title: LNCaP, R1881, pGIPZ, HOXB13 ChIP

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

institute: Emory University

description: Library name: M29

data_processing:
Reads were aligned to hg38 using bowtie2. Bigwig files were created using deeptools' bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig generated from bam files

source_name: Prostate

extract_protocol:
PCa cells were crosslinked with 1% formaldehyde for 10 min at room temperature with gentle rotation and then quenched for 5 min with 0.125 M glycine. Chromatin was sonicated to an average length of 200–600 bp using an E220 focused-ultrasonicator (Covaris).
ChIP–seq libraries were prepared from 3–5 ng of ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: LNCaP cells were infected with control or HOXB13, FOXA1, GATA2 KD lentivirus and subjected to ChIP-seq assay

value: Prostate

value: LNCaP

value: Prostate cancer cell

value: pGIPZ

tag: antibody

value: HOXB13 ChIP


title: 4 Keratinocytes - TNF + IL--17A

status: Public on Mar 04 2026

type: SRA

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description:
Library name: KC_23
2x150 Sequence mode to obtain at approx. 20 million read pairs

library_source: transcriptomic

data_processing:
R package Subread (version 2.10.3)
Raw reads were aligned to the human reference genome (GRCh38.p14 primary assembly)
Gene counts were obtained by uniquely aligned unambiguous reads
Assembly: GRCh38.14 primary assembly
Supplementary files format and content: xlsx

molecule: total RNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
Total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) according to the manufacturer’s instructions
RNA sequencing library was prepared with 100 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

tag: tissue

value: Skin

tag: cell type

value: Primary human keratinocytes

tag: treatment


title: Il5RFP-cre (R5/+) Rptorf/f-1

city: 黄浦区

first: Lin

last: Hu

state: 上海市

address: 重庆南路280号

country: China

institute: 基础医学院

description: Library name: WT1

data_processing:
CLC genomics workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: excel files include FPKM values for each sample

organism: Mus musculus

source_name: adipose tissue

extract_protocol:
Sorting of ILC2 in the adipose tissue,then total RNA extracted by Trizol for sequencing libraries
RNA libraries for RNA-seq were prepared using Smart mRNA-seq library prep kit following manufacturer's protocols

value: adipose tissue


title: HEK 293T, 2WTCT12,rep2

city: Suzhou

first: Tao

last: Zhang

state: Jiangsu

address: No.28 Kehua Road

institute: Suzhou Vocational Health College

description:
Library name: Sample11
CT12-2

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1)
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

source_name: HEK 293T

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with high glucose, supplemented with 10% fetal bovine serum (FBS), 50 U/mL penicillin, and 50 mg/mL streptomycin, and maintained at 37 °C in 5% CO₂.

extract_protocol:
RNA was harvested using Magzol Reagent (Magen，R4801-02). 1.4ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS mRNA Capture Beads（N401）+ VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605-02 following manufacturer's protocols.

treatment_protocol: For synchronization, cells were plated in 3.5 cm plates and treated with 200 nM dexamethasone (DEX, Sigma-Aldrich, MO, USA) in PBS for 0.5 hours and initiated sample collection 24 hours after synchronization. Cells were harvested every 4 hours over a 48-hour period

tag: cell line

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line

tag: genotype

value: Wildtype

value: dexamethasone shock for 30 minutes

tag: batch


title: LNCaP, R1881, shFOXA1, HOXB13 ChIP

department: Urology

country: USA

description: Library name: M31

library_source: genomic

molecule: genomic DNA


title: 1 Keratinocytes - TNF + IL-17A

description:
Library name: KC_5
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 2 Keratinocytes - TNF + IL-17A

description:
Library name: KC_11
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MEFs, 24h +Myf6+F/R/C in iMPC medium, rep2

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: 329951_6-TM19_D1_doxFRC

data_processing:
BWA-MEM used for reference alignment
MACS2 used for narrow peak calling
R package DESeq2 used for differential accessibility analysis based on consensus peaks
R package IRanges used for promoter overlap analysis
MEME suite used for motif analysis
Assembly: GRCm38.p6
Supplementary files format and content: Called narrow peaks in BigWig format
Supplementary files format and content: Consensus peak file in txt format

source_name: Mouse embryonic fibroblasts (MEFs)

growth_protocol: iMPC medium (KnockOut DMEM supplemented with 10% FBS, 10% KnockOut Serum Replacement, 1% MEM Non-Essential Amino Acids Solution (100X), 1% GlutaMAX Supplement (100X), 1% Penicillin-Streptomycin (10,000 U/mL), 0.1% 2-Mercaptoethanol and 10ng/mL bFGF). All cells were cultured at 37°C and 5% CO2.

