title: Endoderm Nepn 12ss b2, scRNA-seq

description:
Nepn_12ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: Endoderm Mnx1GFP 27ss b2, scRNA-seq

status: Public on Jan 15 2025

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
Mnx1GFP_27ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

library_source: transcriptomic single cell

data_processing:
For the Smart-seq3xpress scRNA-seq data, initial quality control was executed with FastQC version 0.11.9 under default settings. Index, primer, and adaptor sequences were then trimmed from paired-end reads using Trimmomatic version 0.39 with default parameters. Alignment of trimmed reads to the Mus musculus Genome assembly GRCm38 (mm10) was accomplished using HISAT version 2.1.0.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

molecule: total RNA

organism: Mus musculus

source_name: Endoderm

extract_protocol:
Endodermal and gut tissues from 9SS to 27SS, were enzymatically dissociated using 0.25% trypsin (Gibco, 25200-056) for roughly 4 minutes at 37°C. The reaction was halted by the addition of 0.4 volumes of fetal bovine serum (FBS). The resultant cell suspension was centrifuged at 1000 rpm for 5 minutes at 4°C, followed by supernatant removal. To prepare single-cell suspensions from endodermal and gut samples, cells were incubated with anti-EpCAM-APC antibody (Invitrogen, 17-5791-82, dilution 1:100) in FACS buffer (comprising HBSS buffer with 1% FBS) for 20 minutes at 4°C in darkness. Following incubation, cells were washed with FACS buffer and subjected to analysis and sorting using BD FACSAriaTM Fusion flow cytometers. Dead cells were excluded from the analysis through staining with 1 µg/mL DAPI (Macklin, D807022).
The Smart-seq3xpress libraries were prepared following Smart3-seq3xpress's protocols.

tag: tissue

value: Endoderm

tag: strain

tag: genotype

value: Mnx1-CreER-EGFP; Rosa-RFP

tag: time


title: Endoderm Mnx1GFP 27ss b1, scRNA-seq

description:
Mnx1GFP_27ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos


title: T25.4_NA

type: RNA

city: Oullins-Pierre-Bénite

first: Marion

last: Debombourg

address: 165 chemindu grand revoyet

country: France

institute: biomerieux

hyb_protocol: NanoString nCounter, a hybridization-based multiplex assay.

scan_protocol: Data were collected and analyzed using the nCounter Digital Analyze according to the manufacturer instructions (NanoStrings Technologies, Seattle, WA).

data_processing: Normalization was performed using internal controls and 3 housekeeping genes (DECR1, HPRT1, POLR2A)

label: biotin

organism: Homo sapiens

source_name: whole blood

label_protocol: Biotin & color-coded tag, 300 ng of total RNA from each sample was analyzed for the detection of a 144-gene panel according to the manufacturers instructions.

growth_protocol: Patient's blood was directly collected in a PaxGene tube and then stabilized at room temperature for 2H

extract_protocol: Total RNA was extracted using the PaxGene Blood RNA kit (PreAnalytiX/QIAGEN) according to manufacturer instructions

treatment_protocol: After the 2h stabilization, the tube was stored at -80°C

tag: cohort

value: FIGHT

tag: status

value: Healthy Volunteer

tag: support

value: PaxGene

tag: stimulus


title: AL_132.4_NA

value: Patient


title: AL_131.4_NA


title: Human Islet 4

city: Ann Arbor

first: Anne

last: Lietzke

state: MI

address: 1000 Wall Street

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
FastQC (v0.11.8) was used to ensure the quality of data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1).
Alignment options followed ENCODE standards for RNA-seq.
FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Data were pre-filtered to remove genes with 0 counts in all samples.
Differential gene expression analysis was performed using DESeq2, using a negative binomial generalized linear model (thresholds: log2(fold change) >0.5 or <-.5, FDR (Padj) <0.05). Plots were generated using variations of DESeq2 plotting functions and other packages with Genialis (Boston, MA, USA).
Assembly: Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1).
Supplementary files format and content: Processed data file for each sample contain the following columns in order: Feature ID, Gene Symbol, Raw Count, TPM, and CPM.

source_name: Primary human islets

growth_protocol: HUES8 and H1 cell lines were differentiated to SC-islets in a 6 stage differentiation protocol (Hogrebe et al. 2021, PMID: 34349281). Primary human islets were received and cultured per protocol (Prodo Labs).

extract_protocol:
Total RNA was isolated from human islet and stem cell samples and DNase treated using commercially available kits (Omega Biotek and Ambion, respectively).
Libraries were constructed and subsequently subjected to 151bp paired-end cycles on the NovaSeq-6000 platform (Illumina).

treatment_protocol: H1 Stage 6 cells were treated for 7 days starting at stage 6 day 3 with vehicle or WY14643.

value: Primary human islets


title: RECQL5, biological replicate 1

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description: Gene expression data from mid-log yeast cells in minimal medium glucose (2%) expressing human helicase RECQL5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were normalized by RMA (Robust Microarray Average) to allow direct comparison between expression values in different experiments. Statistical analysis was performed by LIMMA (Linear Models for Microarray Analysis) using the program affylmGUI. Genes showing at least 1.5-fold linear expression change compared to wild-type strain with a p-value FDR < 0.1, were considered as altered. Expression values were obtained with the anti-log of RMA values

organism: Saccharomyces cerevisiae

source_name: Total RNA from W303 cells expressing tetp::RECQL5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Each strain was growing in minimal medium supplemented with glucose 2% without uracil.

extract_protocol: Total RNA was isolated with the Rneasy Midi kit (QIAGEN)

value: W303-1A + pCM189::RECQL5-FLAG

tag: phenotype


title: RECQL5, biological replicate 2

source_name: Total RNA from W303 cells expressing tetp::RECQL6


title: WT, biological replicate 1

description: Gene expression data from mid-log yeast cells in minimal medium glucose (2%) carrying an empty pCM189 plasmid

source_name: Total RNA from W303 cells carrying and empty pCM189 plasmid


title: RECQL5, biological replicate 3

source_name: Total RNA from W303 cells expressing tetp::RECQL7


title: AL_130.4_NA


title: Endoderm Mnx1GFP 24ss b2, scRNA-seq

description:
Mnx1GFP_24ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: Human Islet 3


title: Human Islet 2


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #5

city: Boston

first: Omar

last: Albastaki

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

description: Non-Phagocytic

data_processing:
The processing of the RNA-seq data (transcript assembly and quantification) was based on the HISAT, Stringtie, and Ballgown pipeline. Reads were aligned to the ‘mm10’ reference genome. Transcript abundances were imported into R (version 4.1.2) for all downstream bioinformatics analyses using several packages.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts (DESeq2) for each sample

source_name: Brain

extract_protocol:
TBI-induced lesion was injected with labelled apoptotic neurons on day 6 post-injury for 16 hours and on day 7 post-injury for 4 hours. We performed bulk RNA-seq on phagocytic and non-phagocytic microglia isolated at 4 and 16 hours post-injection following traumatic brain injury and nasal anti-CD3 treatment. Briefly, isolated microglia were lysed in 5ul TCL buffer + 1% β-mercaptoethanol. RNA was extracted with RNeasy® columns (Qiagen). cDNA libraries were generated from sorted cells using the Smart-seq2 protocol.
Preparation for RNA libraries for sequencing was performed using standard Illumina protocols.

value: Brain

tag: cell type

value: Microglia

tag: treatment

value: Nasal Anti-CD3 (aCD3)


title: AL_129.4_NA


title: Endoderm Mnx1GFP 24ss b1, scRNA-seq

description:
Mnx1GFP_24ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: AL_128.4_NA


title: T24.4_NA


title: Endoderm Nepn 12ss b1, scRNA-seq

description:
Nepn_12ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos

value: Nepn-CreER-EGFP; Rosa-RFP


title: Human Islet 1


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #4

description: Non-Phagocytic


title: Endoderm Mnx1GFP 21ss b2, scRNA-seq

description:
Mnx1GFP_21ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: Endoderm Nepn 09ss b1, scRNA-seq

description:
Nepn_09ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #3

description: Non-Phagocytic


title: AL_127.4_NA


title: Human Islet 5


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #6

description: Non-Phagocytic


title: Endoderm Mnx1GFP 21ss b1, scRNA-seq

description:
Mnx1GFP_21ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: PN0524_0024-Cold-OP

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

country: Denmark

institute: Queen’s University Belfast

library_source: genomic

data_processing:
We performed quality checks using FastQC to assess the overall quality of the bisulfite-converted sequencing (BS-Seq) reads.  Following quality control, adapter sequences were trimmed using TrimGalore. The human reference genome (GRCh38) was prepared using the bismark_genome_preparation utility from Bismark to account for bisulfite conversion. Subsequently, high-quality, adapter-trimmed reads were mapped to the prepared reference genome using Bismark (v0.22.3). Methylated cytosines were extracted from the mapped reads using MethylDackel, considering all three methylation contexts: CpG, CHG, and CHH (dpryan79/MethylDackel: A (mostly) universal methylation extractor for BS-seq experiments GitHub repository).
Assembly: GRCh38
Supplementary files format and content: Bed files

molecule: genomic DNA

extract_protocol:
For gDNA purification samples were added to the nuclease-free water (Thermo AM9939) to the final volume of 100µl. Then 3µl of RNase A (Thermo R1253) was added to the samples and incubated for 20 minutes at 37oC. Further DNA was purified using Monarch® Genomic DNA Purification Kit (NEB T3010S) according to the manufacturer's instructions with minor modifications. 1µl of Proteinase K (Thermo EO0491) was added to the samples and 100µl of lysis buffer was added and incubated for 5 min at 57oC followed by 400µl of binding buffer was added and loaded to the purification columns. Washed twice with wash buffer and eluted with 15µl of elution buffer. Purified DNA samples were quantified using Qubit high-sensitivity dsDNA Quantification assay (Thermo Q32854). The quality of the gDNA was analysed using Agilent TapeStation systems with high-sensitivity genomic DNA tapes.
Library preparation performed with NEBNext Enzymatic Methyl-Seq Kit.

