title: KO, rep5

city: Edmonton

first: René

last: Jacobs

state: Alberta

address: Room 4002E, Li Ka Shing Building, 11300 87 Ave NW

department: Department of Agricultural, Food and Nutritional Science

country: Canada

institute: University of Alberta

data_processing:
STAR[1](version 2.5.2b) was used to align RNA-Seq data to the genome reference; RSEM[2](version 1.3.0) was used to quantify gene and isoform expression; Ensembl gene annotation GTF[3]was used to build the RSEM reference, and add gene and transcript specific information to the .results file
Differential expression (DE) analysis was performed using R[4](version R-4.0.2) and DESeq2[5]package (version 1.28.1), using raw read count (gene-level abundances) as input data. When applying DESeq2, the functions DESeqDataSetFromMatrix and DESeq were used.
When performing DE analysis, genes were filtered out if the median counts from either test group or control group < 25. An expected Benjamini-Hochberg (FDR) adjusted p-value less than 0.05 as regarded as significant
Fold enrichment analysis was performed to determine biological processes that were up or down regulated.
GO terms were determined with the online DAVID resource with default parameters
Assembly: mm10
Supplementary files format and content: Tab delimited text files, with columns for NCBI official gene symbol, Ensembl gene ID, and FPKM values for each animal

source_name: Liver

growth_protocol: Etnppl KO and WT mice were fed a chow diet for 20 weeks

extract_protocol:
Total RNA was extracted with Trizol, cleaned up with RNEasy columns.mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA was synthesized from heat-denaturated purified mRNA using the following kits: a Maxima H Minus First Strand cDNA Synthesis kit (Thermo-Fisher, USA) to synthesize first-strand cDNA; PCR Clean DX (Aline Biosciences) bead purification; and the NEBNext Ultra 12 Directional Second Strand cDNA Synthesis protocol (New England Biolabs)

treatment_protocol: Livers were harvested and snap frozen.

value: Liver

value: Etnppl KO

value: 20 week Chow diet

value: female


title: WT1 LP Second

status: Public on Nov 25 2024

type: SRA

city: London

first: Patricia

last: Barral

address: Great Maze Pond

department: CIBCI

country: United Kingdom

institute: King's College London

library_source: transcriptomic

data_processing:
Sample quality was assessed with FastQC with MultiQC used to inspect all samples together. Fastq files were trimmed using Cutadapt with a quality threshold of 10
Trimmed sequence reads were mapped to GRCm38.p6 mouse reference genome using RSEM/Bowtie2
QC of alignment was performed with Picard Tools (MarkDuplicates, CollectAligmentSummaryMetrics and CollectRnaSeqMetrics tools) to generate alignment metrics that were then inspected with MultiQC
FeatureCounts program from the subread package was used to aggregate the total read counts for each gene or exon. The raw count data was then imported into R and analysed using DESeq to identify differentially expressed genes (false discovery threshold(FDR) of 0.05) between tissues.
Assembly: Grcm38.p6
Supplementary files format and content: tab-delimited file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Small intestine lamina propria

extract_protocol:
RNA was harvested using Rneasy mini kit (QIAGEN). RNA was then quantified using with Nanodrop and submitted for RNA-sequencing.
Library preparation and whole transcriptome profiling was performed by The Francis Crick Institute Advanced sequencing facility. Sequencing libraries were prepared with 100ng total RNA with RN integrity (RIN) values of more than 7. The Nugen Ovation ultralow kit was used to prepare the sequencing libraries following manufacturer’s instructions. Libraries were barcoded and run on an Illumina HiSeq 2500system with paired-end read lengths of 101 bp

tag: tissue

value: Small intestine lamina propria

tag: cell type

value: iNKT cell

tag: genotype


title: WT4 LP First


title: J1158_NAC

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

country: USA

institute: University of Pittsburgh

data_processing:
FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of the data. Per base sequence quality was high (Quality score generally > 30) indicating good data quality. HISAT2 (HISAT2v2.1.0) was used to align reads to the reference (Mus musculus Ensembl GRCm38) using default parameters.
Assembly: GRCm38
Supplementary files format and content: mouse_filteredCounts_NACPFC.csv; mouse_filteredCounts_SCN.csv

source_name: NAC

extract_protocol:
Mice exposed to adolescent CRD and adult CRD, as well as matching controls, were euthanized approximately 4 wks after the CRD or control paradigm ended by cervical dislocation and rapid decapitation at ZT6. Brains were flash frozen on dry ice and stored at –80 °C until used for punching.
Libraries were prepared with 10 ng of RNA from each sample using the Smartseq HT ultra-low input sample preparation kits (Illumina).

value: NAC


title: Tmem cells, HP1a KO, R1

city: Toulouse

first: Olivier

last: Joffre

address: CHU Purpan

department: Infinity UMR1291

country: France

institute: Inserm

data_processing:
nf-core RNAseq pipeline v.3.9
Sequence reads were trimmed for adapter/low-quality sequence using nf-core/rnaseq pipeline (default parameters)
Trimmed sequence reads were mapped to the GRCm39/mm39 genome using nf-core/rnaseq pipeline (STAR aligner with default parameters)
Read count extraction was performed using nf-core/rnaseq pipeline (Salmon with default parameters)
Assembly: GRCm39 v.107
Supplementary files format and content: raw_counts.tsv: tab-delimited text file with length of each gene and their raw count values for each sample
Supplementary files format and content: tpm_counts.tsv: tab-delimited text file with TPM values for each sample

molecule: polyA RNA

source_name: Spleen

growth_protocol: Treg were isolated from B6 Foxp3-Thy1.1 mice and cultured in complete medium (RPMI 1640 with 10% Fetal Calf Serum (FCS), 1 IU/mL penicillin, 1 μg/mL streptomycin, non-essential amino acids, 50 μM 2-Mercaptoethanol, 2 mM glutamine and 1 μM HEPES) supplemented with 500 IU/mL recombinant human IL-2, 0.1 ng/mL recombinant human TGFb 1 and anti-CD3/CD28 coated Dynabeads (1 bead per cell). After three days of culture, TCR stimulation was removed and cells were further cultured in fresh medium for 5 to 7 additional days.

extract_protocol:
RNA was harvested using Rneasy micro kit. 50 to 100 ng of total RNA was used for the constructio of the librairies.
RNA librairies for RNA-seq were prepared using Illumina Stranded mRNA Prep Ligation Kit following manufacturer's protocols.

value: Spleen

value: Tmem

value: HP1a KO

tag: treatment

value: Treg transferred with HP1a WT Tconv


title: Blood_AD157_EPIC

type: genomic

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

hyb_protocol: Bisulfite-converted DNA samples were randomly assigned to a chip well on the Infinium Human Methylation EPIC v2 BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.

data_processing: For the EPIC processing, the data were processed at TruDiagnostic (Inc., Lexington, KY) using a custom EPIC v2 array that include all the probes from the regular EPICv2 array and 6,930 additional probes spiked in. To preprocess the DNA methylation values, we utilized the sesame package  due to its compatibility with custom arrays. Specifically, we employed the readIDATpair followed by the getBetas functions, which require the IDAT file locations and the custom manifest to generate a beta value matrix. To visualize the distribution of beta values we employed the densityPlot function from the minfi package

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral Whole Blood

extract_protocol: For the preparation of samples, 200 ng of DNA were bisulfite converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions.

treatment_protocol: A pilot case control study of 50 cases and 50 controls was also conducted at the Duke Memory Clinic. Peripheral whole blood was collected by the lancet and capillary method into lysis buffer and DNA extracted. In total, DNA samples from 17 individuals were randomly selected. Among them, 10 were Alzheimer’s disease cases and 7 were controls. All the samples were processed twice using the Human Imprintome array to assess the performance of the array. Moreover, three more controls were randomly selected to process them with the Human Imprintome array and the EPICv2 array

value: Peripheral Whole Blood

tag: Sex

value: M

tag: race

value: EAA

tag: disease

value: Control


title: WT3 LP First


title: KO, rep4


title: J1021_NAC


title: J1017_NAC


title: KO, rep3


title: WT, rep5

value: Etnppl WT


title: KO, rep2


title: WT, rep4


title: WT, rep2


title: KO, rep1


title: WT, rep3


title: J1020_NAC


title: WT, rep1


title: J1162_NAC


title: Blood_AD173_EPIC

scan_protocol: Bisulfite-converted DNA samples were randomly assigned to a chip well on the Infinium Human Methylation EPIC v2 BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.

value: AA


title: J1157_NAC


title: Mouse muscle endothelial cells Young 4

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
RNA-seq reads were counted with Kallisto using the genome build GENCODE Mus musculus GRCm39 M26
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GENCODE Mus musculus GRCm39 M26
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

source_name: Skeletal muscle

extract_protocol:
Mice were euthanized and leg muscles were immediately dissected and placed in a Petri dish on ice. Tissues were minced with a scalpel until a homogeneous paste-like mash was formed. Subsequently, the tissue was enzymatically digested in a buffer containing 2 mg/ml Dispase II (D4693, Sigma-Aldrich, Steinheim, Germany), 2 mg/ml Collagenase IV (17104019, ThermoFisher Scientific, Zurich, Switzerland), 2 mM CaCl2 and 2% BSA in PBS at 37°C for 10 min (lungs) or 25 min (muscle), with gentle shaking every 3 min. The reaction was stopped by immediately adding an equal volume of ice cold HBSS containing 20% FBS and the suspension was passed through a 70-μm cell strainer (#431751, Corning, New York, USA) then 40-μm cell strainer (#431750, Corning, New York, USA) to remove tissue debris. Cell suspension was centrifuged at 500 g for 5 min at 4°C, then the pellet was washed with ice cold HBSS (+20% FBS) followed by a centrifugation at 400 g for 5 min in 4°C. Next, the cell pellet was re-suspended in antibody medium (EGM2 CC-3162, Lonza, Basel, Switzerland) with anti-mouse CD31 PE antibody (1:400) (553373, BD Biosciences, Basel, Switzerland) and anti-mouse CD45 PerCP antibody (1:400) (557235 BD Biosciences, Basel, Switzerland) and placed on ice for 20 min in the dark. Before sorting, the cell suspension was washed in FACS buffer (1xPBS+1%BSA) and centrifuged at 400G for 5 min, 4°C, then the washed cell pellet was re-suspended in FACS buffer containing cell viability dye, SYTOX blue (1:1000) (S34857, Thermo Fischer Scientific, Zurich, Switzerland). Viable ECs (CD31+, CD45-, SYTOX blue-) were sorted by a FACS Aria III (BD Bioscience) sorter. ECs were were put in culture in EGM2 cell culture medium (CC-3162, Lonza, Basel, Switzerland) or directly sorted (70μm nozzle) into 700 μl RNA lysis buffer for , RNA extraction using RNeasy Plus Micro Kit (74034 QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skeletal muscle

value: Endothelial cells

tag: age

value: Young


title: Mouse muscle endothelial cells Young 3


title: J1016_NAC


title: Mouse muscle endothelial cells Old 3

value: Old


title: J1015_NAC


title: L_3

city: lanzhou

first: Wenwen

last: Ren

address: xiaoxihu

country: China

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

description: yak milk-derived exosomes at low altitude

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: excel,expression profiles

organism: Bos grunniens

source_name: yak milk-derived exosomes

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (v4.2) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: yak milk-derived exosomes


title: L_2


title: Mouse muscle endothelial cells Old 1


title: Blood_AD125_EPIC

label_protocol: Bisulfite-converted DNA samples were randomly assigned to a chip well on the Infinium Human Methylation EPIC v2 BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.

value: F


title: J980_NAC

value: NAC


title: Mouse muscle endothelial cells Young 1


title: L_1


title: BMDM, soluble LPS, replicate 2

city: Amherst

first: Alissa

last: Rothchild

state: MA

address: 661 N Pleasant Street

department: Veterinary and Animal Sciences Department

institute: University of Massachusetts Amherst

data_processing:
The read pairs were aligned to the mouse genome (mm10) using the gsnap aligner.
Concordantly mapping read pairs (~20 million / sample) that aligned uniquely were assigned to exons using the 25iocond program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
Genes with low expression were filtered using the “filterByExpr” function in the edgeR package.
Assembly: mm10
Supplementary files format and content: rawCounts.csv, contains the raw counts for each sample generated by subRead

source_name: Bone marrow-derived macrophages

growth_protocol: For BMDMs, bone marrow was isolated from murine femurs by flushing the bone with RPMI. Cells were filtered, spun down and plated on 15 cm non-TC treated plates. Cells were cultured for 6 days in RPMI with 10% FBS, 1% L-glutamine, 1% penicillin-streptomycin, and 0.01% recombinant human M-CSF. BMDMs were counted and replated before use.