extract_protocol:
For ATAC-Seq, the protocol modifications of the Kestner Lab of the Omni-ATAC protocol were used (Ackermann et al., 2016; Corces et al., 2017). Cells were washed 1x with PBS and collected by incubating them with Accutase cell detachment solution at 37°C in 5% CO2 for 7 minutes. After inactivation with iMPC medium, cells were centrifuged and resuspended in sterile-filtered 2% BSA (Albumin (BSA) Fraction V, (pH 7.0)) in PBS. 50k cells per condition were transferred into 1.5mL Protein Lo-Bind tube. Cells were then spun down at 500g for 5 minutes at 4°C, washed with ice-cold PBS, spun down again with the same settings and resuspended in nuclei isolation buffer containing 10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Igepal, 0.1% TWEEN 20 and 0.01% Digitonin. After incubation for 3 minutes on ice, wash buffer containing 10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2 and 0.1% TWEEN 20 was added to the nuclei and the samples were centrifuged at 500g at 4°C for 10 minutes. Each nuclei preparation was then resuspended in transposition reaction mix containing 25µL 2x Tagment DNA buffer (Illumina, 20034197), 16.5µL PBS, 0.5µL 10% TWEEN 20, 0.5µL 1% Digitonin, 2.5uL TDE1 Tagment DNA Enzyme (Illumina, 20034197) and 5µL nuclease-free H2O. The samples were then incubated at 37°C for 30mins at 1,000rpm. Tagmented DNA was then isolated and purified using MinElute Reaction Cleanup Kit according to manufacturer’s protocol and eluted in 10µL.
The purified transposed DNA was then amplified for 12 cycles using NEBNext High-Fidelity 2X PCR Master Mix and the custom Nextera PCR primers Ad1_noMX and Ad2.1-6 indexing primers at 1.25µM from Buenrostro et al., 2013. The amplified libraries were then purified from primers with a single left-side 1.8x AMPure XP Beads-Based Reagent beads purification. Samples were then eluted in 22µL elution buffer and a 1:15 dilution was analyzed on the 4200 TapeStation System (Agilent Technologies) using the D5000 High Sensitivity ScreenTapes and reagents.

treatment_protocol: iMPC medium was used either alone or supplemented with doxycycline (2µg/mL doxycycline hyclate) to induce Myf6 overexpression and/or F/R/C (F: 5µM Forskolin; R: 5µM RepSox; C: 3µM CHIR99021).

value: Mouse embryonic fibroblasts (MEFs)

tag: strain

value: M2-rtTA x TetO-Myf6

value: heterozygous for both alleles

value: iMPC medium+Myf6+F/R/C

tag: time


title: MLE-12 cells,Hyperoxia+Exo2,24h

city: Wuxi

first: Yahui

last: Zhou

address: No. 299-1 Qingyang Road, Liangxi District, Wuxi, Jiangsu, China

department: Department of Neonatology

institute: Affiliated Children’s Hospital of Jiangnan University

description: Library name: Sample Exo-O2-2

data_processing:
Raw sequencing reads were filtered to remove adaptor sequences, rRNA reads, low-quality reads, and short fragments.
Clean reads were aligned to the reference genome using HISAT2 (version 2.0.4).
Transcript assembly and quantification were performed using StringTie (version 1.3.0), and gene expression levels were calculated as FPKM values.
Differential gene expression analysis was conducted using edgeR. Genes with FDR ≤ 0.05 and fold change ≥ 2 were considered significantly differentially expressed.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files contain raw read counts for each sample.
Supplementary files format and content: CSV files contain normalized gene expression values (FPKM) for each sample.

growth_protocol: The lung AT II cell line (MLE-12)was cultured in 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin. The cells were incubated in an in-cubator at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from samples using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. RNA quantity and quality were assessed prior to library construction.
RNA libraries were prepared using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following the manufacturer’s instructions. Briefly, poly(A)+ mRNA was enriched using oligo(dT) magnetic beads, followed by fragmentation and cDNA synthesis. Libraries were quantified using Qubit 2.0 Fluorometer and validated using Agilent 2100 Bioanalyzer. Sequencing was performed on the Illumina NovaSeq 6000 platform.

treatment_protocol: Two types of cell models were established to model bronchopulmonary dysplasia (BPD) in vitro. One was induced by hyperoxia, and the other was induced by lipopolysaccharide (LPS). The cells in the hyperoxia group were placed in a high-oxygen incubator and exposed to 85% oxygen. The cells in the LPS group were maintained under normal oxygen conditions (21% O2) and treated with 100 ng/mL LPS. In the intervention groups, M2 macrophage-derived exosomes (M2-Exo) were added after hyperoxia or LPS treatment. The final concentration of M2-Exo was 10 µg/mL.