tag: disease

value: Rasmussen’s encephalitis

value: OP

value: Cold


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #2

description: Non-Phagocytic


title: PN0524_0023-Cold-CING

value: CING


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #1

description: Non-Phagocytic


title: AL_126.4_NA


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #5

description: Phagocytic


title: Endoderm Mnx1GFP 18ss b2, scRNA-seq

description:
Mnx1GFP_18ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: Endoderm Mnx1GFP 18ss b1, scRNA-seq

description:
Mnx1GFP_18ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: PN0524_0021-Cold-SFG

value: SFG


title: AL_124.4_NA


title: PN0524_0022-Cold-MFG

value: MFG


title: Endoderm Mnx1GFP 15ss b2, scRNA-seq

description:
Mnx1GFP_15ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos

value: Endoderm

value: Mnx1-CreER-EGFP; Rosa-RFP


title: PN0524_0020-Spread-CING

value: Spread


title: AL_125.4_NA

value: FIGHT

value: PaxGene


title: AL_123.4_NA

value: Patient


title: Endoderm Mnx1GFP 15ss b1, scRNA-seq

description:
Mnx1GFP_15ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: AL_122.4_NA


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #2

description: Phagocytic


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #3

description: Phagocytic


title: Endoderm Mnx1GFP 12ss b1, scRNA-seq

description:
Mnx1GFP_12ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: AL_119.4_NA


title: PN0524_0018-Cold-HIPP

value: HIPP


title: PN0524_0017-Onset-HIPP

value: Brain

value: Onset


title: PN0524_0019-Cold-MTG

value: MTG


title: Endoderm Mnx1GFP 09ss b2, scRNA-seq

description:
Mnx1GFP_09ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: AL_121.4_NA


title: PN0524_0016-Onset-TP

value: non-lesional temporal lobe epilepsy

value: TP


title: Endoderm Mnx1GFP 09ss b1, scRNA-seq

description:
Mnx1GFP_09ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #1

description: Phagocytic

value: Microglia

value: Nasal Anti-CD3 (aCD3)


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #5

description: Non-Phagocytic

value: Isotype (Iso)


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #6

description: Non-Phagocytic


title: Endoderm Mnx1 27ss b2, scRNA-seq

description:
Mnx1_27ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Mnx1-CreER; Rosa-RFP


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #4

description: Phagocytic


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #4

description: Non-Phagocytic


title: AL_118.4_NA


title: AL_116.4_NA


title: PN0524_0015-Cold-IFG

value: IFG

value: Cold


title: AL_117.4_NA


title: AL_115.4_NA


title: PN0524_0014-Cold-ORB

value: ORB


title: Endoderm Mnx1 27ss b1, scRNA-seq

description:
Mnx1_27ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Endoderm


title: Endoderm Mnx1GFP 12ss b2, scRNA-seq

description:
Mnx1GFP_12ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos

value: Mnx1-CreER-EGFP; Rosa-RFP


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #3

description: Non-Phagocytic


title: Endoderm Mnx1 24ss b2, scRNA-seq

description:
Mnx1_24ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: PN0524_0013-Cold-SFG

value: SFG


title: AL_113.4_NA

value: FIGHT

value: Patient

value: PaxGene


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #2

description: Non-Phagocytic

value: Brain


title: PN0524_0012-Cold-INS

value: INS


title: Endoderm Mnx1 24ss b1, scRNA-seq

description:
Mnx1_24ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #1

description: Non-Phagocytic


title: PN0524_0011-Spread-ITG

value: non-lesional temporal lobe epilepsy

value: ITG

value: Spread


title: Endoderm Mnx1 21ss b2, scRNA-seq

description:
Mnx1_21ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: AL_112.4_NA


title: AL_111.4_NA


title: Phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #5

description: Phagocytic

value: Microglia


title: PN0524_0010-Spread-MTG

value: MTG


title: PN0524_0009-Onset-HIPP

value: HIPP

value: Onset


title: Endoderm Mnx1 18ss b2, scRNA-seq

description:
Mnx1_18ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos

value: Mnx1-CreER; Rosa-RFP


title: Endoderm Mnx1 21ss b1, scRNA-seq

description:
Mnx1_21ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: AL_110.4_NA


title: Phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #3

description: Phagocytic

value: Isotype (Iso)


title: PN0524_0008-Onset-MTG


title: AL_109.4_NA


title: Endoderm Mnx1 18ss b1, scRNA-seq

description:
Mnx1_18ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos

value: Endoderm


title: AL_108.4_NA


title: AL_106.4_NA


title: Phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #2

description: Phagocytic


title: Phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #1

description: Phagocytic


title: Endoderm Mnx1 15ss b2, scRNA-seq

description:
Mnx1_15ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: Endoderm Mnx1 15ss b1, scRNA-seq

description:
Mnx1_15ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: PN0524_0006-Cold-IFG

value: focal cortical dysplasia

value: IFG

value: Cold


title: Phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 16 h post-injection of apoptotic neurons, Sample #4

description: Phagocytic


title: PN0524_0007-Onset-SMA

value: SMA


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #4

description: Non-Phagocytic

value: Nasal Anti-CD3 (aCD3)


title: AL_105.4_NA

value: FIGHT

value: Patient

value: PaxGene


title: PN0524_0005-Cold-CING

value: Brain

value: CING


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #3

description: Non-Phagocytic

value: Microglia


title: Endoderm Mnx1 12ss b2, scRNA-seq

description:
Mnx1_12ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: AL_104.4_NA


title: PN0524_0004-Onset-FCD

value: FCD


title: Endoderm Mnx1 12ss b1, scRNA-seq

description:
Mnx1_12ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #2

description: Non-Phagocytic


title: AL_102.4_NA


title: Endoderm Mnx1 09ss b2, scRNA-seq

description:
Mnx1_09ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: PN0524_0003-Spread-TOJ

value: TOJ

value: Spread


title: AL_100.4_NA


title: Endoderm Mnx1 09ss b1, scRNA-seq

description:
Mnx1_09ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos

value: Mnx1-CreER; Rosa-RFP


title: Non-phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #1

description: Non-Phagocytic


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #4

description: Phagocytic


title: Endoderm Hhex 27ss b2, scRNA-seq

description:
Hhex_27ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Hhex-CreER-RFP; Ai6


title: Endoderm Hhex 27ss b1, scRNA-seq

description:
Hhex_27ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Endoderm


title: GFB-15565-Cold-CING

data_processing:
Adapter sequences were removed from raw FASTQ files using Cutadapt (v4.9)42. Subsequently, high-quality, adapter-trimmed reads were mapped against the human reference genome (GRCh38) using the STARlong utility within the STAR aligner43. Quantification of gene expression was performed using FeatureCounts at default parameters for each electrode from different brain regions in each disorder (Liao et al., 2014).
Assembly: GRCh38
Supplementary files format and content: Normalised count matrix

growth_protocol: For the total nucleic acids extraction, snap-frozen sEEG electrodes were cut into small pieces using sterile nuclease-free scissors into microfuge tubes and the total nucleic acids were extracted using PicoPure™ RNA Isolation Kit (Thermo KIT0204) according to the manufacturer's instructions with minor modifications.

extract_protocol:
For the RNA purification samples were first treated with DNase I (Thermo EN0521) to remove the DNA and purified using GeneJET RNA Purification Kit (Thermo K0732) according to the manufacturer's instructions. Purified RNA samples were quantified using Qubit high-sensitivity RNA Quantification assay (Thermo Q32852). The quality of the RNA was analysed using Agilent TapeStation systems with high-sensitivity RNA tapes with RIN numbers.
FLASH-seq protocol (https://www.protocols.io/view/bulk-flash-seq-3byl4jynolo5/v2)

value: Rasmussen’s encephalitis


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #3

description: Phagocytic


title: Endoderm Hhex 24ss b1, scRNA-seq

description:
Hhex_24ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: PN0524_0001-Cold-HIPP

value: focal cortical dysplasia

value: HIPP


title: GFB-15566-Cold-OP

value: OP

value: Cold


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #2

description: Phagocytic

value: Nasal Anti-CD3 (aCD3)


title: AL_91.4_NA

value: FIGHT

value: Patient


title: PN0524_0002-Cold-MTG

value: Brain

value: MTG


title: Endoderm Hhex 24ss b2, scRNA-seq

description:
Hhex_24ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: AL_64.4_NA

value: PaxGene


title: AL_67.4_NA


title: AL_99.4_NA


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #3

description: Non-Phagocytic

value: Microglia

value: Isotype (Iso)


title: GFB-15562-Spread-CING

value: CING

value: Spread


title: Endoderm Hhex 21ss b2, scRNA-seq

description:
Hhex_21ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos

value: Hhex-CreER-RFP; Ai6


title: AL_98.4_NA


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #2

description: Non-Phagocytic


title: GFB-15563-Cold-SFG

value: SFG


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #4

description: Non-Phagocytic


title: Phagocytic Microglia from TBI-aCD3 mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #1

description: Phagocytic


title: AL_60.4_NA


title: Endoderm Hhex 21ss b1, scRNA-seq

description:
Hhex_21ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos

value: Endoderm


title: GFB-15564-Cold-MFG

value: Rasmussen’s encephalitis

value: MFG


title: GFB-15561-Cold-MTG


title: AL_59.4_NA


title: Non-phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #1

description: Non-Phagocytic


title: GFB-15560-Onset-HIPP

value: HIPP

value: Onset


title: Endoderm Hhex 18ss b2, scRNA-seq

description:
Hhex_18ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: Phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #3

description: Phagocytic


title: AL_57.4_NA


title: GFB-15557-Cold-SFG

value: non-lesional temporal lobe epilepsy

value: Cold


title: GFB-15556-Cold-INS

value: INS


title: GFB-15559-Onset-TP

value: Brain

value: TP


title: Endoderm Hhex 18ss b1, scRNA-seq

description:
Hhex_18ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: Phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #2

description: Phagocytic


title: AL_46.4_NA

value: FIGHT

value: Patient

value: PaxGene


title: Endoderm Hhex 15ss b2, scRNA-seq

description:
Hhex_15ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: GFB-15558-Cold-ORB

value: ORB


title: AL_49.4_NA


title: aCD3_Total_CD4+_3

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of Total CD4+ Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #3

extract_protocol:
Bulk RNA-sequencing analysis was performed on sorted microglia single cell suspensions from the ipsilateral hemisphere of the mouse brains at 7 days and 30 days following traumatic brain injury and adoptive transfer. Briefly, isolated microglia were lysed in 5ul TCL buffer + 1% β-mercaptoethanol. RNA was extracted with RNeasy® columns (Qiagen). cDNA libraries were generated from sorted cells using the Smart-seq2 protocol.
Preparation for RNA libraries for sequencing was performed using standard Illumina protocols.

