title: GSC23 shCONT rep1

description:
Library name: Sample1
GSC23NT_1

value: GBM tissue

tag: cell line

tag: cell type

value: Glioblastoma stem cell

value: shCONT


title: RR

status: Public on Apr 08 2026

type: SRA

city: ShenZhen

first: Lin

last: Ma

state: Guangdong Province

address: Lihu Campus: Xueyuan Avenue, Nanshan District, Shenzhen

department: Medical School

country: China

institute: ShenZhen University

description: Library name: Sample 3

library_source: transcriptomic

data_processing:
The basic reads were converted into sequence data (also called raw data/reads) by base calling. Low quality reads were filtered, and the reads with 5’ primer contaminants and poly (A) were removed. The reads without 3’adapter and insert tag, the reads shorter than 15 nt or longer than 41 nt from the raw data were filtered, and the clean reads were obtained
The length distribution of the clean sequences in the reference genome was determined, then the sequences were aligned and subjected to the Bowtie search against Rfam v.10.1 (http://www.sanger.ac.uk/software/Rfam), rRNA, scRNA, Cis-reg, snRNA, tRNA and other RNAs were annotated and filtered. Then, cDNA sequence and Repbase database of species repeat sequence were also identified with Bowtie software. The mature miRNAs were identified by aligning against miRBase v22 database (http://www.mirbase.org/), and the expression patterns in different samples were analyzed. After that, unannotated reads were analyzed by miRDeep2 to predict novel miRNAs. Based on the hairpin structure of a pre-miRNA and the miRBase database, the corresponding miRNA star sequence and miRNA mature sequence were also identified.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for All Samples

molecule: total RNA

organism: Homo sapiens

source_name: RR

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's protocol. Quantitation of total RNA was carried out using the Nanodrop 2000 (Thermo Fisher Scientific Inc., USA). RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technology, USA). 1 μg total RNA of each sample was used for the small RNA library construction using NEBNext Small RNA Library Prep Set for Illumina kit (Cat. No. NEB#E7330S, NEB, USA) following the manufacturer’s recommendations
Briefly, total RNA were ligated to adapters at each end. Then the adapter-ligated RNA were reverse transcribed to cDNA and performed PCR amplification. The PCR products ranging from 140–160 bp were isolated and purified as small RNA libraries. Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were finally sequenced using the Illumina Novaseq 6000 platform. 150 bp paired-end reads were generated.

tag: treatment


title: RNA-Seq, Tetraodon ventral retina, biol rep1

city: Baton Rouge

first: Patricia

last: Schneider

state: Louisiana

address: LSU 131 Life Sciences Building

department: Biological Sciences

country: USA

institute: Louisiana State University

description: Library name: Tn_V1

data_processing:
High quality sequencing reads were mapped to Tetraodon nigroviridis Genome Asselmby tetNig2 using STAR V2.7.10b. Read count extraction was performed using featureCounts v2.0.6. Read count normalization and DGE analysis were performed using DEseq2.
Assembly: tetNig2
Supplementary files format and content: tab-delimited text file including raw counts for each sample

molecule: polyA RNA

organism: Tetraodon nigroviridis

source_name: Ventral retina

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen_ThermoFIsher).
mRNA enriched librraies were preparaed and sequenced at Novogene (https://www.novogene.com/us-en). Briefly, for each sample, 1 µg RNA was used to generated RNA sequencing librarires using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB,USA), follwing the manufacturee's recommendation.

tag: tissue

value: Ventral retina

tag: genotype

value: WT

tag: batch


title: Neuro B1 | 017 | TME

city: Woolloongabba

first: Fernando

last: Guimaraes

state: QLD

address: 37 Kent Street

country: Australia

institute: Frazer Institute - University of Queensland

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
Supplementary files format and content: rawdata.csv: raw count data, normdata.csv: normalised count data (We performed quality control steps to all the samples, then removed samples with nuclei count < 200 and performed normalization of all samples that  passed the quality control steps.)
Library strategy: Spatial Transcriptomics

source_name: Neuroblastoma

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring GeoMx DSP WTA kit according to manufacture's construction

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: TME

tag: staging

value: Staging  I

tag: age dx_class

value: <12 months

tag: histology

value: Poorly diferentiated

tag: mycn amplification

value: non-amplified

tag: gender

value: M

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

value: Alive

tag: risk classification

value: Low


title: Mock

description: Library name: Sample 2

source_name: Mock

tag: cell line

tag: treatment

value: IR


title: KOT3

type: RNA

city: Beijing

first: Wu

last: Meng yao

address: No.27 Taiping Road, Haidian District

institute: Beijing Institute of Basic Medical Sciences

description: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.3, LPS 4h

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: MOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

organism: Mus musculus

source_name: BMDMs,100 ng/mL LPS, 4 h,replicate 3

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: BMMs were generated by flushing bone marrow cells from femurs and tibiae of mice. Cells were cultured in RPMI 1640 medium containing 15% (v/v) FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, and 50 µM β-mercaptoethanol with 100 ng/ml M-CSF (Cetus) for 7 days.

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: With or without 100ng/ml LPS (Sigma) treatment for 4 hours.

tag: tissue

value: bone marrow

tag: cell type

value: BMDMs

tag: genotype

tag: age

value: 6-8 week


title: Neuro B1 | 017 | Tumour

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Tumor


title: CC

description: Library name: Sample 1

source_name: CC

tag: cell line

tag: treatment

value: Ctrl


title: RNA-Seq, Tetraodon dorsal retina, biol rep3

description: Library name: Tn_D3

source_name: Dorsal retina

tag: tissue

value: Dorsal retina

tag: genotype

value: WT

tag: batch


title: RNA-Seq, Tetraodon dorsal retina, biol rep4

description: Library name: Tn_D4


title: RNA-Seq, Tetraodon dorsal retina, biol rep2

description: Library name: Tn_D2


title: with OSM biol rep 2

city: Guangzhou

last: Haibin

address: Waihuan east road

institute: South china university of technology

description:
Library name: sample 20
rawcounts.xlsx

data_processing:
Sequencing was performed by Novogene (Beijing, China) on an Illumina HiSeq X-Tensequencer with 150 bp paired-end sequencing reaction. Differentially expressed genes (DEGs) were analyzed by DESeq2 using counts. Genes with P value ≤ 0.05 and fold change ≥ 2 was identified as DEGs.
Assembly: GRCh38
Supplementary files format and content: xlsx file include raw counts for each sample

source_name: H9 differentiated cells

extract_protocol:
Total RNA of organoids were extracted using RNAiso Plus kit according to the manufacturer’s instructions.
The cDNA libraries for RNA sequencing were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB).

tag: cell type

value: H9 differentiated cells

tag: sample group

value: with OSM


title: KOC3

description: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.3, no stimulation

source_name: BMDMs,100 ng/mL LPS, 0 h,replicate 3

tag: age


title: with IL6 biol rep 3

description:
Library name: sample 18
rawcounts.xlsx

value: with IL6


title: KOT1

description: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.1, LPS 4h

source_name: BMDMs,100 ng/mL LPS, 4 h,replicate 1


title: Neuro B1 | 013 | Tumour

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: staging

value: Staging  II

tag: age dx_class

value: <12 months

tag: histology

tag: mycn amplification

tag: gender

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

tag: risk classification


title: KOC2

description: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.2, no stimulation

source_name: BMDMs,100 ng/mL LPS, 0 h,replicate 2

tag: tissue

tag: cell type

tag: genotype

tag: age


title: Tetraodon dorsal retina, biol rep2

description: Library name: Tn2_D

library_source: genomic

data_processing:
Adapter sequences were removed from the reads using NGmerge (version 0.3) (Gaspar, 2018). The trimmed reads were aligned to theTetraodon reference genome (tetNig2) using Bowtie2 (version 2.2.5). Alignments were output as a BAM file, which was indexed using Samtools (version 1.18) (Li et al., 2009). The fragment size distribution graph was created using the ATACseqQC package (version 1.24.0) (Ou et al., 2018) in RStudio (version 4.3.1). The trimmed reads were name-sorted using Samtools (version 1.18) (Li et al., 2009) and further processed with Genrich (version 0.6.1) to call narrow peaks using the parameters -j -y -r -v -m -e -a -f, to remove duplicate reads, multimapped reads, and reads mapped to mitochondrial chromosomes. Downstream analysis of the ATAC-seq data was performed using DiffBind.
Assembly: tetNig2
Supplementary files format and content: tab-delimited text file including differential chromatin accessibility peaks identified from ATAC-seq data

molecule: genomic DNA

extract_protocol:
ATAC-seq libraries were prepared following the Active Motif ATAC seq protocol, which is based on a combination of the Buenrostro et al., 2013 and the Corces et al., 2017. Dorsal and ventral retinas were dissected and subsequently used for nuclei extraction.
All ATAC-seq libraries were performed from 50,000 cells and were amplified within 10 total PCR cycles. After PCR amplification, the libraries were purified with magnetic beads following the manufacturer’s protocol. Libraries were sequenced by Novogene Corporation Inc. The sequencing was performed using Nova-seq Paired-end 150.

