title: chr14_105151525_F_rep1

description: Library name: EW36


title: Geniad339

status: Public on Aug 06 2025

type: SRA

city: Camperdown

first: Søren

last: Madsen

state: NSW

address: D17 Charles Perkins Centre – School of L, The University of Sydney

country: Australia

institute: University of Sydney

description:
Library name: SAM24456385
Colname in processed data - same as title

library_source: transcriptomic

data_processing:
bcl2fastq - demultiplexing
Quality of sequencing data was assessed with multiQC (Ewels et al, 2016). Gene expression levels were quantified with Kallisto (Bray et al, 2016) version 0.50.1 with the following flags: kallisto quant -b 100 --single -l 50 -s 20. Mouse index file was downloaded from (November 2023): https://github.com/pachterlab/kallisto-transcriptome-indices/releases. Transcript levels were estimated with the r package tximport (Soneson et al, 2015) and EdgeR (Robinson et al, 2010) was used to filter lowly expressed genes. No samples were excluded.
Assembly: mm10
Supplementary files format and content: tab-delimited file includes log(CPM) for individual samples

molecule: total RNA

organism: Mus musculus

source_name: quadriceps muscles

extract_protocol:
combined TRIzol/chloroform/RNeasy kit (Invitogen/Sigma Aldrich/Qiagen) spin column protocol
KAPA mRNA HyperPrep Kit (Roche) was used for RNA sequencing library preparation following manufacturer's instructions with 500 ng of RNA as input

treatment_protocol: Animals are ~18-20 weeks old and have been fed standard rodent chow their whole life

tag: tissue

value: quadriceps muscles

tag: treatment

value: Chow


title: NOVA02_Blood_Phase_2_SD5

type: RNA

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

description: Gene expression profiling of PBMC  from influenza infected humans

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from PBMCs in Paxgene tubes according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: PBMCs  collected from humans  and stored in Paxgene tubes  according to manufacturer's instructions.

tag: disease state

value: influenza

value: PBMC

tag: study group

value: Vaccinated

tag: study date


title: NOVA10_Blood_Phase_2_SD5


title: chr14_105168266_F_rep1

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: EW34

data_processing:
Reads were trimmed using cutadpat for adapter removal (AGATCGGAAGAGC) and quality trimming (-m 30)
Reads were then aligned to hg38 with STAR [--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix alignment/${sample}/ --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD]
Counts were generated for each annotated gene (GENCODE Human Release 42 (GRCh38.p13)) with htseq-count using the intersection-nonempty method and non-stranded counting.
Assembly: hg38
Supplementary files format and content: comma-delimited text file of raw counts
Supplementary files format and content: meta data csv

molecule: polyA RNA

growth_protocol: NPCs were maintained in 2:1 DMEM:Ham's F12 supplemented with hFGF, hEGF, and heparin. NPCs were differentiated following the BrainPhys protocol from Bardy, et al. (doi:10.1073/pnas.1504393112)

extract_protocol:
Neurons were harvested for RNA isolation at day 14 of differentiation, following the Norgen Total RNA Purification kit (Norgen 37500) with the RNase-free DNase I kit (Norgen 25720)
100 ng total RNA per replicate was sent to Novogene for Eukaryotic mRNA library preparation with poly A enrichment. Samples were sequenced on a NovaSeq X Plus PE-150 flowcell, targeting 20 million reads per sample.

tag: cell line

tag: cell type

value: Neurons


title: chr11_124936086_F_rep1

description: Library name: EW33


title: Geniad40

description:
Library name: SAM24456384
Colname in processed data - same as title


title: chr11_124935297_F_rep1

description: Library name: EW32


title: chr11_124953964_F_rep1

description: Library name: EW31


title: chr11_82758310_F_rep1

description: Library name: EW30


title: Geniad273

description:
Library name: SAM24456383
Colname in processed data - same as title


title: SafeHarbor_318_rep4

description: Library name: EW39


title: Geniad276

description:
Library name: SAM24456382
Colname in processed data - same as title


title: NOVA29_Blood_Phase_2_SD5


title: chr11_83071905_F_rep1

description: Library name: EW28


title: Geniad121

description:
Library name: SAM24456381
Colname in processed data - same as title


title: SafeHarbor_318_rep3

description: Library name: EW27


title: chr11_82756421_F_rep1

description: Library name: EW29


title: SafeHarbor_317_rep3

description: Library name: EW26


title: chr14_105152528_F_rep1

description: Library name: EW35


title: chr1_12617218_F_rep2

description: Library name: EW23


title: Geniad457

description:
Library name: SAM24456380
Colname in processed data - same as title


title: chr1_12615462_F_rep2

description: Library name: EW24_1


title: NOVA52_Blood_Phase_2_SD5

value: Unvaccinated


title: NOVA39_Blood_Phase_2_SD5


title: chr9_87667926_F_rep2

description: Library name: EW21


title: NOVA41_Blood_Phase_2_SD5


title: chr9_87668396_F_rep2

description: Library name: EW20


title: chr9_87497930_F_rep2

description: Library name: EW19


title: Geniad283

description:
Library name: SAM24456378
Colname in processed data - same as title


title: NOVA19_Blood_Phase_2_SD5


title: NOVA31_Blood_Phase_2_SD5


title: chr8 _22222266_F_rep2

description: Library name: EW18


title: Geniad346

description:
Library name: SAM24456377
Colname in processed data - same as title


title: Geniad191

description:
Library name: SAM24456376
Colname in processed data - same as title


title: chr8_22057016_F_rep2

description: Library name: EW16_1


title: chr1_12618085_F_rep2

description: Library name: EW22


title: NOVA30_Blood_Phase_2_SD5


title: SafeHarbor_318_rep2

description: Library name: EW15_1


title: chr1_12615462_F_rep1

description: Library name: EW12


title: Geniad122

description:
Library name: SAM24456375
Colname in processed data - same as title


title: SafeHarbor_317_rep2

description: Library name: EW14


title: chr1_12618085_F_rep1

description: Library name: EW10


title: Geniad42

description:
Library name: SAM24456379
Colname in processed data - same as title


title: NOVA18_Blood_Phase_2_SD5


title: NOVA28_Blood_Phase_2_SD5


title: chr1_12617218_F_rep1

description: Library name: EW11


title: NOVA23_Blood_Phase_2_SD5


title: Geniad37

description:
Library name: SAM24456374
Colname in processed data - same as title


title: NOVA08_Blood_Phase_2_SD5


title: chr9_87667926_F_rep1

description: Library name: EW9


title: chr9_87668396_F_rep1

description: Library name: EW8


title: chr8_22222165_F_rep2

description: Library name: EW17_1


title: Geniad56

description:
Library name: SAM24456373
Colname in processed data - same as title


title: chr9_87497930_F_rep1

description: Library name: EW7


title: duodenum_GSDMD_CKO

city: hangzhou

first: Qianzhou

last: Yu

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

description:
Library name: KO
scRNA_Seq

library_source: transcriptomic single cell

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment, and count quantification.
Downstream analysis was applied with the Seurat package (v4.0.1) 47. Low-quality cells with ‘nFeature’ < 200 or > 6000, and nCount < 500, and cells with mitochondrial encoded transcripts representing > 50% were excluded from analysis. Doublets were excluded from analysis using R package Doubletfinder.
The raw gene expression matrix after quality control was cell-normalized over total expression, and 2000 variable features were selected for the integration of 2 samples (Gsdmdf/f, GsdmdΔIEC). FindAllMarkers was used to determine the signature marker genes of each cluster, and each cell type was partitioned into epithelial, stromal, and immune compartments based on the expression of the following known marker genes: epithelial cells (Epcam, Krt8, and Krt18), stromal cells (Col1Aa1, COl1a2, COl6a1, COl6a2, Vwf, Plvap, Cdh5, and S100b), and immune cells (Cd52, Cd2, Cd3d, Cd3g, Cd3e, Cd79a, Cd79b, Cd14, Cd16, Cd68, Cd83, Csf1r, and Fcer1g).
Assembly: mm10
Supplementary files format and content: genes.tsv
Supplementary files format and content: barcode.tsv
Supplementary files format and content: matrix.mtx

source_name: duodenum

extract_protocol:
2 cm of duodenum was collected from mice with the indicated genotype. After washing with ice-cold PBS, the tissue was minced into 2-3 mm pieces, washed twice with ice-cold PBS, digested with digestion buffer [2 mg/mL Collagenase II (Sigma), 0.05 mg/mL Dnase I (Solarbio), and 2 mg/mL Dispase (Worthington)] at 37℃ with 100 rpm for 40 min, and stopped with three times the volume of ice-cold RPMI 1640 (Gibco). Cell suspensions were passed through a 70 µm filter, and centrifuged at 350 g for 5 min at 4℃. The supernatant was carefully removed, the cell pellets were collected and red blood cells were removed using 1 ml Red Blood Cell Lysis Solution. Then they were resuspended in 1× DPBS (0.04% BSA) and centrifuged twice at 300 g for 10 min at 4℃. Single-cell suspensions were counted using a cell counter (Countstar), and the final concentration was adjusted to 700-1200 cells/μL.
The single-cell suspensions were loaded on a 10X Genomics GemCode Single-cell instrument to generate single-cell Gel Beads-In-EMulsion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3′ Reagent Kits v3.1.

value: duodenum

tag: genotype

value: Gsdmd CKO

tag: batch


title: chr8_22222165_F_rep1

description: Library name: EW5


title: NOVA12_Blood_Phase_2_SD5


title: duodenum_WT

description:
Library name: WT
scRNA_Seq

value: WT


title: NOVA27_Blood_Phase_2_SD5


title: SafeHarbor_318_rep1

description: Library name: EW3


title: chr8_22057016_F_rep1

description: Library name: EW4


title: distal colon3_GSDMD_CKO

description: Library name: ck3-5

data_processing:
FastQC was used for quality control with default parameters. After adaptor trimming with Cutadapt, read pairs with length >30 bp were kept, and aligned to the mouse reference genome GRCm38.102 using star.
Differentially-expressed genes were called using DESeq2.
GSEA enrichment analysis was applied with ClusterProfiler according to the default pipeline. Volcano plots and other visualizations were based on ggplot2.
Assembly: mm10
Supplementary files format and content: read count and fpkm value for all sample

source_name: distal colon

extract_protocol:
1 cm of each indicated segment of the intestine from WT and GsdmdΔIEC mice was isolated. Total RNA was isolated and purified using TRIzol reagent (Invitrogen) following the manufacturer's procedure.
The amount and purity of each RNA sample was quantified with NanoDrop ND-1000 (NanoDrop) and RNA integrity was assessed by a Bioanalyzer 2100 (Agilent) with RNA Integrity Number >7.0, and further confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA was purified from 1 μg total RNA using Dynabeads Oligo (dT) (25-61005, Thermo Fisher) using two rounds of purification, followed by fragmentation using the Magnesium RNA Fragmentation Module (cat.e6150, NEB) at 94℃ for 5-7 min. Cleaved RNA fragments were reverse-transcribed to create cDNA with SuperScript™ II Reverse Transcriptase (cat.1896649, Invitrogen), then were next used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (cat.m0209, NEB), RNase H (cat.m0297, NEB), and dUTP solution (cat.R0133, Thermo Fisher). After PCR amplification, the average insert size for the final cDNA library was 300 ± 50 bp.

