title: Subject 1.20304, Visit 6

description: Library name: 1.20304.Visit.6


title: piR-1873-3

status: Public on Aug 13 2026

type: SRA

city: Qingdao

first: yajun

last: zhang

address: No. 16 Jiangsu Road, Shinan District

department: Department of Cardiac Ultrasound

country: China

institute: The Affiliated Hospital of Qingdao University

description:
Library name: piR-1873-3
cells in the piR-1873 mimic group were transfected with piR-1873 mimic to overexpress piR-1873.

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
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 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: tab-delimited text files include gene count for each Sample

molecule: total RNA

organism: Mus musculus

source_name: cell culture

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

tag: tissue

value: cell culture

tag: cell line

value: mouse atrial cardiomyocyte cell line

tag: treatment


title: Subject 1.20304, Visit 3

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

description: Library name: 1.20304.Visit.3

data_processing:
Sequencing data were aligned to a composite reference of GRCh38 with Ensemble annotation version 100 and SARS-CoV-2 reference assembly MN985325.1 using STAR v2.7.3a. Transcript abundance estimates were calculated by using the
STAR “quantMode GeneCounts” option using the algorithm of htseq-count.
Assembly: GRCh38-100, MN985325.1
Supplementary files format and content: Tab delimited text with counts for each sample in columns and transcript in rows.

organism: Homo sapiens

source_name: Whole blood

growth_protocol: Whole blood collected in Paxgene tubes. No growth

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific). RNA quality was assessed using a TapeStation 4200 and one microgram of total RNA was subjected to globin transcript depletion using the human GLOBINclear Kit (ThermoFisher Scientific).
Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent)

treatment_protocol: Whole blood collected 1, 2, 3 or 7 days after primary, secondary or tertiary vaccinations

value: Whole blood

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Primary

tag: infection status

value: Infected

tag: infection category

value: Prior

tag: study

value: AZ


title: piR-1873-2

description:
Library name: piR-1873-2
cells in the piR-1873 mimic group were transfected with piR-1873 mimic to overexpress piR-1873.


title: Subject 1.20304, Visit 2

description: Library name: 1.20304.Visit.2


title: piR-1873-1

description:
Library name: piR-1873-1
cells in the piR-1873 mimic group were transfected with piR-1873 mimic to overexpress piR-1873.


title: Subject 1.20304, Visit 1

description: Library name: 1.20304.Visit.1


title: CON-3

description:
Library name: CON-3
Cells in the CON group were transfected with negative control mimic


title: Subject 1.20224, Visit 8

description: Library name: 1.20224.Visit.8

value: Secondary

value: Uninfected

value: Healthy


title: CON-2

description:
Library name: CON-2
Cells in the CON group were transfected with negative control mimic


title: Subject 1.20414, Visit 1

description: Library name: 1.20414.Visit.1


title: Mtb, phoR::Tn, propionate, pH 7.0, Rep A

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

description: Library name: Prop_Tn_7A_S14_L001_R1_001.fastq.gz

data_processing:
After the sequencing runs, reads were demultiplexed and converted fastq format using Illumina bcl2fastq (v1.8.4) script.  The reads in the raw files were then subjected to trimming of low quality bases and removal of adapter sequences using Trimmomatic (v0.30) with a 4bp sliding window, cutting when the read quality dropped below 15, or read length was less than 36 bp.  Trimmed reads were aligned to the WT erdman genome using bowtie with the -S option to produce SAM files as output.
SAM files produced by bowtie were converted to BAM files and coverage depth was calculated using SAM tools resulting in 98% coverage.  Aligned reads were then counted gene feature in WT erdman genome using the HTSeq software suite.  Data were normalized by estimating effective library sizes using robust regression within the DEseq package.  Statistical analysis and differential gene expression was performed in R studio by fitting a negative binomial model to each set of conditions and testing for differences utilizing the DESeq package.
Assembly: M. tuberculosis Erdman (ATCC 35801), GCA\_000350205.1
Supplementary files format and content: Processed files are presented as an .xlsx spreadsheet with calculated CPMs of each Rep presented.
Supplementary files format and content: Dataset_GEO.xlsx

organism: Mycobacterium tuberculosis

source_name: Bacterial Cell

growth_protocol: Mtb cultures were cultured for 3 days  in T-75 standing flasks in a 37C incubator (with 5% CO2).

extract_protocol:
RNA was extracted using the method Rohde, Abramovitch and Russell, Cell Host and Microbe, 2007. Briefly,  RNA was stabilized and isolated using a guanidine thiocyanate-based lysis buffer as previously described. Pelleted mycobacteria were lysed using 5 μg/ml lysozyme, hot Trizol, and physical disruption with silica beads in a BeadBeater. Total RNA was isolated by chloroform extraction followed by direct application to QIAGEN RNeasy column purification. Residual DNA contamination was removed using Turbo DNAfree DNase (Ambion).  RNA quality and integrity were examined using an Agilent Bioanalyzer prior to subjecting samples to rRNA depletion using the Epicentre Ribo-Zero depletion kit.
DNA libraries were constructed using the illumina true seq RNA library preparation kit omiting the polyA selection step.  After library quality control, samples were pooled and sequenced in one lane Illumina HiSeq 2500 Rapid Run flow (v1) in 50 bp, single end read format (SE50).

treatment_protocol: 8 conditions conditions, and three strains,WTERDMAN, phoR::Tn and phoT::Tn were examined with two biological replicates. The conditions examined include: 1)WT, 2mM propionate acidic, pH 7.0; 2) WT, 2mM propionate acidic, pH 5.7, 3) phoR::TN, 2mM propionate, pH 7.0, 4) phoR::TN, 2mM propionate, pH 5.7; 5) WT, 4 mM lacate,  pH7.0, 6) WT, 4 mM lactate, pH 5.7; 7) phoT::Tn 4 mM lactate, pH 7.0, 8) phoT::Tn, 4 mM lacate, pH 5.7.   Following, a 3 day incubation, total bacterial RNA was extracted.

tag: cell type

value: Bacterial Cell


title: CON-1

description:
Library name: CON-1
Cells in the CON group were transfected with negative control mimic


title: Subject 1.20224, Visit 7

description: Library name: 1.20224.Visit.7


title: CKD3

city: Hangzhou

first: Linnan

last: Bai

address: 3 East Qingchun Road

institute: Zhejiang University School of Medicine Sir Run Run Shaw Hospital

description:
Library name: Sample 6
CKD3

data_processing:
Illumina HiSeq X Ten
Raw data (raw reads) were processed using Trimmomatic . The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
Gene-level raw read counts were generated using HTSeq-count based on the reference gene annotation. The processed data file contains the raw count matrix for all genes across all samples. Differential expression analysis was performed using the DESeq R package; size factors were estimated with estimateSizeFactors, and differential expression was tested using nbinomTest.
Assembly: mm9
Supplementary files format and content: RNAseq_raw_counts_matrix.txt: Tab-delimited text file containing gene-level raw read counts for all samples. Rows represent genes, columns represent samples, and the first column contains gene identifiers.

source_name: Heart

extract_protocol:
Total RNA was extracted using the mirVana microRNA isolation kit (Ambion, Austin, TX, USA), and RNA integrity was evaluated by the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

tag: genotype

value: wild type

tag: batch


title: Subject 1.20224, Visit 6

description: Library name: 1.20224.Visit.6


title: Subject 1.20224, Visit 2

description: Library name: 1.20224.Visit.2


title: CKD2

description:
Library name: Sample 5
CKD2


title: Subject 1.20224, Visit 1

description: Library name: 1.20224.Visit.1


title: CKD1

description:
Library name: Sample 4
CKD1


title: Subject 1.20201, Visit 8

description: Library name: 1.20201.Visit.8


title: Sham3

description:
Library name: Sample 3
Sham3


title: Subject 1.20201, Visit 7

description: Library name: 1.20201.Visit.7


title: Sham2

description:
Library name: Sample 2
Sham2


title: Sham1

description:
Library name: Sample 1
Sham1


title: Subject 1.20201, Visit 6

description: Library name: 1.20201.Visit.6


title: Baclofen-treated DNP whole brain replicate 3

city: Dongguan

first: Kaisheng

last: Ye

address: No. 111 Humen Avenue, Humen Town, Dongguan City

institute: Binhaiwan Central Hospital of Dongguan

description: Library name: GA-3

data_processing:
Raw paired-end sequencing reads were assessed for sequencing quality using FastQC v0.11.9.
Adapter sequences were removed using fastp. Bases with quality scores below 20 at the 3-prime end were trimmed, reads shorter than 25 bp were discarded, and reads matching ribosomal RNA were removed computationally.
Reads matching ribosomal RNA reference sequences were identified using Bowtie2 v2.3.4.1 and removed. The remaining clean paired-end reads were aligned to the Mus musculus reference genome GRCm38 using HISAT2 v2.1.0.
Gene and transcript expression was quantified using StringTie v1.3.3b. Gene-level read counts and FPKM values were generated for each sample.
Gene-level raw count and FPKM matrices were compiled across all nine samples for downstream transcriptomic analyses.
Assembly: Mus musculus reference genome GRCm38
Supplementary files format and content: Tab-delimited gene-by-sample matrix containing raw gene-level read counts for all nine RNA-seq samples. Rows represent genes and columns represent individual biological samples.
Supplementary files format and content: Tab-delimited gene-by-sample matrix containing gene-level FPKM expression values for all nine RNA-seq samples. Rows represent genes and columns represent individual biological samples.

molecule: polyA RNA

source_name: whole brain

growth_protocol: Specific pathogen-free male C57BL/6 mice, 7 weeks of age and weighing 20-22 g, were housed under controlled conditions at 23 ± 1 °C and 50% ± 10% relative humidity with a 12-h light/12-h dark cycle. Mice had ad libitum access to standard rodent chow and water and were acclimatized for 3-5 days before experimentation.

extract_protocol:
After completion of behavioral testing, mice were deeply anesthetized and whole-brain tissues were rapidly collected on ice, frozen in liquid nitrogen, and stored at -80 °C. Total RNA was extracted from whole-brain tissues using RNAiso Plus according to the manufacturer's instructions. RNA concentration and purity were assessed before library preparation.
Poly(A)-enriched RNA was used for library construction. Non-strand-specific cDNA libraries were prepared according to the sequencing service provider's standard protocol and sequenced in paired-end 150-bp mode on an Illumina sequencing platform.

treatment_protocol: To establish diabetic neuropathic pain, mice were fed a 60% high-fat diet for 4 weeks and then administered streptozotocin at 50 mg/kg by intraperitoneal injection once daily for 7 consecutive days after a 6-h fast. Diabetic status was confirmed by fasting blood glucose levels of at least 16.7 mmol/L. Neuropathic hypersensitivity was assessed 4 weeks after streptozotocin administration. Mice in the baclofen-treated group received baclofen at 8 mg/kg by intraperitoneal injection once daily for 7 days. Control and untreated diabetic neuropathic pain mice received an equivalent volume of saline vehicle.