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol. RNA was quantified with the Bioanalyzer RNA 6000 Pico Kit (Agilent)
cDNA libraries were constructed and amplified using the SMART-Seq v4 Ultra Low Input RNA kit (TaKaRa) per the manufacturers instructions. Libraries were amplified and then sequenced on an IlluminaNovaSeq 6000 (150bp paired-end).

treatment_protocol: Polysciences Fluoresbrite Carboxylate Microspheres 1.00 µm (YG) were incubated overnight with 100 µg/mL LPS (R595 S. Minnesota) in PBS or PBS alone at 4 degrees. The next day, the beads were washed 10X in PBS. Each wash was followed by centrifugation at 10,000 x g for 5 minutes. Beads were then resuspended in PBS. For AM treatment, beads were aerosolized using a LC Sprint® Reusable Nebulizer (PARI) attached to a mouse cage with a vacuum pump and air flow regulator. Beads were resuspended in 4 mL of ddH2O and delivered at 3 liters/minute for 20 minutes. Beads were delivered to BMDMs in cell culture media. Soluble LPS was given at 10 ng/ml.

value: Bone marrow-derived macrophages

tag: strain

value: WT

value: soluble LPS

tag: bead-status

tag: time

value: 4 hours


title: J1019_NAC


title: H_3

description: yak milk-derived exosomes at high altitude


title: BMDM, untreated, replicate 2


title: BMDM, PBS-bead positive, replicate 2

value: PBS-bead

value: bead+


title: H_1


title: J1011_NAC


title: AM, PBS-bead positive, replicate 2

source_name: Lung

value: Lung

value: Alveolar macrophages


title: AM, LPS-bead bystander, replicate 2

value: LPS-bead

value: bystander


title: J1014_NAC


title: BMDM, soluble LPS, replicate 1


title: H_2


title: Mouse muscle endothelial cells Young 2

value: Skeletal muscle


title: AM, LPS-bead positive, replicate 2


title: BMDM, LPS-bead bystander, replicate 2


title: Sorted A375 tumor cells, day 50

city: 上海

first: Xu

last: Jiaojiao

state: 上海Shanghai

address: Zhangheng Road

institute: Fudan university

description: 10× genomics

library_source: transcriptomic single cell

data_processing:
The sample raw sequencing data were aligned and quantified using the Cell Ranger (version 3.0.1, 10× Genomics) to the GRCH38 human or mm10 mouse reference genome dependent on the experiment setup. The gene expression matrix was then processed and analyzed by Seurat R (version 4.0) package.
The cells detected with fewer than 200 genes or more than 10% mitochondrial reads or more than 10% red cell reads were removed. The cells predicted to be potential cell doublets using Python Scrublet package were also excluded.
For each sample dataset of the filtered gene-barcode matrix, top 2000 highly variable genes (HVGs) were used for the subsequent principal component analysis (PCA) to reduce dimensionality by “RunPCA” function.
Then t-distributed stochastic neighbor embedding (t-SNE) was performed on the top 30 principal components for visualizing the cells using ‘RunTSNE’ function. Cluster marker genes were identified by applying differential gene expression testing, which was performed using ‘FindAllMarkers’ function with a filter condition of logfc.threshold = 0.1, min.pct = 0.01. DGEs between the cases and the controls were performed using “FindMarkers” function and then filtered with the condition |log2FC| > 0.585 and P < 0.05.
GO enrichment analysis for DEGs was performed by TopGO R package and the KEGG pathway enrichment analysis was performed using the Hypergeometric test in R. Significantly enriched GO terms and KEGG pathways were selected by a threshold FDR (adjusted P-value) ≤ 0.05.
For sorted A375 tumor cell sample, CytoTRACE was performed to predicted the cancer stem cell population.
Assembly: GRCH38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens/Mus musculus xenograft

source_name: human melanoma xenograft mouse model

extract_protocol:
For whole A375 tumor sample, human tumor dissociation kit (Miltenyi Biotec, 130-095-929) was used to obtain the single suspension. For sorted A375 tumor cell sample, A375-GFP tumor model was established and sorted based on the human HLA-A,B,C antibody and GFP signal.
The result signle cells were barcode labelled and library constructed by Single Cell 3' Reagent Kits v3 (10× genomics, Genergy BIO-technology, Shanghai, China). The constructed library was sequenced on an Illumina NovaSeq 6000 System.

value: human melanoma xenograft mouse model

tag: cell line

value: FACS sorted human derived cells

value: adoptively transferred engineered macrophage-based therapy


title: J1018_NAC


title: J1013_NAC


title: AM, PBS-bead bystander, replicate 2


title: BMDM, LPS-bead positive, replicate 1


title: Mouse muscle endothelial cells Old 2

value: Endothelial cells

value: Old


title: BMDM, untreated, replicate 1


title: Whole A375 tumors, day 50

description: 10× genomics

value: pooled whole A375 tumors derived cells


title: BMDM, LPS-bead bystander, replicate 1

value: Bone marrow-derived macrophages


title: BMDM, LPS-bead positive, replicate 2

value: WT


title: J1198_PFC

source_name: PFC

value: PFC


title: BMDM, PBS-bead positive, replicate 1

value: 4 hours


title: AM, LPS-bead positive, replicate 1


title: J1165_PFC


title: AM, LPS-bead bystander, replicate 1


title: AM, PBS-bead positive, replicate 1

value: PBS-bead


title: J1160_PFC


title: Brain_E_Exposed_S64

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

institute: UCL

data_processing:
nf-core RNASeq pipeline v3.14.0 using Nextflow 24.04.2
Raw reads were trimmed with trim galore, mappes with star, then gene counts quantified with Salmon
Assembly: BIMP3.0 JBEUIP000000000, SUB14541561
Supplementary files format and content: tab delimitd file with the raw counts for each sample (brain and fatbody in separate tsv files)

organism: Bombus impatiens

source_name: Brain tissue

extract_protocol:
Qiagen RNEasy Mini Kit
Quant-Seq mRNA libraries were prepared by the Iowa State University DNA Facility following manufacturer’s protocols, and subjected to Illumina Quant-Seq using a HiSEQ 3000 Sequencer

treatment_protocol: Control or exposed to metal

value: Brain tissue


title: AM, PBS-bead bystander, replicate 1

value: Lung


title: Brain_E_Exposed_S63


title: Day 7, RAG KO

city: White/Caucasian

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: UNMC

description:
D7_KO
scRNA-seq RAG Craniotomy Matrix.h5

data_processing:
Sequencing data was aligned to the mouse genome using 10X Genomics Cell Ranger before importing into Partek Flow Genomics Suite (RRID: SCR_011860) for the remainder of the analysis.
A standard quality control pipeline was implemented to safeguard against contamination by low-quality cells/reads.
Resulting single-cell count matrices were normalized within Partek Flow using counts per million, add 1, and log base 2 transformed. Samples were then integrated for all downstream analyses.
Assembly: mm10
Supplementary files format and content: Hierarchical Data Format .h5 files containing count matricies for each sample

source_name: Brain

extract_protocol:
Mice were euthanized at the indicated intervals using an overdose of inhaled isoflurane prior to tissue collection. The vasculature was perfused with sterile 1X PBS, whereupon the brain was collected and placed in 1X PBS supplemented with 10% FBS on ice. The ipsilateral hemisphere of the brain was removed and disrupted by passing through a 70 µm cell strainer and rinsed with 1X PBS. Brain homogenates required further processing to obtain single-cell suspensions. Briefly, tissues were disrupted with collagenase IV (Cat. #C9891, Sigma-Aldrich) and DNase I (Cat. #AAJ62229MC, Fisher Scientific) for 15 min at 37°C followed by the addition of FBS to inactivate enzymatic digestion, whereupon the cell suspension was subjected to Percoll density gradient centrifugation (25% Percoll (GE Heatlhcare) with 3% FBS) at 520 x g for 20 min with no brake. The upper myelin layer down to the pellet was discarded, and the pellet was resuspended in 1X PBS to obtain a single cell suspension. Target CD45+ cell populations were enriched via FACS before submission to a core facility at UNMC for scRNA-seq.
Illumina-compatible cDNA libraries were quantified with a Qubit-30 Fluorometer and assessed using a fragment analyzer before loading on a Novaseq6000 instrument at a final concentration of 300pM for generation of 75 bp pair-end reads.

value: Brain

tag: strain background

value: CD45+ Immune Cells

value: RAG KO

tag: time point

value: Day 7


title: J1141_PFC


title: Day 3, Wildtype

description:
D3_WT
scRNA-seq RAG Craniotomy Matrix.h5

value: Wildtype

value: Day 3


title: Day 3, RAG KO

description:
D3_KO
scRNA-seq RAG Craniotomy Matrix.h5


title: Brain_E_Exposed_S66


title: J1164_PFC


title: Brain_E_Exposed_S62


title: Brain CD3+, Day 3

description:
D3_S2
scRNA-seq CD3 Craniotomy Matrix.h5

extract_protocol:
Mice were euthanized at the indicated intervals using an overdose of inhaled isoflurane prior to tissue collection. The vasculature was perfused with sterile 1X PBS, whereupon the brain was collected and placed in 1X PBS supplemented with 10% FBS on ice. The ipsilateral hemisphere of the brain was removed and disrupted by passing through a 70 µm cell strainer and rinsed with 1X PBS. Brain homogenates required further processing to obtain single-cell suspensions. Briefly, tissues were disrupted with collagenase IV (Cat. #C9891, Sigma-Aldrich) and DNase I (Cat. #AAJ62229MC, Fisher Scientific) for 15 min at 37°C followed by the addition of FBS to inactivate enzymatic digestion, whereupon the cell suspension was subjected to Percoll density gradient centrifugation (25% Percoll (GE Heatlhcare) with 3% FBS) at 520 x g for 20 min with no brake. The upper myelin layer down to the pellet was discarded, and the pellet was resuspended in 1X PBS to obtain a single cell suspension. Target CD3+ cell populations were enriched via FACS before submission to a core facility at UNMC for scRNA-seq.
Illumina-compatible cDNA libraries were quantified with a Qubit-30 Fluorometer and assessed using a fragment analyzer before loading on a Novaseq6000 instrument at a final concentration of 300pM for generation of 75 bp pair-end reads.

value: CD3+ T cells

value: craniotomy infection


title: Day 7, Wildtype

description:
D7_WT
scRNA-seq RAG Craniotomy Matrix.h5


title: Brain_E_Exposed_S60


title: Brain_E_Exposed_S61


title: WT4 SIO + NKTs

data_processing:
Sample quality was assessed with FastQC with MultiQC used to inspect all samples together. Fastq files were trimmed using Cutadapt with a quality threshold of 10
Trimmed sequence reads were mapped to GRCm39 mouse reference genome using Hisat2
QC of alignment was performed with Picard Tools (MarkDuplicates, CollectAligmentSummaryMetrics and CollectRnaSeqMetrics tools) to generate alignment metrics that were then inspected with MultiQC
FeatureCounts program from the subread package was used to aggregate the total read counts for each gene or exon. The raw count data was then imported into R and analysed using DESeq to identify differentially expressed genes (FDR of 0.05) between genotypes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Small intestine derived organoid

extract_protocol:
RNA was harvested using Rneasy mini kit (QIAGEN). RNA was then quantified using with Nanodrop and submitted for RNA-sequencing.
Library preparation and whole transcriptome profiling was performed by The Francis Crick Institute Advanced sequencing facility. Sequencing libraries were prepared with 100ng total RNA with RN integrity (RIN) values of more than 7. The KAPA mRNA HyperPrep Kit for Illumina sequencing (Roche) was used to prepare the sequencing libraries following manufacturer’s instructions. The quality and fragment size distributions of the purified libraries was assessed by a 4200 TapeStation Instrument (Agilent Technologies).

