title: NC05-2_Xenium

type: RNA

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description:
Xenium Analyzer
Xenium prime assay (2 slides, 5k pool (human), cell segmentation

hyb_protocol: Human bone marrow core biopsies (NC=2 and CH=2) were processed as specified before and tested for RNA quality. All samples yield a DV200>30%. Xenium 5K Custom panel Add on  Design ID#X33D9K, design included 100 genes from the Immuno-Oncology panel, cell segmentation kit was used. For non-CHIP samples, two sections per patient were placed in the slides.

scan_protocol: Samples were run on the Xenium Analyzer.

data_processing:
GENCODE human reference genome v38
Data was then aligned and analyzed with the Xenium onboard analysis version 4.0.1.0

label: Xenium probe set

source_name: Bone marrow biopsy

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Bone marrow trabecular fragments were obtained from femoral head neck, femoral canal and acetabulum. Samples were collected in RPMI media supplemented with 5% fetal bovine serum (FBS) and 1% penicillin streptomycin. Samples were processed in three steps: flushing, crushing and enzymatic digestion. For flushing, samples, washed 3 times with media and cell suspension was filtered through a 70 μm cell strainer. Bone pieces were then crushed using a mortar and cell suspension was filtered. Fractions from flushing and crushing were combined and mononuclear cell (MNC) isolation was performed by Ficoll density gradient separation (Millipore, Sigma). MNCs were frozen in 90% fetal bovine serum (FBS) with 10% dimethyl sulfoxide (DMSO) and stored in liquid nitrogen until further use. For digestion, remaining bone marrow fragments were digested using a modified protocol, in filtered 4 mg/mL dispase II (Sigma), and 1 mg/mL collagenase II (Invitrogen) in PBS for 90 minutes on a rocker at 37C. Supernatant was filtered through a 70-um cell strainer and bone fragments were washed with PBS containing 2% FBS.

value: Bone marrow biopsy

value: Non-CHIP

tag: gender

value: Female


title: Subject 1.20176, Visit 3

status: Public on Aug 13 2026

type: SRA

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: 1.20176.Visit.3

library_source: transcriptomic

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.

molecule: total RNA

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

tag: tissue

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: After

tag: study

value: AZ


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

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: INF_H307_F_Ctrl_Liver_GEX46_B1

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

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

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: Liver

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: genotype

value: Wildtype

tag: treatment

tag: disease

tag: disease stage


title: NC05_Xenium

tag: tissue

tag: gender


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

description: Library name: INF_H307_F_Ctrl_Kidney_GEX48_A1

source_name: Kidney

value: Kidney

tag: strain


title: Subject 1.20176, Visit 2

description: Library name: 1.20176.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: NC03-2_Xenium

value: Male


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

description: Library name: INF_H307_F_Ctrl_Bulb_GEX54_C1

source_name: Olfactory bulb

value: Olfactory bulb

tag: mouse id

tag: Sex

tag: age

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: Subject 1.20176, Visit 1

description: Library name: 1.20176.Visit.1

tag: tissue

tag: subject


title: CH15_Xenium

value: Bone marrow biopsy

tag: treatment

value: CHIP

tag: gender


title: NC03_Xenium

value: Non-CHIP


title: Spatial transcriptomics of mus musculus: young female lung mouse BNI-H306

description: Library name: INF_H306_F_Ctrl_Lung_GEX51_D1

source_name: Lung

value: Lung

tag: strain

tag: technology

tag: genotype

tag: disease

tag: disease stage


title: LUHMES neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 2, biological rep 2

city: Ithaca

first: Joel

middle: D

last: Baines

state: NY

address: 235 Hungerfordhill Rd

institute: Cornell University

description:
in-house precision nuclear run on library preparation follwing previously published protocols (Birkenhuer, Danki, and Baines, 2018, Journal of Virology)
LL-2
Lund human mesencephalic neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 2, biological replicate 2

data_processing:
library strategy: PRO-seq
raw fastq files were concatenated
sequences were aligned to  using the Danko lab PRO-seq1.0 pipeline, which includes adapter trimming with cutadapt, a bwa alignment to the reference genome, and a final data processing step which converts the .BAM files to .bw files to report only the 5' end position of the read
regions of high polymerase activity on the host genome were expolred using a Deseq2 analysis
regions of hight polymerase activyt on the viral genome were determined using statistical analysis with JMP software
Assembly: the reference genome used was a concatenated genome containing the HSV-1 strain 17 genome with masked terminal repeats, human hg38 genome build, and the drosophila dm3 reference genome
Supplementary files format and content: .bw files are bigwig files with the mapped lcoation of the 5' end of the seqencing read, and are strand specific as indicated by the _plus or _minus desgingation

organism:
Drosophila melanogaster
Homo sapiens
Human alphaherpesvirus 1 strain 17

source_name: Lund human mesencephalic (LUHMES) neuronal cells

growth_protocol: Luhmes cells were propagated following the protocol found in Edwards and Bloom, 2019, Journal of Virology

extract_protocol:
Nuclei were isolated and precision nuclear run on were carried out following the potocol found in Birkenheuer, Danko, and Baines, 2018, Journal of Virology
PRO-seq libraries were prepared as previously described in Birkenheuer, Danko, and Baines, 2018, journal of virology which consited NaOH base hydrolysis to fragment the RNA followed by the 3' RNA adapter ligation.  The 5'caps were then removed with RPPH and the 5' hydroxyl repaired using polynucleotide kinase before ligation to the 5' RNA adapter.  The final RNA library was reverse transcribed and PCR amplified.  The library was purified using an 8% polyacrylamide gel with electrophoresis before being submitted for sequencing.

treatment_protocol: infected cells were treated infected with HSV-1 strain 17 syn + for 2 days in the presence of 50 𝜇M of acyclovir.  Acyclovir was then removed and infected cells were cultured for an additional 9 days.  At this time nuclei were isolated for the latent and LL samples or were treated with  1𝜇M of wortmannin for 1hr, 3hr, or 18hr.

tag: cell line

tag: cell type

value: Drosophila melanogaster S2

value: HSV-1 infected with acyclovir-induced latency that are from experiment 2


title: Spatial transcriptomics of mus musculus: young female liver mouse BNI-H306

description: Library name: INF_H306_F_Ctrl_Liver_GEX45_C1

tag: mouse id

tag: Sex

tag: age

tag: slide


title: Subject 1.20161, Visit 8

description: Library name: 1.20161.Visit.8

value: Whole blood

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Secondary

tag: infection status

value: Uninfected

tag: infection category

value: Healthy

tag: study


title: LUHMES neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 2, biological rep 1

description:
in-house precision nuclear run on library preparation follwing previously published protocols (Birkenhuer, Danki, and Baines, 2018, Journal of Virology)
LL_1
Lund human mesencephalic neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 2, biological replicate 1

value: Lund human mesencephalic (LUHMES) neuronal cells

tag: treatment


title: Subject 1.20161, Visit 7

description: Library name: 1.20161.Visit.7

tag: tissue

tag: subject

value: AZ


title: LUHMES neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 1, biological rep 3

description:
in-house precision nuclear run on library preparation follwing previously published protocols (Birkenhuer, Danki, and Baines, 2018, Journal of Virology)
Luhmes_3
Lund human mesencephalic neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 1, biological replicate 3

value: HSV-1 infected with acyclovir-induced latency


title: CH02_Xenium

tag: gender


title: Spatial transcriptomics of mus musculus: young female kidney mouse BNI-H306

description: Library name: INF_H306_F_Ctrl_Kidney_GEX47_C1

tag: strain

value: female

value: 2 months

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Infection

tag: technology

value: 10x Visium

tag: genotype

value: Wildtype

tag: disease

tag: disease stage


title: LUHMES neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 1, biological rep 2

description:
in-house precision nuclear run on library preparation follwing previously published protocols (Birkenhuer, Danki, and Baines, 2018, Journal of Virology)
Luhmes_2
Lund human mesencephalic neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 1, biological replicate 2

tag: cell line

tag: cell type


title: Subject 1.20161, Visit 6

description: Library name: 1.20161.Visit.6

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

tag: infection category

tag: study


title: Subject ZA0010802, Visit 2

description: Library name: ZA0010802.Visit.2

tag: tissue

tag: subject

value: Tertiary

value: NX


title: LUHMES neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 1, biological rep 1

description:
in-house precision nuclear run on library preparation follwing previously published protocols (Birkenhuer, Danki, and Baines, 2018, Journal of Virology)
Luhmes_1
Lund human mesencephalic neuronal cells with latent HSV-1 strain 17 infection (MOI3) , experiment 1, biological replicate 1

tag: treatment


title: Spatial transcriptomics of mus musculus: young female olfactory bulb mouse BNI-H306

description: Library name: INF_H306_F_Ctrl_Bulb_GEX54_B1

value: Olfactory bulb

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


title: YP_009508864.1_ssDNA-SELEX_cycle4_Rep2

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hongkong·

description: Library name: YP_009508864.1_ssDNA-SELEX_cycle4_Rep2

library_source: genomic

data_processing:
Quality control of the raw sequencing data using FastQC with default parameters.Sequences from the 40-nt random region without bases annotated as N were extracted using custom script.Autoseed software was used for motif analysis.
Supplementary files format and content: ssDNA-SELEX_PWM.xlsx

molecule: genomic DNA

organism: synthetic construct

source_name: synthetic construct

growth_protocol: During the purification of the protein, the culture conditions for the Escherichia coli strain were set at 37°C with shaking at 220 rpm, until the optical density at 600 nm (OD600) reached 0.6.

