title: Lib2_Air

city: New York

first: Dr. Shruti

last: Naik

state: NY

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: 2.F23710AA.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

library_source: other

data_processing:
The final library was sequenced on Illumina® Nextseq™ with a P1 reagent kit (600 cycles). The sequencing was performed with 30% PhiX spike-in.
QIIME2 pipeline (version: 2024.5) (PMID: 31341288) was used for training the classifier and for all downstream analysis of 16s data. Paired end demultiplexed FASTQ files were first imported into QIIME2 workflow, using import function with data type set to ‘SampleData[PairedEndSequencesWithQuality]’ and input format set to ‘PairedEndFastqManifestPhred33V2’. The data was denoised with DADA2 (PMID: 27214047) to trim and truncate reads to remove low quality reads. Output from DADA2 denoising included representative sequences, features table and DADA2 denoising stats.
New classifier was trained specifically for V1-V3 region of Bacterial genome using Silva 138 database (PMID: 23193283). The representative sequences were then tabulated to generate read counts using feature table function to generate feature counts tabulations based on the sample metadata. The representative reads / sequences were also aligned to the custom classifier generated for V1-V3 region and output taxonomic classifications were generated. The taxonomy data was then used to tabulate read counts and an output taxa bar plot was generated using the condition column from metadata to group the samples.
The taxonomy and feature data output from QIIME2 was then imported into an R programming environment and mia package (doi:10.18129/B9.bioc.mia) was used for subsequent analysis. ImportQIIME2 function was used to import the data into R. The imported microbiome data was stored in TreeSummarizedExperiment object in R.
Feature table and Taxonomic mapping were extracted from TreeSummarizedExperiment object in R.
Assembly: V1-V3 bacterial genomic region
Supplementary files format and content: Feature table with raw read counts (no normalization) stored in .csv file format.
Supplementary files format and content: Taxonomic mapping for features found in the read counts file, stored in .csv file format.
Library strategy: 16S rRNA-seq

molecule: other

organism: air metagenome

source_name: Air control

extract_protocol:
ZymoBIOMICS® DNA Miniprep Kit (Zymo Research, Irvine, CA) was used for low biomass samples such as skin swabs, as it permits for a lower elution volume, resulting in more concentrated DNA samples.
Bacterial 16S ribosomal RNA gene targeted sequencing was performed using the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA). The bacterial 16S primers amplified the V1-V3 region of the 16S rRNA gene. These primers have been custom-designed by Zymo Research to provide the best coverage of the 16S gene while maintaining high sensitivity.  The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned with the Select-a-Size DNA Clean & Concentrator™ (Zymo Research, Irvine, CA), then quantified with TapeStation®(Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA).

value: Air control

tag: injury time

value: f

tag: site

value: finger

tag: injury type

value: cut


title: DSP-1001660002551-C-G06_S17-18548

status: Public on Dec 31 2025

type: SRA

city: New Haven

first: Thazin

middle: Nwe

last: Aung

address: 310 Cedar Street

country: USA

institute: Yale University

description: Library name: DSP-1001660002551-C-G06

library_source: transcriptomic

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Assembly: hg19
Supplementary files format and content: CD45_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the leukocyte (CD45) compartment
Supplementary files format and content: CD68_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the macrophage (CD68) compartment
Supplementary files format and content: CK_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the tumor (CK) compartment
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Lung Cancer

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx-DSP protocol (MAN-10150-01). Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5-666 nm, excitation 645-19 nm, emission 683-30 nm), CD45 for lymphocyte compartment (Texas Red-615 nm, excitation 588-19 nm, emission 623-30 nm), S100B (Cy3-568 nm, excitation 538-19 nm, emission 564-15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

tag: tissue

value: Lung Cancer

tag: treatment

value: immunotherapy

tag: batch


title: Lib15_Air

description:
Library name: 15.M30821SA.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

tag: Sex

value: m

tag: age


title: photoreceptor, Day 10, ZT16, rep 1

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

data_processing:
Adaptors trimmed using Trimmomatic
Alignment using HISAT2
SAM file processing using SAMtools
BigWigs generated using deepTools, CPM-normalized
Assembly: BDGP6.46 (GCA_000001215.4)
Supplementary files format and content: CPM-normalized BigWigs

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Outer photoreceptors

growth_protocol: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle.

extract_protocol:
400 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by RNA isolation and purification.
6 ng of nuclear RNA was used to prepare libraries using the Ovation® SoLo® RNA-Seq library preparation kit from Tecan with Drosophila AnyDeplete probes.

value: Outer photoreceptors

value: adult, day 10

tag: time

value: male

tag: genotype


title: DSP-1001660002551-C-G04_S17-16092

description: Library name: DSP-1001660002551-C-G04


title: photoreceptor, Day 10, ZT16, rep 2


title: DSP-1001660002551-C-G05_S17-18548

description: Library name: DSP-1001660002551-C-G05


title: photoreceptor, Day 10, ZT16, rep 3


title: photoreceptor, Day 10, ZT12, rep 3


title: Lib12_Air

description:
Library name: 12.F2487W.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: Lib13_Air

description:
Library name: 13.F30810W.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: scratch


title: scRNAseq_E14_CTX_dHET_3000cells

city: Montreal

first: Benoit

middle: Charles

last: Boulan

state: Quebec

address: 110, avenue des Pins Ouest

country: Canada

institute: IRCM

description: Library name: Sample 5

library_source: transcriptomic single cell

data_processing:
scRNA-seq sequencing data were aligned to the mm10-2020-A genome using CellRanger version 6.1.1 or later (Cell Ranger software, 10x Genomics,).  Cortex dataset : Raw feature-barcode matrices from Cellranger count were imported in R package Seurat (v4.1.3) for downstream analyses. Each experiment was first examined individually in order to identify and filter out empty/dead cells or doublets based on the number of transcripts and number of unique genes present in each cell and also on the percentage of mitochondrial reads. Individual filtered samples were normalized, scaled and 3000 highly variable genes identified using the SCTransform method. All 4 samples were then integrated using Seurat’s anchor-based integration approach. Linear dimensionality reduction performed on the integrated object by principal component analysis (PCA). Only the first 20 PCs were selected for subsequent analyses. Integrated datasets were then transferred in H5ad format for further analysis using Scanpy (Wolf et al., 2018) software on Python. Unbiased clustering of single cells was performed using the Leiden algorithm. Differential gene expression analysis was performed using the t-test with overestimated variance method. Uniform Manifold Approximation and Projection (UMAP) was applied for visualization purposes.  Retina dataset The Retina dataset was directly analyzed using Scanpy for cell quality assessment, principal component analysis, and dimensionality reduction using the UMAP algorithm. Unbiased clustering of single cells was performed using the Leiden algorithm. Differential gene expression analysis was performed using the t-test with overestimated variance method. Uniform Manifold Approximation and Projection (UMAP) was applied for visualization purposes.
Assembly: mm10-2020-A
Supplementary files format and content: Cell ranger software output files  containing count matrix, features and barcodes and Scanpy annotated data matrix  files containing analysed and annotated datasets

organism: Mus musculus

source_name: cortex

extract_protocol:
E14.5 or E17.5 littermate heads were harvested and stored in HibernateTM-E media (ThermoFisher, A1247601) supplemented with B-27™ (ThermoFisher, 17504044) (2%) and GlutaMAX™ (1%) (ThermoFisher, 35050061) for around 3 hours during genotyping. E14.5 cortices and E17.5 retinas from dHET and dKO littermates were then dissected into HibernateTM-E media before dissociation in Papain solution (NaOH (0,05%), Papain (10 units/mL), DNAse (0,004%), L-cysteine, in DPBS) during 2 to 4 min at 37ºC. Then mechanical dissociation was done adding Lo Ovomucoid solution and flushing cells in 1mL pipette tips. Eventually cells were filtered with a 60 μm filter and counted to resuspend them at 1000 cell/μL in PBS, 0,04% BSA.
RNA library generation were generated using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 Dual Index (10x Genomics, Pleasanton, CA)

value: cortex

tag: cell count

value: ~3000 cells

tag: mouse line

value: Gpsm2 +/- Sapcd2 +/-

tag: strain

tag: developmental stage

value: E14.5 embryo

tag: condition

value: Dissection of E14.5 cortex


title: scRNAseq_E14_CTX_dKO_50000cells

description: Library name: Sample 4

value: Gpsm2 -/- Sapcd2 -/-


title: DSP-1001660002551-C-G03_S17-16092

description: Library name: DSP-1001660002551-C-G03


title: scRNAseq_E14_CTX_dKO_3000cells

description: Library name: Sample 6


title: photoreceptor, Day 10, ZT12, rep 2


title: Lib11B_Air

description:
Library name: 11.F2383W.B.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Air control


title: DSP-1001660002551-C-G02_S17-16092

description: Library name: DSP-1001660002551-C-G02


title: photoreceptor, Day 10, ZT12, rep 1


title: scRNAseq_E17_RTN_dKO

description: Library name: Sample 2

source_name: retina

value: retina

value: ~3500 cells

value: E17.5 embryo

value: Dissection of E17.5 retina


title: DSP-1001660002551-C-G01_S17-16092

description: Library name: DSP-1001660002551-C-G01

value: Lung Cancer

value: immunotherapy


title: Lib11_Air

description:
Library name: 11.F2382W.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: f

value: finger

value: cut


title: photoreceptor, Day 10, ZT8, rep 3

value: Outer photoreceptors

value: adult, day 10

value: male


title: scRNAseq_E17_RTN_dHET

description: Library name: Sample 1

value: Gpsm2 +/- Sapcd2 +/-


title: Lib10_Air

description:
Library name: 10.F36724AA.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: puncture