value: whole brain

tag: strain

tag: Sex

value: male

value: A 60% high-fat diet for 4 weeks followed by streptozotocin at 50 mg/kg by intraperitoneal injection once daily for 7 consecutive days; baclofen at 8 mg/kg by intraperitoneal injection once daily for 7 days after confirmation of diabetic neuropathic pain.


title: Subject 1.20201, Visit 2

description: Library name: 1.20201.Visit.2


title: Subject 1.20201, Visit 1

description: Library name: 1.20201.Visit.1


title: Baclofen-treated DNP whole brain replicate 1

description: Library name: GA-1


title: Subject 1.20201, Visit 3

description: Library name: 1.20201.Visit.3


title: Subject 1.20158, Visit 8

description: Library name: 1.20158.Visit.8


title: Baclofen-treated DNP whole brain replicate 2

description: Library name: GA-2


title: Diabetic neuropathic pain whole brain replicate 3

description: Library name: DM1-3

value: A 60% high-fat diet for 4 weeks followed by streptozotocin at 50 mg/kg by intraperitoneal injection once daily for 7 consecutive days; saline vehicle after confirmation of diabetic neuropathic pain.


title: Subject 1.20158, Visit 7

description: Library name: 1.20158.Visit.7


title: Diabetic neuropathic pain whole brain replicate 2

description: Library name: DM1-2


title: Subject 1.20158, Visit 6

description: Library name: 1.20158.Visit.6


title: Diabetic neuropathic pain whole brain replicate 1

description: Library name: DM1-1


title: Subject 1.20158, Visit 3

description: Library name: 1.20158.Visit.3


title: Control whole brain replicate 2

description: Library name: con-2

value: Saline vehicle.


title: Subject 1.20158, Visit 2

description: Library name: 1.20158.Visit.2


title: Control whole brain replicate 3

description: Library name: con-3


title: Control whole brain replicate 1

description: Library name: con-1


title: Subject 1.20158, Visit 1

description: Library name: 1.20158.Visit.1


title: Subject 1.20138, Visit 7

description: Library name: 1.20138.Visit.7


title: Subject 1.20138, Visit 6

description: Library name: 1.20138.Visit.6


title: E12.5 TRIM28nCKO heart_H3K9me3 cuttag

city: Shanghai

first: Yuze

last: Wang

address: Shanghai Minhang District Dongchuan Road No. 800

institute: Shanghai Jiao Tong University

description: Library name: E12.5 TRIM28nCKO heart_H3K9me3 cuttag

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NovaSeq output. Paired-end reads were aligned to the mouse reference genome (GRCm38/mm10) using Bowtie2 v2.5.4 with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Mapped reads were converted to BAM format, sorted and indexed using SAMtools v1.20. BigWig tracks for visualization were generated using deepTools bamCoverage with a bin size of 50 bp and read extension. For peak calling, mapped reads were converted to BED format and filtered to retain fragments with both mates mapped to the same chromosome and insert size < 1,000 bp using bedtools. Filtered fragments were normalized by a scale factor (10⁴ / total fragments) to generate BedGraph files via bedtools genomecov. Significant peaks were identified using SEACR v1.3 in stringent mode with a threshold of 0.01.
Assembly: CRCm38/mm10
Supplementary files format and content: bigWig.narrowPeak(except for IgG sample)
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
formaldehyde-crosslinked primary cardiomyocyte suspensions were permeabilized in cell membrane permeabilization(CMPB) buffer and then incubated with pre-washed ConA magnetic beads at room temperature to conjugate the cardiomyocytes to the beads. Cardiomyocytes conjugated ConA beads were incubated with the primary antibody overnight at 4 °C and followed by a room-temperature incubation with secondary antibody. The intervening wash steps were carried out after each antibody incubation. The targeted tagging of genomic DNA was conducted at 37 °C for 1 hour after adding the ChiTag transposome to antibody-bound chromatin which was further terminated by an incubation with a stop buffer supplemented with Proteinase K at 55 °C for 2 h. The reversely crosslinked and tagged DNA were isolated via a magnetic bead-based purification
CUT&Tag libraries were prepared using the NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (Novoprotein, N259-YH01) .Libraries were amplified using 12–15 cycles on the thermocycler . Post amplification libraries were size selected at 200–500 bp in length using DNA purification beads provided in the kit. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: age

value: mixed embryonic cardiac cells

value: TRIM28 knockdown

tag: cut&tag antibody


title: Subject 1.20138, Visit 3

description: Library name: 1.20138.Visit.3

tag: tissue

value: Whole blood

value: Primary


title: E10.5 WT heart_TRIM28 cuttag

description: Library name: E10.5 WT heart_TRIM28 cuttag

value: WT


title: E12.5 WT heart_H3K9me3 cuttag

description: Library name: E12.5 WT heart_H3K9me3 cuttag


title: Subject 1.20138, Visit 2

description: Library name: 1.20138.Visit.2

value: AZ


title: E12.5 Hey2nCKO heart_TRIM28 cuttag

description: Library name: E12.5 Hey2nCKO heart_TRIM28 cuttag

value: Hey2 knockdown


title: Subject 1.20138, Visit 1

description: Library name: 1.20138.Visit.1

value: Uninfected


title: E12.5 WT heart_TRIM28 cuttag

description: Library name: E12.5 WT heart_TRIM28 cuttag


title: Subject 1.20111, Visit 8

description: Library name: 1.20111.Visit.8

value: Secondary

value: Infected

value: Prior


title: E12.5 WT heart_Hey2 cuttag

description: Library name: E12.5 WT heart_Hey2 cuttag

value: Heart


title: E12.5 WT heart_IGg cuttag

description: Library name: E12.5 WT heart_IGg cuttag

value: IGg


title: Subject 1.20111, Visit 7

description: Library name: 1.20111.Visit.7


title: Subject 1.20111, Visit 6

description: Library name: 1.20111.Visit.6


title: Adult wild-type mouse lung cells

city: Phoenix

first: Ying-Wei

last: Lan

address: 475 N. 5th Street

department: Child Health

institute: The University of Arizona College of Medicine-Phoenix

description:
Library name: WT_Lung
Filtered single-cell gene expression matrix from adult wild-type mouse lung cells.

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using Cell Ranger count v7.0.1 (10x Genomics) with a custom Mus musculus reference based on the mm10 (GRCm38) genome assembly. Intronic reads were included in the gene expression count matrix.Reads were aligned to the mm10 (GRCm38) mouse genome, and filtered gene-by-cell UMI count matrices were generated using Cell Ranger. Cells with at least 400 UMIs, at least 200 detected genes, log10GenesPerUMI greater than 0.8, and less than 20% mitochondrial transcript content were retained. Data were normalized using SCTransform and analyzed using Seurat v4.4.0. Dimensionality reduction was performed using PCA and UMAP, followed by shared nearest-neighbor clustering. KIT-positive endothelial cells were stratified into Foxf1-positive capEPCs and Foxf1-negative endothelial cells. Differentially expressed genes were identified using FindAllMarkers.
Assembly: GRCm38/mm10
Supplementary files format and content: Filtered gene-by-cell UMI count matrix in 10x Genomics Matrix Exchange (MEX) format, including cell barcodes, gene features, and a sparse count matrix.

source_name: lung

extract_protocol:
Mouse lungs were harvested, mechanically minced, and enzymatically digested to generate single-cell suspensions. Cells were filtered to remove tissue debris, and red blood cells were lysed. Live lung cells were isolated by FACS and processed immediately for single-cell RNA sequencing.
Single-cell gene expression libraries were generated using the Chromium Next GEM Single Cell 3′ Gene Expression v3 kit (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end sequencing.

value: lung

tag: cell line

value: lung cells

value: wild type

tag: treatment

value: untreated


title: Subject 1.20111, Visit 3

description: Library name: 1.20111.Visit.3

tag: subject

tag: visit


title: labyrinth, WT_E16.5_6

city: Leuven

first: Katrien

last: De Clercq

address: Herestraat 49, box 611

country: Belgium

institute: KU Leuven

description: Library name: S44

data_processing:
Reads were aligned against the mouse GENCODE gene set release M27 (tissues) or M28 (Cells)  using the STAR aligner (v2.7.10b) and gene and isoform expression levels were estimated using the RSEM (v1.3.1) software package (tissues) or Salmon (v1.10.3) package (cells)
Assembly: GENCODE M27 (GRCm39) (tissues) or GENCODE M28 (GRCm39) (cells)
Supplementary files format and content: Sxxx.genes.results: RSEM 1.3.1 output file; tab-delimited expression estimates (expected count, TPM, FPKM)
Supplementary files format and content: Sxxx.quant.sf: SALMON 1.10.3 quantification output file; tab-delimited expression estimates (TPM, number of reads)

source_name: placenta

extract_protocol:
Cells: RNeasy mini kit, Tissues: TriPure Isolation Reagent
cells: Illumina Stranded mRNA prep; Tissues: Illumina Trueq Stranded mRNA prep