value: distal colon

value: gsdmd cko


title: THP1 UBA1 M41V MUT

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: THP1 UBA1 M41V MUT
Isogenic mutant UBA1 cell line

library_source: genomic

data_processing:
Libraries are sequenced on an Illumina NovaSeq X Plus, generating > 25 million 100 bp read pairs and analyzed using Illumina’s Dragen (4.1.23) enrichment pipeline. Reads were aligned using a functionally equivalent pipeline, as previously defined70. Specifically, each read pair was separately aligned to the appropriate reference (GRCh38) genome using bwa-mem version 0.7.17 with the -M option. The resulting SAM files are first sorted and converted to BAM with Picard SortSam (V2.18.22), then all resulting BAMs are merged and duplicate marked with Picard MarkDuplicates (https://broadinstitute.github.io/picard/) using the “OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500” command line flag. Variants were filtered and subsetted using BCFtools (v1.9, https://samtools.github.io/bcftools/) and annotated with Variant Effect Predictor (VEP, https://useast.ensembl.org/info/docs/tools/vep/).
Assembly: GRCh38
Supplementary files format and content: WT.hard-filtered.vcf.gz, VCF format with called variants
Supplementary files format and content: MUT.hard-filtered.vcf.gz, VCF fortmat with called variants

molecule: genomic DNA

growth_protocol: THP1 were cultured in RPMI-1640 media with 10% of FBS and 1% penicillin/streptomycin

extract_protocol:
The cells were collected, and DNA was extracted using Qiagen Dneasy kit.
Following initial sample dsDNA quality control for quantity with a Qubit fluorometer and size distribution with an Agilent Fragment Analyzer, 50 ng of gDNA is enzymatically fragmented using Twist Bioscience’s Library Preparation EF Kit 2.0 (Twist Bioscience, 104207). Index adapters (Twist Bioscience, 100577) are ligated onto the DNA fragments, and then amplified with 10 cycles of PCR. Libraries are purified with Binding and Purification beads (Twist Bioscience, 100983), quantified with a Qubit fluorometer, and checked again on a Fragment Analyzer. Up to 8 libraries of like organisms are pooled together with a total mass of 1500 ng/pool. Human DNA is then hybridized with Twist’s Comprehensive Exome probes (Twist Bioscience, 102032). Samples are hybridized for 30 minutes with Twist’s Fast Hybridization Reagents (Twist Bioscience, 104180) before being bound to streptavidin beads and washed with Twist’s Fast Hybridization and Wash Kit (Twist Bioscience, 104180). Following hybridization, hybridized pools are amplified with 8 cycles of PCR using primers and master mix from the Library Preparation Kit EF. Final libraries are purified with Twist’s Binding and Purification beads, quantified with a Qubit fluorometer, and their size checked with a Fragment Analyzer.

value: UBA1 M41V MUT


title: SafeHarbor_317_rep1

description: Library name: EW2


title: distal colon2_GSDMD_CKO

description: Library name: ck2-5


title: LS foreskin, biol rep 3

city: Chengdu

first: Lede

last: Lin

state: Sichuan

address: No.37 Guoxue Lane, Wuhou District, Chengdu, Sichuan, P. R. China

institute: West China Hospital of Sichuan University

description:
Library name: LS3
10x Genomics

data_processing:
The FASTQ files were aligned to the human GRCh38 reference genome using the Cell Ranger v7.1.0 toolkit from 10X Genomics. Following this, the scRNA-seq data underwent quality control (QC) analysis using the Seurat v5.0.3 package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Foreskin

extract_protocol:
The procedure initiated with the fastidious creation of a single-cell suspension, succeeded by a rigorous assessment of its viability. It was ascertained that the cells exhibited a remarkable degree of activity, surpassing the 85% threshold, and were distinguished by their excellent uniformity and minimal impurities. To augment the efficiency of isolating individual cells, the cell concentration was carefully fine-tuned to an exact range of 700 to 1200 cells per microliter.
During the construction of the single-cell RNA sequencing (scRNA-seq) library, each cell, along with its associated cellular enzymes, was attached to a gel bead. This assembly was subsequently encapsulated within an oil droplet, forming a single-cell gel bead-in-emulsion (GEM). Each gel bead was uniquely labeled with a distinct barcode, incorporated a unique molecular identifier (UMI) sequence, and was equipped with a poly-dT primer sequence designed to initiate reverse transcription. The GEM droplets were then collected in Eppendorf tubes, where cell membranes were lysed using specifically designed recovery reagents, releasing the mRNA. The liberated mRNA interacted with the enzymes, dNTP substrates, and the poly-dT primer sequence within the droplets. Under precisely controlled conditions in a polymerase chain reaction (PCR) apparatus, reverse transcription was initiated, resulting in the synthesis of complementary DNA (cDNA). In the final step, the cDNA underwent PCR amplification, thereby completing the construction of the scRNA-seq library.

value: Foreskin


title: distal colon3_WT

description: Library name: cw3-5


title: distal colon1_GSDMD_CKO

description: Library name: ck1-5


title: LS foreskin, biol rep 1

description:
Library name: LS1
10x Genomics


title: LS foreskin, biol rep 2

description:
Library name: LS2
10x Genomics


title: THP1 UBA1 WT-control

description:
Library name: THP1 UBA1 WT-control
Isogenic control cell line

value: UBA1 WT


title: paraLS foreskin, biol rep 3

description:
Library name: paraLS3
10x Genomics


title: chr8 _22222266_F_rep1

description: Library name: EW6


title: distal colon2_WT

description: Library name: cw2-5


title: Normal foreskin, biol rep 3

description:
Library name: N3
10x Genomics


title: distal colon1_WT

description: Library name: cw1-5


title: NOVA37_Blood_Phase_2_SD5


title: paraLS foreskin, biol rep 2

description:
Library name: paraLS2
10x Genomics


title: Normal foreskin, biol rep 2

description:
Library name: N2
10x Genomics


title: NOVA09_Blood_Phase_2_SD5


title: NOVA47_Blood_Phase_2_SD5


title: NOVA68_Blood_Phase_2_SD5


title: NOVA07_Blood_Phase_2_SD5


title: proximal colon3_GSDMD_CKO

description: Library name: ck3-4

source_name: proximal colon

value: proximal colon


title: Normal foreskin, biol rep 1

description:
Library name: N1
10x Genomics


title: NOVA16_Blood_Phase_2_SD5


title: TCR-seq: chip 2 pool 7

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Library name: chip2pool7 - TCR

data_processing:
GEX, TCR, and CITE-seq libraries were analyzed with cell ranger multi v8.0.1 on the 10x Genomics Cloud.
GEX and CITE-seq libraries were aggregated with cell ranger aggr v8.0.1 on the 10x Genomics Cloud.
Since TCR library preparation also included primers designed to amplify TCRγ/δ sequences, we also performed MiXCR analysis with the mixcr analyze 10x-sc-xcr-vdj pipeline (MiXCR version 4.6.0). Cells were first assigned a TCR, if available, from cell ranger vdj output. Cells with unassigned TCRs were then assigned a TCR based on MiXCR results.
Assembly: GRCh38 (refdata-cellranger-GRCh38-2024-A)
Supplementary files format and content: Combined pools: cell ranger web summary files. GEX and CITE-seq: aggregated cellranger count output. TCR-seq libraries: individual library cellranger vdj outputs.

source_name: Tumor

extract_protocol:
Bioposied or resected tumors were cut into small pieces with scissors and enzymatically digested by shaking for 1 hour at 37 degrees in RPMI with 10% fetal bovine serum, 0.125 mg/ml collagenase I, 0.125 mg/ml collagenase IV, 0.05 mg/ml DNase I, and 0.05 mg/ml elastase. After digestion, tissue was forced through a cell strainer and lymphocytes were isolated by collecting the interface of a 44%/67% Percoll gradient. Cells were washed with 2% FBS in PBS and viably cryopreserved in FBS with 10% DMSO.  Cryopreserved cells were thawed simultaneously to avoid batch effects, and T cells from each patient were isolated in a single experiment by fluorescence-activated cell sorting by isolating live CD45+CD3+ cells from each sample. Cells with compatible hashing barcodes were pooled together for single-cell RNA-sequencing.
From each pool, gene expression (GEX), CITE-seq, and T cell receptor (TCR) libraries were generated with the 10x Genomcs GEM-X reagents according to the manufacturer's protocols (10x Genomics User Guide CG000734). For TCR amplification, primers were also included to amplify γ/δ TCRs. Primers were for TCRγ (outer: TGTGTCGTTAGTCTTCATGGTGTTCC, inner: GATCCCAGAATCGTGTTGCTC), and for TCRδ (outer: AGCTTGACAGCATTGTACTTCC, inner: TCCTTCACCAGACAAGCGAC).