value: Microglia

value: Nasal Anti-CD3 (aCD3)


title: GFB-15555-Spread-ITG

value: ITG

value: Spread


title: Endoderm Hhex 12ss b2, scRNA-seq

description:
Hhex_12ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos

value: Endoderm

value: Hhex-CreER-RFP; Ai6


title: AL_48.4_NA


title: AL_44.4_NA


title: AL_47.4_NA


title: Endoderm Hhex 09ss b1, scRNA-seq

description:
Hhex_09ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: aCD3_Total_CD4+_1

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of Total CD4+ Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #1


title: aCD3_Total_CD4+_4

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of Total CD4+ Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #4


title: Endoderm Hhex 12ss b1, scRNA-seq

description:
Hhex_12ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: AL_42.4_NA


title: Endoderm Hhex 09ss b2, scRNA-seq

description:
Hhex_09ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: Endoderm Hhex 15ss b1, scRNA-seq

description:
Hhex_15ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: aCD3_Total_CD4+_2

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of Total CD4+ Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #2


title: AL_41.4_NA


title: GFB-15554-Spread-MTG

value: MTG


title: aCD3_FoxP3(ve)GFP_4

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of CD4+FoxP3(-ve) T cells from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #4


title: Phagocytic Microglia from TBI-Isotype mice 7 days post-TBI and 4 h post-injection of apoptotic neurons, Sample #1

description: Phagocytic

value: Isotype (Iso)


title: GFB-15553-Onset-HIPP

value: non-lesional temporal lobe epilepsy

value: HIPP

value: Onset


title: GFB-15552-Onset-MTG

value: Brain


title: Day 245 rep1

city: Chengdu

first: Rhea

last: Chen

address: No.211 Huimin Road, Wenjiang District, Chengdu, Sichuan, China

institute: Sichuan Agricultural University

data_processing:
Raw reads were mapped to the pig reference genome of Ensembl (Sus Scrofa 110) via Celescope (version 1.17.0). The number of UMIs per gene per cell was estimated by counting the reads with the same cell barcode and UMI. The UMI count tables of each cellular barcode were imported for downstream analysis. SoupX (version 1.6.2) is used to remove low levels of ambient RNA contamination, and high proportions of putative doublets identified by the DoubletFinder  (version 2.0.3) which were cells subsequently discarded.
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: Tab-separated values files and matrk files

organism: Sus scrofa

source_name: latissimus dorsi muscle

extract_protocol:
Skeletal muscle tissue was harvested from the longissimus dorsi muscles of 170-day-old and 245-day-old large white pigs, respectively, and were washed in pre-cooled PBSE (PBS buffer containing 2 mM EGTA). Nuclei isolation was carried out using GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies, Nanjing, China) refer to the manufacturer's product manual. Isolated nuclei were resuspended in PBSE to 106 nuclei per 400μl, fltered through a 40μm cell strainer, and counted with Trypan blue. Nuclei enriched in PBSE were stained with DAPI (1:1,000) (TermoFisher Scientifc, D1306). Nuclei were defned as DAPI-positive singlets.
The concentration of single nucleus suspension was adjusted to 3-4 × 105 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single NucleusRNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies). The resulting snRNA-seq libraries were sequenced on an Illumina HiSeq X10 instrument with 150 bp paired end reads

value: Skeletal muscle

value: 245 Day


title: GFB-15551-Onset-SMA

value: focal cortical dysplasia

value: SMA


title: AL_50.4_NA

value: FIGHT

value: Patient

value: PaxGene


title: AL_40.4_NA


title: Day 170 rep2

value: 170 Day


title: Day 245 rep2


title: aCD3_FoxP3(ve)GFP_2

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of CD4+FoxP3(-ve) T cells from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #2

value: Microglia

value: Nasal Anti-CD3 (aCD3)


title: GFB-15550-Cold-CING

value: CING

value: Cold


title: AL_34.4_NA


title: Day 170 rep1


title: aCD3_FoxP3(ve)GFP_1

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of CD4+FoxP3(-ve) T cells from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #1


title: AL_33.4_NA


title: Sample 4

type: genomic

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

institute: ISABIAL

description: Glioblastoma, IDH wildtype

hyb_protocol: Bisulphite converted and restored DNA from brain tumor samples were hybridized to the Illumina Infinium HumanMethylationEPIC version 2.0 microarray following manufacturer's instructions

scan_protocol: Arrays were imaged with iScan (Illumina)

data_processing: Initial processing and analysis were performed using the 'minfi' package in R. Samples were filtered to retain only those with a mean detection p-value of less than 0.01. Probe-level filtering was subsequently applied, retaining probes with a detection p-value below 0.01 across all samples and excluding probes located on sex chromosomes (XY) as well as those containing single nucleotide polymorphisms (SNPs). The original probe IDs were modified using the aggregate_to_probes() function to ensure accurate identification and aggregation in subsequent analyses

label: Cy3 and Cy5

source_name: FFPE-derived biomaterial

label_protocol: Standard Illumina protocol

extract_protocol: Paraffin was removed using mineral oil (QIAGEN). DNA from FFPE brain tumor tissue was then extracted using the QIAamp DNA Mini kit (QIAGEN). DNA concentration was assessed using Qubit dsDNA BR Assay Kits. DNA quality was assessed by quantitative PCR (Infinium HD FFPE QC kit, Illumina): samples with a ΔCq value < 5 were processed treated with bisulphite (Zymo EZ-96 DNA Methylation kit) and restored (Infinium HD FFPE DNA Restore kit, Illumina) following manufacturer’s protocol.

value: Brain tumor


title: Iso_total_Total_CD4+_4

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of Total CD4+ Tregs from injured mice treated with nasal isotype (Iso), Biological Replicate #4

value: Isotype (Iso)


title: Sample 238

description: Glioblastoma, IDH wildtype


title: Iso_total_Total_CD4+_3

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of Total CD4+ Tregs from injured mice treated with nasal isotype (Iso), Biological Replicate #3


title: GFB-15548-Cold-HIPP

value: HIPP


title: Sample 421

description: Glioblastoma, IDH wildtype


title: AL_30.4_NA

source_name: whole blood


title: Iso_total_Total_CD4+_2

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of Total CD4+ Tregs from injured mice treated with nasal isotype (Iso), Biological Replicate #2


title: Sample 400

description: Glioblastoma, IDH wildtype


title: AL_28.4_NA


title: AL_32.4_NA


title: G507, replicate5, scRNASeq

city: Aurora

first: Kejun

last: Guo

state: Colorado

department: Division of Infectious Diseases

institute: University of Colorado Anschutz Medical Campus

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (http://support.10genomics.com/single-cell-gene-expression/software/piplines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: LPMC

extract_protocol:
Cryo-preserved LPMCs were thawed and negatively select for CD4 T cells using EasySep Human CD4 T cell isolation kit from Stem Cell technologies.  After magnetic separation, the purified CD4 T cells were further isolated by florescence cell sorting.  CD4 T cells were stained for viability and surface markers CD45RO, CD3 CD4, and CD8. On average, the viable gut CD4 T cells were enriched to 99.5% among 6 donors.
The Thromium Single Cell 3’ Libray and Gel Bead Kit V3 (10x Genomics) was used to capture, label, and generate transcriptome libraries of individual cells.

value: LPMC

tag: cell line

value: Primary cells

value: CD4 T cells

value: E coli lysate


title: aCD3_FoxP3(ve)GFP_3

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of CD4+FoxP3(-ve) T cells from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #3

value: Brain


title: AL_27.4_NA


title: BG59, replicate4, scRNASeq

description: 10x Genomics


title: Sample 342

description: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted, grade 2


title: TBI_aCD3_FoxP3Negative_2

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of CD4+ T cells depleted of Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #2


title: TBI_aCD3_FoxP3Negative_3

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of CD4+ T cells depleted of Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #3


title: BG57, replicate3, scRNASeq

description: 10x Genomics


title: GFB-15549-Cold-MTG

source_name: Brain

value: focal cortical dysplasia

value: MTG


title: AL_19.4_NA

value: FIGHT

value: Patient


title: AL_21.4_NA

value: PaxGene


title: TBI_aCD3_FoxP3Negative_1

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of CD4+ T cells depleted of Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #1

value: Microglia


title: Sample 301

description: Glioblastoma, IDH wildtype


title: G447, replicate2, scRNASeq

description: 10x Genomics


title: BG44, replicate1, scRNASeq

description: 10x Genomics


title: G509, replicate6, scRNASeq

description: 10x Genomics


title: TBI_aCD3_FoxP3_3

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of FoxP3+ Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #3

value: Nasal Anti-CD3 (aCD3)


title: patient_10

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
STARsolo (version 2.7.10a) was used to perform sample and cell demultiplexing, and alignment of reads to the human genome (hg38) and UMI counting on gene models from Ensembl 104 excluding Locus Reference Genomic sequences (with options -- outFilterType=BySJout --outFilterMultimapNmax=10 --outSAMmultNmax=1 -- outFilterScoreMin=30 --soloCBmatchWLtype=1MM_multi_Nbase_pseudocounts -- soloUMIfiltering=MultiGeneUMI_CR --soloUMIdedup=1MM_CR --soloType=CB_UMI_Simple --soloStrand=Forward --clipAdapterType=CellRanger4 --soloUMIlen=12 --soloCellFilter=None --soloMultiMappers=EM).
Processing of the UMI counts matrix was performed using Bioconductor (version 3.16) packages, notably DropletUtils (function emptyDrops using 5000 iterations, the option test.ambient=TRUE, a lower threshold of 100 UMIs and an FDR threshold of 0.1%), scran and scater, following mostly the steps illustrated in the OSCA book (http://bioconductor.org/books/3.16/OSCA/). Cells with 0% or more than 12% of UMI counts attributed to mitochondrial genes, with less than 3000 UMI counts, or with less than 1500 detected genes were excluded. The presence of doublet cells was investigated with the scDblFinder package (version 1.12.0), and suspicious cells were filtered out (score<0.2). The package SingleR (version 2.0.0) was used for cell-type annotation of the cells using the following celldex human references: MonacoImmuneData, HumanPrimaryCellAtlasData, BlueprintEncodeData and DatabaseImmuneCellExpressionData. The assigned pruned labels were used and the cells not annotated to monocyte subtypes in these references were excluded.
Systematic differences between samples were removed using the fastMNN function (k=30) of the batchelor package (version 1.14.1). A UMAP embedding for visualization of cells was calculated using the batch-corrected low-dimensional coordinates for cells (n_neighbors=50, min_dist=0.5). Shared nearest-neighbor graph clustering was performed using the Leiden algorithm for finding community structure (k=10), resulting in 17 clusters which were merged into 7 clusters based on manual inspection of the cluster-specific genes, to reflect the continuum between classical monocytes, non-classical monocytes and M- MDSCs.
Assembly: hg38
Supplementary files format and content: UMIsMatrix.txt.gz: TSV file (tab separated values) including UMI counts for each cell and gene (ENSEMBL ID release 104). Column headers include the sample ID and cell barcode sequence separated by a dash (e.g., "patient_7-AAACCCAAGCGAGAAA")
Supplementary files format and content: CellMetadata.txt.gz: TSV file (tab separated values) including metadata for cells used in the paper. The information includes the samples metadata, cluster assignments and UMAP coordinates.