value: placenta

tag: group

value: labyrinth


title: labyrinth, WT_E16.5_5

description: Library name: S43


title: labyrinth, WT_E16.5_4

description: Library name: S42


title: Subject 1.20101, Visit 8

description: Library name: 1.20101.Visit.8

value: Whole blood

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Healthy


title: labyrinth, Trpv2 KO_E16.5_6

description: Library name: S41

value: KO


title: labyrinth, Trpv2 KO_E16.5_5

description: Library name: S40


title: Subject 1.20101, Visit 7

description: Library name: 1.20101.Visit.7

tag: infection status

tag: infection category

tag: study

value: AZ


title: Subject 1.20101, Visit 6

description: Library name: 1.20101.Visit.6


title: labyrinth, Trpv2 KO_E16.5_4

description: Library name: S39

tag: genotype


title: Subject 1.20111, Visit 1

description: Library name: 1.20111.Visit.1

value: Primary


title: Subject 1.20101, Visit 3

description: Library name: 1.20101.Visit.3

value: Uninfected


title: Subject 1.20384, Visit 8

description: Library name: 1.20384.Visit.8

value: Secondary


title: Subject 1.20384, Visit 7

description: Library name: 1.20384.Visit.7


title: labyrinth, WT_E16.5_3

description: Library name: S38

value: WT


title: labyrinth, WT_E16.5_2

description: Library name: S37


title: Subject 1.20101, Visit 2

description: Library name: 1.20101.Visit.2


title: Subject 1.20101, Visit 1

description: Library name: 1.20101.Visit.1


title: labyrinth, WT_E16.5_1

description: Library name: S36


title: Subject 1.20061, Visit 8

description: Library name: 1.20061.Visit.8

value: Infected

value: Prior


title: labyrinth, Trpv2 KO_E16.5_3

description: Library name: S35


title: Subject 1.20111, Visit 2

description: Library name: 1.20111.Visit.2


title: labyrinth, Trpv2 KO_E16.5_1

description: Library name: S33


title: Subject 1.20061, Visit 7

description: Library name: 1.20061.Visit.7


title: labyrinth, Trpv2 KO_E16.5_2

description: Library name: S34


title: Subject 1.20061, Visit 6

description: Library name: 1.20061.Visit.6


title: labyrinth, WT_E14.5_6

description: Library name: S32


title: Subject 1.20061, Visit 1

description: Library name: 1.20061.Visit.1


title: Subject 1.20061, Visit 2

description: Library name: 1.20061.Visit.2


title: labyrinth, WT_E14.5_5

description: Library name: S31


title: Subject 1.20054, Visit 8

description: Library name: 1.20054.Visit.8


title: labyrinth, WT_E14.5_4

description: Library name: S30


title: Subject 1.20054, Visit 7

description: Library name: 1.20054.Visit.7


title: labyrinth, Trpv2 KO_E14.5_5

description: Library name: S28


title: Subject 1.20054, Visit 6

description: Library name: 1.20054.Visit.6


title: labyrinth, Trpv2 KO_E14.5_4

description: Library name: S27


title: labyrinth, Trpv2 KO_E14.5_6

description: Library name: S29


title: labyrinth, WT_E14.5_3

description: Library name: S26


title: Subject 1.20054, Visit 2

description: Library name: 1.20054.Visit.2


title: Subject 1.20054, Visit 1

description: Library name: 1.20054.Visit.1


title: Subject 1.20025, Visit 8

description: Library name: 1.20025.Visit.8


title: labyrinth, WT_E14.5_2

description: Library name: S25


title: labyrinth, WT_E14.5_1

description: Library name: S24


title: labyrinth, Trpv2 KO_E14.5_3

description: Library name: S23


title: Subject 1.20025, Visit 7

description: Library name: 1.20025.Visit.7


title: labyrinth, Trpv2 KO_E14.5_2

description: Library name: S22


title: Subject 1.20054, Visit 3

description: Library name: 1.20054.Visit.3


title: Subject 1.20025, Visit 6

description: Library name: 1.20025.Visit.6


title: Subject 1.20025, Visit 3

description: Library name: 1.20025.Visit.3


title: labyrinth, Trpv2 KO_E14.5_1

description: Library name: S21


title: Subject 1.20025, Visit 1

description: Library name: 1.20025.Visit.1


title: Spleen Dox

city: Omaha

first: Venkatasai Rahul

last: Dogiparthi

state: NE

address: 985805 Nebraska Medical Center

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

description:
Library name: Sample 4
Seq-well

data_processing:
The demultiplexing, barcoded processing, alignment and digital gene expression extracting were made using the DropSeq pipeline (v2.0.0) (Macosko., et al. Cell (2015). https://github.com/broadinstitute/Drop-seq/blob/v2.4.0/doc/Drop-seq_Alignment_Cookbook.pdf)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values matrix files for each sample after doing quality control

source_name: Spleen

extract_protocol:
Leukemia cells were enriched using the MagniSort Mouse Hematopoietic Lineage Depletion kit (Invitrogen) then single cell RNA sequencing (scRNA-Seq) was performed using the Seq-well, nanowell-based high throughput platform
Library was performed according to the Seq-well protocol from Gierahn, et al. (2017, Nat Method). Briefly, beads binding with cells were removed and resuspended with reverse transcription master mix to make single strand cDNA. Then the samples were treated with Exonuclease I. Following second strand synthesis using dN-SMRT oligo, a PCR with KAPA HiFi Hotstart mix was used to do the Whole Transcriptome Amplification (WTA). After purification with SPRI beads and pooling,  quality was checked to be within 0.7-2kbps by BioAnalyzer. Following that cDNA Tagmentation was done by Nextera XT kit. And the library was constructed by adding paired-end adapter of P5 and N7 sequences and a sample index were added. Further, each sample was purified with SPRI beads and quality checked to be within 400-800bp before sequencing.

treatment_protocol: Mice were treated with control (5% sucrose) and Doxycycline (3ug/ml) for 7 days. After sacrifice, the spleen and bone marrow was harvested.

value: Spleen

value: Primary cells

tag: cell type

value: Leukemia

value: Dox


title: Subject 1.30113, Visit 8

description: Library name: 1.30113.Visit.8


title: Subject 1.20001, Visit 1

description: Library name: 1.20001.Visit.1

value: After


title: Spleen Control

description:
Library name: Sample 3
Seq-well

value: Control


title: Bone Marrow Dox

description:
Library name: Sample 2
Seq-well

source_name: Bone Marrow

value: Bone Marrow


title: Subject 1.30113, Visit 6

description: Library name: 1.30113.Visit.6

value: Whole blood


title: Bone Marrow Control

description:
Library name: Sample 1
Seq-well


title: Subject 1.30113, Visit 3

description: Library name: 1.30113.Visit.3

value: Healthy


title: SS_KO

city: Los Angeles

first: Jina

last: Kim

address: 8700 Beverly Blvd

institute: cedars-sinai medical center

description: Library name: Sample 4

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Rnager software(v2.1.1)
Assembly: GRCm38
Supplementary files format and content: Tab seperated values and matrix files

source_name: gWAT (perigonadal white adipose tissue)

extract_protocol:
The cell suspensions were prepared from macrophages sorted from the perigonadal white adipose tissue (gWAT). Cells were counted, assessed for viability, and diluted to the recommended concentration for the 10x Genomics Chromium Single Cell 3′ workflow. Only samples with high viability were used for library preparation.
Illumina NovaSeq 6000

value: gWAT (perigonadal white adipose tissue)

value: total macrophages (live CD45+Lin-CD11b+CD64+)

value: Macrophages

value: CKO

value: Normal diet


title: Subject 1.30113, Visit 2

description: Library name: 1.30113.Visit.2

value: Primary

value: Uninfected

value: AZ


title: Subject 1.30113, Visit 1

description: Library name: 1.30113.Visit.1


title: HFD_KO

description: Library name: Sample 2

value: High fat diet


title: SS_WT

description: Library name: Sample 3

value: WT


title: Subject 1.301, Visit 8

description: Library name: 1.30100.Visit.8

value: Secondary


title: Subject 1.301, Visit 7

description: Library name: 1.30100.Visit.7


title: HFD_WT

description: Library name: Sample 1


title: Subject 1.301, Visit 6

description: Library name: 1.30100.Visit.6


title: 7059_adipo_S4_R1

description: Library name: Sample 4

data_processing:
Raw sequencing data quality was assessed with FastQC
Clean reads were aligned to the mouse reference genome (GRCm38) using STAR aligner (v2.7.5c).
Normalization was performed using the TMM method, followed by log2 transformation.
Assembly: GRCm38.p6.genome.fa / vM22 annotation
Supplementary files format and content: log2_normalised_counts,csv format

extract_protocol:
Total RNA was isolated from gWAT adipocytes using TRIzol (Invitrogen, Cat# 15596026) and purified using a RNeasy Micro Kit (Qiagen, Cat# 74104).
Illumina NovaSeq 6000

value: total adipocytes

value: adipocytes


title: 7058_adipo_S3_R1

description: Library name: Sample 3


title: 7056_adipo_S2_R1

description: Library name: Sample 2


title: 7055_adipo_S1_R1

description: Library name: Sample 1


title: Subject 1.301, Visit 3

description: Library name: 1.30100.Visit.3


title: Subject 1.301, Visit 2

description: Library name: 1.30100.Visit.2


title: Subject 1.301, Visit 1

description: Library name: 1.30100.Visit.1


title: Subject 1.20466, Visit 8

description: Library name: 1.20466.Visit.8


title: ED

city: Houston

first: Junjun

last: Zheng

state: TX

address: 6670 Bertner Ave, Houston, TX 77030

department: Houston Methodist Neal Cancer Center

institute: Houston Methodist Research Institute

description:
Library name: FX_69500
10x Genomic

data_processing:
The FASTQ data were processed using CellRanger (version 7.1.0)
Assembly: Mouse mm10
Supplementary files format and content: Raw_feature_bc_matrix from Cell Ranger

extract_protocol:
Mice received a sublethal 550 cGy (RS 2000) irradiaion at the Comparative Medicine of Houston Methodist Hospital. This dose of irradiation is sufficient to induce myeloablation and evident damage to the bone marrow vasculature. Pooled bone marrow cells (n=3-4/genotype; female and male mixed) were collected from 2 tibias and 2 femurs on day 11-12 after irradiation.
The scRNA-seq libraries were generated by Chromium Next-GEM Single Cell 3' v3.1 kit (PN-1000263, 10x Genomics, Pleasanton, CA) according to the manufacturer's protocol. Pre-made libraries were sequenced on a Novaseq 6000 (Illumina) instrument to obtain a minimum of 30,000 paired-end reads per cell.

value: ED; Endothelial-specific DLL4 knockout


title: Ctrl

description:
Library name: FX_69499
10x Genomic

value: Bone Marrow

value: Ctrl


title: Subject 1.20466, Visit 7

description: Library name: 1.20466.Visit.7

value: Whole blood

value: Healthy


title: T3M4 cells, sgMETTL13, replicate 3

city: Stanford

first: Shuo

last: Liu

address: 327 Campus Drive

department: Department of Biology

description:
Library name: Sample 6
Column name in differential_expression_results.csv contains: KD

data_processing:
Sequence reads were trimmed for reads of low quality, reads with adaptor sequences and reads with high levels of N base using BGI's internal software SOAPnuke (v1.5.2, parameters: -l 15 -q 0.2 -n 0.01)
Clean reads were aligned to the Homo sapiens (human) genome hg38 using HISAT2 (v2.0.4, Parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000).
Clean reads were mapped to the reference genes using Bowtie2 (v2.2.5, Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no- mixed--no-discordant -p1-k200).
Gene expression was standardized by FPKM (Fragments Per Kilobase per Million mapped fragments) using RSEM (v1.2.12) with default settings.
Differentially expression genes between KD and WT groups were identified using DEseq2 algorithms. DEseq2 is based on the negative binomial distribution, performed as described at Michael I, et al. (PMID: 25516281). P-values represent the statistical significance of differential expression, and Q-values represent FDR-adjusted p-values to control for multiple testing.
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: csv file includes differential mRNA expression analysis results comparing KD samples to WT samples

source_name: pancreatic tumor

growth_protocol: T3M4 (human pancreatic cancer, Riken RCB1021) cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco 11965118) supplemented with 10% fetal bovine serum (FBS, Gibco A3160502) and 100 U/mL penicillin/streptomycin.

extract_protocol:
RNA samples were extracted from cells using TRIzol reagent (Thermo 15596026).
The RNA-seq libraries were constructed by BGI (Hong Kong, China).