title: photoreceptor, Day 10, ZT8, rep 1


title: WT-Foxp3-rep1.bigwig

city: Shanghai

first: Weiqi

last: Zhang

address: 280 South Chongqing Road, Shanghai, China

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: WT-Foxp3-rep1

library_source: genomic

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Fastp（version 0.24.1）to be high quality clean data.  Reference genome sequences and gene model annotation files of relative species are downloaded from UCSC. Bowtie2-build is used to index reference genome sequence. Clean data is aligned to reference genome via software Bowtie2 (version 2.2.6). Use MACS[1](V2)  to analyze peaks quality control, peaks calling and peaks annotation.
Assembly: GRCm39/mm9
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: spleen

extract_protocol:
For T-bet and  Foxp3 CUT&Tag assay, 2×10^5 WT and V408M Treg cells sorted as described  above from WT and V408M mice were prepared for each reaction. Treg cells were isolated and subjected to CUT&Tag profiling using the Vazyme CUT&Tag Kit (TD904-01) according to the manufacturer’s instructions. Briefly, purified Treg cells were incubated with primary antibodies, followed by binding of secondary antibody and pA-Tn5 transposase complex to enable site-specific tagmentation. After activation of transposase, genomic DNA fragments containing sequencing adapters were released and purified. For ATAC-seq, freshly isolated Treg cells were processed for nuclei preparation, followed by transposition using Tn5 transposase to simultaneously fragment accessible chromatin and insert sequencing adapters. Transposed DNA fragments were then purified and PCR-amplified to construct sequencing libraries.
CUT&Tag DNA samples were quantified using a Qubit 3.0 Fluorometer (Invitrogen) and qualified by Agilent Bioanalyzer 2100(Agilent Technologies). Next generation sequencing library preparations were constructed following the manufacturer’s protocol. For each sample, CUT&Tag product was used for library preparation. The CUT&Tag product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dAtailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptor-ligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer. Then libraries with different indices were multiplexed and loaded on an Illumina Novaseq instrument according to manufacturer’s instruction.

value: spleen

tag: cell line

value: primary T cell

tag: cell type

value: splenic CD4+CD25+ Treg cells

value: Wild-type


title: scRNAseq_E14_CTX_dHET_50000cells

description: Library name: Sample 3

value: cortex

value: E14.5 embryo

value: Dissection of E14.5 cortex


title: DSP-1001660002551-C-F11_S16-26594

description: Library name: DSP-1001660002551-C-F11

value: Lung Cancer


title: photoreceptor, Day 10, ZT4, rep 2


title: LN Treg_3

city: London

first: Niwa

last: Ali

address: King’s College London, 28th Floor, Tower Wing  Guy’s Hospital, Great Maze Pond

country: United Kingdom

institute: King's College London

description: Library name: bulk LN Treg_3

data_processing:
For bulk RNA-seq data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: csv file contains FPKM values.

source_name: Skin

extract_protocol:
Where applicable, RNA was extracted using miRvana miRNeasy kit as per manufacturer's protocol.
RNA sequencing libraries were constructed by Genewiz using a standard protocol in which total RNA quality is first assessed, followed by enrichment of polyadenylated mRNA using oligo(dT) magnetic beads or depletion of rRNA for total RNA applications; the resulting RNA is fragmented (typically to ~200 bp) and subjected to first- and second-strand cDNA synthesis, after which fragments are end-repaired, 3' adenylated, and ligated to Illumina-compatible indexed adapters; the adapter-ligated products are then PCR-amplified to enrich for properly ligated fragments, and the final libraries are quality controlled for size distribution and concentration before sequencing on an Illumina platform

value: Skin

value: Tregs


title: Lib1B_Air

description:
Library name: 1.0629M35A.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Air control

tag: injury time

value: m

value: finger


title: Lib8_Air

description:
Library name: 8.M26720SA.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

tag: site

value: cut


title: LN Treg_2

description: Library name: bulk LN Treg_2


title: DSP-1001660002551-C-F09_S16-26594

description: Library name: DSP-1001660002551-C-F09

value: immunotherapy


title: photoreceptor, Day 10, ZT4, rep 3

value: Outer photoreceptors

value: adult, day 10

value: male


title: DSP-1001660002551-C-F08_S15-15403

description: Library name: DSP-1001660002551-C-F08


title: photoreceptor, Day 10, ZT4, rep 1


title: DSP-1001660002551-C-F10_S16-26594

description: Library name: DSP-1001660002551-C-F10


title: KI-Foxp3-rep1.bigwig

description: Library name: KI-Foxp3-rep1

value: spleen

value: primary T cell

value: Foxp3V408M Knock-in


title: Lib9_Air

description:
Library name: 9.F20721H.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: f

value: hand

tag: injury type


title: Lib7_Air

description:
Library name: 7.714M26SA.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

tag: tissue

value: forehead

value: blister


title: Thbs1wt/wt/Lyz2-Cre

city: Madison

first: Bo

last: Liu

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin - Madison

description:
Library name: Sample 1
10x Genomics Chromium Single Cell 3’ v3.1 Reagent Kit

data_processing:
Raw Illumina sequencing reads were aligned to mm10 (GENCODE vM23/Ensembl 98) reference genome and, subsequently, genes were quantified as UMI counts using Simpleaf (alevin-fry pipline, V0.9.0).
Assembly: mm10
Supplementary files format and content: h5ad

source_name: Abdominal aorta

extract_protocol:
Mouse abdominal aortas were digested sequentially in two digestion buffers (PBS containing  collagenase I (200U/mL; SCR103, Sigma Aldrich), elastase 0.05 U/mL; (E1250, Sigma Aldrich), neutral protease (5 U/mL, LS02111, Worthington), and deoxyribonuclease I (0.3 U/mL, M6101, Promega) for 20 minutes, followed by DMEM containing collagenase type II (5 mg/mL, C6885, Sigma-Aldrich) and elastase (0.5 mg/mL, LS002292, Worthington Biochemistry]) for 2.5 minutes at 37°C). The tissue suspension was filtered with a 40 μm cell strainer, then centrifuged at 500 g for 5 minutes. Cells were resuspended with PBS containing BSA (0.04% wt/vol). Single-cell suspensions from 5 Thbs1wt/wt/Lyz2-Cre or 5 Thbs1fl/fl/Lyz2-Cre were pooled together as one sample.
Ten thousand cells per sample were loaded on a Chromium Controller (10x Genomics). The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ v3.1 Reagent Kit according to the manufacturer’s guidelines (10x Genomics). cDNA libraries were uniquely sample indexed and pooled for sequencing.

value: Abdominal aorta

tag: treatment

value: PCSK9-AAV/Angiotensin II


title: Thbs1fl/fl/Lyz2-Cre

description:
Library name: Sample 2
10x Genomics Chromium Single Cell 3’ v3.1 Reagent Kit


title: DSP-1001660002551-C-F07_S15-15403

description: Library name: DSP-1001660002551-C-F07

value: Lung Cancer

tag: batch


title: photoreceptor, Day 10, ZT0, rep 2

tag: Sex


title: LN Treg_1

description: Library name: bulk LN Treg_1

value: Skin

value: Tregs


title: DSP-1001660002551-C-F12_S16-26594

description: Library name: DSP-1001660002551-C-F12


title: Lib6_Air

description:
Library name: 6.M33713W.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Air control

value: m

value: cut

tag: age


title: DSP-1001660002551-C-F06_S15-15403

description: Library name: DSP-1001660002551-C-F06

value: immunotherapy


title: Skin Treg_2

description: Library name: bulk skin Treg_2


title: photoreceptor, Day 10, ZT0, rep 3

value: Outer photoreceptors

value: adult, day 10

tag: time

value: male


title: Lib5_Air

description:
Library name: 5.M38712WH.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: knee

value: scratch


title: Muscle,LIGEL,24day,rep6

city: Beijing

first: Xun

last: Hu

address: Student Dormitory, No. 17, Panjiayuan So

institute: Department of Imaging Diagnosis National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

description:
Library name: Sample24
Column name in gene_count.txt: A18_1

data_processing:
Illumina Casava1.8 software used for basecalling.
After filtering the raw data, checking the sequencing error rate, and checking the GC content distribution, clean reads were obtained for subsequent analysis. HISAT2 software was used to quickly and accurately align the clean reads with the reference genome to obtain the location information of the reads on the reference genome.
Based on the mapping positions of genes on the reference genome, the number of reads covering each gene (including newly predicted genes) from start to stop was counted. Reads with mapping quality values below 10, reads on non-contig mappings, and reads mapped to multiple regions of the genome were filtered out. This analysis utilized the featureCounts tool in the subread software.
FPKM and FPKM were used to correct for sequencing depth and gene length, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each
Supplementary files format and content: Samplecsv files include FPK values for each Sample

source_name: pancreatic tumor

extract_protocol:
The pancreatic tumor was removed, frozen on dry ice, and then RNA was extracted from the tissue using Trizol reagent and standard extraction methods. The RNA samples were then subjected to strict quality control, mainly through the Agilent 2100 bioanalyzer.
RNA libraries were prepared for sequencing using standard llumina protocols

value: pancreatic tumor


title: Skin Treg_1

description: Library name: bulk skin Treg_1

tag: genotype


title: Muscle,LIGEL,24day,rep5

description:
Library name: Sample23
Column name in gene_count.txt:A17_1


title: Lib3_Air

description:
Library name: 3.F35712WH.AB.Air
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: f