tag: batch


title: Neuro B1 | 016 | Tumour

tag: treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: roi

value: Staging  IV

value: Poorly diferentiated

value: non-amplified

value: M

value: Alive


title: Neuro B1 | 015 | TME

tag: tissue

tag: alignedreads

value: TME

tag: staging

value: Staging  I

tag: age dx_class

tag: histology

tag: mycn amplification

tag: gender

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

tag: risk classification

value: Low


title: with OSM biol rep 3

description:
Library name: sample 21
rawcounts.xlsx

tag: cell type

tag: sample group


title: Neuro B1 | 015 | Tumour

tag: treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

value: Tumor


title: with OSM biol rep 1

description:
Library name: sample 19
rawcounts.xlsx


title: RNA-Seq, Tetraodon dorsal retina, biol rep1

description: Library name: Tn_D1

tag: tissue

value: Dorsal retina

tag: genotype

value: WT

tag: batch


title: Tetraodon ventral retina, biol rep2

description: Library name: Tn2_V

value: Ventral retina


title: Tetraodon ventral retina, biol rep1

description: Library name: Tn1_V


title: Neuro B1 | 014 | Tumour

tag: alignedreads

tag: scanoffsety

tag: roi

tag: staging

tag: age dx_class

value: >18 months

tag: histology

tag: mycn amplification

value: amplified

tag: gender

value: F

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

value: Death

tag: risk classification

value: High


title: Neuro B1 | 011 | Tumour

value: Neuroblastoma

tag: treatment

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

value: Staging  IV

value: unknown


title: KOC1

description: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.1, no stimulation

source_name: BMDMs,100 ng/mL LPS, 0 h,replicate 1

tag: tissue

value: bone marrow

tag: cell type

value: BMDMs

tag: genotype

tag: age

value: 6-8 week


title: KOT2

description: BMMs from Uba3(flox/flox; lyz2-cre) mouse No.2, LPS 4h

source_name: BMDMs,100 ng/mL LPS, 4 h,replicate 2


title: with IL6 biol rep 2

description:
Library name: sample 17
rawcounts.xlsx

value: H9 differentiated cells

tag: sample group

value: with IL6


title: WTC3

description: BMMs from Uba3(flox/flox) mouse No.3, no stimulation


title: with IL6 biol rep 1

description:
Library name: sample 16
rawcounts.xlsx


title: Neuro B1 | 012 | Tumour

tag: treatment

tag: alignedreads

tag: scanoffsety

tag: roi

value: Tumor

tag: staging

value: Staging  II

tag: age dx_class

value: <12 months

tag: histology

value: Poorly diferentiated

tag: mycn amplification

value: non-amplified

tag: gender

value: M

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

value: Alive

tag: risk classification

value: Low


title: Tetraodon dorsal retina, biol rep1

description: Library name: Tn1_D

tag: tissue

value: Dorsal retina

tag: genotype

value: WT

tag: batch


title: Neuro B1 | 009 | Tumour

value: Neuroblastoma

tag: treatment

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

value: Staging  IV

value: >18 months

value: Death

value: High


title: WTT3

description: BMMs from Uba3(flox/flox) mouse No.3, LPS 4h

value: bone marrow

tag: cell type

value: BMDMs

tag: age

value: 6-8 week


title: Neuro B1 | 007 | TME

tag: tissue

tag: alignedreads

tag: scanoffsety

tag: roi

value: TME

tag: staging

value: Staging  I

tag: age dx_class

value: <12 months

tag: histology

tag: mycn amplification

tag: gender

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

tag: risk classification


title: L. lactis subps. cremoris MG1363_2xMS2-sLLM1042+_rep3

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Life sciences center

country: Lithuania

institute: Vilnius Universitye

description: Library name: Sample 6

data_processing:
Raw data quality was investigated using FastQC. Reads were trimmed using trimGalore!.
Cleaned reads were mapped to the reference genome using hisat2 and quantified using StringTie.
Assembly: NC_009004.1
Supplementary files format and content: TXT format file with gene identificator and gene expression.

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: bacteria

growth_protocol: Lactococcus lactis subsp. cremoris MG1363 ΔsLLM1042+ strains, harboring either pMSP3545-2xMS2-sLLM1042+ or pMSP3545-sLLM1042+, were cultivated at 30°C in BD™ Difco™ M17 broth supplemented with 0.5% glucose (GM17) and 10 mg/l erythromycin. Overnight cultures were diluted 1:50 in fresh GM17 medium containing the same antibiotic and grown to an OD600 of 0.8.

extract_protocol:
25 ml of cells were harvested by centrifugation at 5,000 × g for 10 min at 4°C, resuspended in 2 ml of 1× PBS supplemented with 1 mM DTT and 0.4 mM PMSF, and homogenized twice for 40 s at 5 m/s using MP Biomedicals homogenizer. Lysates were clarified by centrifugation at 15,000 × g for 15 min at 4°C. 25 μl of Glutathione Sepharose 4B resin (Fisher Scientific) per sample was pelleted at 500 × g for 5 min and washed 3 times with 1× PBS containing 1 mM DTT and 0.4 mM PMSF. 10 μg (25 μl) of purified GST-2xMCP protein was added and incubated for 10 min at 4°C with rotation. The resin was washed twice with 0.5 ml of the same buffer. Cleared lysate was applied to the resin, followed by 4 washes with 0.5 ml of the same buffer. RNA was eluted in 1× PBS containing 1 mM DTT and 10 mM reduced glutathione. An equal volume of Roti-Aqua-PCI solution (Carl Roth) was added, mixed, and centrifuged at 13,000 × g for 5 min at 4°C. RNA was precipitated by adding 3 volumes of 99.9% ethanol, followed by centrifugation at 13,000 × g for 40 min at 4°C. Pellets were washed twice with 70% ethanol and centrifuged at 13,000 × g for 10 min at 4°C.
Libraries were prepared by Novogene following DNase treatment and rRNA depletion, according to their standard prokaryotic directional mRNA library preparation protocol.

treatment_protocol: Expression of sRNA was induced with 5 ng/ml nisin for 15 min.

value: bacteria


title: Neuro B1 | 010 | Tumour

tag: treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

value: Tumor

value: Poorly diferentiated

value: unknown

value: F


title: L. lactis subps. cremoris MG1363_sLLM1042+_rep3

description: Library name: Sample 3

tag: cell type


title: CKO-DCM-3

city: Harbin

first: miao

last: yan

address: Harbin

institute: Harbin Medical University

description:
Library name: Sample 6
Total RNA from heart tissue, poly(A) selected, paired-end 150 bp RNA-seq

data_processing:
Paired-end 150 bp reads; adapters trimmed with Cutadapt; reads aligned using HISAT2; transcript abundance estimated with StringTie; DEGs analyzed with Ballgown; alternative splicing detected with rMATS
Assembly: Mouse reference genome GRCm38 (GENCODE M25) transcripts were used as primary reference for maximum historical ENSMUSG ID coverage. Missing genes were supplemented with GENCODE M38 (GRCm39) transcripts. Genes without direct mapping to current transcripts were retrieved from GRCm39 genome coordinates. All data are mapped to standard transcripts or GRCm39 coordinates; no additional fallback sequences are included.
Supplementary files format and content: Tab-delimited TXT file; first column gene_id, subsequent columns sample_name (DCM1–DCM3, CKO-DCM1–CKO-DCM3); values are FPKM

source_name: Heart

growth_protocol: N/A – tissue collected from mouse heart

extract_protocol:
Total RNA extracted from heart tissue using standard methods; RNA integrity verified via agarose gel and NanoDrop
1–2 µg total RNA used; libraries prepared with KAPA Stranded RNA-Seq Kit (Roche) using poly(A) selection or rRNA depletion; library quality assessed via Bioanalyzer and qPCR

treatment_protocol: N/A – no treatment applied prior to RNA extraction

tag: tissue

value: Heart

value: cardiomyocyte

tag: genotype

value: Mmut CKO

value: Diabetic cardiomyopathy


title: mature Day 12 biol rep 2

description:
Library name: sample 14
rawcounts.xlsx

value: H9 differentiated cells

tag: sample group

value: mature Day 12


title: mature Day 12 biol rep 3

description:
Library name: sample 15
rawcounts.xlsx


title: WTT2

description: BMMs from Uba3(flox/flox) mouse No.2, LPS 4h

value: bone marrow

tag: age


title: WTT1

description: BMMs from Uba3(flox/flox) mouse No.1, LPS 4h

value: BMDMs


title: L. lactis subps. cremoris MG1363_2xMS2-sLLM1042+_rep2

description: Library name: Sample 5


title: mature Day 6 biol rep 2

description:
Library name: sample 11
rawcounts.xlsx

value: mature Day 6


title: CKO-DCM-2

description:
Library name: Sample 5
Total RNA from heart tissue, poly(A) selected, paired-end 150 bp RNA-seq

tag: treatment


title: mature Day 12 biol rep 1

description:
Library name: sample 13
rawcounts.xlsx


title: CKO-DCM-1

description:
Library name: Sample 4
Total RNA from heart tissue, poly(A) selected, paired-end 150 bp RNA-seq


title: L. lactis subps. cremoris MG1363_sLLM1042+_rep2

description: Library name: Sample 6

data_processing:
Reads were quality trimmed using BBDUK (38.41) according to the manufacturers recommendations. Reads mapping to the ribosomes were removed and clean reads mapped to the reference genome using hisat2 (2.2.1) and quantified using stringTie (2.1.5).
Assembly: NC_009004.1
Supplementary files format and content: TXT format file containing gene identificator, start, end, strand, coverage, FPKM and TPM values (as calculated using StringTie).

growth_protocol: Lactococcus lactis subsp. cremoris MG1363, harboring either the control plasmid pVE3916, plasmid M-31-D3 carrying the sLLM2- sequence, or pVE3916-sLLM1042+ carrying the sLLM1042+ sequence, was cultivated at 30°C in BD™ Difco™ M17 broth supplemented with 0.5% glucose (GM17) and 5 µg/ml chloramphenicol. Overnight cultures were used to inoculate fresh GM17 medium containing the same antibiotic to an initial OD600 of 0.05–0.1 and grown until OD600 reached 0.8.

extract_protocol:
Bacteria were mixed with 1/8 volume of ice-cold STOP solution (95% ethanol and 5% acid phenol) and centrifuged at 1,800 × g for 20 min at 4°C. Cells were ground to a fine powder using liquid nitrogen and total RNA was extracted with RNAzolRT (RN 190) (Molecular Research Center, Inc.).
Total RNA was treated with DNase I, RNase-free (Thermo Scientific), and purified using RNA Clean & Concentrator-5 Kit (Zymo Research). rRNA was depleted using the modified RiboMinus Transcriptome Isolation Kit (Invitrogen), bacteria, where 3,5 μl of commercial probes and 0,5 μl of a 100 μM mix of three custom-designed probes specific to L. lactis 5S rRNA were used. After ethanol precipitation, libraries were further prepared in ThermoFisher Scientific facilities using Invitrogen™ Collibri™ Stranded RNA Library Prep Kit for Illumina.