value: pancreatic tumor

value: pancreatic ductal adenocarcinoma cell

value: METTL13 knockdown


title: T3M4 cells, sgMETTL13, replicate 2

description:
Library name: Sample 5
Column name in differential_expression_results.csv contains: KD


title: Double_KO

description:
Library name: FX_67135
10x Genomic


title: T3M4 cells, sgMETTL13, replicate 1

description:
Library name: Sample 4
Column name in differential_expression_results.csv contains: KD


title: Subject 1.20466, Visit 6

description: Library name: 1.20466.Visit.6


title: T3M4 cells, sgControl, replicate 3

description:
Library name: Sample 3
Column name in differential_expression_results.csv contains: WT


title: Subject 1.30113, Visit 7

description: Library name: 1.30113.Visit.7


title: EP

description:
Library name: FX_67134
10x Genomic

value: EP; Endothelial-specific PERK knockout


title: T3M4 cells, sgControl, replicate 1

description:
Library name: Sample 1
Column name in differential_expression_results.csv contains: WT


title: Veh_RR_HGS3

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: Library name: Veh_RR_HGS3

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal are performed using FastP version 0.20.1 with the following paramters: ""--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
Processed/cleaned reads were then mapped to the mouse reference genome GRCm39 using STAR_2.7.6a with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx".
Genelevel read quantification was derived using the subread-2.0.1 package (featureCounts) with a M31 GTF annotation file and the following parameters: "-s 2 -t exon -g gene_name".
Differential expression analysis was performed using DESeq2-1.28.1 with a P-value threshold of 0.05 within R version 4.0.2 (https://www.R-project.org/).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
Supplementary files format and content: tab delimited deSeq2 counts files

source_name: peritoneal wall

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) per manufacturers recommendations. The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
The Illumina Stranded Total Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols.

value: peritoneal wall


title: T3M4 cells, sgControl, replicate 2

description:
Library name: Sample 2
Column name in differential_expression_results.csv contains: WT


title: Subject 1.20466, Visit 3

description: Library name: 1.20466.Visit.3

value: Primary

value: Uninfected


title: GAN-AAV-sil1rap 3-3-1

city: hefei

first: xiezong

last: hu

state: anhui province

address: shushanqu huangshanlu443

institute: university of science and technology of china

data_processing:
Raw sequencing reads were quality-filtered using fastp to remove adapters and low-quality reads.
Clean reads were aligned to the mouse reference genome.
Gene-level read counts were generated using HTSeq.
Gene expression levels were calculated as counts, TPM and FPKM values.
Differential expression analysis was performed between experimental groups, followed by pathway enrichment analysis.
Assembly: Mouse mm10
Supplementary files format and content: Excel file containing gene-level raw count matrix for all samples.
Supplementary files format and content: Excel files containing gene-level TPM and FPKM expression matrices for all samples.

source_name: liver

extract_protocol:
Total RNA was extracted from mouse liver tissues. RNA quality and quantity were assessed before library construction.
Poly(A)-enriched bulk mRNA-seq libraries were prepared from total RNA and sequenced on the DNBSEQ-T7 platform using paired-end 150 bp sequencing.

treatment_protocol: Mice were assigned to chow control, GAN diet-induced MASH plus control AAV vector, or GAN diet-induced MASH plus AAV-sIL1RAP groups. Liver tissues were collected at the experimental endpoint.

value: liver


title: Subject 1.20466, Visit 2

description: Library name: 1.20466.Visit.2

value: AZ


title: Veh_R_HGS3

description: Library name: Veh_R_HGS3


title: GAN-AAV-sil1rap 3-2


title: GAN-AAV-sil1rap 3-1


title: Subject 1.20466, Visit 1

description: Library name: 1.20466.Visit.1


title: GAN-AAV-vector 2-3


title: Veh_N_HGS3

description: Library name: Veh_N_HGS3


title: Subject 1.20395, Visit 8

description: Library name: 1.20395.Visit.8

value: Secondary


title: GAN-AAV-vector 2-2


title: GAN-AAV-vector 2-1


title: Veh_LL_HGS3

description: Library name: Veh_LL_HGS3


title: chon 1-3


title: Subject 1.20395, Visit 7

description: Library name: 1.20395.Visit.7


title: chon 1-2


title: UR241_2_R_HGS3

description: Library name: UR241_2_R_HGS3


title: chon 1-1


title: Subject 1.20395, Visit 6

description: Library name: 1.20395.Visit.6


title: Spatial transcriptomics of mus musculus: old male brain4 mouse 12

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

description: Library name: AGE_12_112_Brain4_SS200000953BR_F3

data_processing:
We stitched the image series from the Axio Imager KMAT brightfield microscope using the Zeiss ZEN software (v3.6) and cropped and rotated the resulting high-resolution TIFF files using Fiji. Individual sample images were color corrected where needed to match the other images.
In the next step, we ran Spaceranger (v2.1) with the demultiplexed FASTQ files and the corresponding TIFF images. In brief, Spaceranger aligns the reads to a reference genome (refdata-gex-mm10-2020-A), detects tissue under spots and the fiducial frame in the image, to create a spot x UMI count matrix. For the infection cohort, we additionally built a custom Spaceranger reference genome combining mouse (GRCm39) and Plasmodium berghei -ANKA genome (PBANKA01). For two samples the alignment of the fiducial frame was manually corrected after the automatic detection had failed initially. For the manual image QC of Visium samples we used the 10x Loupe browser tool (v6.5.0).
Based on the Spaceranger reports, we either excluded a sample completely from further analysis, or using the 10x Cloupe tool manually selected small spot regions to exclude from downstream analysis where necessary (e.g. removing corners with uneven permeabilization), and further applied criteria-based spot filtering on each sample, to eventually obtain a high-quality data set. To this end, we inspected the variable distributions for the number of UMIs, the number of read counts, mitochondrial content, as well as spot complexity (=log10(Number of features) / log10(Number of counts)) for each tissue separately, and applied the following filtering criteria on the filtered spot count matrix from Spaceranger after loading into Seurat objects: (Maximum percentage of mitochondrial read content; Minimum number of UMIs; Maximum number of UMIs; Minimum number of detected features; Maximum number of detected features; Minimum spot complexity) Brain: (35; 500; 70,000; 300; 10,000; 0.75), Bulb: (35; 500; 70,000; 300; 10,000; 0.75), Heart: (60; 1000; 25,000; 300; 5000; 0.75), Kidney: (30; 1000; 50,000; 300; 8000; 0.75) Liver: (15; 1000; 40,000; 500; 8000; 0.75), Lung: (10; 1000; 30,000; 300; 8000; 0.75) Spleen: (10; 500; 35,000; 300; 8000; 0.75).
We then rotated the images of the remaining samples to best match the desired orientation for each tissue. We then followed the default Seurat (v4.4) workflow to preprocess each sample by applying NormalizeData, FindVariableFeatures with variance stabilizing transformation for 2000 features, followed by SCTransform (v1), regressing out the percentage of mitochondrial reads and subsetting to 3000 variable features. Subsequently, we performed RunPCA on the SCT assay, FindNeighbors on up to 30 PCs, FindClusters with leiden clustering followed by RunUMAP with up to 30 dimensions. Using the cleaned list of Visium samples, we created one Seurat object for each tissue using the SCT-based integration workflow as follows: set the default assay to SCT, run SelectIntegrationFeatures with 3000 features, then PrepSCTIntegration, and FindIntegrationAnchors followed by IntegrateData, each with “SCT” set as normalization method and up to 30 dimensions. Next, we performed the standard dimension reduction workflow consisting of RunPCA, RunUMAP, FindNeighbors, and FindClusters again with up to 30 dimensions and fixed random seeds.
In case of the STOmics Stereo-seq samples, images were obtained and stitched with the Zeiss Moticam Pro 500i. Combined QC and primary analysis of sequencing and image data was performed using the STOmics analysis workflow (SAW) v1.0 to obtain quantification matrices for the mouse genome (GRCm38). The SAW pipeline was also used to accumulate DNB spot gene expression counts into the specific area and cell binnings.
For the STOmics Stereo-seq samples, we first converted the outputs of the Stereo-Seq Analysis Workflow (SAW) pipeline90 into Seurat objects for both bin200 (200x200 Stereo-seq spots) and cell bins. This is done by using the io.stereo_to_anndata function in the Stereopy package91 (v1.1.0), followed by applying the h5ad2rds.R script provided by BGI. Cell bins were obtained using image-based cell segmentation of the corresponding ssDNA-stained images. Filtering was performed using the following criteria: (Maximum percentage of mitochondrial read content; Minimum number of UMIs; Maximum number of UMIs; Minimum number of detected features; Maximum number of detected features; Minimum spot complexity) Brain (bin200): (35; 500; 100,000; 300; 10,000; 0.75), Brain (cell bin): (35; 100; 10,000; 100; 3,000; 0.75).
In line with the Visium 10x samples we applied a default Seurat preprocessing workflow for each sample. Using the cleaned list of STOmics Stereo-Seq samples, we performed the Harmony-based integration workflow as follows: set the default assay to SCT, run SelectIntegrationFeatures with 5000 features, merge the sample list into one Seurat sample, run RunPCA with 50 components, run RunHarmony on SCT assay and the PCA reduction using Sample_ID and Age as latent variables, run JoinLayers on the RNA assay. Then, we performed the sample dimension reduction workflow as in the Visium samples with up to 50 dimensions.
Assembly: GRCm39
Supplementary files format and content: tif image of H&E stained tissue slice on capture area in high resolution
Supplementary files format and content: jpg image of spaceranger aligned fiducials
Supplementary files format and content: jpg image of spaceranger detected tissue
Supplementary files format and content: h5 of filtered spot barcode-to-feature count matrix from spaceranger
Supplementary files format and content: h5 of raw spot barcode-to-feature count matrix from spaceranger
Supplementary files format and content: json of spaceranger image scale factors
Supplementary files format and content: csv of spatial enrichment results for gene features
Supplementary files format and content: png image of tissue slice on visium capture area in high resolution
Supplementary files format and content: png image of tissue slice on visium capture area in low resolution
Supplementary files format and content: csv of spaceranger spot tissue positions
Supplementary files format and content: tif image of adjacent (before or after) H&E stained tissue slice in high resolution
Supplementary files format and content: cellbin.gef cellbin feature expression matrix records the information of cells individually, including the centroid coordinate, boundary coordinates, expression of genes, and cell area.
Supplementary files format and content: gef feature expression matrix includes the whole information over a complete chip region. It only has bin1 expression counts.
Supplementary files format and content: gem gene expression matrix (GEM) stores gene spatial expression data. SAW generates multiple gene expression matrix files in the workflow, the basic format requires six columns with a header row that shows the column names. The six columns are gene ID, gene name, x coordinate, y coordinate, MID count and exon count. When it comes to cellbin GEM, the seventh column is for cell ID. The header of the expression matrix for the maximum area enclosing rectangle region has several annotation rows starting with "#" before the column rows.
Supplementary files format and content: tissue.gef Feature expression matrix under the tissue coverage region. It is also a visualization GEF that includes expression counts for bin1, 5, 10, 20, 50, 100, 150, 200.
Supplementary files format and content: tissue.gem gene expression matrix (GEM) stores gene spatial expression data for spots under tissue. SAW generates multiple gene expression matrix files in the workflow, the basic format requires six columns with a header row that shows the column names. The six columns are gene ID, gene name, x coordinate, y coordinate, MID count and exon count. When it comes to cellbin GEM, the seventh column is for cell ID. The header of the expression matrix for the maximum area enclosing rectangle region has several annotation rows starting with "#" before the column rows.
Library strategy: Spatial Transcriptomics

source_name: Brain

growth_protocol:
For the aging cohort, male C57BL/6JN mice were shipped from the National Institute on Aging colony (Charles River) to the Stanford ChEM-H animal facility, where they were housed at 12/12h light/dark cycle in cages of 2-3 mice. Water and food were provided ad libitum.
For the infection cohort, C57BL/6 mice were bred at the animal facility of the Bernhard Nocht Institute. P. berghei ANKA parasites were obtained from the blood of sporozoite-infected C57BL/6 mice provided by the Parasitology Section of the Bernhard Nocht Institute. Male C57BL/6 mice (6–8 weeks old) were infected i.p. with 1×10^5 parasitized red blood cells. Parasitemia was determined in Giemsa-stained blood smears from tail blood. Body weight was determined at different time points.

