title: IECs, SETD2-VILKO-96

description: Library name: SETD2-VILKO-96


title: IECs, SETD2-FF-97

status: Public on Aug 12 2026

type: SRA

city: Shanghai

first: Jing

last: Feng

address: Zhizao ju road

department: Gastroenterology

country: China

institute: Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University

description: Library name: SETD2-FF-97

library_source: transcriptomic

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13 HISAT2.1.0 mapping to reference genome
Assembly: mm10/Ensembl v101
Supplementary files format and content: csv file including raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: colon

extract_protocol:
Total RNA was isolated utilizing the Trizol reagent. Subsequently, we employed the Illumina TruSeq RNA Sample Prep Kit to construct sequencing libraries, starting with an initial input of 1 μg of total RNA and strictly adhering to the manufacturer's established protocols.
RNA-seq library was constructed by using NEBNext Ultra Ⅱ RNA Library Prep Kit for illumina.

tag: tissue

value: colon

tag: cell type

value: intestinal epithelial cells

tag: genotype


title: 1952-2.GEX.SamplePool.rs116820

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

country: USA

description:
Library name: 116820
Fig5.seurat.rds
Fig5.counts.rds

data_processing:
CellRanger count
DropletUtils emptyDrops
Seurat Normalize/Scale/PCA
Assembly: GCA_003339765.3
Supplementary files format and content: Sparse count matrix (RDS file)
Supplementary files format and content: Seurat Object (RDS file)

molecule: polyA RNA

organism: Macaca mulatta

source_name: PBMC

extract_protocol: 10x Genomics 5' VDJ scRNA-seq

value: PBMC


title: Mov10 Deletion, Day 0, replicate 1

city: Urbana

first: Stephanie

last: Ceman

state: Illinois

address: 506 S Mathews Ave

department: Cell and Developmental Biology

institute: University of Illinois Urbana-Champaign

description:
Library name: D0_1
Output from Salmon quant

data_processing:
Cutadapt (cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT)
Create decoy-aware transcriptome using Salmon-1.10.0 and transcript annotations from GENCODE—gencode.vM37.transcripts.fa.gz and GRCm39.primary_assembly.genome.fa.gz. Quantify the transcripts using salmon quant with -seqBias --gcBias --recoverOrphans --validateMappings flags.
Differential gene expression was performed in R using DESeq2 with default parameters.
Assembly: GRCm39
Supplementary files format and content: quant.sf files with transcript-level quantifications from Salmon

source_name: Whole brain

extract_protocol:
Whole brains were dissected on ice and flash frozen using liquid nitrogen. Tissues were kept at -80C before being shipped to Biostate.ai in dry ice for RNA extraction and sequencing.
NEBNext Poly(A) mRNA Magnetic Isolation Module

value: Whole brain

value: Mov10 Deletion

tag: treatment

value: Day 0

tag: batch


title: WT, Day 23, replicate 3

description:
Library name: W23_3
Output from Salmon quant

value: WT

value: Day 23


title: IECs, SETD2-FF-63

description: Library name: SETD2-FF-63


title: 1952-2.HTO.SamplePool.rs116819

description:
Library name: 116819
Fig5.seurat.rds
Fig5.counts.rds


title: 1952-1.TCR.SamplePool.rs116818

description:
Library name: 116818
Fig5.seurat.rds
Fig5.counts.rds


title: WT, Day 23, replicate 2

description:
Library name: W23_2
Output from Salmon quant


title: WT, Day 23, replicate 1

description:
Library name: W23_1
Output from Salmon quant


title: 1952-1.GEX.SamplePool.rs116817

description:
Library name: 116817
Fig5.seurat.rds
Fig5.counts.rds


title: 1952-1.HTO.SamplePool.rs116816

description:
Library name: 116816
Fig5.seurat.rds
Fig5.counts.rds


title: WT, Day 14, replicate 3

description:
Library name: W14_3
Output from Salmon quant

value: Day 14


title: WT, Day 14, replicate 2

description:
Library name: W14_2
Output from Salmon quant


title: WT, Day 14, replicate 1

description:
Library name: W14_1
Output from Salmon quant


title: 1878-9.TCR.32619.rs114635

description:
Library name: 114635
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds


title: E13.5 Cnot1 R623W/R623W developing diaphragm replicate 1

city: Bar Harbor

first: Stephen

last: Murray

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Library name: Cnot1_Hom_E135_1

data_processing:
RNA sequencing reads were batch processed using The Jackson Laboratory standard Nextflow RNAseq pipeline (https://github.com/TheJacksonLaboratory/jds-nf-workflows/wiki/RNA-Pipeline-ReadMe), aligning to the mm10 (GRCm38) mouse genome and gencode gene annotation release M25 (GRCm38.6). In brief, sequenced reads were trimmed with Trim Galore, aligned STAR and counts were quantified with Salmon and STRINGTIE. Differential gene and transcript analysis was performed with DESeq2, using standard parameters, on both gene and isoform counts from STAR.
Software versions: bioconductor-deseq2: 1.28.0; r-base: 4.0.3; picard: 3.0.0; salmon: 1.10.1; star: 2.7.9a; samtools: 1.16.1; stringtie: 2.2.1; cutadapt: '3.4'; trimgalore: 0.6.7; Nextflow: 23.04.0; nf-core/rnaseq: 3.11.1
Assembly: mm10 (GRCm38) mouse genome
Supplementary files format and content: Tab delimited files with raw counts for each sample, one for counts mapping to full genes and one for transcript isoform mapping
Supplementary files format and content: Tab delimited files with TPM normalized counts for each sample, one for counts mapping to full genes and one for transcript isoform mapping

source_name: Embryonic diaphragm

extract_protocol:
Total RNA was isolated from snap frozen diaphragms using the Qiagen miRNeasy micro RNA Isolation Kit (Qiagen). Tissues were homogenized in TRIzol (ThermoFisher) using a Pellet Pestle Motor (Kimbal). After the addition of chloroform, the RNA-containing aqueous layer was removed for RNA isolation according to the manufacturer’s protocol.
Stranded libraries were constructed using the KAPA RNA Hyper Prep Kit with RiboErase (HMR) (Roche Sequencing and Life Science), according to the manufacturer’s protocol.

value: Embryonic diaphragm

tag: age

value: Cnot1 R623W/R623W


title: 1878-9.GEX.32619.rs114634

description:
Library name: 114634
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds


title: E14.5 Cnot1 R623W/+ developing diaphragm replicate 3

description: Library name: Cnot1_Het_E145_3

value: Cnot1 R623W/+


title: WT, Day 7, replicate 3

description:
Library name: W7_3
Output from Salmon quant

value: Day 7


title: 1878-8.TCR.32069.rs114633

description:
Library name: 114633
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds


title: 1878-8.GEX.32069.rs114632

description:
Library name: 114632
Fig1_1of2.seurat.rds
Fig1_2of2.seurat.rds
Fig1_1of2.counts.rds
Fig1_2of2.counts.rds


title: WT, Day 7, replicate 2

description:
Library name: W7_2
Output from Salmon quant


title: WT, Day 7, replicate 1

description:
Library name: W7_1
Output from Salmon quant


title: 1703-4.TCR.26910.rs110493

description:
Library name: 110493
Fig4.seurat.rds
Fig4.counts.rds

source_name: CD8+ T cells

value: CD8+ T cells


title: WT, Day 0, replicate 3

description:
Library name: W0_3
Output from Salmon quant


title: WT, Day 0, replicate 2

description:
Library name: W0_2
Output from Salmon quant


title: 1703-4.GEX.26910.rs110492

description:
Library name: 110492
Fig4.seurat.rds
Fig4.counts.rds


title: 1703-3.TCR.26511.rs110490

description:
Library name: 110490
Fig4.seurat.rds
Fig4.counts.rds


title: RNA-seq using wild‑type NIH3T3 cells, rep3

city: Tokyo

first: Yosuke

last: Isota

address: Faculty of Science Bldg.3, Rm126, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, JAPAN

department: Graduate school of science

country: Japan

institute: The University of Tokyo

description: Library name: control3

data_processing:
RNA-seq data were mapped to the mouse genome (mm10) using Bowtie2 in paired-end mode after quality check.
Uniquely mapped reads were retained, while unmapped reads and reads overlapping genomic blacklist regions (mm10-blacklist.v2) were removed.
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file

growth_protocol: NIH3T3 cells were cultured at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% fetal bovine serum (Sigma) and Penicillin-Streptomycin-Glutamine (Gibco).

extract_protocol:
Total RNA was extracted from NIH3T3 cells using ISOGEN II (FUJIFILM Wako Pure Chemical)  according to the manufacturer’s instructions. Purified RNA was treated with Turbo DNase (Thermo Fisher Scientific) at 37 °C for 30 min and subsequently cleaned up by phenol–chloroform extraction and ethanol precipitation. The resulting RNA was resuspended in nuclease-free water.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA following manufacturer's protocols.

tag: cell line

value: fibroblast

value: wild-type


title: 1703-4.HTO.26910.rs110491

description:
Library name: 110491
Fig4.seurat.rds
Fig4.counts.rds


title: WT, Day 0, replicate 1

description:
Library name: W0_1
Output from Salmon quant


title: RNA-seq using wild‑type NIH3T3 cells, rep2

description: Library name: control2


title: 1703-3.GEX.26511.rs110489

description:
Library name: 110489
Fig4.seurat.rds
Fig4.counts.rds


title: 1703-3.HTO.26511.rs110488

description:
Library name: 110488
Fig4.seurat.rds
Fig4.counts.rds


title: RNA-seq using wild‑type NIH3T3 cells, rep1

description: Library name: control1


title: 1684-4.TCR.23824.rs110181

description:
Library name: 110181
Fig4.seurat.rds
Fig4.counts.rds


title: WT, TNF treated, 6h, replicate 3

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

description: Library name: WT_T6h4

data_processing:
QC - fastQC
Adapter trimming - Trimmomatic
Alignment to ref genome - STAR
Quantification and raw counts matrix obtention - featureCounts
Assembly: mm10 GENCODE ref M27
Supplementary files format and content: Raw counts matrix

growth_protocol: Tumor cell lines were cultured in RPMI 1640 medium (Gibco) supplemented with 10%FBS (Sigma), 100U/ml penicillin, 100ug/ml streptomycin (Gibco), mouse cell lines were supplemented with 5x10-5 mol/L 2-mercaptoethanol (Gibco), and B16-OVA cell line was also supplemented with 400μg/mL of geneticin (Gibco). All tumor cell lines were maintained in a humidified incubator at 5% CO 2 and 37ᵒC for at least 7 days before being inoculated into mice. Mycoplasma contamination tests were routinely performed on all cell lines using the MycoAlert Mycoplasma Detection Kit (Lonza). To generate murine TNFR1 KO cell variants, each cell line was seeded at high cell density, one day prior to transfection with a customized vector from Genescript encoding a gRNA, Cas9, and GFP, using Lipofectamine 2000 (Thermo). gRNA was designed using several platforms (Benchling, Breaking-Cas, CHOP-CHOP, and Cas-Offinder), which predict the probability of on- and off-target gene editing. gRNA with the highest score across multiple platforms was selected. gRNA sequence is provided in supplementary figure 1. The gene-edited cells were sorted out twice using MoFlo Astrios EQ sorter (Beckman Coulter): first by GFP expression, and then by the absence of TNFR1 expression stained with anti-CD120a (Biolegend; 113003) to obtain several monoclonal TNFR1 KO cell lines. To analyse the tumour engraftment capability following TNFR1 silencing, C57BL/6, Rag1 -/- or Batf3 -/- [35] mice were subcutaneously injected on day 0 with 0.5x10 6 of wild-type or TNFR1 KO tumour cell lines suspended in 50μl of saline buffer.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen;74104) and sent for RNA-seq sequencing analysis to Macrogen (South Korea).
Done by Macrogen (South Korea)

treatment_protocol: For transcriptomic analyses, EO771 and HT29 tumor cell lines were collected at 6 and 24 hours after treatment with 1000 U/mL of TNFα.