value: Tumor

value: CD3+ T cells


title: TCR-seq: chip 2 pool 6

description: Library name: chip2pool6 - TCR


title: proximal colon2_GSDMD_CKO

description: Library name: ck2-4


title: proximal colon3_WT

description: Library name: cw3-4


title: NOVA36_Blood_Phase_2_SD5


title: proximal colon1_GSDMD_CKO

description: Library name: ck1-4


title: TCR-seq: chip 2 pool 4

description: Library name: chip2pool4 - TCR


title: TCR-seq: chip 2 pool 3

description: Library name: chip2pool3 - TCR


title: TCR-seq: chip 2 pool 2

description: Library name: chip2pool2 - TCR


title: TCR-seq: chip 2 pool 5

description: Library name: chip2pool5 - TCR


title: proximal colon2_WT

description: Library name: cw2-4


title: TCR-seq: chip 1 pool 8

description: Library name: chip1pool8 - TCR


title: TCR-seq: chip 2 pool 16

description: Library name: chip2pool16 - TCR


title: TCR-seq: chip 1 pool 7

description: Library name: chip1pool7 - TCR


title: paraLS foreskin, biol rep 1

description:
Library name: paraLS1
10x Genomics


title: TCR-seq: chip 1 pool 6

description: Library name: chip1pool6 - TCR


title: TCR-seq: chip 1 pool 5

description: Library name: chip1pool5 - TCR


title: TCR-seq: chip 2 pool 1

description: Library name: chip2pool1 - TCR


title: ileum3_GSDMD_CKO

description: Library name: ck3-3

source_name: ileum

value: ileum


title: TCR-seq: chip 1 pool 4

description: Library name: chip1pool4 - TCR


title: TCR-seq: chip 1 pool 3

description: Library name: chip1pool3 - TCR


title: ileum2_GSDMD_CKO

description: Library name: ck2-3


title: TCR-seq: chip 1 pool 2

description: Library name: chip1pool2 - TCR


title: NOVA78_Blood_Phase_2_SD5

value: influenza


title: CITE-seq: chip 2 pool 16

description: Library name: chip2pool16 - CITE

library_source: other

molecule: protein


title: NOVA46_Blood_Phase_2_SD5

value: PBMC


title: CITE-seq: chip 2 pool 7

description: Library name: chip2pool7 - CITE


title: proximal colon1_WT

description: Library name: cw1-4


title: ileum3_WT

description: Library name: cw3-3


title: NOVA60_Blood_Phase_2_SD5


title: TCR-seq: chip 1 pool 1

description: Library name: chip1pool1 - TCR


title: NOVA65_Blood_Phase_2_SD5


title: CITE-seq: chip 2 pool 6

description: Library name: chip2pool6 - CITE


title: CITE-seq: chip 2 pool 5

description: Library name: chip2pool5 - CITE


title: ileum2_WT

description: Library name: cw2-3


title: CITE-seq: chip 2 pool 4

description: Library name: chip2pool4 - CITE


title: CITE-seq: chip 2 pool 3

description: Library name: chip2pool3 - CITE


title: NOVA32_Blood_Phase_2_SD5

value: Vaccinated


title: CITE-seq: chip 2 pool 2

description: Library name: chip2pool2 - CITE


title: NOVA66_Blood_Phase_2_SD5


title: NOVA21_Blood_Phase_2_SD5


title: CITE-seq: chip 2 pool 1

description: Library name: chip2pool1 - CITE


title: ileum1_GSDMD_CKO

description: Library name: ck1-3


title: jejunum3_GSDMD_CKO

description: Library name: ck3-2

source_name: jejunum

value: jejunum


title: CITE-seq: chip 1 pool 7

description: Library name: chip1pool7 - CITE


title: NOVA56_Blood_Phase_2_SD5

value: Unvaccinated


title: NOVA62_Blood_Phase_2_SD5


title: CITE-seq: chip 1 pool 6

description: Library name: chip1pool6 - CITE


title: CITE-seq: chip 1 pool 8

description: Library name: chip1pool8 - CITE


title: NOVA53_Blood_Phase_2_SD5


title: jejunum2_GSDMD_CKO

description: Library name: ck2-2


title: NOVA73_Blood_Phase_2_SD5


title: NOVA71_Blood_Phase_2_SD5


title: CITE-seq: chip 1 pool 5

description: Library name: chip1pool5 - CITE


title: CITE-seq: chip 1 pool 4

description: Library name: chip1pool4 - CITE


title: CITE-seq: chip 1 pool 3

description: Library name: chip1pool3 - CITE


title: ileum1_WT

description: Library name: cw1-3


title: jejunum3_WT

description: Library name: cw3-2


title: CITE-seq: chip 1 pool 1

description: Library name: chip1pool1 - CITE


title: Gene expression: chip 2 pool 16

description: Library name: chip2pool16 - GEX


title: Gene expression: chip 2 pool 7

description: Library name: chip2pool7 - GEX


title: jejunum2_WT

description: Library name: cw2-2


title: Gene expression: chip 2 pool 6

description: Library name: chip2pool6 - GEX


title: NOVA63_Blood_Phase_2_SD5


title: NOVA81_Blood_Phase_2_SD5


title: NOVA75_Blood_Phase_2_SD5


title: NOVA77_Blood_Phase_2_SD5


title: NOVA80_Blood_Phase_2_SD5


title: CITE-seq: chip 1 pool 2

description: Library name: chip1pool2 - CITE


title: Gene expression: chip 2 pool 4

description: Library name: chip2pool4 - GEX


title: NOVA49_Blood_Phase_2_SD5


title: Gene expression: chip 2 pool 2

description: Library name: chip2pool2 - GEX


title: duodenum2_GSDMD_CKO

description: Library name: ck2-1

value: duodenum


title: duodenum3_GSDMD_CKO

description: Library name: ck3-1


title: NOVA50_Blood_Phase_2_SD5


title: jejunum1_GSDMD_CKO

description: Library name: ck1-2


title: Gene expression: chip 1 pool 7

description: Library name: chip1pool7 - GEX


title: duodenum1_GSDMD_CKO

description: Library name: ck1-1


title: Gene expression: chip 1 pool 8

description: Library name: chip1pool8 - GEX


title: Gene expression: chip 2 pool 3

description: Library name: chip2pool3 - GEX


title: duodenum3_WT

description: Library name: cw3-1


title: jejunum1_WT

description: Library name: cw1-2


title: NOVA76_Blood_Phase_2_SD5


title: Gene expression: chip 1 pool 6

description: Library name: chip1pool6 - GEX


title: Gene expression: chip 1 pool 5

description: Library name: chip1pool5 - GEX


title: Gene expression: chip 2 pool 1

description: Library name: chip2pool1 - GEX


title: NOVA82_Blood_Phase_2_SD5


title: duodenum2_WT

description: Library name: cw2-1


title: Gene expression: chip 1 pool 4

description: Library name: chip1pool4 - GEX


title: Gene expression: chip 2 pool 5

description: Library name: chip2pool5 - GEX


title: Gene expression: chip 1 pool 3

description: Library name: chip1pool3 - GEX


title: duodenum1_WT

description: Library name: cw1-1


title: NOVA11_Blood_Phase_2_SD5


title: NOVA48_Blood_Phase_2_SD5


title: Gene expression: chip 1 pool 2

description: Library name: chip1pool2 - GEX


title: NOVA25_Blood_Phase_2_SD5


title: Gene expression: chip 1 pool 1

description: Library name: chip1pool1 - GEX


title: invitro KPN DCAplus, tRNAseq, rep3

city: Chicago

first: Mohammad Amin

last: Bayat Tork

state: IL

address: 929 East 57th Street

department: Biochemistry and Molecular Biophysics

institute: University of Chicago

description: Library name: Sample12

data_processing:
Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to a curated Mus musculus tRNA, rRNA and reference genome.
The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/, Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads.
Assembly: GRCm39
Supplementary files format and content: tsv files with gene name and abundance per sample
Supplementary files format and content: .sam.tsv files with mutation, deletion, coverage for each gene position per sample

source_name: Organoid

growth_protocol: These organoids were cultured and maintained as described previously [PMID: 31526760] using advanced DMEM/F12 (Gibco, ThermoFisher, 12634010) supplemented with penicillin/streptomycin (100U/mL) (Gibco, ThermoFisher, 15140122), 200 mM L-Glutamine (Gibco, ThermoFisher, 25030081), 1 M HEPES (Gibco, ThermoFisher, 15630080), N2-supplement (ThermoFisher, 17502001), B27-supplement (ThermoFisher, 17504044), Recombinant Human EGF (1 ng/ml) (Peprotech, AF-100-15), and Recombinant Murine Noggin (5 ng/ml) (Peprotech, 250-38). The complete media used for culture consisted of 88% DMEM/F12, 4.7% EGF, 1.9% Noggin, 1.9% B27 supplement, 0.9% N2 supplement, 0.9% HEPES, 0.9% L-Glutamine, and 0.9% penicillin/streptomycin by volume. Organoids were grown in Matrigel scaffolding (Corning, 356255) with a 2:1 ratio of Matrigel to organoids suspended in complete media. 50 μL dots this Matrigel/Organoid mixture were bathed in complete media and grown for 48 hours prior to passaging or collection for deoxycholic acid(DCA).

extract_protocol:
RNA-seq experiments were performed on 3 independent replicates. RNA was extracted and purified using RNeasy Mini Kit(Qiagen, Cat:74104). The samples were further purified using the RNA Clean & Concentrator-5 Kit (Zymo Research, R1013). 1 ug of total RNA was used for the construction of sequencing libraries.RNA quality and quantity were assessed using the Agilent bio-analyzer.
MSR-seq (PMID 35513407)

treatment_protocol: DCA (Sigma, D2510) was dissolved in DMSO to prepare a stock solution with a concentration of 185 mM. After two days of growth, AKPT and KPN cells were replenished with fresh media supplemented with either 50 mM DCA or an equivalent volume of DMSO, which served as the control.

value: Organoid

value: villinCreER KrasG12D/+ Trp53fl/fl Rosa26N1icd/+

value: treated with 50 μM of DCA (Deoxycholic acid) for 48 h


title: TCR sequences of CD4 T cells from patient 8

description: Library name: pt8_CD4

data_processing:
Sequenced TCR-seq libraries were analyzed with MiXCR v4.6.0, using the mixcr analyze takara-human-rna-tcr-umi-smartseq pipeline preset and the --assemble-clonotypes-by CDR3 option.
Assembly: human TCR from MiXCR v4.6.0
Supplementary files format and content: MiXCR output for TCR-beta clones
Library strategy: TCR-Seq

source_name: PBMCs

extract_protocol:
DNA and RNA were extracted from sorted T cells with Qiagen AllPrep DNA/RNA Micro kit. Only RNA was used in this experiment.
TCR-sequencing libraries were generated from isolated RNA with the SMART-Seq Human TCR-seq with UMIs kit (Takara Bio) according to the manufacturer’s protocol.

value: PBMCs

value: CD4 T cells


title: TCR sequences of CD8 T cells from patient HD5

description: Library name: HD5_CD8

value: CD8 T cells


title: TCR sequences of CD4 T cells from patient 26

description: Library name: pt26_CD4


title: TCR sequences of CD4 T cells from patient 17

description: Library name: pt17_CD4


title: invitro KPN DCAplus, tRNAseq, rep1

description: Library name: Sample10


title: TCR sequences of CD4 T cells from patient HD5

description: Library name: HD5_CD4


title: TCR sequences of CD4 T cells from patient 21

description: Library name: pt21_CD4


title: invitro KPN DCAminus, tRNAseq, rep2

description: Library name: Sample8

value: untreated


title: NOVA17_Blood_Phase_2_SD5


title: invitro KPN DCAminus, tRNAseq, rep3

description: Library name: Sample9


title: TCR sequences of CD4 T cells from patient 11

description: Library name: pt11_CD4


title: TCR sequences of CD4 T cells from patient 14

description: Library name: pt14_CD4


title: TCR sequences of CD4 T cells from patient HD4

description: Library name: HD4_CD4


title: TCR sequences of CD4 T cells from patient HD3

description: Library name: HD3_CD4


title: invitro KPN DCAminus, tRNAseq, rep1

description: Library name: Sample7


title: TCR sequences of CD4 T cells from patient 10

description: Library name: pt10_CD4


title: NOVA43_Blood_Phase_2_SD5


title: invitro KPN DCAplus, tRNAseq, rep2

description: Library name: Sample11


title: invitro AKPT DCAplus, tRNAseq, rep3

description: Library name: Sample6

value: villinCreER Apcfl/fl KrasG12D/+ Trp53fl/fl TrgfbrIfl/fl


title: TCR sequences of CD8 T cells from patient 14

description: Library name: pt14_CD8


title: NOVA22_Blood_Phase_2_SD5


title: NOVA15_Blood_Phase_2_SD5


title: TCR sequences of CD4 T cells from patient 25

description: Library name: pt25_CD4


title: TCR sequences of CD4 T cells from patient 7

description: Library name: pt7_CD4


title: NOVA04_Blood_Phase_2_SD5


title: invitro AKPT DCAplus, tRNAseq, rep2

description: Library name: Sample5


title: TCR sequences of CD8 T cells from patient HD4

description: Library name: HD4_CD8


title: invitro AKPT DCAplus, tRNAseq, rep1

description: Library name: Sample4


title: NOVA57_Blood_Phase_2_SD5


title: TCR sequences of CD4 T cells from patient 4

description: Library name: pt4_CD4


title: TCR sequences of CD4 T cells from patient 12

description: Library name: pt12_CD4


title: invitro AKPT DCAminus, tRNAseq, rep3

description: Library name: Sample3


title: invitro AKPT DCAminus, tRNAseq, rep2

description: Library name: Sample2


title: TCR sequences of CD4 T cells from patient 2

description: Library name: pt2_CD4


title: TCR sequences of CD4 T cells from patient 1

description: Library name: pt1_CD4


title: TCR sequences of CD4 T cells from patient 23

description: Library name: pt23_CD4


title: TCR sequences of CD8 T cells from patient 13

description: Library name: pt13_CD8


title: NOVA34_Blood_Phase_2_SD5


title: TCR sequences of CD4 T cells from patient HD2

description: Library name: HD2_CD4


title: TCR sequences of CD4 T cells from patient 16

description: Library name: pt16_CD4


title: TCR sequences of CD4 T cells from patient 5

description: Library name: pt5_CD4


title: TCR sequences of CD8 T cells from patient 18

description: Library name: pt18_CD8


title: TCR sequences of CD4 T cells from patient HD1

description: Library name: HD1_CD4


title: TCR sequences of CD4 T cells from patient 19

description: Library name: pt19_CD4


title: TCR sequences of CD4 T cells from patient 18

description: Library name: pt18_CD4


title: NOVA51_Blood_Phase_2_SD5


title: CD206+LYVE1+ Macrophages, KCL_HO_1i, rep 1

city: London

first: James

middle: N

last: Arnold

address: New Hunt’s House, Great Maze Pond

department: Cancer and Pharmaceutical Sciences

country: United Kingdom

institute: King's College London

description:
Library name: KCL_HO_1i_1
PY119.3f

data_processing:
Sample read quality was checked using FastQC v0.11.9
Read alignment was done using the STAR aligner v2.7.9a
Count table was generated using the quant function from Salmon v1.9.0
Transcript level counts was summarized to Gene level counts using the tximport package in R
Differential Analysis was done using the DeSeq2 package in R
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for all the samples

source_name: Breast

growth_protocol: FVB/N-Tg(MMTV-PyVT)634Mul/J mice used in this study were housed under specific pathogen-free conditions in individually ventilated cages at a temperature of 21°C with water and food ad libitum.

extract_protocol:
RNA was collected using The RNeasy Mini Kit  manufactured by Qiagen and RNA extraction was performed according to manufacturer’s protocol.
Library was prepared using the NEBNext Ultra II Directional RNA Library Prep Kit according to the manufacturer's instructions

treatment_protocol: The mice were treated in a acute setting for 36 hours prior tumor collection. For drug treatments, drugs were freshly prepared on the day of injection and administered by intraperitoneal (i.p.) injection using a 26 G needle. KCL-HO-1i was produced in house and administrated at 25 µmol/kg/daily.