value: Small intestine derived organoid

value: Epithelial cell

value: LP iNKT cell 3 day coculture


title: WT3 SIO + NKTs


title: J1178_PFC


title: Brain_E_Exposed_S59


title: WT2 SIO + NKTs


title: WT1 SIO + NKTs


title: Brain_E_Exposed_S58


title: Brain CD3+, Day 14

description:
D14_S3
scRNA-seq CD3 Craniotomy Matrix.h5

value: Day 14


title: J1177_PFC

value: PFC


title: Brain_E_Exposed_S65


title: J1163_PFC


title: WT4 SIO


title: Brain_E_Exposed_S56


title: WT1 SIO


title: IECs,WT4

data_processing:
Sample quality was assessed with FastQC with MultiQC used to inspect all samples together. Fastq files were trimmed using Cutadapt with a quality threshold of 10
Trimmed sequence reads were mapped to GRCm39 mouse reference genome using Hisat2
QC of alignment was performed with Picard Tools (MarkDuplicates, CollectAligmentSummaryMetrics and CollectRnaSeqMetrics tools) to generate alignment metrics that were then inspected with MultiQC
FeatureCounts program from the subread package was used to aggregate the total read counts for each gene or exon. The raw count data was then imported into R and analysed using DESeq to identify differentially expressed genes (false discovery threshold(FDR) of 0.05) between treatment groups.
Assembly: GRCm39
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Proximal small intestine

value: Proximal small intestine


title: J1019_PFC


title: J1021_PFC


title: Brain_D_Exposed_S54


title: WT2 SIO


title: WT3 SIO


title: J1157_PFC


title: Brain CD3+, Day 7

description:
D7_S1
scRNA-seq CD3 Craniotomy Matrix.h5


title: Brain_E_Exposed_S57


title: IECs,WT2


title: Brain_E_Exposed_S55


title: IECs,WT1


title: J1014_PFC


title: IECs, CD1dKO3

value: CD1d1/2 KO


title: Brain_D_Exposed_S53

value: Brain tissue


title: Brain_D_Exposed_S52


title: IECs, CD1dKO4


title: J1015_PFC


title: J965_PFC


title: Brain_D_Exposed_S51


title: IECs, Sample9, aGal, 72h, Rep3

data_processing:
Sequence reads were mapped to GRCm38/mm10 using HISAT2
Read quantification was performed using featureCounts from the subRead package
Differential gene expression analysis was conducted using DESeq2 (v 1.42.0)
Assembly: GRCm38/mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalised counts (output from DESeq2) for each sample

source_name: Small intestine epithelium

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
NEBNext Ultra II Directional +ribodepletion
100bp reads

treatment_protocol:
To activate intestinal NKT cells, mice were i.p. injected with the prototypical lipid anitgen α-Galactosylceramide (αGal; 2μg), or PBS as a control.
At 18h/72h post-injection, the proximal small intestine was harvested, and crypt cells were isolated by enzymatic and mechanical digestion, before selection of live intestinal epithelial cells by FACS based on EpCAM+, Ter119−, CD31−, CD45− gating.
Cells were lysed by sorting directly into buffer RLT containing ß-ME before storage at -80C.

value: Small intestine epithelium

value: female

value: Intestinal epithelial cells

value: WT

value: α-Galactosylceramide (αGal)


title: IECs, CD1dKO2


title: J1018_PFC


title: IECs, Sample7, aGal, 72h, Rep1


title: IECs,WT3


title: Brain_D_Exposed_S50


title: IECs, Sample5, aGal, 18h, Rep2


title: IECs, Sample6, aGal, 18h, Rep3


title: IECs, Sample4, aGal, 18h, Rep1


title: IECs, Sample3, PBS, 18h, Rep3

value: PBS


title: IECs, Sample2, PBS, 18h, Rep2


title: Brain_D_Exposed_S48


title: IECs, Sample1, PBS, 18h, Rep1


title: Brain_D_Exposed_S49


title: 48h RFA rep 4

city: Verona

first: Francesco

last: De Sanctis

address: Piazzale L.A. Scuro, 10

department: Department of Medicine

country: Italy

institute: University and Hospital Trust of Verona

data_processing:
The first 11 bases of the reads were trimmed using cutadapt v1.15.
Trimmed sequence reads were mapped to GRCm38/mm10 and quantified using RSEM v1.3.1 (parameters: --star)
Assembly: mm10
Supplementary files format and content: RSEM output files

source_name: KPC-derived PDAC

extract_protocol:
RNA was extracted by Trizol solution (Thermo Fisher Scientific, Waltham, MA, USA) and miRNeasy Kit (Qiagen, Hilden, DEU)
RNA libraries were prepared using the QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen GmbH, Austria)

value: KPC-derived PDAC

value: tumor microenvironment

value: KPC (Kras+ / LSL-G12D; Trp53+ / LSL-R172H; Pdx1-Cre)

value: RFA


title: 48h RFA rep 3


title: Brain_D_Exposed_S47


title: IECs, CD1dKO1

value: Epithelial cell


title: Treg_WT_HP1a_KO_R3

data_processing:
nf-core RNAseq pipeline v.3.9
Sequence reads were trimmed for adapter/low-quality sequence using nf-core/rnaseq pipeline (default parameters)
Trimmed sequence reads were mapped to the GRCm39/mm39 genome using nf-core/rnaseq pipeline (STAR aligner with default parameters)
Read count extraction was performed using nf-core/rnaseq pipeline (Salmon with default parameters)
Assembly: GRCm39 v.107
Supplementary files format and content: salmon.merged.gene_counts.tsv: tab-delimited text file with length of each gene and their raw count values for each sample
Supplementary files format and content: salmon.merged.gene_tpm.tsv: tab-delimited text file with TPM values for each sample

extract_protocol:
RNA were harvested using Rneasy Micro Kit (Qiagen). 500ng of total RNA was used for the construction of sequencing libraries.
RNA librairies for RNA-seq were prepared using Truseq Stranded total RNA LP  following manufacturer's protocols (Illumina).

value: Spleen

value: Treg

tag: condition

value: Treg transferred with HP1a KO Tconv


title: 48h RFA rep 2


title: IECs, Sample8, aGal, 72h, Rep2


title: Treg_WT_HP1a_KO_R2


title: Treg_WT_HP1a_WT_R3

value: Treg transferred with HP1a WT Tconv


title: Brain_D_Exposed_S45


title: Treg_WT_HP1a_WT_R2


title: 48h CTRL rep 4

value: No treatment


title: Brain_D_Exposed_S44

value: Brain tissue


title: 48h CTRL rep 3


title: Naive_HP1g_KO_RNA-seq_R3

description:
column name in processed files: NaivesHP1g.S6
RNAseq-NaivesHP1g-S6

data_processing:
nf-core RNAseq pipeline v.3.9
Sequence reads were trimmed for adapter/low-quality sequence using nf-core/rnaseq pipeline (default parameters)
Trimmed sequence reads were mapped to the GRCm39/mm39 genome using nf-core/rnaseq pipeline (STAR aligner with default parameters)
Read count extraction was performed using nf-core/rnaseq pipeline (Salmon with default parameters)
Assembly: GRCm39 v.107
Supplementary files format and content: salmon.merged.gene_counts.tsv: tab-delimited text file with length of each gene and their raw count values for each sample

extract_protocol:
RNA were harvested using Rneasy Micro Kit (Qiagen). 10 pg of total RNA was used for the construction of sequencing libraries.
RNA librairies for RNA-seq were prepared using SMART-seq V4 PLUS and SMARTer RNA Unique Dual Index kits following manufacturer's protocols (Takara).

value: CD4 T cells

value: HP1g KO

value: Naive


title: J1013_PFC

value: PFC


title: Brain_D_Exposed_S43


title: Naive_HP1g_KO_RNA-seq_R1

description:
column name in processed files: NaivesHP1g.S4
RNAseq-NaivesHP1g-S4


title: 48h CTRL rep 2


title: Naive_HP1g_WT_RNA-seq_R1

description:
column name in processed files: NaivesHP1g.S1
RNAseq-NaivesHP1g-S1

value: HP1g WT


title: Naive_HP1g_WT_RNA-seq_R2

description:
column name in processed files: NaivesHP1g.S2
RNAseq-NaivesHP1g-S2


title: 48h CTRL rep 1


title: Naive_HP1a_KO_RNA-seq_R3

description:
column name in processed files: NaivesHP1a.S6
RNAseq-NaivesHP1a-S6

value: HP1a KO


title: J1159_PFC


title: Brain_D_Exposed_S46


title: Treg_WT_HP1a_KO_R1

value: WT


title: Brain_C_Control_S41


title: RFA and Immuno rep 4

treatment_protocol: RFA (15W 10''), Gemcitabin (100mg/kg), ICI (5mg/kg)

value: KPC-derived PDAC

value: tumor microenvironment

value: RFA and Immunotherapy


title: Brain_C_Control_S42


title: Naive_HP1a_KO_RNA-seq_R2

description:
column name in processed files: NaivesHP1a.S5
RNAseq-NaivesHP1a-S5


title: 48h RFA rep 1

value: KPC (Kras+ / LSL-G12D; Trp53+ / LSL-R172H; Pdx1-Cre)