value: TNF treated, 6h


title: 1684-4.GEX.23824.rs110180

description:
Library name: 110180
Fig4.seurat.rds
Fig4.counts.rds


title: 1684-4.HTO.23824.rs110179

description:
Library name: 110179
Fig4.seurat.rds
Fig4.counts.rds


title: WT, TNF treated, 6h, replicate 1

description: Library name: WT_T6h1


title: WT, TNF treated, 24h, replicate 3

description: Library name: WT_T24h4

value: TNF treated, 24h


title: 1684-3.TCR.23230.rs110178

description:
Library name: 110178
Fig4.seurat.rds
Fig4.counts.rds


title: WT, TNF treated, 6h, replicate 2

description: Library name: WT_T6h2


title: WT, TNF treated, 24h, replicate 2

description: Library name: WT_T24h2


title: 1684-3.GEX.23230.rs110177

description:
Library name: 110177
Fig4.seurat.rds
Fig4.counts.rds


title: 1684-3.HTO.23230.rs110176

description:
Library name: 110176
Fig4.seurat.rds
Fig4.counts.rds


title: WT, TNF treated, 24h, replicate 1

description: Library name: WT_T24h1


title: 1683-3.TCR.25688.rs110166

description:
Library name: 110166
Fig4.seurat.rds
Fig4.counts.rds


title: WT, untreated, 6h, replicate 3

description: Library name: WT_6h4

value: Untreated, 6h


title: 1683-3.GEX.25688.rs110165

description:
Library name: 110165
Fig4.seurat.rds
Fig4.counts.rds


title: WT, untreated, 6h, replicate 2

description: Library name: WT_6h2


title: 1169-10.TCR.26511.rs97125

description:
Library name: 97125
Fig5.seurat.rds
Fig5.counts.rds

source_name: Ilio-sacral LN,Liver,PBMC,PLN

value: Ilio-sacral LN,Liver,PBMC,PLN


title: 1683-3.HTO.25688.rs110164

description:
Library name: 110164
Fig4.seurat.rds
Fig4.counts.rds


title: 1169-10.GEX.26511.rs97124

description:
Library name: 97124
Fig5.seurat.rds
Fig5.counts.rds


title: WT, untreated, 6h, replicate 1

description: Library name: WT_6h1


title: WT, untreated, 24h, replicate 3

description: Library name: WT_24h4

value: Untreated, 24h


title: WT, untreated, 24h, replicate 1

description: Library name: WT_24h1


title: 1169-10.HTO.26511.rs97123

description:
Library name: 97123
Fig5.seurat.rds
Fig5.counts.rds


title: WT, untreated, 24h, replicate 2

description: Library name: WT_24h3


title: 1169-9.TCR.26511.rs97122

description:
Library name: 97122
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,MesLN,Spleen

value: Bone marrow,Colon,MesLN,Spleen


title: TNFR1 KO bulk, TNF treated, 6h, replicate 2

description: Library name: Bulk_T6h3

value: TNFR1 KO bulk


title: 1169-9.GEX.26511.rs97121

description:
Library name: 97121
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO bulk, TNF treated, 6h, replicate 1

description: Library name: Bulk_T6h2


title: 1169-9.HTO.26511.rs97120

description:
Library name: 97120
Fig5.seurat.rds
Fig5.counts.rds


title: 1169-8.TCR.26511.rs97119

description:
Library name: 97119
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,Ilio-sacral LN,PLN

value: Bone marrow,Colon,Ilio-sacral LN,PLN


title: TNFR1 KO bulk, TNF treated, 24h, replicate 3

description: Library name: Bulk_T24h4


title: TNFR1 KO bulk, TNF treated, 24h, replicate 2

description: Library name: Bulk_T24h3


title: 1169-8.GEX.26511.rs97118

description:
Library name: 97118
Fig5.seurat.rds
Fig5.counts.rds


title: 1169-8.HTO.26511.rs97117

description:
Library name: 97117
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO bulk, TNF treated, 6h, replicate 3

description: Library name: BulkKo_T6h4


title: 1169-7.TCR.26511.rs97116

description:
Library name: 97116
Fig5.seurat.rds
Fig5.counts.rds

source_name: Liver,MesLN,PBMC,Spleen

value: Liver,MesLN,PBMC,Spleen


title: TNFR1 KO bulk, TNF treated, 24h, replicate 1

description: Library name: Bulk_T24h1


title: TNFR1 KO bulk, untreated, 6h, replicate 3

description: Library name: BulkKo_6h4


title: 1169-7.GEX.26511.rs97115

description:
Library name: 97115
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO bulk, untreated, 6h, replicate 2

description: Library name: Bulk_6h3


title: 1169-7.HTO.26511.rs97114

description:
Library name: 97114
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO bulk, untreated, 6h, replicate 1

description: Library name: Bulk_6h2


title: 1169-6.TCR.26511.rs97113

description:
Library name: 97113
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO bulk, untreated, 24h, replicate 2

description: Library name: Bulk_24h2


title: TNFR1 KO bulk, untreated, 24h, replicate 3

description: Library name: Bulk_24h4


title: 1169-5.TCR.26511.rs97110

description:
Library name: 97110
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2H8, TNF treated, 6h, replicate 3

description: Library name: 2H8_T6h3

value: TNFR1 KO clone


title: 1169-6.GEX.26511.rs97112

description:
Library name: 97112
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2H8, TNF treated, 6h, replicate 2

description: Library name: 2H8_T6h2


title: 1169-5.GEX.26511.rs97109

description:
Library name: 97109
Fig5.seurat.rds
Fig5.counts.rds


title: 1169-6.HTO.26511.rs97111

description:
Library name: 97111
Fig5.seurat.rds
Fig5.counts.rds


title: 1169-5.HTO.26511.rs97108

description:
Library name: 97108
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2H8, TNF treated, 6h, replicate 1

description: Library name: 2H8_T6h1


title: 1169-4.TCR.26511.rs97107

description:
Library name: 97107
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2H8, TNF treated, 24h, replicate 3

description: Library name: 2H8_T24h4


title: TNFR1 KO clone 2H8, TNF treated, 24h, replicate 2

description: Library name: 2H8_T24h3


title: 1169-4.HTO.26511.rs97105

description:
Library name: 97105
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2H8, TNF treated, 24h, replicate 1

description: Library name: 2H8_T24h1


title: 1169-3.TCR.26511.rs97104

description:
Library name: 97104
Fig5.seurat.rds
Fig5.counts.rds


title: 1169-3.GEX.26511.rs97103

description:
Library name: 97103
Fig5.seurat.rds
Fig5.counts.rds


title: 1169-4.GEX.26511.rs97106

description:
Library name: 97106
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2H8, untreated, 6h, replicate 3

description: Library name: 2H8_6h4


title: TNFR1 KO clone 2H8, untreated, 6h, replicate 2

description: Library name: 2H8_6h3


title: TNFR1 KO bulk, untreated, 24h, replicate 1

description: Library name: Bulk_24h1


title: 1169-3.HTO.26511.rs97102

description:
Library name: 97102
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2H8, untreated, 6h, replicate 1

description: Library name: 2H8_6h1


title: 1169-2.TCR.26511.rs97101

description:
Library name: 97101
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,Liver,PBMC

value: Bone marrow,Colon,Liver,PBMC


title: TNFR1 KO clone 2H8, untreated, 24h, replicate 3

description: Library name: 2H8_24h4


title: TNFR1 KO clone 2H8, untreated, 24h, replicate 2

description: Library name: 2H8_24h3


title: 1169-2.HTO.26511.rs97099

description:
Library name: 97099
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2H8, untreated, 24h, replicate 1

description: Library name: 2H8_24h1


title: 1169-2.GEX.26511.rs97100

description:
Library name: 97100
Fig5.seurat.rds
Fig5.counts.rds


title: 1169-1.TCR.26511.rs97098

description:
Library name: 97098
Fig5.seurat.rds
Fig5.counts.rds

source_name: Ilio-sacral LN,MesLN,PLN,Spleen

value: Ilio-sacral LN,MesLN,PLN,Spleen


title: 1169-1.GEX.26511.rs97097

description:
Library name: 97097
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2B9, TNF treated, 6h, replicate 2

description: Library name: 2B9_T6h3


title: TNFR1 KO clone 2B9, TNF treated, 6h, replicate 3

description: Library name: 2B9_T6h4


title: TNFR1 KO clone 2B9, TNF treated, 6h, replicate 1

description: Library name: 2B9_T6h1


title: 1169-1.HTO.26511.rs97096

description:
Library name: 97096
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-1.GEX.25688.rs105383

description:
Library name: 105383
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2B9, TNF treated, 24h, replicate 3

description: Library name: 2B9_T24h4


title: 1420-10.TCR.25688.rs103989

description:
Library name: 103989
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2B9, TNF treated, 24h, replicate 2

description: Library name: 2B9_T24h3


title: 1420-10.GEX.25688.rs103988

description:
Library name: 103988
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-9.GEX.25688.rs103985

description:
Library name: 103985
Fig5.seurat.rds
Fig5.counts.rds

source_name: Colon,MesLN,Spleen

value: Colon,MesLN,Spleen


title: TNFR1 KO clone 2B9, untreated, 6h, replicate 1

description: Library name: 2B9_6h1


title: 1420-10.HTO.25688.rs103987

description:
Library name: 103987
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2B9, untreated, 6h, replicate 3

description: Library name: 2B9_6h4


title: TNFR1 KO clone 2B9, TNF treated, 24h, replicate 1

description: Library name: 2B9_T24h2


title: TNFR1 KO clone 2B9, untreated, 6h, replicate 2

description: Library name: 2B9_6h2


title: 1420-9.TCR.25688.rs103986

description:
Library name: 103986
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-9.HTO.25688.rs103984

description:
Library name: 103984
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2B9, untreated, 24h, replicate 3

description: Library name: 2B9_24h4


title: Niche, CH06

status: Public on Aug 13 2026

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description:
Library name: HS_11
10x Genomics Single Cell 3’ V4