title: mature Day 6 biol rep 3

description:
Library name: sample 12
rawcounts.xlsx


description: Library name: Sample 2


title: Neuro B1 | 008 | Tumour

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: alignedreads

tag: scanoffsety

tag: roi

tag: staging

value: Staging  IV

tag: age dx_class

value: >18 months

tag: histology

tag: mycn amplification

tag: gender

value: M

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

value: Death

tag: risk classification

value: High


title: with GA017 biol rep 2

description:
Library name: sample 8
rawcounts.xlsx

tag: cell type

tag: sample group

value: with GA017


title: L. lactis subps. cremoris MG1363_2xMS2-sLLM1042+_rep1

description: Library name: Sample 4

value: bacteria


title: DCM-3

description:
Library name: Sample 3
Total RNA from heart tissue, poly(A) selected, paired-end 150 bp RNA-seq

tag: tissue

value: Heart

value: cardiomyocyte

tag: genotype

value: WT

tag: treatment


title: Neuro B1 | 004 | Tumour

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

value: Tumor

value: Staging  III

value: 12-18 months

value: Poorly diferentiated

value: unknown

value: Alive


title: WTC1

description: BMMs from Uba3(flox/flox) mouse No.1, no stimulation

value: bone marrow

tag: cell type

value: BMDMs

tag: age

value: 6-8 week


title: with GA017 biol rep 3

description:
Library name: sample 9
rawcounts.xlsx

value: H9 differentiated cells

tag: sample group


title: L. lactis subps. cremoris MG1363_sLLM1042+_rep1

description: Library name: Sample 5


title: DCM-1

description:
Library name: Sample 1
Total RNA from heart tissue, poly(A) selected, paired-end 150 bp RNA-seq

tag: tissue

tag: genotype

tag: treatment

value: Diabetic cardiomyopathy


title: WTC2

description: BMMs from Uba3(flox/flox) mouse No.2, no stimulation


title: L. lactis subps. cremoris MG1363_sLLM2-_rep2

description: Library name: Sample 4


title: Neuro B1 | 007 | Tumour

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roi

tag: staging

value: Staging  I

tag: age dx_class

value: <12 months

tag: histology

tag: mycn amplification

value: non-amplified

tag: gender

value: M

tag: follow up_months

tag: overall survival_months

tag: overall survival_years

tag: death

tag: risk classification

value: Low


title: Neuro B1 | 006 | Tumour

tag: tissue

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

value: Tumor

value: Staging  IV

value: >18 months

value: Death

value: High


title: mature Day 6 biol rep 1

description:
Library name: sample 10
rawcounts.xlsx

tag: cell type

tag: sample group

value: mature Day 6


title: Neuro B1 | 003 | TME

tag: treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roi

value: TME

tag: staging

tag: age dx_class

tag: histology

value: Poorly diferentiated

tag: mycn amplification

tag: gender

tag: follow up_months

tag: overall survival_months

value: Alive


description: Library name: Sample 1

value: bacteria


title: DCM-2

description:
Library name: Sample 2
Total RNA from heart tissue, poly(A) selected, paired-end 150 bp RNA-seq

tag: tissue

value: Heart

value: cardiomyocyte

tag: genotype

value: WT

value: Diabetic cardiomyopathy


title: Neuro B1 | 005 | Tumour

value: Neuroblastoma

value: Pre-treatment

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

value: unknown

tag: overall survival_years

tag: death

tag: risk classification


title: S-heporg biol rep 3

description:
Library name: sample 6
rawcounts.xlsx

tag: cell type

value: H9 differentiated cells

tag: sample group

value: S-heporg


title: with GA017 biol rep 1

description:
Library name: sample 7
rawcounts.xlsx

value: with GA017


title: NC_4

city: Wenzhou

first: gaozhi

last: chen

address: Chashan Higher Education Park, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

description: Library name: NC_4

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/) to map reads to the reference genome of homo sapiens Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: renal

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 400±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ X Plus (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: tissue

value: renal


title: NC_3

description: Library name: NC_3


title: L. lactis subps. cremoris MG1363_sLLM2-_rep1

description: Library name: Sample 3


title: S-heporg biol rep 2

description:
Library name: sample 5
rawcounts.xlsx


title: L. lactis subps. cremoris MG1363_control_rep2

description: Library name: Sample 2


title: G-heporg biol rep 1

description:
Library name: sample 1
rawcounts.xlsx

value: G-heporg


title: S-heporg biol rep 1

description:
Library name: sample 4
rawcounts.xlsx


title: G-heporg biol rep 2

description:
Library name: sample 2
rawcounts.xlsx


title: AKI_A_mcherry_4

description: Library name: AKI_A_mcherry_4


title: Neuro B1 | 002 | Tumour

tag: treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roi

value: Tumor

tag: staging

value: Staging  IV

tag: age dx_class

value: <12 months

tag: histology

tag: mycn amplification

value: non-amplified

tag: gender

value: M

tag: follow up_months

tag: overall survival_months

value: Low


title: NC_2

description: Library name: NC_2


title: Neuro B1 | 003 | Tumour

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

value: Staging  I

value: Poorly diferentiated

tag: overall survival_years

tag: death

value: Alive


title: L. lactis subps. cremoris MG1363_control_rep1

description: Library name: Sample 1

tag: cell type

value: bacteria


title: NC_1

description: Library name: NC_1

tag: tissue


title: IFN_2_2

city: Pittsburgh

first: YUE

last: ZHANG

state: PA

address: 4400 Fifth Ave

department: Biological Science

institute: Carnegie Mellon University

description: Library name: SAMPLE4

data_processing:
Raw sequencing reads were quality-controlled and aligned to the mouse reference genome using a splice-aware aligner. Gene-level read counts were generated for downstream differential expression analysis.
Assembly: mm10
Supplementary files format and content: Gene-level raw read counts for all samples generated using featureCounts. Rows represent Entrez Gene IDs and columns represent individual samples.

extract_protocol:
RNA was extrated from cells with TRIZOL reagent and chloroform, and then precipitate with isopropanol.
Total RNA was extracted from cells and mRNA was enriched using oligo(dT)-attached magnetic beads. The enriched mRNA was fragmented and reverse transcribed using random primers. Strand-specific libraries were generated using a dUTP-based method for second-strand synthesis. After end repair, adapter ligation, PCR amplification, libraries were circularized and sequenced on the DNBSEQ platform with paired-end 100 bp reads.

tag: cell line

value: Colon cancer cells

tag: genotype

value: WT

tag: treatment

value: IFN-gamma,hypoxia


title: Neuro B1 | 001 | Tumour

value: Neuroblastoma

value: Pre-treatment

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: roi

tag: staging

tag: age dx_class

tag: histology

tag: mycn amplification

tag: gender

tag: follow up_months

tag: overall survival_months

tag: risk classification


title: G-heporg biol rep 3

description:
Library name: sample 3
rawcounts.xlsx

tag: cell type

value: H9 differentiated cells

tag: sample group


title: Ctrl_2_1

description: Library name: SAMPLE2

tag: cell line

tag: genotype

value: Untreated control, hypoxia


title: IFN_1_2

description: Library name: SAMPLE3

tag: treatment

value: IFN-gamma,normoxia


title: Input PDM257

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

country: Italy

institute: University of Udine

description: Pooling of PDM-257

data_processing:
ChIP-seq reads were clipped form their adapter sequences using the Trimmomatic software (v0.35), discrading reads below the 36 bases long and an overall sequence mean quality lower than 28.
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.5.1 with default configuration for paired reads
Duplicate reads were flagged using samtools but no duplicates were removed
peaks were called using MACS2 version 2.2.9.1  in its paired-end  analysis mode ('-f BAMPE')
Assembly: GRCh38 (Ensembl 107)
Supplementary files format and content: Coverage tracks were generated using the bamCoverage (deepTools) tool, taking an alignment of reads as input (BAM file) and generating a coverage track (bigWig) as output, applying the following parameters: --outFileFormat bigwig --binSize 50 -p 6 --normalizeUsing RPKM
Supplementary files format and content: narrowPeak, peak location

source_name: Colorectal cancer patient's derived organoid

growth_protocol: Patient-derived CRC organoids PDM96 (HCM-CSHL-0143-C20) and PDM257 (HCM-CSHL-0248-C19) were from ATCC (Virginia, USA). Organoids were embedded in a 1:1 mixture of Cultrex (R&D Systems, USA) and ECM Gel (Sigma-Aldrich, Italy) and grown in Advanced DMEM/F12 (Gibco, USA) supplemented with 2 mM L-glutamine (Euroclone, Italy), 10 mM Hepes (Thermo Fisher Scientific, USA), 1X B-27 supplement (Gibco, USA), 10 mM Nicotinamide (Sigma-Aldrich, Germany), 1,25 mM N-acetylcysteine (Sigma-Aldrich, Germany), 50 ng/ml EGF, 100 ng/ml Noggin and 500 ng/ml R-spondin recombinant proteins (all from Pepro Tech, UK), 3 μM SB202190 (Sigma-Aldrich, Italy). Y27632 analogue Pro-survival Compound (Sigma-Aldrich, Italy) was added for the first days of organoids culture after thawing. After 4 days of culture, medium was changed and PDOs were treated as described for the following 48h.

extract_protocol:
After 10 minutes fixation with 1% formaldeyde, chromatin was extracted and shared with Bioruptor Plus (Diagenode). DNA was purified with Zymo ChIP columns. Three independent experiments were pulled.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Untreated: DMSO; OxPt: DMSO 48h, last 24h with OxPt 50 µM; OxPt + #11: Protac compound #11 1 µM for 48h, last 24h with OxPt 50 µM; OxPt + Tsq: Tsq 1 µM for 48h, last 24h with OxPt 50 µM

tag: tissue

value: patient's derived CRC organoid

value: Pooling of PDM-257


title: Input PDM96

description: Pooling of PDM-96

value: Colorectal cancer patient's derived organoid

value: Pooling of PDM-96


title: H3K27ac in PDM257 OxPt+Tsq

description: PDM-257 treated with #11 (1µM 48h), last 24h with OxPt 50 µm

value: OxPt + Tsq


title: Biphasic pleural mesothelioma spatial transcriptomics sample 198900-1

city: Durham

first: David

last: Severson

state: North Carolina

address: 2301 Erwin Road

department: Department of Surgery

institute: Duke University Health System

description: FFPE pleural mesothelioma tissue section from case 27278, anatomic site 1, manuscript ID 198900-1, diagnosis Biphasic. Archive contains Xenium raw and processed outputs including morphology.ome.tif, transcripts.parquet, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and cell_feature_matrix.h5.