extract_protocol:
After overnight induction of protein expression, collect the cell pellet and suspend it in Buffer A (0.5 mg/ml lysozyme, 50 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM imidazole, 1 mM DTT, 1 mM PMSF). Ultrasonicate the cells on ice at 30% power for 10 minutes, with a 6 seconds on/6 seconds off cycle. Subsequently, centrifuge at 12,000 rpm for 15 minutes at 4°C to collect the supernatant. Next, incubate the supernatant with Ni-NTA beads pre-equilibrated by Buffer A at 4 °C for 45–60 min. After incubation, rinse the beads with 5 column volumes of Buffer A, followed by another 5 column volumes of Buffer B (Buffer A supplemented with 50 mM imidazole) to remove non-specific binding proteins. The target protein is finally eluted using Buffer A containing 300 mM imidazole.
For the ssDNA input library, the dsDNA library was reamplified to append a T7 promoter sequence in a 25-μL reaction containing 12.5 μL 2× Phanta Max Master Mix (Vazyme, P515-03), 1 μL each of 10 μM Illumina-T7-F and Illumina-SELEX-R primers, and 3 μL dsDNA template. PCR cycling was conducted as follows: 95°C for 3 min; 10 cycles of 95°C for 15 s, 55°C for 15 s, and 72°C for 30 s; followed by 72°C for 5 min and hold at 4°C. RNA transcription was subsequently performed using the T7 High Yield RNA Transcription Kit (Vazyme, TR101-02) in a 20-μL reaction containing 2 μL 10× transcription buffer, 0.4 μL each of ATP, CTP, GTP, and UTP, 5 μL of T7-promoter-modified DNA, 0.5 μL RNase inhibitor, and 2 μL T7 RNA polymerase mix. Samples were incubated at 37°C for 16 h, followed by digestion of remaining DNA templates with 1 μL DNase I (RNase-free) (Takara, 2270B) at 37°C for 15 min. To obtain clean RNA for downstream reactions, transcription products were purified using VAHTS RNA Clean Beads (Vazyme, N412-01) at a 2.5× bead-to-sample ratio, then eluted in nuclease-free water. For secondary structure unfolding, 1.5 μg RNA was mixed with 2 μL 20 μM Illumina-SELEX-R primer in a total volume of 10 μL, heated at 70°C for 5 min, and snap-cooled on ice for 2 min. Reverse transcription was then performed using the HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, R312-02) in a 20-μL reaction (10 μL RNA, 2 μL 10× RT buffer, 2 μL enzyme mix) at 37°C for 45 min, followed by inactivation at 85°C for 5 s to generate RNA-DNA hybrids. The RNA strand was then removed using Ribonuclease H (RNase H, Thermo, EN0202) in a 15 μL system (2 μL enzyme, 1.5 μL 10× reaction buffer) incubated at 37°C for 40 min. Finally, the ssDNA products were purified using VAHTS DNA Clean Beads (Vazyme, N411-02) at a 2.5× bead-to-sample ratio, eluted in 10 μL nuclease-free water, and used directly for ssDNA-SELEX. HT-SELEX and ssDNA-SELEX were performed using identical experimental procedures, as described below. 400 ng of protein and 5 µl of DNA input were added to the binding buffer (10 mM Tris pH 7.5, 50 mM NaCl, 1 mM DTT, 1 mM MgCl2, 4% glycerol, 0.5 mM EDTA, 5 µg/mL poly-dIdC) to a total volume of 25 µl, and the DNA and protein were incubated at room temperature for 1 hour under 800 rpm. Subsequently, the protein-DNA complex and 10 µL of pre-equilibrated Ni Sepharose 6 Fast Flow resin (GE Healthcare, 17-5318-01) were added to 150 µL of binding buffer. The entire system was transferred to a 96-well plate and incubated at room temperature for 1 hour under 800 rpm. After that, the 96-well plate was placed in a washing machine with the washing program set up, using a wash solution (10 mM Tris pH 7.5, 50 mM NaCl, 1 mM DTT, 1 mM MgCl2, 4% glycerol, 0.5 mM EDTA) to wash 12 times to remove unbound DNA ligands. Next, the beads were resuspended in 50 μL of ddH2O to elute the DNA that preferentially binds to the protein. Finally, the eluted DNA was amplified by PCR with primers shown in Table S1b. For dsDNA-SELEX, the purified PCR products were directly applied as input templates for the subsequent selection cycle. For ssDNA-SELEX, the PCR products were subjected to T7 ligation, in vitro transcription, reverse transcription and RNase H digestion to generate single-stranded DNA, which served as the input for the next round. This process was repeated four times. Each PCR products were purified and sequence using Illumina NovaSeq X Plus PE150.

treatment_protocol: Add 1 mM IPTG (isopropyl β-D-1-thiogalactopyranoside) to the E. coli culture medium, set the constant temperature shaker to 17°C at 220 rpm, and induce protein expression for 14-16 hours.

tag: cell line

value: synthetic construct

tag: cell type


title: YP_009508864.1_ssDNA-SELEX_cycle4_Rep1

description: Library name: YP_009508864.1_ssDNA-SELEX_cycle4_Rep1


title: YP_009116878.1_ssDNA-SELEX_cycle4_Rep2

description: Library name: YP_009116878.1_ssDNA-SELEX_cycle4_Rep2


title: Subject 1.20161, Visit 2

description: Library name: 1.20161.Visit.2

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Primary

tag: infection status

tag: infection category


title: YP_009116878.1_ssDNA-SELEX_cycle4_Rep1

description: Library name: YP_009116878.1_ssDNA-SELEX_cycle4_Rep1


title: Spatial transcriptomics of mus musculus: young female brain mouse BNI-H306

description: Library name: INF_H306_F_Ctrl_Brain_GEX55_B1

source_name: Brain

tag: tissue

value: Brain

tag: strain

tag: mouse id

tag: technology

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: Subject 1.20161, Visit 3

description: Library name: 1.20161.Visit.3

value: Whole blood

tag: subject

tag: study


title: YP_008431134.1_ssDNA-SELEX_cycle4_Rep2

description: Library name: YP_008431134.1_ssDNA-SELEX_cycle4_Rep2

tag: cell line

tag: cell type


title: Subject 1.20161, Visit 1

description: Library name: 1.20161.Visit.1

tag: visit

tag: day post_primary

value: Uninfected


title: Spatial transcriptomics of mus musculus: young male liver mouse BNI-H304

description: Library name: INF_H304_M_Ctrl_Liver_GEX47_B1

value: Liver

tag: Sex

value: male

tag: age

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: YP_008431134.1_ssDNA-SELEX_cycle4_Rep1

description: Library name: YP_008431134.1_ssDNA-SELEX_cycle4_Rep1


title: Subject 1.20135, Visit 8

description: Library name: 1.20135.Visit.8

tag: tissue

tag: day post_prior_vaccition

tag: prior vaccition

value: Secondary

tag: infection status

tag: infection category

value: Healthy

value: AZ


title: FUS_ssDNA-SELEX_cycle4_Rep2

description: Library name: FUS_ssDNA-SELEX_cycle4_Rep2

tag: cell line


title: Spatial transcriptomics of mus musculus: young male kidney mouse BNI-H304

description: Library name: INF_H304_M_Ctrl_Kidney_GEX49_A1

value: Kidney

tag: strain

tag: mouse id

value: 2 months

tag: technology

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: FUS_ssDNA-SELEX_cycle4_Rep1

description: Library name: FUS_ssDNA-SELEX_cycle4_Rep1

tag: cell type


title: Spatial transcriptomics of mus musculus: young male olfactory bulb mouse BNI-H304

description: Library name: INF_H304_M_Ctrl_Bulb_GEX52_C1

tag: Sex

tag: age

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

value: Infection

value: 10x Visium


title: FUS_ssDNA-SELEX_cycle0_Rep2

description: Library name: FUS_ssDNA-SELEX_cycle0_Rep2


title: Subject 1.20135, Visit 7

description: Library name: 1.20135.Visit.7

tag: tissue

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

tag: study


title: FUS_ssDNA-SELEX_cycle0_Rep1

description: Library name: FUS_ssDNA-SELEX_cycle0_Rep1

tag: cell line


title: YP_009508864.1_ssDNA-SELEX_cycle0

description: Library name: YP_009508864.1_ssDNA-SELEX_cycle0


title: Subject 1.20135, Visit 6

description: Library name: 1.20135.Visit.6

tag: infection category


title: Spatial transcriptomics of mus musculus: young male brain mouse BNI-H304

description: Library name: INF_H304_M_Ctrl_Brain_GEX53_C1

tag: strain

tag: mouse id

tag: slice thickness_(um)

tag: cohort

tag: technology

tag: genotype

value: Wildtype

tag: treatment

tag: disease

tag: disease stage


title: YP_009116878.1_ssDNA-SELEX_cycle0_Rep2

description: Library name: YP_009116878.1_ssDNA-SELEX_cycle0_Rep2

tag: cell type


title: YP_008431134.1_ssDNA-SELEX_cycle0_Rep2

description: Library name: YP_008431134.1_ssDNA-SELEX_cycle0_Rep2


title: Spatial transcriptomics of mus musculus: young male lung mouse BNI-H303

description: Library name: INF_H303_M_Ctrl_Lung_GEX50_D1

tag: tissue

value: Lung

tag: Sex

tag: age

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)


title: YP_009116878.1_ssDNA-SELEX_cycle0_Rep1

description: Library name: YP_009116878.1_ssDNA-SELEX_cycle0_Rep1

tag: cell line


title: Subject 1.20135, Visit 3

description: Library name: 1.20135.Visit.3

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: YP_008431134.1_ssDNA-SELEX_cycle0_Rep1

description: Library name: YP_008431134.1_ssDNA-SELEX_cycle0_Rep1

tag: cell type


title: Subject 1.20135, Visit 2

description: Library name: 1.20135.Visit.2

tag: tissue


title: NP_671816.1_SELEX_cycle4

description: Library name: NP_671816.1_SELEX_cycle4

library_source: other

data_processing:
Quality control of the raw sequencing data using FastQC with default parameters.Sequences from the 40-nt random region without bases annotated as N were extracted using custom script.Autoseed software was used for motif analysis.
Supplementary files format and content: SELEX_PWM.xlsx

molecule: protein

extract_protocol:
After overnight induction of protein expression, collect the cell pellet and suspend it in Buffer A (0.5 mg/ml lysozyme, 50 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM imidazole, 1 mM DTT, 1 mM PMSF). Ultrasonicate the cells on ice at 30% power for 10 minutes, with a 6 seconds on/6 seconds off cycle. Subsequently, centrifuge at 12,000 rpm for 30 minutes at 4°C to collect the supernatant, which is then filtered through a 0.45 μm filter. Next, incubate the supernatant with Ni-NTA beads, pre-equilibrated with Buffer A, at 4°C for 30 minutes, wash off the non-specific proteins with 50 mM imidazole, and finally elute the target protein using Buffer A containing 300 mM imidazole.
The random ligand library of HT-SELEX was generated using primers from Supplementary Table S1b and 40 bp random oligonucleotides as templates, followed by PCR amplification. The library was sequenced using the Illumina NovaSeq X Plus PE150 sequencer to analyze the uniformity of each base (A, T, C, G). Subsequently, 400 ng of protein and 5 µl of DNA input were added to the binding buffer (10 mM Tris pH 7.5, 50 mM NaCl, 1 mM DTT, 1 mM MgCl2, 4% glycerol, 0.5 mM EDTA, 5 µg/mL poly-dIdC) to a total volume of 25 µl, and the DNA and protein were incubated at room temperature for 30 minutes.Subsequently, the protein-DNA complex and 10 µL of pre-equilibrated Ni Sepharose 6 Fast Flow resin (GE Healthcare, 17-5318-01) were added to 150 µL of binding buffer. The entire system was transferred to a 96-well plate and incubated at room temperature for 1 hour under 800 rpm. After that, the 96-well plate was placed in a washing machine with the washing program set up, using a wash solution to wash 12 times to remove unbound RNA ligands. Next, the beads were resuspended in 50 μL of UPD H2O to elute the DNA that preferentially binds to the protein. Finally, the eluted DNA was amplified by PCR using primers listed in Table S1b, and the obtained PCR products were used as DNA templates for the next cycle. This process was repeated four times.Each PCR products were purified and sequence using Illumina NovaSeq X Plus PE150.