title: DSP-1001660002551-C-F05_S15-15403

description: Library name: DSP-1001660002551-C-F05


title: IC02_IC90-K

description: Library name: Bulk RNA skin_11

value: FullDT


title: DSP-1001660002551-C-F02_S15-15344

description: Library name: DSP-1001660002551-C-F02


title: 3C-seq of C. steedae stationary phase

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

data_processing:
Raw contact maps were built as described previously (Lioy and Cournac 2018). Briefly, each read was assigned to a restriction fragment. Non- informative events such as self-circularized restriction fragments, or uncut co- linear restriction fragments were discarded. The chromosome of each bacterium was divided into 5 kb bins and the frequencies of contacts between genomic loci for each bin were assigned. Contact frequencies were visualized as heatmaps. Raw contact maps used for comparative analyses were built using 1 million valid reads. Raw contact maps were normalized using Iterative correction and eigenvector decomposition (ICE; Imakaev, et all 2012 https://pubmed.ncbi.nlm.nih.gov/22941365/). To facilitate visualization, normalized contact matrices are visualized as log matrices. A Gaussian filter of H=0.5 is used when plotting the matrices. To quantify the frequency of interactions in the secondary diagonals (Supplementary Figure 4), we applied to our data a method based on the filtering of significant 3C contacts and developed as described (Wang et al, science, 2015).
Assembly: CP097501.1
Supplementary files format and content: raw and ICE-normalized matrices
Library strategy: 3C-Seq

organism: Conchiformibius steedae DSM 2580

source_name: bacterial cell culture

extract_protocol:
3C libraries were prepared as previously described (Lioy et al., 2021b, 2018; Marbouty et al., 2015b). Cells were plated from glycerol stock onto agar plates and grown at 37C for 24 hours and 48 hours, after which they were scraped off and transferred to BSTSY/FBS containing 6% f.c formaldehyde, fully resuspended, and fixed at room temperature at 120 rpm, followed by 30 min more at 4C. Glycine (250 mM f.c.) was added, and the cells incubated 30 min at 4C at 120 rpm. After fixation, cells were collected by centrifugation for 10 min at 3,500 g at 4C, resuspended in fresh medium, collected again by centrifugation, and resuspended in 1 ml fresh medium before final collection by centrifugation. Cell pellets were stored at -70C. For digestion, cell pellets were thawed on ice for 10 min, resuspended in 500 l Tris 10 mM EDTA 0.5 mM (TE) (pH 8), and lysed using 4 l Ready-lyse lysozyme (Epicentre) for 20 min at 37C, 300 rpm. SDS (0.5% f.c.) was added and incubated for 10 min at room temperature. 500 l lysed cells were then transferred to a tube containing 4.5 ml digestion buffer (1% Triton X-100, 1x Cutsmart buffer (New England Biolabs)), and 100 l cells (non-digested control) were transferred to a tube containing 0.9 ml of digestion buffer. 100U of HpaII (New England Biolabs) were added to the 5 ml digestion mix. Both tubes were incubated for 3 h at 37C. After digestion, 1 ml of digestion mix was put on ice (digested control) together with the non-digested control. The remaining digestion mix was split into 4 parts, centrifuged for 20 min at 20,000 g, and pellets were carefully resuspended in 1 ml water each, and pooled into 7 ml ligation buffer (1X ligation buffer 3 (New England Biolabs; without ATP), 1mM ATP, 1 mg/ml BSA, 500 U of T4 DNA ligase 5 U/l (ThermoFisher)). Ligation was carried out at 16C for 4 h, followed by incubation together with the two control tubes overnight at 65C with proteinase K (0.25 mg/ml f.c.) and EDTA (6 mM f.c.). The next day, DNA of the ligated sample was precipitated with 1/10 volume of 3 M sodium acetate (pH 5.2) and 2 volumes of isopropanol, and after one hour at -80C, DNA was pelleted by centrifugation for 30 min at 10,000 g at 4C, and resuspended in 500 l 1X TE buffer. DNA in all tubes (ligation and two controls) were extracted once with 400 l phenol-chloroform pH 8.0 (vortexed for 1 min and centrifuged for 5 min 16,000 g at 4C), precipitated (see above; 30 min at -80C, followed by centrifugation for 20 min at 16,000 x g at 4C), washed with 400 l 80% cold ethanol, and diluted in 30 l 1X TE buffer supplemented with RNase A (1 mg/ml f.c.; ThermoFisher). Tubes containing ligated DNA were pooled. A 1% agarose gel was run with aliquots of the ligated and two control DNA to check for efficiency of digest and ligation. Ligated DNA was adjusted with water for 130 l with approx. 5 g, and sheared using a Covaris S220 (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 s for 4 cycles), and the DNA purified using the QIAquick PCR purification kit (40 l elution buffer; Quiagen), and DNA end-repaired with 1X T4 DNA ligase buffer (New England Biolabs), 0.4 mM dNTP mix, 15 U T4 polynucleotide kinase (New England Biolabs), 5U Klenow DNA polymerase (Roche), and incubated for 30 min at RT. DNA was purified using MinElute columns (Qiagen). A-tailing was done with 1X NEBuffer 2 (New England Biolabs), 0.2 mM dATP, and 15 U Klenow exo (New England Biolabs), for 30 min at 37C before inactivation for 20 min at 65C, and DNA again purified using MinElute columns (Qiagen). Sequencing adapters were ligated with 0.5 mM custom-made adapters, 2.106 U T4 DNA ligase, and 1X T4 DNA ligase buffer, for 2 hours at RT, followed by inactivation for 20 min at 65C. DNA fragments were purified in a size from 400 to 900 bp using a PippinPrep apparatus (SAGE Science). Each library was amplified in 12 cycles with 1X Phusion Buffer (ThermoFisher) , 0.2 dNTPs, 0.2 M Illumina primers PE1.0 (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA) and PE2.0 (CAAGCAGAAGACGGCATACGAGAT), 3 l of 3C library, and 1U of Taq Phusion polymerase (ThermoFisher; 98 C 30 s, 12 cycles of 65C 30 s, and 72C 30 s, and 72C for 7 min). The PCR reaction was purified using MinElute PCR purification kit (Qiagen), and libraries sequenced on an Illumina NextSeq500 with 75 bp paired-end reads. Reads have been trimmed of adapter sequences and deduplicated (see paper for details).
Ligated DNA (5 µg) was adjusted with water to 130 µl, and sheared using a Covaris S220 (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 s for 4 cycles), and the DNA purified using the QIAquick PCR purification kit (40 µl elution buffer; Qiagen), and DNA end-repaired with 1X T4 DNA ligase buffer (New England Biolabs), 0.4 mM dNTP mix, 15 U T4 polynucleotide kinase (New England Biolabs), 5 U Klenow DNA polymerase (Roche), and incubated for 30 min at RT. DNA was purified using MinElute columns (Qiagen). A-tailing was done with 1X NEBuffer 2 (New England Biolabs), 0.2 mM dATP, and 15 U Klenow exo (New England Biolabs), for 30 min at 37°C before inactivation for 20 min at 65°C, and DNA again purified using MinElute columns (Qiagen). Sequencing adapters were ligated with 0.5 mM custom-made adapters, 2.106 U T4 DNA ligase, and 1X T4 DNA ligase buffer, for 2 hours at RT, followed by inactivation for 20 min at 65°C. DNA fragments were purified in a size from 400 to 900 bp using a PippinPrep apparatus (SAGE Science). Each library was amplified in 12 cycles with 1X Phusion Buffer (ThermoFisher) , 0.2 mM dNTPs, 0.2 µM Illumina primers PE1.0 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA-3’) and PE2.0 (5’-CAAGCAGAAGACGGCATACGAGAT-3’), 3 µl of 3C library, and 1U of Taq Phusion polymerase (ThermoFisher; 98 °C 30 s, 12 cycles of 65°C 30 s, and 72°C 30 s, and 72°C for 7 min). The PCR reaction was purified using MinElute PCR purification kit (Qiagen), and libraries sequenced on an Illumina NextSeq500 with 75 bp paired-end reads.

value: bacterial cell culture

tag: group

value: stationary phase


title: Muscle,LIGEL,24day,rep3

description:
Library name: Sample21
Column name in gene_count.txt: A13_1


title: Muscle,LIGEL,24day,rep4

description:
Library name: Sample22
Column name in gene_count.txt:A16_1


title: DSP-1001660002551-C-F01_S14-7026-2

description: Library name: DSP-1001660002551-C-F01

value: Lung Cancer


title: IC02_IC90-I

description: Library name: Bulk RNA skin_9

value: Skin


title: Muscle,LIGEL,24day,rep2

description:
Library name: Sample20
Column name in gene_count.txt: A3_2


title: DSP-1001660002551-C-F03_S15-15344

description: Library name: DSP-1001660002551-C-F03


title: 3C-seq of C. steedae plate

value: plate


title: Skin Treg_3

description: Library name: bulk skin Treg_3

value: Tregs


title: photoreceptor, Day 10, ZT0, rep 1


title: DSP-1001660002551-C-E12_S14-7026-1

description: Library name: DSP-1001660002551-C-E12


title: Muscle,LIGEL,24day,rep1

description:
Library name: Sample19
Column name in gene_count.txt:A3_1


title: 3C-seq of A. filiformis plate with 25 ug/ml Chloramphenicol for 30 min

data_processing:
Raw contact maps were built as described previously (Lioy and Cournac 2018). Briefly, each read was assigned to a restriction fragment. Non- informative events such as self-circularized restriction fragments, or uncut co- linear restriction fragments were discarded. The chromosome of each bacterium was divided into 5 kb bins and the frequencies of contacts between genomic loci for each bin were assigned. Contact frequencies were visualized as heatmaps. Raw contact maps used for comparative analyses were built using 1 million valid reads. Raw contact maps were normalized using Iterative correction and eigenvector decomposition (ICE; Imakaev, et all 2012 https://pubmed.ncbi.nlm.nih.gov/22941365/). To facilitate visualization, normalized contact matrices are visualized as log matrices. A Gaussian filter of H=0.5 is used when plotting the matrices. To quantify the frequency of interactions in the secondary diagonals (Supplementary Figure 4), we applied to our data a method based on the filtering of significant 3C contacts and developed as described (Wang et al, science, 2015).
Assembly: CP083931.1
Supplementary files format and content: raw and ICE-normalized matrices
Library strategy: 3C-seq