hyb_protocol: FFPE tissue sections from pleural mesothelioma tumor sites previously assayed by scRNA-seq were mounted onto Xenium slides. Sections were deparaffinized, permeabilized, and hybridized with the Xenium Human Immuno-Oncology panel plus additional custom probes according to the manufacturer’s protocol. Following probe hybridization, slides were washed and loaded onto the Xenium Analyzer for imaging, decoding, and downstream processing using default manufacturer parameters.

scan_protocol: Hybridized slides were processed on the 10x Genomics Xenium Analyzer. High-resolution morphology images were acquired, transcripts were decoded, and initial cell segmentation was performed using the Xenium Analyzer with default manufacturer parameters.

label: Xenium probe set

source_name: pleural mesothelioma

label_protocol: Xenium probe set

growth_protocol: Not applicable. Human surgical tissue specimens were profiled and no growth protocol was used.

extract_protocol: tissue preparation protocol: Formalin-fixed paraffin-embedded (FFPE) tissue sections from pleural mesothelioma tumor sites adjacent to regions analyzed by scRNA-seq were mounted onto Xenium slides. Sections underwent deparaffinization and permeabilization according to the manufacturer’s protocol prior to probe hybridization.

treatment_protocol: No experimental treatment was applied prior to Xenium profiling. Tissue sections represent clinical surgical specimens collected from pleural mesothelioma tumor sites.

value: pleural mesothelioma

tag: tissue preservation method

value: formalin-fixed paraffin-embedded

value: Biphasic

value: not applicable


title: Epithelioid pleural mesothelioma spatial transcriptomics sample 133261-0

description: FFPE pleural mesothelioma tissue section from case 26599, anatomic site 5, manuscript ID 133261-0, diagnosis Epithelioid. Archive contains Xenium raw and processed outputs including morphology.ome.tif, transcripts.parquet, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and cell_feature_matrix.h5.

data_processing: Hybridized slides were processed on the 10x Genomics Xenium Analyzer. High-resolution morphology images were acquired, transcripts were decoded, and initial cell segmentation was performed using the Xenium Analyzer with default manufacturer parameters.

value: Epithelioid


title: AKI_A_mcherry_1

description: Library name: AKI_A_mcherry_1

value: renal


title: AKI_A_mcherry_3

description: Library name: AKI_A_mcherry_3


title: H3K27ac in PDM257 OxPt+#11

description: PDM-257 treated with Tasquinimod (1µM 48h), last 24h with OxPt 50 µm

value: OxPt + #11


title: Cortical organoids, isogenic set 1, 3 Month, Batch 3

city: La Jolla

first: Jeffery

last: Kelly

state: California

address: 10550 North Torrey Pines Road

department: Chemistry

institute: The Scripps Research Institute

description:
Library name: ca_ns_0453_2
tp3MgtX33 tp3MgtY33 tp3MgtZ33

library_source: transcriptomic single cell

data_processing:
The raw sequencer results were aligned to the GRCh38 genome assembly and de-multiplexed using Cell Ranger (v7.0.1 & v7.1.0, 10x Genomics) with default parameters. The aligned gene expression matrices were then processed on R via Seurat (ver.4.3.0.1).
Assembly: GRCh38
Supplementary files format and content: For each sample library: barcodes as tab-separated values (.tsv) files
Supplementary files format and content: features as tab-separated values (.tsv) files
Supplementary files format and content: matrices as matrix (.mtx) files

source_name: iPSC-derived cerebrocortical organoid

extract_protocol:
Individual COs of ~7 weeks and 3 months of age were washed 4x in PBS and then dissociated with a Worthington Papain Dissociation kit (Worthington Biochemical Corp.) following a modified manufacturer’s protocol. In brief, live organoids were placed in an Ultra-Low Attachment 6-well plate, manually minced in a Papain+DNase solution in Earle’s medium, and incubated at 37 °C in an orbital shaker at 100 RPM for 30 minutes. Then, the pieces were gently broken up with a 1 mL pipette before returning to shaking in an incubator for an additional 20-30 minutes. Afterwards, using a 10 mL pipette, the solution with the minced-up pieces was gently mixed up and down 10 times and transferred to an empty 15 mL conical tube to allow undissociated debris to settle for ~2 minutes. Subsequently, the cell suspension was transferred to a 3:8-diluted ovomucoid protease inhibitor solution in Earle’s medium, mixed, and then centrifuged at 300 x g for 7 minutes. The supernatant was then discarded, and the cells were gently resuspended in 1% BSA-supplemented basal medium before filtering through a 40 µm mesh filter. Cells were then counted and confirmed to have viabilities above 85% using a Countess II Cell Counter (Thermo-Fisher).
Using the Chromium Next GEM single cell 3’ Cellplex v3.1 and Chip G kits (10x Genomics), the single cell partitioning, cDNA preparation, and sequencing libraries were prepared according to the manufacturer’s protocol, using one 10x reaction for each experiment. After labeling the samples and amplifying the transcriptomic libraries, they were sequenced using on an Illumina Novaseq 6000 (SP or S1, depending on the run size). An average depth of ~30,000 reads per cell was targeted.

value: iPSC-derived cerebrocortical organoid

tag: age

value: 3 Mo

tag: parent line

tag: genotypes

value: Isogenic PSEN1_M146V/WT, APP_swe/WT, and control (1)

tag: batch


title: Ctrl_1_1

description: Library name: SAMPLE1

value: Colon cancer cells

value: WT

value: Untreated control, normoxia


title: H3K27ac in PDM257 UNT

description: PDM-257 Untreated (DMSO)

value: patient's derived CRC organoid

value: Untreated


title: AKI_A_mcherry_2

description: Library name: AKI_A_mcherry_2


title: Cortical organoids, isogenic set 2, 3 Month, Batch 2, Replicates 1-3

description:
Library name: ca_no_0262
tp3MgtA11 tp3MgtA12 tp3MgtB11 tp3MgtB12 tp3MgtB13

value: CV-hIPS-B

value: Isogenic PSEN1_delE9/WT and control (2)


title: AKI_A_FGF23_R176QR179Q_5

description: Library name: AKI_A_FGF23_R176QR179Q_5


title: Biphasic pleural mesothelioma spatial transcriptomics sample 135496-1

description: FFPE pleural mesothelioma tissue section from case 27278, anatomic site 6, manuscript ID 135498-1, diagnosis Biphasic. Archive contains Xenium raw and processed outputs including morphology.ome.tif, transcripts.parquet, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and cell_feature_matrix.h5.

value: pleural mesothelioma


title: H3K27ac in PDM96 OxPt+#11

description: PDM-96 treated with Tasquinimod (1µM 48h), last 24h with OxPt 50 µm

value: Colorectal cancer patient's derived organoid


title: Sarcomatoid pleural mesothelioma spatial transcriptomics sample 164109-1

description: FFPE pleural mesothelioma tissue section from case 27306, anatomic site 4, manuscript ID 164109-1, diagnosis Sarcomatoid. Archive contains Xenium raw and processed outputs including morphology.ome.tif, transcripts.parquet, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and cell_feature_matrix.h5.

value: formalin-fixed paraffin-embedded

value: Sarcomatoid


title: Cortical organoids, isogenic set 1, 3 Month, Batch 2, Replicates 1-2

description:
Library name: ca_ns_0453_1
tp3MgtX31 tp3MgtX32 tp3MgtY31 tp3MgtY32 tp3MgtZ31 tp3MgtZ32


title: AKI_A_FGF23_R176QR179Q_3

description: Library name: AKI_A_FGF23_R176QR179Q_3


title: Cortical organoids, isogenic set 1, 2 Month, Batch 1, Replicates 1-3, GEX

description:
Library name: ca_no_0244_GEX
tp2MgtX01 tp2MgtX02 tp2MgtX03 tp2MgtY01 tp2MgtY02 tp2MgtY03 tp2MgtZ01 tp2MgtZ02 tp2MgtZ03

value: 2 Mo


title: H3K27ac in PDM96 OxPt+Tsq

description: PDM-96 treated with #11 (1µM 48h), last 24h with OxPt 50 µm

value: OxPt + Tsq


title: AKI_A_FGF23_R176QR179Q_2

description: Library name: AKI_A_FGF23_R176QR179Q_2

value: renal


title: H3K27ac in PDM257 OxPt

description: PDM-257 treated with DMSO (48h), last 24h with OxPt 50 µm

value: OxPt


title: Cortical organoids, isogenic set 1, 2 Month, Batch 1, Replicates 1-3, CELLMULTI

description:
Library name: ca_no_0244_CELLMULTI
tp2MgtX01 tp2MgtX02 tp2MgtX03 tp2MgtY01 tp2MgtY02 tp2MgtY03 tp2MgtZ01 tp2MgtZ02 tp2MgtZ03

value: iPSC-derived cerebrocortical organoid


title: Cortical Organoids, isogenic set 2, 2 Month, Batch 1, Replicates 1-3, GEX

description:
Library name: ca_no_0237_GEX
tp2MgtA01 tp2MgtA02 tp2MgtA03 tp2MgtB01 tp2MgtB02 tp2MgtB03


title: SK_N_BE_03_ML210

description: Library name: Sample 12

data_processing:
Fastq files underwent quality checks using FastQC then trimmed using Trimmomatic (v.1.4) with the following parameters: removal of low-quality bases from the start and end of reads (LEADING=20, TRAILING=20) and a minimum read length threshold of 35 bases (MINLEN=35). The trimmed reads were then aligned to the GRCh38 (hg38) human reference genome using HISAT2 (v. 2.2.1). A raw counts matrix was generated from mapped reads using featureCounts (v.2.0.5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file inculdes raw counts for each sample

extract_protocol:
RNA was extracted from ex vivo cultured neuroblastoma cell lines using the RNeasy Plus Mini Kit (#74134, QIAGEN), according to the manufacturer’s instructions.
Libraries were prepared using Illumina’s Stranded mRNA prep Kit with 10nt UDIs. Final libraries were quality checked using the Agilent Fragment Analyzer 5200 NGS assay, before normalization and sequencing on an Illumina NovaSeq 6000 to generate a minimum of 30 million reads per sample.