value: RFA


title: RFA and Immuno rep 3


title: Naive_HP1a_WT_RNA-seq_R3

description:
column name in processed files: NaivesHP1a.S4
RNAseq-NaivesHP1a-S4

value: Spleen

value: HP1a WT


title: Treg_WT_HP1a_WT_R1

value: Treg

value: Treg transferred with HP1a WT Tconv


title: Brain_C_Control_S40

value: Brain tissue


title: Naive_HP1a_KO_RNA-seq_R1

description:
column name in processed files: NaivesHP1a.S2
RNAseq-NaivesHP1a-S2

value: CD4 T cells


title: Brain_C_Control_S39


title: Naive_HP1a_WT_RNA-seq_R2

description:
column name in processed files: NaivesHP1a.S3
RNAseq-NaivesHP1a-S3


title: RFA and Immuno rep 2


title: Naive_HP1g_KO_RNA-seq_R2

description:
column name in processed files: NaivesHP1g.S5
RNAseq-NaivesHP1g-S5

value: HP1g KO


title: TconvTreg_HP1g_WT_RNA-seq_R2

description:
column name in processed files: HP1g.S9
RNAseq-HP1g-S9

value: Tconv transferred with Treg


title: Brain_C_Control_S38


title: RFA and Immuno rep 1


title: Naive_HP1g_WT_RNA-seq_R3

description:
column name in processed files: NaivesHP1g.S3
RNAseq-NaivesHP1g-S3

value: Naive


title: Tconv_HP1g_KO_RNA-seq_R3

description:
column name in processed files: HP1g.S8
RNAseq-HP1g-S8

value: Tconv


title: Brain_C_Control_S37


title: Tconv_HP1g_KO_RNA-seq_R2

description:
column name in processed files: HP1g.S7
RNAseq-HP1g-S7


title: Tconv_HP1g_WT_RNA-seq_R3

description:
column name in processed files: HP1g.S6
RNAseq-HP1g-S6

value: HP1g WT


title: RFA rep 4


title: TconvTreg_HP1g_WT_RNA-seq_R1

description:
column name in processed files: HP1g.S3
RNAseq-HP1g-S3


title: TconvTreg_HP1g_KO_RNA-seq_R1

description:
column name in processed files: HP1g.S4
RNAseq-HP1g-S4


title: RFA rep 2


title: Tconv_HP1g_WT_RNA-seq_R2

description:
column name in processed files: HP1g.S5
RNAseq-HP1g-S5


title: RFA rep 3


title: RFA rep 1


title: TconvTreg_HP1g_KO_RNA-seq_R2

description:
column name in processed files: HP1g.S11
RNAseq-HP1g-S11


title: Brain_C_Control_S36


title: Brain_C_Control_S34


title: Tconv_HP1g_KO_RNA-seq_R1

description:
column name in processed files: HP1g.S2
RNAseq-HP1g-S2


title: Brain_C_Control_S35


title: Tconv_HP1g_WT_RNA-seq_R1

description:
column name in processed files: HP1g.S1
RNAseq-HP1g-S1


title: Naive_HP1a_WT_RNA-seq_R1

description:
column name in processed files: NaivesHP1a.S1
RNAseq-NaivesHP1a-S1


title: Brain_C_Control_S33


title: Immuno rep 4

value: Immunotherapy


title: TconvTreg_HP1g_WT_RNA-seq_R3

description:
column name in processed files: HP1g.S10
RNAseq-HP1g-S10


title: TconvTreg_HP1a_KO_RNA-seq_R3

description:
column name in processed files: HP1a.S36
RNAseq-HP1a-S36

value: HP1a KO


title: TconvTreg_HP1a_KO_RNA-seq_R2

description:
column name in processed files: HP1a.S35
RNAseq-HP1a-S35


title: TconvTreg_HP1g_KO_RNA-seq_R3

description:
column name in processed files: HP1g.S12
RNAseq-HP1g-S12


title: Brain_C_Control_S31


title: Immuno rep 3

value: KPC-derived PDAC

value: tumor microenvironment


title: J965_NAC

value: NAC


title: TconvTreg_HP1a_KO_RNA-seq_R1

description:
column name in processed files: HP1a.S34
RNAseq-HP1a-S34


title: Immuno rep 2

value: KPC (Kras+ / LSL-G12D; Trp53+ / LSL-R172H; Pdx1-Cre)


title: TconvTreg_HP1a_WT_RNA-seq_R3

description:
column name in processed files: HP1a.S33
RNAseq-HP1a-S33

value: Spleen


title: Brain_B_Exposed_S30


title: Immuno rep 1


title: TconvTreg_HP1a_WT_RNA-seq_R2

description:
column name in processed files: HP1a.S32
RNAseq-HP1a-S32

value: HP1a WT


title: Brain_B_Exposed_S29


title: Tconv_HP1a_KO_RNA-seq_R3

description:
column name in processed files: HP1a.S30
RNAseq-HP1a-S30


title: Brain_C_Control_S32


title: Tconv_HP1a_KO_RNA-seq_R1

description:
column name in processed files: HP1a.S28
RNAseq-HP1a-S28


title: Tconv_HP1a_WT_RNA-seq_R3

description:
column name in processed files: HP1a.S27
RNAseq-HP1a-S27


title: CTRL rep 3

value: No treatment


title: Brain_B_Exposed_S28


title: Tconv_HP1a_WT_RNA-seq_R2

description:
column name in processed files: HP1a.S26
RNAseq-HP1a-S26


title: Brain_B_Exposed_S27


title: CTRL rep 2


title: Brain_B_Exposed_S26


title: Tconv_HP1a_WT_RNA-seq_R1

description:
column name in processed files: HP1a.S25
RNAseq-HP1a-S25


title: CTRL rep 1


title: Naive_HP1g_KO_ATAC-seq_R3

description:
ATACseq-NaivesHP1g-S6
counts.txt
peaks.bed

library_source: genomic

data_processing:
Sequence reads were trimmed for adapter/low-quality sequence using TrimGalore V.0.6.7.
Trimmed sequences reads were mapped to GRCm39/mm39 genome using BWA_MEM 2 v.2.2.
Duplicated reads are removed using MarkDuplicates. Reads not properly paired, mapped inblacklisted regions, not primary aligned and/or with an alignment quality below 30 were filtered out using Samtools.
Peaks were called using HMMRATAC v.1.2.10. Cinsensus peaks were generated by merging all the peaks detected for each sample using bedtools.
Raw coverage of DNA fragments at each consensus peak coordiante was calculated using featureCounts v.2.0.3. BigWig files were generated from filtered BAM files using deeptools. Scores represent the normalized coverage of DNA fragments at a given genomic range.
Assembly: GRCm39 v.107
Supplementary files format and content: counts.txt: tab-delimited text file containing the coordinates of consensus peaks and the raw count values for each sample.
Supplementary files format and content: bigWig and BED files

extract_protocol:
Cells were lysed in ice-cold lysis buffer and the transposition reaction was performed using the ILMN Tagment DNA Enzyme and Buffer kit (Illumina) at 37°C for 30 min. DNA was purified using the Qiagen MinElute kit.
Sequencing librairies were prepared using the NEBNext High-Fidelity 2X PCR Master Mix(New England Biolabs). They were then purified twice using AMPure XP beads (Beckman) followinf a double-sided protocol.


title: Cancer Sox10 Low, rep4

data_processing:
The quality of sequenced data was assessed using fastqc application, and 10 poor-quality bases were trimmed from the 5’-end. The remaining good-quality reads were aligned to the Zebrafish reference genome (danRer10) downloaded from the Ensembl database using STAR aligner. Per-gene counts of uniquely mapped reads were calculated using htseq-count script from the HTSeq Python package for each replicate.
Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF  gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions
Assembly: danRer10
Supplementary files format and content: csv format  read count

organism: Danio rerio

source_name: C, Sox10, Low

growth_protocol: Zebrafish housed and maintained under standard conditions

extract_protocol:
RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer
RNA-seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina (NEB).
RNA-seq-double ended

treatment_protocol: Ocular tissues were removed, enzymatically dissociated, and processed by FACS

value: Cancer Microenvironment

value: Sox10 Low


title: Brain_B_Exposed_S25

value: Brain tissue


title: Naive_HP1g_KO_ATAC-seq_R2

description:
ATACseq-NaivesHP1g-S5
counts.txt
peaks.bed

value: CD4 T cells

value: HP1g KO


title: Cancer Sox10 Low, rep3


title: Brain_B_Exposed_S24


title: Brain_B_Exposed_S23


title: CR, seedlings, rep3

city: Athens

first: Gerasimos

last: Daras

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

data_processing:
RNA-seq data were analyzed using SOAPnuke (version 1.5.2) with parameters “-l 15 -q 0.2 -n 0.05"
We used Bowtie2 to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM to calculate the gene expression level of each sample. DESeq2 was used to identify differentially expressed genes.
Bowtie2 version：v2.2.5 | Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM version：v1.2.8 | Parameters：-p 8 --forward-prob 0.5 --paired-end
Assembly: Arabidopsis_thaliana_NCBI_GCF_000001735.4_TAIR10.1
Supplementary files format and content: Excel file with gene expression values and log2FoldChange between samples as generated by DEseq2

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized and sown in 120×120 mm2 Petri dishes containing 0.5×Murashige and Skoog (MS) medium (Duchefa, Haarlem, the Netherlands), pH 5.7, supplemented with 1% sucrose and solidified with 0.4% phytagel (Sigma, Gillingham, UK). After 48h of stratification at 4oC, seedlings were positioned to grow at 22oC in a Fitotron (Weiss Gallenkamp, Loughborough, UK) growth chamber under a long-day photoperiod with 16h of light and 8h of darkness per day and 150 μmol m−2s−1 light intensity.

extract_protocol:
Total RNA was extracted  from seedlings using the Direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis.
RNA-seq libraries were generated using the polyA Strand-Specific Transcriptome Library method of BGI for DNBSEQ platform.
Sequencing was performed on DNBSEQ-G400 platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample.

treatment_protocol: Col -0 (wild-type) (CR) seedlings were treated with 0.6 mM Riboflavin for 8 hours during the dark cycle.

value: seedlings


title: TconvTreg_HP1a_WT_RNA-seq_R1

description:
column name in processed files: HP1a.S31
RNAseq-HP1a-S31

value: Tconv transferred with Treg


title: Scyliorhinus canicula retina, female, 11.1 cm

city: Santiago de Compostela

first: Nicolás

last: Vidal-Vázquez

state: A Coruña

address: Av. Lope Gómez de Marzoa s/n

department: Departamento de Bioloxía Funcional

country: Spain

institute: Universidade de Santiago de Compostela

data_processing:
Genome indexing and library mapping was performed with STAR (v2.7.10a).
Assembly: sScyCan1.1
Supplementary files format and content: Tab-separated values file for barcodes
Supplementary files format and content: Tab-separated values file for features
Supplementary files format and content: Matrix file

molecule: nuclear RNA

organism: Scyliorhinus canicula

source_name: Retina

growth_protocol: Animals were kindly provided by the Aquarium Finisterrae (A Coruña, Spain) and kept in artificial seawater tanks under standard conditions of temperature (15-16 °C), pH (7.5-8.5) and salinity (35 g/L). All procedures were performed in accordance with European and Spanish guidelines for animal experimentation.

extract_protocol:
Animals were deeply anaesthetised with 0.5% tricaine methanesulfonate in seawater. The animals were removed from water and the retinas were dissected out under a stereomicroscope. Retinas were immediately frozen in liquid nitrogen, and kept at -80 °C until further processing.
Retina nuclei were extracted following a published protocol (Krishnaswami et al. 2016, Nat. Protoc. https://doi.org/10.1038/nprot.2016.015) with small modifications. Briefly, the frozen retinas were homogenised using a micropestle in 400 µL ice-cold homogenisation buffer. The homogenates were triturated gently using a p1000 tip for 10 times, incubated on ice for 5 min and then centrifuged at 100 g for 1 min at 4 °C. The supernatant was transferred into another 1.5 mL Eppendorf tube and centrifuged at 400 g for 4 min at 4 °C to collect nuclei. The nuclei were washed twice in 400 µL homogenisation buffer and strained using a 40 µm Flowmi strainer (Sigma) during the second wash step to remove nuclei aggregates. The final nuclei pellet was resuspended in 30-50 µL Nuclei Buffer (10x Genomics). To estimate the nuclei concentration, nuclei aliquots were diluted in PBS with Hoechst and PI DNA dyes and counted on Countless II FL Automated Cell Counter (Thermo Fisher Scientific). Around 15,000 nuclei were used as input for the snRNA-seq experiment. The Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (PN-1000121, PN-1000120, and PN-1000213) were used to make snRNA-seq libraries. Libraries were quantified on a Qubit Fluorometer (Thermo Fisher Scientific) and quality checked on a Fragment Analyzer (Agilent). Libraries were sequenced on NextSeq550 (Illumina; 28 cycles for Read 1, 56 cycles for Read 2, 8 cycles for i7 index).