value: lung epithelial cell


title: MLE-12 cells,Hyperoxia+Exo1,24h

description: Library name: Sample Exo-O2-1


title: MLE-12 cells,Hyperoxia3,24h

description: Library name: Sample O2-3


title: MLE-12 cells,Hyperoxia2,24h

description: Library name: Sample O2-2


title: 2 Keratinocytes - TNF

description:
Library name: KC_10
2x150 Sequence mode to obtain at approx. 20 million read pairs

value: TNF


title: 4 Keratinocytes - TNF

description:
Library name: KC_22
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 3 Keratinocytes - TNF

description:
Library name: KC_16
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MLE-12 cells,Hyperoxia1,24h

description: Library name: Sample O2-1


title: 1 Keratinocytes - TNF

description:
Library name: KC_4
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Il5RFP-cre (R5/+) Rptor+/+-1

description: Library name: KO1


title: HEK 293T, 2WTCT0,rep1

description:
Library name: Sample1
CT0-1


title: MLE-12 cells,LPS+Exo3,24h

description: Library name: Sample Exo3


title: 2 Keratinocytes - IL-17A

description:
Library name: KC_8
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 3 Keratinocytes - IL-17A

description:
Library name: KC_14
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MLE-12 cells,LPS+Exo1,24h

description: Library name: Sample Exo1


title: MLE-12 cells,LPS3,24h

description: Library name: Sample LPS3


title: DXO treated rat 8

city: Laval

first: Geraldine

last: Delbes

state: QC

address: 531 boulevard des Prairies

country: Canada

institute: Institut national de la recherche scientifique

description:
Library name: DXO-8
Column name in raw_counts_all_samples.csv: i5.DXO-8

data_processing:
Library quality was confirmed via Illumina Library QC prior to sequencing on an Illumina NovaSeq platform with paired-end 100 bp reads (PE100), generating a total of approximately 3200 million reads across all libraries (±200 million reads per sample). Raw reads were quality-checked using FastQC v0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and MultiQC v1.12 (Ewels et al., 2016). Adapters were trimmed with fastp v0.23.2 Trimmomatic (Chen et al., 2018).
Assembly: Reads were aligned to the Rattus norvegicus reference transcriptome (rn6) using Kallisto v0.48.0 (Bray et al., 2016).Gene expression quantification was done with featureCounts, and differential expression analysis was conducted using DESeq2 v1.40.2 (Love et al., 2014). To identify significantly differentially expressed genes (DEGs), we applied a threshold of |log2 fold change| ≥ 2 and a Benjamini–Hochberg adjusted p-value (FDR) < 0.05.
Supplementary files format and content: csv files include raw count for each samples

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Testis

extract_protocol:
Arcturus PicoPure RNA isolation kit (Thermofisher, #KIT0204)
A subset of RNA samples with RIN above eight (n=4/group) were used for polyA-enriched RNA libraries preparation using standard protocols at Genome Quebec

value: Testis

value: SSC

value: Germ cells

value: Transgenic Sprague-Dawley  (GCS-EGFP)

value: 5mg/kg of Doxorubicin


title: DXO treated rat 6

description:
Library name: DXO-6
Column name in raw_counts_all_samples.csv: i5.DXO-6


title: Control rat 9

description:
Library name: CTRL-9
Column name in raw_counts_all_samples.csv: i5.CTRL-9


title: DXO treated rat 3

description:
Library name: DXO-3
Column name in raw_counts_all_samples.csv: i5.DXO-3


title: DXO treated rat 2

description:
Library name: DXO-2
Column name in raw_counts_all_samples.csv: i5.DXO-2


title: Control rat 5

description:
Library name: CTRL-5
Column name in raw_counts_all_samples.csv: i5.CTRL-5


title: MLE-12 cells,LPS+Exo2,24h

description: Library name: Sample Exo2


title: D7 TAK 1

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

description:
Library name: PRCH575
CAAGCAGAAGACGGCATACGAGATACAGTGGTGTCTCGTGGGCTCGGAGATGT

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Reads were mapped to the Homo sapiens genome (hg38) using the ENCODE ATAC pipeline v2.2.2 utilizing Bowtie2 v2.3.4.3 (parameter: -X2000).
Reads were filtered using samtools view v1.9 (parameters: -F 1804 -q 30), and duplicates were marked with Picard MarkDuplicates v2.20.7 and removed using samtools (parameter: -F 1804).
Peak calling was performed on samples separately using macs2 v2.2.4 within the ENCODE ATAC pipeline v2.2.2 with the following parameters: –shift 75 –extsize 150 –nomodel -B –SPMR –keep-dup all –call-summits.
Peak calling was performed on samples separately using macs2 v2.2.4 within the ENCODE ATAC pipeline v2.2.2 with the following parameters: –shift 75 –extsize 150 –nomodel -B –SPMR –keep-dup all –call-summits.
BigWig files were generated using Deeptools bamCoverage v3.5 with the parameters: -of bigwig -bs 10 –normalizeUsing CPM –effectiveGenomeSize 2913022398 –skipNonCoveredRegions –extendReads.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Adipose tissue

extract_protocol:
Cells were lysed and incubated with transposase to tag accessible DNA regions. TAGmented DNA fragments were PCR amplified.
Quality of the PCR-amplified library was assessed on a Bioanalyzer. Amplicons of 200 - 600bp were size-selected and purified 2x with SPRIselect beads and the quality once more assessed by Bioanalyzer and sent for sequencing.