value: Neuroblastoma cells


title: AKI_A_FGF23_R176QR179Q_1

description: Library name: AKI_A_FGF23_R176QR179Q_1


title: Sarcomatoid pleural mesothelioma spatial transcriptomics sample 164504-1

description: FFPE pleural mesothelioma tissue section from case 27306, anatomic site 5, manuscript ID 164504-1, diagnosis Sarcomatoid. Archive contains Xenium raw and processed outputs including morphology.ome.tif, transcripts.parquet, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and cell_feature_matrix.h5.

value: not applicable


title: H3K27ac in PDM96 OxPt

description: PDM-96 treated with DMSO (48h), last 24h with OxPt 50 µm


title: H3K27ac in PDM96 UNT

description: PDM-96 Untreated (DMSO)


title: Epithelioid pleural mesothelioma spatial transcriptomics sample 170147-2

description: FFPE pleural mesothelioma tissue section from case 29891, anatomic site 1, manuscript ID 170147-2, diagnosis Epithelioid. Archive contains Xenium raw and processed outputs including morphology.ome.tif, transcripts.parquet, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and cell_feature_matrix.h5.

value: Epithelioid


title: Cortical Organoids, isogenic set 2, 2 Month, Batch 1, Replicates 1-3, CELLMULTI

description:
Library name: ca_no_0237_CELLMULTI
tp2MgtA01 tp2MgtA02 tp2MgtA03 tp2MgtB01 tp2MgtB02 tp2MgtB03


title: SK_N_BE_02_ML210

description: Library name: Sample 11

value: WT


title: Biphasic pleural mesothelioma spatial transcriptomics sample 182968-1

description: FFPE pleural mesothelioma tissue section from case 27278, anatomic site 5, manuscript ID 182968-1, diagnosis Biphasic. Archive contains Xenium raw and processed outputs including morphology.ome.tif, transcripts.parquet, cells.parquet, cell_boundaries.parquet, nucleus_boundaries.parquet, and cell_feature_matrix.h5.

value: Biphasic


title: G2-3

city: Daegu

first: Mookyung

last: Cheon

address: 61, Cheomdan-ro, Dong-gu

department: Dementia Research Group

country: South Korea

institute: Korea Brain Research Institute

description:
Library name: G2-3_Visium_6-month-old
Fresh frozen spatial transcriptome sequencing

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

source_name: Brain

growth_protocol: Male G2-3 (A53T alpha-synuclein) and wild-type mice were maintained under standard housing conditions and used at 6 months of age.

extract_protocol: Tissue slides and Visium CytAssist Spatial Gene Expression v2 Slides were used as input for the CytAssist instrument. Tissue sections were methanol-fixed, H&E-stained, imaged, and destained. Probe hybridization was then performed, followed by ligation of probe pairs bound to target transcripts. The resulting ligation products were transferred to the Visium slide using the CytAssist instrument, extended with UMI, spatial barcode, and partial Read 1 sequences, and then harvested. Libraries were amplified by sample index PCR, purified using SPRIselect, quantified by qPCR, quality-checked using the Agilent Bioanalyzer, and sequenced on the Illumina NovaSeq platform.

value: Brain

value: G2-3 (A53T alpha-synuclein)

tag: Sex

value: Male


title: WT

description:
Library name: WT-Visium_6-month-old
Fresh frozen spatial transcriptome sequencing

value: Wild Type


title: Mouse lung tissue, OVA-induced asthma + Rg3 treatment, biological replicate 4

city: Huai'an

first: Xiuqin

last: Ni

address: No.4 Mei Cheng Road, Higher Education Park

institute: Jiangsu Food and Pharmaceutical Science College

description:
Library name: Rg3_Lung_4
Mouse lung tissue with OVA-induced allergic asthma, treated with Ginsenoside Rg3

data_processing:
Raw sequencing data (FASTQ files) were filtered to remove low-quality reads, adapter sequences, and reads containing more than 5% N bases using Trimmomatic software to obtain clean reads.
Read counts of each gene were calculated using featureCounts software, and the gene expression matrix was generated.
Assembly: Mus musculus reference genome, GRCm39 (mm39).
Supplementary files format and content: Processed data files are in XLSX format, including the gene-level expression matrix (Expression_Gene.xlsx). Rows represent genes (with Ensembl gene ID and gene symbol), columns include gene annotation information (locus, strand, gene type) and sample expression values (e.g., Con1, OVA1, Rg3-1), recording the expression level of each gene in each sample.

source_name: Lung

growth_protocol: Wild type Mus musculus (mice) were raised under specific pathogen-free (SPF) conditions, with a 12-hour light/dark cycle, free access to food and water, and maintained at a constant temperature of 22±2℃ and humidity of 50±5% until the experimental period.

extract_protocol:
Total RNA was extracted from mouse lung tissue using Trizol reagent (Invitrogen) according to the manufacturer's instructions. The purity and integrity of RNA were detected by NanoDrop and agarose gel electrophoresis, respectively, to ensure RNA quality meets sequencing requirements (OD260/OD280 = 1.8-2.0, RNA integrity number ≥ 7.0).
RNA libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina). Briefly, mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented, reverse-transcribed into cDNA, and then subjected to end repair, A-tailing, adapter ligation, and PCR amplification. The constructed libraries were quantified by Qubit and qualified by agarose gel electrophoresis before sequencing.

treatment_protocol: Mice were divided into three groups: NC group (normal saline, no OVA induction, no Rg3 treatment), OVA group (OVA induction, no Rg3 treatment), and Rg3 group (OVA induction + Ginsenoside Rg3 treatment). OVA induction was performed by intraperitoneal injection and aerosol inhalation; Ginsenoside Rg3 (20 mg/kg) was administered by gavage at the corresponding dose during OVA induction.

value: Lung

value: Wild type

value: Ovalbumin (OVA) induction + Ginsenoside Rg3 (20 mg/kg)  treatment

value: Batch 1


title: Type 2 Diabetes DM-2

city: Washington

first: Somiranjan

last: Ghosh

state: DC

address: 415 College Street EE JUST HALL BIOLOGY EE JUST HALL BIOLOGY

department: Biology

institute: Howard University

description: Gene expression data from whole blood, particepants were clinically diagnosed of T2D based on HbA1C, plasma glucose (mg/dl) level.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HuGene-2_0-st Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The stained probe array is then scanned with a laser, and the fluorescent signals emitted from each probe are measured. The intensity of the signal from each probe reflects the amount of target RNA that has hybridized to it.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software

label: biotin

source_name: Whole Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted using the PAXgene Blood RNA kit (Qiagen, Cat. # 762164, PreAnalytiX GmbH, Germany) following the manufacturer's instructions.

value: Female

tag: specimen type

value: Peripheral blood


title: cko3

city: wuhan

first: wang

last: yi

address: no.1095 Jiefang Avenue

institute: Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: cko3

data_processing:
we used StringTie(v2.1.5) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq2 (v1.30.1) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant padj≤0.05. At the  same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Assembly: mm39
Supplementary files format and content: excel

source_name: spleen

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after the total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop spectrophotometer (Thermo Scientific) and Qubit 4.0; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit was used for quantitative . The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded circular DNA. Single-stranded circular DNA is amplified by a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative.

value: spleen


title: cko1

description: Library name: cko1


title: SK_N_BE_03_Control

description: Library name: Sample 9

value: Control


title: Mouse lung tissue, OVA-induced asthma + Rg3 treatment, biological replicate 3

description:
Library name: Rg3_Lung_3
Mouse lung tissue with OVA-induced allergic asthma, treated with Ginsenoside Rg3


title: Mouse lung tissue, OVA-induced asthma + Rg3 treatment, biological replicate 5

description:
Library name: Rg3_Lung_5
Mouse lung tissue with OVA-induced allergic asthma, treated with Ginsenoside Rg3

value: Ovalbumin (OVA) induction + Ginsenoside Rg3 (20 mg/kg) treatment


title: Ctrl3

description: Library name: Ctrl3


title: Mouse lung tissue, OVA-induced asthma model, biological replicate 5

description:
Library name: OVA_Lung_5
Mouse lung tissue with OVA-induced allergic asthma, no Rg3 treatment

value: Ovalbumin (OVA) induction (no Rg3)


title: cko2

description: Library name: cko2


title: SK_N_BE_02_Control

description: Library name: Sample 8

value: Neuroblastoma cells


title: Mouse lung tissue, OVA-induced asthma + Rg3 treatment, biological replicate 2

description:
Library name: Rg3_Lung_2
Mouse lung tissue with OVA-induced allergic asthma, treated with Ginsenoside Rg3


title: Mouse lung tissue, OVA-induced asthma model, biological replicate 4

description:
Library name: OVA_Lung_4
Mouse lung tissue with OVA-induced allergic asthma, no Rg3 treatment


title: SK_N_AS_02_ML210

description: Library name: Sample 5

source_name: SK-N-AS

value: SK-N-AS

value: WT


title: Type 2 Diabetes DM-1

tag: gender


title: SK_N_BE_01_Control

description: Library name: Sample 7


title: SK_N_AS_03_ML210

description: Library name: Sample 6


title: Mouse lung tissue, OVA-induced asthma + Rg3 treatment, biological replicate 1

description:
Library name: Rg3_Lung_1
Mouse lung tissue with OVA-induced allergic asthma, treated with Ginsenoside Rg3


title: Ctrl2

description: Library name: Ctrl2


title: Ctrl1

description: Library name: Ctrl1


title: CONTROL-C-2

description: Gene expression data from whole blood, particepants were free from any major reported illness and had not undergone any major surgical procedures during the last 5 years.