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were processed using CellRanger version 8.0.1 (10X Genomics). RNA counts were generated by aligning to the GRCh38 (hg38) reference using SC3Pv3 or SC3Pv4 for 10Xv3 or 10Xv4 3’ pair end sequencing respectively. HTO counts were generated using the same method, by aligning to their respective barcodes.
Assembly: GENCODE human reference genome v38
Supplementary files format and content: Gene expression – Raw counts

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Niche fraction - Digested cell suspension were depleted for hematopoietic cells using automated magnetic cell separation system (AUTOMACS). Cells were stained with biotin anti-human CD45 and biotin anti-human glycophorin A (Biolegend).  Depleted fraction was stained for 1 hour at 4 degrees with the following antibodies: CD45-BUV395 (BD), GlyA-FITC (Biolegend), CD38-PECy7 (Biolegend), CD34-APCCy7 (Biolegend), NGFR-AF647 (Biolegend) and CD31-PE (Biolegend) and FVS575V was used for dead cell exclusion. Cells were sorted on a BD Aria Fusion. Two populations were sorted: CD45-GlyA-CD38-  niche fraction and CD45lowCD34+ HSPC fraction. Niche fraction was resuspended in PBS + 0.04% BSA and loaded into the 10x Genomics Chip G or X.  Hematopoietic fraction - Frozen mononuclear cell fractions were thawed using X-VIVO medium (Lonza) supplemented with 50% FBS and 110 mg/mL DNase. The suspension was centrifuged at 1200 rpm for 8 mins, cells were resuspended in RPMI with 10% FBS and counted. 4-5x106 MNC cells were resuspended in staining buffer (2% BSA,0.01% Tween in PBS) in conical bottom polypropylene FACS tubes. Cells were incubated with Fc Blocking reagent at a dilution of 1:10 (FcX, BioLegend) for 10 minutes on ice. After FcX block incubation, 0.1ug (per 1x106 cells) of unique TotalSeq™-B Hashing antibody (Biolegend) was added and incubated for 30 minutes on ice. Cells were washed 5 times with 1 ml Staining buffer (2%BSA/0.01%Tween, PBS), spined at 4˚C for 5 minutes at 350g. After the final wash, cells were resuspended in FACS buffer (PBS 2% FBS) and stained with the following antibodies: Lineage cocktail-FITC, CD45-PECy7, CD34-APCCy7 for 1 hour at 4 degrees. DAPI was used for dead cell exclusion. Cells were filtered and sorted on a BD Aria Fusion. Three hematopoietic populations were sorted: Mature cells (Lineage+), committed progenitors (Lineage-CD45+) and hematopoieitc progenitors (Lineage-CD45lowCD34+).  Samples were pooled evenly for two library preparations: Mature library (Mature cells and committed progenitors) and HSPC library. Pooled samples were delivered to the Princess Margaret Genomics Center (PMGC) for single cell sequencing preparation using the 10X platform.
We used Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and Chromium GEM-X Single Cell 3', Library & Gel Bead Kit v4 and followed the protocol as provided by 10x Genomics. Sorted HSPC fraction was frozen until further use.

value: Bone Marrow

tag: disease state

value: CHIP

tag: Sex

value: Female

tag: compartment

value: BM Niche


title: WT8425_1

city: Ribeirão Preto

first: Matheus

middle: Mertz

last: Ribeiro

state: São Paulo

address: Av. Prof. Dr. Zeferino Vaz - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900

department: Faculty of Pharmaceutical Sciences of Ribeirão Preto

country: Brazil

institute: University of São Paulo

description:
Library name: WT8425_1
Column name in RNAseq_Macrophage.csv : WT8425

data_processing:
Data processing  Raw sequencing data generated from multiple sequencing lanes were concatenated for each biological sample prior to downstream analyses. Sequence quality was assessed using FastQC, and adapter sequences and low-quality bases were removed using fastp. Filtered paired-end reads were aligned to the appropriate reference genome using HISAT2. Fungal reads were aligned against the Aspergillus nidulans FGSC A4 (ASM1142v1) or Aspergillus fumigatus A1163 reference genomes, while host reads were aligned against the *Mus musculu* reference genome (GRCm39). Alignment files were sorted and indexed using SAMtools. Gene-level read counts were generated using featureCounts based on the corresponding genome annotations (GTF/GFF3). Differential gene expression analyses were performed using the DESeq2 package in R. Raw counts were normalized using the median-of-ratios method, and differential expression was assessed using the Wald test with Benjamini–Hochberg correction for multiple testing. Genes with an adjusted *P* value < 0.05 were considered significantly differentially expressed. Genome build:*Mus musculus GRCm39;Aspergillus nidulans FGSC A4 (ASM1142v1); Aspergillus fumigatus A1163.  Supplementary files format and content: Tab-delimited text files containing raw gene counts.
Assembly: GCA_000002655.1 (A. fumigatus Af293) - GCA_000001635.9 (Mus musculus GRCm39) -  GCA_000011425.1 (A. nidulans A4)
Supplementary files format and content: RNAseq_Macrophage.csv
Supplementary files format and content: RNAseq_fumigatus.csv
Supplementary files format and content: RNAseq_nidulans.csv

source_name: murine macrophages

extract_protocol:
Total RNAs of cultures of early dual biofilm interactions of 24 and 48 h were extracted by the TRIzol method, treated with RQ1 RNase-free DNase I (Promega), and purified using the RNAeasy kit (Qiagen) according to the manufacturer’s instructions. The total RNA was quantified using a NanoDrop, and its integrity was analyzed using an Agilent 2100 Bioanalyzer. All RNA had a minimum RNA integrity number value of 8.0. For RNA sequencing, the cDNA libraries were constructed using the TruSeq Total RNA with Ribo Zero (Illumina, San Diego, CA, USA).
mRNA library  preparation (poly A enrichment)

tag: sample group

value: murine macrophages

value: Macrophage WT + A. nidulans 8425

value: Coculture

tag: time


title: WTMO_1

description:
Library name: WTMO_1
Column name in RNAseq_Macrophage.csv : WTMO

value: WTMO

value: Macrophage WT

value: Monoculture


title: 1420-8.TCR.25688.rs103983

description:
Library name: 103983
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 2B9, untreated, 24h, replicate 2

description: Library name: 2B9_24h2

value: Untreated, 24h


title: 1420-8.GEX.25688.rs103982

description:
Library name: 103982
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,Ilio-sacral LN,PLN


title: Mov10 Deletion, Day 23, replicate 2

description:
Library name: D23_2
Output from Salmon quant

value: Whole brain

value: Mov10 Deletion

value: Day 23


title: TNFR1 KO clone 2B9, untreated, 24h, replicate 1

description: Library name: 2B9_24h1

value: TNFR1 KO clone


title: 1420-7.TCR.25688.rs103980

description:
Library name: 103980
Fig5.seurat.rds
Fig5.counts.rds

value: Liver,MesLN,PBMC,Spleen


title: TNFR1 KO clone 1D2, TNF treated, 6h, replicate 3

description: Library name: 1D2_T6h3

value: TNF treated, 6h


title: TNFR1 KO clone 1D2, TNF treated, 6h, replicate 2

description: Library name: 1D2_T6h2


title: 1420-7.GEX.25688.rs103979

description:
Library name: 103979
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-8.HTO.25688.rs103981

description:
Library name: 103981
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-7.HTO.25688.rs103978

description:
Library name: 103978
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-6.TCR.25688.rs103977

description:
Library name: 103977
Fig5.seurat.rds
Fig5.counts.rds

value: Ilio-sacral LN,Liver,PBMC,PLN


title: TNFR1 KO clone 1D2, TNF treated, 24h, replicate 3

description: Library name: 1D2_T24h41

value: TNF treated, 24h


title: TNFR1 KO clone 1D2, TNF treated, 24h, replicate 2

description: Library name: 1D2_T24h3


title: TNFR1 KO clone 1D2, TNF treated, 6h, replicate 1

description: Library name: 1D2_T6h1


title: 1420-6.GEX.25688.rs103976

description:
Library name: 103976
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 1D2, TNF treated, 24h, replicate 1

description: Library name: 1D2_T24h1


title: TNFR1 KO clone 1D2, untreated, 6h, replicate 3

description: Library name: 1D2_6h3

value: Untreated, 6h


title: TNFR1 KO clone 1D2, untreated, 6h, replicate 2

description: Library name: 1D2_6h2


title: 1420-5.GEX.25688.rs103973

description:
Library name: 103973
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,MesLN,Spleen


title: TNFR1 KO clone 1D2, untreated, 6h, replicate 1

description: Library name: 1D2_6h1


title: 1420-6.HTO.25688.rs103975

description:
Library name: 103975
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-4.TCR.25688.rs103971

description:
Library name: 103971
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-5.TCR.25688.rs103974

description:
Library name: 103974
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-4.GEX.25688.rs103970

description:
Library name: 103970
Fig5.seurat.rds
Fig5.counts.rds


title: TNFR1 KO clone 1D2, untreated, 24h, replicate 1

description: Library name: 1D2_24h1


title: KO_FGO 3

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description: Library name: sample6

data_processing:
Raw reads were trimmed to remove low-quality bases and adaptor sequences using Trim Galore v0.6.7. Reads were further mapped to the mouse (mm10) genomes using STAR v2.7.10a.
Uniquely mapped reads were applied for gene expression quantification using FeatureCounts v2.0.2.
The gene transcript abundance was further analyzed using the DESeq2 R package. An adjusted p-value of < 0.05, and fold change (FC) of APEXflox/+;Gdf9-Cre/WT > 2 were considered statistically significant to identify primordial follicle oocyte mRNAs.
Transcripts per million mapped reads (TPM) was calculated to validate gene expression and normalized to gene length and sequencing depth.
Assembly: mm10
Supplementary files format and content: countlist.xlsx includes raw counts for each sample

source_name: full-grown oocyte

extract_protocol:
The oocytes and 2-cells were lysed and then RNA was enriched for sequencing.
RNAs were diluted to 0.2 ng/μL and 2.5 μL samples were performed library constructions. The samples were incubated with oligo(dT) primers (a deoxynucleoside triphosphate mixture) for 3 min at 72 °C, and cDNA pools were obtained by Smart-seq2 reverse transcription reactions. After the first-strand reaction, the cDNAs were pre-amplified with limited cycles (~ 12 cycles). Sequencing libraries were then constructed with 0.5 ng cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (TD503; Vazyme, Nanjing, China) according to the manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform in the 151 bp paired-end mode.