organism: Alysiella filiformis DSM 16848


title: IC02_IC90-H

description: Library name: Bulk RNA skin_8

value: LateDT


title: Lib1A_Air

description:
Library name: 1.0629M35A.AC
V1V3 16S rRNA sequencing of air control. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Air control

value: m

value: finger

value: puncture


title: 3C-seq of A. filiformis plate with 25 ug/ml Rifampicin for 30 min


title: DSP-1001660002551-C-E11_S14-7026-1

description: Library name: DSP-1001660002551-C-E11

value: immunotherapy


title: Muscle,IGEL,24day,rep6

description:
Library name: Sample18
Column name in gene_count.txt:A24_1


title: IC02_IC90-F

description: Library name: Bulk RNA skin_6


title: DSP-1001660002551-C-F04_S15-15344

description: Library name: DSP-1001660002551-C-F04


title: IC02_IC90-J

description: Library name: Bulk RNA skin_10


title: 3C-seq of A. filiformis stationary phase


title: 3C-seq of C. steedae exponential phase

value: exponential phase


title: DSP-1001660002551-C-E10_S14-25109

description: Library name: DSP-1001660002551-C-E10


title: IC02_IC90-E

description: Library name: Bulk RNA skin_5

value: EarlyDT


title: Muscle,IGEL,24day,rep5

description:
Library name: Sample17
Column name in gene_count.txt:A23_1

value: pancreatic tumor


title: 3C-seq of A. filiformis exponential phase, replicate 2


title: Muscle,IGEL,24day,rep4

description:
Library name: Sample16
Column name in gene_count.txt:A22_1


title: DSP-1001660002551-C-E09_S14-25109

description: Library name: DSP-1001660002551-C-E09


title: Muscle,IGEL,24day,rep3

description:
Library name: Sample15
Column name in gene_count.txt: A20_1


title: IC02_IC90-D

description: Library name: Bulk RNA skin_4


title: IC02_IC90-G

description: Library name: Bulk RNA skin_7


title: 3C-seq of A. filiformis exponential phase, replicate 1


title: 3C-seq of A. filiformis plate, replicate 2


title: DSP-1001660002551-C-E08_S14-25109

description: Library name: DSP-1001660002551-C-E08


title: DSP-1001660002551-C-E06_S14-1694

description: Library name: DSP-1001660002551-C-E06


title: Muscle,IGEL,24day,rep2

description:
Library name: Sample14
Column name in gene_count.txt: A14_1


title: Muscle,IGEL,24day,rep1

description:
Library name: Sample13
Column name in gene_count.txt: A1_1


title: DSP-1001660002551-C-E07_S14-1694

description: Library name: DSP-1001660002551-C-E07


title: IC02_IC90-A

description: Library name: Bulk RNA skin_1

value: PBS


title: IC02_IC90-B

description: Library name: Bulk RNA skin_2


title: DSP-1001660002551-C-E05_S14-1694

description: Library name: DSP-1001660002551-C-E05


title: 3C-seq of A. filiformis plate, replicate 1


title: Muscle,GEM,24day,rep6

description:
Library name: Sample12
Column name in gene_count.txt:A21_1


title: Patient 796

type: RNA

city: Oslo

first: Andreas

middle: Hagen

last: Røssevold

email: andreashr@gmail.com, anharo@ous-hf.no

address: Ullernchausséen 70

country: Norway

institute: Oslo University Hospital

hyb_protocol: Hybridization of mRNA and capture and reporter probes was done using the nCounter XT Assay protocol (NanoString Technologies) and incubated at 65 °C for 20 hours.

scan_protocol: The nCounter Digital Analyzer (NanoString Technologies) was used for digital counting and data collection with field of view (FOV) set to 555. Best practice for the BC360 assays was followed.

data_processing: Raw gene counts were normalized based on the expression values of 40 housekeeping genes predefined by NanoString, in accordance with NanoString's Gene Expression Data Analysis Guidelines (MAN-C0011-04). Log2 transformation was performed after normalization.

label: not provided

source_name: primary breast cancer

label_protocol: nCounter PanCancer Immune Profiling Panel

extract_protocol: RNA isolation of the collected tumor tissue was done using the High Pure FFPET RNA Isolation Kit (Roche, 06650775001) and protocol, with the 55 °C incubation time increased to 2 hours.

treatment_protocol: FFPE biopsy slides were deparaffinized using (R)-(+)-Limonene (Merck, 183164) and rehydrated absolute ethanol and air-dried for a minimum of 15 minutes

value: LumA

value: II

tag: histology

value: IDC

tag: er

tag: pr

tag: chemo


title: Muscle,GEM,24day,rep5

description:
Library name: Sample11
Column name in gene_count.txt:A19_1


title: Exper3

city: Changchun City

first: bin

last: yang

state: Jilin

address: No. 4110, Yatai Street, Nanguan District, Changchun City, Jilin Province

institute: jilin university

description:
Library name: sample6
FPKM.Exper3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ensemblv112
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

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.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: cell line

tag: cell line


title: DSP-1001660002551-C-E04_S14-14165

description: Library name: DSP-1001660002551-C-E04

value: Lung Cancer


title: DSP-1001660002551-C-E03_S14-14165

description: Library name: DSP-1001660002551-C-E03


title: Exper2

description:
Library name: sample5
FPKM.Exper2


title: Exper1

description:
Library name: sample4
FPKM.Exper1


title: Patient 625

value: III


title: IC02_IC90-C

description: Library name: Bulk RNA skin_3

value: Skin


title: contr3

description:
Library name: sample3
FPKM.contr3


title: DSP-1001660002551-C-E01_S14-14165

description: Library name: DSP-1001660002551-C-E01


title: Patient 614


title: Muscle,GEM,24day,rep2

description:
Library name: Sample8
Column name in gene_count.txt: A2_1


title: contr2

description:
Library name: sample2
FPKM.contr2


title: Muscle,GEM,24day,rep1

description:
Library name: Sample7
Column name in gene_count.txt: A1_2


title: contr1

description:
Library name: sample1
FPKM.contr1


title: Patient 539

value: I


title: DSP-1001660002551-C-D12_S14-10489

description: Library name: DSP-1001660002551-C-D12


title: Muscle,GEM,24day,rep4

description:
Library name: Sample10
Column name in gene_count.txt: A11_1


title: Muscle,PBS,24day,rep6

description:
Library name: Sample6
Column name in gene_count.txt:A15_1


title: Patient 389


title: DSP-1001660002551-C-D11_S14-10489

description: Library name: DSP-1001660002551-C-D11


title: DSP-1001660002551-C-D10_S14-10489

description: Library name: DSP-1001660002551-C-D10


title: Male WT Ventral Hippocampus, Rep 3

city: Charleston

first: Jessica

middle: H

last: Hartman

state: South Carolina

address: 70 President St., Drug Discovery Bldg/Rm DD220

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description:
Library name: Sample 48
M_WT_V_3

data_processing:
Novogene performed data analysis in the Novogene platform
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignments were performed with HISAT2 v2.0.5 by Novogene
Differentially expressed genes were determined with the R package DESeq2
Assembly: mm39
Supplementary files format and content: spreadsheet containing gene counts

molecule: polyA RNA

source_name: Ventral Hippocampus

growth_protocol: Mice were maintained in co-housed cages on normal chow in controlled temperature and humidity until 16 weeks of age.

extract_protocol:
Liver lysates were prepared by homogenization in the bullet blender and RNA was isolated using the RNeasy Qiagen kit with the optional DNaseI on-column digestion step
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Ventral Hippocampus

value: 16-week old


title: Patient 375

value: LumB


title: Patient 182


title: Male WT Ventral Hippocampus, Rep 1

description:
Library name: Sample 46
M_WT_V_1


title: DSP-1001660002551-C-D09_S14-10489

description: Library name: DSP-1001660002551-C-D09


title: DSP-1001660002551-C-D08_S13-8074

description: Library name: DSP-1001660002551-C-D08


title: Muscle,GEM,24day,rep3

description:
Library name: Sample9
Column name in gene_count.txt:A2_2


title: DSP-1001660002551-C-E02_S14-14165

description: Library name: DSP-1001660002551-C-E02


title: Muscle,PBS,24day,rep4

description:
Library name: Sample4
Column name in gene_count.txt: A10_1


title: Muscle,PBS,24day,rep3

description:
Library name: Sample3
Column name in gene_count.txt: A9_1


title: Male WT medial Prefrontal Cortex, Rep 3

description:
Library name: Sample 45
M_WT_P_3

source_name: medial Prefrontal Cortex

value: medial Prefrontal Cortex


title: Patient 435


title: Patient 140


title: Patient 138


title: Muscle,PBS,24day,rep2

description:
Library name: Sample2
Column name in gene_count.txt: A8_1


title: Male WT medial Prefrontal Cortex, Rep 2

description:
Library name: Sample 44
M_WT_P_2


title: DSP-1001660002551-C-D05_S13-7196

description: Library name: DSP-1001660002551-C-D05

value: immunotherapy


title: Patient 115


title: Male WT medial Prefrontal Cortex, Rep 1

description:
Library name: Sample 43
M_WT_P_1


title: Patient 020

value: Other Infitrating Ca


title: Muscle,PBS,24day,rep5

description:
Library name: Sample5
Column name in gene_count.txt: A12_1


title: Male WT Dorsal Hippocampus, Rep 3

description:
Library name: Sample 42
M_WT_D_3

source_name: Dorsal Hippocampus

value: Dorsal Hippocampus


title: Male WT Ventral Hippocampus, Rep 2

description:
Library name: Sample 47
M_WT_V_2


title: DSP-1001660002551-C-D04_S13-7196

description: Library name: DSP-1001660002551-C-D04


title: Patient 921

data_processing:
Raw gene counts were normalized based on the expression values of 40 housekeeping genes predefined by NanoString, in accordance with NanoString's Gene Expression Data Analysis Guidelines (MAN-C0011-04)
NOTE:
CXCL4 is labelled PF4 (CXCL4) in some RCC files.
RhoC is labelled RHOC in some RCC files.
STING is labelled TMEM173 (Sting) in some RCC files.