title: H4, express mClover3-0N4R-P301L with fibril, replicate4

city: Santa Barbara

first: Andrew

middle: Paul

last: Longhini

address: 6139 Biological Sciences II

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

description:
Library name: H4_mClover3_0N4R_P301L_with_jR2R3_P301L_Fibrils_Sample4
Column name in raw_counts_matrix.tsv: H4_mClover3_0N4R_P301L_with_jR2R3_P301L_Fibrils_Sample4

data_processing:
Raw sequencing reads from multiple lanes per sample were concatenated prior to analysis.
Quality control was performed using FastQC.
Reads were then quantified using Salmon with quasi-mapping against the human reference transcriptome to obtain transcript-level abundance estimates, which were summarized to gene-level counts for downstream analysis.
Assembly: Reads were quantified using Salmon (v1.10.3) with quasi-mapping against a human reference transcriptome (GRCh38, GENCODE annotation).
Supplementary files format and content: Processed data files include a tab-delimited gene-level count matrix derived from featureCounts output. The deposited raw counts matrix contains one row per gene and one column per sample, with the first column listing gene identifiers and subsequent columns listing counts for the 12 samples.

source_name: brain

growth_protocol: H4 HTB-148 neuroglioma cells were maintained in DMEM supplemented with 10% heat inactivated fetal bovine serum and 1% pencillin/streptamycin in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
Total RNA was extracted from cultured H4 cells using TRIzol reagent according to the manufacturer’s protocol. Briefly, cells were lysed directly in TRIzol, and phase separation was performed by addition of chloroform followed by centrifugation. The aqueous phase was recovered, and RNA was precipitated with isopropanol, washed with 75% ethanol, and resuspended in nuclease-free water. RNA quantity and quality were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA using the Illumina TruSeq RNA Library Preparation Kit v2 according to the manufacturer’s protocol, including poly(A) selection, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

value: brain

value: neuoglioma

value: jR2R3 P301L Fibrils


title: mouse heart

city: Melbourne

first: Maria Rosaria

last: Nucera

state: VICTORIA

address: 50, Flemington road

department: Paediatrics

institute: University of Melbourne

description:
Library name: mouse_heart_tissue_21weeks
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the SAW pipeline
Images in format .czi were converted into .ipr and .tar format using ImageStudio software.
Assembly: mm10 for mouse tissue and GRCh38 for human organoids
Supplementary files format and content: file.gef : output of SAW pipeline
Supplementary files format and content: anndata.h5ad : output of SAW pipeline
Supplementary files format and content: image.ipr : image converted using ImageStudio, input of SAW pipeline
Supplementary files format and content: image.tar : image converted using ImageStudio, input of SAW pipeline
Library strategy: Spatial Transcriptomics

source_name: heart tissue

extract_protocol:
Samples were prepared and processed using the STOmics Transcriptomics kit (STOmics Cat# 111KT114) in accordance with manufacturer’s instructions (BGI Stereo-seq Transcriptomics set for Chip-on-a-slide user manual version B) with slight variations.
The cDNA purification and library preparation of each sample was constructed using the STOmics library preparation kit (STOmics Cat# 111KL114) in accordance with manufacturer’s instructions (BGI STOmics Stereo-seq Transcriptomics set for Chip-on-a-slide user manual version B).

treatment_protocol: the tissues are fresh frozen

value: heart tissue

value: Wild-type

tag: time

value: 21 weeks


title: Mouse lung tissue, OVA-induced asthma model, biological replicate 3

description:
Library name: OVA_Lung  3
Mouse lung tissue with OVA-induced allergic asthma, no Rg3 treatment

value: Lung

value: Wild type


title: Azlzheimr's Disease-AD-2

description: Gene expression data from whole blood, particepants were clinically diagnosed of AD using standard methodologies including neurological examinations, magnetic resonance imaging (MRI), or computed tomography (CT).

value: Male


title: H4, express mClover3-0N4R-P301L with fibril, replicate2

description:
Library name: H4_mClover3_0N4R_P301L_with_jR2R3_P301L_Fibrils_Sample2
Column name in raw_counts_matrix.tsv: H4_mClover3_0N4R_P301L_with_jR2R3_P301L_Fibrils_Sample2


title: SK_N_BE_01_ML210

description: Library name: Sample 10


title: H4, express mClover3-0N4R-P301L with fibril, replicate1

description:
Library name: H4_mClover3_0N4R_P301L_with_jR2R3_P301L_Fibrils_Sample1
Column name in raw_counts_matrix.tsv: H4_mClover3_0N4R_P301L_with_jR2R3_P301L_Fibrils_Sample1


title: Mouse lung tissue, OVA-induced asthma model, biological replicate 1

description:
Library name: OVA_Lung_1
Mouse lung tissue with OVA-induced allergic asthma, no Rg3 treatment

value: Batch 1


title: CD4+ T cells treated with MAPK13-IN-1 2

description:
M2
gene_count_matrix.txt

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp (v0.21.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.1.0.
We used StringTie(v2.1.5) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq2 (v1.30.1) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant padj≤0.05. At the same time, we used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Spleen

growth_protocol: CD4+ lymphocyte cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after the total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop spectrophotometer (Thermo Scientific) and Qubit 4.0; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit was used for quantitative. The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded circular DNA. Single-stranded circular DNA is amplified by a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative.

treatment_protocol:
Proliferation of CD4+ lymphocyte cells was induced by treatment of CD3/CD28. Cells were fed with RPMI 1640 supplemented with 10% fetal bovine serum (FBS) until day 1. Cells were fed with RPMI 1640 supplemented with 10% fetal bovine serum (FBS) until day 1. Then 17.1μM MAPK13 inhibitor (MCE) was added into culture medium.
Proliferation of CD4+ lymphocyte cells was induced by treatment of CD3/CD28. Cells were fed with RPMI 1640 supplemented with 10% fetal bovine serum (FBS) until day 1. Cells were fed with RPMI 1640 supplemented with 10% fetal bovine serum (FBS) until day 1. Then 0.1ul DMSO (Sigma) was added into culture medium.

value: Spleen

value: CD3/CD28 costimulation

tag: inhibitor


title: mouse head

description:
Library name: mouse_head_tissue_E13.5
Fresh frozen Spatial transcriptome sequencing

source_name: head tissue

value: head tissue


title: SK_N_AS_01_Control

description: Library name: Sample 1

value: Control


title: Mouse lung tissue, OVA-induced asthma model, biological replicate 2

description:
Library name: OVA_Lung_2
Mouse lung tissue with OVA-induced allergic asthma, no Rg3 treatment

value: Ovalbumin (OVA) induction (no Rg3)


title: SK_N_AS_01_ML210

description: Library name: Sample 4

value: SK-N-AS

value: Neuroblastoma cells


title: CD4+ T cells treated with MAPK13-IN-1 3

description:
M3
gene_count_matrix.txt

value: WT


title: KYSE30-3-IgG

city: guangzhou

first: yong

last: she

state: Guangdong

address: Sun Yat-sen University Cancer Prevention and Treatment Center, No. 651 Dongfeng East Road, Guangzhou

institute: Sun Yat-sen University Cancer Center

description: Library name: sample 12

data_processing:
Paired-end reads were aligned to GRCh38 human reference genome (hg38) using Bowtie2 version 2.5.4 .
Peak calling was performed using MACS2 (version 2.2.9.1) with threshold at p value of 0.001 as a cutoff based on input.
Assembly: GRCh38
Supplementary files format and content: merged tdf files, KYSE150_merge.tdf, KYSE30_merge.tdf
Library strategy: CUT&Tag

source_name: cell line

extract_protocol:
Cells are resuspended in tagmentation buffer (10mM MgCl2 in dig-300 buffer) and incubated at 37°C for 1 hour to allow for the tagmentation reaction to occur.
DNA Purification: Using Tagment DNA Extract Beads to purify the DNA after the tagmentation reaction. Primer Mixing: Mixing the purified DNA with universal and barcoded primers. PCR Amplification: Amplifying the DNA using NEBNext HiFi 2× PCR Master mix and specific cycling conditions. Post-PCR Clean-up: Cleaning up the amplified DNA using XP beads to obtain the final library.

value: cell line


title: CD4+ T cells treated with DMSO 2

description:
C2
gene_count_matrix.txt


title: SK_N_AS_03_Control

city: Woolloongabba

last: Guimaraes

address: 37 Kent Street

institute: Frazer Institute - University of Queensland

description: Library name: Sample 3


title: CD4+ T cells treated with DMSO 3

description:
C3
gene_count_matrix.txt


title: H4, express mClover3-0N4R-P301L, replicate4

description:
Library name: H4_mClover3_0N4R_P301L_Sample4
Column name in raw_counts_matrix.tsv: H4_mClover3_0N4R_P301L_Sample4

value: brain

value: neuoglioma


title: Azlzheimr's Disease-AD-1

value: Female

value: Peripheral blood


title: H4, express mClover3-0N4R-P301L with fibril, replicate3

description:
Library name: H4_mClover3_0N4R_P301L_with_jR2R3_P301L_Fibrils_Sample3
Column name in raw_counts_matrix.tsv: H4_mClover3_0N4R_P301L_with_jR2R3_P301L_Fibrils_Sample3

value: jR2R3 P301L Fibrils


title: H4, express mClover3-0N4R-P301L, replicate2

description:
Library name: H4_mClover3_0N4R_P301L_Sample2
Column name in raw_counts_matrix.tsv: H4_mClover3_0N4R_P301L_Sample2


title: Mouse lung tissue, normal control, biological replicate5

description:
Library name: Con_Lung_5
Normal mouse lung tissue without OVA induction and Rg3 treatment

value: Lung

value: Wild type

value: Normal saline (no OVA, no Rg3)


title: H4, express mClover3-0N4R-P301L, replicate3

description:
Library name: H4_mClover3_0N4R_P301L_Sample3
Column name in raw_counts_matrix.tsv: H4_mClover3_0N4R_P301L_Sample3