value: full-grown oocyte

value: KO


title: 1420-3.TCR.25688.rs103968

description:
Library name: 103968
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-5.HTO.25688.rs103972

description:
Library name: 103972
Fig5.seurat.rds
Fig5.counts.rds


title: 1420-4.HTO.25688.rs103969

description:
Library name: 103969
Fig5.seurat.rds
Fig5.counts.rds


title: KO_FGO 2

description: Library name: sample5


title: TNFR1 KO clone 1D2, untreated, 24h, replicate 3

description: Library name: 1D2_24h3


title: TNFR1 KO clone 1D2, untreated, 24h, replicate 2

description: Library name: 1D2_24h2


title: Niche, NC01

description:
Library name: HS_7
10x Genomics Single Cell 3’ V4

value: Bone Marrow

value: Non-Carrier

value: Female

value: BM Niche


title: LUHMES pSG5-miR-133b 1

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

data_processing:
Sample primary processing was performed with miRMaster (Fehlmann et al., Nucleic Acids Res, 2021) using standard parameters. Mapping to the genome was performed allowing up to 5 mulit-mapping hits with Bowtie. One mismatch was allowed for the quantification of isomiRs.  As output, miRMaster generated a list with the expression of 80,668 RNAs from 10 RNA classes. The data were normalized to expression in one million reads and further processed with R (R 4.0.4 GUI 1.74 Catalina build (7936)). To limit the effect of low-abundance miRNAs, we considered miRNA isoforms as expressed if at least five in 10 million mapped miRNA reads were found for at least three independent samples.
Supplementary files format and content: Reads per million mapped miRNA normalzed counts for each sample and human miRNA from miRBase v22.

source_name: LUHMES

growth_protocol: The cell lines HEK293T (ACC 635), SH-SY5Y (ACC 209) and HeLa (ACC 57) were purchased from the German collection of microorganisms and cell cultures (DSMZ). The authenticity of the cell lines was confirmed by STR fingerprinting by the supplier. Cell lines were cultivated in DMEM (Life Technologies, Darmstadt, Germany) supplemented with penicillin (100 U/ml), streptomycin (100 µg/ml) and either 10% [v/v] FCS for 293T and HeLa cells or 20% [v/v] FCS for SH-SY5Y cells. Lund human mesencephalic (LUHMES) cells were purchased from the American Type Culture Collection (ATCC; CRL-2927). The cells were cultured as previously described by Scholz et al. We performed one passage for all cell lines after purchasing them and cryo-conserved them. All cell lines are from female. All cell lines were subcultured two times a week for no more than three months after the start of the culture.

extract_protocol:
0, 4, 8, 24, 48 h after transfections for miR-7 and 48 h for miRNAs miR-34a, -129, -133b, 873, cells were lysed by QIAzol Lysis Reagent (Qiagen, Hilden, Germany), and total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Library preparation for small RNA sequencing was performed using the MGIEasy Small RNA Library Prep Kit according to the manufacturer’s recommendations. In detail, after 3’ and 5’ adapter ligation, RNAs were reverse transcribed and PCR amplified (21 cycles). PCR products were purified using 6% TBE gels, excising only the 110 bp band corresponding to the PCR product of miRNAs. Subsequently, twelve samples were pooled equimolar into one library, and the library was further circularized and purified. Circularized libraries were sent to BGI Hong Kong for sequencing using the standard MPS protocol as described previously (Li et al., Nucleic Acids Res, 2021).

treatment_protocol: Sequence inserts representing miRNA precursor sequences with additional nucleotides up- and downstream of the precursor sequence for mir-129 and mir-873 were either synthesized by Eurofins Genomics (Ebersberg, Germany) or PCR amplified using sequence-specific primers with human genomic DNA as a template and subsequently cloned into the expression plasmid pSG5 (Agilent Technologies, Santa Clara, California) using EcoR I and BamH I restriction sites. The expression plasmid pSG5-miR-129 harbors nucleotides 128207756-128208053[+] of human chromosome 7 (GRCh38/hg38) and pSG5-miR-873 nucleotides 28888786-28889058[-] of human chromosome 9 (GRCh38/hg38). Cloned sequences of miRNA expression plasmids were verified by Sanger sequencing. Cloning of the pSG5-miR-133b, pSG5-miR-34a and pSG5-miR-7 expression vectors was described previously (Alles et al., Nucleic Acids Res, 2019; Hart et al., Oncotarget, 2016; Kern et al., Nucleic Acids Res, 2021).  For ectopic expression of the respective miRNAs for NGS of miR-transfected HEK293T and HeLa cells, 4x105 cells were seeded out in 6-well plates. Twenty-four hours later, the cells were transfected with the respective DNA amounts (0.5 µg, 1 µg, 2 µg for miR-7, 2 µg for mir-34a, -129, -133b, 873) using PolyFect transfection reagent (Qiagen, Hilden, Germany). For the transfection of the different amounts of mir-7 (0.5 µg, 1 µg) in HEK293T cells, the pSG5-miR-7 expression plasmids were supplemented with the respective amount of pSG5 empty vector to achieve equal amounts of transfected DNA in all samples. For ectopic expression of the respective miRNAs of miR-transfected SH-SY5Y (4,5x105 cells/well) and 4x105 LUHMES (4x105 cells/well) cells for NGS, cells were seeded out in 6-well plates. Twenty-four hours later, the cells were transfected with 2 µg of the respective expression plasmids for mir-7, mir-34a, mir-129, mir-133b, mir-873 or the pSG5-empty vector using Lipofectamine™ 2000 transfection reagent (Invitrogen, Karlsbad, USA). All experiments were conducted 3 times.

value: LUHMES

tag: plasmid

tag: concentration

value: 48 hr


title: Bulk RNA-seq of brain endothelial cells CTRL-2

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description:
Library name: CTRL_2
RNA-seq

data_processing:
Adapter trimming was performed using fastp (v0.20.1) and reads were aligned to the GRCm39 reference genome using hisat2 (v2.1.0). To count reads overlapping genes, featureCounts v2.0.6 was used, and the output was loaded into R (v4.2.2) for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: counts table

source_name: Brain

growth_protocol: 6-week-old C57BL/6 mice mice were anesthetized with a ketamine/xylazine injection and perfused with 20ml of ice-cold PBS. Cortices were homogenized with GentleMACS tissue dissociator (Mylteni Biotech) in prewarmed DMEM supplemented with 2% Bovine Calf Serum (BCS, HyClone), 25µg/ml Liberase DL, 100µg/ml Dispase, 0.5mg/ml Papain, 10µg/ml DNase-I (all enzymes from Sigma) for 30 min at 37°C. After homogenization the cell suspension was filtered through a 70 μm strainer and myelin depletion was performed in 30% isotonic percoll (800g for 20 min at 4°C). Brain cell pellets were stained with anti-CD45-AlexaFluor 647 (1:200), anti-CD31-PE (1:100), and anti-Ly6C-APCCy7 (1:200) for 30 minutes on ice (all antibodies from Biolegend). DAPI was used for live/dead cells discrimination. The DAPI−CD45−CD31+Ly6C+ population was sorted on FACS Aria-III (BD Bioscience) using a 100 µm nozzle. Approximately 600,000 brain endothelial cells (BEC) per sample were sorted (two brains were pooled for each sample). BECs were collected into Endothelial Cell Medium (Cell Biologics, M1168), plated onto a Matrigel-coated 24-well plate and expanded for 12 days in Endothelial Cell Medium at 37°C with 5% CO2. Matrigel was removed using Cell Recovery Solution (Corning) prior to RNA extraction.

extract_protocol:
Cells were lysed in 450µl of lysis buffer for RNA extraction. The lysate was mixed by pipetting and briefly shaken for 1 minute at room temperature. Lysates were collected, and RNA was purified using the RNeasy Micro Kit (Qiagen 74004), following the manufacturer’s protocol. Purified RNA was stored at -80°C until analysis.
Library preparation was performed with 5-10ng of total RNA per sample. ds-cDNA was made using the low-input SMARTseq mRNA kit (Takarabio) according to manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Libraries were pooled and sequenced on an Illumina NovaSeqX Plus (2x150 sequencing recipe), targeting 50M reads per sample. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

treatment_protocol: On the day of the experiment, cells were incubated in serum-free medium for 2 hours prior to stimulation with recombinant mouse GAS6 (250 ng/mL; R&D Systems) and recombinant mouse IGF-I (200 ng/mL; PeproTech), or PBS as a control. After 6 hours stimulation, the medium was removed, and wells were washed with PBS.

value: Brain

value: Endothelial cells

value: Wild-type

value: PBS


title: 293T 48h pSG5-miR-7 2µg 1


title: Niche, NC04

description:
Library name: HS_9
10x Genomics Single Cell 3’ V4

value: Male


title: 1420-2.TCR.25688.rs103965

description:
Library name: 103965
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,Liver,PBMC


title: KO_FGO 1

description: Library name: sample4


title: IgG control CUT&RUN in microglia

description: Library name: MG_IgG

library_source: genomic

data_processing:
Adapter trimming was performed using fastp (v0.20.1), reads were aligned to the mm10 reference genome using hisat2 (v2.1.0), and duplicates were removed using “Picard markDuplicates” (v2.18.29) (https://github.com/broadinstitute/picard).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

molecule: genomic DNA

source_name: brain

extract_protocol:
n=16 brains from P0 Bl6 pups were mechanically dissociated and approximately 100,000 CD206+MHCII− BAMs and microglia were sorted separately and resuspended in PBS at 1,000 cells/µl.
Cell were bound to Concanavalin A-coated magnetic beads and permeabilized with Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and one Roche Complete protein inhibitor tablet per 50 mL) containing 0.05% digitonin (Dig Wash). The cells were incubated with anti-cMAF antibody (Abcam, ab77071 at 1:25 dilution) or IgG negative control antibody (Antibodies-online ABIN101961) or H3K27me3 positive control antibody (Cell Signaling 9733S) overnight at 4°C. The slurry was then washed twice with Dig Wash buffer and incubated with Protein A/G-MNase (Epicypher, 15-1016) for 1 hour at 4°C, followed by two additional washes with Dig Wash. Tubes were placed on ice and incubated with Dig Wash containing 2 mM CaCl₂ to initiate MNase digestion of bound fragments. After 30 minutes incubation, 4X STOP buffer (80 mM EGTA, 0.05% Digitonin, 100 μg/mL RNase A) was added to stop the reaction, and fragments were released by incubation for 30 minutes at 37°C. The supernatant containing cleaved DNA fragments was transferred to a new tube and used directly as input for barcoded Illumina libraries, as previously described109. Libraries were pooled and sequenced on an Illumina NovaSeqX Plus targeting 150M reads.