value: Breast

value: CD206+LYVE1+ Macrophages

tag: strain

value: WT


title: TCR sequences of CD8 T cells from patient HD2

description: Library name: HD2_CD8


title: CD206+LYVE1+ Macrophages, KCL_HO_1i, rep 3

description:
Library name: KCL_HO_1i_3
PY120.1f


title: CD206+LYVE1+ Macrophages, Control, rep 3

description:
Library name: Control_3
PY121.1e

value: Vehicle


title: invitro AKPT DCAminus, tRNAseq, rep1

description: Library name: Sample1


title: TCR sequences of CD8 T cells from patient 22

description: Library name: pt22_CD8


title: CD206+LYVE1+ Macrophages, Control, rep 2

description:
Library name: Control_2
PY121.1k


title: TCR sequences of CD4 T cells from patient 3

description: Library name: pt3_CD4


title: NOVA61_Blood_Phase_2_SD5

value: influenza

value: PBMC


title: TCR sequences of CD4 T cells from patient 13

description: Library name: pt13_CD4


title: NOVA03_Blood_Phase_2_SD5

value: Vaccinated


title: NOVA40_Blood_Phase_2_SD5


title: CD206+LYVE1+ Macrophages, Control, rep 1

description:
Library name: Control_1
PY121.1i


title: NOVA64_Blood_Phase_2_SD5

value: Unvaccinated


title: TCR sequences of CD4 T cells from patient 22

description: Library name: pt22_CD4


title: TCR sequences of CD4 T cells from patient 9

description: Library name: pt9_CD4


title: NOVA33_Blood_Phase_2_SD5


title: NOVA59_Blood_Phase_2_SD5


title: TCR sequences of CD8 T cells from patient 23

description: Library name: pt23_CD8


title: invitro KPN DCAplus, rep3

description:
Library name: KPN50UM_3
KPN50_S3

data_processing:
Trimmed sequence reads were aligned using HISAT2 with GRCm39 genome.
Samtools were used for sorting and indexing to generate the bam file.
HTSeq-count was used for quantifying the transcripts expression.
Assembly: GRCm39
Supplementary files format and content: csv file includes row counts for each sample

extract_protocol:
RNA-seq experiments were performed on 3 independent replicates. RNA was extracted and purified using RNeasy Mini Kit(Qiagen, Cat:74104). The samples were further purified using the RNA Clean & Concentrator-5 Kit (Zymo Research, R1013). 1 ug of total RNA was used for the construction of sequencing libraries.RNA quality and quantity were assessed using the Agilent bio-analyzer.
RNA-SEQ libraries were prepared using a TruSEQ based mRNA-SEQ library protocol (Illumina). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).


title: NOVA29_Blood_Phase_2_SD3


title: NOVA47_Blood_Phase_2_SD3


title: NOVA01_Blood_Phase_2_SD5


title: CD206+LYVE1+ Macrophages, KCL_HO_1i, rep 2

description:
Library name: KCL_HO_1i_2
PY120.1e


title: NOVA05_Blood_Phase_2_SD5


title: TCR sequences of CD8 T cells from patient 3

description: Library name: pt3_CD8


title: invitro KPN DCAplus, rep2

description:
Library name: KPN50UM_2
KPN50_S2


title: NOVA73_Blood_Phase_2_SD3


title: TCR sequences of CD4 T cells from patient 6

description: Library name: pt6_CD4


title: NOVA25_Blood_Phase_2_SD3


title: TCR sequences of CD8 T cells from patient 5

description: Library name: pt5_CD8


title: TCR sequences of CD8 T cells from patient 12

description: Library name: pt12_CD8


title: TCR sequences of CD4 T cells from patient 27

description: Library name: pt27_CD4


title: invitro KPN DCAminus, rep3

description:
Library name: KPN0UM_3
KPN0_S3


title: invitro KPN DCAplus, rep1

description:
Library name: KPN50UM_1
KPN50_S1


title: TCR sequences of CD8 T cells from patient 16

description: Library name: pt16_CD8


title: TCR sequences of CD8 T cells from patient 2

description: Library name: pt2_CD8


title: TCR sequences of CD8 T cells from patient HD3

description: Library name: HD3_CD8


title: invitro KPN DCAminus, rep2

description:
Library name: KPN0UM_2
KPN0_S2


title: TCR sequences of CD4 T cells from patient 28

description: Library name: pt28_CD4


title: invitro KPN DCAminus, rep1

description:
Library name: KPN0UM_1
KPN0_S1


title: TCR sequences of CD8 T cells from patient 9

description: Library name: pt9_CD8


title: NOVA70_Blood_Phase_2_SD3


title: TCR sequences of CD8 T cells from patient 7

description: Library name: pt7_CD8


title: TCR sequences of CD8 T cells from patient 8

description: Library name: pt8_CD8


title: TCR sequences of CD8 T cells from patient 10

description: Library name: pt10_CD8


title: TCR sequences of CD8 T cells from patient 19

description: Library name: pt19_CD8


title: invitro AKPT DCAplus, rep2

description:
Library name: AKPT50UM_2
AKPT50_S2


title: TCR sequences of CD8 T cells from patient 1

description: Library name: pt1_CD8


title: NOVA69_Blood_Phase_2_SD3


title: TCR sequences of CD8 T cells from patient 17

description: Library name: pt17_CD8


title: TCR sequences of CD8 T cells from patient 28

description: Library name: pt28_CD8


title: NOVA63_Blood_Phase_2_SD3


title: invitro AKPT DCAplus, rep1

description:
Library name: AKPT50UM_1
AKPT50_S1


title: TCR sequences of CD8 T cells from patient 11

description: Library name: pt11_CD8


title: invitro AKPT DCAminus, rep3

description:
Library name: AKPT0UM_3
AKPT0_S3


title: TCR sequences of CD4 T cells from patient 15

description: Library name: pt15_CD4


title: TCR sequences of CD8 T cells from patient HD1

description: Library name: HD1_CD8


title: TCR sequences of CD4 T cells from patient 20

description: Library name: pt20_CD4


title: NOVA77_Blood_Phase_2_SD3


title: NOVA78_Blood_Phase_2_SD3


title: TCR sequences of CD8 T cells from patient 20

description: Library name: pt20_CD8


title: NOVA71_Blood_Phase_2_SD3


title: invitro AKPT DCAminus, rep2

description:
Library name: AKPT0UM_2
AKPT0_S2


title: TCR sequences of CD8 T cells from patient 27

description: Library name: pt27_CD8


title: NOVA11_Blood_Phase_2_SD3


title: invitro AKPT DCAplus, rep3

description:
Library name: AKPT50UM_3
AKPT50_S3


title: NOVA20_Blood_Phase_2_SD3


title: invitro AKPT DCAminus, rep1

description:
Library name: AKPT0UM_1
AKPT0_S1


title: NOVA79_Blood_Phase_2_SD3


title: NOVA53_Blood_Phase_2_SD3


title: hippocampus, AAV-TAU

first: Wei

last: Cao

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

description: Library name: AAV-TAU

data_processing:
The raw scRNA-seq data were processed using CellRanger v4.0, which performed initial data alignment, filtering, and UMI counting. The mouse reference genome (mm10) was utilized for accurate mapping of sequencing reads to genes. After preprocessing with CellRanger, the resulting gene-barcode matrices were imported into R for downstream analyses. The quality control and preprocessing steps were performed using Seurat (v4.4.0), and batch effect removal was performed using Harmony. To preprocess the scRNA-seq data, we applied stringent quality control thresholds to ensure the reliability and biological relevance of the downstream analysis. Cells were filtered based on the following criteria: a minimum of 200 detected genes (nFeature_RNA > 200) to exclude low-quality or empty droplets, and a total RNA count between 1,000 and 20,000 (1000 < nCount_RNA < 20000) to eliminate cells with extremely low or high RNA content, which could indicate technical artifacts or doublets. Additionally, cells with a mitochondrial gene percentage exceeding 5% (percent.mt < 5) were excluded to remove cells with potential stress or apoptosis signals.
Assembly: mouse genome (mm10)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
The mouse hippocampus was dissected and snap-frozen at -80°C. Tissue (100 mg) was powdered on dry ice using a scalpel and transferred to a 1.5-mL microtube. Homogenization was performed by adding 0.5 mL of freshly prepared Homogenization Buffer (320 mM Sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 0.1 mM EDTA, 0.1% NP40, 0.1 mM Protease inhibitor, 1 mM Beta-mercaptoethanol, 1 U/μL RNase inhibitor), followed by gentle pipetting and incubation on ice for 10 minutes. The homogenate was passed through a 30-μm strainer and centrifuged at 300g for 3 minutes at 4°C. The pellet was resuspended in 0.5 mL Homogenization Buffer and mixed with 0.5 mL Upper Gradient Centrifugation Buffer (50% OptiPrep Gradient, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 0.1 mM Protease inhibitor, 1 mM Beta-mercaptoethanol, 1 U/μL RNase inhibitor). The mixture was gently layered on top of 1 mL of Lower Gradient Centrifugation Buffer (29% OptiPrep Gradient, 1 U/μL RNase inhibitor) in a 2-mL microtube. The gradient was centrifuged at 7,200g for 15 minutes at 4°C. The supernatant was carefully discarded. The nuclei pellet was resuspended in the PBS containing 0.04% BSA and 1 U/μL RNase inhibitor to achieve a concentration of 700-1200 nuclei/μL.
Nuclei (∼20,000 per sample) were loaded onto a 10x Genomics Next GEM chip G. Libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 (10x Genomics), following the manufacturer's protocol, and sequenced on an Illumina NovaSeq 6000.

value: brain


title: TCR sequences of CD8 T cells from patient 4

description: Library name: pt4_CD8


title: TCR sequences of CD8 T cells from patient 15

description: Library name: pt15_CD8


title: NOVA34_Blood_Phase_2_SD3


title: hippocampus, AAV-STOP

description: Library name: AAV-STOP


title: Rat, rep2, snATAC

description:
Library name: Rat2_snATAC
Rat2_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Data was processed using cellranger-arc (v2.0.0).
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: h5 files contain all snRNA and snATAC-seq counts for each sample. Fragment files included for snATAC-seq.

organism: Rattus norvegicus

source_name: cortex

extract_protocol:
At least 10 – 20 mg of frozen tissue was obtained from each sample using a metallic block and hammer to take a portion of the dissected cortex tissue. The tissue was then sealed inside of a Covaris Tissue TUBE (Covaris, cat. Nos. 520021 and 520023) and thoroughly pulverized using the chilled hammer and metallic block, with intermittent submerging into liquid nitrogen to maintain cold temperature and brittleness. Using a clean, pre-chilled scoopula, pulverized tissue was then transferred to a pre-chilled 2 mL DNA LoBind tube. RNA was isolated using the miRNeasy Mini Kit according to manufacturer instructions (QIAGEN, cat. no. 217084). RIN scores were calculated by a 2100 BioAnalzyer (Agilent) using the RNA 6000 Nano Kit following manufacturer instructions (Agilent cat. no. 50671511) .
Transposition, nuclei isolation, barcoding, and library preparation were performed according to the 10X Genomics Chromium Next GEM Single Cell Multiome protocol CG000338 Rev E with the following alterations. Each sample was loaded on one lane of the Chromium Next GEM Chip J. Nuclei were loaded according to manufacturer’s recommendations to target recovery of 10,000 nuclei per lane.