treatment_protocol: Add 1 mM IPTG (isopropyl β-D-1-thiogalactopyranoside) to the E. coli culture medium, set the constant temperature shaker to 17°C at 220 rpm, and induce protein expression for 17-20 hours.

tag: protein id

tag: cycle


title: Spatial transcriptomics of mus musculus: young male liver mouse BNI-H303

description: Library name: INF_H303_M_Ctrl_Liver_GEX45_A1

tag: strain

tag: mouse id

tag: Sex

tag: age

tag: slide

tag: slice thickness_(um)

tag: cohort

tag: technology

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: NP_671816.1_SELEX_cycle0

description: Library name: NP_671816.1_SELEX_cycle0


title: Subject 1.20135, Visit 1

description: Library name: 1.20135.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: YP_007518320.1_SELEX_cycle4

description: Library name: YP_007518320.1_SELEX_cycle4

tag: tissue

tag: protein id

tag: cycle


title: YP_007518320.1_SELEX_cycle0

description: Library name: YP_007518320.1_SELEX_cycle0


title: Subject 1.20112, Visit 8

description: Library name: 1.20112.Visit.8


title: Spatial transcriptomics of mus musculus: young male olfactory bulb mouse BNI-H303

description: Library name: INF_H303_M_Ctrl_Bulb_GEX52_A1

value: Olfactory bulb

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


title: Spatial transcriptomics of mus musculus: young male kidney mouse BNI-H303

description: Library name: INF_H303_M_Ctrl_Kidney_GEX49_D1

tag: technology

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: YP_717937.1_SELEX_cycle4

description: Library name: YP_717937.1_SELEX_cycle4

tag: tissue

value: synthetic construct

tag: protein id


title: Spatial transcriptomics of mus musculus: young male brain mouse BNI-H303

description: Library name: INF_H303_M_Ctrl_Brain_GEX53_A1

tag: strain


title: Subject 1.20112, Visit 7

description: Library name: 1.20112.Visit.7

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: YP_717937.1_SELEX_cycle0

description: Library name: YP_717937.1_SELEX_cycle0

tag: cycle


title: YP_009137113.1_SELEX_cycle4

description: Library name: YP_009137113.1_SELEX_cycle4


title: Spatial transcriptomics of mus musculus: infected young male liver mouse BNI-H300

description: Library name: INF_H300_M_Day6_Liver_GEX46_C1

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

value: Plasmodium berghei ANKA infection

value: Cerebral malaria

value: Day 6 post-infection


title: YP_005271181.1_SELEX_cycle4

description: Library name: YP_005271181.1_SELEX_cycle4

tag: tissue

tag: protein id


title: Subject 1.20112, Visit 6

description: Library name: 1.20112.Visit.6

value: Whole blood

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Uninfected


title: YP_005271181.1_SELEX_cycle0

description: Library name: YP_005271181.1_SELEX_cycle0

tag: cycle


title: NP_050210.1_SELEX_cycle4

description: Library name: NP_050210.1_SELEX_cycle4


title: NP_050210.1_SELEX_cycle0

description: Library name: NP_050210.1_SELEX_cycle0


title: Subject 1.20112, Visit 3

description: Library name: 1.20112.Visit.3

value: Primary

tag: infection status

tag: infection category

tag: study


title: YP_010796333.1_SELEX_cycle4

description: Library name: YP_010796333.1_SELEX_cycle4


title: Spatial transcriptomics of mus musculus: infected young male lung mouse BNI-H299

description: Library name: INF_H299_M_Day6_Lung_GEX50_B1

tag: strain

tag: mouse id

tag: Sex

value: male

tag: age

tag: slide

tag: area

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: Spatial transcriptomics of mus musculus: infected young male olfactory bulb mouse BNI-H300

description: Library name: INF_H300_M_Day6_Bulb_GEX56_C1

tag: tissue

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology


title: Subject 1.20112, Visit 1

description: Library name: 1.20112.Visit.1

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

tag: infection status

tag: infection category

value: Healthy

tag: study


title: YP_009508805.1_SELEX_cycle4

description: Library name: YP_009508805.1_SELEX_cycle4

tag: protein id

tag: cycle


title: YP_010796333.1_SELEX_cycle0

description: Library name: YP_010796333.1_SELEX_cycle0


title: Subject 1.20073, Visit 8

description: Library name: 1.20073.Visit.8

value: Secondary

value: Infected

value: After

value: AZ


title: Spatial transcriptomics of mus musculus: infected young male liver mouse BNI-H299

description: Library name: INF_H299_M_Day6_Liver_GEX45_B1

value: Liver

tag: strain

tag: mouse id

tag: Sex

tag: age

value: 2 months

tag: slide

tag: area

value: Infection

value: 10x Visium

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: Spatial transcriptomics of mus musculus: infected young male kidney mouse BNI-H299

description: Library name: INF_H299_M_Day6_Kidney_GEX49_B1

tag: tissue

value: Kidney

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology

value: Wildtype


title: YP_009508805.1_SELEX_cycle0

description: Library name: YP_009508805.1_SELEX_cycle0

value: synthetic construct

tag: protein id

tag: cycle


title: YP_009058895.1_SELEX_cycle4

description: Library name: YP_009058895.1_SELEX_cycle4


title: YP_009030018.1_SELEX_cycle4

description: Library name: YP_009030018.1_SELEX_cycle4


title: Subject 1.20073, Visit 7

description: Library name: 1.20073.Visit.7

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: YP_009030018.1_SELEX_cycle0

description: Library name: YP_009030018.1_SELEX_cycle0


title: YP_009111420.1_SELEX_cycle4

description: Library name: YP_009111420.1_SELEX_cycle4


title: Spatial transcriptomics of mus musculus: infected young male olfactory bulb mouse BNI-H299

description: Library name: INF_H299_M_Day6_Bulb_GEX52_B1

value: Olfactory bulb

tag: strain

tag: mouse id

tag: Sex

tag: age

tag: slide

tag: area

tag: genotype

tag: treatment

value: Plasmodium berghei ANKA infection

tag: disease

value: Cerebral malaria

tag: disease stage

value: Day 6 post-infection


title: Subject 1.20073, Visit 6

description: Library name: 1.20073.Visit.6

tag: tissue

value: Whole blood

tag: subject

tag: visit


title: YP_005271187.1_SELEX_cycle4

description: Library name: YP_005271187.1_SELEX_cycle4

tag: protein id

tag: cycle


title: Spatial transcriptomics of mus musculus: infected young male brain mouse BNI-H299

description: Library name: INF_H299_M_Day6_Brain_GEX53_B1

value: Brain

value: male

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology


title: Subject 1.20073, Visit 2

description: Library name: 1.20073.Visit.2

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: Primary

tag: infection status

value: Infected

tag: infection category

tag: study


title: YP_001974456.1_SELEX_cycle4

description: Library name: YP_001974456.1_SELEX_cycle4


title: Spatial transcriptomics of mus musculus: old male kidney mouse 15

description: Library name: AGE_15_112_Kidney_GEX8_D1

tag: strain

tag: mouse id

tag: Sex

tag: age

value: 112 weeks

tag: slide

tag: area

value: Aging

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: YP_002213784.1_SELEX_cycle4

description: Library name: YP_002213784.1_SELEX_cycle4

tag: tissue

tag: protein id

tag: cycle


title: Subject 1.20073, Visit 1

description: Library name: 1.20073.Visit.1

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition

value: After

value: AZ


description: Library name: YP_002213784.1_SELEX_cycle0, YP_009058895.1_SELEX_cycle0


title: Spatial transcriptomics of mus musculus: old male heart mouse 15

description: Library name: AGE_15_112_Heart_GEX21_A1

source_name: Heart

value: Heart

tag: strain

tag: mouse id

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology

value: 10x Visium


title: YP_009553535.1_SELEX_cycle4

description: Library name: YP_009553535.1_SELEX_cycle4


title: Subject 1.10052, Visit 8

description: Library name: 1.10052.Visit.8

value: Secondary

tag: infection status

tag: infection category

value: Prior

tag: study


title: YP_009553535.1_SELEX_cycle0

description: Library name: YP_009553535.1_SELEX_cycle0

tag: tissue

value: synthetic construct

tag: protein id


title: Subject 1.10052, Visit 7

description: Library name: 1.10052.Visit.7

tag: subject


title: YP_008431134.1_SELEX_cycle4

description: Library name: YP_008431134.1_SELEX_cycle4

tag: cycle


title: YP_008431134.1_SELEX_cycle0

description: Library name: YP_008431134.1_SELEX_cycle0


title: Spatial transcriptomics of mus musculus: old male brain4 mouse 15

description: Library name: AGE_15_112_Brain4_GEX32_D1

tag: Sex

tag: age

tag: slide

tag: area

tag: genotype

value: Wildtype

tag: treatment

tag: disease

tag: disease stage


title: Spatial transcriptomics of mus musculus: old male brain5 mouse 15

description: Library name: AGE_15_112_Brain5_GEX33_D1

tag: strain

tag: mouse id

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: YP_003457415.1_SELEX_cycle4

description: Library name: YP_003457415.1_SELEX_cycle4

tag: tissue

tag: protein id


title: Subject 1.10052, Visit 6

description: Library name: 1.10052.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: YP_003457415.1_SELEX_cycle0

description: Library name: YP_003457415.1_SELEX_cycle0

tag: cycle


title: NP_957885.1_SELEX_cycle4

description: Library name: NP_957885.1_SELEX_cycle4


title: Subject 1.10052, Visit 3

description: Library name: 1.10052.Visit.3


title: Spatial transcriptomics of mus musculus: old male brain3 mouse 15

description: Library name: AGE_15_112_Brain3_GEX32_C1

tag: strain

tag: Sex

tag: age

tag: slide

tag: area

tag: technology

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: NP_957885.1_SELEX_cycle0

description: Library name: NP_957885.1_SELEX_cycle0

tag: tissue

tag: protein id


title: Spatial transcriptomics of mus musculus: old male brain2 mouse 15

description: Library name: AGE_15_112_Brain2_GEX32_B1

tag: mouse id

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: YP_010377141.1_SELEX_cycle4