extract_protocol:
We followed the standard protocol for fresh frozen tissues (compare document CG000239 - Rev F) using the Visium Spatial Gene Expression (GEX) Slide & Reagent Kits with recommended reagents (10x Genomics, PN-1000193). In brief, after H&E staining and imaging (10x magnification, Axio Imager KMAT - ZEISS), tissues were permeabilized with the previously defined permeabilization time. After reverse transcription on the slide and denaturation, second strand synthesis is performed. For further processing, cDNA is released via denaturation. To determine cycle number for amplification the KAPA SYBER FAST qPCR Master Mix Kit (KAPA Biosystems) is used in a qPCR. All samples in this study were amplified using 14 – 19 PCR cycles. After bead purification using SPRIselect beads (Beckman Coulter, Product No. B233318), cDNA is quantified via 2100 Bioanalyzer using the Bioanalyzer High Sensitivity DNA kit (Agilent, cat.no.:5067-4626).
For each brain, five 10µm sections (Bregma: –1.7, -2.06, -2.7, -3.52 and -4.72) identical to the Visium cohort were collected and loaded onto the StereoSeq Chip T-Slide according to manufacturer´s protocol. In short, after fixation of the tissue using ice-cold methanol, cell nuclei were stained using the ssDNA Qubit dye (Thermo Fisher) and imaged in 10x resolution in FITC channel. Subsequently, brain tissue was permeabilized for 14 min at 37°C, releasing mRNAs from the cells onto the Chip T-Slide. Reverse transcription of mRNAs was conducted for 3 hours at 42°C generating cDNA with sequence barcodes indicating their unique location on the T-Slide. Afterwards, the tissue was removed using tissue removal buffer for 10 min at 55°C and cDNA was collected from the chip o/n at 55°C. CDNA was then purified, amplified and size distribution was checked using High Sensitivity DNA Bioanalyser Kit (Agilent).
The library construction was either performed manually or using the MGISP-100 liquid handling system according to the 10x Visium user guide. In short, the following steps were performed: fragmentation, end repair, A-tailing, double sided size selection, adaptor ligation, post ligation cleanup, sample index PCR, double sided size selection; followed by post library construction QC performed using the Bioanalyzer High Sensitivity DNA kit (Agilent, cat.no.:5067-4626) and KAPA Library Quantification Kit (Roche, KK4824). Libraries were pooled in an equimolar fashion with up to 15 samples in one library, pooling only samples originating from the same organ whenever possible. All libraries were sequenced using NovaSeq 6000 (Illumina).
Library Preparation was performed using Stereo-seq Library Preparation Kit (MGI) using 30ng of cDNA and 13 cycles of amplification following the manufacturer´s protocol. Final quality check of the size distribution of the library was performed using High Sensitivity DNA Bioanalyzer Kit.

treatment_protocol:
For the aging cohort, tissues from brain, heart, kidney, liver, lung and spleen were collected after anaesthetization with 2.5% v/v Avertin and transcardial perfusion with 20 mL cold PBS and flash frozen in isopentane cooled with liquid nitrogen, all between 10:15 AM- 12:00 PM on a single day. For brain samples, the right and left hemisphere were separated before freezing and stored separately. Samples were stored at -80°C until embedding in OCT. Samples were embedded for sectioning in precooled OCT on dry ice.
For the infection cohort, tissues samples were collected on consecutive days, from 9:30 AM (Ctrl.) and 10:30 AM (day 6 post-infection) until 12 PM. To prevent lung deflation, the tracheae were sutured, and the lungs were inflated with a 1:1 mixture of PBS and OCT. The small lung lobe was separated and frozen separately from the residual lung tissue. Brains were frozen without separating the hemispheres. All tissues were simultaneously frozen while embedded in OCT, in an isopentane bath cooled with liquid nitrogen and stored at -80°C.
Cryosectioning and section mounting were performed according to the manufacturer’s protocol, in a Leica cryostat (LEICA CM3050 S) set to -15°C with a slice thickness of 16 µm (except for the spleen of the infection cohort; 10 µm). For the aging cohort, five brain sections were mounted using visual landmarks and the Allen Mouse Brain Atlas, resulting in sections from bregma –1.7, -2.06, -2.7, -3.52 and -4.72. For the infection cohort, two brain sections were mounted, namely from bregma –2.06 and bregma 3.89 (Olfactory bulb). Sections were mounted on designated capture areas and stored at -80°C until further processing. After tissue mounting on the slide, an additional 10-15 sections were collected for RNA Quality assessment. All samples used in this study had a RIN value between 3.0 and 9.0.

value: Brain

tag: strain

tag: mouse id

tag: Sex

value: male

value: 112 weeks

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Aging

tag: technology

value: STOmics Stereo-seq

value: Wildtype

tag: disease

tag: disease stage


title: Subject 1.20395, Visit 3

description: Library name: 1.20395.Visit.3

tag: tissue

value: Whole blood

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

value: Healthy


title: UR241_2_N_HGS3

description: Library name: UR241_2_N_HGS3


title: Spatial transcriptomics of mus musculus: old male brain5 mouse 12

description: Library name: AGE_12_112_Brain5_SS200000953BR_F5

tag: strain

tag: mouse id

tag: Sex

tag: age

tag: genotype

tag: treatment


title: Spatial transcriptomics of mus musculus: old male brain3 mouse 12

description: Library name: AGE_12_112_Brain3_SS200000953BR_D6

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: UR241_2_LL_HGS_3

description: Library name: UR241_2_LL_HGS_3

tag: tissue


title: Spatial transcriptomics of mus musculus: old male brain2 mouse 12

description: Library name: AGE_12_112_Brain2_SS200000953BR_E6

tag: technology

tag: disease

tag: disease stage


title: Spatial transcriptomics of mus musculus: old male brain1 mouse 12

description: Library name: AGE_12_112_Brain1_SS200000953BR_E4


title: Subject 1.20395, Visit 2

description: Library name: 1.20395.Visit.2

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

tag: infection category

tag: study


title: UR241_2_L_HGS3

description: Library name: UR241_2_L_HGS3


title: Case_17, Chondrosarcoma

status: Public on Aug 14 2026

type: genomic

city: Bern

first: Jon

last: Brugger

address: Private Address

country: Switzerland

institute: Private

description: Sample ID: 206644410004_R04C01

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using mepylome version 0.10.0 and python 3.13
[processed value definition]  Beta values, calculated with mepylome using the Illumina method

label: Cy5 and Cy3

source_name: KRYO

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

value: Chondrosarcoma

tag: grade

value: high-grade

tag: origin

value: NL

value: MUT

value: Humerus

tag: age

tag: gender

tag: follow-up

tag: status

value: alive

value: KRYO


title: Thal_CON_F_18

city: Zürich

first: Juliet

last: Richetto

address: Winterthurerstrasse 260

institute: University of Zürich

description: Library name: 562_T

data_processing:
Reads were quality-checked using FastQC. Low-quality ends were clipped (5’: 4 bases; 3’: 4 bases) and sequencing adaptors removed using Fastp. Trimmed reads were mapped to the mouse genome (GRCm39 release M31-2023-01-30) and gene-level quantifications were calculated with Kallisto using the SUSHI data analysis framework
Assembly: GRCm39 release M31-2023-01-30
Supplementary files format and content: ene-level quantifications calculated with Kallisto

source_name: Brain - Thalamus

extract_protocol:
RNA was extracted with the Qiagen AllPrep DNA/RNA mini kit
RNA libraries for RNA-seq were prepared using thew Illumina Stranded mRNA Prep, Ligation following the manufacturers instructions.

tag: tissue

value: Brain - Thalamus

tag: treatment

value: Maternal housing control

tag: Sex

value: Female


title: 149311_Esophagus_Tumor

city: Boston

first: Liyang

last: Diao

state: MA

address: 201 Brookline Ave. Suite 1001

institute: Rome Therapeutics

description: Library name: 616901FT2

data_processing:
RNA-seq reads were aligned to the human reference genome using STAR aligner (Dobin et al., 2013) with default parameters.
Locus-specific LINE-1 expression was quantified using L1EM (McKerrow & Fenyö, 2020) restricted to intact LINE-1 loci from L1Base2.
Expression was normalized to transcripts per million (TPM) and summed across intact loci.
For comparative analyses, repeat-naïve quantifications were also generated by counting reads mapping to L1Hs loci without ORF filtering.
Expression values were merged with protein expression and immunopeptidomics results for downstream correlation analyses.
Assembly: Human genome reference GRCh38 (GENCODE/Ensembl annotation; L1Base2 intact LINE-1 loci set).
Supplementary files format and content: L1EM locus-level output files in comma-delimited format with normalized TPM values.

source_name: Esophagus

extract_protocol:
Frozen esophageal tumor, tumor-adjacent normal, and healthy control tissues were pulverized using a Covaris cryoPREP instrument. Total RNA was extracted using standard column-based RNA purification according to the manufacturer’s instructions. RNA integrity was assessed by Bioanalyzer prior to library preparation.
RNA-seq libraries were prepared from high-quality total RNA using a poly(A)-enrichment method followed by stranded mRNA library construction (Illumina TruSeq stranded mRNA kit or equivalent). Indexed libraries were quantified by qPCR and pooled for sequencing.

value: Esophagus

tag: disease state

value: Tumor


title: Subject 1.20395, Visit 1

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

description: Library name: 1.20395.Visit.1

data_processing:
Sequencing data were aligned to a composite reference of GRCh38 with Ensemble annotation version 100 and SARS-CoV-2 reference assembly MN985325.1 using STAR v2.7.3a. Transcript abundance estimates were calculated by using the
STAR “quantMode GeneCounts” option using the algorithm of htseq-count.
Assembly: GRCh38-100, MN985325.1
Supplementary files format and content: Tab delimited text with counts for each sample in columns and transcript in rows.