value: cortex


title: Rat, rep2, snRNA

description: Library name: Rat2_snRNA


title: NOVA22_Blood_Phase_2_SD3


title: cKOEmx1_4

city: Taipei City

first: Yi-Shuian

last: Huang

address: No. 128, Section 2, Academia Rd, Nangang District

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

data_processing:
Raw data was converted into raw sequenced reads using CASAVA base calling and stored in FASTQ format
Trimmomatic was employed to filter out low-quality reads, trim adapter sequences, and eliminate poor-quality bases from the obtained raw paired-end reads.
These clean reads were used for downstream analysis.
The read pairs from each sample were mapped to the corresponding reference genome using HISAT2, and the number of reads mapped to individual genes was counted using featureCounts.
Assembly: GRCm38
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: text files contain FPKM values for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was isolated using Rneasy mini kit (Qiagen). 1μg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Hippocampus

value: conditional knockout


title: Rat, rep1, snRNA

description: Library name: Rat1_snRNA


title: Rat, rep1, snATAC

description:
Library name: Rat1_snATAC
Rat1_filtered_feature_bc_matrix.h5


title: NOVA05_Blood_Phase_2_SD3

description: Gene expression profiling of PBMC  from influenza infected humans


title: cKOEmx1_2


title: Rat, rep2

description:
Library name: Rat2
Bulk RNA-seq from cortex

data_processing:
Reads were trimmed using cutadpat for adapter removal (AGATCGGAAGAGC) and quality trimming (-m 30).
Reads were then aligned to to corresponding reference genome with STAR [--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix alignment/${sample}/ --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD].
Duplicate reads were filtered using picard MarkDuplicates.
Counts were generated using  htseq-count using the intersection-nonempty method and non-stranded counting.
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: Raw counts tsv

source_name: Cortex

extract_protocol:
At least 10 – 20 mg of frozen tissue was obtained from each sample using a metallic block and hammer to take a portion of the dissected cortex tissue. The tissue was then sealed inside of a Covaris Tissue TUBE (Covaris, cat. Nos. 520021 and 520023) and thoroughly pulverized using the chilled hammer and metallic block, with intermittent submerging into liquid nitrogen to maintain cold temperature and brittleness. Using a clean, pre-chilled scoopula, pulverized tissue was then transferred to a pre-chilled 2 mL DNA LoBind tube. RNA was isolated using the miRNeasy Mini Kit according to manufacturer instructions (QIAGEN, cat. no. 217084). Approximately 100,000 NeuN+ nuclei were sorted into 650 μL cold Trizol for RNA isolation. RNA isolation was performed using the Direct-zol RNA microprep kit  (Zymo Research. cat. no. R2060) per manufacturer instructions.
Sequencing libraries were prepared following the SMARTer Stranded Total RNA-seq Kit v2 – Pico Input (Takara Bio, cat. no. 634411).

value: Cortex


title: TCR sequences of CD8 T cells from patient 26

description: Library name: pt26_CD8

value: PBMCs


title: Rat, rep1, NEUN sorted

description:
Library name: Rat1-NEUN
NeuN+ RNA-seq from crotex

value: Neurons


title: NeuN+ ATAC-seq, Rat, rep2

description: Library name: ATA_Rat2-NEUN

data_processing:
Samples were processed using the standard ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline v.1.7.0).
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: ATAC-seq peak calls, tagAlign alignment files

extract_protocol:
After centrifugation to remove sucrose gradient, nuclei were labeled by resuspending the pellet in 1 mL blocking buffer with NeuN-488 antibody (Millipore, cat. no. MAB377X) at 1:4,000 and 4,6-diamidino-2-phenylindole at 1:20,000 for at least 30 minutes at 4°C with rotation. Nuclei were then centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was removed the pellet was resuspended in 500 μL cold 1% BSA in PBS with RNase Inhibitor. Nuclei were then filtered through a 35 μm filter, washing the filter with an additional 100 μL 1% BSA in PBS. Nuclei were then sorted using a Sony MA900 device with a 70-μm nozzle and pressure not exceeding a pressure setting of 7. Gates were set to capture those populations that were positive for 488 signal (NeuN+). Both the NeuN+ and NeuN- populations were collected and held at 4°C . Purity of selected samples was typically >95% based on reanalysis of sorted samples.
Approximately 100,000 NeuN+ nuclei were isolated from cortex tissues and used for ATAC-seq library preparation as per standard protocols (PMID: 24097267, PMID: 25559105, PMID: 28846090) with the following modifications. Briefly, 50 μL of cold 5x lysis buffer was added to sorted nuclei to reach a final concentration of 1x (1- mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and incubated for 20 min on ice followed by centrifugation for 10 minutes. The transposition reaction was incubated for 30 minutes at 37°C with agitation at 1000 rpm (Illumina Tagment DNA Enzyme and Buffer kit, cat. no. 20034198). After column clean up via the QIAGEN MinElute Reaction Cleanup kit (QIAGEN, cat. no. 28204) and PCR amplification of libraries, an additional clean up with AMPure XP beads (0.8X ratio) was performed with two 80% ethanol washes before quantification using a DNA High-Sensitivity chip on a 2100 BioAnalyzer (Agilent). Libraries were sequenced paired-end with the Illumina dual indexes on a NovaSeq X Plus 10 B 300 cycle flowcell targeting 100 million reads per sample.


title: Rat, rep2, NEUN sorted

description:
Library name: Rat2-NEUN
NeuN+ RNA-seq from crotex


title: NeuN+ ATAC-seq, Rat, rep1

description: Library name: ATAC_Rat1-NEUN


title: Rat, rep1

description:
Library name: Rat1
Bulk RNA-seq from cortex


title: NOVA10_Blood_Phase_2_SD3


title: cKOEmx1_1


title: cWT_3

value: conditional wildtype


title: cKOEmx1_3


title: NOVA52_Blood_Phase_2_SD3


title: TCR sequences of CD8 T cells from patient 6

description: Library name: pt6_CD8

value: CD8 T cells


title: parthenote1 [WGBS]

city: Columbus

first: Jinsoo

last: Ahn

state: OH

address: 2029 Fyffe Rd

institute: The Ohio State University

description: Library name: PA1_WGBS

data_processing:
The raw WGBS reads were trimmed and filtered, using the default parameters of Trim Galore (v0.12.1).
The resulting cleaned reads were mapped to the pig reference genome (Sscrofa11.1/susScr11) using the Bismark aligner (v0.22.3) with default parameters.
Deduplication was performed with deduplicate_bismark and methylation percentages for cytosines in CpGs were determined using bismark_methylation_extractor.
Assembly: susScr11
Supplementary files format and content: methylation ratios in bedGraph format.

organism: Sus scrofa

source_name: whole embryo

growth_protocol: After electric stimulation of oocytes followed by 2 h of stabilization period, parthenogenetic embryos were placed into oviducts of each of the two surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.

extract_protocol:
From the whole collected embryos of CN and PA, genomic DNA was isolated and fragmented.
For optimization of bisulfite conversion of genomic DNA, Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Inc. Ann Arbor, MI, USA) was used according to the manufacturer`s instructions.

treatment_protocol: In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.

value: whole embryo

value: parthenogenesis


title: parthenote2 [WGBS]

description: Library name: PA2_WGBS


title: cWT_2


title: cWT_1


title: Moderate MAFLD 3, female

city: Pittsburgh

first: Irina

middle: M

last: Bochkis

state: PA

address: 707A Scaife Hall, 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

description: H F Moderate MAFLD 3

data_processing:
RNA-Seq reads were aligned using STAR 18 to human genome (hg19; NCBI build 37). Expression levels were calculated using RSEM 19 . Differential expression analysis of RNA-seq (P-value < 0.05) was performed in R using edgeR package) 11 with a Benjamini–Hochberg FDR of 5%.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw expression counts, RPKM, TPM values for each sample

source_name: Liver

extract_protocol:
Isolation of total cellular RNA from cultured hepatocytes or liver was pertranscription factors are expressed. formed using the RNeasy Kit (Qiagen)
The quality of the RNA samples was analyzed using an Agilent RNA 6000 nano kit (Bioanalyzer, Agilent Technologies). Samples with RIN scores above 9.5 were used in library preparation. One microgram of total RNA was used to isolate mRNA (NEBNext Poly(A) mRNA magnetic isolation module). Libraries of the resulting mRNA were prepared using a NEBNext Ultra II RNA library preparation kit. All samples were sequenced on an Illumina NextSeq 2000. Three replicates were sequenced for each category (female: Normal, Mild, Moderate; male: Normal, Moderate, Severe).

value: Liver

tag: subject status

value: Moderate MAFLD

tag: gender

value: female


title: control2 [WGBS]

description: Library name: CN2_WGBS

value: untreated


title: NOVA39_Blood_Phase_2_SD3

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

extract_protocol: Total RNA was isolated from PBMCs in Paxgene tubes according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

value: influenza

value: PBMC

value: Vaccinated


title: NOVA23_Blood_Phase_2_SD3


title: NOVA02_Blood_Phase_2_SD3


title: Moderate MAFLD 1, female

description: H F Moderate MAFLD 1


title: scRNAseq_KO

first: Chi-Yuan

last: Yao

address: No.7, Chung Shan S. Rd.

department: Hematology

institute: National Taiwan University Hospital

data_processing:
The FASTQ files were mapped to the mouse reference genome (GRCm38) using the CellRanger software (v3.0.1).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited barcodes, features, and matrix files.

source_name: GFP+Lin- cells

extract_protocol:
We FACS sorted for GFP+Lin- cells from recipient mice bone marrow. The cells were washed and resuspended in PBS.
The sequencing library was constructed using the Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (10X Genomics).

value: GFP+Lin- cells

value: KO


title: Mild MAFLD 3, female

description: H F Mild MAFLD 3

value: Mild MAFLD


title: Mild MAFLD 2, female

description: H F Mild MAFLD 2


title: scRNAseq_WT

value: WT


title: Mild MAFLD 1, female

description: H F Mild MAFLD 1


title: Moderate MAFLD 2, female

description: H F Moderate MAFLD 2


title: NOVA24_Blood_Phase_2_SD3


title: NOVA18_Blood_Phase_2_SD3


title: Severe MAFLD 3, male

description: H M Severe MAFLD 3

value: Severe MAFLD

value: male


title: Thymus obtained from model mouse number 25

city: Fuzhou

first: Qiao

middle: ting

last: Hu

state: Fujian

address: 420 Fuma Road, Jin'an District

department: Medical oncology

institute: Fujian medical University

data_processing:
Software used for data processing：python: 2.7; R: 3.5.0; FastQC: 0.11.7; Cutadapt: 1.17; hisat2: 2.1.0; StringTie: 1.3.3; ballgown: 2.10.0; CAPT: 1.2.4; GSEA: 2.2.4; rMATs: 4.0.1; rmats2sashimiplot: 2.0.2
Agarose gel electrophoresis was used to assess the integrity of total RNA samples.
The quality and concentration of the sequencing libraries were evaluated using an Agilent 2100 Bioanalyzer.
Sequencing data quality control: When assessing sequencing quality, Q30 was calculated for the raw sequences of each sample, where Q = -10log10(P). For example, Q = 30 represents a probability of misidentification of 0.1%, which means an error rate of 0.1% and an accuracy rate of 99.9%.
Sequencing data alignment: After sequencing quality control, the raw data underwent preprocessing to obtain trimmed data, which was then aligned to the reference genome.
Assembly: mm10
Supplementary files format and content: Excel file includes RPKM values for each sample.

source_name: HCC nodule

extract_protocol:
RNA was harvested using NEB Next® Poly(A) mRNA Magnetic Isolation Module. 1-2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit(Roche) following manufacturer's protocols.

treatment_protocol:
Normal mice i.p. with corn oil. Model mice i.p. with DEN and CCl4.
Livers/HCC nodules and corresponding thymus were harvested from normal mice and model mice.
mRNA extracted from livers/HCC nodules/thymi was sequenced by Illumina NovaSeq 6000.