description: Library name: YP_010377141.1_SELEX_cycle4

tag: cycle


title: Subject 1.10052, Visit 2

description: Library name: 1.10052.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: YP_010377141.1_SELEX_cycle0

description: Library name: YP_010377141.1_SELEX_cycle0


title: Spatial transcriptomics of mus musculus: old male brain1 mouse 15

description: Library name: AGE_15_112_Brain1_GEX32_A1

tag: strain

tag: Sex

tag: age

tag: slide

tag: area

tag: technology

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: YP_009508864.1_SELEX_cycle4

description: Library name: YP_009508864.1_SELEX_cycle4

tag: tissue

tag: protein id

tag: cycle


title: YP_009508864.1_SELEX_cycle0

description: Library name: YP_009508864.1_SELEX_cycle0


title: Subject 1.10052, Visit 1

description: Library name: 1.10052.Visit.1

tag: subject

tag: visit

tag: day post_primary

tag: day post_prior_vaccition

tag: prior vaccition


title: Spatial transcriptomics of mus musculus: middle-aged male spleen mouse 14

description: Library name: AGE_14_73_Spleen_GEX36_C1

source_name: Spleen

value: Spleen

tag: strain

tag: mouse id

tag: Sex

value: 73 weeks

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: TC28a2, RNAseq

city: Gainesville

first: Darius

last: Ramkhalawan

address: 1200 Newell Drive

institute: University of Florida

description: Library name: DR45

data_processing:
RNAseq alignment and counting were performed using nf-core's RNAseq pipeline with the salmon pseudo aligner option
Assembly: hg19
Supplementary files format and content: RNAseq gene tpm counts are in a 2 column tsv format file

extract_protocol:
RNA was simultaneously isolated from TC28a2 human chondrocytes cells using the RNeasy mini kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. Paired-end RNA sequencing was carried out on an Illumina NovaSeq6000.

tag: cell line

tag: cell type

value: chondrocyte


title: YP_009508841.1_SELEX_cycle0

description: Library name: YP_009508841.1_SELEX_cycle0

tag: tissue


title: YP_009508841.1_SELEX_cycle4

description: Library name: YP_009508841.1_SELEX_cycle4

tag: protein id


title: YP_009116878.1_SELEX_cycle4

description: Library name: YP_009116878.1_SELEX_cycle4

tag: cycle


title: Spatial transcriptomics of mus musculus: middle-aged male lung mouse 14

description: Library name: AGE_14_73_Lung_GEX6_D1

value: Lung

tag: age

tag: slide

tag: area

tag: technology

tag: genotype

tag: treatment

tag: disease

tag: disease stage


title: THP-1 cells, deltadotA Legionella infection, 5h post-infection, biol rep 3

city: Clayton

first: Kathleen

last: McCaffrey

state: VIC

address: 25-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

description: Library name: Sample 12

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.6.0 and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. RTA performs real-time base calling on the NovaSeq instrument computer. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Trimmed reads were mapped to hg38 using Tophat2 v2.1.1
Read counts were generated using featureCounts v1.5.0
Assembly: Homo sapiens genome (hg38)
Supplementary files format and content: tab delimited text file including raw counts for each Sample

source_name: Blood

growth_protocol: THP-1 monocytes [Homo sapiens, male] (ATCC Cat#TIB-202) were cultured in RPMI 1640 supplemented with Glutamax (Gibco Cat#61870036) and 10 % foetal bovine serum (FBS) (Bovagen Cat#SFBS-AU) at 37C and 5 % CO2. THP-1 monocytes were seeded at 2.5x105 cells/cm2 in tissue-culture dishes and differentiated for 48 h prior to infection using 50 ng/mL phorbol 12-myristate 13-acetate (PMA) (Sigma Aldrich Cat#P8139).

extract_protocol:
At 5 h post-infection, RNA was extracted from cell monolayers using the ISOLATE II RNA Mini Kit (Bioline Cat# BIO-52073) according to the manufacturer’s instructions and analysed using a 2100 Bioanalyzer (Agilent).
cDNA libraries were prepared for three independent replicates per condition using the TruSeq® Stranded mRNA Library Prep (Illumina Cat# 20020594) according to the manufacturer’s instructions

treatment_protocol: THP-1 cell monolayers were infected with either L. pneumophila 130b or thelegC4 strain at a MOI of 10. At 2 h post-infection, cell monolayers were incubated with gentamicin at 100 g/mL (Gibco Cat#15750060) for 1 h to kill any remaining extracellular bacteria followed by washing and the addition of fresh media.

value: Blood

value: Monocyte

value: PMA differentiated, 48 h


title: YP_009116878.1_SELEX_cycle0

description: Library name: YP_009116878.1_SELEX_cycle0


title: Spatial transcriptomics of mus musculus: middle-aged male liver mouse 14

description: Library name: AGE_14_73_Liver_GEX39_C1

value: Liver

tag: strain

tag: mouse id

tag: Sex

value: male

tag: sequencing primer


title: YP_001129451.1_SELEX_cycle4

description: Library name: YP_001129451.1_SELEX_cycle4


title: THP-1 cells, deltadotA Legionella infection, 5 h post-infection, biol rep 2

description: Library name: Sample 11

tag: cell line


title: YP_001129451.1_SELEX_cycle0

description: Library name: YP_001129451.1_SELEX_cycle0


title: AVM80381.1_SELEX_cycle4

description: Library name: AVM80381.1_SELEX_cycle4


title: Spatial transcriptomics of mus musculus: middle-aged male kidney mouse 14

description: Library name: AGE_14_73_Kidney_GEX9_A1

value: Kidney

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Aging


title: THP-1 cells, deltadotA Legionella infection, 5 h post-infection, biol rep 1

description: Library name: Sample 10

tag: tissue

tag: cell type


title: AVM80381.1_SELEX_cycle0

description: Library name: AVM80381.1_SELEX_cycle0

tag: protein id

tag: cycle


title: Spatial transcriptomics of mus musculus: middle-aged male heart mouse 14

description: Library name: AGE_14_73_Heart_GEX43_D1

value: Heart

tag: age

tag: slide

tag: area

tag: technology


title: YP_006272959.1_SELEX_cycle4

description: Library name: YP_006272959.1_SELEX_cycle4


title: THP-1 cells, 130b Legionella infection, 5h post-infection, biol rep 3

description: Library name: Sample 9

tag: treatment


title: YP_006272959.1_SELEX_cycle0

description: Library name: YP_006272959.1_SELEX_cycle0


title: Spatial transcriptomics of mus musculus: middle-aged male brain5 mouse 14

description: Library name: AGE_14_73_Brain5_GEX33_A1

value: Brain

tag: strain

value: 10x Visium

tag: genotype

tag: disease

tag: disease stage


description: Library name: YP_009246379.1_SELEX_cycle0, YP_005271187.1_SELEX_cycle0


title: THP-1 cells, 130b Legionella infection, 5 h post-infection, biol rep 2

description: Library name: Sample 8

tag: cell line


title: YP_009246379.1_SELEX_cycle4

description: Library name: YP_009246379.1_SELEX_cycle4


title: YP_001111258.1_SELEX_cycle4

description: Library name: YP_001111258.1_SELEX_cycle4


title: THP-1 cells, 130b Legionella infection, 5 h post-infection, biol rep 1

description: Library name: Sample 7


title: Spatial transcriptomics of mus musculus: middle-aged male brain4 mouse 14

description: Library name: AGE_14_73_Brain4_GEX31_D1

tag: mouse id

tag: Sex

tag: sequencing primer

tag: permeabilization time_(minutes)


title: YP_001111256.1_SELEX_cycle4

description: Library name: YP_001111256.1_SELEX_cycle4

tag: tissue


title: Spatial transcriptomics of mus musculus: middle-aged male brain3 mouse 14

description: Library name: AGE_14_73_Brain3_GEX31_C1

tag: slice thickness_(um)

tag: cohort


title: THP-1 cells, deltalpg1666 Legionella infection, 5h post-infection, biol rep 3

description: Library name: Sample 6

tag: cell type


title: YP_001111256.1_SELEX_cycle0

description: Library name: YP_001111256.1_SELEX_cycle0

tag: protein id

tag: cycle


title: YP_010782993.1_SELEX_cycle4

description: Library name: YP_010782993.1_SELEX_cycle4


title: THP-1 cells, deltalpg1666 Legionella infection, 5 h post-infection, biol rep 2

description: Library name: Sample 5


title: Spatial transcriptomics of mus musculus: middle-aged male brain2 mouse 14

description: Library name: AGE_14_73_Brain2_GEX31_B1

tag: age

tag: slide

tag: area

tag: technology


title: YP_001111258.1_SELEX_cycle0

description: Library name: YP_001111258.1_SELEX_cycle0


title: YP_010782993.1_SELEX_cycle0

description: Library name: YP_010782993.1_SELEX_cycle0


title: Spatial transcriptomics of mus musculus: middle-aged male brain1 mouse 14

description: Library name: AGE_14_73_Brain1_GEX31_A1

tag: strain

tag: genotype

tag: treatment

tag: disease


title: NP_043126.1_SELEX_cycle4

description: Library name: NP_043126.1_SELEX_cycle4


title: THP-1 cells, deltalpg1666 Legionella infection, 5 h post-infection, biol rep 1

description: Library name: Sample 4

tag: cell line


title: YP_717939.1_SELEX_cycle4

description: Library name: YP_717939.1_SELEX_cycle4


description: Library name: NP_043126.1_SELEX_cycle0,YP_001974456.1_SELEX_cycle0,YP_009137113.1_SELEX_cycle0


description: Library name: YP_717939.1_SELEX_cycle0, YP_009111420.1_SELEX_cycle0


title: THP-1 cells, WT Legionella infection, 5 h post-infection, biol rep 3

description: Library name: Sample 3


title: Spatial transcriptomics of mus musculus: young male spleen mouse 13

description: Library name: AGE_13_17_Spleen_GEX44_B1

tag: mouse id

tag: Sex

value: 17 weeks

tag: sequencing primer

tag: disease stage


title: Spatial transcriptomics of mus musculus: young male lung mouse 13

description: Library name: AGE_13_17_Lung_GEX6_A1

tag: tissue

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: YP_010509362.1_SELEX_cycle4