value: Retina


title: Cancer Sox10 Low, rep2


title: CTRL rep 4


title: Naive_HP1g_WT_ATAC-seq_R3

description:
ATACseq-NaivesHP1g-S3
counts.txt
peaks.bed

source_name: Spleen

value: HP1g WT

value: Naive


title: Tconv_HP1a_KO_RNA-seq_R2

description:
column name in processed files: HP1a.S29
RNAseq-HP1a-S29

value: HP1a KO

value: Tconv


title: Brain_B_Exposed_S22


title: Scyliorhinus canicula retina, female, 10.5 cm


title: Scyliorhinus canicula retina, female, 11.0 cm


title: CR, seedlings, rep2

value: treated with 0.6 mM Riboflavin for 8 hours during the dark cycle


title: Cancer Sox10 Low, rep1


title: CR, seedlings, rep1


title: Cancer Sox10 High, rep4

source_name: C, Sox10, High

value: Cancer Cells

value: Sox10 High


title: Naive_HP1g_WT_ATAC-seq_R2

description:
ATACseq-NaivesHP1g-S2
counts.txt
peaks.bed

value: Spleen


title: melin, seedlings, rep3

value: melinoe, EMS mutant of FMN/FHY gene (At4g21470)


title: Cancer Sox10 High, rep3


title: Brain_B_Exposed_S20


title: melin, seedlings, rep2


title: Brain_B_Exposed_S21


title: Naive_HP1g_WT_ATAC-seq_R1

description:
ATACseq-NaivesHP1g-S1
counts.txt
peaks.bed


title: Brain_B_Exposed_S19


title: Cancer Sox10 High, rep2


title: Naive_HP1a_KO_ATAC-seq_R3

description:
ATACseq-NaivesHP1a-S6
counts.txt
peaks.bed


title: Naive_HP1g_KO_ATAC-seq_R1

description:
ATACseq-NaivesHP1g-S4
counts.txt
peaks.bed


title: Cancer Sox10 High, rep1


title: Naive_HP1a_KO_ATAC-seq_R2

description:
ATACseq-NaivesHP1a-S5
counts.txt
peaks.bed


title: melin, seedlings, rep1


title: Col-0, seedlings, rep3


title: Brain_A_Control_S17


title: Control Sox10 Low, rep1

source_name: Control

value: Control Microenvironment

value: Control


title: Naive_HP1a_WT_ATAC-seq_R2

description:
ATACseq-NaivesHP1a-S3
counts.txt
peaks.bed

value: HP1a WT


title: Brain_A_Control_S16

value: Brain tissue


title: Naive_HP1a_WT_ATAC-seq_R3

description:
ATACseq-NaivesHP1a-S4
counts.txt
peaks.bed

value: CD4 T cells


title: Col-0, seedlings, rep1

value: seedlings


title: Control Sox10 Low, rep3

value: 5.O MO


title: Brain_A_Control_S14


title: Brain_A_Control_S13


title: Naive_HP1a_WT_ATAC-seq_R1

description:
ATACseq-NaivesHP1a-S1
counts.txt
peaks.bed


title: Brain_A_Control_S12


title: Col-0, seedlings, rep2


title: Ctrl-3

city: Guangzhou，China

first: sen

middle: da

last: XIE

state: Guangdong

address: 54 Xianlie Road

institute: Zhongshan ophthemology center

description: The replication 3 for Ctrl group of adult mice was subjected to a normoxic exposure. At P17, mice were sacrificed by carbon dioxide euthanasia and eyes were enucleated for further investigation.

data_processing:
P17 mouse retinal tissue were enzymatically dissociated as described above and 15 µl of single-cell suspension at a concentration of ~900,000 cells/ml was loaded into one channel of the ChromiumTM Single Cell B Chip (10X Genomics，1000073), aiming for a recovery of 8000-9000 cells. Cell populations were isolated from mouse retinal. Retinas of the eyes of two mice were taken at a time The Chromium Single Cell 3’Library & Gel Bead Kit v3 (10X Genomics, 1000075) was used for single-cell barcoding, cDNA synthesis and library preparation, following manufacturer’s instructions according to the Single Cell 3’Reagent Kits User Guide Version 3. Libraries were sequenced on Illumina novaseq 6000 using paired-end 150 bp.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Murine retinal endothelial cells

extract_protocol:
Cell populations were isolated from mouse retinal, In brief, the tissue was incubated in dissociation buffer containing 1 mg/ml hyaluronidase（sigma,H3506） and 20,000U/ml DNase I（sigma,DN25） for 15 min at 37 C. Enzymatic digestion was quenched with Dulbecco’s Modifified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, 10270106, Gibco). Cells were resuspended at a concentration of 1 million cells per ml and stained with PBST containing 1% FCS
P17 mouse retinal tissue were enzymatically dissociated as described above and 15 µl of single-cell suspension at a concentration of ~900,000 cells/ml was loaded into one channel of the ChromiumTM Single Cell B Chip (10X Genomics，1000073), aiming for a recovery of 8000-9000 cells. Cell populations were isolated from mouse retinal. Retinas of the eyes of two mice were taken at a time The Chromium Single Cell 3’Library & Gel Bead Kit v3 (10X Genomics, 1000075) was used for single-cell barcoding, cDNA synthesis and library preparation, following manufacturer’s instructions according to the Single Cell 3’Reagent Kits User Guide Version 3. Libraries were sequenced on Illumina novaseq 6000 using paired-end 150 bp.

value: Murine retinal endothelial cells


title: Pre Cancerous Sox10 Low, rep2

source_name: PreC, Sox10, Low

value: Precancerous Microenvironment

value: Sox10 Low


title: Control Sox10 Low, rep2


title: Ctrl-1

description: The replication 1 for Ctrl group of adult mice was subjected to a normoxic exposure. At P17, mice were sacrificed by carbon dioxide euthanasia and eyes were enucleated for further investigation.


title: Ctrl-2

description: The replication 2 for Ctrl group of adult mice was subjected to a normoxic exposure. At P17, mice were sacrificed by carbon dioxide euthanasia and eyes were enucleated for further investigation.


title: Brain_A_Control_S15


title: Pre Cancerous Sox10 Low, rep3


title: Brain_A_Control_S18


title: Brain_A_Control_S11


title: OIR-3

description: The replication 3 for OIR group of adult mice was subjected to a 75% oxygen environment from P7 to P12, Followed by 5 days of normoxic exposure. At P17, mice were sacrificed by carbon dioxide euthanasia and eyes were enucleated for further investigation.


title: Pre Cancerous Sox10 Low, rep1


title: Tconv_HP1g_KO_ATAC-seq_R2

description:
ATACseq-HP1g-S7
counts.txt
peaks.bed

value: HP1g KO


title: Pre Cancerous Sox10 High, rep3

source_name: PreC, Sox10, High

value: Precancerous Cells


title: Brain_A_Control_S10


title: OIR-2

description: The replication 2 for OIR group of adult mice was subjected to a 75% oxygen environment from P7 to P12, Followed by 5 days of normoxic exposure. At P17, mice were sacrificed by carbon dioxide euthanasia and eyes were enucleated for further investigation.


title: Naive_HP1a_KO_ATAC-seq_R1

description:
ATACseq-NaivesHP1a-S2
counts.txt
peaks.bed

value: HP1a KO

value: Naive


title: Tconv_HP1g_WT_ATAC-seq_R3

description:
ATACseq-HP1g-S6
counts.txt
peaks.bed

value: HP1g WT

value: Tconv


title: TconvTreg_HP1g_WT_ATAC-seq_R2

description:
ATACseq-HP1g-S9
counts.txt
peaks.bed

value: Spleen

value: Tconv transferred with Treg


title: OIR-1

description: The replication 1 for OIR group of adult mice was subjected to a 75% oxygen environment from P7 to P12, Followed by 5 days of normoxic exposure. At P17, mice were sacrificed by carbon dioxide euthanasia and eyes were enucleated for further investigation.


title: Brain_A_Control_S9


title: Pre Cancerous Sox10 High, rep1

value: Sox10 High


title: Brain_A_Control_S8


title: Brain_A_Control_S7


title: TconvTreg_HP1g_KO_ATAC-seq_R1

description:
ATACseq-HP1g-S4
counts.txt
peaks.bed


title: Tconv_HP1g_WT_ATAC-seq_R2

description:
ATACseq-HP1g-S5
counts.txt
peaks.bed


title: SKHEP-1 cell, lung metastatic tumor cell, mini-CRISPR library, R4-2

city: Hangzhou

first: yilong

last: Zou

state: Zhejiang

address: 18 Shilongshan Street, Xihu District

institute: Westlake University

description:
NGS
mini-SK-sample-20

library_source: other

data_processing:
MAGeCK v0.5.9.4
Assembly: hg38
Supplementary files format and content: tab-delimited txt files includes normalized counts for each sample

molecule: other

extract_protocol:
Cell pellets were dissolved by STE buffer, proteinase K and SDS and incubated at 65℃ overnight. Saturated NaCl solution and chloroform were used for phase separation, followed by isopropanol for DNA precipitation. DNA pellets were then washed twice by 70% ethanol solution and dissolved by ultra-pure water. 30μg DNA per sample was used for subsequent library construction.
NGS library construction was followed to Feng Zhang's protocol in 2017.

value: hepatocarcinoma cell


title: Tconv_HP1g_KO_ATAC-seq_R3

description:
ATACseq-HP1g-S8
counts.txt
peaks.bed


title: SKHEP-1 cell, lung metastatic tumor cell, mini-CRISPR library, R3-2

description:
NGS
mini-SK-sample-18


title: SKHEP-1 cell, lung metastatic tumor cell, mini-CRISPR library, R4-1

description:
NGS
mini-SK-sample-19


title: Tconv_HP1g_WT_ATAC-seq_R1

description:
ATACseq-HP1g-S1
counts.txt
peaks.bed


title: TconvTreg_HP1g_WT_ATAC-seq_R1

description:
ATACseq-HP1g-S3
counts.txt
peaks.bed


title: SKHEP-1 cell, lung metastatic tumor cell, mini-CRISPR library, R2-2

description:
NGS
mini-SK-sample-16


title: Fatbody_F_Exposed_S67

source_name: Fat body

value: Fat body


title: TconvTreg_HP1g_KO_ATAC-seq_R3

description:
ATACseq-HP1g-S12
counts.txt
peaks.bed

value: CD4 T cells


title: Fatbody_F_Exposed_S65


title: Fatbody_F_Exposed_S64


title: SKHEP-1 cell, lung metastatic tumor cell, mini-CRISPR library, R2-1

description:
NGS
mini-SK-sample-15


title: Tconv_HP1g_KO_ATAC-seq_R1

description:
ATACseq-HP1g-S2
counts.txt
peaks.bed


title: Fatbody_F_Exposed_S63


title: SKHEP-1 cell, lung metastatic tumor cell, mini-CRISPR library, R1-2

description:
NGS
mini-SK-sample-14


title: TconvTreg_HP1g_KO_ATAC-seq_R2

description:
ATACseq-HP1g-S11
counts.txt
peaks.bed


title: Pre Cancerous Sox10 High, rep2


title: SY3

city: Beijing

first: Chao

last: Liu

state: Beijing

address: No 5 Bei Xiange Road

department: Clinical Laboratory

institute: Guang’anmen Hospital, China Academy of Chinese Medical Sciences

description: Library name: Sample 6

data_processing:
Illumina Casava 2.19 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell
Supplementary files format and content: fpkm

growth_protocol: The culture conditions for the HepG2.2.15 cell line are DMEM medium containing 10% fetal bovine serum, 1%Penicillin-Streptomycin and 0.4ug/ml G418.