source_name: blood

extract_protocol:
Blood samples from 15 patients, including 6 healthy donors, 4 patients with compensated cirrhosis and 5 with decompensated cirrhosis, were processed for scRNA-seq, across 8 batches from July 2019 to August 2021. Enriched monocytes isolated by magnetic cell separation (MACS) were stained for viability and monocyte markers (CD14, CD16, HLA-DR) and sorted using BD FACSMelody Cell Sorter.
For each sample, an estimated count of 20,000 monocytes were loaded onto a single 10X channel, for a targeted recovery of 10,000 cells. cDNA and library preparation was performed with a Single Cell 3' v3 Reagent Kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed on an Illumina platform to produce 90nt-long R2 reads.

value: blood

value: primary cells

value: monocytes

tag: disease state

value: Decompensated cirrhosis


title: AL_18.4_NA


title: Sample 246

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: Iso_total_Total_CD4+_1

source_name: Microglia isolated from injured but untreated mice (1 month post-TBI), following the adoptive transfer of Total CD4+ Tregs from injured mice treated with nasal isotype (Iso), Biological Replicate #1

value: Isotype (Iso)


title: Sample 162

description: Glioblastoma, IDH wildtype


title: Sample 457

description: Glioblastoma, IDH wildtype


title: AL_14.4_NA


title: patient_3


title: AL_4.4_NA


title: TBI_aCD3_FoxP3_1

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of FoxP3+ Tregs from injured mice treated with nasal anti-CD3 (aCD3) , Biological Replicate #1


title: TBI_Iso_FoxP3_3

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of FoxP3+ Tregs from injured mice treated with nasal isotype (Iso), Biological Replicate #3


title: healthy_control_3

value: Healthy


title: patient_2


title: TBI_Iso_FoxP3_2

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of FoxP3+ Tregs from injured mice treated with nasal isotype (Iso), Biological Replicate #2


title: Sample 83

description: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted, grade 3

source_name: FFPE-derived biomaterial


title: Sample 197


title: healthy_control_2


title: AL_2.4_NA


title: Sample 436

description: Glioblastoma, IDH wildtype


title: AL_3.4_NA


title: TBI_Iso_FoxP3_1

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of FoxP3+ Tregs from injured mice treated with nasal isotype (Iso), Biological Replicate #1


title: AL_17.4_NA


title: T30.2_LPS

growth_protocol: Incubation inside a Truculture stimulation tube (from Myriad RBM), 37C, 22h.

extract_protocol: A modified protocol of the NucleoSpin 96 RNA tissue kit (Macherey-Nagel) was followed using a vaccum system

treatment_protocol: At the end of the incubation period, upon removal of the liquid supernatant cell pellets were resuspended in 2ml Trizol LS (Sigma) and vortexed for 2min, rested for 10 min at RT before storage at -80°C

value: Healthy Volonteer

value: TruCulture

value: LPS


title: healthy_control_6


title: TBI_aCD3_FoxP3_2

source_name: Microglia isolated from injured but untreated mice (7 days post-TBI), following the adoptive transfer of FoxP3+ Tregs from injured mice treated with nasal anti-CD3 (aCD3), Biological Replicate #2

value: Brain


title: patient_5

value: Compensated cirrhosis


title: Sample 6

description: Supratentorial ependymoma, NOS


title: TBI_aCD3+aIL10R_3_1m

source_name: TBI-aCD3 (anti-CD3) and anti-IL10 receptor (aIL10) blocking antibody 1 Month (1m) post-TBI, Biological Replicate #3

extract_protocol:
The IL-10 receptor was blocked in vivo through intraperitoneal administration of anti-IL-10 receptor blocking antibody every 3 days post-injury. Bulk RNA-sequencing analysis was performed on sorted microglia single cell suspensions from the ipsilateral hemisphere of the mouse brains using the microglia-specific 4D4+ antibody at 30 days following traumatic brain injury. Briefly, isolated microglia were lysed in 5ul TCL buffer + 1% β-mercaptoethanol. RNA was extracted with RNeasy® columns (Qiagen). cDNA libraries were generated from sorted cells using the Smart-seq2 protocol.
Preparation for RNA libraries for sequencing was performed using standard Illumina protocols.

value: Nasal Anti-CD3 (aCD3) + anti-IL10 receptor (aIL10R) blocking antibody


title: Sample 410

description: Glioblastoma, IDH wildtype


title: Sample 75

description: Glioblastoma, IDH wildtype


title: Sample 331

description: Glioblastoma, IDH wildtype


title: patient_1


title: healthy_control_5


title: TBI_aCD3+aIL10R_2_1m

source_name: TBI-aCD3 (anti-CD3) and anti-IL10 receptor (aIL10) blocking antibody 1 Month (1m) post-TBI, Biological Replicate #2


title: T28.3_SEB

source_name: whole blood

value: FIGHT

value: SEB


title: Sample 242

description: Glioblastoma, IDH wildtype


title: TBI_aCD3+aIL10R_1_1m

source_name: TBI-aCD3 (anti-CD3) and anti-IL10 receptor (aIL10) blocking antibody 1 Month (1m) post-TBI, Biological Replicate #1

value: Microglia


title: healthy_control_1


title: T28.2_LPS


title: Sample 120

description: Glioblastoma, IDH wildtype


title: patient_9


title: T30.3_SEB


title: TBI_Iso_3_1m_for_aIL10_cohort

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #3


title: T28.1_NUL

value: NUL


title: patient_4

value: blood


title: Sample 408

description: Glioblastoma, IDH wildtype


title: TBI_aCD3+aIL10R_4_1m

source_name: TBI-aCD3 (anti-CD3) and anti-IL10 receptor (aIL10) blocking antibody 1 Month (1m) post-TBI, Biological Replicate #4


title: healthy_control_4

value: primary cells


title: TBI_Iso_2_1m_for_aIL10_cohort

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #2


title: Sample 450

description: Glioblastoma, IDH wildtype


title: T25.2_LPS


title: patient_8

value: monocytes


title: patient_7


title: T25.1_NUL


title: Sample 233

description: Glioblastoma, IDH wildtype


title: TBI_Iso_1_1m_for_aIL10_cohort

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #1


title: Sham_Iso_4_1m_for_aIL10_cohort

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #4


title: T30.1_NUL


title: Sample 456

description: Glioblastoma, IDH wildtype


title: T24.2_LPS


title: Hours_48_72_96_rep2

first: Michigan

middle: CDB

last: Bioinformatics

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

data_processing:
BCL Convert Conversion Software v4 (Illumina)
(4830-KJ) samples were run through Cell Ranger v7.0.1 count against reference GRCh38-2020-A. (9704-BC) samples were run through Cell Ranger v7.1.0 multi against reference GRCh38-2020-A; config_9704_CellRanger_Multi.csv supplied to recreate the hd5 files
Assembly: GRCh38-2020-A
Supplementary files format and content: hd5 files from cellranger count or multi (see 10x website for format)
Supplementary files format and content: config_9704_CellRanger_Multi.csv is the configuration file for cellranger multi for the 9704 sample fastq

growth_protocol: Human pluripotent stem cells were grown in defined pluripotency maintenance media mTeSR1 at low density with 0.1% ROCK inhibitor in an incubator at 37C and 5% CO2

extract_protocol:
Samples (9704-BC) for single-cell RNA sequencing were harvested with the 10x Flex fixation kit based on the manufacturer’s manual. Samples (4830-KJ) were collected using accutase and resuspended in ice cold PBS. Cells were barcoded using the 10x Genomics Chromium system (part numbers 1000268, 1000120, 1000215). For quality control cDNA was quantified by Qubit High Sensitivity DNA assay and Agilent TapeStation
For both samples (9704-BC & 4830-KJ), the University of Michigan Advanced Genomics Core performed library preparation.

treatment_protocol: To differentiate cells for 2D gastruloids by micropatterning, cells were pre-incubated for 24 hours in mTeSR before adding the 50ng/ml BMP4 treatment by a full medium change. Full media changes with 50ng/ml BMP4 were performed every 24 hours.

value: human embryonic stem cells

value: 50ng/ml BMP4


title: Sample 260

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: TBI_Iso_4_1m_for_aIL10_cohort

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #4

value: Isotype (Iso)


title: Sample 351

description: Astrocytoma, IDH-mutant, grade 3


title: T24.3_SEB

value: Healthy Volonteer


title: Sample 413

description: Glioblastoma, IDH wildtype


title: T25.3_SEB

value: TruCulture


title: Sham_Iso_1_1m_for_aIL10_cohort

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #1


title: T24.1_NUL


title: T21.3_SEB


title: Hour_72_rep1


title: Sham_Iso_3_1m_for_aIL10_cohort

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #3


title: Sample 326

description: Glioblastoma, IDH wildtype


title: T21.2_LPS

value: LPS


title: Sham_Iso_2_1m_for_aIL10_cohort

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #2

value: Brain


title: Hour_96_rep1


title: Sample 340

description: Glioblastoma, IDH wildtype


title: TBI_aCD3_4_1m_Female_Severe_TBI

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #4

extract_protocol:
Bulk RNA-sequencing analysis was performed on sorted microglia single cell suspensions from the ipsilateral hemisphere of the mouse brains using the microglia-specific 4D4+ antibody at 7 days and 30 days following traumatic brain injury. Briefly, 2,000 isolated microglia CD45+CD11b+ Ly6C-4D4+ were lysed in 5ul TCL buffer + 1% β-mercaptoethanol. RNA was extracted with RNeasy® columns (Qiagen). cDNA libraries were generated from sorted cells using the Smart-seq2 protocol.
Preparation for RNA libraries for sequencing was performed using standard Illumina protocols.