value: Adipose tissue

value: hTERT-A41hWAT-SVF CRL-3398

value: White adipocyte SVF cells

value: WT

value: adipogenic differentiation with transient TAK-981 treatment in preadipocytes


title: 1 Keratinocytes - IL-17A

description:
Library name: KC_2
2x150 Sequence mode to obtain at approx. 20 million read pairs

value: Skin

value: Primary human keratinocytes


title: Control rat 4

description:
Library name: CTRL-4
Column name in raw_counts_all_samples.csv: i5.CTRL-4


title: Control rat 1

description:
Library name: CTRL-1
Column name in raw_counts_all_samples.csv: i5.CTRL-1


title: 4 Keratinocytes - Vehicle

description:
Library name: KC_19
2x150 Sequence mode to obtain at approx. 20 million read pairs

value: Vehicle


title: D7 DMSO 2

description:
Library name: PRCH574
CAAGCAGAAGACGGCATACGAGATATCACGACGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3397

value: adipogenic differentiation with transient DMSO treatment in preadipocytes


title: 4 Keratinocytes - IL-17A

description:
Library name: KC_20
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: MLE-12 cells,LPS1,24h

description: Library name: Sample LPS1

value: lung epithelial cell


title: 24 months AF cells MDL-800 treated 30

city: Philadelphia

first: Makarand

middle: V

last: Risbud

address: 1025 Walnut St.

institute: Thomas Jefferson University

description:
Library name: Sample 20
total RNA

data_processing:
the sequence reads were aligned by STAR 2.7.11b, and counts data were retrieved by --quantMode option
Assembly: mm10
Supplementary files format and content: FPKM counts in csv format

source_name: intervertebral disc

extract_protocol:
NP and AF tissues were isolated under microscope and placed in RNA later immediately. Samples were stored in -80 until extraction. RNA was isolated using RNA-easy mini kit (Qiagen).
Libraries for whole transcriptome RNA sequencing were prepared using the Stranded Total RNAseq with Ribo-zero Plus kit (Illumina, San Diego, CA) as per manufacturer’s instructions starting with an input of 50 ng of RNA and 14 cycles of final PCR amplification. Library size was assessed using the 4200 TapeStation and the DNA D5000 ScreenTape assay (Agilent, Santa Clara, CA). Library concentration was determined using the Qubit Fluorometer 2.0 (ThermoFisher Scientific, Waltham, MA).

treatment_protocol: 18 months old BL6 mice were randomly divided into two groups Vehicle and MDL. Vehicle group received DMSO IP injections per week for 6 months and MDL group received MDL-800 dissolved in same amount of DMSO as Vehicle group IP injections per week for 6 months. Mice were euthanized at 24 months of age by CO2 asphyxiation.

value: intervertebral disc

value: Primary cells

value: Annulus fibrosus


title: 3 Keratinocytes - Vehicle

description:
Library name: KC_13
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: D7 TAK 2

description:
Library name: PRCH576
CAAGCAGAAGACGGCATACGAGATCAGATCCAGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3399


title: D7 DMSO 1

description:
Library name: PRCH573
CAAGCAGAAGACGGCATACGAGATTGCCTCTTGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3396


title: 24 months AF cells MDL-800 treated 29

description:
Library name: Sample 19
total RNA


title: 12h TAK 2

description:
Library name: PRCH572
CAAGCAGAAGACGGCATACGAGATCAGCCTCGGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3395


title: MLE-12 cells,LPS2,24h

description: Library name: Sample LPS2


title: 12h TAK 1

description:
Library name: PRCH571
CAAGCAGAAGACGGCATACGAGATAGCGTAGCGTCTCGTGGGCTCGGAGATGT

value: Adipose tissue

value: hTERT-A41hWAT-SVF CRL-3394


title: 1 Keratinocytes - Vehicle

description:
Library name: KC_1
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 12h DMSO 1

description:
Library name: PRCH569
CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3392

value: White adipocyte SVF cells


title: 24 months AF cells MDL-800 treated 28

description:
Library name: Sample 18
total RNA


title: 12h DMSO 2

description:
Library name: PRCH570
CAAGCAGAAGACGGCATACGAGATCCTCTCTGGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3393

value: WT


title: 24 months AF cells MDL-800 treated 27

description:
Library name: Sample 17
total RNA


title: 4 Fibroblasts - TNF + IL-17A

description:
Library name: FB_23
2x150 Sequence mode to obtain at approx. 20 million read pairs

value: Skin

value: Primary human fibroblasts


title: D0 DMSO 2

description:
Library name: PRCH566
CAAGCAGAAGACGGCATACGAGATGCTCAGGAGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3389


title: 3 Fibroblasts - TNF + IL-17A

description:
Library name: FB_17
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: D0 TAK 2

description:
Library name: PRCH568
CAAGCAGAAGACGGCATACGAGATCATGCCTAGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3391

value: adipogenic differentiation with transient TAK-981 treatment in preadipocytes


title: 24 months AF cells MDL-800 treated 25

description:
Library name: Sample 16
total RNA

value: intervertebral disc


title: D0 DMSO 1

description:
Library name: PRCH565
CAAGCAGAAGACGGCATACGAGATTTCTGCCTGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3388