extract_protocol:
The HepG2.2.15 cell culture supernatants were removed by centrifugation, HepG2.2.15 cells frozen on dry ice, and RNA was harvested using Trizol reagent. lllumina TruSeq RNA Sample Prep Kit(Cat#FC-122-10)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The YQSHJD freeze-dried powder dilution and PBS were added to HepG2.2.15 cells and incubated for 3 days with the drug constituting 10% of the culture medium

value: Hepatocellular carcinoma cell line

value: WT

value: YQSHJD drug


title: SY2

description: Library name: Sample 5


title: Fatbody_F_Exposed_S62


title: TconvTreg_HP1a_KO_ATAC-seq_R3

description:
ATACseq-HP1a-S36
counts.txt
peaks.bed


title: SY1

description: Library name: Sample 4


title: SKHEP-1 cell, lung metastatic tumor cell, mini-CRISPR library, R1-1

description:
NGS
mini-SK-sample-13


title: Fatbody_F_Exposed_S61


title: TconvTreg_HP1a_KO_ATAC-seq_R2

description:
ATACseq-HP1a-S35
counts.txt
peaks.bed


title: DZ3

description: Library name: Sample 3

value: physiological saline


title: SKHEP-1 cell, lung metastatic tumor cell, mini-CRISPR library, R3-1

description:
NGS
mini-SK-sample-17


title: Fatbody_F_Exposed_S66


title: SKHEP-1 cell, subcutaneous tumor cell, mini-CRISPR library, R4

description:
NGS
mini-SK-sample-12


title: Fatbody_E_Exposed_S60


title: TconvTreg_HP1a_KO_ATAC-seq_R1

description:
ATACseq-HP1a-S34
counts.txt
peaks.bed


title: SKHEP-1 cell, subcutaneous tumor cell, mini-CRISPR library, R2

description:
NGS
mini-SK-sample-10


title: SKHEP-1 cell, subcutaneous tumor cell, mini-CRISPR library, R3

description:
NGS
mini-SK-sample-11


title: DZ2

description: Library name: Sample 2


title: Fatbody_E_Exposed_S58


title: SKHEP-1 cell, subcutaneous tumor cell, mini-CRISPR library, R1

description:
NGS
mini-SK-sample-9


title: DZ1

description: Library name: Sample 1


title: TconvTreg_HP1a_WT_ATAC-seq_R3

description:
ATACseq-HP1a-S33
counts.txt
peaks.bed

value: HP1a WT


title: Fatbody_E_Exposed_S59


title: Fatbody_E_Exposed_S57


title: TconvTreg_HP1g_WT_ATAC-seq_R3

description:
ATACseq-HP1g-S10
counts.txt
peaks.bed


title: SKHEP-1 cell, in_vitro_culture_7.doubling, mini-CRISPR library, R4

description:
NGS
mini-SK-sample-8


title: Fatbody_E_Exposed_S56


title: TconvTreg_HP1a_WT_ATAC-seq_R2

description:
ATACseq-HP1a-S32
counts.txt
peaks.bed


title: Tconv_HP1a_KO_ATAC-seq_R3

description:
ATACeq-HP1a-S30
counts.txt
peaks.bed


title: SKHEP-1 cell, in_vitro_culture_7.doubling, mini-CRISPR library, R3

description:
NGS
mini-SK-sample-7


title: AD2, SZ, Replicate2

city: Munich

first: Moritz

middle: J

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

country: Germany

description:
Library name: SCZ_2_hNGN2
SCZ_2_hNGN2

data_processing:
bcl2fast2
Star Alignment
htseq-count
DESeq2 Normalisation
Assembly: GRCh38.107
Supplementary files format and content: Raw Counts
Supplementary files format and content: Normalised Counts

source_name: iNeurons

growth_protocol: NPC were seeded at a density of 4.29x104/cm2 on PLO/Laminin-coated 12-well plates in Neural Progenitor medium (day in vitro (DIV)-1). On DIV0, cells were transduced with pLV-TetO-hNGN2-eGFP-Puro + FUdeltaGW-rtTA (Addgene #79823 (23), #19780 (24)) for differentiation into glutamatergic neurons (NGN2) and TetO-Ascl1-puro + DLX2-hygro + FUdeltaGW-rtTA (Addgene #97329 (25), #97330 (25), #19780) for differentiation into GABAergic neurons (AD2) in separate wells according to published protocols (23, 26). On DIV1, the medium was changed to Neural Progenitor Medium containing 1 µg/ml of Doxycycline (Sigma-Aldrich #D9891), to induce tetracycline-dependent transgene expression. After 24h (DIV2), selection of transduced cells was performed by addition of the respective antibiotics to the medium (2 µg/ml puromycine (Thermo Fisher Scientific) for NGN2-transduced cells, 2 µg/ml of puromycine + 250 µg/ml of hygromycin (Carl Roth) for AD2-transduced cells). On DIV3, NGN2 and AD2 neurons were detached with Accutase and seeded into monocultures or co-cultures at a ratio of 80:20 on PLO/Laminin-coated plates. The total seeding density was 1.25x105 neurons/cm2 for types of cultures. Neurons were cultured in Neurobasal Plus medium, supplemented with 1 x B27 Plus supplement, 1 x N2 supplement, 1 µg/ml of laminin, 20 ng/ml of GDNF (Peprotech), 20 ng/ml of BDNF (Peprotech), 35 µg/ml of L-Ascorbic Acid (Sigma-Aldrich), 1x Penicillin/Streptomycin and 1 µg/ml of Doxycycline. After neurons attached to the plate bottom, 3.125x104/cm2 primary mouse astrocytes were added to all cultures. 50 % medium changes with neuronal medium (without Doxycycline) were performed until DIV24, when the medium was again supplemented with 1 µg/ml Doxycycline to support neuronal maturation at the final stages of the differentiation process until DIV28.

extract_protocol:
Samples were lysed with RLT Buffer and extracted with Micro Rneasy (Qiagen) kit after shredding. Eluted in 14 ul of H20
SmartSeq V4 Ultra Low Input RNA & Nextera-XT Library Prep

value: iNeurons

value: hNGN2 Neurons

value: Schizophrenic


title: AD2, SZ, Replicate3

description:
Library name: SCZ_4_hNGN2
SCZ_4_hNGN2


title: AD2, SZ, Replicate4

description:
Library name: SCZ_5_hNGN2
SCZ_5_hNGN2


title: Fatbody_E_Exposed_S55


title: SKHEP-1 cell, in_vitro_culture_7.doubling, mini-CRISPR library, R2

description:
NGS
mini-SK-sample-6


title: Fatbody_E_Exposed_S54


title: Tconv_HP1a_KO_ATAC-seq_R1

description:
ATACseq-HP1a-S28
counts.txt
peaks.bed

value: HP1a KO


title: AD2, SZ, Replicate1

description:
Library name: SCZ_1_hNGN2
SCZ_1_hNGN2


title: hNGN2 Neurons, Control, Replicate3

description:
Library name: Control_3_hNGN2
Control_3_hNGN2

value: Control


title: SKHEP-1 cell, pre-injected cell, mini-CRISPR library, R4

description:
NGS
mini-SK-sample-4


title: Tconv_HP1a_WT_ATAC-seq_R3

description:
ATACseq-HP1a-S27
counts.txt
peaks.bed

value: Tconv


title: SKHEP-1 cell, in_vitro_culture_7.doubling, mini-CRISPR library, R1

description:
NGS
mini-SK-sample-5


title: hNGN2 Neurons, Control, Replicate2

description:
Library name: Control_2_hNGN2
Control_2_hNGN2


title: Tconv_HP1a_WT_ATAC-seq_R2

description:
ATACeq-HP1a-S26
counts.txt
peaks.bed

value: Spleen


title: Fatbody_E_Exposed_S51


title: Fatbody_E_Exposed_S52


title: SKHEP-1 cell, pre-injected cell, mini-CRISPR library, R3

description:
NGS
mini-SK-sample-3


title: Fatbody_E_Exposed_S50


title: Tconv_HP1a_WT_ATAC-seq_R1

description:
ATACseq-HP1a-S25
counts.txt
peaks.bed


title: hNGN2 Neurons, Control, Replicate1

description:
Library name: Control_1_hNGN2
Control_1_hNGN2


title: AD2 Neurons, SZ, Replicate4

description:
Library name: SCZ_5_AD2
SCZ_5_AD2

value: AD2 Neurons


title: AD2 Neurons, SZ, Replicate3

description:
Library name: SCZ_4_AD2
SCZ_4_AD2


title: Fatbody_E_Exposed_S49


title: TconvTreg_HP1a_WT_ATAC-seq_R1

description:
ATACseq-HP1a-S31
counts.txt
peaks.bed

value: Tconv transferred with Treg


title: SKHEP-1 cell, pre-injected cell, mini-CRISPR library, R2

description:
NGS
mini-SK-sample-2

value: hepatocarcinoma cell


title: td+, bleomycin, scRNA-seq

city: New York

first: Yinshan

last: Fang

state: New York

address: 650W 168th Street

institute: Columbia University Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: matrix files

source_name: lung

extract_protocol:
To obtain single cell suspension, lung tissues were dissected, washed with PBS and then minced with a razor blade followed by digesting in a digestion buffer (2 mg/ml collagenase-IV, 2 mg/ml dispase II and 10 U/ml DNase I) for 30 min at 37°C. DMEM containing 10% FBS was added to stop digestion and then the cells were filtered through 100-μm and 40-μm strainers. After centrifuged at 300g for 5 min, the cell pellet was resuspended in red blood cell lysis buffer (Sigma), incubated for 2 min at 37°C, washed with HBSS containing 10% FBS and then centrifuged at 300g for 5 min to obtain cell pellet. To isolate Tdtomato+ cells for Single cell RNA sequencing (scRNA-seq), single cell suspension was applied to sort live Tdtomato+ cells by using BD Influx cell Sorter.
Single Cell 3’ V2 chemistry kit (10x Genomics) was used to produce single-cell barcoded droplets and libraries according to the manufacturer's protocol.

value: lung

value: 8-10 weeks

value: tdtomato+ cells

value: bleomycin


title: Fatbody_D_Exposed_S48

city: London

data_processing:
nf-core RNASeq pipeline v3.14.0 using Nextflow 24.04.2
Raw reads were trimmed with trim galore, mappes with star, then gene counts quantified with Salmon
Assembly: BIMP3.0 JBEUIP000000000, SUB14541561
Supplementary files format and content: tab delimitd file with the raw counts for each sample (brain and fatbody in separate tsv files)

extract_protocol:
Qiagen RNEasy Mini Kit
Quant-Seq mRNA libraries were prepared by the Iowa State University DNA Facility following manufacturer’s protocols, and subjected to Illumina Quant-Seq using a HiSEQ 3000 Sequencer

value: Fat body


title: SKHEP-1 cell, pre-injected cell, mini-CRISPR library, R1

description:
NGS
mini-SK-sample-1


title: Tconv_HP1a_KO_ATAC-seq_R2

description:
ATACseq-HP1a-S29
counts.txt
peaks.bed

value: CD4 T cells


title: td+, saline, scRNA-seq

description: 10x Genomics

value: saline


title: AD2 Neurons, SZ, Replicate2

description:
Library name: SCZ_2_AD2
SCZ_2_AD2

value: iNeurons


title: Fatbody_E_Exposed_S53


title: ES-2-MC2-Liver cell, in_vitro_culture_7.days, mini-CRISPR library, R1

description:
NGS
mini-ES-2-sample_21

value: ovary cancer cell


title: ES-2-MC2-Liver cell, in_vitro_culture_7.days, mini-CRISPR library, R2

description:
NGS
mini-ES-2-sample_22


title: Fatbody_D_Exposed_S47


title: AD2 Neurons, Control, Replicate3

description:
Library name: Control_3_AD2
Control_3_AD2


title: MPNST ST88-14 p125

city: Houston

first: Keila

middle: E.

last: Torres

state: TX

address: 1515 Holcombe Blvd

department: Surgical Oncology

institute: The University of Texas MD Anderson Cancer Center

description:
MPNST Cell Line
200123530003_R01C01

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: All raw data were processed and normalized using Minfi19 in R v3.4.4.

label: Cy3 and Cy5

source_name: MPNST Cell Line

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA from the FF and FFPE tissue specimens and cell lines was isolated (phenol-chloroform extraction and QIAamp DNA FFPE Tissue Kit, DNeasy Blood & Tissue Kit; Qiagen), followed by bisulfite conversion using a Zymo Direct Kit (Zymo Research), according to the manufacturers’ protocols.

value: MPNST Cell Line

value: Cancer


title: Fatbody_D_Exposed_S46


title: MPNST ST88-14 p127

description:
MPNST Cell Line
200123530003_R03C01


title: MPNST ST88-14 p126

description:
MPNST Cell Line
200123530003_R02C01


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, mini-CRISPR library, R4

description:
NGS
mini-ES-2-sample_20


title: MPNST S462 p47

description:
MPNST Cell Line
101178130142_R06C02


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, mini-CRISPR library, R3

description:
NGS
mini-ES-2-sample_19


title: Fatbody_D_Exposed_S45


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, mini-CRISPR library, R2

description:
NGS
mini-ES-2-sample_18


title: AD2 Neurons, Control, Replicate1

description:
Library name: Control_1_AD2
Control_1_AD2

value: Control


title: Fatbody_D_Exposed_S44


title: MPNST S462 p46

description:
MPNST Cell Line
101178130142_R05C02


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, mini-CRISPR library, R1

description:
NGS
mini-ES-2-sample_17


title: Fatbody_D_Exposed_S43


title: MPNST S462 p45

description:
MPNST Cell Line
101178130142_R04C02


title: Fatbody_D_Exposed_S42


title: NSC Lot8757 p4

description:
Normal Schwann Cell Line
101178130142_R03C01

source_name: Normal Schwann Cell Line

value: Normal Schwann Cell Line

value: Normal


title: Fatbody_D_Exposed_S41


title: NCM, GNAQ wildtype, rep2

city: Montreal

first: Bioinformatics

last: Platform

state: Quebec

address: 1001 Decarie Blvd

institute: RI-MUHC

data_processing:
The raw Fastq files were preprocessed using fastp. The trimmed FASTQ files were aligned to human reference GRCh37 using STAR. The aligned reads were processed with HTSEQ to obtain the read counts.
Assembly: GRCh37
Supplementary files format and content: Raw counts in text format for each sample

source_name: Human choroid

growth_protocol: 92.1 was cultured in RPMI-1640 (CorningTM or Wisent Inc.) supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES, 2 mM glutagro, 1 mM NaPyruvate, 1% penicillin and streptomycin (pen/strep) and 10 µg/ml insulin (Roche). NCM and MutCM were cultured in Melanocyte Growth Medium M2 (PromoCell).