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific). RNA quality was assessed using a TapeStation 4200 and one microgram of total RNA was subjected to globin transcript depletion using the human GLOBINclear Kit (ThermoFisher Scientific).
Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent)

tag: subject

tag: visit

value: Primary

value: Uninfected

value: AZ


title: c-MAF ChIP-seq in BMDMs

first: Julia

last: Belk

state: California

address: 450 Serra Mall

description:
Library name: BMDMs_ChIP_CMAF
TruSeq ChIP Library Preparation Kit

data_processing:
Reads were trimmed with fastp
Reads were aligned to the mm10 genome with hisat2
Reads were deduplicated using picard
Peaks were called using macs2
Normalized bigwig files were generated using Rtracklayer
Assembly: mm10
Supplementary files format and content: Normalized genome coverage file (bigwig file)

source_name: Bone marrow

growth_protocol: C57BL/6J bone marrow cells were collected from femurs and tibias crushed in a mortar, filtered through a 70 μm strainer in 50 ml PBS and centrifuged 450 x g for 5 min. Cell pellets underwent RBC lysis, before being filtered and centrifuged as before. Bone marrow cells were differentiated in IMDM medium supplemented with 20% FBS, 10% L929-conditioned medium containing M-CSF, 2mM L-glutamine, 5mM 2-mercaptoethanol and antibiotics (penicillin G 100 U/ml and streptomycin sulfate 100 U/ml). After 6 days of culture, BMDMs were collected for downstream analyses.

extract_protocol:
Upon differentiation, 108 BMDMs were fixed with 1% formaldehyde, and nuclear fractions isolated and lysed. Fragmented chromatin was obtained using Covaris E220 focused-ultrasonicator and nuclear extracts were incubated overnight at 4°C with Dynabeads Protein G, previously coupled with 10µg of anti-C-MAF antibody (Abcam, ab77071). DNA fragments were immunoprecipitated in a 96-well magnet, and de-crosslinked overnight at 65°C. DNA was then purified with AMPure XP beads and quantified with Qubit 3.0.
ChIP DNA (5 ng) was used for library preparation with Illumina TruSeq ChIP Library Prep kit and sequenced on Illumina NovaSeq6000 (1x75bp reads) following manufacturer’s instruction.

value: Bone marrow

tag: cell type

value: BMDMs

tag: genotype

value: wild-type

tag: batch


title: Spatial transcriptomics of mus musculus: middle-aged male brain5 mouse 11

description: Library name: AGE_11_73_Brain5_SS200000953BR_F2

value: Brain

tag: strain

tag: mouse id

value: male

value: 73 weeks

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Aging

tag: technology

value: STOmics Stereo-seq

value: Wildtype

tag: disease

tag: disease stage


title: Spatial transcriptomics of mus musculus: middle-aged male brain4 mouse 11

description: Library name: AGE_11_73_Brain4_SS200000953BR_E2

tag: tissue

tag: Sex

tag: age

tag: treatment


title: Spatial transcriptomics of mus musculus: middle-aged male brain3 mouse 11

description: Library name: AGE_11_73_Brain3_SS200000953BR_E1

tag: genotype


title: Subject 1.20329, Visit 8

description: Library name: 1.20329.Visit.8

source_name: Whole blood

value: Whole blood

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Secondary

tag: infection status

tag: infection category

value: Healthy

tag: study


title: Spatial transcriptomics of mus musculus: middle-aged male brain2 mouse 11

description: Library name: AGE_11_73_Brain2_SS200000953BR_D3

tag: strain

tag: mouse id

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: Subject 1.20329, Visit 7

description: Library name: 1.20329.Visit.7

tag: tissue


title: Smart-seq BMDMs wild-type 3

description:
Library name: BMDMs_Ctrl_UT_C
Smart-seq2

data_processing:
Reads were aligned to the mm10 mouse reference genome using STAR aligner (v 2.5.3)
The featureCounts function from Rsubread package (v 1.24.2) was used to compute reads over RefSeq Mus musculus transcriptome (mm10), setting minMQS option to 255
Downstream analyses were performed in R (v 3.4.1) with edgeR R package (v. 3.20.7).
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing DEGs with RPKM for each sample as well as fold change and p value information

growth_protocol: C57BL/6J bone marrow cells were collected from femurs and tibias crushed in a mortar, filtered through a 70 μm strainer in 50 ml PBS and centrifuged 450 x g for 5 min. Cell pellets underwent RBC lysis, before being filtered and centrifuged as before. Ribonucleoprotein (RNP) complexes of Cas9-sgRNAs were obtained by incubating 5μg of Cas9 (Thermo Fisher) with 6 μg sgRNA targeting Maf and Mafb for 15 min at room temperature. Bone marrow cells (5x105, day 0 of differentiation) were resuspended in P3 solution (Primary Cell 4D-Nucleofector kit), mixed with RNP complex and electroporated using ED-113 program of the 4D-Nucleofector System (Lonza). Wild-type BMDMs used as controls were electroporated with scrambled gRNA + Cas9. Bone marrow cells were differentiated in IMDM medium supplemented with 20% FBS, 10% L929-conditioned medium containing M-CSF, 2mM L-glutamine, 5mM 2-mercaptoethanol and antibiotics (penicillin G 100 U/ml and streptomycin sulfate 100 U/ml). The culture medium was replaced 24 hours after nucleofection. After 6 days of culture, gene-edited BMDMs were collected for analysis.  Gene-editing efficiency was confirmed via Non-Homologous End Joining (NHEJ) at targeted sites and western blot.

extract_protocol:
Total RNA from wild-type and Maf/Mafb double knock-out BMDMs was purified using the ReliaPrep RNA Cell Miniprep System (Promega).
RNA-Seq libraries were generated using the Smart-seq2 method. Briefly, 5ng of RNA were retrotranscribed, cDNA was PCR-amplified for 15 cycles and purified with AMPure XP beads. After purification, the concentration was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system. Then, the tagmentation reaction was performed starting from 0.5 ng of cDNA for 30 min at 55°C followed by PCR amplification for 12 cycles. Libraries were then purified with AMPure XP beads, quantified using Qubit 3.0, assessed for fragment size distribution on an Agilent 4200 TapeStation system. Sequencing was performed on an Illumina NovaSeq6000 (1x75bp reads) following manufacturer’s instruction.

tag: cell type

tag: genotype

value: Wild-type

tag: batch


title: Spatial transcriptomics of mus musculus: middle-aged male brain1 mouse 11

description: Library name: AGE_11_73_Brain1_SS200000953BR_D1

tag: Sex

tag: age

tag: technology

tag: treatment

tag: disease

tag: disease stage


title: Spatial transcriptomics of mus musculus: young male brain5 mouse 10

description: Library name: AGE_10_17_Brain5_SS200000953BR_C1

tag: strain

tag: mouse id

value: 17 weeks


title: Smart-seq BMDMs wild-type 2

description:
Library name: BMDMs_Ctrl_UT_B
Smart-seq2


title: Spatial transcriptomics of mus musculus: young male brain4 mouse 10

description: Library name: AGE_10_17_Brain4_SS200000953BR_B6

tag: slide

tag: area


title: Subject 1.20329, Visit 6

description: Library name: 1.20329.Visit.6

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

tag: infection category

tag: study


title: Subject 1.20329, Visit 3

description: Library name: 1.20329.Visit.3

tag: tissue

value: Primary


title: Smart-seq BMDMs wild-type 1

description:
Library name: BMDMs_Ctrl_UT_A
Smart-seq2

tag: cell type

tag: genotype

tag: batch


title: Smart-seq BMDMs Maf/Mafb double knock-out 3

description:
Library name: BMDMs_MAFdKO_UT_C
Smart-seq2

value: Maf/Mafb double knock-out


title: Spatial transcriptomics of mus musculus: young male brain3 mouse 10

description: Library name: AGE_10_17_Brain3_SS200000953BR_B5

tag: Sex

tag: age

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology

tag: treatment

tag: disease

tag: disease stage


title: Spatial transcriptomics of mus musculus: young male brain1 mouse 10

description: Library name: AGE_10_17_Brain1_SS200000838BL_C2

tag: strain

tag: mouse id

tag: slide

tag: area


title: Spatial transcriptomics of mus musculus: young male brain2 mouse 10

description: Library name: AGE_10_17_Brain2_SS200000838BL_C3

tag: tissue


title: WT_TME419, IP-H3K4me3, RepC

city: Saint Louis

first: Kerrigan

last: Gilbert

state: MO

address: 975 N Warson Rd

institute: Donald Danforth Plant Science Center

description: Library name: WT_C_IP-H3K4me3

data_processing:
Raw sequencing data from the ChIP-seq experiment was trimmed using trim_galore.
Trimmed reads were aligned to the haplotype-resolved cassava genome of variety TME204 using bowtie2 and samtools was used to convert to bam format. Bam files for samples with more than 1 lane of sequencing data were merged to create a single bam file for all subsequent steps.
Picard MarkDuplicates was used to mark duplicates (version 3.1.1; http://broadinstitute.github.io/picard), and used as input to bamCoverage from deeptools (version 3.5.5; (Ramírez et al. 2016)) to generate bigwig files using RPKM as normalization and bin size of 50
Assembly: Manihot esculenta TME204 GCA_020916445.1
Supplementary files format and content: bigwig files of RPKM normalized read counts in 50 nt bins across the genome

organism: Manihot esculenta

source_name: leaf

growth_protocol: Plants were maintained in the glasshouse at 32ºC/27ºC (day/night) temperature at 70-95% relative humidity

extract_protocol:
A total of 5 grams of tissue was collected from the first two fully formed leaves of approximately 6 month old greenhouse grown cassava plants. Processed samples were divided into 4 separate aliquots: 100 ul for the input sample and the remaining 3.9 mL was split into 3 tubes for either bead only control, or 1 µl of anti-H3K4me3 (catalog number 04-745R, Millipore), or 1 µl of anti-H3 antibody (catalog number ab1791, abcam). After overnight incubation the DNA was precipitated and the pellet is washed with 70% ethanol, and resuspended in13 ul of Buffer EB (catalog number 19086, Qiagen).
Libraries were constructed with the NuGen Ultralow V2 kit and sequenced on an Illumina NovaSeq X plus sequencer.

value: leaf

tag: chip antibody

tag: genotype

value: wildtype TME419

tag: grna target_1

tag: grna target_2

tag: grna target_3


title: Subject 1.20329, Visit 2

institute: Stanford University

description: Library name: 1.20329.Visit.2

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

value: Uninfected

tag: infection category

tag: study

value: AZ


title: WT_TME419, IP-H3, RepC

description: Library name: WT_C_IP-H3


title: Smart-seq BMDMs Maf/Mafb double knock-out 2

description:
Library name: BMDMs_MAFdKO_UT_B
Smart-seq2

value: Bone marrow

tag: cell type

value: BMDMs

tag: batch


title: WT_TME419, input, RepC

description: Library name: WT_C_input

value: input


title: Subject 1.20329, Visit 1

description: Library name: 1.20329.Visit.1


title: WT_TME419, bead, RepC

description: Library name: WT_C_bead

value: bead control


title: Subject 1.20281, Visit 7

description: Library name: 1.20281.Visit.7


title: WT_TME419, IP-H3K4me3, RepA

description: Library name: WT_A_IP-H3K4me3


title: Smart-seq BMDMs Maf/Mafb double knock-out 1

description:
Library name: BMDMs_MAFdKO_UT_A
Smart-seq2


title: WT_TME419, IP-H3, RepA

description: Library name: WT_A_IP-H3


title: WT_TME419, input, RepA

description: Library name: WT_A_input


title: Subject 1.20281, Visit 6

description: Library name: 1.20281.Visit.6


title: WT_TME419, bead, RepA

description: Library name: WT_A_bead


title: Spatial transcriptomics of mus musculus: infected young female lung mouse BNI-H311