description: Library name: YP_010509362.1_SELEX_cycle4

value: synthetic construct

tag: protein id

tag: cycle


title: THP-1 cells, WT Legionella infection, 5 h post-infection, biol rep 2

description: Library name: Sample 2

tag: cell type


title: YP_010509362.1_SELEX_cycle0

description: Library name: YP_010509362.1_SELEX_cycle0


title: NP_570541.1_SELEX_cycle4

description: Library name: NP_570541.1_SELEX_cycle4


title: Spatial transcriptomics of mus musculus: young male liver mouse 13

description: Library name: AGE_13_17_Liver_GEX39_A1

tag: age

tag: slide

tag: area

tag: technology

value: Wildtype


title: NP_570541.1_SELEX_cycle0

description: Library name: NP_570541.1_SELEX_cycle0


title: THP-1 cells, WT Legionella infection, 5 h post-infection, biol rep 1

description: Library name: Sample 1

tag: treatment


title: C2C12_2xFS-hsRTL1_T2a_GFP_dox

city: New York

first: Benjamin

last: Kleaveland

address: 1300 York Ave

department: Pathology and Lab Medicine

institute: Weill Cornell Medicine

description:
Library name: C2C12_2xFS-hsRTL1_T2a_GFP_dox
stranded
C2C12_hsRTL1_DESeq2.csv

data_processing:
Alignment and differential expression of the RNA-seq libraries was performed using the nf-core pipeline. Briefly, the default RNAseq pipeline was used, specifying STAR alignment and using a salmon counter. Reads were aligned to the mouse genome (mm39) using STAR v2.7.1a and Gencode annotations (m39.gencode.vM25.basic.annotation.gtf; downloaded 7/10/23). For mouse tissues, the gtf file was modified to include Rtl1as using the same coordinates as Rtl1 exon 2. For C2C12 cell lines, the mouse genome and gtf annotation file were modified to include the corresponding piggyBac sequences and either Rtl1, RTL1, or Halo transgenes as an artificial chromosome. As no reads mapped to the endogenous Rtl1 locus in Halo-expressing C2C12 cells, we excluded endogenous Rtl1 from any downstream analysis. Count files were merged to generate tables of gene counts for each tissue organized by genotype. For mouse tissue libraries, salmon.merged.gene_counts_length_scaled.tsv were imported directly into DESeq2; for C2C12 libraries, salmon.merged.gene_counts.tsv and salmon.merged.gene_lengths.tsv were imported into DESeq2 via tximport. Differential expression was performed using DESeq2 without the lfcShrink function.80
Assembly: mm39
Supplementary files format and content: comma-separated text file of DESeq2 output includes gene name, baseMean, log2 fold change, lfcSE, stat, p-value, adjusted p-value, raw counts, and normalized counts

extract_protocol:
Total RNA was extracted from mouse tissues using TRI Reagent (ThermoFisher) according to the manufacturer’s protocol with the following modifications. Mouse tissues were rapidly dissected after CO2-based euthanasia and flash frozen in Eppendorf tubes in liquid N2. Tissue was transferred to a 15 mL conical tube, 1–2 mL of TRI Reagent was added, and the tissue was homogenized with a TissueRuptor (Qiagen) and disposable probes. Samples were transferred to Eppendorf tubes (1 mL per tube) and phase separated with 200 μL chloroform (J.T. Baker Analytical). After isopropanol precipitation and two 70% ethanol washes, total RNA was resuspended in water. Small-RNA sequencing libraries were prepared with 2 μg of total RNA from each diaphragm (n = 2–3 biological replicates per genotype). RNAs that co-migrated within the range of 17 and 32 nt radiolabeled internal standards run in adjacent lanes were isolated on a 15% polyacrylamide urea gel. Gel slices were macerated and RNA was eluted overnight at 4C in 400 μL of 0.3 M NaCl. After Spin-X column (Corning CLS8170) cleanup, RNA was precipitated for >2 hours at –20C with 3 μL of GlycoBlue (ThermoFisher AM9515) and 1 mL of 100% ethanol and then resuspended in 8 μL RNase-free H2O.
NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760) was used to generate stranded, poly(A)-selected RNA-seq libraries. Briefly, 1 μg of total RNA was poly(A) enriched and then reverse transcribed into double-strand cDNA. The cDNA samples were fragmented, end-repaired, and polyadenylated before ligation of TruSeq adapters containing an index sequence for multiplex sequencing. Multiplexing fragments containing TruSeq adapters on both ends were selectively enriched with 8–9 PCR cycles. All libraries were sequenced on the NovaseqX (Illumina) with 100 nt paired-end reads and ~20 million reads per sample.

tag: cell line

value: Treated


title: Spatial transcriptomics of mus musculus: young male heart mouse 13

description: Library name: AGE_13_17_Heart_GEX43_C1

tag: strain

tag: mouse id

tag: genotype

tag: disease


title: TEX_RVU120_72h-3

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

description: Library name: S6577Nr30

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2). The quality of the FASTQ files was analyzed with FastQC (version 0.11.5)
The resulting fastq files were mapped to the reference genome (hg38) using STAR aligner (PMID: 23104886) version 2.7.10a with default parameters.
The read assignments per gene were counted using htseq-count (version 0.11.1), using default counting mode and reverse string assignment to genes.
Assembly: hg38
Supplementary files format and content: htseq-count files

source_name: TEX

growth_protocol: TEX cells were cultured in a humidified 5% CO₂ atmosphere at 37°C  in IMDM medium, supplemented with 15% FBS, 20 ng/ml SCF, and 2 ng/ml IL-3 (PeproTech, Cranbury, NJ, USA).

extract_protocol:
Total RNA was isolated from 1 million cells TEX using the DirektZol kit (Zymo Research), all samples were DNase-treated, and eluted with 50 µl of water.  The quality and quantity of isolated RNA was analyzed using the 2100 Bioanalyzer System (Agilent 2100 bioanalyzer Eukaryote Total RNA Nano Series II Kit). RNA sequencing was performed by the CeGaT company (≥ 1 µg of RNA with a concentration of ≥ 40 ng/µl in at least 25 µl total volume)
The libraries were prepared at CeGaT using 100ng of input mRNA and the TruSeq Stranded mRNA kit and then sequenced there on NovaSeq 6000 using 2x 100bp sequencing.

treatment_protocol: TEX cells were treated with RVU120 (0.5mM), CCT251921 (0.5mM), or DMSO (5%) for 3h, 24h, and 72h in three biological replicates.

value: TEX

tag: time point


title: C2C12_2xFS-hsRTL1_T2a_GFP_no_dox

description:
Library name: C2C12_2xFS-hsRTL1_T2a_GFP_no_dox
stranded
C2C12_hsRTL1_DESeq2.csv

value: Untreated


title: C2C12_hsRTL1-Halo_T2a_GFP_dox

description:
Library name: C2C12_hsRTL1-Halo_T2a_GFP_dox
stranded
C2C12_hsRTL1_DESeq2.csv


title: TEX_RVU120_72h-2

description: Library name: S6577Nr29


title: C2C12_hsRTL1-Halo_T2a_GFP_no_dox

description:
Library name: C2C12_hsRTL1-Halo_T2a_GFP_no_dox
stranded
C2C12_hsRTL1_DESeq2.csv


title: Spatial transcriptomics of mus musculus: young male brain4 mouse 13

description: Library name: AGE_13_17_Brain4_GEX29_D1

tag: tissue

tag: Sex

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: disease stage


title: Spatial transcriptomics of mus musculus: young male brain5 mouse 13

description: Library name: AGE_13_17_Brain5_GEX30_A1

tag: slice thickness_(um)

tag: cohort


title: C2C12_hsRTL1_T2a_GFP_dox

description:
Library name: C2C12_hsRTL1_T2a_GFP_dox
stranded
C2C12_hsRTL1_DESeq2.csv


title: TEX_RVU120_72h-1

description: Library name: S6577Nr28


title: C2C12_hsRTL1_T2a_GFP_no_dox

description:
Library name: C2C12_hsRTL1_T2a_GFP_no_dox
stranded
C2C12_hsRTL1_DESeq2.csv


title: Spatial transcriptomics of mus musculus: young male brain3 mouse 13

description: Library name: AGE_13_17_Brain3_GEX29_C1

tag: age

tag: slide


title: TEX_Merck_72h-3

description: Library name: S6577Nr27


title: C2C12_2xFS-mmRtl1_T2a_GFP_dox

description:
Library name: C2C12_2xFS-mmRtl1_T2a_GFP_dox
stranded
C2C12_mmRtl1_DESeq2.csv


title: Spatial transcriptomics of mus musculus: young male brain2 mouse 13

description: Library name: AGE_13_17_Brain2_GEX29_B1

tag: area

tag: technology


title: C2C12_mmRtl1-Halo_T2a_GFP_dox

description:
Library name: C2C12_mmRtl1-Halo_T2a_GFP_dox
stranded
C2C12_mmRtl1_DESeq2.csv

tag: cell line

tag: treatment


title: TEX_Merck_72h-2

description: Library name: S6577Nr26


title: C2C12_2xFS-mmRtl1_T2a_GFP_no_dox

description:
Library name: C2C12_2xFS-mmRtl1_T2a_GFP_no_dox
stranded
C2C12_mmRtl1_DESeq2.csv


title: C2C12_mmRtl1-Halo_T2a_GFP_no_dox

description:
Library name: C2C12_mmRtl1-Halo_T2a_GFP_no_dox
stranded
C2C12_mmRtl1_DESeq2.csv


title: Spatial transcriptomics of mus musculus: young male brain1 mouse 13

description: Library name: AGE_13_17_Brain1_GEX29_A1

tag: strain

tag: mouse id


title: C2C12_mmRtl1_T2a_GFP_dox

description:
Library name: C2C12_mmRtl1_T2a_GFP_dox
stranded
C2C12_mmRtl1_DESeq2.csv


title: C2C12_mmRtl1_T2a_GFP_no_dox

description:
Library name: C2C12_mmRtl1_T2a_GFP_no_dox
stranded
C2C12_mmRtl1_DESeq2.csv


title: TEX_Merck_72h-1

description: Library name: S6577Nr25


title: TEX_DMSO_72h-3

description: Library name: S6577Nr24

value: DMSO


title: C2C12_2xFS-Halo_T2a_GFP_no_dox_Rep3

description:
Library name: C2C12_2xFS-Halo_T2a_GFP_no_dox_Rep3
stranded
C2C12_Halo_DESeq2.csv