value: Basal

tag: til

tag: tls

tag: gc


title: Male WT Dorsal Hippocampus, Rep 2

description:
Library name: Sample 41
M_WT_D_2


title: Patient 911


title: Male WT Cerebellum, Rep 3

description:
Library name: Sample 39
M_WT_C_3

source_name: Cerebellum

value: Cerebellum


title: DSP-1001660002551-C-D03_S13-7196

description: Library name: DSP-1001660002551-C-D03


title: 16_miR_onc

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Huh7, miR_onc

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Huh7 cells were grown in DMEM with 10% FBS and Pen-Strep. Cells were seeded in 6-well plates in DMEM without antibiotics for the transfection experiments. 24h post seeding, cells were transfected.

extract_protocol: 48h post transfection, cells were trypsinized and harvested, and total RNA was extracted. miRNA expression was validated by qPCR before sending the samples for gene expression profiling.

treatment_protocol: Huh7 cells were transiently transfected with scramble control or miRNA mimic to see the effect on global gene expression.


title: DSP-1001660002551-C-D07_S13-8074

description: Library name: DSP-1001660002551-C-D07


title: DSP-1001660002551-C-D06_S13-8074

description: Library name: DSP-1001660002551-C-D06


title: Patient 832


title: Patient 811


title: Patient 791


title: DSP-1001660002551-C-C12_S13-28478

description: Library name: DSP-1001660002551-C-C12


title: DSP-1001660002551-C-D02_S13-7196

description: Library name: DSP-1001660002551-C-D02


title: Male WT Cerebellum, Rep 2

description:
Library name: Sample 38
M_WT_C_2


title: Male CYP2E1-KO Ventral Hippocampus, Rep 3

description:
Library name: Sample 36
M_KO_V_3


title: Muscle,PBS,24day,rep1

description:
Library name: Sample1
Column name in gene_count.txt: A7_1

value: pancreatic tumor


title: DSP-1001660002551-C-C10_S13-28478

description: Library name: DSP-1001660002551-C-C10


title: Patient 768


title: Male WT Cerebellum, Rep 1

description:
Library name: Sample 37
M_WT_C_1


title: Male WT Dorsal Hippocampus, Rep 1

description:
Library name: Sample 40
M_WT_D_1


title: DSP-1001660002551-C-C11_S13-28478

description: Library name: DSP-1001660002551-C-C11


title: Patient 771


title: Patient 762


title: Male CYP2E1-KO Ventral Hippocampus, Rep 2

description:
Library name: Sample 35
M_KO_V_2


title: DSP-1001660002551-C-C09_S11-32143

description: Library name: DSP-1001660002551-C-C09


title: 15_miR_onc


title: DSP-1001660002551-C-D01_S13-28478

description: Library name: DSP-1001660002551-C-D01


title: Male CYP2E1-KO Ventral Hippocampus, Rep 1

description:
Library name: Sample 34
M_KO_V_1


title: DSP-1001660002551-C-C08_S11-32143

description: Library name: DSP-1001660002551-C-C08


title: Patient 761


title: Male CYP2E1-KO medial Prefrontal Cortex, Rep 3

description:
Library name: Sample 33
M_KO_P_3


title: DSP-1001660002551-C-C07_S11-32143

description: Library name: DSP-1001660002551-C-C07


title: 10_miRsup

source_name: Huh7, miRsup

value: miRsup


title: Patient 738

value: IDC


title: Male CYP2E1-KO medial Prefrontal Cortex, Rep 2

description:
Library name: Sample 32
M_KO_P_2


title: DSP-1001660002551-C-C06_S11-32143

description: Library name: DSP-1001660002551-C-C06

source_name: Lung Cancer


title: Male CYP2E1-KO medial Prefrontal Cortex, Rep 1

description:
Library name: Sample 31
M_KO_P_1


title: DSP-1001660002551-C-C05_R7_C3

description: Library name: DSP-1001660002551-C-C05


title: 13_miR_onc


title: Patient 709


title: Patient 727


title: Male CYP2E1-KO Dorsal Hippocampus, Rep 3

description:
Library name: Sample 30
M_KO_D_3


title: DSP-1001660002551-C-C04_R7_C3

description: Library name: DSP-1001660002551-C-C04


title: Renal tissue, CKD_2

city: Kunming

first: Chunjuan

last: Xia

address: 374 Dianmian Avenue

institute: The Second Affiliated Hospital of Kunming Medical University

data_processing:
RseQC 4.0.0, fastp 0.20.1, hisat2 2.1.0, and htseq-count 0.11.2 were applied to perform  quality control of RNA, quality assessment of raw reads, QC of raw reads bases, genome comparison, and gene quantification, respectively.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

organism: Rattus norvegicus

source_name: Renal tissue

extract_protocol:
Total RNA was extracted using the TRIzol reagent  according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using VAHTS Universal V5 RNA-seq Library Prep kit following manufacturer's protocols

value: Renal tissue

value: WT

tag: disease state

value: CKD


title: Renal tissue, CKD_3

tag: tissue


title: Male CYP2E1-KO Dorsal Hippocampus, Rep 2

description:
Library name: Sample 29
M_KO_D_2


title: 8_control

source_name: Huh7, control

tag: treatment

value: control


title: Patient 708

value: III


title: Male CYP2E1-KO Dorsal Hippocampus, Rep 1

description:
Library name: Sample 28
M_KO_D_1


title: Renal tissue, CKD_1


title: 4_miRsup


title: Patient 696


title: Patient 670


title: Renal tissue, Sham_3

value: Sham


title: DSP-1001660002551-C-C02_R5_C7

description: Library name: DSP-1001660002551-C-C02

value: Lung Cancer

tag: batch


title: 9_miRsup


title: 3_miRsup


title: 14_miR_onc


title: Male CYP2E1-KO Cerebellum, Rep 3

description:
Library name: Sample 27
M_KO_C_3

value: 16-week old


title: Patient 659


title: Renal tissue, Sham_2


title: 2_control


title: 7_control


title: DSP-1001660002551-C-C01_R5_C7

description: Library name: DSP-1001660002551-C-C01


title: Patient 619


title: Male CYP2E1-KO Cerebellum, Rep 2

description:
Library name: Sample 26
M_KO_C_2


title: 1_control


title: DSP-1001660002551-C-B12_R5_C7

description: Library name: DSP-1001660002551-C-B12


title: Renal tissue, Sham_1


title: Male CYP2E1-KO Cerebellum, Rep 1

description:
Library name: Sample 25
M_KO_C_1


title: Female WT Ventral Hippocampus, Rep 3

description:
Library name: Sample 24
F_WT_V_3

value: Ventral Hippocampus


title: DSP-1001660002551-C-B11_R4_C2

description: Library name: DSP-1001660002551-C-B11

value: immunotherapy


title: Patient 615

value: Other Infitrating Ca


title: DSP-1001660002551-C-C03_R5_C7

description: Library name: DSP-1001660002551-C-C03


title: RAW 264.7 CELLS, HPDM group, 3days 3

city: 南充市

first: Cai-Ping

last: Yan

state: sichuan

address: No. 1 The South of Maoyuan Road

department: orthopedics

institute: North sichuan medical college

description:
Library name: R-H-3
RAW264.7_ref_trans_full_table.txt

data_processing:
After passing the library quality inspection, high-throughput sequencing was performed using the Illumina NovaSeq6000 platform in paired-end 150bp (PE150) mode.
Assembly: The sequencing data was analyzed through the BMK Cloud platform (www.biocloud.net).
Supplementary files format and content: FPKM, count valus for each Sample

growth_protocol: The third-generation cells were seeded at 5×10^3 cells/well in a 96-well plate, with 200μL of material extract added to each well. After 48 hours of incubation (5% CO2, 37°C), the extract was aspirated and discarded, followed by washing the cells with PBS three times.

extract_protocol:
Upon reaching the predetermined time points, the cells were lysed with TRIzol, cooled in liquid nitrogen for 5-10 minutes, and stored at −80°C.
The NanoDrop 2000 spectrophotometer was used to measure the purity and concentration of RNA, while the Agilent 2100/LabChip GX assessed RNA integrity. After passing sample quality control, library construction and quality control were performed.