value: adipogenic differentiation with transient DMSO treatment in preadipocytes


title: D0 TAK 1

description:
Library name: PRCH567
CAAGCAGAAGACGGCATACGAGATAGGAGTCCGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3390


title: 2 Keratinocytes - Vehicle

description:
Library name: KC_7
2x150 Sequence mode to obtain at approx. 20 million read pairs

value: Primary human keratinocytes

value: Vehicle


title: D-2 2

description:
Library name: PRCH564
CAAGCAGAAGACGGCATACGAGATCTAGTACGGTCTCGTGGGCTCGGAGATGT

value: Adipose tissue

value: hTERT-A41hWAT-SVF CRL-3387

value: Adipogenic differentiation


title: 2 Fibroblasts - TNF + IL-17A

description:
Library name: FB_11
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: D-2 1

description:
Library name: PRCH563
CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGGAGATGT

value: hTERT-A41hWAT-SVF CRL-3386

value: White adipocyte SVF cells


title: 1 Fibroblasts - TNF + IL-17A

description:
Library name: FB_5
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 24 months AF cells Vehicle Control 13

description:
Library name: Sample 15
total RNA

value: Primary cells

value: Annulus fibrosus


title: In-vivo WM4007 scRNAseq Day20 Dabrafenib/Trametinib treated

first: Yeqing

last: Chen

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description: Library name: WM4007_D20_scRNAseq

library_source: transcriptomic single cell

data_processing:
The reads alignment was performed using Cell Ranger v8.0.0 (10x Genomics). For in-vivo PDX samples, the raw sequencing reads were first aligned to a human-mouse combined reference genome (refdata-gex-GRCh38_and_GRCm39-2024-A) to identify mouse reads contamination. Cells with more than 20% of counts originating from mouse genome were excluded. For barcoded samples, the raw sequencing reads were aligned to a customized reference genome by incorporating our barcode vector sequence into the human genome (GRCh38-2024-A). Otherwise, the raw sequencing reads were aligned to the human genome (GRCh38-2024-A) directly.
Assembly: GRCh38-2024-A
Supplementary files format and content: rds

source_name: In-vivo PDX

growth_protocol: WM4237-1 cells are cultured in TU2% media consisting of 80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4 mM CaCl2, and passaged using 0.05% trypsin-EDTA. Melanoma cells (5 × 10⁵ in 100 μL of a 1:1 mixture of RPMI and Matrigel [Corning]) were subcutaneously injected into the right flanks of 6–8-week-old male NSG mice. Tumor growth was monitored using calipers, and volumes were calculated using the formula (W² × L)/2.

extract_protocol:
Post-treatment WM4237-1 cells were trypsinized, washed, and processed with Dead Cell Removal Kit (Miltenyi Biotec) following manufacturer’s instructions. Tumor chunks from three replicates were pooled, minced, and dissociated (0.2–1 g) using the Tumor Dissociation Kit and gentleMACS Octo Dissociator (Miltenyi Biotec) with heating. Cells were filtered (70 μm nylon mesh), centrifuged (250 × g, 7 min), RBC-lysed with 1 mL ACK buffer (Quality Biological, 118-156-101), diluted, and centrifuged again (250 × g, 5 min). Pellets were processed with the Mouse Cell Depletion Kit and Dead Cell Removal Kit (Miltenyi Biotec). Final pellets were resuspended in 80 µL PBS, kept on ice, and used for cell counting and scRNA-seq.
Single cell droplets were generated using the Chromium Next GEM single cell 3’ kit v3.1 (10x Genomics). cDNA synthesis and amplification, library preparation and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics), according to manufacturer’s instructions. Overall library size was determined using the Agilent Bioanalyzer 2100 and the High Sensitivity DNA assay and libraries were quantitated using KAPA real-time PCR. Libraries were pooled and sequenced on the NovaSeq 6000 (Illumina, San Diego, CA) using a S2 300 cycle kit (Illumina), paired end run with the following run parameters: 26 base pair x 8 base pair (dual index) x 280 base pair.

treatment_protocol: WM4237-1 cells were treated for one week with media containing 0.3 µM dabrafenib and 30 nM trametinib refreshed every two days. Once tumors reached approximately 100-500 mm³, mice were treated with a rodent diet supplemented with 150 mg/kg dabrafenib and 1.5 mg/kg trametinib (Bio-Serv, S7581). Tumors were harvested at defined time points and pooled for single-cell sample preparation.