value: HCC nodule

value: mouse i.p. with DEN+CCl4


title: NOVA31_Blood_Phase_2_SD3


title: Thymus obtained from model mouse number 15


title: Severe MAFLD 2, male

description: H M Severe MAFLD 2


title: Severe MAFLD 1, male

description: H M Severe MAFLD 1


title: Moderate MAFLD 3, male

description: H M Moderate MAFLD 3


title: control1 [WGBS]

description: Library name: CN1_WGBS

value: whole embryo


title: NOVA41_Blood_Phase_2_SD3


title: Thymus obtained from model mouse number 8


title: Thymus obtained from normal mouse number 5, Control 3

source_name: Normal liver

value: Normal liver

value: mouse i.p. with corn oil


title: Moderate MAFLD 2, male

description: H M Moderate MAFLD 2

value: Liver

value: Moderate MAFLD


title: Normal Liver 3, female

description: H F Normal 3

value: healthy

value: female


title: NOVA12_Blood_Phase_2_SD3

value: influenza

value: PBMC


title: Normal Liver 2, female

description: H F Normal 2


title: Normal Liver 3, male

description: H M Normal 3


title: Thymus obtained from normal mouse number 2, Control 1


title: Normal Liver 1, female

description: H F Normal 1


title: Thymus obtained from normal mouse number 3, Control 2


title: Normal Liver 2, male

description: H M Normal 2


title: Macrophages,Naive,0dpi,Rep6

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos labs

description: Library name: F029493_E5-7

data_processing:
RNA-seq FASTQ files were trimmed, aligned to the mouse reference genome (GRCm39, v108), and quantified using the nf-core/rnaseq pipeline with the star_salmon option (v3.12.0). Gene-level length-scaled counts were used for all downstream analyses.
Assembly: GRCm39
Supplementary files format and content: quant.sf files from salmon quantification.

source_name: Whole Brain

extract_protocol:
MDMs (tdTomato+), microglia (CD11b+, CD45mid/low, tdTomato-) and “classical” monocytes (Ly6G-,Ly6Chi) were sorted from brain and blood of female and male Ms4a3-cre::Ai14D mice at 7 and 30 days with and without TBI. Naïve samples were collected from untreated mice.
cDNAs were generated using the SMART-Seq® mRNA LP (with UMIs) kit for sequencing (Takara bio,634765), according to the vendor protocol. cDNA amplification cycle was adjusted to 19 cycles. PCR-amplified cDNA was purified by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol, and cDNA is eluted with ~15ul of Elution Buffer. Subsequently, 8 ul of cDNA 0.125 ng/μL was used as a starting material for library preparation using the the Unique Dual Index (UDI) kits (Takara bio, 634752-5) according to the vendor protocol, with final library PCR amplification of 14 cycles. PCR-amplified library was purified individually by immobilization on NucleoMag NGS Clean-up and Size Select beads. The beads were then washed with 80% ethanol and the library eluted with nuclease-free water.
Quality control and quantification was performed using the Qubit dsDNA HS Assay Kit (Thermofisher, 32854) and TapeStation D5000 Reagents (Agilent, 5067-5589) and Screentape (Agilent, 5067-5588). Samples were normalized and pooled individually for sequencing. An additional double-sided SPRI selection was performed on the pool prior to sequencing. Libraries were sequenced using the NextSeq 2000 P3, 300 cycles kit (Illumina, 20040561).

value: Whole Brain

value: Monocyte-derived Macrophages

value: Naive

tag: time

tag: mouse id

tag: library prep_date

tag: lysis plate_id


title: Big HCC nodule obtained from model mouse number 25


title: Small HCC nodule obtained from model mouse number 25


title: Macrophages,Naive,0dpi,Rep5

description: Library name: F029488_E5-7


title: NOVA66_Blood_Phase_2_SD3

value: Unvaccinated


title: NOVA28_Blood_Phase_2_SD3

value: Vaccinated


title: Microglia,Naive,0dpi,Rep6

description: Library name: F029493_E1-3

value: Microglia


title: NOVA27_Blood_Phase_2_SD3


title: Monocytes,Naive,0dpi,Rep6

description: Library name: F029492_E1-3

source_name: Blood

value: Blood

value: Monocytes


title: NOVA36_Blood_Phase_2_SD3


title: Small HCC nodule obtained from model mouse number 15

value: HCC nodule

value: mouse i.p. with DEN+CCl4


title: NOVA75_Blood_Phase_2_SD3


title: Microglia,Naive,0dpi,Rep5

description: Library name: F029488_E1-3


title: Big HCC nodule obtained from model mouse number 15


title: Monocytes,SHAM,30dpi,Rep2

description: Library name: F029490_E1-3

value: SHAM


title: NOVA65_Blood_Phase_2_SD3


title: Monocytes,Naive,0dpi,Rep5

description: Library name: F029487_E1-3


title: NOVA09_Blood_Phase_2_SD3


title: Macrophages,TBI,7dpi,Rep8

description: Library name: F029532_D5-7

value: TBI


title: Macrophages,SHAM,7dpi,Rep3

description: Library name: F029533_D5-7


title: Macrophages,Naive,0dpi,Rep4

description: Library name: F029493_D5-7


title: Normal Liver 1, male

description: H M Normal 1

value: Liver

value: male


title: Big HCC nodule obtained from model mouse number 8


title: Small HCC nodule obtained from model mouse number 8


title: Microglia,SHAM,7dpi,Rep3

description: Library name: F029533_D1-3


title: Macrophages,Naive,0dpi,Rep3

description: Library name: F029488_D5-7


title: Moderate MAFLD 1, male

description: H M Moderate MAFLD 1

value: Moderate MAFLD


title: Microglia,TBI,7dpi,Rep8

description: Library name: F029532_D1-3


title: NOVA30_Blood_Phase_2_SD3_rehyb

value: influenza


title: NOVA19_Blood_Phase_2_SD3

value: PBMC


title: Liver obtained from normal mouse number 3, Control 2

value: Normal liver

value: mouse i.p. with corn oil


title: Monocytes,SHAM,7dpi,Rep3

description: Library name: F029494_D1-3


title: Monocytes,Naive,0dpi,Rep4

description: Library name: F029492_D1-3

value: Naive


title: Liver obtained from normal mouse number 2, Control 1


title: Monocytes,SHAM,30dpi,Rep1

description: Library name: F029490_D1-3


title: Microglia,Naive,0dpi,Rep4

description: Library name: F029493_D1-3

value: Whole Brain


title: K907A_3

city: University Park

first: Adam

middle: Bleier

last: Glick

address: 108 AVBS Building

department: Department of Veterinary and Biomedical Sciences

institute: Pennsylvania State University

description: SM_K907A_4_S37_R1_001starAligned.sortedByCoord.out.bam

data_processing:
Demultiplexed reads were obtained as fastQ files and were checked for quality using FastQC (version 0.11.9) (Andrews, 2010).
Adapter contamination, polyA read through, and low-quality tails were removed using BBDuk BBMap (version 37.62) (https://sourceforge.net/projects/bbmap/).
The STAR aligner (Dobin et al., 2013) was used to align the filtered reads to the mouse reference genome of strain C57BL/6J GRCm38 (mm10)
The quality of the alignment was checked using Qualimap (Okonechnikov, Conesa and García-Alcalde, 2016), visualized in IGV, and aligned BAM files were quantified using featureCounts (version: 2.0.1) (Liao, Smyth and Shi, 2014).
Normalized and transformed read counts were generated by DESeq2 algorithm to normalize the raw counts data from featureCounts (version: 1.22.2) using R studio (R version: 3.5.2)  An arbitrary cut-off of 2 log2FoldChange was used to determine the significantly up- and down-regulated genes versus the C57-T control. Statistical significance was determined by q-value < 0.05.  Gene annotation was performed by BiomaRt (version: 2.38.0).
Assembly: mm10
Supplementary files format and content: Matrix table text file with raw gene counts for every gene and every sample

growth_protocol: C57-T immortalized mouse keratinocytes expressing doxycycline-inducible wildtype (WT) or mutant IRE1alpha constructs were routinely cultured in EMEM media contaning 0.05 mM calcium and 8% chelated FBS. For generation of spheroids, 5000 keratinocytes were plated in presence of 0.25 mg/ml Corning Matrigel with doxycycline in a Corning ultra-low attachment (ULA), U-bottom 96-well trays. Plates were centrifuged at 4degrees C and spheroids were allowed to form by passive aggregation. All spheroids were harvested for experiments after 24h.

extract_protocol:
Total RNA was extracted from 30 spheroids pooled per condition to generate RNA per replicate using Qiagen RNasy Micro kit.
Unique indexed library generated by Lexogen QuantSeq Library kit

treatment_protocol: Spheroids were generated in keratinocytes media (EMEM, 0.05 mM calcium , 8% chelated FBS) with either 500 ng/ml or 1000 ng/ml doxycycline for 24h to induce expression of wildtype (WT) or mutant forms of IRE1alpha

value: SV40 Large T Ag-immortalized keratinocytes

tag: genetic modification

value: IRE1alpha K907A mutation overexpression

value: Spheroids generated in ultra-low attachment wells

value: Doxycycline for 24h


title: Pancreas, KC HOM, Mouse 8

city: Edinburgh

first: Carla

last: Salomo Coll

address: Crewe Rd S

department: Institute of Genetics and Cancer - CRUK Scotland Centre

institute: University of Edinburgh

data_processing:
Data was processed using the nf-core/rnaseq v3.12.0 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020). The pipeline was executed with Nextflow v23.04.2 (Di Tommaso et al., 2017) on the Edinburgh Compute and Data Facility (ECDF) Linux Compute Cluster (Eddie) with the following command: nextflow run nf-core/rnaseq -params-file nf-params.json -profile eddie -resume
Assembly: Mus musculus GRCCm39
Supplementary files format and content: tab-separated values file include scaled counts for each sample

source_name: Pancreas

extract_protocol:
RNA extraction was performed as described in (Smith et al., 2022). Frozen pancreas was pulverised while covered in liquid nitrogen, transfer to TRIzol and homogenised. RNA was isolated with the phenol/chloroform extraction method and purified using the Qiagen RNeasy kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: tissue

value: Pancreas

value: PDX CCPG1

value: KC Ccpg1-delta-Panc

tag: Sex

value: F

tag: age (days)


title: NOVA57_Blood_Phase_2_SD3

first: kathie

last: walters

address: 401 Terry Ave N

institute: Institute for Systems Biology

tag: disease state

tag: study group

value: Unvaccinated


title: NOVA62_Blood_Phase_2_SD3

tag: study date


title: Pancreas, KC HOM, Mouse 7


title: K907A_2

description: SM_K907A_3_S36_R1_001starAligned.sortedByCoord.out.bam

tag: cell line

tag: cell type

tag: treatment


title: Microglia,Naive,0dpi,Rep3

description: Library name: F029488_D1-3

value: Microglia

tag: genotype


title: Liver obtained from normal mouse number 3, Control 3


title: NOVA32_Blood_Phase_2_SD3

value: Vaccinated


title: Pancreas, KC WT, Mouse 8

tag: strain

value: KC Ccpg1+/+


title: Monocytes,TBI,7dpi,Rep8

description: Library name: F029495_D1-3

value: Blood

value: Monocytes

value: TBI


title: Monocytes,Naive,0dpi,Rep3

description: Library name: F029487_D1-3

value: Naive


title: NOVA43_Blood_Phase_2_SD3

value: influenza

value: PBMC


title: K907A_1

description: SM_K907A_2_S35_R1_001starAligned.sortedByCoord.out.bam

value: SV40 Large T Ag-immortalized keratinocytes

value: IRE1alpha K907A mutation overexpression


title: NOVA39_Blood_Phase_2_SD3_rehyb


title: Macrophages,SHAM,7dpi,Rep2

description: Library name: F029533_C5-7

value: Whole Brain

value: Monocyte-derived Macrophages

value: SHAM


title: R635W_3

description: SM_R635W_3_S28_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha R635W mutation overexpression