value: brain

value: primary cells

value: microglia

value: wild-type

tag: antibody

value: IgG


title: WT_FGO 3

description: Library name: sample3

value: full-grown oocyte

value: WT


title: 1420-3.GEX.25688.rs103967

description:
Library name: 103967
Fig5.seurat.rds
Fig5.counts.rds

value: Liver,MesLN,PBMC,Spleen


title: Niche, NC06

description:
Library name: HS_4
10x Genomics Single Cell 3’ V3

value: Bone Marrow

value: Non-Carrier

value: BM Niche


title: KO_L2C_3

description: Library name: sample12

source_name: embryos

value: embryos


title: WT_FGO 1

description: Library name: sample1


title: KO_L2C_2

description: Library name: sample11


title: WT_L2C_3

description: Library name: sample9


title: 1420-1.HTO.25688.rs103960

description:
Library name: 103960
Fig5.seurat.rds
Fig5.counts.rds

value: Ilio-sacral LN,MesLN,PLN,Spleen


title: 1420-1.TCR.25688.rs103962

description:
Library name: 103962
Fig5.seurat.rds
Fig5.counts.rds


title: WT_L2C_2

description: Library name: sample8


title: 1371-2.GEX.23824.rs103682

description:
Library name: 103682
Fig5.seurat.rds
Fig5.counts.rds


title: 1371-1.GEX.23824.rs103676

description:
Library name: 103676
Fig5.seurat.rds
Fig5.counts.rds


title: 1371-5.GEX.23824.rs103559

description:
Library name: 103559
Fig5.seurat.rds
Fig5.counts.rds

value: Bone marrow,Colon,MesLN,Spleen


title: WT_L2C_1

description: Library name: sample7


title: 1371-10.GEX.23824.rs103703

description:
Library name: 103703
Fig5.seurat.rds
Fig5.counts.rds

value: Ilio-sacral LN,Liver,PBMC,PLN


title: WT_PN3_3

description: Library name: sample3


title: 1371-7.GEX.23824.rs103541

description:
Library name: 103541
Fig5.seurat.rds
Fig5.counts.rds


title: KO_PN3_2

description: Library name: sample5


title: WT_PN3_1

description: Library name: sample1


title: 1408-8.HTO.25688.rs103431

description:
Library name: 103431
Fig5.seurat.rds
Fig5.counts.rds


title: 1408-4.TCR.25688.rs103421

description:
Library name: 103421
Fig5.seurat.rds
Fig5.counts.rds


title: LTA9_siUBA1

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
Library name: LTA9_siUBA1
UBA1 siRNAs replicate 4

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm39/mm39 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include TPM values for all 8 samples

source_name: skeletal muscles

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase.
RNA sequencing libraries for each sample were prepared with 1 ug total RNA by using the TruSeq RNA Sample Prep v2 Kit (Illumina) per the manufacturer’s instructions, and sequencing was completed on the Illumina NovaSeq 6000.

value: skeletal muscles

value: electroporated with siRNAs targeting UBA4


title: 1408-4.GEX.25688.rs103420

description:
Library name: 103420
Fig5.seurat.rds
Fig5.counts.rds


title: LTA7_siUBA1

description:
Library name: LTA7_siUBA1
UBA1 siRNAs replicate 3

value: electroporated with siRNAs targeting UBA3


title: 1371-10.TCR.23824.rs102675

description:
Library name: 102675
Fig5.seurat.rds
Fig5.counts.rds


title: LTA1_siUBA1

description:
Library name: LTA1_siUBA1
UBA1 siRNAs replicate 1

value: electroporated with siRNAs targeting UBA1


title: 1371-10.HTO.23824.rs102673

description:
Library name: 102673
Fig5.seurat.rds
Fig5.counts.rds


title: RTA9_siNT

description:
Library name: RTA9_siNT
control siRNAs replicate 4

value: electroporated with non-targeting (NT) control siRNAs


title: 1371-9.GEX.23824.rs102671

description:
Library name: 102671
Fig5.seurat.rds
Fig5.counts.rds

value: Colon,MesLN,Spleen


title: RTA6_siNT

description:
Library name: RTA6_siNT
control siRNAs replicate 2


title: 1371-9.HTO.23824.rs102670

description:
Library name: 102670
Fig5.seurat.rds
Fig5.counts.rds


title: RTA1_siNT

description:
Library name: RTA1_siNT
control siRNAs replicate 1


title: Tdp2 cKO, 6mo, Rep3

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: cKO3

data_processing:
Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed to remove adapter sequences using Trimmomatic, and aligned to the mm10 (GRCm38.p6) reference genome using TopHat.
Aligned reads were processed by HTSeq-Count to obtain raw read counts, and deSeq2 (p < 0.05, log fold-change > 0.5 or < -0.5) was used to identify differentially regulated transcripts.
BamCoverage was used to convert aligned read files into BigWig signal tracks for visualization.
Assembly: mm10
Supplementary files format and content: tab delimited text file (Raw_Counts) includes raw counts for each sample
Supplementary files format and content: tab delimited text file (TPMs) includes calculated TPM values for each sample
Supplementary files format and content: bigwig files include merged, TPM-normalized RNA-seq signals for each genotype

source_name: Cortex

growth_protocol: Wild-type (Tdp2fl/fl, CAMKII:Cre negative) and Tdp2 conditional knockout (Tdp2fl/fl, CAMKII:Cre positive) mice were maintained in standard housing conditions until 6 months of age.

extract_protocol:
Fresh cortical tissue was dissected from 6-month old WT and Tdp2cKO mice, flash frozen in liquid nitrogen, and stored at -80°C. For RNA purification, samples were dissociated and lysed in 500µL Trizol using a manual homogenizer. RNA was extracted using a standard Trizol procedure, treated with DNase (NEB) for 1 hour at 37℃, and purified using an RNA clean and concentrator kit (Zymo).
The concentration and quality of purified RNA samples were assessed using an Agilent Tapestation 4200 both before and after library construction. Samples with a RIN score of 8 or higher were prepared for sequencing using a paired-end library preparation kit (Illumina) according to the manufacturer’s instructions.

value: Cortex

tag: strain

value: Tdp2 cKO

value: 6 months


title: Tdp2 cKO, 6mo, Rep2

description: Library name: cKO2


title: 1371-8.HTO.23824.rs102667

description:
Library name: 102667
Fig5.seurat.rds
Fig5.counts.rds

source_name: Ilio-sacral LN,PLN

value: Ilio-sacral LN,PLN


title: 1371-7.HTO.23824.rs102664

description:
Library name: 102664
Fig5.seurat.rds
Fig5.counts.rds

value: Liver,MesLN,PBMC,Spleen


title: 1371-6.TCR.23824.rs102663

description:
Library name: 102663
Fig5.seurat.rds
Fig5.counts.rds

source_name: Ilio-sacral LN,Liver,PBMC,PLN


title: WT, 6mo, Rep1

description: Library name: WT1

value: WT


title: 1371-6.GEX.23824.rs102662

description:
Library name: 102662
Fig5.seurat.rds
Fig5.counts.rds


title: Bone marrow cells and bone cells, Mdm2 conditional knockout mice

city: Wuhan

first: Xin

last: Liu

address: Luojia Hill, Wuchang District

institute: Wuhan University

description:
Library name: Sample 2
10X Genomisc

data_processing:
Raw sequencing data were filtered and processed with Cellrange-7.0.0 (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) which includes: demultiplexing by cell barcodes and UMIs, spliced read alignment to the reference genome, and UMI-based gene expression quantification for each gene and cell. Potential doublets were identified and removed using the scDblFinder package (v1.12.0) for each sample.
Quality control was performed to filter low quality cells following the rules below: Cells with fewer than 200 detected genes were excluded, cells with extreme gene counts were filtered by removing those in the top and bottom 2% quantiles, cells with total UMI counts (nUMI) in the top or bottom 2% were discarded, cells with mitochondrial gene expression exceeding 20% of total reads were eliminated, and low-complexity cells by retaining only those with a log10(Genes per UMI) > 0.8 (novelty score) were excluded to ensure high-quality transcriptional profiles.
Raw count matrices were processed using Seurat (v4.3.0) in R (v4.2.3). For each sample, gene expression was normalized and variance stabilized via SCTransform, selecting 3,000 highly variable genes (HVGs) while excluding housekeeping genes, TCR/BCR, and immunoglobulin genes (IGV). Multiple samples were merged and batch-corrected using IntegrateData. Integrated data were centered and subjected to principal component analysis (PCA, 50 dimensions).
Clustering was performed using FindNeighbors and FindClusters. Nonlinear dimensionality reduction was conducted via Uniform Manifold Approximation and Projection (UMAP) for visualization. Automated annotation was performed using SingleR, PanglaoDB, and CellMarker. Manual refinement was applied based on canonical marker genes. FindAllMarkers function was applied in Seurat to detect DEGs among different clusters of the datasets. Pathway enrichment analysis was conducted by R package clusterProfiler (version 4.2.3).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Bones from Mdm2cKO mice

growth_protocol: Dmp1-Cre mediated conditional Mdm2 knockout in osteoocytes (Mdm2cKO). Mdm2cKO mice and the control littermates were sacrificed at 2-month old.

extract_protocol:
Bone marrow cells isolated through flushing, while cells from bone pieces were digested with 2.4 mg/mL collagenase I (Biosharp) and 5 mM EDTA alternately as previously described80,86. Specifically, periosteum cells were digested by collagenase I for two consecutive 15 minutes and cells were discarded. OLCs were digested according to the following steps: Collagenase I for two consecutive 15 minutes, EDTA for 20 minutes, Collagenase I for 20 minutes, EDTA for 20 minutes and finally Collagenase I for 20 minutes. All the digestion processes were performed on the shaker at 90 rpm, 37℃. Cells from five 2-month-old mice (3 males, 2 females) were pooled for each experimental group. Hematopoietic cell depletion was achieved using the Lineage Cell Depletion Kit (Miltenyi Biotec) according to the manufacturer`s instructions, followed by fluorescence-activated cell sorting to enrich CD45-; TER119-; CD71- cells by flow cytometry.
A single cell library was generated with Chromium Next GEM Single Cell 3ʹ Kit v3.1(10x Genomics) and sequenced on a Illumina NovaSeq 6000 system, targeting >30000 reads per cell for robust gene coverage.

value: Bones from Mdm2cKO mice

value: Bone marrow cells and bone cells

value: Mdm2 conditional knoockout in osteocytes


title: 1371-6.HTO.23824.rs102661

description:
Library name: 102661
Fig5.seurat.rds
Fig5.counts.rds


title: Secondary disease 2

city: Omaha

first: Kate

last: Hyde

state: NE

address: 985802 Nebraska Medical Center

institute: University of Nebraska Medical Center

description: Library name: SPrelapse2

data_processing:
The original fastq format reads were trimmed by Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 20).
The trimmed fastq files were processed by FastQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data; available online at:http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and MultiQC for quality control (QC).
The QC passed trimmed fastq files were mapped to GRCm38 reference genome using STAR aligner and RSEM to quantifiy the mapped reads
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Supplementary files format and content: Tab-delimited text file with raw gene counts for all genes and all samples

source_name: Spleen

extract_protocol:
For RNA extractions, after harvesting samples were homognised into single cells to break down the nucleoprotein complex using TRIZOL. They were treated briefly with chloroform and RNA percipitation was done to separate the aqueous phase using isopropanol. The RNA was washed couple of times with 75% ethanol. Once RNA pellet was seen, supernatant removed and pellet was air dried. The pellets were resuspended in RNAse free water. This was then store in -80C with 500ul Trizol reagent.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Spleen

value: Leukemia cells

tag: transduction

value: CM cells transduced with shRNA

value: Doxycycline (Dox)


title: 1371-5.HTO.23824.rs102658

description:
Library name: 102658
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,MesLN,Spleen

tag: tissue

value: Bone marrow,Colon,MesLN,Spleen


title: Normal

city: Suzhou

first: Haiying

last: Li

state: Jiangsu

address: 188 Shizi Street

department: Department of Neurosurgery

institute: The First Affiliated Hospital of Soo-chow University

description:
Library name: Sample 1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v 5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: ipsilateral regional normal brain tissue,n=3

growth_protocol: Mice were subjected to subarachnoid hemorrhage (SAH) through the endovascular puncture method. After 12 hours of modeling, the mice were euthanized.