value: In-vivo PDX

value: Melanoma

value: BRAF V600E

value: Dabrafenib/Trametinib


title: 4 Fibroblasts - TNF

description:
Library name: FB_22
2x150 Sequence mode to obtain at approx. 20 million read pairs

value: Skin

value: Primary human fibroblasts

value: TNF


title: 24 months AF cells Vehicle Control 12

description:
Library name: Sample 14
total RNA

value: intervertebral disc


title: In-vivo WM4007 scRNAseq Day13 Dabrafenib/Trametinib treated

description: Library name: WM4007_D13_scRNAseq


title: 24 months AF cells Vehicle Control 10

description:
Library name: Sample 13
total RNA


title: In-vivo WM4007 scRNAseq Day89 Dabrafenib/Trametinib treated

description: Library name: WM4007_EP_scRNAseq


title: OVCAR-8, Untreated, 1

city: Oklahoma City

first: Dongin

last: Kim

state: Oklahoma

address: 1110 N Stonewall Ave

department: Pharmaceutical Sciences

institute: University of Oklahoma Health Sciences Center

description: Library name: Sample 12

data_processing:
Raw RNA-seq reads were preprocessed for quality control using fastp (v0.23.4) with adapter trimming, poly-G, and poly-X removal. Following QC, gene-level quantification was performed using salmon (version 1.7.0) in quasi-mapping mode.
Assembly: The reads were mapped to the GRCh38.p13 v39 transcriptome index (GENCODE annotations).
Supplementary files format and content: Processed data includes raw gene counts, differential expression reports (DEGs), PCA plots, MA plots, volcano plots, and heat maps.

extract_protocol:
Total RNA was extracted using TRIzol reagent, following the manufacturer’s protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer, and concentrations were determined using ThermoFisher’s NanoDrop.
Stranded RNA-seq libraries were constructed using the NEBNext poly(A) mRNA isolation kit, followed by the IDT XGen Broad Range RNA Library Prep Kit, according to the manufacturer’s protocol. 1 µg of RNA was used for library construction, and libraries were indexed for multiplexed sequencing.

value: Ovarian cancer cell

value: WT

value: No


title: OVCAR-8, Untreated, 3

description: Library name: Sample 14


title: 24 months AF cells Vehicle Control 9

description:
Library name: Sample 12
total RNA

value: Vehicle


title: 2 Fibroblasts - TNF

description:
Library name: FB_10
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: OVCAR-8, Untreated, 2

description: Library name: Sample 13


title: OVCAR-8, AB-TSEV, 2

description: Library name: Sample 11

value: Antibody decorated CD8+ T cell sEV


title: OVCAR-8, AB-TSEV, 1

description: Library name: Sample 10


title: 24 months AF cells Vehicle Control 8

description:
Library name: Sample 11
total RNA


title: 1 Fibroblasts - TNF

description:
Library name: FB_4
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 4 Fibroblasts - IL-17A

description:
Library name: FB_20
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: OVCAR-8, TSEV, 2

description: Library name: Sample 8

value: CD8+ T cell sEV


title: OVCAR-8, TSEV, 1

description: Library name: Sample 7


title: OVCAR-8, TSEV, 3

description: Library name: Sample 9


title: 24 months NP cells MDL-800 treated 22

description:
Library name: Sample 10
total RNA

value: nucleus pulposus


title: OVCAR-8, ASAB, 3

description: Library name: Sample 6

value: ASAB


title: 24 months NP cells MDL-800 treated 20

description:
Library name: Sample 9
total RNA

value: Primary cells


title: 3 Fibroblasts - IL-17A

description:
Library name: FB_14
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: OVCAR-8, ASAB, 1

description: Library name: Sample 4


title: 24 months NP cells MDL-800 treated 18

description:
Library name: Sample 7
total RNA


title: OVCAR-8, AB, 2

description: Library name: Sample 2

value: Antibody


title: 3 Fibroblasts - TNF

description:
Library name: FB_16
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 1 Fibroblasts - IL-17A

description:
Library name: FB_2
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: TAKRosi3

description: Library name: PRCH504

data_processing:
Image analysis and base calling were performed using RTA and bcl2fastq.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 4.2. Reads were mapped onto the hg38 assembly of Homo sapien genome using STAR version 2.7.10b. Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.13.5, with annotations from Ensembl version 110 and “union” mode.
Assembly: hg38
Supplementary files format and content: Tab-separated text file with raw read counts per Ensembl Gene.

source_name: hTERT-A41hWAT-SVF CRL-3386

growth_protocol: Human white pre-adipocytes (hTERT-A41hWAT-SVF, ATCC, CRL-3386) were maintained and differentiated based on previously established protocols (Herbers et al, 2022, PMID: 35422865). Cells were maintained in StableCellTM DMEM High Glucose Medium (Sigma, D0819), supplied with 10% Fetal Bovine Serum (FBS, F7524) and 1% Penicillin/Streptomycin (PenStrep, Gibco, 15140-122) at 37°C in a humidified incubator at 5% CO2 in air atmosphere. In advance to differentiation induction, the pre-adipocytes were grown to full confluence and kept at full confluence for 2 days. After two days at full confluency, differentiation was induced.