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

description: Library name: AGE_12_112_Spleen_GEX36_B1

value: Spleen

value: 112 weeks

tag: genotype

tag: disease


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

description: Library name: AGE_12_112_Lung_GEX6_C1

tag: tissue

value: Lung


title: E125-CKO3

city: Shanghai

first: Yuze

last: Wang

address: Shanghai Minhang District Dongchuan Road No. 800

institute: Shanghai Jiao Tong University

description:
Library name: CKO3
Column name in_raw_counts_All_samples.txt:CKO3

data_processing:
CLC Genomics Workbench
Assembly: CRCm38/mm10
Supplementary files format and content: Tab-delimited text file; gene-level raw read counts across all samples

extract_protocol:
RNA was extracted from E12.5 embryonic hearts using RNAprep Pure Micro Kit(TIANGE, China) ,500ng of total RNA was used for construction of sequencing libraries
Sequencing libraries were prepared with NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) and subjected to the next_x001E_generation sequencing on a Illumina HiSeq platform

tag: cell type

value: mixed embryonic cardiac cells

value: TRIM28 knockdown


title: TEX_DMSO_72h-2

description: Library name: S6577Nr23

tag: time point


title: E125-CKO2

description:
Library name: CKO2
Column name in_raw_counts_All_samples.txt:CKO2


title: C2C12_2xFS-Halo_T2a_GFP_dox_Rep2

description:
Library name: C2C12_2xFS-Halo_T2a_GFP_dox_Rep2
stranded
C2C12_Halo_DESeq2.csv


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

description: Library name: AGE_12_112_Liver_GEX37_A1

value: Liver

tag: Sex

value: male

tag: sequencing primer

tag: permeabilization time_(minutes)


title: TEX_DMSO_72h-1

description: Library name: S6577Nr22


title: C2C12_2xFS-Halo_T2a_GFP_no_dox_Rep2

description:
Library name: C2C12_2xFS-Halo_T2a_GFP_no_dox_Rep2
stranded
C2C12_Halo_DESeq2.csv


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

description: Library name: AGE_12_112_Heart_GEX43_A1

value: Heart

tag: slice thickness_(um)

tag: cohort

value: Aging

tag: disease stage


title: C2C12_2xFS-Halo_T2a_GFP_dox_Rep1

description:
Library name: C2C12_2xFS-Halo_T2a_GFP_dox_Rep1
stranded
C2C12_Halo_DESeq2.csv


title: E125-CKO1

description:
Library name: CKO1
Column name in_raw_counts_All_samples.txt:CKO1


title: TEX_RVU120_3h-3

description: Library name: S6577Nr21


title: E125-CTR3

description:
Library name: CTR3
Column name in_raw_counts_All_samples.txt:CTR3

value: WT


title: TEX_RVU120_3h-2

description: Library name: S6577Nr20


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

description: Library name: AGE_11_73_Spleen_GEX36_A1

tag: age

value: 73 weeks

tag: slide

tag: area

value: 10x Visium


title: C2C12_2xFS-Halo_T2a_GFP_no_dox_Rep1

description:
Library name: C2C12_2xFS-Halo_T2a_GFP_no_dox_Rep1
stranded
C2C12_Halo_DESeq2.csv

tag: cell line

tag: treatment


title: E125-CTR2

description:
Library name: CTR2
Column name in_raw_counts_All_samples.txt:CTR2


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

description: Library name: AGE_11_73_Lung_GEX6_B1

tag: strain

tag: mouse id

tag: technology

value: Wildtype


title: TEX_RVU120_3h-1

description: Library name: S6577Nr19


title: E19Placenta_AGO2_CDN3

description:
Library name: E19Placenta_AGO2_CDN3
stranded
E19Placenta_CDNvPN_DESeq2.csv

source_name: Placenta

tag: tissue

value: Placenta

tag: Stage

tag: genotype

tag: background

value: C57BL/6J and C57BL/6N


title: E125-CTR1

description:
Library name: CTR1
Column name in_raw_counts_All_samples.txt:CTR1

tag: cell type


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

description: Library name: AGE_11_73_Liver_GEX3_A1

tag: Sex

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: disease


title: TEX_Merck_3h-3

description: Library name: S6577Nr18

value: TEX

tag: time point


title: E19Placenta_AGO2_PN4

description:
Library name: E19Placenta_AGO2_PN4
stranded
E19Placenta_CDNvPN_DESeq2.csv


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

description: Library name: AGE_11_73_Heart_GEX43_B1

tag: age

tag: slide

tag: slice thickness_(um)

tag: cohort

tag: disease stage


title: BKV, Experimental, 3dpi, HVEC6

city: Pittsburgh

first: Jim

last: Pipas

state: PA

address: 5th and Tennyson

institute: University of Pittsburgh

description:
Library name: BKV_R9
InDrops scRNAseq

library_source: transcriptomic single cell

data_processing:
Indrops software (https://github.com/indrops/indrops) was used to process the raw reads. The min-reads argument for the “quantify” step of Indrops was set independently for each library to obtain a number of cells similar to the number of cells sequenced.
Assembly: ENSEMBL hg38 release 90 version + the BKV genome (NC_001538.1) was used for alignment
Supplementary files format and content: InDrops raw counts.tsv file, Cell barcodes (rows) X Gene symbols (columns)

source_name: Lung vascular endothelium

extract_protocol:
Citation: An P, Cantalupo PG, Zheng W, Sáenz-Robles MT, Duray AM, Weitz D, Pipas JM. 2021. Single-cell transcriptomics reveals a heterogeneous cellular response to BK virus infection. J Virol 95:e02237-20. https://doi.org/10.1128/JVI.02237-20.
Citation: An P, Cantalupo PG, Zheng W, Sáenz-Robles MT, Duray AM, Weitz D, Pipas JM. 2021. Single-cell transcriptomics reveals a heterogeneous cellular response to BK virus infection. J Virol 95:e02237-20. https://doi.org/10.1128/JVI.02237-20.

value: Lung vascular endothelium

tag: cell line

value: HVEC

value: Endothelial

tag: treatment

value: BKV infection

tag: batch

value: RunB

tag: donor number


title: TEX_Merck_3h-2

description: Library name: S6577Nr17


title: Subject ZA0010752, Visit 1

description: Library name: ZA0010752.Visit.1

tag: tissue

value: Whole blood

tag: subject

tag: visit

tag: day post_prior_vaccition

tag: prior vaccition

value: Tertiary

tag: infection status

value: Uninfected

tag: infection category

value: Healthy

tag: study

value: NX


title: E19Placenta_AGO2_PN2

description:
Library name: E19Placenta_AGO2_PN2
stranded
E19Placenta_CDNvPN_DESeq2.csv

tag: Stage

tag: genotype

tag: background


title: Mock, Control, 3dpi, HVEC6

description:
Library name: Mock_R9
InDrops scRNAseq

tag: cell type

value: Mock infection


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

description: Library name: AGE_10_17_Spleen_GEX35_D1

value: Spleen

tag: strain

tag: mouse id

tag: Sex

value: male

tag: age

value: 17 weeks

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: Aging

tag: technology

tag: disease

tag: disease stage


title: TEX_Merck_3h-1

description: Library name: S6577Nr16

tag: cell line

tag: treatment

tag: time point


title: TEX_DMSO_3h-3

description: Library name: S6577Nr15

value: DMSO


title: E19Placenta_AGO2_CDN2

description:
Library name: E19Placenta_AGO2_CDN2
stranded
E19Placenta_CDNvPN_DESeq2.csv

tag: tissue

value: Placenta

tag: Stage

tag: genotype

tag: background

value: C57BL/6J and C57BL/6N


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

description: Library name: AGE_10_17_Liver_GEX38_B1

value: Liver

tag: strain

tag: mouse id

tag: Sex

tag: age

value: 10x Visium

value: Wildtype


title: E19Placenta_AGO2_PN1

description:
Library name: E19Placenta_AGO2_PN1
stranded
E19Placenta_CDNvPN_DESeq2.csv


title: BKV, Experimental, 3dpi, HVEC4

description:
Library name: BKV_R5
InDrops scRNAseq

value: Lung vascular endothelium

value: HVEC

tag: cell type

value: Endothelial

value: BKV infection

tag: batch

value: RunA

tag: donor number


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

description: Library name: AGE_10_17_Kidney_GEX8_C1

value: Kidney

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology


title: Mock, Control, 3dpi, HVEC4

description:
Library name: Mock_R5
InDrops scRNAseq

tag: tissue

tag: cell line

tag: treatment

value: Mock infection


title: TEX_DMSO_3h-2

description: Library name: S6577Nr14

value: TEX

tag: time point


title: E19Placenta_AGO2_CDN1

description:
Library name: E19Placenta_AGO2_CDN1
stranded
E19Placenta_CDNvPN_DESeq2.csv

tag: Stage

tag: genotype

tag: background


title: ECN90 INS-KO-3

city: Paris

first: Farah

last: Kobaisi

address: 123 Bvd Port Royal

country: France

institute: Institute Cochin

description:
Library name: Sample 6
coloumn name in normalized counts-all samples.tsv: INS-KO_DMEM-F12_3

data_processing:
STAR algorithm (version 2.7.6a)
Reads were then count using RSEM (v1.3.1) and the statistical analyses on the read counts were performed with R (version 3.6.3) and the DESeq2 package (DESeq2_1.26.0) to determine the proportion of differentially expressed genes between two conditions.
We used the standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function)
Assembly: the Ensembl Homo Sapiens GRCh38 reference, release 101.
Supplementary files format and content: txt file including RSEM normalized counts for all samples

source_name: pancreas

extract_protocol:
RNA was extracted using RNeasy Mini kit (Qiagen)  For library construction, 5ng of total RNA for each sample in triplicate
RNA libraries were prepared using Ovation Solo RNA-seq Kit (NuGEN) according to the manufacturer’s instructions. library amplification, rRNA was depleted using AnyDeplete (NuGEN)

value: pancreas

tag: cell type

value: pancreatic beta cell line

value: INS-KO


title: TEX_DMSO_3h-1

description: Library name: S6577Nr13

value: DMSO


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

description: Library name: AGE_10_17_Heart_GEX42_A1

value: Heart

tag: strain

tag: mouse id

tag: Sex

value: male

tag: age

value: 17 weeks

value: Aging

tag: disease

tag: disease stage


title: E19Lung_AGO2_CDN3

description:
Library name: E19Lung_AGO2_CDN3
stranded
E19Lung_CDNvPN_DESeq2.csv

value: Lung

value: C57BL/6J and C57BL/6N


title: TEX_TO-3

description: Library name: S6577Nr12


title: E19Lung_AGO2_PN3

description:
Library name: E19Lung_AGO2_PN3
stranded
E19Lung_CDNvPN_DESeq2.csv


title: ECN90 INS-KO-2

description:
Library name: Sample 5
coloumn name in normalized counts-all samples.tsv: INS-KO_DMEM-F12_2