value: Nasal Anti-CD3 (aCD3)


title: TBI_aCD3_3_1m_Female_Severe_TBI

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #3


title: Sample 333

description: Glioblastoma, IDH wildtype

source_name: FFPE-derived biomaterial


title: SAM24419056, replicate 1, scRNASeq

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

data_processing:
Read pseudoalignment: kallisto (version 0.46.2)
BUS file processing and gene count matrix creation: bustools (version 0.40.0)
Assembly: GRCh38 / Ensembl 90
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast

growth_protocol: T-47D cell line was barcoded with TraCe-seq barcoding libraries and expanded in culture to establish the starting TraCe-seq cell populations. A fraction of the starting population was profiled by single cell RNA-sequencing (scRNA-seq) to capture the relative clonal abundance and transcriptional profile of each barcoded clones right before drug treatment. In parallel, the rest of the cells were treated with giredestrant alone, palbociclic alone, or both drugs in combination until resistant clones emerged and expanded. We conducted scRNA-seq profiling to capture acute responses to the treatment at 1, 4,8, and 26 days post treatment as well as after resistance development to capture adaptive changes. These time points were chosen to allow us capture the differential transcriptional responses in the resistant versus sensitive clones, and compare the responses to individual single agent versus giradestrant + palbociclib combination at individual clone and single cell level.

extract_protocol:
Cultured cells were trypsinized into single cell suspensions in PBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Breast

value: Giredestrant + Palbociclib

tag: time point

value: Month 6


title: AL_132.3_SEB

value: FIGHT

value: Patient

value: SEB


title: Sample 451

description: Glioblastoma, IDH wildtype


title: Hour_48_rep1


title: Sample 305

description: Glioblastoma, IDH wildtype


title: TBI_aCD3_1_1m_Female_Severe_TBI

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #1

value: Microglia


title: TBI_aCD3_2_1m_Female_Severe_TBI

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #2


title: SAM24412247, replicate 1, scRNASeq

value: Giredestrant 200nm

value: Day 26


title: SAM24412248, replicate 1, scRNASeq


title: AL_132.2_LPS

source_name: whole blood


title: AL_132.1_NUL

value: NUL


title: Sample 406

description: Pilocytic astrocytoma

value: Brain tumor


title: TBI_Iso_5_1m_Female_Severe_TBI

source_name: TBI-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #5

value: Isotype (Iso)


title: SAM24412246, replicate 1, scRNASeq

value: Palbociclib 200nm


title: Sample 399

description: Glioblastoma, IDH wildtype


title: TBI_Iso_4_1m_Female_Severe_TBI

source_name: TBI-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #4


title: TBI_aCD3_5_1m_Female_Severe_TBI

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #5


title: T21.1_NUL

value: Healthy Volonteer

value: TruCulture


title: SAM24412245, replicate 2, scRNASeq

value: Day 8


title: SAM24412245, replicate 1, scRNASeq


title: Sample 347

description: Glioblastoma, IDH wildtype


title: TBI_Iso_3_1m_Female_Severe_TBI

source_name: TBI-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #3

value: Brain


title: TBI_Iso_2_1m_Female_Severe_TBI

source_name: TBI-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #2


title: AL_131.2_LPS

value: LPS


title: SAM24412244, replicate 1, scRNASeq

value: Breast


title: AL_131.1_NUL


title: Sample 397

description: Astrocytoma, IDH-mutant, grade 2


title: TBI_Iso_1_1m_Female_Severe_TBI

source_name: TBI-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #1


title: SAM24412243, replicate 1, scRNASeq


title: Sample 369

description: Glioblastoma, IDH wildtype


title: Sham_Iso_5_1m_Female_Severe_TBI

source_name: Sham-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #5


title: AL_131.3_SEB


title: Sample 336

description: Glioblastoma, IDH wildtype


title: SAM24412243, replicate 2, scRNASeq


title: Sham_Iso_4_1m_Female_Severe_TBI

source_name: Sham-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #4


title: Sham_Iso_3_1m_Female_Severe_TBI

source_name: Sham-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #3


title: Sample 282

description: Glioblastoma, IDH wildtype


title: SAM24412241, replicate 1, scRNASeq

value: Day 4


title: SAM24412244, replicate 2, scRNASeq


title: SAM24412242, replicate 1, scRNASeq

value: Giredestrant + Palbociclib


title: AL_129.2_LPS

value: FIGHT

value: Patient


title: Sample 423

description: Supratentorial ependymoma, NOS


title: AL_130.3_SEB

value: SEB


title: Sham_Iso_2_1m_Female_Severe_TBI

source_name: Sham-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #2

value: Microglia


title: AL_129.1_NUL


title: Sample 41

description: Glioblastoma, IDH wildtype


title: Sham_Iso_1_1m_Female_Severe_TBI

source_name: Sham-Isotype (Iso) 1 Month (1m) following severe TBI, Female mice, Biological Replicate #1


title: SAM24412239, replicate 1, scRNASeq

value: Day 1


title: Sample 286

description: Glioblastoma, IDH wildtype


title: SAM24412240, replicate 1, scRNASeq


title: Sample 438

description: Glioblastoma, IDH wildtype


title: AL_130.2_LPS


title: AL_128.2_LPS


title: AL_128.3_SEB


title: AL_130.1_NUL

value: NUL


title: TBI_aCD3_5_1m_delayed

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #5

value: Nasal Anti-CD3 (aCD3)


title: SAM24412238, replicate 1, scRNASeq

value: Giredestrant 200nm


title: Sample 346

description: Supratentorial ependymoma, NOS

source_name: FFPE-derived biomaterial

value: Brain tumor


title: Sample 273


title: SAM24412237, replicate 1, scRNASeq

source_name: Breast

value: Palbociclib 200nm


title: TBI_aCD3_3_1m_delayed

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #3


title: AL_129.3_SEB

value: TruCulture


title: AL_127.3_SEB


title: AL_128.1_NUL


title: SAM24412236, replicate 2, scRNASeq

value: Baseline

value: Day 0


title: Sample 249

description: Glioblastoma, IDH wildtype


title: TBI_aCD3_2_1m_delayed

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #2

value: Brain


title: SAM24412236, replicate 1, scRNASeq

value: Breast


title: AL_127.1_NUL

source_name: whole blood


title: TBI_aCD3_1_1m_delayed

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #1


title: Sample 140

description: Glioblastoma, IDH wildtype


title: AL_127.2_LPS

value: LPS


title: Sample 367

description: Glioblastoma, IDH wildtype


title: S2-Exos-3

city: Nanjing

first: Jing

last: Li

state: Jiangsu

address: No.101 Longmian Avenue, Jiangning District

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

data_processing:
Ttag counts per million aligned miRNAs (TPM) method was used to standardize the original expression of each miRNA. Fold change between the two samples was calculated and differentially expressed miRNAs were screened. The P-value and Fold Change between the two groups of samples (with replicates) were calculated, and the differentially expressed miRNAs were screened.
Assembly: hg38
Supplementary files format and content: All Comparisons.xlsx

source_name: Exosomes of umbilical cord mesenchymal stem

extract_protocol:
Exosomes were resuspended in 500 uL of Trizol (Invitrogen, USA) for high-throughput miRNA sequencing (Cloud-Seq Biotech, Shanghai, China). Briefly, total RNA was extracted and the A260/A280 ratio measured using a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). All samples had an A260/A280 ratio > 1.8.
The small RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq,Inc.) by following the manufacturer’s instructions. Briefly, 3’ and 5’ adaptors were successively ligated to RNA samples. Then, the adaptor-ligated RNA was reversely transcribed into cDNA, followed by PCR amplification. After amplification, the cDNA libraries were size-selected for miRNA fractions before sequencing and then sequenced in a HiSeq platform (Illumina).


title: Sample 227

description: Glioblastoma, IDH wildtype


title: TBI_Iso_5_1m_delayed

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #5

value: Isotype (Iso)


title: AL_126.3_SEB

value: FIGHT


title: AL_126.2_LPS

value: Patient


title: S2-Exos-1

value: Exosomes of umbilical cord mesenchymal stem


title: TBI_Iso_4_1m_delayed

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #4

value: Microglia


title: Sample 159

description: Glioblastoma, IDH wildtype


title: TBI_Iso_3_1m_delayed

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #3


title: TBI_aCD3_4_1m_delayed

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #4


title: S1-Exos-3


title: AL_126.1_NUL


title: S1-Exos-2


title: Sample 54


title: TBI_Iso_2_1m_delayed

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #2


title: Sample 89

description: Glioblastoma, IDH wildtype


title: TBI_Iso_1_1m_delayed

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #1


title: S1-Exos-1


title: Sample 306

description: Glioblastoma, IDH wildtype


title: AL_125.2_LPS


title: Sham_Iso_5_1m_delayed

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #5


title: AL_125.3_SEB

value: SEB


title: S2-Exos-2


title: AL_125.1_NUL

value: NUL


title: Sample 29


title: Sham_Iso_4_1m_delayed

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #4


title: AL_124.3_SEB


title: HCT116PRI_2

city: singapore

first: yi

last: chai

department: CSI

country: Singapore

institute: National University of SIngapore

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to hg38 using STAR v2.4.2a with default parameters settings
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were computed using RSEM v1.2.25 and Gencode v24 annotation.
Assembly: hg38
Supplementary files format and content: Excel file include FPKM values for each sample

extract_protocol:
1 ug of total RNA was used for the construction of sequencing libraries, using Illumina TruSeq Stranded Total RNA Library Preparation Kit (Cat no: RS-122-2201).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: HCT116PRI_3