title: KYSE30-3

description: Library name: sample 11


title: Mouse lung tissue, normal control, biological replicate 4

description:
Library name: Con_Lung_4
Normal mouse lung tissue without OVA induction and Rg3 treatment

value: Batch 1


title: KYSE30-2

description: Library name: sample 9


title: H4, replicate4

description:
Library name: H4_Sample4
Column name in raw_counts_matrix.tsv: H4_Sample4


title: KYSE30-1-IgG

description: Library name: sample 8


title: H4, express mClover3-0N4R-P301L, replicate1

description:
Library name: H4_mClover3_0N4R_P301L_Sample1
Column name in raw_counts_matrix.tsv: H4_mClover3_0N4R_P301L_Sample1


title: KYSE30-2-IgG

description: Library name: sample 10


title: H4, replicate3

description:
Library name: H4_Sample3
Column name in raw_counts_matrix.tsv: H4_Sample3


title: SK_N_AS_02_Control

description: Library name: Sample 2


title: Mouse lung tissue, normal control, biological replicate 2

description:
Library name: Con_Lung_2
Normal mouse lung tissue without OVA induction and Rg3 treatment


title: KYSE30-1

description: Library name: sample 7


title: 3384807_KDM6B_rTreg_TCR3

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description: Library name: sample 12

data_processing:
the reads were trimmed for the Nextera adapter by cutadapt (v1.9, paired-end mode, default parameter with “ -m 6 -O 20”) and aligned to the human genome mm10(GRCm38) by BWA (v0.7.12-r1039, default parameter)(Li and Durbin 2009).
The duplicated reads were then marked with biobambam2 (v2.0.87), and only nonduplicated proper paired reads were kept by samtools (parameter “-q 1 -F 1804,” v1.2)(Li, Handsaker et al. 2009).
After removing the mitochondrial DNA reads, the rest of reads were classified into nucleosome free reads and nucleosome reads by fragment size. The bigwig files were generated by using the center 80-bp fragments and scaled to 20 million nucleosome-free reads. We observed reasonable nucleosome-free peaks and patterns of nucleosome peaks surrounding the nucleosome-free peaks on the Integrative Genomics Viewer (Broad Institute).
All samples exhibited double the ENCODE criteria. Therefore, we concluded the data showed enough depth. Given that almost all of samples exhibited more than 15 million nucleosome free fragments, we were confident that most of the strong
Assembly: mm10(GRCm38)
Supplementary files format and content: bigwig

source_name: Spleen and LNs

extract_protocol:
Following treatment, cells were washed with 1x cold PBS. Then, 300 µl of Lysis Buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% MP-40, Molecular Grade H2O) was added to wells and centrifuged at 1,200 g for 10 mins in a swinging bucket centrifuge. Following removal of supernatant containing lysis buffer and cell debris, the nuclei pellet was then resuspended in 50 µl of tagmentation reaction mix containing Molecular Grade H2O, 2x Tagment DNA Buffer (Illumina), followed by the addition of 2.5 µl TDE1 (Illumina) and incubated at 37°C for 0.5 hr.
Following tagmentation, libraries were purified using the Qiagen Minelute PCR purification kit (Qiagen) and amplified by PCR. To remove primer dimers, libraries were bead purified using one round of 1.0X Ampure XP beads with 80% ethanol, followed by a second round of 0.6X Ampure beads with 80% ethanol. Libraries were sequenced (50-bp paired end reads).

treatment_protocol: CD4 T cells were enriched by EasySep Mouse CD4 T Cell Isolation Kit (STEMCELL) from lymph nodes and spleens. Resting CD4 Treg cells  (rTreg, CD4+CD44-CD62L+YFP+) T cells were further sorted by FACS. The sorted rTreg cells then were stimulated with PBS (NO) or anti-CD3/anti-CD28 coated plate for 3 hours.

value: Spleen and LNs

value: Treg

value: Foxp3Cre x Kdm6bfl/fl

value: anti-CD3/CD28 for 3 hours


title: Mouse lung tissue, normal control, biological replicate 1

description:
Library name: Con_Lung_1
Normal mouse lung tissue without OVA induction and Rg3 treatment


title: CD4+ T cells treated with DMSO

data_processing:
Briefly, raw sequencing data underwent initial filtration using FastQC; low-quality reads were discarded, and adaptor sequences were trimmed accordingly. After quality filtering, each sample yielded approximately 49.5-67.5 million clean reads. These clean reads were then mapped to the Mus musculus GRCm38 reference genome utilizing the hisat2 alignment tool.
Assembly: mm10
Supplementary files format and content: file includes RPKM values for each sample

extract_protocol:
Total RNA was extracted from purified CD4+ T cells using TRIzol (Invitrogen). For stranded RNA sequencing library preparation, 2 μg of total RNA was utilized with a Stranded mRNA Library Prep Kit from DR08502 (Bioyigene) following the manufacturer's instructions.
Library products corresponding to 200-500 bp were enriched, quantified, and sequenced on the DNBSEQ-T7 platform.

value: spleen

value: CD4+ T cells

value: DMSO


title: 3384806_KDM6B_rTreg_TCR2

description: Library name: sample 11


title: 3384805_KDM6B_rTreg_TCR1

description: Library name: sample 10


title: CONTROL-C-1

description: Gene expression data from whole blood, particepants were free from any major reported illness and had not undergone any major surgical procedures during the last 5 years.

value: Male


title: H4, replicate1

description:
Library name: H4_Sample1
Column name in raw_counts_matrix.tsv: H4_Sample1

value: brain

value: WT


title: H4, replicate2

description:
Library name: H4_Sample2
Column name in raw_counts_matrix.tsv: H4_Sample2

value: neuoglioma


title: CD4+ T cells treated with MAPK13-IN-1


title: KYSE150-3

description: Library name: sample 5

value: cell line


title: Input_FNPMxMdPA2_E11.5_WT

city: Basel

first: Filippo

address: Fabrikstrasse 24,

country: Switzerland

institute: FMI

description:
Library name: Sample 9
Wnt1CreRosa.mix, E11.5, WT, Input

data_processing:
Reads were aligned to the mouse GRCm38/mm10 reference genome using the QuasR package (version 1.38.0) through the qAlign function.
BigWig files were generated using the qExportWig function from the QuasR package. The files contain CPM (Counts Per Million) values with a resolution of 100 base pairs and a scaling factor of 1e6.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig files contain cpm values
Supplementary files format and content: wig files contain cpm values

source_name: FNP, Mx, Md, PA2

extract_protocol:
Dissected tissue from E8.5 embryos (i.e. dorsal most portion of the neural plate) and from E10.5 and E11.5 embryos (i.e. FNP, Mx, Md and PA2) were micro-dissected and incubated in trypsin 0.5%/EDTA 1X at 37 °C for 10 minutes, rinsed (DMEM 1X/ FBS 10%, followed by two washes in ice-cold 1× DMEM), dissociated by pipetting, cross-linked with 1% formaldehyde in PBS 1X for 10 minutes at room temperature (RT) and quenched with glycine (final concentration 125 mM) for 5 minutes at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C) and rinsed in ice-cold PBS. CNCCs from E11.5 Wnt1::Cre;ROSARFP and Wnt1::Cre;ROSARFP;Ezh2 flox/flox (Ezh2cKO) embryos were filtered and collected by FACS. ChIP-seq experiments with anti-H3K4me2 (Millipore, Cat. #07-030), anti-H3K27me3 (Millipore, Cat. # 07-449), anti-H3K27ac (abcam, ab4729) and anti-CTCF (Cell Signaling, CST 2899) antibodies were performed as described in Minoux et al., 2017 and Kessler et al., 2023.
ChIP-seq libraries were generated using bar-coded adapters (NEB, E7335) in combination with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370) according to manufacturers’ instructions. The quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single-end) or an Illumina NovaSeq 6000 machine (50 bp read length, paired-end) .

value: FNP, Mx, Md, PA2

tag: developmental stage

value: Cranial neural crest cells

tag: antibody

value: Input


title: Input_FNPMxMdPA2_E11.5_Ezh2cKO

description:
Library name: Sample 10
Wnt1CreRosa.mix , E11.5, Ezh2cKO, Input

tag: cell type


title: 3384804_KDM6B_rTreg_NO3

description: Library name: sample 9

value: PBS


title: technical control replicate; 1893-HCT-15_2

first: Astrid

last: Beerlage

address: Hebelstrasse 10

institute: University of Basel

description: Library name: 1893-HCT-15_2

data_processing:
All processing steps were automatically performed on the HTG EdgeSeq host system by the parser version 5.3.
Assembly: Alignment is automatically performed by the host system. Under the hood it uses bowtie 2 for alignment and a targeted probe list as a genome.
Supplementary files format and content: The processed data files are Excel sheets containing the raw gene counts, as well as QC-filtered normalized counts (CPM and median-ratio). Additionally the processed data sheets contain information on the individual QC steps.

source_name: bone marrow

extract_protocol:
Quantitative nuclease protection assay (qNPA) of FFPE samples, i.e. extraction free.
Library preparation was performed by HTG Molecular Diagnostics, Tucson, AZ, USA using their established protocols. Excess functional DNA nuclease protection probes flanked with universal wing sequences are hybridized to target RNAs. Non-hybridized DNA probes and RNA are digested by S1 nuclease, essentially resulting in a 1:1 ratio of DNA detection probes and initially targeted RNA. DNA protection probes are released after heat denaturalization. Barcodes and adapters were individually added using a 16-cycle PCR reaction. Individual sample purification using AMPure XP beads (Beckman Coulter, Brea, CA, USA) and quantification using  KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA, USA).