extract_protocol:
The entire nuclear suspension preparation process is conducted on ice. The frozen tissue sample is minced in 1 mL of Nuclei Suspension Buffer (NST), which consists of 0.1% NP40, 10 mM Tris-HCl, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, and 40 U/mL RNase inhibitor. The lysis time is 7 minutes. After confirming complete nuclear lysis through trypan blue staining and microscopic examination, 1 mL of ST Wash buffer is added. The ST Wash buffer contains 10 mM Tris-HCl, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 0.01% BSA (NEB B9000S), and 40 U/mL RNase inhibitor. The mixture is then filtered through a 40 µm cell strainer (BD). The filtrate is transferred to a 15 mL centrifuge tube, and the cell strainer is rinsed with an appropriate amount of ST Wash buffer, combining the rinse with the nuclear filtrate. The sample is centrifuged at 500g for 5 minutes in a horizontal rotor at 4°C. The nuclei are resuspended in 5 mL of PBS + 1% BSA, washed by centrifugation, and finally resuspended in 100 µL of PBS + 1% BSA. After trypan blue staining, the nuclei are counted under a microscope and diluted with PBS + 1% BSA to a concentration of 700-1200 nuclei/µL.
The single-cell sequencing and cDNA library amplification were performed following the instructions provided in the 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). For DNA library construction, the Chromium™ Single Cell 3'/5' Library Construction Kit (1000020) was used. The constructed libraries were then sequenced on the Illumina Nova 6000 platform using the PE150 sequencing mode.

treatment_protocol: The entire brain tissue extraction process was conducted on ice to ensure tissue preservation. After carefully removing the brain from the euthanized mice, the ipsilateral hemisphere (the side affected by SAH) was separated. Subsequently, the brain tissue was dissected from the medial prefrontal cortex (mPFC, starting at 2.34 mm anterior to bregma) to the centrolateral nucleus (CL, ending at 2.18 mm posterior to bregma). Finally, the brain tissues from the same region of three SAH mice and three normal mice were separately pooled, placed into cell freezing medium, and stored at -80°C.

value: 6-8 weeks old

value: male

tag: group

value: Normal


title: 1420-3.HTO.25688.rs103966

description:
Library name: 103966
Fig5.seurat.rds
Fig5.counts.rds

source_name: Liver,MesLN,PBMC,Spleen


title: 1420-2.GEX.25688.rs103964

description:
Library name: 103964
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,Liver,PBMC

value: Bone marrow,Colon,Liver,PBMC


title: WT_FGO 2

description: Library name: sample2

value: full-grown oocyte

tag: genotype


title: 1420-2.HTO.25688.rs103963

description:
Library name: 103963
Fig5.seurat.rds
Fig5.counts.rds


title: KO_L2C_1

description: Library name: sample10

value: embryos


title: 1371-4.TCR.23824.rs102657

description:
Library name: 102657
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow,Colon,Ilio-sacral LN,PLN

value: Bone marrow,Colon,Ilio-sacral LN,PLN


title: KO_PN3_1

description: Library name: sample4


title: 1371-3.GEX.23824.rs103672

description:
Library name: 103672
Fig5.seurat.rds
Fig5.counts.rds

value: Liver,MesLN,PBMC,Spleen


title: Ad_OSK_AD3

city: Changsha

first: Meidan

last: Wan

address: Xiangya street

institute: Central South University

description: Library name: Sample9

data_processing:
Raw reads were first processed with SOAPnuke (version 2.0.5) to remove the residual adaptor sequences and the reads with low quality scores. Then the clean reads were mapped to the reference genome and the duplicated reads were removed using Bismark (version 0.20.1). The depth and coverage on chromosomes were calculated with samtools (version 1.4) and bedtools (version 2.26.0). The methylation detection along the whole genome were conducted by Bismark which calculates the proportion of methylated reads at every genome site. The differentially methylated regions (DMRs) between different groups were detected with metilene (version 0.2-7). The pathway enrichment analysis of DMR annotated genes were conducted with KOBAS (version 2.1.1).
Assembly: GRCm39
Supplementary files format and content: Methylation level of each Samples.

growth_protocol: All mice were in groups of 4-5 animals per cage, maintaining a temperature range of 23° to 25°C with 40-60% humidity. All mice were exposed to a 12-hour light/dark cycle and allowed free access to water and standard laboratory pellets.

extract_protocol:
Total DNAs were extracted from samples using the Blood/cell/tissue genomic DNA extraction kit, and more than 2μg DNA was extracted. An aliquot of extracted DNA was electrophoresed on a 0.8% agarose gel to visualize DNA quality and size, and the bands were clear, suggesting no degradation or slight degradation.
2~3μg extracted DNA was digested by MSPI for 30min.The conversion of digested DNA was carried out using the EZ DNA Methylation-Gold™ Kit. Sequencing libraries were prepared using the Accel-NGS® Methyl-Seq DNA Library kit following the manufacturer’s instruction. PCR products corresponding to 300-500 bp were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
Accel-NGS® Methyl-Seq DNA Library.

treatment_protocol: APP/PS1 mice and WT mice were intracerebrally injected into the bilateral hippocampus with adeno-associated virus to induce the expression of Oct4, Sox2, and Klf4 (AAV-OSK) in brain tissue.

value: brain

tag: treatment

value: OSK-treatment


title: 1371-4.HTO.23824.rs102655

description:
Library name: 102655
Fig5.seurat.rds
Fig5.counts.rds

data_processing:
CellRanger count
DropletUtils emptyDrops
Seurat Normalize/Scale/PCA
Assembly: GCA_003339765.3
Supplementary files format and content: Sparse count matrix (RDS file)
Supplementary files format and content: Seurat Object (RDS file)

extract_protocol: 10x Genomics 5' VDJ scRNA-seq


title: 1371-4.GEX.23824.rs102656

description:
Library name: 102656
Fig5.seurat.rds
Fig5.counts.rds


title: 1408-8.TCR.25688.rs103433

description:
Library name: 103433
Fig5.seurat.rds
Fig5.counts.rds


title: WT_PN3_2

description: Library name: sample2


title: 1408-8.GEX.25688.rs103432

description:
Library name: 103432
Fig5.seurat.rds
Fig5.counts.rds


title: Ad_OSK_AD1

description: Library name: Sample7


title: 1371-3.TCR.23824.rs102654

description:
Library name: 102654
Fig5.seurat.rds
Fig5.counts.rds


title: 1408-4.HTO.25688.rs103419

description:
Library name: 103419
Fig5.seurat.rds
Fig5.counts.rds


title: LTA6_siUBA1

description:
Library name: LTA6_siUBA1
UBA1 siRNAs replicate 2

value: skeletal muscles

value: electroporated with siRNAs targeting UBA2


title: Ad_Mock_AD3

description: Library name: Sample6

value: mock


title: 1371-3.HTO.23824.rs102652

description:
Library name: 102652
Fig5.seurat.rds
Fig5.counts.rds


title: 1371-2.TCR.23824.rs102651

description:
Library name: 102651
Fig5.seurat.rds
Fig5.counts.rds


title: Ad_Mock_AD2

description: Library name: Sample5


title: 1371-2.HTO.23824.rs102649

description:
Library name: 102649
Fig5.seurat.rds
Fig5.counts.rds


title: Ad_Mock_AD1

description: Library name: Sample4


title: Ad_Mock_WT3

description: Library name: Sample3

value: WT


title: 1371-9.TCR.23824.rs102672

description:
Library name: 102672
Fig5.seurat.rds
Fig5.counts.rds

source_name: Colon,MesLN,Spleen

value: Colon,MesLN,Spleen


title: Ad_Mock_WT2

description: Library name: Sample2


title: 1371-1.HTO.23824.rs102646

description:
Library name: 102646
Fig5.seurat.rds
Fig5.counts.rds

source_name: Ilio-sacral LN,MesLN,PLN,Spleen

value: Ilio-sacral LN,MesLN,PLN,Spleen


title: Ad_Mock_WT1

description: Library name: Sample1


title: 1352-5.GEX.26910.rs102283

description:
Library name: 102283
Fig5.seurat.rds
Fig5.counts.rds

value: Spleen


title: MCT1 cKO caudal (Ca7/8) intervertebral discs from 4 mice

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut Street

institute: Thomas Jefferson University

description:
Library name: Sample 2
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: spinal motion segment

extract_protocol:
Formalin, fixed paraffin-embedded mouse disc blocks were cut to 5μm paraffin sections using a microtome.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's protocol.

value: spinal motion segment

value: cKO


title: 1352-4.TCR.26910.rs102282

city: Beaverton

first: Benjamin

last: Bimber

address: 505 NW 185th Ave

description:
Library name: 102282
Fig5.seurat.rds
Fig5.counts.rds

source_name: PBMC

value: PBMC


title: AMs control-2

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

description: Library name: Control-2

data_processing:
The raw reads were filtered using the Trimmomatic software to remove adapter and low quality reads. Quality control was processed by FastQC. The resulting clean reads were aligned to the mouse reference genome (mm10) using Burrows-Wheeler Aligner (BWA) program. The Binary Alignment/Map (BAM) file generated by the unique mapped reads was used as an input file. MACS2 (model-based analysis of ChIPseq) software was applied to call ATAC-seq peak regions with cutoff q-value < 0.05. Peaks were annotated by the function of annotatePeak of ChIPseeker. The target genes for peaks are filtered based on the column "distanceToTSS" (the distance from the peak center to the gene TSS) in the peak annotation analysis results (< 100,000 bp). After perfoming the PCA on the signals of merged peaks from all samples, plotPCA will sort the principal components according to the amount of variability of the data. To identify differential peaks between different samples, the ATAC-seq peaks of each sample were merged using the bedtools software. Then the counts of the reads over the bed was determined for each sample using bedtools multicov, and differential accessible peaks were identified using DESeq2, with the thresholds of | log2FC| > 1 and p < 0.05. Example peak views for key geneswere generated using the Integrative Genomics Viewer (IGV) to visualize changes in chromatin accessibility.
Assembly: mm10
Supplementary files format and content: BigWig,narrowPeak

source_name: BALF

growth_protocol: None.