tag: cell type

value: Macrophage

value: HPDM


title: DSP-1001660002551-C-B10_R4_C2

description: Library name: DSP-1001660002551-C-B10


title: Patient 577

tag: age

value: Basal


title: RAW 264.7 CELLS, HPDM group, 3days 2

description:
Library name: R-H-2
RAW264.7_ref_trans_full_table.txt


title: Patient 541


title: Female WT Ventral Hippocampus, Rep 2

description:
Library name: Sample 23
F_WT_V_2


title: DSP-1001660002551-C-B09_R4_C1

description: Library name: DSP-1001660002551-C-B09


title: RAW 264.7 CELLS, HPDM group, 3days 1

description:
Library name: R-H-1
RAW264.7_ref_trans_full_table.txt


title: Female WT Ventral Hippocampus, Rep 1

description:
Library name: Sample 22
F_WT_V_1


title: Patient 540


title: RAW 264.7 CELLS, HP group, 3days 3

description:
Library name: R-B-3
RAW264.7_ref_trans_full_table.txt

value: HP


title: DSP-1001660002551-C-B08_R4_C1

description: Library name: DSP-1001660002551-C-B08


title: Female WT medial Prefrontal Cortex, Rep 3

description:
Library name: Sample 21
F_WT_P_3

value: medial Prefrontal Cortex


title: Patient 513

value: II


title: Patient 517

value: IDC


title: Female WT medial Prefrontal Cortex, Rep 2

description:
Library name: Sample 20
F_WT_P_2


title: DSP-1001660002551-C-B07_R4_C1

description: Library name: DSP-1001660002551-C-B07


title: DSP-1001660002551-C-B06_R4_C1

description: Library name: DSP-1001660002551-C-B06


title: RAW 264.7 CELLS, HP group, 3days 1

description:
Library name: R-B-1
RAW264.7_ref_trans_full_table.txt

value: WT


title: Female WT medial Prefrontal Cortex, Rep 1

description:
Library name: Sample 19
F_WT_P_1


title: Female WT Dorsal Hippocampus, Rep 3

description:
Library name: Sample 18
F_WT_D_3

value: Dorsal Hippocampus


title: MC3T3-E1 CELLS, HPDM@Hu/Ra group, 7days 3

description:
Library name: Control-3
MC3T3_ref_trans_full_table.txt

value: Preosteoblast


title: Female WT Dorsal Hippocampus, Rep 2

description:
Library name: Sample 17
F_WT_D_2


title: DSP-1001660002551-C-B04_R1_C7

description: Library name: DSP-1001660002551-C-B04


title: MC3T3-E1 CELLS, HPDM@Hu/Ra group, 7days 2

description:
Library name: Control-2
MC3T3_ref_trans_full_table.txt


title: Patient 467

value: III


title: DSP-1001660002551-C-B03_R1_C7

description: Library name: DSP-1001660002551-C-B03


title: MC3T3-E1 CELLS, HPDM@Hu/Ra group, 7days 1

description:
Library name: Control-1
MC3T3_ref_trans_full_table.txt


title: Female WT Dorsal Hippocampus, Rep 1

description:
Library name: Sample 16
F_WT_D_1


title: Patient 452


title: Patient 441


title: Patient 449


title: MC3T3-E1 CELLS, HPDM group, 7days 3

description:
Library name: HPDM-3
MC3T3_ref_trans_full_table.txt


title: Female WT Cerebellum, Rep 3

description:
Library name: Sample 15
F_WT_C_3

value: Cerebellum


title: DSP-1001660002551-C-B02_R1_C7

description: Library name: DSP-1001660002551-C-B02

value: Lung Cancer


title: Patient 420


title: RAW 264.7 CELLS, HP group, 3days 2

description:
Library name: R-B-2
RAW264.7_ref_trans_full_table.txt


title: DSP-1001660002551-C-B01_R1_C5

description: Library name: DSP-1001660002551-C-B01


title: Female WT Cerebellum, Rep 2

description:
Library name: Sample 14
F_WT_C_2

value: 16-week old


title: MC3T3-E1 CELLS, HPDM group, 7days 2

description:
Library name: HPDM-2
MC3T3_ref_trans_full_table.txt


title: Patient 402


title: DSP-1001660002551-C-B05_R1_C7

description: Library name: DSP-1001660002551-C-B05


title: MC3T3-E1 CELLS, HPDM group, 7days 1

description:
Library name: HPDM-1
MC3T3_ref_trans_full_table.txt


title: DSP-1001660002551-C-A12_R1_C5

description: Library name: DSP-1001660002551-C-A12


title: Female WT Cerebellum, Rep 1

description:
Library name: Sample 13
F_WT_C_1


title: DSP-1001660002551-C-A11_R7_C8

description: Library name: DSP-1001660002551-C-A11


title: Female CYP2E1-KO Ventral Hippocampus, Rep 3

description:
Library name: Sample 12
F_KO_V_3

value: Ventral Hippocampus


title: MC3T3-E1 CELLS, HPD group, 7days 3

description:
Library name: HPD-3
MC3T3_ref_trans_full_table.txt

value: HPD


title: Patient 385

value: Other Infitrating Ca


title: DSP-1001660002551-C-A10_R7_C8

description: Library name: DSP-1001660002551-C-A10

value: immunotherapy


title: Female CYP2E1-KO Ventral Hippocampus, Rep 2

description:
Library name: Sample 11
F_KO_V_2


title: DSP-1001660002551-C-A09_R7_C8

description: Library name: DSP-1001660002551-C-A09


title: MC3T3-E1 CELLS, HPD group, 7days 2

description:
Library name: HPD-2
MC3T3_ref_trans_full_table.txt


title: Female CYP2E1-KO Ventral Hippocampus, Rep 1

description:
Library name: Sample 10
F_KO_V_1


title: DSP-1001660002551-C-A08_R7_C8

description: Library name: DSP-1001660002551-C-A08


title: Patient 332


title: MC3T3-E1 CELLS, HP group, 7days 3

description:
Library name: HP-3
MC3T3_ref_trans_full_table.txt


title: Patient 329


title: MC3T3-E1 CELLS, HP group, 7days 2

description:
Library name: HP-2
MC3T3_ref_trans_full_table.txt


title: Female CYP2E1-KO medial Prefrontal Cortex, Rep 3

description:
Library name: Sample 9
F_KO_P_3


title: DSP-1001660002551-C-A07_R7_C7

description: Library name: DSP-1001660002551-C-A07


title: Patient 295


title: Female CYP2E1-KO medial Prefrontal Cortex, Rep 2

description:
Library name: Sample 8
F_KO_P_2


title: Patient 397


title: DSP-1001660002551-C-A06_R7_C7

description: Library name: DSP-1001660002551-C-A06


title: Female CYP2E1-KO medial Prefrontal Cortex, Rep 1

description:
Library name: Sample 7
F_KO_P_1


title: DSP-1001660002551-C-A05_R7_C7

description: Library name: DSP-1001660002551-C-A05


title: DSP-1001660002551-C-A04_R7_C7

description: Library name: DSP-1001660002551-C-A04


title: Patient 250


title: 4T1,lymph node,treated

city: Columbus

first: Mark

last: Rubinstein

address: 460 W 12th Ave

department: Internal medicine

institute: The Ohio State University

description: Library name: sample4

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix file

source_name: lymph node

extract_protocol:
Tumors and draining lymph nodes (dLNs) were harvested and processed to generate single-cell suspensions. Tumor tissues were finely minced and enzymatically digested using Collagenase D (Roche, Cat# 11088882001) for 40 minutes at 37 °C with agitation at 250 rpm. dLNs were mechanically dissociated by gently mincing between sterile glass slides. Following dissociation, tissues were passed through a 70 μm cell strainer to remove debris and obtain a single-cell suspension. The cell suspensions were centrifuged, resuspended in completed media, and filtered again through a 30 μm cell strainer. For tumor samples, the single-cell suspension was layered over Histopaque-1077 (Sigma-Aldrich, Cat# 10771) in a 50 mL conical tube and centrifuged at 400 × g for 30 minutes at room temperature with acceleration and brake set to level 1. The upper plasma layer was carefully removed and discarded, and the opaque interface was collected into a fresh conical tube. Collected cells were washed by adding 10 mL of complete media (RPMI-1640 supplemented with 10% FBS, 1% penicillin-streptomycin, NSAA, Sodium pyruvate and β-Me), followed by centrifugation at 250 × g for 10 minutes. This wash step was repeated twice. Final cell pellets were resuspended in 5 mL of complete media and counted using a hemocytometer. For tumors and dLNs, CD8 T cells were enriched using the CD8 (TIL) Isolation Kit (Miltenyi Biotec, Cat# 130-116-478) according to the manufacturer’s instructions.
Live CD8+ T cells from TDLN day 5 post treatment were sorted for single-cell RNA-seq:. Sorted cells were then loaded onto a 10x Chromium Chip A using reagents from the Chromium Single-Cell 5’ Library and Gel Bead Kit (10x Genomics) according to the manufacturer’s protocol. Amplified cDNA was used for both 5’ RNA-seq library generation and TCR V(D)J targeted enrichment using the Chromium Single-Cell V(D) J Enrichment Kit for Mouse T Cells (10x Genomics). 5’ RNA-seq and TCR V(D)J libraries were prepared following the manufacturer’s user guide (10x Genomics). The final libraries were profiled using the Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies) and quantified using the Kapa Library Quantification Kit (Kapa Biosystems)

value: lymph node

value: CD8 T cell


title: Patient 232

value: Basal


title: Female CYP2E1-KO Dorsal Hippocampus, Rep 3

description:
Library name: Sample 6
F_KO_D_3


title: MC3T3-E1 CELLS, HPD group, 7days 1

description:
Library name: HPD-1
MC3T3_ref_trans_full_table.txt


title: Female CYP2E1-KO Dorsal Hippocampus, Rep 2

description:
Library name: Sample 5
F_KO_D_2


title: 4T1,lymph node,control

description: Library name: sample3


title: Patient 225


title: Female CYP2E1-KO Dorsal Hippocampus, Rep 1

description:
Library name: Sample 4
F_KO_D_1


title: Patient 218


title: B16,lymph node, control

description: Library name: sample1


title: Female CYP2E1-KO Cerebellum, Rep 3

description:
Library name: Sample 3
F_KO_C_3


title: DSP-1001660002551-C-A03_R7_C6

description: Library name: DSP-1001660002551-C-A03

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Assembly: hg19
Supplementary files format and content: CD45_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the leukocyte (CD45) compartment
Supplementary files format and content: CD68_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the macrophage (CD68) compartment
Supplementary files format and content: CK_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the tumor (CK) compartment
Library strategy: Spatial Transcriptomics