value: bone marrow


title: technical control replicate; 1893-HCT-15_1

description: Library name: 1893-HCT-15_1


title: ChipSeq_PA2_E11.5_Hoxa2PTE-36kb-del_H3K27me3_1

description:
Library name: Sample 5
PA2 , E11.5, Hoxa2PTE-36kb-del, ChipSeq , H3K27me3


title: KYSE150-1-IgG

description: Library name: sample 2

tag: cell line


title: ChipSeq_FNPMxMdPA2_E11.5_WT_CTCF_1

description:
Library name: Sample 7
Wnt1CreRosa.mix, E11.5, WT, ChipSeq , CTCF

tag: genotype

value: CTCF


title: 3384802_KDM6B_rTreg_NO1

description: Library name: sample 7

value: Spleen and LNs

value: Treg

tag: treatment


title: 3384800_WT_rTreg_TCR2

description: Library name: sample 5

tag: tissue

value: anti-CD3/CD28 for 3 hours


title: KYSE150-2

description: Library name: sample 3


title: bone marrow; sAA; 1893-A043013

description: Library name: 1893-A043013


title: KYSE150-3-IgG

description: Library name: sample 6


title: bone marrow; sAA; 1893-A043012

description: Library name: 1893-A043012


title: 3384799_WT_rTreg_TCR1

description: Library name: sample 4


title: technical control replicate; 1893-HCT-15_3

description: Library name: 1893-HCT-15_3


title: KYSE150-2-IgG

description: Library name: sample 4


title: KYSE150-1

description: Library name: sample 1


title: Input_PA2_E11.5_WT

description:
Library name: Sample 3
PA2 , E11.5, WT, Input


title: 3384801_WT_rTreg_TCR3

description: Library name: sample 6


title: bone marrow; sAA; 1893-A043011

description: Library name: 1893-A043011


title: 3384803_KDM6B_rTreg_NO2

description: Library name: sample 8

value: Foxp3Cre x Kdm6bfl/fl


title: 3384798_WT_rTreg_NO3

description: Library name: sample 3


title: ChipSeq_PA2_E11.5_Hoxa2PTE-36kb-del_H3K27ac_1

description:
Library name: Sample 4
PA2 , E11.5, Hoxa2PTE-36kb-del, ChipSeq , H3K27ac


title: RA MΦs, PBS 1

city: Chicago

first: Shiva

last: Shahrara

address: 840 S. Wood St

institute: University of Illinois Chicago

description: Library name: Sample 1

data_processing:
Sequence reads were mapped to the human genome (GRCh38) reference using STAR aligner (2.7.10b). Raw read counts per gene were then generated by HT-Seq Count (2.0.5). Normalization occurred by calculating the Fragments per kilobase per million mapped reads (FPKM) and TPM (transcripts per kilobase million) values for each gene to correct for sequencing depth and gene length via StringTie (2.2.1).
Assembly: human genome (GRCh38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: RA PBMCs

extract_protocol:
RNA was isolated from cell samples using QIAzol and Chloroform phase separation and purified using RNeasy Mini Kit (Qiagen LLC, Germantown, MD). Isolated RNA sample quality was assessed BioAnalyzer Pico RNA Assay (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 (ThermoFisher, Massachusetts, USA).
Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 500bp with an insert size of about 350bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for [40] M PE reads per sample (20M in each direction).

treatment_protocol: Cells were stimulated with 100 ng/mL GM-CSF for 12 hrs.

value: RA PBMCs

value: macrophages

value: PBS 1


title: bone marrow; sAA; 1893-A043010

description: Library name: 1893-A043010


title: 3384797_WT_rTreg_NO2

description: Library name: sample 2


title: ChipSeq_PA2_E11.5_WT_H3K27ac_1

description:
Library name: Sample 1
PA2 , E11.5, WT, ChipSeq , H3K27ac


title: 3384796_WT_rTreg_NO1

description: Library name: sample 1


title: SCPD_D25.5, scRNAseq

city: Hangzhou

first: Tiancheng

last: Yu

state: Zhejiang

address: Dunyu Road

institute: Westlake University

description: Library name: SAMPLES 1

data_processing:
The demultiplexing, barcoded processing,gene counting and aggregation were made using the Cell Ranger software v7.0.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The organoids were dissociated into single cells using the STEMdiff Cardiomyocyte Dissociation Kit (Stemcell Technologies, #05025). The cell suspension was then loaded into Chromium microfluidic chips for single-cell RNA sequencing.
The cell suspension was processed with 3’ (v2 or v3, depending on the project) chemistry and barcoded using a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was reverse-transcribed, and sequencing libraries were constructed using the Chromium Single Cell 3’ v2 (v2 or v3, depending on the project) reagent kit (10X Genomics), following the manufacturer’s instructions.

value: 3D culture


title: RA MΦs, GM-CSF 1

description: Library name: Sample 4

value: GM-CSF 1


title: Gastrocnemius, KO 4

first: Tony

last: Tiganis

state: Victoria

address: 23 Innovation Walk, Monash University, Clayton

institute: Monash University

description:
Library name: KO 4
column KO 4 in Nox4_RNAseq_counts.csv

data_processing:
Reads were mapped using the nf-core RNAseq pipeline as implemented in Laxy. STAR feature counts outputs were used for the counts matrix.
Assembly: GRCm39
Supplementary files format and content: raw counts matrix (STAR feature counts) as .csv file

source_name: Gastrocnemius muscle

extract_protocol:
Gastrocnemius muscle from 21-month old muscle-specific Nox4 knockout mice (MckCre:Nox4 fl/fl) and age-matched Nox4 fl/fl controls. Total RNA was isolated from homogenised mouse gastrocnemius muscle tissue with RNeasy mini kits (Qiagen, Hilden, Germany) and processed for library preparation (PolyA, unstranded) and sequencing on an Illumina Novaseq PE150 by Azenta Life Sciences (Burlington, MA).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and  add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of  Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Novaseq instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Gastrocnemius muscle

value: MckCre:Nox4 fl/fl (KO)


title: Control patient line 17 replicate 2

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: Control_LCH17_rep2

data_processing:
FASTQ files from sequencing experiments were mapped to hg38. RNA-seq files were mapped using the alignment tool STAR (v2.7.11b).
Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.1.3).
Gene expression raw counts was quantified by HOMER’s ‘analyzeRepeats’
Batch correction was performed using CombatSeq and the sva package (v3.52.0)
Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Quantified read counts were normalized and analyzed using DESeq2 (v1.44.0) to determine differential expression between groups, within the R statistical computing environment (v4.4.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample
Supplementary files format and content: tab-delimited text file inclues raw TPM for each Sample

source_name: iPSC-derived Microglia

extract_protocol:
To perform the mRNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer’s instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries
RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions

value: iPSC-derived Microglia

value: patient line

value: Microglia

value: Control


title: bone marrow; sAA; 1893-A043008

description: Library name: 1893-A043008

value: bone marrow


title: Gastrocnemius, KO 3

description:
Library name: KO 3
column KO 3 in Nox4_RNAseq_counts.csv


title: bone marrow; sAA; 1893-A043009

description: Library name: 1893-A043009


title: Control patient line 17 replicate 1

description: Library name: Control_LCH17_rep1


title: Control patient line 1293 replicate 1

description: Library name: Control_1293_rep1


title: bone marrow; sAA; 1893-A043006

description: Library name: 1893-A043006


title: Gastrocnemius, KO 2

description:
Library name: KO 2
column KO 2 in Nox4_RNAseq_counts.csv


title: Visium_alpha_MHC_MerCreMer_Het

city: Cleveland

first: Lily

last: Wang

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description:
Library name: alpha_MHC_MerCreMer_Het
Visium Spatial

data_processing:
Raw base call files were demultiplexed using Illumina bcl2fastq to generate FASTQ files.
FASTQ files were processed using 10x Genomics Space Ranger software to align reads, assign spatial barcodes, and generate gene expression matrices.
Spatial gene expression matrices were imported into downstream analysis pipelines for normalization, clustering, and differential spatial gene expression analysis.
Differential expression analyses were performed to identify cardiac remodeling, metabolic, and heart failure–associated transcriptional signatures.
Spatial visualization and gene signature mapping were performed using Loupe Browser and custom R-based workflows.
Assembly: Mus musculus reference genome GRCm39 (mm39)
Supplementary files format and content: Processed data include spatial gene expression matrices, spot-level metadata, and tissue position files generated by Space Ranger. Files are provided in HDF5 (.h5), CSV, and Loupe-compatible formats.
Supplementary files format and content: Differential expression results and annotation tables are provided as tab-delimited text files.
Library strategy: Spatial Transcriptomics

source_name: Cardiac Tissue

growth_protocol: α-MHC-MerCreMer and α-MHC-MerCreMer+/− hTOP2BLSL/− mice were maintained under standard specific pathogen–free conditions with ad libitum access to food and water on a 12-hour light/dark cycle. Animals were housed at constant temperature and humidity according to institutional guidelines.

extract_protocol:
Mouse hearts were harvested, fixed in formalin, and embedded in paraffin. FFPE blocks were sectioned at 5 μm thickness and mounted on microscope slides. Sections were deparaffinized, H&E stained, imaged, and processed using the 10x Genomics Visium CytAssist Spatial Gene Expression FFPE workflow, including decrosslinking, probe hybridization, and RNA capture according to manufacturer’s instructions.
Spatial transcriptomic libraries were generated using the 10x Genomics Visium CytAssist Spatial Gene Expression for FFPE protocol. Following probe hybridization and extension, libraries were constructed with paired-end dual indexing. Libraries were quantified, quality controlled, and sequenced on an Illumina NovaSeq platform (28 cycles Read 1, 10 cycles i7, 10 cycles i5, 50 cycles Read 2).

treatment_protocol: For TOP2B induction, both control α-MHC-MerCreMer+/− and α-MHC-MerCreMer+/− hTOP2BLSL/− mice received intraperitoneal tamoxifen injections (single dose 80 mg/kg).

value: Cardiac Tissue

value: Cardiac


title: bone marrow; sAA; 1893-A043007

description: Library name: 1893-A043007


title: alpha_MHC_MerCreMer_Het_TOP2B_LSL

description:
Library name: alpha_MHC_MerCreMer_Het_TOP2B_LSL
Visium Spatial


title: ChipSeq_PA2_E11.5_WT_H3K27me3_1

description:
Library name: Sample 2
PA2 , E11.5, WT, ChipSeq , H3K27me3

value: Cranial neural crest cells

value: WT