description: Library name: INF_H311_F_Day6_Lung_GEX51_C1

source_name: Lung

value: Lung

tag: strain

tag: mouse id

tag: Sex

value: female

tag: age

value: 2 months

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Infection

tag: technology

value: 10x Visium

tag: treatment

value: Plasmodium berghei ANKA infection

tag: disease

value: Cerebral malaria

tag: disease stage

value: Day 6 post-infection


title: Spatial transcriptomics of mus musculus: infected young female liver mouse BNI-H311

description: Library name: INF_H311_F_Day6_Liver_GEX45_D1

source_name: Liver

tag: tissue

value: Liver

tag: genotype

value: Wildtype


title: Line_117, IP-H3K4me3, RepC

description: Library name: 117_C_IP-H3K4me3

value: leaf

tag: chip antibody

tag: grna target_1

tag: grna target_2

tag: grna target_3


title: Subject 1.20281, Visit 3

description: Library name: 1.20281.Visit.3

value: Whole blood

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Primary

tag: infection status

value: Uninfected

tag: infection category

value: Healthy

tag: study


title: Line_117, IP-H3, RepC

description: Library name: 117_C_IP-H3


title: Spatial transcriptomics of mus musculus: infected young female kidney mouse BNI-H311

description: Library name: INF_H311_F_Day6_Kidney_GEX47_D1

source_name: Kidney

value: Kidney

tag: strain

tag: mouse id

tag: Sex

tag: age

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology

tag: treatment


title: Line_117, input, RepC

description: Library name: 117_C_input

tag: tissue

tag: chip antibody

value: input

tag: genotype

tag: grna target_1

tag: grna target_2

tag: grna target_3


title: Subject 1.20281, Visit 2

description: Library name: 1.20281.Visit.2

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

tag: infection category

tag: study

value: AZ


title: Line_117, bead, RepC

description: Library name: 117_C_bead

value: bead control


title: Subject 1.20281, Visit 1

description: Library name: 1.20281.Visit.1


title: Line_117, IP-H3, RepA

description: Library name: 117_A_IP-H3


title: Line_117, input, RepA

description: Library name: 117_A_input


title: Spatial transcriptomics of mus musculus: infected young female olfactory bulb mouse BNI-H311

description: Library name: INF_H311_F_Day6_Bulb_GEX54_A1

source_name: Olfactory bulb

value: Olfactory bulb

tag: strain

tag: mouse id

tag: Sex

value: female

tag: age

value: 2 months

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: disease

tag: disease stage


title: Line_117, IP-H3K4me3, RepA

description: Library name: 117_A_IP-H3K4me3

tag: tissue

tag: chip antibody

tag: genotype

tag: grna target_1

tag: grna target_2

tag: grna target_3


title: Spatial transcriptomics of mus musculus: infected young female brain mouse BNI-H311

description: Library name: INF_H311_F_Day6_Brain_GEX55_C1

value: Brain

tag: strain

tag: mouse id

value: Infection

tag: technology

value: 10x Visium

tag: treatment

value: Plasmodium berghei ANKA infection


title: Line_117, bead, RepA

description: Library name: 117_A_bead


title: Subject 1.20239, Visit 8

description: Library name: 1.20239.Visit.8

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Secondary

tag: infection status

tag: infection category

tag: study


title: Spatial transcriptomics of mus musculus: infected young female lung mouse BNI-H310

description: Library name: INF_H310_F_Day6_Lung_GEX50_A1

tag: tissue

value: Lung

tag: Sex

tag: age

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Wildtype

tag: disease

value: Cerebral malaria

tag: disease stage

value: Day 6 post-infection


title: Clostridioides difficile 630erm, planktonic 6h 3

city: Coleraine

first: Megan

middle: Grace

last: Taggart

state: Co. Londonderry

address: Cromore Road

country: United Kingdom

institute: Ulster University

description: Library name: ERM-PK-3

data_processing:
Raw reads were trimmed of Illumina adapters and low quality (Q<20) nucleotides using TrimGalore (v 0.6.7). Reads shorter than 20 bp were discarded.
Trimmed reads were aligned to Clostridium difficile reference genome LN614756.1, or AM180355.1. StringTie (v 2.2.1) was used to assemble genes and calculate gene abundance.
Assembly: Clostridium difficile reference genome LN614756.1, or AM180355.1
Supplementary files format and content: Raw counts as .csv files

organism: Clostridioides difficile 630

source_name: Clostridioides difficile 630erm

extract_protocol:
RNeasy PowerBiofilm kit, Qiagen. With additional DNase digest step
A NEBNext Ultra II Directional RNA library prep kit for illumina (NEB, USA) was then used with NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs)

tag: cell type

value: Clostridioides difficile 630erm


title: Subject 1.20239, Visit 7

description: Library name: 1.20239.Visit.7

value: Whole blood

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

value: Uninfected

value: Healthy


title: Clostridioides difficile 630erm, planktonic 6h 2

description: Library name: ERM-PK-2


title: Clostridioides difficile 630erm, planktonic 6h 1

description: Library name: ERM-PK-1


title: Subject 1.20239, Visit 6

description: Library name: 1.20239.Visit.6

tag: prior vaccition

tag: infection status

tag: infection category

tag: study

value: AZ


title: Clostridioides difficile 630erm, Biofilm 24h 2

description: Library name: ERM-BF-2


title: Subject 1.20239, Visit 2

description: Library name: 1.20239.Visit.2

tag: tissue

value: Primary


title: Clostridioides difficile 630erm, Biofilm 24h 1

description: Library name: ERM-BF-1


title: Spatial transcriptomics of mus musculus: infected young female kidney mouse BNI-H310

description: Library name: INF_H310_F_Day6_Kidney_GEX49_C1

value: Kidney

tag: strain

tag: mouse id

tag: Sex

value: female

tag: age

tag: slide

tag: area

tag: technology

tag: genotype

tag: treatment


title: Spatial transcriptomics of mus musculus: infected young female liver mouse BNI-H310

description: Library name: INF_H310_F_Day6_Liver_GEX47_A1

value: Liver

value: 2 months

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: disease

tag: disease stage


title: Clostridioides difficile 630erm, Biofilm 24h 3

description: Library name: ERM-BF-3

tag: cell type


title: Spatial transcriptomics of mus musculus: infected young female brain mouse BNI-H310

description: Library name: INF_H310_F_Day6_Brain_GEX53_D1

tag: tissue

value: Brain

value: Infection

value: 10x Visium


title: Subject 1.20239, Visit 1

description: Library name: 1.20239.Visit.1

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

tag: infection category

tag: study


title: Clostridioides difficile 630erm:dnaK, planktonic 6h 3

description: Library name: DNAK-PK-3

source_name: Clostridioides difficile 630erm:dnaK

value: Clostridioides difficile 630erm:dnaK


title: Clostridioides difficile 630erm:dnaK, planktonic 6h 2

description: Library name: DNAK-PK-2


title: Spatial transcriptomics of mus musculus: infected young female lung mouse BNI-H309

description: Library name: INF_H309_F_Day6_Lung_GEX51_A1

value: Lung

tag: strain

tag: mouse id

tag: Sex

tag: age

tag: slide

tag: area

tag: technology

tag: genotype

value: Wildtype

tag: treatment

value: Plasmodium berghei ANKA infection


title: Clostridioides difficile 630erm:dnaK, planktonic 6h 1

description: Library name: DNAK-PK-1

tag: cell type


title: Subject 1.20225, Visit 8

description: Library name: 1.20225.Visit.8

tag: tissue

tag: subject

tag: visit

value: Secondary

value: Infected

value: Prior


title: Clostridioides difficile 630erm:dnaK, Biofilm 24h 3

description: Library name: DNAK-BF-3


title: Subject 1.20225, Visit 7

description: Library name: 1.20225.Visit.7

value: Whole blood

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition


title: Clostridioides difficile 630erm:dnaK, Biofilm 24h 2

description: Library name: DNAK-BF-2


title: Clostridioides difficile 630erm:dnaK, Biofilm 24h 1

description: Library name: DNAK-BF-1


title: Subject 1.20225, Visit 6

description: Library name: 1.20225.Visit.6

tag: infection status

tag: infection category

tag: study

value: AZ


title: Clostridioides difficile 630, planktonic 6h 3

description: Library name: 630-PK-3

source_name: Clostridioides difficile 630

value: Clostridioides difficile 630


title: Spatial transcriptomics of mus musculus: infected young female liver mouse BNI-H309

description: Library name: INF_H309_F_Day6_Liver_GEX46_A1

tag: strain

tag: mouse id

tag: Sex

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: disease

value: Cerebral malaria

tag: disease stage

value: Day 6 post-infection


title: Spatial transcriptomics of mus musculus: infected young female kidney mouse BNI-H309

description: Library name: INF_H309_F_Day6_Kidney_GEX48_B1

tag: tissue

value: Kidney

value: female

tag: age

tag: slide

tag: area

tag: technology

tag: genotype

tag: treatment


title: Clostridioides difficile 630, planktonic 6h 2

description: Library name: 630-PK-2

tag: cell type


title: Clostridioides difficile 630, planktonic 6h 1

description: Library name: 630-PK-1


title: Spatial transcriptomics of mus musculus: infected young female olfactory bulb mouse BNI-H309

description: Library name: INF_H309_F_Day6_Bulb_GEX54_D1

value: Olfactory bulb

tag: strain

value: 2 months


title: Subject 1.20225, Visit 3

description: Library name: 1.20225.Visit.3

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Primary

tag: infection status

tag: infection category

tag: study


title: Clostridioides difficile 630, Biofilm 24h 3

description: Library name: 630-BF-3


title: Clostridioides difficile 630, Biofilm 24h 2

description: Library name: 630-BF-2


title: Spatial transcriptomics of mus musculus: infected young female brain mouse BNI-H309

description: Library name: INF_H309_F_Day6_Brain_GEX55_D1

tag: tissue

value: Brain

tag: mouse id

tag: Sex

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Infection

value: 10x Visium

tag: disease

tag: disease stage


title: Subject 1.20225, Visit 2

description: Library name: 1.20225.Visit.2

tag: subject


title: Subject 1.20225, Visit 1

description: Library name: 1.20225.Visit.1

tag: visit


title: T1 retinal spatial transcriptomic expression library

city: Beijing

first: WEIHONG

last: YU

address: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

institute: Peking Union Medical College Hospital

description:
Library name: T1_expression
The actual sequencing instrument was GeneMind SURFSeq 5000, which is not available in the GEO instrument dropdown list. GenoLab M was selected as the closest available GeneMind platform for template validation. Libraries were sequenced using paired-end 150-bp reads.