extract_protocol:
cells were lysed in cold lysis buffer to extract nuclei (Buenrostro et al., 2015).A total of 40,000 nuclei were treated with transposase (Illumina Nextera) for 30 min at 37°C for transposition reactions.
Transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix and indexed primers. The transposed DNA fragments were purified with a MinElute PCR Purification Kit (Qiagen) and used to generate the library via PCR amplification with barcoded primers using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). The subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and were sequenced on the Illumina Novaseq 6000 platform with a paired-end read of 150bp.

treatment_protocol: CD45.2+ CD11c+ AMs (3 biological replicates) and CD45.2+ CD13+ AMs (2 biological replicates) were sorted from BALF of IWC-immunized and control CD45.2+ cells were isolated from control CD45.2+ mice using fluorescence-activated cell sorting (FACS). Cells were washed with cold PBS and counted for viability >85% using trypan blue. ATAC-Seq of these cells was done by Shanghai Jiayin Biotechnology Co., Ltd.

value: BALF

value: Alveolar macrophages

tag: cell type

value: macrophages

value: Control AMs


title: MCT1 CTR caudal (Ca7/8) intervertebral discs from 4 mice

description:
Library name: Sample 1
FFPE Spatial transcriptome sequencing

value: CTR


title: 1352-4.GEX.26910.rs102281

description:
Library name: 102281
Fig5.seurat.rds
Fig5.counts.rds


title: AMs control-3

description: Library name: Control-3


title: 1352-3.TCR.26910.rs102280

description:
Library name: 102280
Fig5.seurat.rds
Fig5.counts.rds

source_name: Med Mes

value: Med Mes


title: AMs control-1

description: Library name: Control-1


title: 1352-3.GEX.26910.rs102279

description:
Library name: 102279
Fig5.seurat.rds
Fig5.counts.rds


title: 1352-2.TCR.26910.rs102278

description:
Library name: 102278
Fig5.seurat.rds
Fig5.counts.rds

source_name: Liver

value: Liver


title: AMs CD11C+ IWC-3

description: Library name: CD11C-3

value: IWC immunized CD11C+AMs


title: AMs CD11C+ IWC-2

description: Library name: CD11C-2


title: 1352-2.GEX.26910.rs102277

description:
Library name: 102277
Fig5.seurat.rds
Fig5.counts.rds


title: AMs CD11C+ IWC-1

description: Library name: CD11C-1


title: 1352-1.TCR.26910.rs102276

description:
Library name: 102276
Fig5.seurat.rds
Fig5.counts.rds

source_name: Bone marrow

value: Bone marrow


title: AMs CD13+ IWC-2

description: Library name: CD13+-2

value: IWC immunized CD13+ AMs


title: 1056-6.GEX.23244.rs98244

description:
Library name: 98244
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1352-1.GEX.26910.rs102275

description:
Library name: 102275
Fig5.seurat.rds
Fig5.counts.rds


title: DM-4T1-3

city: Shanghai

first: Rui

last: Zeng

address: Dong An Road

institute: Fudan University

description: Library name: Replicate 3

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

source_name: Tumor

extract_protocol:
The dura mater with tumors was dissected from the cranium, then was minced into small pieces and digested with 1 mL of 1 mg/mL Collagenase VIII (#C2139, Sigma) and 0.1 mg/mL of DNase I (#DN25, Sigma) in 5%-FBS DMEM in a water bath at 37°C for 20 minutes. The enzymes were neutralized with 5 mL 5%-FBS DMEM, and samples were filtered through a 40 μm cell strainer, followed by centrifugation at 400×g for 5 minutes at 4°C.
Library was performed according to the manufacture's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix andloaded 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 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: Tumor


title: Ad_OSK_AD2

description: Library name: Sample8

source_name: brain

value: brain

value: OSK-treatment


title: KO_PN3_3

description: Library name: sample6

source_name: embryos

value: embryos


title: 1056-15.GEX.23244.rs98243

description:
Library name: 98243
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: DM-4T1-2

description: Library name: Replicate 2


title: 1056-3.HTO.23244.rs94812

description:
Library name: 94812
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-8.HTO.23244.rs94792

description:
Library name: 94792
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HMD_H3K27me3

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

data_processing:
The raw sequencing data were examined using the illumina analysis pipeline.
Using Bowtie2, the data were aligned to the Mus musculus reference genome (University of California, Santa Cruz, mm10).
The data were further analyzed through the ChIP-seq analysis based on the model (MACS) program (https://github.com/taoliu/MACS).
The enriched binding peaks were identified after normalization with the control input.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: hippocampus

growth_protocol: C57BL/6 male mice (6-8 weeks old) were purchased from the Experimental Animal Center of Shanxi Medical University and fed with a high-methionine diet for more than 8 weeks.

extract_protocol:
The mice were fed with high-methionine or standard diet for 8 weeks, and the hippocampus of the two groups were isolated after being euthanized by cervical dislocation.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 30 cycles on the thermocycler. Post amplification libraries were size selected at 250-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Two mice per cage were housed at a stable temperature (24±2℃), with 12h/12h light/dark time alternation, and constant humidity. Free food and drinks available at all times.

value: hippocampus

value: high methionine feeding


title: 1057-6.TCR.23244.rs93911

description:
Library name: 93911
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: 1057-6.GEX.23244.rs93910

description:
Library name: 93910
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HMD_H3K27ac


title: Con_H3K27me3

value: WT


title: 1057-5.GEX.23244.rs93907

description:
Library name: 93907
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: Con_H3K27ac


title: Con_input

value: input


title: 1057-5.HTO.23244.rs93906

description:
Library name: 93906
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HFD67

city: Wenzhou

first: Liang

last: Xu

address: Chashan Higher Education Zone

department: School of Laboratory Medicine and Life Sciences

institute: Wenzhou Medical University

data_processing:
CLC Genomics Workbench V 11.0.1
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM walues for each Sample

source_name: iWAT

extract_protocol:
Total RNA was isolated by using Optimized RNA isolation kit (Qiagen). 2μg total RNA was used to construct the sequencing library.
RNA libraries for RNA sequencing were prepared using SMARTer RNA-seq prep kit according to the manufacturer's instructions.

value: iWAT


title: 1057-4.TCR.23132.rs93905

description:
Library name: 93905
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HFD66


title: 1057-4.GEX.23132.rs93904

description:
Library name: 93904
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HFD65


title: 1057-4.HTO.23132.rs93903

description:
Library name: 93903
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HFD64

value: wild type


title: 1057-3.TCR.23244.rs93902

description:
Library name: 93902
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HFD63


title: 1057-3.GEX.23244.rs93901

description:
Library name: 93901
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: HFD62


title: 1057-3.HTO.23244.rs93900

description:
Library name: 93900
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1057-2.TCR.23244.rs93899

description:
Library name: 93899
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: scRNA-seq of Prostate specific Pten and Nnmt KO

first: Erick

last: Mitchell-Velasquez

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
The single-cell gene expression data were mapped to the mouse genome (mm10) using the Cell Ranger package (10x Genomics Cell Ranger 7.1.0).
Cells with fewer than 200 expressed genes and greater than 20% mitochondrial reads were filtered out. Genes with less than 1 count were excluded from further analysis.
Subsequently, the counts were normalized per cell to achieve a million reads each. The top 1000 differentially expressed genes were selected for visualization using the SCANPY package (Wolf et al., 2018 Genome Biol).
Counts for these genes were scaled and logarithmized. Clustering was performed using the Louvain algorithm (Blondel et al., 2008) with default parameters.
Principal Component Analysis (PCA) was then conducted on these 1000 genes, retaining the top 15 Principal Components (PCs).
Visualization of the cells was achieved using the UMAP algorithm (Ntranos et al., 2018) by constructing a neighborhood graph with 30 neighbors.
Partition-based graph abstraction (Wolf et al., 2019) was utilized, with Louvain clusters as initial seeds for embedding.
Annotation of clusters was performed by identifying literature-defined markers for each cell type and annotating them based on marker expression within the clusters.
The markers used for cell lines were as follows: Endothelial - Cldn5, Vwf, Erg; Dendritic - Clec9a, Xcr1; B cells - Cd79; T/NK cells - Cd3; Myeloid - Cd68, Aif1; Luminal - Krt8, Krt18, Cd24, Epcam; Basal - Krt5, Krt14, Trp63; Mesenchyme - Wnt2, Wnt6, Rorb, Acta2, Myh11, CD44, Itgb1, Sultle1; Glial - Sox10; Macrophage - Cd68, Cd14, Aif1.
For Gene Set Enrichment Analysis (GSEA), only cells expressing luminal markers were considered, resulting in 1713 cells.
Of these, 1046 cells were from the Pten-/-, condition and 667 were from the Pten-/-;Nnmt-/- condition. Raw expression matrices were constructed for these cells, and phenotype based GSEA analysis was performed using the GSEApy package (Fang, 2022) with the hallmark gene set.
For Gene Ontology (GO) analysis, Differential Expression (DE) analysis was initially conducted using the Wilcoxon rank sum test within the luminal cell clusters.
Subsequently, GO annotation was performed using Enrichr gene sets (Xie et al., 2022) via the GSEApy package.
Assembly: mm10
Supplementary files format and content: expression profiles

source_name: prostate

extract_protocol:
Papain DissociationKit - Worthington Biochemical Corporation
Chromium Single Cell 3' Reagent - 10X genomics

value: prostate

value: epithelial

value: nnmt and pten KO


title: 1057-2.GEX.23244.rs93898

description:
Library name: 93898
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1057-2.HTO.23244.rs93897

description:
Library name: 93897
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549 Cells infected with Mock 48hpi replicate 2

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: A549WT_Mock_48h_rep2

data_processing:
RNA-seq reads were mapped to the hg38-EBOV composite genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Assembly: hg38
Supplementary files format and content: Aligned reads in BigWig format generated by the nf-core RNA-seq pipeline

source_name: Lung

growth_protocol: A549 (CCL-185) cells were purchased from the ATCC and were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) (Corning) supplemented with 10% v/v fetal bovine serum (FBS) (Corning) and 1% v/v penicillin-streptomycin (Corning). PTPN13 knockout cell lines were generated using the lentiCRISPR v2 plasmid (Addgene #52961) produced by the Feng Zhang lab [PMID: 25075903]. Single-guide RNA was designed using http://crispr.mit.edu:8079/ and targeted the PDZ signaling domain of PTPN13. The sgRNA sequence was cloned into the lentiCRISPR v2 plasmid following the directions described [PMID: 24336571]. To generate the knockout cell lines, 500,000 A549 cells per well and 400,000 293T cells per well were plated in 6-well plates. The cells were transfected with 1 ug of plasmid using Lipofectamine 3000 or Mirus LT-1 respectively according to manufacturer recommendations. The A549 cells had their media replaced after 6 hours. 24-hours post transfection, the media was replaced with DMEM containing 10% FBS and 1.5uM puromycin for selection. Cells were grown in media containing puromycin until viable cell growth was detected. Once cells began growing, they were diluted and plated in 96-well plates to produce single clone colonies. Cells were expanded and then moved up to 6-well plates and finally a T75 flask once almost confluent. Knockout was verified by immunoblot.