title: Sham_Iso_3_1m_delayed

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #3


title: HCT116PRI_1


title: Sample 230

description: Glioblastoma, IDH wildtype


title: AL_124.2_LPS


title: Sham_Iso_2_1m_delayed

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #2


title: Sample 278

description: Glioblastoma, IDH wildtype

source_name: FFPE-derived biomaterial


title: HCT116Oxa_3


title: HCT116Oxa_2


title: AL_124.1_NUL


title: Sham_Iso_1_1m_delayed

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, delayed treatment, Biological Replicate #1


title: Sample 313

description: Glioblastoma, IDH wildtype


title: Sample 203

description: Glioblastoma, IDH wildtype


title: AL_123.3_SEB


title: Sample 12

description: Supratentorial ependymoma, NOS


title: TBI_aCD3_4_1m

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, Biological Replicate #4

value: Nasal Anti-CD3 (aCD3)


title: AL_123.2_LPS


title: HCT116Oxa_1


title: AL_123.1_NUL


title: TBI_aCD3_3_1m

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, Biological Replicate #3


title: Sample 8

description: Glioblastoma, IDH wildtype


title: HCT116DMSO_2


title: Sample 287

description: Glioblastoma, IDH wildtype


title: TBI_aCD3_2_1m

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, Biological Replicate #2


title: AL_122.3_SEB

source_name: whole blood


title: TBI_aCD3_1_1m

source_name: TBI-aCD3 (anti-CD3) 1 Month (1m) post-TBI, Biological Replicate #1


title: HCT116DMSO_1


title: Sample 360

description: Glioblastoma, IDH wildtype


title: HCT116DMSO_3


title: HCT116Combi3


title: AL_122.2_LPS


title: TBI_Iso_4_1m

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #4


title: AL_122.1_NUL


title: Sample 343


title: TBI_Iso_3_1m

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #3


title: HCT116Combi2


title: Sample 466

description: Astrocytoma, IDH-mutant, grade 3


title: AL_121.3_SEB


title: HCT116Combi1


title: TBI_Iso_2_1m

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #2


title: AL_121.2_LPS


title: Sample 198

description: Glioblastoma, IDH wildtype


title: TBI_Iso_1_1m

source_name: TBI-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #1


title: Sample 100

description: Glioblastoma, IDH wildtype


title: Sham_Iso_4_1m

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #4


title: DLD1PRImet_3


title: AL_121.1_NUL


title: DLD1PRImet_2


title: AL_119.3_SEB


title: Sample 141

description: Glioblastoma, IDH wildtype


title: Sham_Iso_3_1m

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #3


title: Sham_Iso_2_1m

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #2


title: DLD1PRImet_1


title: DLD1Oxa_3


title: AL_119.1_NUL


title: Sample 330

description: Glioblastoma, IDH wildtype


title: Sham_Iso_1_1m

source_name: Sham-Isotype (Iso) 1 Month (1m) post-TBI, Biological Replicate #1


title: AL_118.3_SEB


title: DLD1Oxa_1


title: Sample 68

description: Ganglioglioma


title: TBI_aCD3_4_7d

source_name: TBI-aCD3 (anti-CD3) 1 Week (7d) post-TBI, Biological Replicate #4


title: DLD1Oxa_2


title: Sample 73

description: Glioblastoma, IDH wildtype


title: Sample 411

description: Glioblastoma, IDH wildtype


title: DLD1DMSO_3


title: AL_118.1_NUL


title: TBI_aCD3_3_7d

source_name: TBI-aCD3 (anti-CD3) 1 Week (7d) post-TBI, Biological Replicate #3


title: DLD1DMSO_2.


title: AL_118.2_LPS


title: Sample 225

description: Glioblastoma, IDH wildtype

source_name: FFPE-derived biomaterial


title: TBI_aCD3_2_7d

source_name: TBI-aCD3 (anti-CD3) 1 Week (7d) post-TBI, Biological Replicate #2


title: TBI_aCD3_1_7d

source_name: TBI-aCD3 (anti-CD3) 1 Week (7d) post-TBI, Biological Replicate #1


title: AL_117.3_SEB


title: AL_117.2_LPS


title: DLD1DMSO_1


title: Sample 110

description: Glioblastoma, IDH wildtype


title: Sample 138

description: Glioblastoma, IDH wildtype


title: TBI_Iso_4_7d

source_name: TBI-Isotype (Iso) 1 Week (7d) post-TBI, Biological Replicate #4


title: AL_117.1_NUL


title: AL_119.2_LPS


title: DLD1Combi_3


title: TBI_Iso_3_7d

source_name: TBI-Isotype (Iso) 1 Week (7d) post-TBI, Biological Replicate #3


title: Sample 344

description: Glioblastoma, IDH wildtype


title: DLD1Combi_2


title: Sample 190

description: Glioblastoma, IDH wildtype


title: TBI_Iso_2_7d

source_name: TBI-Isotype (Iso) 1 Week (7d) post-TBI, Biological Replicate #2


title: DLD1Combi_1


title: AL_116.3_SEB

source_name: whole blood


title: AL_116.2_LPS


title: Sample 166

description: Glioblastoma, IDH wildtype


title: Sham_Iso_4_7d

source_name: Sham-Isotype (Iso) 1 Week (7d) post-TBI, Biological Replicate #4


title: Sample 361

description: Glioblastoma, IDH wildtype


title: AL_116.1_NUL


title: Sham_Iso_3_7d

source_name: Sham-Isotype (Iso) 1 Week (7d) post-TBI, Biological Replicate #3


title: NF3, shControl, rep3

city: Bangkok

first: Pichaya

last: Chanpanitkitchote

address: Phayathai

department: Molecular Medicine

country: Thailand

institute: Mahidol University

data_processing:
CLC Gnomics Workbench v 21.0
Sequence reads were trimmed for adapter seqence/low-quality sequence using CLC Genomic Workbench
Trimmed sequence reads were mapped to GRCh38 using CLC Genomic Workbench
Reads count extraction and normalization were performed using CLC genomic workbench
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes total counts, RPKM,TPM, CPM for each sample

source_name: Oral

growth_protocol: FADU cells were cultured in EMEM, supplemented with 10% FBS. CAL27 and all fibroblast cell  were cultured in DMEM medium with 10% FBS. All cultures were supplemented with antibiotic-microtic (100 U/ml penicillin, 100 μg/ml streptomycin, and 0.25 μg/ml amphotericin B), and 25 mM HEPES in a humidified 5% CO2 at 37°C.

extract_protocol:
Total RNA extraction was done by using RNeasy mini kit (74104, Qiagen).
RNA libraries for RNA sequencing using the Human TruSeq standard mRNA protocol (Illumina, Inc.) .

value: Oral

value: Normal fibroblast

value: primary fibroblast

value: control


title: AL_115.3_SEB

value: TruCulture


title: Sample 160

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: Sham_Iso_2_7d

source_name: Sham-Isotype (Iso) 1 Week (7d) post-TBI, Biological Replicate #2

value: Brain


title: AL_115.1_NUL


title: Sample 158

description: Astrocytoma, IDH-mutant, grade 2


title: AL_115.2_LPS


title: NF3, shControl, rep1


title: Sham_Iso_1_7d

source_name: Sham-Isotype (Iso) 1 Week (7d) post-TBI, Biological Replicate #1


title: NF3, shEMILIN1, rep2

value: EMILIN1 knockdown


title: NF3, shEMILIN1, rep3


title: AL_113.3_SEB


title: Sample 102

description: Supratentorial ependymoma, NOS


title: TBI_aCD3_2_Treg_Blood

source_name: Blood FoxP3+ Tregs, TBI-aCD3, 7 days post-TBI, Sample #2

extract_protocol:
CD4+Foxp3(GFP)+ Treg cells were FACS-isolated from the pericontusional brains tissue and from blood of the sham and injured mice at 7 days post-TBI. Between 800-1000 isolated CD4+FoxP3(GFP+) cells from the brain and blood were processed. RNA was extracted with RNeasy® columns (Qiagen). cDNA libraries were generated from sorted cells using the Smart-seq2 protocol.
Preparation for RNA libraries for sequencing was performed using standard Illumina protocols.

value: Blood

value: Tregs


title: NF3, shEMILIN1, rep1


title: Sample 443

description: Glioblastoma, IDH wildtype


title: AL_113.2_LPS

value: FIGHT

value: LPS


title: TBI_aCD3_1_Treg_Blood

source_name: Blood FoxP3+ Tregs, TBI-aCD3, 7 days post-TBI, Sample #1


title: TBI_Iso_1_7d

source_name: TBI-Isotype (Iso) 1 Week (7d) post-TBI, Biological Replicate #1

value: Isotype (Iso)


title: NF2, shControl, rep3

source_name: Hypopharyx

value: Hypopharyx


title: AL_113.1_NUL

value: Patient


title: TBI_Iso_2_Treg_Blood

source_name: Blood FoxP3+ Tregs, TBI-Iso, 7 days post-TBI, Sample #2


title: NF2, shControl, rep2


title: Sample 122

description: Glioblastoma, IDH wildtype

source_name: FFPE-derived biomaterial


title: AL_112.3_SEB

value: SEB


title: Sample 67

description: Glioblastoma, IDH wildtype


title: AL_112.2_LPS


title: NF2, shControl, rep1


title: Sample 157

description: Glioblastoma, IDH wildtype


title: Sham_2_Treg_Blood

source_name: Blood FoxP3+ Tregs, Sham, 7 days post-TBI, Sample #2


title: Sham_1_Treg_Blood

source_name: Blood FoxP3+ Tregs, Sham, 7 days post-TBI, Sample #1


title: NF2, shEMILIN1, rep3


title: NF2, shEMILIN1, rep2


title: Sample 255

description: Astrocytoma, IDH-mutant, grade 3


title: AL_111.3_SEB


title: NF2, shEMILIN1, rep1


title: AL_111.2_LPS


title: TBI_aCD3_2_Treg_Brain

source_name: Brain FoxP3+ Tregs, TBI-aCD3, 7 days post-TBI, Sample #2

value: Nasal Anti-CD3 (aCD3)