data_processing:
Raw reads were processed with fastp to remove primer sequences, low-quality trailing bases, and trailing ambiguous bases; reads with more than 80% failed bases or a post-trimming length below 60 bp were discarded.
SeekSpace Tools v1.0.2 was used for sequencing quality assessment, spatial-barcode processing, and generation of the gene-by-nucleus count matrix.
Reads were aligned to the mouse mm10 reference genome using STAR; spatial coordinates were retained in the expression object.
Quality control and downstream analyses were performed using SeekSoul Online and Seurat v4.1.1. The supplied processed data should include the complete gene-by-nucleus count matrix and spatial coordinates for T1.
Cell-type annotation and inferred cell-cell communication analyses were performed using the methods described in the manuscript; computationally inferred regulatory and communication networks require independent experimental validation.
Assembly: mm10
Supplementary files format and content: The complete gene-by-nucleus count matrix and spatial coordinate table for T1 should be supplied as processed data. T1_HE.tif is the original HE image used for spatial registration. Exact processed-data filenames must be added to the SAMPLES section before submission.
Supplementary files format and content: Processed data should include quantitative values for all genes and nuclei, together with spatial coordinates and any sample-level cell metadata required to interpret the T1 dataset.
Library strategy: Spatial Transcriptomics

source_name: retina

growth_protocol: C57BL/6J mice were housed in an SPF facility under a 12-hour light/dark cycle with ad libitum access to standard chow and water.

extract_protocol:
Fresh-frozen mouse retinas were embedded in OCT compound and cryosectioned at 10 um under RNase-free conditions. One 10-um retinal section from one eye was mounted on a SeekSpace spatial capture chip; tissue was fixed, imaged for transcriptome registration, lysed, homogenized, and nuclei were isolated by washing and filtration.
Single-nucleus RNA-seq and spatial-barcode libraries were prepared using the SeekSpace Single Cell Spatial Transcriptome-seq Kit (K02501-08) according to the manufacturer's instructions. Libraries were sequenced on a GeneMind SURFSeq 5000 instrument using paired-end 150-bp reads.

treatment_protocol: No experimental treatment was administered.

value: retina


title: T1 retinal spatial-barcode library

description:
Library name: T1_spatial
The actual sequencing instrument was GeneMind SURFSeq 5000, which is not available in the GEO instrument dropdown list. GenoLab M was selected as the closest available GeneMind platform for template validation. Libraries were sequenced using paired-end 150-bp reads.


title: Bulk RNA-seq from cryoinjured platyfish ventricles - replicate 3

city: Fribourg

first: Anna

last: Jaźwińska

address: Chemin du Musée 10

institute: University of Fribourg

description:
Library name: PF_7dpci_III
PF_7dpci_III

data_processing:
The quality of the RNA-seq data was assessed using fastqc and RSeQC (v4.0.0).
The reads were mapped to the reference genome using HiSat2 (v2.2.1)
FeatureCounts (v2.0.1) was used to count the number of reads overlapping with each gene as specified in the genome annotation.
DESeq2 (v1.38.3) was used to test for differential gene expression between the experimental groups.
Gene set enrichment analysis were achieved with ClusterProfiler (v4.7.1) using genesets from KEGG and MSigDb
Assembly: Danio_rerio.GRCz11.94 Xiphophorus_maculatus.X_maculatus-5.0-male.95
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: The CSV file includes the normalised read counts, log₂ fold change (log₂FC) and p-value for each gene, obtained using DESeq2.

organism: Xiphophorus maculatus

source_name: Heart ventricles

growth_protocol: Adult zebrafish and platyfish were raised in system water at a temperature of ~27°C, a pH of ~7.5 and a conductivity of ~485 µS. They were fed twice daily from Monday to Friday (dry food at 9 am and Artemia at 4 pm) and once at the weekend.

extract_protocol:
RNA were extracted using usual Trizol procedure, followed by DNAse treatment.
TruSeq Stranded mRNA library preparation kit (Illumina) was used following the manufacturer's protocol.

treatment_protocol: Twenty-four zebrafish and twenty-four platyfish underwent a ventricular cryoinjury procedure on day 0. On day 7, their hearts were collected and their ventricles were separated from the bulbus arteriosus and atrium. These were then pooled in three tubes, with eight ventricles in each tube. For the control group, the same number of uninjured ventricles from zebrafish and platyfish that had not been manipulated in any way were distributed in three tubes for each species, with eight ventricles per tube.

value: Heart ventricles

tag: cell type

value: Mixed

tag: genotype

value: WT

tag: treatment

value: Cryoinjured zebrafish ventricles

tag: batch

value: replicate 3


title: Clostridioides difficile 630, Biofilm 24h 1

description: Library name: 630-BF-1

value: Clostridioides difficile 630


title: Spatial transcriptomics of mus musculus: young female lung mouse BNI-H308

description: Library name: INF_H308_F_Ctrl_Lung_GEX56_A1

value: Lung

tag: strain

tag: age

tag: slide

tag: area

tag: technology

value: Wildtype


title: Subject 1.20176, Visit 8

description: Library name: 1.20176.Visit.8

tag: tissue

value: Whole blood

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Secondary

tag: infection status

value: Infected

tag: infection category

value: After

tag: study

value: AZ


title: Spatial transcriptomics of mus musculus: young female liver mouse BNI-H308

description: Library name: INF_H308_F_Ctrl_Liver_GEX46_D1

value: Liver

tag: mouse id

tag: Sex

value: female

value: 2 months

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: disease

tag: disease stage


title: Bulk RNA-seq from cryoinjured platyfish ventricles - replicate 2

description:
Library name: PF_7dpci_II
PF_7dpci_II

tag: cell type

tag: genotype

tag: treatment

tag: batch

value: replicate 2


title: Spatial transcriptomics of mus musculus: young female kidney mouse BNI-H308

description: Library name: INF_H308_F_Ctrl_Kidney_GEX48_C1

tag: tissue

value: Kidney

tag: strain

tag: age

tag: slide

tag: area

value: Infection

tag: technology

value: 10x Visium


title: Bulk RNA-seq from cryoinjured platyfish ventricles - replicate 1

description:
Library name: PF_7dpci_I
PF_7dpci_I

value: Heart ventricles

value: Mixed

value: WT

value: Cryoinjured zebrafish ventricles

value: replicate 1


title: Bulk RNA-seq from uninjured platyfish ventricles - replicate 3

description:
Library name: PF_Uninj_III
PF_Uninj_III

value: Uninjured platyfish ventricles

value: replicate 3


title: Subject 1.20176, Visit 7

description: Library name: 1.20176.Visit.7

value: Whole blood

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Secondary

tag: infection status

value: Infected

tag: infection category

tag: study


title: Spatial transcriptomics of mus musculus: young female lung mouse BNI-H307

description: Library name: INF_H307_F_Ctrl_Lung_GEX51_B1

value: Lung

tag: mouse id

tag: Sex

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: genotype

value: Wildtype

tag: disease

tag: disease stage


title: Bulk RNA-seq from uninjured platyfish ventricles - replicate 2

description:
Library name: PF_Uninj_II
PF_Uninj_II

tag: tissue

tag: cell type

tag: treatment

tag: batch


title: Subject 1.20176, Visit 6

description: Library name: 1.20176.Visit.6

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: After

value: AZ


title: Bulk RNA-seq from uninjured platyfish ventricles - replicate 1

description:
Library name: PF_Uninj_I
PF_Uninj_I


title: Multiplexed E6.5-7 and E8.5-9 mouse embryos + Actvin and BMP4 combinatorially-treated mESC-derived embyroid bodies

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Ave N, Mailstop D2-100

department: Translational Science and Therapeutics

institute: Fred Hutchinson Cancer Center

description: Library name: sciChem_HSC_3

data_processing:
Expression matrices, cell annotations and gene annotations were generated according to the protocol described in Srivatsan et al. 2020 Science 367(6473) p.45-51.
Assembly: Mouse mm10
Supplementary files format and content: tab separated values, comma separated values and matrix files

source_name: embryoid body

growth_protocol: Embryoid Bodies: mESCs were collected and dissociated into single cell suspension by incubation in Accutase. Cells were washed in serum-free media, resuspended in StemPro-34 serum-free media and plated onto 100 mm petri dishes at a density of 2x10^6 cells per plate to allow for EB formation. EBs were cultured in StemPro-34 for 51 hours, EBs were then collected into 15 mL conical tubes (no more than 2x 100 mm dishes per tube) and allowed to gravity settle for 10 minutes at 37°C. Once settled, media was gently removed, 1 mL TrypLE per dish was added, and cells were resuspended by gently flicking the tube 2-3 times. Cells were incubated in 37°C water bath for 3 minutes with gentle swirling and 1-2 flicks halfway through the incubation to keep the EBs suspended. An equivalent volume of StemPro-34 was added and cells were gently triterated 10x times with a 1000 uL pipette to fully dissociate EBs. Cells were then pooled, if applicable, washed in serum-free media, and resuspended in 300 uL of StemPro-34. 30 uL of DNase was added and cells were incubated for 10 minutes at room temperature. Following DNase treatment, cells were washed in serum-free media and resuspended in StemPro-34 containing recombinant vascular endothelial growth factor (VEGF) at 10 ng/mL and a combinatorial gradient of Activin and bone morphogenetic protein 4 (BMP4). Cells were plated onto 24-well low-adherence plates at 4x10^5 cells per well to allow for EB reformation. Following 72 hours of incubation (Day 5 of the differentiation protocol), the Activin concentration in the media was lowered. To do this, EBs were collected, gravity settled, and media was replaced with StemPro-34 containing 10 ng/mL VEGF, 5 ng/mL Activin and BMP4.  Following media swap, EBs were gently replated onto new 24-well low-adherence plates.  Embryos: Embryos were harvested from pregnant females, as previously described (Hadland et al. 2015 J Clin Invest 152(5) p.2032-45). Embryo age was determined by morphology (E6.5-7) or by counting somite pairs (E8.5-9). For E6.5-7 and E8.5-9, whole embryo/extra-embryonic tissue, or yolk sac and P-Sp region of the embryo proper were collected, respectively. Dissected tissues were treated with 0.25% collagenase for 30 minutes at 37°C, pipetted to single cell suspension, and washed with PBS containing 10% FBS. The resulting single cell suspension was process for Sci-plex library prep and sequencing as previously described (Srivatsan et al. 2020 Science 367(6473) p.45-51)

extract_protocol:
Embryoid Bodies: EBs were collected and dissociated to single-cell suspension in PBS containing 10% FBS as described above (see growth protocol) over the course of differentiation (day 4, 5, and 6) to assess transcriptional expression by Sci-plex as previously described (Srivatsan et al. 2020 Science 367(6473) p.45-51)  Embryos: Embryos were harvested from pregnant females, as previously described (Hadland et al. 2015 J Clin Invest 152(5) p.2032-45). Embryo age was determined by morphology (E6.5-7) or by counting somite pairs (E8.5-9). For E6.5-7 and E8.5-9, whole embryo/extra-embryonic tissue, or yolk sac and P-Sp region of the embryo proper were collected, respectively. Dissected tissues were treated with 0.25% collagenase for 30 minutes at 37°C, pipetted to single cell suspension, and washed with PBS containing 10% FBS. The resulting single cell suspension was process for Sci-plex library prep and sequencing as previously described (Srivatsan et al. 2020 Science 367(6473) p.45-51)
Sci-Plex libraries were constructed as described in Srivatsan et al. 2020 Science 367(6473) p.45-51

value: embryo proper (EP)

value: yolk sac (YS)

value: embryoid body

value: combinatorial Activn and BMP4 gradient (embryoid body), or none (embryo)