extract_protocol:
Cells were collected in TRIzole Reagent (Life Technologies, MAN0001271) and 200µL of chloroform was added per 1ml of TRIzole Reagent used. Samples were vortexed thoroughly and incubated on ice for 5 minutes before centrifugation at 13,200 RPM for 10 minutes at 4°C. The aqueous phase containing the RNA was collected and the RNA precipitated with 100% isopropanol and incubated on ice for 5 minutes. The RNA pellets were centrifuged at 13,200 RPM for 10 minutes at 4°C. The supernatant was removed and the RNA pellet washed in 70% ethanol, followed by incubation on ice for 5 minutes. After centrifugating the RNA at 13,200 RPM for 5 minutes at 4°C the supernatant was removed, and the RNA pellet briefly air dried. Finally, the RNA was resuspended in RNAse-free H2O and incubated on ice for 20 minutes. RNA concentrations were determined using Nanodrop 3000 and 200ng of total RNA sent for sequencing.
Total RNA-Seq libraries were generated from 200 ng of total RNA using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and IDT for Illumina RNA UD Indexes, Ligation (Illumina, San Diego, USA), according to manufacturer's instructions. DNA library were amplified using 15cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France). The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: Differentiation was induced by adding StableCellTM DMEM High Glucose Medium (D0819, Sigma), supplied with 2% Fetal Bovine Serum (F7524, Sigma), 1% PenStrep ( 15140-122, ThermoFisher), 1 µM Dexamethasone (D4902, Sigma), 0.5 mM 3-Isobutyl-1-methylxanthine (I5879, Sigma), 0.1 µM human insulin (91077C, Sigma), 17 µM Pantothenate (P5155, Sigma), 22 µM Biotin (B4639, Sigma) and 1 µM Rosiglitazone (R2408, Sigma) for 7 days. On Day 7 (D7), the induction medium was replaced with the maintenance medium, consisting of StableCellTM DMEM High Glucose Medium, supplied with 2% FBS, 1% PenStrep, 1 µM Dexamethasone, 0.1 µM human insulin, 17 µM Pantothenate and 22 µM Biotin for at least 14 days. The medium was refreshed every second or third day. The cells marked as DMSORosi and TAKRosi were continuously differentiated with Rosiglitazone.The SUMOylation inhibitor TAK-981 (Takara) was added at 0.5 µM to the cells prior to differentiation induction for 48hrs. After the treatment, the cells were washed with phosphate-buffered saline (PBS) and differentiation was started. As a control, cells were treated with DMSO for 48hrs the same way.

value: hTERT-A41hWAT-SVF CRL-3386

value: adipogenic differentiation with transient TAK-981 treatment in pre-adipocytes and chronic Rosiglitazone treatment during differentiation


title: OVCAR-8, AB, 3

description: Library name: Sample 3


title: 2 Fibroblasts - IL-17A

description:
Library name: FB_8
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: OVCAR-8, ASAB, 2

description: Library name: Sample 5


title: 24 months NP cells Vehicle control 6

description:
Library name: Sample 5
total RNA


title: 24 months NP cells MDL-800 treated 15

description:
Library name: Sample 6
total RNA


title: 4 Fibroblasts - Vehicle

description:
Library name: FB_19
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: TAKRosi1

description: Library name: PRCH502


title: TAKRosi2

description: Library name: PRCH503


title: 3 Fibroblasts - Vehicle

description:
Library name: FB_13
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 24 months NP cells MDL-800 treated 19

description:
Library name: Sample 8
total RNA


title: 2 Fibroblasts - Vehicle

description:
Library name: FB_7
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 24 months NP cells Vehicle control 3

description:
Library name: Sample 3
total RNA


title: TAK2

description: Library name: PRCH500

value: adipogenic differentiation with transient TAK-981 treatment  in preadipocytes


title: 24 months NP cells Vehicle control 5

description:
Library name: Sample 4
total RNA


title: DMSORosi3

description: Library name: PRCH498

value: adipogenic differentiation with transient DMSO treatment in preadipocytesand chronic Rosiglitazone treatment during differentiation


title: 24 months NP cells Vehicle control 2

description:
Library name: Sample 2
total RNA


title: 1 Fibroblasts - Vehicle

description:
Library name: FB_1
2x150 Sequence mode to obtain at approx. 20 million read pairs

value: Skin

value: Primary human fibroblasts


title: DMSORosi2

description: Library name: PRCH497


title: TAK3

description: Library name: PRCH501

value: adipogenic differentiation with transient TAK-981 treatment in preadipocytes


title: THP-1 CoCl2 treated 3

city: Paris

first: Beibhinn

last: O'Hora

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description: Library name: THP1 TREAT BioRep3

data_processing:
Raw sequencing data was assessed using FastQC (v0.12.1) and MultiQC (v1.12) . Reads were trimmed to improve low-quality bases and adapter sequences using Trimmomatic (v0.39)  using the parameters: ILLUMINACLIP: TruSeq3-PE.fa:2:30:10; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:20; MINLEN:36. Trimmed reads were aligned to the human reference genome (GENCODE_GRCh38.p14) using STAR alignment tool (v2.7.11b) . Alignment quality metrics were summarised using MultiQC (v1.12) , and gene counts were extracted using featureCounts function from the Subread package (v2.0.0). Differential expression analysis was performed in R (v4.4.3) within the RStudio environment using the DESEQ2 package (v1.46.0) . Differentially Expressed Genes. (DEGs) were identified with a threshold of adjusted p-value 1.5. DEGS were subjected to Gene Ontology (GO) enrichment analysis for Biological Processes (BP) using the clusterProfiler package (v4.14.6) and to Gene Set Enrichment Analysis (GSEA) using the fgsea package (v1.32.4) . Data visualisations were performed using base R, ggplot2 (v4.4.0)  and pheatmap (v1.0.13) .
Assembly: GENCODE GRCh38.p14
Supplementary files format and content: raw gene counts and normalized gene counts in csv format