title: Patient 211


title: Patient 321


title: B16, lymph node, treated

description: Library name: sample2


title: DSP-1001660002551-C-A02_R7_C6

description: Library name: DSP-1001660002551-C-A02


title: DSP-1001660002550-B-H12_R7_C6

description: Library name: DSP-1001660002550-B-H12


title: MC3T3-E1 CELLS, HP group, 7days 1

description:
Library name: HP-1
MC3T3_ref_trans_full_table.txt

value: HP


title: Female CYP2E1-KO Cerebellum, Rep 2

description:
Library name: Sample 2
F_KO_C_2


title: Patient 161


title: Female CYP2E1-KO Cerebellum, Rep 1

description:
Library name: Sample 1
F_KO_C_1


title: SY1_2

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: SY1_2
SY1_2

data_processing:
The raw paired-end FASTQ reads were processed using the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq which utilizes STAR aligner.
Assembly: mm10
Supplementary files format and content: Gene counts in a txt file

extract_protocol:
Total RNA was isolated from the mice tumor nodules and cell lines using the miRNeasy Tissue/Cells Advanced Micro Kit with on-column DNase I treatment
Libraries were prepared using the TruSeq mRNA Library Prep Kit v2

value: YAP-SY-CCA


title: SY1_1

description:
Library name: SY1_1
SY1_1


title: DSP-1001660002550-B-H11_R7_C6

description: Library name: DSP-1001660002550-B-H11


title: Patient 128

value: IDC


title: Patient 179

value: II


title: SB1_3

description:
Library name: SB1_3
SB1_3

value: YAP-S-CCA


title: PreFrontal Cortex, Saline, Plexxikon-treated, Male, Sample05

city: Bordeaux

first: Charlotte

last: Madore

address: 146 rue Leo Saignat

department: Alimentation Humaine

country: France

institute: INRAE

description:
Library name: PFC_Sal_PLX_M_05
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_M_05

data_processing:
R sfotware and Rstudio were used;
Reads were trimmed using Trimmomatic package followed by feature count generation (Rsubread).
Reads were mapped to the mouse reference transcriptome GRCm39, v27 using STAR (v2.6.1d)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: prefrontal cortex

extract_protocol:
RNA was extracted using the miRNeasy Micro kit (Qiagen). 200ng of total RNA was used to construct RNA libraries.
RNA libraries were prepared using the Illumina Stranded mRNA Ligation Sample Prep kit following manufacturer's protocol.

tag: csf1r inhibitor

value: Plexxikon

value: prefrontal cortex

tag: Sex

value: Male

value: Saline injection


title: DSP-1001660002550-B-H10_R7_C5

city: New Haven

first: Thazin

last: Aung

address: 310 Cedar Street

institute: Yale University

description: Library name: DSP-1001660002550-B-H10

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx-DSP protocol (MAN-10150-01). Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5-666 nm, excitation 645-19 nm, emission 683-30 nm), CD45 for lymphocyte compartment (Texas Red-615 nm, excitation 588-19 nm, emission 623-30 nm), S100B (Cy3-568 nm, excitation 538-19 nm, emission 564-15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

value: Lung Cancer


title: SY1_3

description:
Library name: SY1_3
SY1_3

tag: genotype


title: DSP-1001660002550-B-H08_R7_C5

description: Library name: DSP-1001660002550-B-H08


title: Patient 042

value: III

tag: histology

value: ILC


title: Patient 004

tag: er


title: DSP-1001660002550-B-H07_R7_C5

description: Library name: DSP-1001660002550-B-H07


title: SB1_2

description:
Library name: SB1_2
SB1_2


title: PreFrontal Cortex, Saline, Plexxikon-treated, Male, Sample04

description:
Library name: PFC_Sal_PLX_M_04
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_M_04


title: SB1_1

description:
Library name: SB1_1
SB1_1


title: PreFrontal Cortex, Saline, Plexxikon-treated, Male, Sample06

description:
Library name: PFC_Sal_PLX_M_06
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_M_06


title: DSP-1001660002550-B-H09_R7_C5

description: Library name: DSP-1001660002550-B-H09


title: DSP-1001660002550-B-H05_R7_C4

description: Library name: DSP-1001660002550-B-H05


title: YAP-SY_M3

description:
Library name: YAP-SY_M3
Mut1_M3

source_name: Tumor

value: Tumor

value: YAP-SY-Mixed

value: myr-AKT and YAP S127A/Y357F


title: DSP-1001660002550-B-H06_R7_C4

description: Library name: DSP-1001660002550-B-H06

value: immunotherapy


title: PreFrontal Cortex, Saline, Plexxikon-treated, Male, Sample01

description:
Library name: PFC_Sal_PLX_M_01
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_M_01


title: Donor 4 MePyr [autoimmunity panel]

first: Adebowale

last: Bamidele

state: Minnesota

address: Medicine, 200 First Street SW, Guggenheim 10

department: Medicine

hyb_protocol: Total RNA  was hybridized with the NanoString nCounter Human Autoimmune Profiling Panel, which includes Reporter and Capture probe pairs for targeted immune-related gene transcripts. Hybridization was performed according to the manufacturer's protocol (NanoString Technologies), involving  hybridization at 65°C for 16 hours (without enzymatic amplification). The Reporter Probes carry fluorescent barcodes for digital counting, while the biotin-labeled Capture Probes facilitate immobilization on a streptavidin-coated cartridge. No additional labeling was performed.

scan_protocol: Post-hybridization processing and data collection were performed using the nCounter Prep Station and Digital Analyzer.

data_processing: Raw RCC files were imported into nSolver Analysis Software, and data were background-corrected, normalized to internal positive controls and housekeeping genes, and log2-transformed before analysis.

source_name: naïve CD4 T cells

growth_protocol: Human naive cells were differentiated into effector Th1 cells in cRPMI 1640 media (RPMI 1640 + L-Glutamine [Gibco] supplemented with 10% FCS, 10 mmol/L HEPES pH 7.4, 1 mmol/L sodium pyruvate, 2 mmol/L L-glutamine, 1% non-essential amino acids, penicillin, streptomycin, and 50 µmol/L β-mercaptoethanol)

extract_protocol: Total RNA was extracted with Rneasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.

value: Th1 cells

value: MePyr

tag: sample group

value: Test


title: YAP-SY_M8

description:
Library name: YAP-SY_M8
Mut1_M8

value: YAP-SY-CCA


title: Donor 3 MePyr [autoimmunity panel]


title: DSP-1001660002550-B-H04_R7_C4

description: Library name: DSP-1001660002550-B-H04


title: YAP-S_M9

description:
Library name: YAP-S_M9
Control_M9

value: YAP-S-Mixed

value: myr-AKT and YAPS127A


title: DSP-1001660002550-B-H03_R7_C4

description: Library name: DSP-1001660002550-B-H03


title: Donor 1 MePyr [autoimmunity panel]


title: PreFrontal Cortex, Saline, Plexxikon-treated, Female, Sample05

description:
Library name: PFC_Sal_PLX_F_05
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_F_05

value: Plexxikon

value: Female


title: PreFrontal Cortex, Saline, Plexxikon-treated, Female, Sample06

description:
Library name: PFC_Sal_PLX_F_06
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_F_06

value: prefrontal cortex


title: Donor 4 LY2090314 [autoimmunity panel]


title: PreFrontal Cortex, Saline, Plexxikon-treated, Female, Sample04

description:
Library name: PFC_Sal_PLX_F_04
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_F_04

value: Saline injection


title: YAP-SY_M9

description:
Library name: YAP-SY_M9
Mutant_M9


title: PreFrontal Cortex, Saline, Plexxikon-treated, Male, Sample03

description:
Library name: PFC_Sal_PLX_M_03
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_M_03

value: Male


title: YAP-SY_M6

description:
Library name: YAP-SY_M6
Mutant_M6


title: Donor 3 LY2090314 [autoimmunity panel]


title: PreFrontal Cortex, Saline, Plexxikon-treated, Male, Sample02

description:
Library name: PFC_Sal_PLX_M_02
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_M_02


title: PreFrontal Cortex, Saline, Plexxikon-treated, Female, Sample03

description:
Library name: PFC_Sal_PLX_F_03
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_F_03


title: YAP-SY_M5

description:
Library name: YAP-SY_M5
Mutant_M5


title: DSP-1001660002550-B-H01_R7_C3

description: Library name: DSP-1001660002550-B-H01

value: Lung Cancer


title: DSP-1001660002550-B-G12_R7_C3

description: Library name: DSP-1001660002550-B-G12


title: PreFrontal Cortex, Saline, Plexxikon-treated, Female, Sample02

description:
Library name: PFC_Sal_PLX_F_02
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_F_02


title: Donor 2 MePyr [autoimmunity panel]


title: YAP-SY_M1

description:
Library name: YAP-SY_M1
Mutant_M1


title: DSP-1001660002550-B-G11_R7_C3

description: Library name: DSP-1001660002550-B-G11


title: Donor 2 LY2090314 [autoimmunity panel]


title: Donor 4 Vehicle [autoimmunity panel]

value: Vehicle

value: Control


title: PreFrontal Cortex, Saline, Plexxikon-treated, Female, Sample01

description:
Library name: PFC_Sal_PLX_F_01
Column name in normalized_counts_all_samples.txt: PFC_Sal_PLX_F_01


title: DSP-1001660002550-B-G10_R7_C2

description: Library name: DSP-1001660002550-B-G10


title: Donor 1 LY2090314 [autoimmunity panel]


title: YAP-S_M7

description:
Library name: YAP-S_M7
Control_M7

value: Tumor


title: YAP-S_M5

description:
Library name: YAP-S_M5
Control_M5

value: YAP-S-CCA


title: PreFrontal Cortex, Saline, Control, Male, Sample06

description:
Library name: PFC_Sal_CTRL_M_06
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_M_06


title: DSP-1001660002550-B-H02_R7_C3

description: Library name: DSP-1001660002550-B-H02

value: immunotherapy


title: DSP-1001660002550-B-G09_R7_C2

description: Library name: DSP-1001660002550-B-G09


title: YAP-S_M4

description:
Library name: YAP-S_M4
Control_M4


title: Donor 3 Vehicle [autoimmunity panel]