title: CAF3, shControl, rep3

value: Oral

value: Cancer associated fibroblast


title: Sample 439

description: Glioblastoma, IDH wildtype


title: NF3, shControl, rep2

value: Normal fibroblast

value: primary fibroblast


title: Sample 156

description: Glioblastoma, IDH wildtype


title: AL_111.1_NUL

value: TruCulture

value: NUL


title: TBI_Iso_2_Treg_Brain

source_name: Brain FoxP3+ Tregs, TBI-Iso, 7 days post-TBI, Sample #2

value: Brain


title: Sample 208

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: AL_110.3_SEB


title: CAF3, shControl, rep2

value: control


title: TBI_Iso_1_Treg_Brain

source_name: Brain FoxP3+ Tregs, TBI-Iso, 7 days post-TBI, Sample #1

value: Tregs


title: CAF3, shControl, rep1


title: AL_110.2_LPS

source_name: whole blood

value: FIGHT


title: Sample 109

description: Glioblastoma, IDH wildtype


title: TBI_Iso_1_Treg_Blood

source_name: Blood FoxP3+ Tregs, TBI-Iso, 7 days post-TBI, Sample #1

value: Blood


title: AL_112.1_NUL


title: Sample 3

description: Glioblastoma, IDH wildtype


title: AL_110.1_NUL


title: CAF3, shEMILIN1, rep3

value: EMILIN1 knockdown


title: Sample 422

description: Glioblastoma, IDH wildtype


title: AL_109.3_SEB


title: CAF3, shEMILIN1, rep2


title: Sham_1_Treg_Brain

source_name: Brain FoxP3+ Tregs, Sham, 7 days post-TBI, Sample #1

value: Isotype (Iso)


title: Sample 442

description: Glioblastoma, IDH wildtype


title: TBI_aCD3_1_Treg_Brain

source_name: Brain FoxP3+ Tregs, TBI-aCD3, 7 days post-TBI, Sample #1


title: Sample_4_Microglia_Xenon

first: Wesley

last: Nogueira Brandao

state: Massachusetts

department: Neurology

data_processing:
Fastq files were processed using Cell ranger. Cells with more than 1000 reads and less than 20 percent mitorchondrial transcripts were selected. Genes were removed if they were expressed in less than 3 cells.Potential dublets were detected using scDblFinder (v1.12.0)
Data was LogNormalized and the mitochondrial percentage was regressed out. The top 26 Principal components were used for UMAP clusterings. Clustree package was used to determine optimal number of clustes (v0.5.0)
Differential expression analysis was performed with FindMarkers with significant DEGs having a pvalue < 0.1 or 0.05. FindAllMarkers was utilized to identify sub cell-state marker genes.
Assembly: mm10
Supplementary files format and content: matrix, features and barcodes file per sample

source_name: Microglia

growth_protocol: APP/PS1 mice were kindly provided by Dr. Mathias Jucker (University of Tubingen). All animal procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women’s Hospital, Harvard Medical School, and Washington University School of Medicine.

extract_protocol:
The myeloid population was sorted  based in CD45 and CD11b and resuspended in 1X PBS containing 0.04% weight/volume BSA, recommended by 10x Genomics.
The Boston University Single Cell Sequencing Core facility and Harvard Medical School Single Cell Core generated the single-cell RNA-seq libraries.

treatment_protocol: We utilized a newly designed inhalation chamber to house up to 12 mice with an airtight 8L volume and a gas recirculation system. Continuous monitoring of Xe, O2, and CO2 concentrations was conducted, with a CO2 absorbent used to maintain CO2 levels between 600-900 ppm. This new system maintained stable gas 30% Xenon concentrations throughout the 40-minute treatment period. The animals were treated once a week from 2-4 months of age.

value: Microglia

tag: Sex

value: Female

value: Xenon


title: Sample 91

description: Supratentorial ependymoma, NOS


title: Sample_3_Microglia_Xenon


title: CAF3, shEMILIN1, rep1

source_name: Oral

value: Oral


title: AL_109.2_LPS

value: Patient

value: LPS


title: CAF2, shControl, rep3

value: Hypopharyx

value: Cancer associated fibroblast

value: primary fibroblast


title: Sample 417

description: Glioblastoma, IDH wildtype


title: Sample 79

description: Pilocytic astrocytoma


title: Sample_2_Microglia_Air

value: Air


title: CAF2, shControl, rep2


title: Sham_2_Treg_Brain

source_name: Brain FoxP3+ Tregs, Sham, 7 days post-TBI, Sample #2

value: Brain


title: CAF2, shControl, rep1

value: control


title: Sample 32

description: Pilocytic astrocytoma

value: Brain tumor


title: Sample_1_Microglia_Air


title: AL_108.3_SEB

value: FIGHT

value: TruCulture

value: SEB


title: CAF2, shEMILIN1, rep3

value: EMILIN1 knockdown


title: Sample_16_Microglia_DN

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: salmon plaint text quantification file (quant.sf)

growth_protocol: Clec7a-CreERT2 mice were developed by Dr. Oleg Butovsky in collaboration with Taconic and funded by the Cure Alzheimer’s Foundation (CAF). All animal procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women’s Hospital, Harvard Medical School, and Washington University School of Medicine.

extract_protocol:
The microglia cells were isolated by cell sorter, and 1000 cells have their RNA extracted by Broad Institute using TCL buffer containing 1% Beta-Mercaptoethanol.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
cDNA libraries were generated from sorted cells using the Smart-seq2 protocol65. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25bp reads.

treatment_protocol: APP/PS1”Clec7a-CreERT2:ROSA26TdTomato mice at 3 months of age were treated with Tamoxifen (TAM) 75mg/kg. One month later, the animals were euthanized.

value: Microglia

value: F

value: DN

tag: age

value: 4 Months


title: Sample 105

description: Glioblastoma, IDH wildtype

tag: tissue


title: AL_106.3_SEB

data_processing: Normalization was performed using internal controls and 3 housekeeping genes (DECR1, HPRT1, POLR2A)

value: Patient


title: AL_108.1_NUL

value: NUL


title: CAF2, shEMILIN1, rep2

value: Hypopharyx


title: Sample 58

description: Glioblastoma, IDH wildtype


title: CAF2, shEMILIN1, rep1

value: Cancer associated fibroblast


title: Sample 81

description: Pilocytic astrocytoma


title: Sample_13_Microglia_TdT

value: TdT


title: AL_109.1_NUL


title: Sample 90

description: Glioblastoma, IDH wildtype


title: CAL27, Control, rep3

value: Oral

value: Head and neck squamous cell carcinoma


title: AL_105.3_SEB


title: Sample_12_Microglia_DN


title: Sample 366

description: Glioblastoma, IDH wildtype


title: Sample_11_Microglia_TdT


title: CAL27, Control, rep1

value: control


title: AL_106.1_NUL


title: Sample 46

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: AL_108.2_LPS

value: FIGHT

value: LPS


title: AL_105.2_LPS

value: TruCulture


title: AL_105.1_NUL


title: Sample 256

description: Glioblastoma, IDH wildtype


title: Sample_15_Microglia_TdT


title: CAL27, OverEMILIN1, rep3

value: EMILIN1 overexpression


title: Sample_10_Microglia_DN

value: Microglia


title: Sample 218

description: Glioblastoma, IDH wildtype


title: Sample_14_Microglia_DN

value: F


title: AL_106.2_LPS


title: AL_104.2_LPS


title: CAL27, OverEMILIN1, rep2


title: AL_104.3_SEB

value: SEB


title: Sample_8_Microglia_DN

value: M

value: DN

value: 4 Months


title: CAL27, OverEMILIN1, rep1


title: CAL27, Control, rep2


title: Sample 364

description: Glioblastoma, IDH wildtype


title: Sample_7_Microglia_TdT


title: FADU, Control, rep3

value: Hypopharyx

value: FADU


title: AL_104.1_NUL

value: Patient

value: NUL


title: AL_102.3_SEB


title: Sample 199

description: Glioblastoma, IDH wildtype


title: FADU, Control, rep2

value: Head and neck squamous cell carcinoma


title: Sample_6_Microglia_DN


title: Sample 430

description: Supratentorial ependymoma, NOS


title: Sample_5_Microglia_TdT

value: TdT


title: FADU, Control, rep1

value: control


title: Sample_9_Microglia_TdT


title: Sample_4_Microglia_DN


title: AL_102.2_LPS

value: FIGHT


title: FADU, OverEMILIN1, rep3


title: AL_102.1_NUL


title: Sample 299

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: Sample_3_Microglia_TdT


title: AL_100.3_SEB

value: TruCulture


title: Sample 416

description: Pilocytic astrocytoma


title: FADU, OverEMILIN1, rep1

value: EMILIN1 overexpression


title: AL_100.2_LPS

value: LPS


title: Sample_1_Microglia_TdT

value: Microglia


title: Sample 134

description: Glioblastoma, IDH wildtype


title: Sample 363

description: Astrocytoma, IDH-mutant, grade 3


title: Pos_C_PDAC

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description:
10x Genomics
Protocol 1