value: Spheroids generated in ultra-low attachment wells

value: Doxycycline for 24h


title: Pancreas, KC WT, Mouse 7

value: Pancreas

value: PDX CCPG1

value: M


title: NOVA68_Blood_Phase_2_SD3

value: Unvaccinated


title: Macrophages,TBI,7dpi,Rep7

description: Library name: F029532_C5-7


title: R635W_2

description: SM_R635W_2_S27_R1_001starAligned.sortedByCoord.out.bam


title: NOVA80_Blood_Phase_2_SD3


title: NOVA81_Blood_Phase_2_SD3


title: Pancreas, KC HOM, Mouse 6

value: KC Ccpg1-delta-Panc


title: Pancreas, KC HOM, Mouse 5

value: F


title: R635W_1

description: SM_R635W_1_S26_R1_001starAligned.sortedByCoord.out.bam


title: NOVA76_Blood_Phase_2_SD3


title: Macrophages,SHAM,7dpi,Rep1

description: Library name: F029488_C5-7


title: Pancreas, KC WT, Mouse 6

value: KC Ccpg1+/+


title: Q780delta_2

description: SM_Q780delta_2_S24_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha Q780delta mutation overexpression


title: Microglia,SHAM,7dpi,Rep2

description: Library name: F029533_C1-3

value: Microglia


title: Q780delta_1

description: SM_Q780delta_1_S23_R1_001starAligned.sortedByCoord.out.bam

value: SV40 Large T Ag-immortalized keratinocytes


title: Pancreas, KC HOM, Mouse 4


title: Microglia,TBI,7dpi,Rep7

description: Library name: F029532_C1-3

value: TBI


title: Monocytes,TBI,7dpi,Rep7

description: Library name: F029495_C1-3

value: Blood

value: Monocytes


title: Pancreas, KC WT, Mouse 4


title: Monocytes,SHAM,7dpi,Rep2

description: Library name: F029494_C1-3

value: SHAM


title: NOVA82_Blood_Phase_2_SD3

value: influenza

value: PBMC


title: E484K_3

description: SM_E484K_3_S34_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha E484K mutation overexpression

value: Spheroids generated in ultra-low attachment wells

value: Doxycycline for 24h


title: NOVA08_Blood_Phase_2_SD3

value: Vaccinated


title: E484K_2

description: SM_E484K_2_S33_R1_001starAligned.sortedByCoord.out.bam


title: Macrophages,TBI,30dpi,Rep3

description: Library name: F029493_C5-7

value: Whole Brain

value: Monocyte-derived Macrophages


title: Pancreas, KC WT, Mouse 3

value: Pancreas

value: PDX CCPG1

value: F


title: Microglia,TBI,30dpi,Rep3

description: Library name: F029493_C1-3

value: Microglia


title: E484K_1

description: SM_E484K_1_S32_R1_001starAligned.sortedByCoord.out.bam

value: SV40 Large T Ag-immortalized keratinocytes


title: NOVA45_Blood_Phase_2_SD3


title: Q780delta_3

description: SM_Q780delta_3_S25_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha Q780delta mutation overexpression


title: NOVA17_Blood_Phase_2_SD3

description: Gene expression profiling of PBMC  from influenza infected humans


title: Monocytes,TBI,30dpi,Rep6

description: Library name: F029492_C1-3

value: Blood

value: TBI


title: NOVA64_Blood_Phase_2_SD3

value: Unvaccinated


title: Pancreas, KC WT, Mouse 5

value: KC Ccpg1+/+


title: S296F_3

description: SM_S296F_5_S31_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha S296F mutation overexpression


title: NOVA48_Blood_Phase_2_SD3

value: influenza

value: PBMC


title: Monocytes,TBI,30dpi,Rep5

description: Library name: F029490_C1-3

value: Monocytes


title: Pancreas, KC HOM, Mouse 2

value: KC Ccpg1-delta-Panc


title: S296F_2

description: SM_S296F_2_S30_R1_001starAligned.sortedByCoord.out.bam

value: Spheroids generated in ultra-low attachment wells

value: Doxycycline for 24h


title: Microglia,SHAM,7dpi,Rep1

description: Library name: F029488_C1-3

value: Whole Brain

value: SHAM


title: Pancreas, KC HOM, Mouse 1

value: Pancreas

value: PDX CCPG1

value: F


title: S296F_1

description: SM_S296F_1_S29_R1_001starAligned.sortedByCoord.out.bam

value: SV40 Large T Ag-immortalized keratinocytes


title: NOVA21_Blood_Phase_2_SD3

value: Vaccinated


title: Pancreas, KC WT, Mouse 1

value: M


title: Monocytes,SHAM,7dpi,Rep1

description: Library name: F029487_C1-3

value: Blood


title: Pancreas, KC HOM, Mouse 3


title: Y628F_3

description: SM_Y628F_4_S22_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha Y628F mutation overexpression


title: Macrophages,TBI,7dpi,Rep6

description: Library name: F029533_B5-7

value: Monocyte-derived Macrophages

value: TBI


title: Sample 15_MTX+Nit-5

city: beijing

first: Xin

last: Wen

address: awfa

institute: Capital Medical University

description: Sample 15

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/MM10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: processed data-gene count.xlsx

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1.3μg of total RNA was used for the construction of sequencing libranies.
RNA libraries for RNA-seq were prepared using SMARTER Mrna-Seq Library Prep Kit following manufacturer's protocols.

value: Liver

value: WT

value: MTX+Nitrate


title: Y628F_2

description: SM_Y628F_3_S21_R1_001starAligned.sortedByCoord.out.bam

value: Spheroids generated in ultra-low attachment wells


title: Pancreas, KC WT, Mouse 2

value: KC Ccpg1+/+


title: Sample 14_MTX+Nit-4

description: Sample 14


title: NOVA16_Blood_Phase_2_SD3

value: influenza

value: PBMC


title: Sample 13_MTX+Nit-3

description: Sample 13


title: NOVA33_Blood_Phase_2_SD3

value: Unvaccinated


title: A414T_3

description: SM_A414T_4_S19_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha A414T mutation overexpression

value: Doxycycline for 24h


title: Macrophages,TBI,30dpi,Rep2

description: Library name: F029493_B5-7

value: Whole Brain


title: Macrophages,TBI,7dpi,Rep4

description: Library name: F029489_B5-7


title: NOVA03_Blood_Phase_2_SD3

value: Vaccinated


title: Macrophages,Naive,0dpi,Rep2

description: Library name: F029488_B5-7

value: Naive


title: NOVA07_Blood_Phase_2_SD3


title: NOVA60_Blood_Phase_2_SD3


title: Sample 11_MTX+Nit-1

description: Sample 11


title: NOVA40_Blood_Phase_2_SD3


title: NOVA61_Blood_Phase_2_SD3


title: Macrophages,TBI,7dpi,Rep5

description: Library name: F029532_B5-7


title: Sample 10_MTX-5

description: Sample 10

value: MTX


title: Monocytes,TBI,7dpi,Rep6

description: Library name: F029489_B9-11

value: Blood

value: Monocytes


title: Y628F_1

description: SM_Y628F_2_S20_R1_001starAligned.sortedByCoord.out.bam

value: SV40 Large T Ag-immortalized keratinocytes

value: IRE1alpha Y628F mutation overexpression


title: Microglia,TBI,7dpi,Rep6

description: Library name: F029533_B1-3

value: Microglia

value: TBI


title: A414T_1

description: SM_A414T_1_S17_R1_001starAligned.sortedByCoord.out.bam

value: Spheroids generated in ultra-low attachment wells


title: WT_2

description: SM_WT_2_S15_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha WT overexpression


title: Microglia,TBI,7dpi,Rep5

description: Library name: F029532_B1-3


title: WT_3

description: SM_WT_3_S16_R1_001starAligned.sortedByCoord.out.bam


title: Sample 8_MTX-3

description: Sample 8

value: Liver

value: WT


title: WT_1

description: SM_WT_1_S14_R1_001starAligned.sortedByCoord.out.bam


title: NOVA46_Blood_Phase_2_SD3

value: influenza

value: PBMC


title: A414T_2

description: SM_A414T_2_S18_R1_001starAligned.sortedByCoord.out.bam

value: IRE1alpha A414T mutation overexpression

value: Doxycycline for 24h


title: Monocytes,TBI,7dpi,Rep5

description: Library name: F029495_B1-3


title: Sample 7_MTX-2

description: Sample 7


title: NOVA59_Blood_Phase_2_SD3

value: Unvaccinated


title: C57T_3

description: SM_C57T_3_S13_R1_001starAligned.sortedByCoord.out.bam

value: Parent


title: NOVA56_Blood_Phase_2_SD3


title: C57T_2

description: SM_C57T_2_S12_R1_001starAligned.sortedByCoord.out.bam


title: Sample 6_MTX-1

description: Sample 6

value: MTX


title: Monocytes,TBI,7dpi,Rep4

description: Library name: F029494_B1-3

value: Blood


title: Microglia,TBI,30dpi,Rep2

description: Library name: F029493_B1-3

value: Whole Brain


title: Sample 9_MTX-4

description: Sample 9


title: Sample 5_Ctrl-5

description: Sample 5

value: control


title: NOVA01_Blood_Phase_2_SD3

value: Vaccinated


title: C57T_1

description: SM_C57T_1_S11_R1_001starAligned.sortedByCoord.out.bam

value: SV40 Large T Ag-immortalized keratinocytes


title: NOVA04_Blood_Phase_2_SD3


title: NOVA52_Blood_Phase_2_SD1


title: Monocytes,TBI,30dpi,Rep4

description: Library name: F029492_B1-3

value: Monocytes

value: TBI


title: NOVA37_Blood_Phase_2_SD3


title: Sample 4_Ctrl-4

description: Sample 4


title: ATAC-Seq ST-rep2

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
ATAC-seq: Raw fastq files were subjected to quality control using FastQC (v0.11.9) and Trim Galore (v0.6.0).
ATAC-seq: Reads were aligned with bowtie2 (v2.3.5.1) and samtools (v1.3.1, options: -Sb -q 20).
ATAC-seq: BAM files were deduplicated with picard (v2.25.7) MarkDuplicates
ATAC-seq: MACS2 (v2.2.7.1) subcommand callpeak was used for peak calling
Assembly: hg19, Sscrofa11
Supplementary files format and content: Peak file

source_name: ST

value: ST

value: Swine testicular cell line


title: Monocytes,TBI,30dpi,Rep3

description: Library name: F029490_B1-3


title: Sample 3_Ctrl-3

description: Sample 3

value: Liver

value: WT


title: ATAC-Seq ST-rep1


title: NOVA48_Blood_Phase_2_SD1

city: Seattle

value: influenza

value: PBMC


title: ATAC-Seq PK15-rep2

value: Porcine kidney


title: Microglia,TBI,7dpi,Rep4

description: Library name: F029489_B1-3

value: Microglia


title: Sample 2_Ctrl-2

description: Sample 2


title: Sample 12_MTX+Nit-2

description: Sample 12

value: MTX+Nitrate


title: ATAC-Seq PK15-rep1


title: Sample 1_Ctrl-1

description: Sample 1


title: Monocytes,Naive,0dpi,Rep2

description: Library name: F029487_B1-3

value: Naive


title: Microglia,Naive,0dpi,Rep2

description: Library name: F029488_B1-3


title: P7_DG_Setdb1_Flag_Igg

city: Shanghai

first: Yunli

last: Xie

state: Shanghai

address: 131 Dong'an Road, Shanghai

department: Institutes of Brain Science

institute: Fudan University

data_processing:
Raw data were aligned to the GRCm38/mm10 genome by Bowtie2 v2.2.5 using parameters: -end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Bam files were converted to paired end BED files using BEDTools v2.30.0 bamtobed with the -bedpe flag, then the read pairs that are on the same chromosome and fragment length less than 1000bp were selected to generate a new BED file, and finally we converted bed file to a bedgraph file using genomecov from BEDTools.
Peaks were called using SEACR v.1.3.0 with the parameters: -0.01 -norm -stringent.
Normalized bigwig files were generated by BamCoverage from Deeptools v3.5.1, which were then visualized on IGV v2.16.2.
Assembly: mm10
Supplementary files format and content: dg_setdb1_merge12_RPKM.bw
Supplementary files format and content: p10_dg_subcell_metadata.csv
Supplementary files format and content: p7_RNA_ko_merge_RPKM.bw
Supplementary files format and content: p7_RNA_wt_merge_RPKM.bw
Supplementary files format and content: p7_dg_ko_atac_RPKM.bw
Supplementary files format and content: p7_dg_wt_atac_RPKM.bw
Library strategy: CUT&Tag

extract_protocol:
In this investigation, Setdb1 binding sites were elucidated employing the Cleavage Under Targets and Tagmentation (CUT&Tag) methodology, adhering to the protocols outlined by the Henikoff laboratory. The analysis encompassed two biological replicates each for both the wild-type (WT) cerebral cortices and those with conditional knockouts (cKO) of Setdb1.
We employed the Mouse anti-Flag antibody (Smart-Lifesciences, Cat#SLAB0101) for specific targeting. The Tn5-tagmented DNA fragments were then amplified using the 2x CAM Mix, a uniquely barcoded i5 primer, and a uniquely barcoded i7 primer, undergoing 12 amplification cycles. Libraries were quantified on a Qubit 4 fluorometer (Thermo Fisher Scientific, Q33226). We performed size-selection on the libraries, isolating DNA fragments exceeding 300 base pairs using VAHTS DNA Clean Beads (Vazyme, Cat#N411). Finally, the pooled libraries were sequenced in a paired-end mode using the Illumina NovaSeq 6000 platform.