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Micro kit following the manufacturer’s protocols. RNA quality and concentration were evaluated by Nanodrop.
polyA Enriched RNA Library Preparation

treatment_protocol: Not applicable.

value: Human choroid

value: Choroidal melanocytes


title: NCM, GNAQ wildtype, rep1


title: AD2 Neurons, SZ, Replicate1

description:
Library name: SCZ_1_AD2
SCZ_1_AD2

value: AD2 Neurons

value: Schizophrenic


title: NCM, GNAQ wildtype, rep3


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, mini-CRISPR library, R3

description:
NGS
mini-ES-2-sample_15


title: NSC Lot8757 p3

description:
Normal Schwann Cell Line
101178130142_R02C01


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, mini-CRISPR library, R4

description:
NGS
mini-ES-2-sample_16


title: MutCM, GNAQ mutant, rep3


title: NSC Lot8757 p2

description:
Normal Schwann Cell Line
101178130142_R01C01


title: Fatbody_D_Exposed_S40


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, mini-CRISPR library, R2

description:
NGS
mini-ES-2-sample_14


title: Fatbody_D_Exposed_S39


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, mini-CRISPR library, R1

description:
NGS
mini-ES-2-sample_13


title: MutCM, GNAQ mutant, rep2


title: AD2 Neurons, Control, Replicate2

description:
Library name: Control_2_AD2
Control_2_AD2


title: MutCM, GNAQ mutant, rep1


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, mini-CRISPR library, R4

description:
NGS
mini-ES-2-sample_12


title: Fatbody_D_Exposed_S38


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, mini-CRISPR library, R3

description:
NGS
mini-ES-2-sample_11


title: UM, GNAQ mutant, rep3

value: Uveal melanoma


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, mini-CRISPR library, R2

description:
NGS
mini-ES-2-sample_10


title: UM, GNAQ mutant, rep2


title: GSM1365193

label: Cy3 and Cy9

source_name: Nerve

value: Nerve


title: GSM1365191

label: Cy3 and Cy7


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, mini-CRISPR library, R1

description:
NGS
mini-ES-2-sample_9


title: GSM1365190

label: Cy3 and Cy6


title: Fatbody_C_Control_S35


title: ES-2-MC2-Liver cell, in_vitro_culture_7.doubling, mini-CRISPR library, R4

description:
NGS
mini-ES-2-sample_8


title: Fatbody_D_Exposed_S37


title: Fatbody_C_Control_S34


title: VES25-2

city: Chicago

first: Yanhong

last: Cui

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: University of Chicago

data_processing:
After sequencing, FastQC (version 0.11.7) was used to assess sequencing quality.
Trimmomatic (version 0.36) was used to remove adapters and filter reads (Phred score >33).
Reads were then aligned to the reference genome (hg38) using STAR (version 2.6.1d). Picard (version 2.18.29) was used to mark and remove duplicate reads.
FeatureCounts of Subread (version 1.5.3) was used to count aligned reads.
Assembly: hg38
Supplementary files format and content: fastq.GZ file for raw file; Text file for processed data file

source_name: Skin Melanoma

growth_protocol: MEL624 maintained in DMEM with 10% FBS and antibiotics in 5% CO2 incubator at 37oC

extract_protocol:
total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) and RNA was purified after treated with DNase for sequencing.
Oligo dT mRNA directional

treatment_protocol: At 72-h VES (25uM) treatment

value: Skin Melanoma

value: WT

value: VES


title: UM, GNAQ mutant, rep1


title: Fatbody_C_Control_S36

value: Fat body


title: GFS4664

source_name: NF

value: NF


title: GSM1365194

label: Cy3 and Cy10


title: GFS4660


title: VES25-1


title: ES-2-MC2-Liver cell, in_vitro_culture_7.doubling, mini-CRISPR library, R2

description:
NGS
mini-ES-2-sample_6

value: ovary cancer cell


title: GFS4658


title: ES-2-MC2-Liver cell, in_vitro_culture_7.doubling, mini-CRISPR library, R1

description:
NGS
mini-ES-2-sample_5


title: Fatbody_C_Control_S32


title: GSM1365192

label: Cy3 and Cy8


title: Vehicle-2

value: Vehicle


title: Vehicle-1


title: GFS4657


title: ES-2-MC2-Liver cell, pre-injected cell, mini-CRISPR library, R4

description:
NGS
mini-ES-2-sample_4


title: Fatbody_C_Control_S31


title: Fatbody_C_Control_S33


title: [ATAC-seq] LT -E2 MCF-7 Rep3

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

description: [ATAC-seq] long-term estrogen-deprived MCF-7 replicate 3

data_processing:
Adapters were removed and reads were trimmed using fastP.
Reads were aligned to hg38 using STAR 2.7.
Bedgraphs were generated using deeptools. Reads were normalized to total library size (RPM).
Assembly: hg38
Supplementary files format and content: .fastq.gz files contain raw trimmed reads.
Supplementary files format and content: .bedgraph files contain mapped reads normalized to library size (RPM).

source_name: breast adenocarcinoma

growth_protocol: Cells were grown in phenol red free DMEM + 5% charcoal-stripped FBS with 1x PenStrep, 1x Glutamax, 1x Sodium Pyruvate, 1x non-essential aminoacids, and 0.01mg/ml insulin.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy mini kit and treated with Dneasy prior to library construction; ATAC-seq was prepared using OMNI-ATAC protocol from Corces et. al. (2017).
Libraries were prepared using standard Illumina TruSeq protocols.

treatment_protocol: Long-term estrogen treated (LT +E2 MCF-7) cells were treated with 10nM b-estradiol for 1 year; 48 hour estrogen treated (48hr +E2 MCF-7) cells were treated with 10nM b-estradiol for 48 hours; long-term estrogen-deprived (LT -E2 MCF-7) cells were treated with DMSO as a mock treatment.

value: breast adenocarcinoma

value: epithelial cell

value: long-term estrogen deprived


title: ES-2-MC2-Liver cell, pre-injected cell, mini-CRISPR library, R3

description:
NGS
mini-ES-2-sample_3


title: ES-2-MC2-Liver cell, in_vitro_culture_7.doubling, mini-CRISPR library, R3

description:
NGS
mini-ES-2-sample_7


title: [ATAC-seq] LT -E2 MCF-7 Rep2

description: [ATAC-seq] long-term estrogen-deprived MCF-7 replicate 2


title: GFS4653


title: ES-2-MC2-Liver cell, pre-injected cell, mini-CRISPR library, R2

description:
NGS
mini-ES-2-sample_2


title: Fatbody_C_Control_S29


title: GFS4651


title: Fatbody_C_Control_S28


title: [ATAC-seq] 48hr +E2 MCF-7 Rep 3

description: [ATAC-seq] 48-hours estrogen-treated MCF-7 replicate 3

value: 48-hours estrogen treated


title: Fatbody_C_Control_S27


title: [ATAC-seq] LT -E2 MCF-7 Rep1

description: [ATAC-seq] long-term estrogen-deprived MCF-7 replicate 1


title: GFS4644


title: Fatbody_C_Control_S30


title: ES-2-MC2-Liver cell, plasmid, metabolic library

description:
NGS
metab-sample_14


title: GFS4640


title: [ATAC-seq] 48hr +E2 MCF-7 Rep 2

description: [ATAC-seq] 48-hours estrogen-treated MCF-7 replicate 2


title: Fatbody_C_Control_S26


title: Fatbody_C_Control_S25


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, metabolic library, R5

description:
NGS
metab-sample_13


title: [ATAC-seq] 48hr +E2 MCF-7 Rep 1

description: [ATAC-seq] 48-hours estrogen-treated MCF-7 replicate 1


title: Fatbody_B_Exposed_S24


title: [ATAC-seq] LT +E2 MCF-7 Rep 3

description: [ATAC-seq] long-term estrogen-treated MCF-7 replicate 3

value: long-term estrogen treated


title: GFS4638


title: GFS4655


title: [ATAC-seq] LT +E2 MCF-7 Rep 2

description: [ATAC-seq] long-term estrogen-treated MCF-7 replicate 2


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, metabolic library, R3

description:
NGS
metab-sample_11


title: GFS4637


title: Fatbody_B_Exposed_S23


title: ES-2-MC2-Liver cell, pre-injected cell, mini-CRISPR library, R1

description:
NGS
mini-ES-2-sample_1


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, metabolic library, R2

description:
NGS
metab-sample_10


title: GFS4632


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, metabolic library, R1

description:
NGS
metab-sample_9


title: [RNA-seq] LT -E2 MCF-7 Rep3

description: [RNA-seq] long-term estrogen-deprived MCF-7 replicate 3


title: GFS4642


title: Fatbody_B_Exposed_S20


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, metabolic library, R5

description:
NGS
metab-sample_8


title: [RNA-seq] LT -E2 MCF-7 Rep2

description: [RNA-seq] long-term estrogen-deprived MCF-7 replicate 2


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, metabolic library, R4

description:
NGS
metab-sample_7


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, metabolic library, R4

description:
NGS
metab-sample_12


title: GFS4621


title: Fatbody_B_Exposed_S19


title: Fatbody_B_Exposed_S18


title: GFS4663


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, metabolic library, R3

description:
NGS
metab-sample_6


title: [RNA-seq] LT -E2 MCF-7 Rep1

description: [RNA-seq] long-term estrogen-deprived MCF-7 replicate 1


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, metabolic library, R2

description:
NGS
metab-sample_5


title: GFS4659


title: [RNA-seq] 48hr +E2 MCF-7 Rep 2

description: [RNA-seq] 48-hours estrogen-treated MCF-7 replicate 2


title: [RNA-seq] 48hr +E2 MCF-7 Rep 1

description: [RNA-seq] 48-hours estrogen-treated MCF-7 replicate 1


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, metabolic library, R1

description:
NGS
metab-sample_4


title: [ATAC-seq] LT +E2 MCF-7 Rep 1

description: [ATAC-seq] long-term estrogen-treated MCF-7 replicate 1


title: GFS4628


title: Fatbody_B_Exposed_S17


title: Fatbody_B_Exposed_S16


title: Fatbody_B_Exposed_S22


title: Fatbody_B_Exposed_S21


title: GFS4656


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, metabolic library, R3

description:
NGS
metab-sample_3


title: GFS4623


title: GFS4654


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, metabolic library, R2

description:
NGS
metab-sample_2


title: [RNA-seq] LT +E2 MCF-7 Rep 3

description: [RNA-seq] long-term estrogen-treated MCF-7 replicate 3


title: Fatbody_B_Exposed_S15


title: [RNA-seq] 48hr +E2 MCF-7 Rep 3

description: [RNA-seq] 48-hours estrogen-treated MCF-7 replicate 3


title: [RNA-seq] LT +E2 MCF-7 Rep 2

description: [RNA-seq] long-term estrogen-treated MCF-7 replicate 2


title: ES-2-MC2-Liver cell, pre-injected cell, metabolic library, R1

description:
NGS
metab-sample_1


title: GFS4650


title: Fatbody_B_Exposed_S14


title: [RNA-seq] LT +E2 MCF-7 Rep 1

description: [RNA-seq] long-term estrogen-treated MCF-7 replicate 1


title: Fatbody_B_Exposed_S13


title: GFS4652


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, phosphatase library, R3

description:
NGS
ph-sample_12


title: GFS4641


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, phosphatase library, R2

description:
NGS
ph-sample_11


title: HNSR3

city: Guangzhou

first: Jingting

last: Li

address: No 1, Zhongshan 2 Road, 12th Floor

department: Institue of Precision Medicine

institute: The First Affiliated Hospital, Sun Yat-sen University

description: single cell RNA-Seq

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Briefly, reads with low-quality barcodes and UMIs were filtered out and then mapped to the reference genome. Reads uniquely mapped to the transcriptome and intersecting an exon at least 50% were considered for UMI counting.
Before quantification, the UMI sequences would be corrected for sequencing errors, and valid barcodes were identified based on the EmptyDrops method.[1] The cell by gene matrices were produced via UMI counting and cell barcodes calling.
The cell by gene matrices for each sample were individually imported to Seurat [2] version 3.1.1 for downstream analysis.
Cells with unusually high number of UMIs (≥8000) or mitochondrial gene percent (≥10%) were filtered out. We also excluded cells with less than 500 or more than 4000 genes detected.
Genome_build: hg38