value: Th1 cells


title: DSP-1001660002550-B-G08_R7_C2

description: Library name: DSP-1001660002550-B-G08


title: Donor 2 Vehicle [autoimmunity panel]


title: PreFrontal Cortex, Saline, Control, Male, Sample05

description:
Library name: PFC_Sal_CTRL_M_05
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_M_05


title: PreFrontal Cortex, Saline, Control, Male, Sample04

description:
Library name: PFC_Sal_CTRL_M_04
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_M_04


title: DSP-1001660002550-B-G07_R7_C2

description: Library name: DSP-1001660002550-B-G07


title: Patient_3_Metastasis_LRS

city: Tianjin

first: liu

last: tianxiang

address: No.94 Weijin Road, Nankai District

institute: Nankai University

description:
Library name: M3_LRS
M3

data_processing:
LRS: Two major steps were performed to obtain full-length non-chimeric (FLNC) reads: (i) Poly(A) tails and concatemers were identified and removed to refine high-quality full-length (FL) reads; (ii) The resulting FL reads were clustered to generate high-confidence transcript isoforms. The processed FLNC reads were then aligned using pbmm2 with the ISOSEQ preset. Aligned BAM files were subsequently sorted and indexed with samtools, and data from multiple SMRT cells of the same sample were merged prior to clustering.Sorted bam files from long read were quantified using isoquant
SRS: Raw sequencing reads were maaped using STAR. The resulting alignments were subsequently sorted and indexed with samtools. Gene-level counts were then obtained using featurecounts.Transcript-level counts were quantified using stringtie.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw trancript and gene counts from Isoquant for each LRS sample
Supplementary files format and content: tab-delimited text file includes raw trancript and gene counts from stringtie2 for each SRS sample

source_name: omentum

extract_protocol:
Total RNA was extracted using TRIeasyTM Total RNA Extraction Reagent according to the manufacturer’s instruction.
LRS:Using the Iso-Seq Express 2.0 kit, polyadenylated RNA molecules were enriched with Oligo(dT) primers and reverse-transcribed to synthesize cDNA, followed by PCR amplification to generate barcoded cDNA. The Kinnex Full-Length RNA kit was then used to amplify the cDNA and introduce sticky ends, allowing concatenation of eight cDNA fragments in series while ligating barcoded adapters at both ends. Damage repair was performed, and exonuclease treatment was applied to remove incompletely ligated fragments, yielding the final sequencing library. After quantification, the library templates of a certain concentration and volume and enzyme complexes were loaded into the nanopores of the PacBio Revio sequencing system for single-molecule real-time (SMRT) sequencing.
SRS:Eukaryotic mRNA was enriched using Oligo(dT) magnetic beads. The enriched mRNA was then fragmented using fragmentation buffer. Using the fragmented mRNA as a template, first- and second-strand cDNA were synthesized and subsequently purified. The purified double-stranded cDNA underwent end repair, A-tailing, adapter ligation, and fragment size selection to obtain cDNA fragments of approximately 350 bp. Finally, PCR amplification was performed to generate the cDNA library.The double-stranded cDNA was then denatured at high temperature to produce single-stranded DNA, followed by the addition of a circularization primer to form a single-stranded circular library. The constructed libraries were quality-checked using Qubit 3.0 and Agilent 2100 systems. Libraries that passed quality assessment were sequenced on a high-throughput sequencing platform with a PE150 strategy.

value: omentum


title: Donor 1 Vehicle [autoimmunity panel]


title: YAP-S_M2

description:
Library name: YAP-S_M2
Control_M2


title: PreFrontal Cortex, Saline, Control, Male, Sample03

description:
Library name: PFC_Sal_CTRL_M_03
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_M_03


title: Patient_2_Metastasis_LRS

description:
Library name: M2_LRS
M2


title: DSP-1001660002550-B-G06_R7_C1

description: Library name: DSP-1001660002550-B-G06


title: Lung CD140b+ cells, KO, rep2

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University

description: Library name: KO2

data_processing:
FASTQ files were aligned to the genome (mm10) with HISAT2. Gene counts were obtained with FeatureCounts in Subread tool. DESeq2 was used for differential expression testing.
Assembly: mm10
Supplementary files format and content: tab-delimited text file for raw count for each sample
Supplementary files format and content: csv file for DESeq2 analysis

source_name: Lung

extract_protocol:
Lung lobes were finely minced and digested with an enzyme solution containing 5 µg/mL Dispase (Corning, 354235), 0.025 mg/mL DNase I (Roche, 10104159001), and 480 µg/mL Collagenase Type I (Thermo Fisher, 17100017) in PBS at 37°C for 30 minutes with periodic agitation. Single-cell suspensions were generated using a gentleMACS Dissociator (Miltenyi Biotec). The digested tissues were washed with FACS buffer (PBS with 1 mM EDTA, 25 mM HEPES, and 0.5% BSA), filtered through a 70-µm cell strainer, and treated with 1× RBC Lysis Buffer (BioLegend, 420301) for 5 minutes on ice to eliminate red blood cells. The samples were then blocked with anti-mouse CD16/32 (FcR) antibody (BioLegend, 101301) at 4°C for 1 hour. The FcR-blocked single-cell suspensions were incubated with biotin-conjugated anti-CD140b (PDGFRβ) antibody at 4°C for 1 hour, followed by anti-biotin microbeads (Miltenyi Biotec, 130-090-485) for 30 minutes. PDGFRβ+ cells bound to microbeads were enriched using LS columns (Miltenyi Biotec) and washed with FACS buffer.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs)

value: Lung

value: Sorted CD140b+ cells


title: DSP-1001660002550-B-G05_R7_C1

description: Library name: DSP-1001660002550-B-G05


title: PreFrontal Cortex, Saline, Control, Male, Sample01

description:
Library name: PFC_Sal_CTRL_M_01
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_M_01


title: Lung CD140b+ cells, KO, rep1

description: Library name: KO1


title: Patient_3_Primary_tumor _LRS

description:
Library name: P3_LRS
P3

source_name: ovary

value: ovary


title: PreFrontal Cortex, Saline, Control, Female, Sample06

description:
Library name: PFC_Sal_CTRL_F_06
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_F_06


title: DSP-1001660002550-B-G04_R7_C1

description: Library name: DSP-1001660002550-B-G04


title: Lung CD140b+ cells, Ctrl, rep1

description: Library name: Ctrl1


title: Patient_2_Primary_tumor _LRS

description:
Library name: P2_LRS
P2


title: DSP-1001660002550-B-G03_R7_C1

description: Library name: DSP-1001660002550-B-G03


title: PreFrontal Cortex, Saline, Control, Female, Sample05

description:
Library name: PFC_Sal_CTRL_F_05
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_F_05


title: Patient_1_Primary_tumor _LRS

description:
Library name: P1_LRS
P1


title: YAP-S_M3

description:
Library name: YAP-S_M3
Control_M3

value: myr-AKT and YAPS127A


title: mut-5_R1

city: New York

first: Jun

last: Wang

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description: Library name: Mut-2, OTI, 48h

data_processing:
The DEGs between groups were analyzed using the R package DESeq2 (version v1.42.1) with the cutoff as |log2FoldChange|>1 and p-value <0.05.
The Gene Ontology (GO) enrichment analysis was performed to analyze the functions of DEGs by R clusterProfiler (version v4.6.2). The analyses were based on the GO resource (http://www.geneontology. org), p < 0.05 was considered statistically significant enrichment.
Assembly: mm10
Supplementary files format and content: Text file with raw counts for each sample

source_name: splenocytes

extract_protocol:
RNA was extracted from cells using an RNA extraction kit (Qiagen) after 48 hours of stimulation.
Libraries were constructed at Azenta LifeSciences

value: splenocytes

value: naive primary CD8 T cells

value: OT-I

value: SIINFEKL


title: PreFrontal Cortex, Saline, Control, Female, Sample04

description:
Library name: PFC_Sal_CTRL_F_04
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_F_04

value: prefrontal cortex

value: Female

value: Saline injection


title: PreFrontal Cortex, Saline, Control, Female, Sample03

description:
Library name: PFC_Sal_CTRL_F_03
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_F_03

value: Control


title: DSP-1001660002550-B-G01_R6_C8

description: Library name: DSP-1001660002550-B-G01

value: Lung Cancer


title: Patient_3_Normal_tissue_LRS

description:
Library name: N3_LRS
N3


title: Patient_2_Normal_tissue_LRS

description:
Library name: N2_LRS
N2


title: PreFrontal Cortex, Saline, Control, Female, Sample02

description:
Library name: PFC_Sal_CTRL_F_02
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_F_02


title: iso-4_R1

description: Library name: Iso-4, OTI, 48h


title: Patient_1_Metastasis_LRS

description:
Library name: M1_LRS
M1


title: Patient_1_Normal_tissue_LRS

description:
Library name: N1_LRS
N1


title: PreFrontal Cortex, Saline, Control, Male, Sample02

description:
Library name: PFC_Sal_CTRL_M_02
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_M_02

value: Male


title: DSP-1001660002550-B-F12_R6_C8

description: Library name: DSP-1001660002550-B-F12

value: immunotherapy


title: DSP-1001660002550-B-F11_R6_C7

description: Library name: DSP-1001660002550-B-F11


title: PreFrontal Cortex, Saline, Control, Female, Sample01

description:
Library name: PFC_Sal_CTRL_F_01
Column name in normalized_counts_all_samples.txt: PFC_Sal_CTRL_F_01


title: Lung CD140b+ cells, Ctrl, rep2

description: Library name: Ctrl2


title: DSP-1001660002550-B-F10_R6_C7

description: Library name: DSP-1001660002550-B-F10