extract_protocol:
Wildtype and PTPN13 knockout cells were infected at MOI=5 with EBOV, and RNA was isolated at 24 or 48 hours post infection.
RNA was enriched for Poly(A) RNa from total RNA using oligo(dT)-attached magnetic beads. First- and second-strand synthesis, adaptor ligation, and amplification of the library were performed using the Illumina TruSeq RNA sample preparation kit as recommended by the manufacturer (Illumina). Library quality was evaluated using an Agilent DNA-1000 chip on an Agilent 2100 Bioanalyzer. Quantification of library DNA templates was performed using qRT-PCR and a known-size reference standard. Cluster formation of the library DNA templates was performed using TruSeq PE cluster kit v3 (Illumina) and the Illumina cBot workstation under conditions recommended by the manufacturer.

treatment_protocol: A549  and PTPN13-KO cells were infected with EBOV strain Mayinga-76 originating from the CDC and maintained at the University of Texas Medical Branch at Galveston

value: Lung

value: epithelial cell

value: Wild type

value: Mock


title: Testis, Spo11-KO

city: Urbana

first: Huanyu

last: Qiao

address: 2001 South Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois Urbana-Champaign

description: 10x Genomics

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

source_name: Testis

extract_protocol:
Wild-type and mutant testes were dissected and soaked in ice-cold PBS buffer. The tunica albuginea was carefully removed, and the seminiferous tubules were transferred to digestion buffer 1 (2mg/ml Collagenase I, 10% KSR in α-MEM). Subsequentially, the tissue was shaken to facilitate the dispersion and release the cell. The sample was then incubated in a 34°C water bath and rotate at 215 rpm for 30 min. Every 5 min, a wide pore pipette was used to gently pipette up and down five times. To release more single cells, the sample was then washed with 1X HBSS and immersed in digestion buffer 2 (700ug/ml trypsin dissolved in HBSS) for further digestion at 34°C and 215 rpm for another 10 minutes. The resulting cell suspension was filtered through a 40-µm cell strainer, washed with HBSS, and resuspended in 1ml of HBSS containing 0.04% BSA.
The library was constructed with the 10x Single Cell 3' V3 kit and sequenced on one 2x150nt lane in a NovaSeq 6000 SP flowcell.

value: Testis

value: testicular cells

tag: age

value: 6-8 week


title: 1056-24.TCR.23244.rs93893

description:
Library name: 93893
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-24.HTO.23244.rs93891

description:
Library name: 93891
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549 Cells infected with Mock 24hpi replicate 2

description: Library name: A549WT_Mock_24h_rep2

tag: cell line


title: Testis, WT

description: 10x Genomics


title: 1056-24.GEX.23244.rs93892

description:
Library name: 93892
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-23.TCR.23244.rs93890

description:
Library name: 93890
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: sample1_to_sample8 (combined)

data_processing:
The sequences RAW data were analyzed using Seven Bridges Genomics platform with BD WTA Multiplex Rhapsody Analysis Pipeline Version 1.8. Sample multiplex is selected using Sample Tags Version used Single-Cell Multiplex Kit - Mouse. Sample tag sequnce is:SMK_FKDL202598339-1a, The pipeline automatically adds the Sample Tag sequences to the FASTA reference file and seperate the 8 samples. The output files were used for downstream bioinformatic analysis.
The  prcessed data for 8 samples were analyzed with SeqGeq software from BD. The 8 samples were first concatenated to one sample to do downstream analysis. First QC and normalization were down with SeqGeq software. The the cells passed QC were analyzed with plugins of Seurat to do the dimensionality reduction with UMAP, clustering, and differential expressed gene analysis between clusters. After that, each amples were divided by sample ID. The same UMAP and clustering were applied to each sample to compare the difference.
Transcriptome annotation used gencodevM19-20181206.gtf
Genome_build: Reference: GRCm38-PhiX-gencodevM19-20181206.tar
Supplementary_files_format_and_content: Processed data files are  molecules per gene per cell, based on RSEC, CSV format.

source_name: BALF and AMs

growth_protocol: For sample 7 and sample 8, alveolar macrophages (AM) were isolated from BALF and cultured in DMEM and sample 8 was stimulated with IWC(ab) for 7 days.

extract_protocol:
The cells from each group were then labeled with a separate Sample Tag from the Single-Cell Multiplexing Kit.  Then the 8  samples of cell suspension with multiplexing sample tags were pooled together  to load onto a BD Rhapsody™ Cartridges. A single-cell suspension of ~20,000 cells was captured from all isolated cells, without selection, on an array of > 200,000 microwells through a limited dilution approach using BD Rhapsody system (BD Biosciences) following the manufacturer’s instruction.
Library was constructed for whole transcriptome assay analysis pipeline and SMK library according to the BD  RhapsodyTM  instruction. The the libraries were sequenced on Illumina nova6000.

treatment_protocol: Three WT mice /group were intranasal treatment with different stimuli for 7 days.  The BALF was harvested from animals at day7 and 3 mice were pooled together for downstream process. Viability of the final cell suspension was calculated using a hemocytometer and Trypan blue (Corning) exclusion and was routinely > 85%.

value: BALF

tag: molecule

value: single cell RNA

tag: sample tag


title: RNA-seq: A549 Cells infected with Mock 24hpi replicate 1

description: Library name: A549WT_Mock_24h_rep1


title: 1xAZA-5_RNAseq

city: Daejeon

first: Hanyong

last: Go

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: KRIBB

description: Library name: 1xAZA-8

data_processing:
The reference genome indexing and read mapping of liver tissue samples were performed using STAR software (v2.7.3a).
Assembly: mm10
Supplementary files format and content: tsv format file include raw count values of transcripts.

extract_protocol:
Total RNA was isolated from mouse liver tissues using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany).
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) and sequenced on the Illumina HiSeq2500 platform to generate 150-bp paired-end reads.

value: Liver

tag: diet

value: MASLD diet


title: 1056-23.HTO.23244.rs93888

description:
Library name: 93888
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds

value: PBMC


title: 1056-23.GEX.23244.rs93889

description:
Library name: 93889
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549 Cells infected with EBOV 48hpi replicate 2

description: Library name: A549WT_EBOV_48h_rep2

value: EBOV


title: 1056-22.TCR.23132.rs93887

description:
Library name: 93887
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1057-5.TCR.23244.rs93908

description:
Library name: 93908
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-22.GEX.23132.rs93886

description:
Library name: 93886
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1xAZA-4_RNAseq

description: Library name: 1xAZA-4


title: 1056-22.HTO.23132.rs93885

description:
Library name: 93885
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-21.TCR.23244.rs93884

description:
Library name: 93884
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1xAZA-2_RNAseq

description: Library name: 1xAZA-2


title: RNA-seq: A549 Cells infected with EBOV 48hpi replicate 1

description: Library name: A549WT_EBOV_48h_rep1


title: 1056-21.GEX.23244.rs93883

description:
Library name: 93883
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549 Cells infected with EBOV 24hpi replicate 2

description: Library name: A549WT_EBOV_24h_rep2


title: 0.1xAZA-4_RNAseq

description: Library name: 0.1xAZA-4


title: 1056-20.GEX.23244.rs93880

description:
Library name: 93880
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-20.TCR.23244.rs93881

description:
Library name: 93881
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549 Cells infected with EBOV 24hpi replicate 1

description: Library name: A549WT_EBOV_24h_rep1


title: scRNA-seq of Prostate specific Pten KO

value: pten KO


title: 0.1xAZA-3_RNAseq

description: Library name: 0.1xAZA-3


title: 1056-21.HTO.23244.rs93882

description:
Library name: 93882
FigS1.seurat.rds
FigS1.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-20.HTO.23244.rs93879

description:
Library name: 93879
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549-PTPN13KO Cells infected with Mock 48hpi replicate 2

description: Library name: A549_PTPN13KO_Mock_48h_rep2


title: 1056-19.TCR.23132.rs93878

description:
Library name: 93878
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549 Cells infected with Mock 48hpi replicate 1

description: Library name: A549WT_Mock_48h_rep1


title: 0.1xAZA-1_RNAseq

description: Library name: 0.1xAZA-1


title: 1056-19.GEX.23132.rs93877

description:
Library name: 93877
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549-PTPN13KO Cells infected with Mock 48hpi replicate 1

description: Library name: A549_PTPN13KO_Mock_48h_rep1


title: 1056-19.HTO.23132.rs93876

description:
Library name: 93876
Fig2.seurat.rds
Fig2.counts.rds
Fig3_CD4data.seurat.rds
Fig3_CD8data.seurat.rds
Fig3_CD4data.counts.rds
Fig3_CD8data.counts.rds
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: MASLD-5_RNAseq

description: Library name: MASLD-5


title: 1056-18.TCR.23244.rs93875

description:
Library name: 93875
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549-PTPN13KO Cells infected with Mock 24hpi replicate 2

description: Library name: A549_PTPN13KO_Mock_24h_rep2


title: 1056-18.GEX.23244.rs93874

description:
Library name: 93874
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-18.HTO.23244.rs93873

description:
Library name: 93873
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549-PTPN13KO Cells infected with Mock 24hpi replicate 1

description: Library name: A549_PTPN13KO_Mock_24h_rep1


title: MASLD-4_RNAseq

description: Library name: MASLD-4


title: MASLD-3_RNAseq

description: Library name: MASLD-3


title: 1056-17.TCR.23244.rs93872

description:
Library name: 93872
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-17.GEX.23244.rs93871

description:
Library name: 93871
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-17.HTO.23244.rs93870

description:
Library name: 93870
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549-PTPN13KO Cells infected with EBOV 48hpi replicate 2

description: Library name: A549_PTPN13KO_EBOV_48h_rep2


title: SD-5_RNAseq

description: Library name: SD-5

value: Standard diet


title: 1056-15.TCR.23244.rs93866

description:
Library name: 93866
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: 1056-15.HTO.23244.rs93864

description:
Library name: 93864
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: SD-4_RNAseq

description: Library name: SD-4


title: 1056-14.TCR.23244.rs93863

description:
Library name: 93863
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549-PTPN13KO Cells infected with EBOV 24hpi replicate 2

description: Library name: A549_PTPN13KO_EBOV_24h_rep2


title: SD-3_RNAseq

description: Library name: SD-3


title: 1056-14.GEX.23244.rs93862

description:
Library name: 93862
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds


title: RNA-seq: A549-PTPN13KO Cells infected with EBOV 24hpi replicate 1

description: Library name: A549_PTPN13KO_EBOV_24h_rep1


title: 1056-14.HTO.23244.rs93861

description:
Library name: 93861
ModelTrainingData.seurat.rds
ModelTrainingData.counts.rds