source_name: Skin

growth_protocol: Skin tissues were harvested and digested into single cell suspension.

extract_protocol:
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.
Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA.

value: Human scar tissue

value: untreated


title: Fatbody_A_Control_S12


title: Fatbody_A_Control_S11


title: HNSR2

description: single cell RNA-Seq


title: ES-2-MC2-Liver cell, lung metastatic tumor cell, phosphatase library, R1

description:
NGS
ph-sample_10


title: HNSR1

description: single cell RNA-Seq


title: GFS4636


title: Fatbody_A_Control_S10


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, phosphatase library, R3

description:
NGS
ph-sample_9


title: GFS4631


title: Fatbody_A_Control_S9


title: HNS6

description: single cell RNA-Seq

value: Normal human skin tissue


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, phosphatase library, R2

description:
NGS
ph-sample_8


title: HNS4

description: single cell RNA-Seq


title: GFS4627


title: ES-2-MC2-Liver cell, subcutaneous tumor cell, phosphatase library, R1

description:
NGS
ph-sample_7


title: GFS4622


title: HNS3

description: single cell RNA-Seq


title: Fatbody_A_Control_S7


title: Fatbody_A_Control_S8


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, phosphatase library, R2

description:
NGS
ph-sample_6


title: GFS4620


title: Fatbody_A_Control_S6


title: HK-NS2

description: single cell RNA-Seq

value: Normal human skin tissue around keloid


title: Fatbody_A_Control_S5


title: Pancreas, 6 months old, rep2

city: changsha

first: yan

last: cheng

state: Hunan

address: Changsha, Hunan, China

institute: Institute of Subtropical Agriculture, Chinese Academy of Sciences

description: DY2 (biol rep 2)

data_processing:
The scRNA-seq libraries were checked for quality using the Agilent Bioanalyzer High Sensitivity chip.
Sequencing results were converted to FASTQ files using Illumina bcl2fastq software (version 5.01).
Raw data were demultiplexed, barcode and mapped to the goat reference genome using the Cell Ranger package (version 3.1.0).
Feature-barcode raw digital gene expression matrix (UMI counts per gene per cell) was filtered and normalized by using the R package Seurat  (Version 3.1.1).
Genes detected in fewer than one cell were filtered out, and cells were removed if they expressed fewer than 500 detected genes, UMI counts less than Inf, and the percent of mitochondrial-DNA derived gene-expression < 25%. The Doublet Finder package (version 2.0.3) was also used to remove doublets.
Assembly: GCF_001704415.1_ARS1

organism: Capra hircus

source_name: Pancreas

extract_protocol:
The pancreas tissues were quickly isolated from goats, divided into three portions on ice and rinsed with 1× PBS. One portion of the tissues from twin female goats (n=2/group) was minced into 2-3 mm pieces and then incubated in a 37 °C water bath with multiple enzymes (1.0 mg/mL collagenase IV, 2.0 mg/mL dispase, and 50 U/mL DNase I) at 100 × rpm for 30 min. It was worth noting that the suspension should be taken and counted to adjust the digestion time during the digestion process. The digestion was stopped by adding 10% FBS, followed by a filtration step through 70-μm and 30-μm Smart Strainer (Miltenyi Biotec, Bergisch Gladbach, Germany). The suspension was transferred to a 15-mL centrifuge tube and centrifuged at 400 × g for 7 min at 12 °C, and then the supernatant was discarded. Dissociated cells were centrifuged at 300 × g for 5 min at 12 °C, washed twice with 1× DPBS, and resuspended in 2 mL of 1640 (Gibco). Isolated single cells were applied to Red Blood Cell Lysis Buffer and the MACS Dead Cell Removal Kit (Miltenyi Biotec, Bergisch Gladbach, Germany) to remove red blood cells, dead cells and cellular debris following the manufacturer’s recommendations. After that, the cells were counted using a haemocytometer (Thermo Fisher Scientific) and checked for viability via trypan blue (Thermo Fisher Scientific, Waltham, MA, USA). Finally, all the single-cell suspensions of each sample were free of cell debris and had high viability (over 90%). The appropriate volume was calculated for a target capture of 8000 cells, and then the cells were further diluted to a user guide concentration (700–1200 cells/μL) with 1× PBS with 0.04% BSA for 10X Genomics sequencing.
The scRNA-seq libraries were constructed using the 10x Genomics 3' Reagent Kits v3.

value: Pancreas

value: acinar_cell, immune_cell, activated_pancreatic_stellate_cell, beta_cell, ductal_cell, endocrine_like_cell, endothelial_cell, delta_cell


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, phosphatase library, R1

description:
NGS
ph-sample_5


title: Pancreas, 6 months old, rep1

description: DY1 (biol rep 1)


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, phosphatase library, R5

description:
NGS
ph-sample_3


title: GFS4639


title: HK3

description: single cell RNA-Seq

value: Human keloid tissue


title: Fatbody_A_Control_S3


title: Pancreas, 10 days old, rep2

description: XY2 (biol rep 2)


title: ES-2-MC2-Liver cell, pre-injected cell, phosphatase library, R1

description:
NGS
ph-sample_2


title: Fatbody_A_Control_S4


title: HK2

description: single cell RNA-Seq


title: Pancreas, 10 days old, rep1

description: XY1 (biol rep 1)


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, phosphatase library, R4

description:
NGS
ph-sample_1


title: HK1

description: single cell RNA-Seq


title: Fatbody_A_Control_S1


title: Fatbody_A_Control_S2


title: HK-NS3

description: single cell RNA-Seq


title: MLO-Y4 cells with 50% B16F10 CM for 48h_03

status: Public on Nov 24 2024

city: Erlangen

first: Yewei

last: Jia

address: Werner-von-Siemens-Straße 7

department: Department of Internal Medicine 3

institute: Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen

data_processing:
Raw reads of FASTQ format were processed through fastp. Clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality. Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl). Paired-end clean reads were aligned to the reference genome using theSTAR (v2.5) software. STAR used the method of Maximal Mappable Prefix (MMP), which can generate a precise maping result forjunction reads.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and read counts mapped to this gene.
Supplementary files format and content: Excel file (xlsx) contains raw counts for each sample
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

growth_protocol: The MLO-Y4 murine osteocytes were cultured on plates pre-coated with rat tail collagen type I (Corning, Cat. #354236, 0.15 mg/ml), and in α-MEM supplemented with 2.5% FBS, 2.5% bovine calf serum (BCS, VWR, Cat. #HYCLSH30072.3), and penicillin-streptomycin at 37°C and 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries
Sequencing libraries were generated using  NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA), and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina).

value: Murine Osteocyte-like Cell Line

value: Treatment


title: MLO-Y4 cells with 50% B16F10 CM for 48h_01


title: MLO-Y4 cells without treatment_02

value: Control


title: MLO-Y4 cells without treatment_03


title: Interneurons grafted into human organoids

city: Santa Cruz

first: Mohammed

middle: Andres

last: Mostajo-Radji

state: CA

address: 2300 Delaware Ave

department: Genomics Institute

institute: University of California Santa Cruz

description: 10X Genomics

data_processing:
Transcriptomes were aligned to both the human (GRCh38) and mouse (mm10) reference genomes, integrating the td-Tomato sequence into the mouse genome. Alignments were performed using Cell Ranger version 5 . Cells aligning to the human genome and td-Tomato-negative mouse cells were excluded, resulting in a final dataset of 225 td-Tomato-positive mouse cells. Subsequent analysis was carried out in Scanpy 1.10.2 . The raw counts expression matrix was loaded as an AnnData object, normalized by read depth, log-transformed, and scaled per gene across the dataset. Cells with fewer than 200 detected genes and genes expressed in fewer than three cells were filtered out.
Assembly: mm10
Supplementary files format and content: h5ad with gene symbols

source_name: medial ganglionic emminence

growth_protocol: Embryonic day 13.5 mouse cortical interneurons (cINs) progenitors were grafted onto FBS-depleted human cortical organoids (cell line H2B.-1323.4; female; RRID: CVCL_0G84). The cINs were labeled genetically by breeding the Nkx2.1-Cre (C57BL/6J-Tg(Nkx2-1-cre)2Sand/J; The Jackson Laboratory #008661) and the Ai14 (B6;129S6-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J; The Jackson Laboratory #007908) mice. 10 organoids were grafted at 6 weeks in vitro.

extract_protocol:
At 14 days post graft (DPG) the organoids were dissociated using the Worthington Papain Dissociation System. The cells were isolated through Fluorescent-Activated Cell Sorting (FACS). 75,000 events were isolated.
Sequencing libraries were prepared using the 10X Chromium Single Cell 3’ reagent kit V3 according to manufacture's instructions

value: medial ganglionic emminence

value: Primary mouse interneurons

value: Genetically labeled mouse interneurons

value: Grafted onto FBS-depleted human organoids


title: MLO-Y4 cells without treatment_01


title: B16F10 bone metastasis treated with 10 mg/kg RXD (RXD group) rep3

source_name: long bone without bone marrow

value: long bone without bone marrow


title: MLO-Y4 cells with 50% B16F10 CM for 48h_02


title: B16F10 bone metastasis treated with 10 mg/kg RXD (RXD group) rep1


title: B16F10 bone metastasis treated with DMSO (RXD group) rep3


title: HK-NS1

description: single cell RNA-Seq


title: B16F10 bone metastasis treated with DMSO (RXD group) rep2


title: ES-2-MC2-Liver cell, liver metastatic tumor cell, phosphatase library, R3

description:
NGS
ph-sample_4

value: ovary cancer cell


title: B16F10 bone metastasis treated with 10 mg/kg RXD (RXD group) rep2


title: B16F10 bone metastasis treated with DMSO (RXD group) rep1


title: mice without treatment rep2


title: B16F10 bone metastasis treated with 10 mg/kg Znpp (Znpp group) rep3


title: B16F10 bone metastasis treated with 10 mg/kg Znpp (Znpp group) rep1


title: B16F10 bone metastasis treated with 10 mg/kg Znpp (Znpp group) rep2


title: B16F10 bone metastasis treated with DMSO (Znpp group) rep3


title: B16F10 bone metastasis treated with DMSO (Znpp group) rep2


title: mice without treatment rep1


title: B16F10 bone metastasis treated with DMSO (Znpp group) rep1