tag: batch


title: Spatial transcriptomics of mus musculus: old male lung mouse 9

description: Library name: AGE_9_112_Lung_GEX5_B1

value: 112 weeks

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

value: 10x Visium

value: Wildtype


title: TEX_TO-2

description: Library name: S6577Nr11

tag: cell line

tag: treatment

tag: time point


title: E19Lung_AGO2_CDN4

description:
Library name: E19Lung_AGO2_CDN4
stranded
E19Lung_CDNvPN_DESeq2.csv

tag: tissue

tag: Stage

tag: genotype

tag: background


title: Spatial transcriptomics of mus musculus: old male spleen mouse 9

description: Library name: AGE_9_112_Spleen_GEX35_C1

value: Spleen

tag: strain

tag: mouse id

tag: Sex

tag: age

tag: technology


title: ECN90 INS-KO-1

description:
Library name: Sample 4
coloumn name in normalized counts-all samples.tsv: INS-KO_DMEM-F12_1

tag: cell type

tag: batch


title: Spatial transcriptomics of mus musculus: old male liver mouse 9

description: Library name: AGE_9_112_Liver_GEX37_C1

value: Liver

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: disease

tag: disease stage


title: TEX_TO-1

description: Library name: S6577Nr10

tag: cell line

tag: treatment

tag: time point


title: ECN90 WT-3

description:
Library name: Sample 3
coloumn name in normalized counts-all samples.tsv: ECN90_DMEM-F12_3

tag: tissue

tag: genotype

value: WT

value: untreated


title: E19Lung_AGO2_PN4

description:
Library name: E19Lung_AGO2_PN4
stranded
E19Lung_CDNvPN_DESeq2.csv

tag: Stage

tag: background


title: TEX_RVU120_24h-3

description: Library name: S6577Nr9

value: TEX


title: ECN90 WT-2

description:
Library name: Sample 2
coloumn name in normalized counts-all samples.tsv: ECN90_DMEM-F12_2

value: pancreas

value: pancreatic beta cell line


title: Spatial transcriptomics of mus musculus: old male kidney mouse 9

description: Library name: AGE_9_112_Kidney_GEX9_C1

value: Kidney

tag: strain

tag: mouse id

tag: Sex

tag: age

tag: slice thickness_(um)

tag: cohort


title: E19Lung_AGO2_PN2

description:
Library name: E19Lung_AGO2_PN2
stranded
E19Lung_CDNvPN_DESeq2.csv


title: Subject 1.30037, Visit 2

description: Library name: 1.30037.Visit.2

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: Report says after

tag: study

value: AZ


title: Subject 1.30097, Visit 6

description: Library name: 1.30097.Visit.6

tag: tissue

value: Secondary

value: Uninfected

value: Healthy


title: ECN90 WT-1

description:
Library name: Sample 1
coloumn name in normalized counts-all samples.tsv: ECN90_DMEM-F12_1

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: batch


title: E19Lung_AGO2_CDN2

description:
Library name: E19Lung_AGO2_CDN2
stranded
E19Lung_CDNvPN_DESeq2.csv

value: Lung

tag: Stage

tag: background

value: C57BL/6J and C57BL/6N


title: TEX_RVU120_24h-1

description: Library name: S6577Nr7

tag: time point


title: SM24_NFIX_THKO_3x

city: HOUSTON

first: Sanjana

last: Murali

state: TX

address: 7600 Kirby Drive

institute: Baylor College of Medicine

description: Library name: SAMPLE 24

data_processing:
Quality control was performed using fastQC (v0.10.1) and MultiQC (v0.9) . Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). In R(v3.5.2) Bioconductor packages GenomicAlignments (v1.16.0) and GenomicFeatures (v1.32.2) were used to build count matrices (Lawrence et al., 2013). UCSC transcripts were downloaded from Illumina iGenomes in GTF file format. Normalization and differential gene expression analysis were performed using DESeq2 (v1.20.0). Gene Ontologies were determined using Enrichr and visualized using GOplot (v1.0.2).
Assembly: Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a).
Supplementary files format and content: csv file with raw counts for each sample

source_name: Thalamus

extract_protocol:
RNA was extracted from sorted cells using RNeasyMicro Kit (Cat.No. 4004, QIAGEN). RNA integrity (RINR8.0) was assessed using the High Sensitivity RNA Analysis Kit (DNF-472-0500, Agilent) on a 12-Capillary Fragment Analyzer.
cDNA synthesis and Illumina sequencing libraries with 8-bp single indices were constructed from 10 ng total RNA using the Revelo RNA-seq High Sensitivity kit (Cat.No. 30184149, TECAN).

value: Thalamus

value: KO


title: Spatial transcriptomics of mus musculus: old male brain5 mouse 9

description: Library name: AGE_9_112_Brain5_GEX30_D1

value: Brain

tag: strain

tag: mouse id

tag: Sex

value: male

tag: age

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: 10x Visium

value: Wildtype

tag: disease

tag: disease stage


title: SM23_NFIX_THKO_2x

description: Library name: SAMPLE 23

tag: tissue

tag: genotype


title: TEX_Merck_24h-3

description: Library name: S6577Nr6

tag: cell line

value: TEX

tag: treatment


title: Spatial transcriptomics of mus musculus: old male brain4 mouse 9

description: Library name: AGE_9_112_Brain4_GEX28_D1

tag: strain


title: E19Liver_AGO2_PN3

description:
Library name: E19Liver_AGO2_PN3
stranded
E19Liver_CDNvPN_DESeq2.csv

value: Liver

tag: Stage

tag: background


title: Spatial transcriptomics of mus musculus: old male brain3 mouse 9

description: Library name: AGE_9_112_Brain3_GEX28_C1

tag: mouse id

tag: Sex

tag: age


title: TEX_Merck_24h-2

description: Library name: S6577Nr5

tag: time point


title: E19Liver_AGO2_CDN4

description:
Library name: E19Liver_AGO2_CDN4
stranded
E19Liver_CDNvPN_DESeq2.csv


title: SM21_NFIX_THcontrol_3x

description: Library name: SAMPLE 21

value: WT


title: Spatial transcriptomics of mus musculus: old male brain2 mouse 9

description: Library name: AGE_9_112_Brain2_GEX28_B1

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)


title: TEX_Merck_24h-1

description: Library name: S6577Nr4


title: E19Liver_AGO2_PN4

description:
Library name: E19Liver_AGO2_PN4
stranded
E19Liver_CDNvPN_DESeq2.csv


title: Spatial transcriptomics of mus musculus: old male brain1 mouse 9

description: Library name: AGE_9_112_Brain1_GEX28_A1

tag: slice thickness_(um)

tag: cohort

tag: technology

tag: disease


title: TEX_DMSO_24h-3

description: Library name: S6577Nr3

tag: cell line

value: DMSO


title: E19Liver_AGO2_PN2

description:
Library name: E19Liver_AGO2_PN2
stranded
E19Liver_CDNvPN_DESeq2.csv

tag: tissue

tag: genotype


title: Spatial transcriptomics of mus musculus: middle-aged male spleen mouse 8

description: Library name: AGE_8_73_Spleen_GEX35_A1

value: Spleen

tag: strain

value: 73 weeks

tag: treatment

tag: disease stage


title: E19Liver_AGO2_CDN2

description:
Library name: E19Liver_AGO2_CDN2
stranded
E19Liver_CDNvPN_DESeq2.csv

tag: Stage

tag: background


title: Spatial transcriptomics of mus musculus: middle-aged male kidney mouse 8

description: Library name: AGE_8_73_Kidney_GEX8_A1

value: Kidney

tag: mouse id

tag: Sex

tag: age


title: SM18_NFIX_CTXKO_3x

description: Library name: SAMPLE 18

source_name: Cortex

value: Cortex


title: E19Liver_AGO2_CDN1

description:
Library name: E19Liver_AGO2_CDN1
stranded
E19Liver_CDNvPN_DESeq2.csv

value: C57BL/6J and C57BL/6N


title: TEX_DMSO_24h-1

description: Library name: S6577Nr1

tag: time point


title: SM17_NFIX_CTXKO_2x

description: Library name: SAMPLE 17


title: Spatial transcriptomics of mus musculus: middle-aged male heart mouse 8

description: Library name: AGE_8_73_Heart_GEX42_C1

value: Heart

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)


title: E19Heart_AGO2_CDN3

description:
Library name: E19Heart_AGO2_CDN3
stranded
E19Heart_CDNvPN_DESeq2.csv


title: Spatial transcriptomics of mus musculus: middle-aged male brain5 mouse 8

description: Library name: AGE_8_73_Brain5_GEX30_B1

tag: slice thickness_(um)

tag: cohort

tag: technology

tag: disease


title: SM16_NFIX_CTXKO_1x

description: Library name: SAMPLE 16

tag: tissue

tag: genotype

value: KO


title: PC3, RNA-seq, TKT-siRNA1

first: Zixian

address: 130 Dong'an Road, Xuhui District, Shanghai

institute: Fudan University

description:
Library name: PC3-TKT-siRNA1
PC3-RNAseq.count.tsv
PC3-RNAseq.tpm.tsv

data_processing:
ChIP-seq: Raw reads were assessed with FastQC (v0.11.9) and adapter/low-quality sequences removed using TrimGalore (v0.6.7). Clean reads were aligned to the GRCh38 reference genome with Bowtie2 (v2.2.5) under default parameters. Alignments with mapping quality < 30 or flagged as unmapped, secondary, or PCR/optical duplicates (−F 3844) were discarded using SAMtools (v1.9). Duplicate reads were further marked and removed with Picard (v2.25.1). Library complexity and enrichment were evaluated with ENCODE's Phantompeakqualtools (run_spp.R), providing fragment-length estimates for downstream analyses. Peak calling was performed with MACS3 (v3.0.0a6) using the options “--nomodel --shift 0 --extsize <fragment_length>” and a significance threshold of p < 1 × 10-3.
RNA-seq: The raw data quality was evaluated with FastQC (v0.11.9). Adapter sequences and low-quality bases were removed using AdapterRemoval (v2.3.2). The resulting clean reads were aligned to the human reference genome (GRCh38) with STAR (v2.7.9a), and the alignments were sorted with SAMtools (v1.13). Gene-level read counts were generated from the sorted BAM files using htseq-count (v0.13.5). Differentially expressed genes (DEGs) were identified with DESeq2, applying thresholds of |fold change| > 2 and FDR < 0.05. Transcript abundance in transcripts per million (TPM) was quantified using StringTie (v2.2.1).
scRNA-seq: The raw sequencing data were processed using Fastp to trim adapter sequences and low-quality bases, followed by alignment to the human GRCh38 reference genome using SeekOne®Tools for gene expression matrix generation. Subsequent analysis was performed using 10x Genomics Cell Ranger and the Seurat package (v5.2.1) in R (v4.4.2), beginning with stringent quality control to select high-quality cells based on the following criteria: 200 < nFeature_RNA < 7000, nCount_RNA > 1000 (excluding the top 3% of cells by nCount_RNA), mitochondrial gene content < 10%, and ribosomal gene content between 0-60%.
Assembly: hg38
Supplementary files format and content: bigwig and narrowPeak for ChIP-seq data (except for input sample); gene expression matrix for RNA-seq and scRNA-seq data.