data_processing:
human
Raw sequencing data were processed with CellRanger pipeline (v7.0.0) (PMID: 28091601). Cellranger “mkfastq” command was used to demultiplex the different samples and Cellranger “count” command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender(v0.2.0)with standard parameters. Human Genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates(PMID: 33270111).   Downstream analysis was performed in R with Seurat (v4.3.0) (PMID: 34062119) and customized R scripts. Data from Negative samples ((Neg_C_PDAC, Neg_Control, Neg_WS_PDAC) and positive samples (Pos_C_PDAC, Pos_Control, Pos_WS_PDAC) were merged into a unique single cell object. Both Negative and Positive samples were analyzed individually.   Positive Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 20017 genes and 5796 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.3 for Louvain clustering and UMAP. Batch correction was performed using Harmony. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).  Negative Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 20017 genes and 11527 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.3 for Louvain clustering and UMAP. Batch correction was performed using Harmony. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9). Differential expression analysis: To identify differentially expressed genes in Negatives and Positive samples. 1. Neg Control vs Neg Cachetic PDAC (Neg_Control  vs Neg_C_PDAC)  2. Neg Control vs Neg Weight Stable PDAC (Neg_Control  vs Neg_WS_PDAC)  3.  Neg Cachetic PDAC  vs Neg Weight Stable PDAC (Neg_C_PDAC  vs Neg_WS_PDAC) 4. Pos Control vs Pos Cachetic PDAC (Pos_Control  vs Pos_C_PDAC)  5. Pos Control vs Pos Weight Stable PDAC (Pos_Control  vs Pos_WS_PDAC)  6.  Pos Cachetic PDAC  vs Pos Weight Stable PDAC (Pos_C_PDAC  vs Pos_WS_PDAC) in each defined cell types, the R package LIBRA (v1.0.0) with option wilcox was used to perform zero-inflated regression analysis (PMID: 34584091). Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2.
Assembly: Homo Sapiens hg38
Supplementary files format and content: HDF5 Feature-Barcode Matrix
mouse
Raw sequencing data were processed with CellRanger pipeline (v7.0.0) (PMID: 28091601). Cellranger “mkfastq” command was used to demultiplex the different samples and Cellranger “count” command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender(v0.2.0)with standard parameters. Mouse Genome mm10 was used for the alignment and gencode vM25 was used for gene annotation and coordinates (PMID: 33270111).   Downstream analysis was performed in R with Seurat (v4.3.0) (PMID: 34062119) and customized R scripts. Data from Negative samples (CtrlNeg and KppNeg) were merged into a unique single cell object and positive samples (CtrlPos and KppPos) were merged into a unique single cell object. Both Negative and Positive samples were analyzed individually.   Positive Samples: Cells with <30000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 21850 genes and 17462 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.4 for Louvain clustering and UMAP. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).   Negative Samples: Cells with <10000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) (PMID: 35814628) for a resultant expression matrix with 21850 genes and 35352 cells. The SCTransform workflow was used for count normalization (VST transformation) and data integration (PMID: 31870423) using 30 principal components and resolution of 0.4 for Louvain clustering and UMAP. Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers, from Tirosh and colleagues. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. Cell annotation was performed using gene markers by manually curation. Gene markers used for identification FAPS(PRG4,PDGFRA), Skeletal Cells(ACTA, TTN), MuSCs and Progenitors(APOC1), Endothelial(PECAM1, VWF), Pericytes(ACTA2), Tcells(CD3G), Mast Cells(TPSAB), Macrophages(C1QA) and Neutrophils(S100A9).
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: Skeletal Muscle

extract_protocol: Dual-indexed libraries were pooled to and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 (S4 flow cell) to a depth of approximately 25 million paired-end 150 bp reads per library.

value: Skeletal Muscle


title: Sample_13_Microglia_M-CSF+TGFB XE

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters
Supplementary files format and content: Bigwig file format, which was created from sorted BAM files and normalization against mouse genome length using deeptools.

growth_protocol: Primary mouse microglia cultures were isolated from 2-month-old C57BL/6 and plated in a 96-well plate (50,000 cells per well). The cells were cultured for 5 days with M-CSF (10ng/mL, R&D Systems 416-ML-010/CF) and human TGF-β (50ng/mL, Miltenyi Biotec 130-095-067) to maintain them in a homeostatic state (M0), or with GM-CSF (10 ng/mL, R&D Systems 415-ML-010/CF) to induce an MGnD-like signature.

treatment_protocol: On day 6 of culture, cells were treated with  Xenon 75% exposure for 24 hours.

value: Female

tag: polarization

value: M-CSF+TGFB XE

value: XEN

value: 2 Months


title: Neg_C_PDAC

description:
10x Genomics
Protocol 1


title: AL_99.3_SEB

value: SEB


title: Sample 205

description: Glioblastoma, IDH wildtype


title: AL_100.1_NUL

value: Patient


title: Sample_12_Microglia_M-CSF+TGFB XE


title: Pos_Control

description:
10x Genomics
Protocol 1


title: Sample 458

description: Glioblastoma, IDH wildtype


title: AL_99.2_LPS


title: Neg_Control

description:
10x Genomics
Protocol 1


title: Sample 192

description: Glioblastoma, IDH wildtype


title: FADU, OverEMILIN1, rep2

value: Hypopharyx

value: FADU

tag: genotype


title: AL_99.1_NUL

value: NUL


title: Sample 36

description: Glioblastoma, IDH wildtype


title: Sample_2_Microglia_DN

value: M

value: DN

value: 4 Months


title: Sample 16

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: Sample_10_Microglia_M-CSF+TGFB

value: M-CSF+TGFB

value: AIR


title: Sample 294

description: Glioblastoma, IDH wildtype


title: Neg_WS_PDAC

description:
10x Genomics
Protocol 1


title: Pos_WS_PDAC

description:
10x Genomics
Protocol 1


title: AL_98.2_LPS

value: FIGHT

value: TruCulture

value: LPS


title: Sample 448


title: Sample_8_Microglia_M-CSF+TGFB

value: Microglia

value: Female


title: Sample 461

description: Glioblastoma, IDH wildtype


title: Sample_9_Microglia_M-CSF+TGFB

value: 2 Months


title: AL_98.1_NUL


title: Sample 219

description: Glioblastoma, IDH wildtype


title: Sample_7_Microglia_GM-CSF XE

value: GM-CSF XE

value: XEN


title: Sample_11_Microglia_M-CSF+TGFB XE

value: M-CSF+TGFB XE


title: Sample_6_Microglia_GM-CSF XE


title: Sample 280

description: Glioblastoma, IDH wildtype


title: Sample_5_Microglia_GM-CSF XE


title: Sample 440


title: Sample 95

description: Glioblastoma, IDH wildtype


title: Sample_4_Microglia_GM-CSF XE


title: Sample_3_Microglia_GM-CSF

value: GM-CSF


title: AL_67.3_SEB

value: Patient

value: SEB


title: AL_98.3_SEB


title: Sample 322

description: Pilocytic astrocytoma


title: Sample_2_Microglia_GM-CSF


title: Sample 415

description: Glioblastoma, IDH wildtype


title: Sample 66

description: Glioblastoma, IDH wildtype


title: Sample_1_Microglia_GM-CSF


title: AL_67.2_LPS


title: AL_67.1_NUL

value: NUL


title: Sample_16_Microglia_Xenon_14Days

growth_protocol: APP/PS1mice were kindly provided by Dr. Mathias Jucker (University of Tubingen). All animals received water and food ad libitum. Procedures and experiments were performed under guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at Brigham and Women's Hospital, Harvard Medical School, and Washington University School of Medicine

treatment_protocol: We treated 3-month-old APP/PS1 mice with a single dose of 30% Xe for 40 minutes.

value: Xenon

tag: timepoint

value: 3 months


title: AL_64.3_SEB

tag: cohort


title: AL_64.2_LPS

tag: status


title: Sample 254

description: Supratentorial ependymoma, NOS

value: Brain tumor


title: AL_91.3_SEB

tag: support


title: Sample 372

description: Astrocytoma, IDH-mutant, grade 2


title: AL_64.1_NUL

tag: stimulus


title: AL_60.2_LPS


title: Sample_15_Microglia_Xenon_14Days


title: Sample 31

description: Glioblastoma, IDH wildtype


title: Sample_13_Microglia_Xenon_14Days


title: Sample 61

description: Pilocytic astrocytoma


title: AL_91.1_NUL


title: AL_91.2_LPS


title: AL_60.3_SEB


title: AL_60.1_NUL


title: Sample_12_Microglia_Xenon_14Days


title: Sample_11_Microglia_Xenon_7Days


title: Sample 465

description: Astrocytoma, IDH-mutant, grade 2


title: AL_59.3_SEB


title: Sample_10_Microglia_Xenon_7Days


title: AL_59.2_LPS


title: Sample 184


title: Sample 161

description: Glioblastoma, IDH wildtype


title: Sample_9_Microglia_Xenon_7Days


title: Sample_8_Microglia_Xenon_7Days


title: AL_59.1_NUL


title: AL_57.3_SEB


title: Sample 445

description: Glioblastoma, IDH wildtype


title: Sample 2

description: Glioblastoma, IDH wildtype


title: Sample_14_Microglia_Xenon_14Days


title: AL_57.2_LPS


title: Sample_7_Microglia_Xenon_3Days


title: Sample_6_Microglia_Xenon_3Days


title: AL_57.1_NUL


title: Sample 132

description: Glioblastoma, IDH wildtype


title: AL_50.3_SEB


title: Sample_5_Microglia_Xenon_3Days


title: Sample 171

description: Glioblastoma, IDH wildtype


title: Sample_4_Microglia_Xenon_3Days


title: Sample 214

description: Glioblastoma, IDH wildtype


title: Sample_3_Microglia_AIR_14Days

value: AIR


title: AL_50.2_LPS

value: FIGHT


title: AL_50.1_NUL

value: TruCulture


title: Sample 193

description: Glioblastoma, IDH wildtype


title: Sample_2_Microglia_AIR_14Days


title: Sample_1_Microglia_AIR_14Days


title: Sample_16_Tcell_Xenon

source_name: Tcells

value: Tcells


title: AL_49.2_LPS

value: LPS


title: Sample 42

description: Glioblastoma, IDH wildtype


title: Sample 365

description: Ganglioglioma


title: AL_49.3_SEB


title: Sample_15_Tcell_Xenon

value: Female


title: AL_48.3_SEB


title: Sample 426

description: Glioblastoma, IDH wildtype


title: Sample 121

description: Glioblastoma, IDH wildtype


title: Sample_14_Tcell_Xenon


title: Sample 320

description: Glioblastoma, IDH wildtype


title: Sample 77

description: Glioblastoma, IDH wildtype


title: Sample_13_Tcell_Xenon


title: AL_49.1_NUL


title: AL_48.2_LPS


title: AL_48.1_NUL


title: AL_47.3_SEB


title: Sample_12_Tcell_Xenon


title: Sample 76

description: Glioblastoma, IDH wildtype


title: Sample_11_Tcell_Xenon


title: Sample 328


title: Sample 144

description: Glioblastoma, IDH wildtype


title: Sample_10_Tcell_Xenon


title: AL_47.1_NUL


title: AL_47.2_LPS


title: AL_46.3_SEB


title: Sample 35

description: Glioblastoma, IDH wildtype


title: Sample_9_Tcell_Xenon


title: Sample 453

description: Astrocytoma, IDH-mutant, grade 3


title: Sample_8_Tcell_Xenon