value: brain

value: mouse brain cells

value: wild type

value: postnatal day 7


title: ST-rep3

data_processing:
CUT&Tag: Raw fastq files were subjected to quality control using FastQC (v0.11.9) and Trim Galore (v0.6.0).
CUT&Tag: Reads were aligned with bowtie2 (v2.3.5.1) and samtools (v1.3.1, options: -Sb -q 20).
CUT&Tag: BAM files were deduplicated with picard (v2.25.7) MarkDuplicates
CUT&Tag: MACS2 (v2.2.7.1) subcommand callpeak was used for peak calling
Assembly: hg19, mm10, Sscrofa11
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Living cells with a 10 minutes’ incubation at room temperature
Cleavage Under Targets and Tagmentation (CUT&Tag) have been described in detail (KayaOkur et al. 2019; Wang et al. 2019) with some modifications. Briefly, cells were incubated with activated concanavalin A-coated magnetic beads (Smart-Lifesciences). The bead-bound cells were permeabilized and incubated first with BG4 primary antibody, followed by anti-Flag M2 antibody (Sigma-Aldrich), and lastly with rabbit antimouse IgG antibody. Diluted pA-Tn5 adapter complex was then added followed by the tagmentation reaction. Extracted DNA fragments were used for library preparation. More details of this experiment and data analysis are described in following.

tag: chip antibody


title: NOVA29_Blood_Phase_2_SD1

value: Vaccinated


title: Macrophages,TBI,7dpi,Rep3

description: Library name: F029533_A5-7

value: Whole Brain

value: Monocyte-derived Macrophages

tag: time


title: P7_DG_Setdb1_Flag_rep2


title: NOVA18_Blood_Phase_2_SD1


title: ST-rep2

value: ST


title: Macrophages,TBI,7dpi,Rep2

description: Library name: F029532_A5-7

value: TBI

tag: mouse id


title: NOVA15_Blood_Phase_2_SD1


title: NOVA23_Blood_Phase_2_SD1


title: NOVA51_Blood_Phase_2_SD3

value: Unvaccinated


title: P7_DG_ATAC_Setdb1_cKO_rep3

data_processing:
Bowtie2 v2.2.5 was used for alignment to the UCSC mm10 genome with parameters: -X 1000, -phred33. After removing duplicates, Samtools v1.7 was used to sort and index the alignment files. Normalized bigwig files were generated using BamCoverage from Deeptools v3.5.1, which were then visualized on IGV v2.16.2.
Assembly: mm10
Supplementary files format and content: dg_setdb1_merge12_RPKM.bw
Supplementary files format and content: p10_dg_subcell_metadata.csv
Supplementary files format and content: p7_RNA_ko_merge_RPKM.bw
Supplementary files format and content: p7_RNA_wt_merge_RPKM.bw
Supplementary files format and content: p7_dg_ko_atac_RPKM.bw
Supplementary files format and content: p7_dg_wt_atac_RPKM.bw

extract_protocol:
The acquisition of dentate gyrus cells refers to the cell preparation protocol for single-cell sequencing. Nuclei from 100,000 cells were obtained using nuclear extraction buffer [0.32 M sucrose, 10 mM tris-HCl (pH8.0), 0.1% NP-40, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM EDTA].
The library was constructed utilizing components from the TruePrep DNA Library Preparation Kit V2 for Illumina (Vazyme, Cat#TD501), adhering to the manufacturer's protocol with certain adjustments. The amplified library DNA underwent purification and size fractionation using SPRIselect Beads (Beckman Coulter, Cat#B23317). Final libraries were sequenced on NovaSeq6000 Illumina instrument.


title: NOVA42_Blood_Phase_2_SD1


title: Macrophages,TBI,7dpi,Rep1

description: Library name: F029489_A5-7

tag: library prep_date


title: NOVA08_Blood_Phase_2_SD1


title: NOVA24_Blood_Phase_2_SD1


title: PK15-rep2


title: PK15-rep1


title: P7_DG_ATAC_Setdb1_cKO_rep1


title: P7_DG_ATAC_Control_rep2


title: Macrophages,Naive,0dpi,Rep1

description: Library name: F029488_A5-7

tag: lysis plate_id


title: ST-rep1

value: Swine testicular cell line


title: Frail_13

city: Jakarta

first: Ariel

last: Pradipta

state: Jakarta

address: Jl. Salemba Raya No.6

department: Biochemistry and Molecular Biology

country: Indonesia

institute: Faculty of Medicine Universitas Indonesia

description:
Library name: F13
RRMS Adaptive Sampling Strategy

data_processing:
Basecalling was performed using the Dorado model, version 7.8.3, which is embedded in MinKNOW, version 25.03.9. The high-accuracy model was used, and reads with a quality score lower than 9 were filtered, along with base modifications for the detection of 5mC and 5hmC methylation.
Minimap2 2.28-r1209 was used for genome mapping with the GRCh38 build and the genome version GCA_000001405.15.
ModKit 0.4.3 was used to tabulate the bedMethyl pileup file.
Assembly: GRCh38
Supplementary files format and content: The BAM file includes the MM and ML methylation tags, which indicate the methylation sites and confidence.
Supplementary files format and content: The BED file contains bedMethyl tables that tabulate the number of base modifications in each sequencing read at every aligned reference genomic position.

source_name: PBMC

growth_protocol: no growth protocol

extract_protocol:
Approximately 2–3 million PBMCs were centrifuged to obtain a cell pellet, which was then processed for DNA extraction using the Monarch Genomic DNA Purification Kit (T3010, New England Biolabs), following the protocol for Cells, Blood, and Tissues. The eluted DNA was quantified using a Qubit 4 Fluorometer (Invitrogen), and its purity was assessed with a Nanophotometer N50 (Implen). DNA fragment size was evaluated using the TapeStation (4150 Agilent), targeting a fragment length of approximately 10–12 kb.
After shearing, 2,000 ng of DNA was used as the input for preparing the library with the Ligation Sequencing Kit V14 (SQK-LSK114, Oxford Nanopore Technologies), according to the Reduced Representation Methylation Sequencing (RRMS) protocol.

treatment_protocol: no treatment protocol

tag: age (y.o)

tag: cfs score

value: Female


title: Monocytes,TBI,7dpi,Rep3

description: Library name: F029489_A9-11

tag: tissue

value: Blood

value: Monocytes


title: NOVA68_Blood_Phase_2_SD1

description: Gene expression profiling of PBMC  from influenza infected humans

value: influenza

value: PBMC


title: P7_DG_Setdb1_Flag_rep1


title: P7_DG_ATAC_Control_rep1


title: Frail_12

description:
Library name: F12
RRMS Adaptive Sampling Strategy

tag: Sex


title: Microglia,TBI,7dpi,Rep3

description: Library name: F029533_A1-3

value: Microglia


title: Frail_5

description:
Library name: F5
RRMS Adaptive Sampling Strategy

value: Male


title: P7_DG_Setdb1_cKO_rep3

data_processing:
raw data were first trimmed using Trim Galore v.0.6.7 then mapped to the mm10 genome by HISAT2 v2.2.1 with default parameters.
The number of reads mapping to each gene were counted by featureCounts v2.0.1 with parameters: -a gencode.vM20.annotation.gtf. And transcripts per million (TPM) were calculated.
Assembly: mm10
Supplementary files format and content: dg_setdb1_merge12_RPKM.bw
Supplementary files format and content: p10_dg_subcell_metadata.csv
Supplementary files format and content: p7_RNA_ko_merge_RPKM.bw
Supplementary files format and content: p7_RNA_wt_merge_RPKM.bw
Supplementary files format and content: p7_dg_ko_atac_RPKM.bw
Supplementary files format and content: p7_dg_wt_atac_RPKM.bw

extract_protocol:
Total RNA was isolated from Dentate gyrus at P7 using TRIzol reagent (ThermoScientific) according to the manufacturer’s instructions.
RNA-seq was performed at Genergy Biotech Co., Ltd. Shanghai, China.

value: brain

value: mouse brain cells


title: Macrophages,TBI,30dpi,Rep1

description: Library name: F029493_A5-7


title: P7_DG_ATAC_Setdb1_cKO_rep2

value: postnatal day 7


title: NOVA71_Blood_Phase_2_SD1

tag: disease state


title: Frail_1

description:
Library name: F1
RRMS Adaptive Sampling Strategy


title: NOVA69_Blood_Phase_2_SD1

tag: study group


title: P7_DG_Setdb1_cKO_rep2


title: Robust_12

description:
Library name: R12
RRMS Adaptive Sampling Strategy


title: NOVA47_Blood_Phase_2_SD1

tag: study date


title: Monocytes,TBI,7dpi,Rep2

description: Library name: F029495_A1-3


title: Monocytes,TBI,7dpi,Rep1

description: Library name: F029494_A1-3


title: Healthy Thymus3

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

country: Belgium

institute: Ugent

description: Library name: Thymus3

data_processing:
alignment by Dorado-integrated minimap2
Basecalled using the rna004_130bps_sup@v5.1.0 m6A_DRACH aware model.
Assembly: GRCh38
Supplementary files format and content: bedmethyl files summarizing m6A methylation information obtained using Nanoporetech modkit toolkit (https://github.com/nanoporetech/modkit)

source_name: Thymus

growth_protocol: The cells were not cultivated prior to the collection.

extract_protocol:
RNA was extracted from the samples by using the RNeasy Plus Micro Kit (Qiagen, 74034) according to the manufacturer’s instructions.
Direct RNA Sequencing Kit (SQK-RNA004) was used for library preparation with 1ug of total RNA as input, according to manufacturers instructions

value: Thymus

tag: cell line

value: Primary material

value: Thymocytes

tag: condition


title: NOVA27_Blood_Phase_2_SD1

value: Vaccinated


title: Microglia,TBI,30dpi,Rep1

description: Library name: F029493_A1-3

value: Whole Brain

tag: cell type

tag: treatment

value: TBI


title: P7_DG_Control_rep3

tag: genotype

value: wild type


title: NOVA73_Blood_Phase_2_SD1

value: Unvaccinated


title: NOVA19_Blood_Phase_2_SD1


title: NOVA09_Blood_Phase_2_SD1


title: Healthy Thymus2

description: Library name: Thymus2


title: Monocytes,TBI,30dpi,Rep2

description: Library name: F029492_A1-3

value: Blood


title: Microglia,TBI,7dpi,Rep2

description: Library name: F029532_A1-3


title: Healthy Thymus1

description: Library name: Thymus1


title: P7_DG_Control_rep2


title: NOVA65_Blood_Phase_2_SD1


title: NOVA66_Blood_Phase_2_SD1


title: P7_DG_Control_rep1


title: T-ALL Primary3

description: Library name: Primary3

value: T-ALL

value: T-ALL Primary


title: Monocytes,TBI,30dpi,Rep1

description: Library name: F029490_A1-3

value: Monocytes