extract_protocol:
The immunoprecipitated and input DNA was purified using the MinElute PCR Purification Kit (#28006, Qiagen). Total RNA was isolated using the EZ-10 DNAaway RNA Mini-Preps Kit (#B618133, Sangon Biotech). Single-cell RNA-Seq RNA extracted were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (No.K00202, SeekGene Catalog).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (#E7103L, NEB) according to the manufacturer’s instructions. RNA-seq libraries were prepared using the Stranded mRNA-seq Lib Prep Module (RK20349, Abclonal). Single-cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (No.K00202, SeekGene Catalog).

tag: cell line

tag: cell type

value: Prostate cancer cell line


title: E19Heart_AGO2_PN3

description:
Library name: E19Heart_AGO2_PN3
stranded
E19Heart_CDNvPN_DESeq2.csv

tag: Stage

tag: background


title: SM15_NFIX_CTXcontrol 3x

description: Library name: SAMPLE 15


title: SM14_NFIX_CTXcontrol 2x

description: Library name: SAMPLE 14


title: E19Heart_AGO2_CDN4

description:
Library name: E19Heart_AGO2_CDN4
stranded
E19Heart_CDNvPN_DESeq2.csv


title: Spatial transcriptomics of mus musculus: middle-aged male brain3 mouse 8

description: Library name: AGE_8_73_Brain3_GEX27_C1

value: Brain

tag: strain

tag: mouse id

tag: Sex

value: male

tag: treatment

tag: disease stage


title: E19Heart_AGO2_PN4

description:
Library name: E19Heart_AGO2_PN4
stranded
E19Heart_CDNvPN_DESeq2.csv


title: PC3, RNA-seq, ctr1

description:
Library name: PC3-ctr1
PC3-RNAseq.count.tsv
PC3-RNAseq.tpm.tsv


title: Spatial transcriptomics of mus musculus: middle-aged male brain2 mouse 8

description: Library name: AGE_8_73_Brain2_GEX27_B1

tag: age

tag: slide

tag: area

tag: sequencing primer

value: Aging


title: SM13_NFIX_CTXcontrol 1x

description: Library name: SAMPLE 13


title: SM12_NFIX_HCKO_3x

description: Library name: SAMPLE 12

source_name: Hippocampus

value: Hippocampus


title: Spatial transcriptomics of mus musculus: middle-aged male brain1 mouse 8

description: Library name: AGE_8_73_Brain1_GEX27_A1

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort

tag: technology

value: 10x Visium

value: Wildtype


title: PC3, ChIP-seq, TKT

description: Library name: PC3-TKT

tag: cell line


title: E19Heart_AGO2_CDN2

description:
Library name: E19Heart_AGO2_CDN2
stranded
E19Heart_CDNvPN_DESeq2.csv

tag: tissue

tag: genotype


title: Spatial transcriptomics of mus musculus: young male spleen mouse 7

description: Library name: AGE_7_17_Spleen_GEX34_D1

value: 17 weeks

tag: disease


title: 22Rv1, ChIP-seq, Input

description: Library name: 22Rv1-Input

tag: cell type


title: E19Heart_AGO2_CDN1

description:
Library name: E19Heart_AGO2_CDN1
stranded
E19Heart_CDNvPN_DESeq2.csv

tag: Stage

tag: background


title: SM10_NFIX_HCKO_1x

description: Library name: SAMPLE 10


title: Spatial transcriptomics of mus musculus: young male lung mouse 7

description: Library name: AGE_7_17_Lung_GEX4_A1

value: Lung

tag: strain

tag: mouse id

tag: Sex

tag: treatment


title: 22Rv1, ChIP-seq, H3K27ac

description: Library name: 22Rv1-H3K27ac


title: Spatial transcriptomics of mus musculus: young male liver mouse 7

description: Library name: AGE_7_17_Liver_GEX38_A1

source_name: Liver

value: Liver

tag: age

tag: slide

tag: area

tag: disease stage


title: SM9_NFIX_HCcontrol_3x

description: Library name: SAMPLE 9

value: WT


title: LNCaP, ChIP-seq, Input

description: Library name: LNCaP-Input

source_name: LNCaP

value: LNCaP


title: E19Diaphragm_AGO2_CDFL3

description:
Library name: E19Diaphragm_AGO2_CDFL3
stranded
E19Diaphragm_CDFLvPFL_DESeq2.csv

source_name: Diaphragm

value: Diaphragm


title: Spatial transcriptomics of mus musculus: young male kidney mouse 7

description: Library name: AGE_7_17_Kidney_GEX8_B1

source_name: Kidney

value: Kidney

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: slice thickness_(um)

tag: cohort


title: SM8_NFIX_HCcontrol_2x

description: Library name: SAMPLE 8

tag: tissue

tag: genotype


title: LNCaP, ChIP-seq, H3K27ac

description: Library name: LNCaP-H3K27ac

tag: cell line

tag: cell type


title: E19Diaphragm_AGO2_CDFL1

description:
Library name: E19Diaphragm_AGO2_CDFL1
stranded
E19Diaphragm_CDFLvPFL_DESeq2.csv

tag: Stage

tag: background

value: C57BL/6J and C57BL/6N


title: Spatial transcriptomics of mus musculus: young male brain5 mouse 7

description: Library name: AGE_7_17_Brain5_GEX26_D1

tag: strain

tag: mouse id

tag: technology

tag: disease


title: VCaP, ChIP-seq, Input

description: Library name: VCaP-Input

source_name: VCaP

value: VCaP


title: E19Diaphragm_AGO2_PFL2

description:
Library name: E19Diaphragm_AGO2_PFL2
stranded
E19Diaphragm_CDFLvPFL_DESeq2.csv


title: Spatial transcriptomics of mus musculus: young male brain4 mouse 7

description: Library name: AGE_7_17_Brain4_GEX25_D1

tag: Sex

tag: age

tag: slide

tag: treatment


title: SM6_NFIX_OBKO_3x

description: Library name: SAMPLE 6

source_name: Olfactory Bulb

value: Olfactory Bulb

value: KO


title: E19Diaphragm_AGO2_CDFL2

description:
Library name: E19Diaphragm_AGO2_CDFL2
stranded
E19Diaphragm_CDFLvPFL_DESeq2.csv


title: Spatial transcriptomics of mus musculus: young male brain3 mouse 7

description: Library name: AGE_7_17_Brain3_GEX25_C1

source_name: Brain

value: Brain

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: disease stage


title: E19Diaphragm_AGO2_PFL4

description:
Library name: E19Diaphragm_AGO2_PFL4
stranded
E19Diaphragm_CDFLvPFL_DESeq2.csv

tag: tissue

tag: genotype


title: SM5_NFIX_OBKO_2x

description: Library name: SAMPLE 5


title: T728, ChIP-seq, Input

description: Library name: T728-Input

source_name: Human prostate cancer tissue

value: Human prostate cancer tissue


title: E19Diaphragm_AGO2_PN2

description:
Library name: E19Diaphragm_AGO2_PN2
stranded
E19Diaphragm_CDNvPN_DESeq2.csv


title: Spatial transcriptomics of mus musculus: young male brain2 mouse 7

description: Library name: AGE_7_17_Brain2_GEX25_B1

value: male

tag: slice thickness_(um)

tag: cohort

value: Aging


title: SM4_NFIX_OBKO_1x

description: Library name: SAMPLE 4


title: T728, ChIP-seq, H3K27ac

description: Library name: T728-H3K27ac


title: SM7_NFIX_HCcontrol_1x

description: Library name: SAMPLE 7

value: Hippocampus


title: E19Diaphragm_AGO2_CDP3

description:
Library name: E19Diaphragm_AGO2_CDP3
stranded
E19Diaphragm_CDPvPP_DESeq2.csv

tag: Stage

tag: background


title: Spatial transcriptomics of mus musculus: young male brain1 mouse 7

description: Library name: AGE_7_17_Brain1_GEX25_A1

tag: strain

tag: mouse id

value: 10x Visium

value: Wildtype


title: TEX_RVU120_24h-2

description: Library name: S6577Nr8

tag: cell line

value: TEX

tag: time point


title: Spatial transcriptomics of mus musculus: old male heart mouse 9

description: Library name: AGE_9_112_Heart_GEX42_D1

source_name: Heart

value: Heart

tag: Sex

tag: age

value: 112 weeks

tag: technology

tag: disease


title: SM3_NFIX_Obcontrol 3x

description: Library name: SAMPLE 3

value: WT


title: E19Liver_AGO2_CDN3

description:
Library name: E19Liver_AGO2_CDN3
stranded
E19Liver_CDNvPN_DESeq2.csv

value: Liver


title: T342, ChIP-seq, Input

description: Library name: T342-Input


title: E19Diaphragm_AGO2_CDP2

description:
Library name: E19Diaphragm_AGO2_CDP2
stranded
E19Diaphragm_CDPvPP_DESeq2.csv

value: Diaphragm


title: VCaP, ChIP-seq, H3K27ac

description: Library name: VCaP-H3K27ac

tag: cell type

value: Prostate cancer cell line


title: Spatial transcriptomics of mus musculus: old male spleen mouse 6

description: Library name: AGE_6_112_Spleen_GEX34_C1

source_name: Spleen

value: Spleen

tag: slide

tag: area

tag: sequencing primer

tag: permeabilization time_(minutes)

tag: treatment


title: SM22_NFIX_THKO_1x

description: Library name: SAMPLE 22

tag: tissue

value: Thalamus

tag: genotype


title: SM2_NFIX_Obcontrol 2x

description: Library name: SAMPLE 2

value: Olfactory Bulb