source_name: No tissue

growth_protocol: THP-1 cells (ATCC TIB-202) were maintained in Roswell Park Memorial Institute medium (RPMI 1640; Gibco), supplemented with heat-inactivated fetal calf serum (10%), penicillin (50U/mL), streptomycin (50μg/ml) and β-mercaptoethanol (0.05mM) were grown in 150-cm2 cell culture flasks. All experiments were performed with low passage number of cells.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Zymo Research, kit reference R2050) following the manufacturer’s protocol with minor modifications. Briefly, cells were lysed in 1 mL of TRIzol reagent (or 500 µL for 12-well plates), followed by immediate vortexing and incubation at room temperature for 10 minutes or freezing at −80°C. Chloroform (200 µL) was added to each sample, which were then vortexed for 10 seconds and incubated for 2 minutes at room temperature before centrifugation at 16,000 × g for 15 minutes at 4°C. The aqueous phase was carefully collected, avoiding the interphase and organic phase, and RNA was precipitated by adding 300 µL of isopropanol, mixing thoroughly by pipetting. The mixture was then loaded onto Zymo-Spin IICR columns and centrifuged at 16,000 × g for 30 seconds at room temperature. Columns were washed with RNA Wash Buffer and subjected to on-column DNase I treatment (5 µL DNase I in 75 µL DNA Digestion Buffer) for 15 minutes at room temperature to remove residual genomic DNA. Following DNase treatment, columns were washed twice with Direct-zol RNA PreWash buffer and once with RNA Wash Buffer, with centrifugations at 16,000 × g for 30 seconds to 1 minute. The RNA was eluted in 60 µL of DNase/RNase-free water after a final centrifugation at 16,000 × g for 30 seconds.
2ug of RNA was sent to Genewiz who carried out library prep and subsequent sequencing.

value: No tissue

value: THP-1 cell line (ATCC)

value: Monocytes

value: CoCl2 treated


title: 24 months NP cells Vehicle control 1

description:
Library name: Sample 1
total RNA

value: intervertebral disc

value: Vehicle


title: DMSORosi1

description: Library name: PRCH496


title: OVCAR-8, AB, 1

description: Library name: Sample 1

value: Ovarian cancer cell

value: WT


title: THP-1 CoCl2 treated 2

description: Library name: THP1 TREAT BioRep2


title: DMSO3

description: Library name: PRCH495

value: adipogenic differentiation with transient DMSO treatment in preadipocytes


title: TAK1

description: Library name: PRCH499


title: p3_PB_M3_VDJ

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

description:
Library name: p3_PB_M3_VDJ
10x Genomics

library_source: other

data_processing:
scRNA-seq and scTCR-seq data were demultiplexed, aligned to the human reference (GRCh38) and the feature-barcode matrix was quantified using Cell Ranger (v6.0.1) from 10X Genomics. Further computational analysis was performed using Seurat (v3.1.5).
Assembly: GRCh38
Supplementary files format and content: CellRanger output files scRNAseq: sample_barcodes.tsv.gz, sample_features.tsv.gz, sample_matrix.mtx.gz
Supplementary files format and content: CellRanger output files scTCRseq: sample_VDJ_filtered_contig_annotations.csv
Library strategy: TCR-Seq

molecule: other

source_name: PBMC

extract_protocol:
PB nad BM-derived cells  were incubated with scFv-BT (Jackson Immunoresearch) for CAR detection, washed with PBS/BSA and stained with Streptavidine-BV421 (BD Biosciences). CAR T cells were then sorted either with BD FACSAria IIu or Moflo ASTRIOS BC.
FACS-sorted CAR T cells from BM and PB samples of MM patients were subjected to scRNA-seq using the Chromium Single Cell 5′ Reagent Kit (10X Genomics) according to manufacturer’s instructions.
TCRα/β sequencing was performed with 10X Genomics Single Cell V(D)J Immune Profiling Solution (10x Genomics).

value: PBMC

value: CAR T cell

tag: cell fraction_strategy

value: CAR+ fraction


title: exFoxp3, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 5

city: Adelaide

first: Sarah

last: Robertson

state: South Australia

address: 4 North Terrace

department: Discipline of Obstetrics and Gynaecology

country: Australia

institute: The University of Adelaide

description: Library name: exTreg_5

data_processing:
Read quality was checked with FastQC v0.12.1 (Babraham Bioinformatics, Cambridge, UK) before and after adapter trimming with bbduk v39.03.
Reads were aligned to the GRCh39/mm39 mouse reference genome using STAR v2.7.10b_alpha_230301-GCC-11.2.0 and indexed with SAMtools v1.17-GCC-11.2.0.
Read count extraction and normalization were performed with R.
Assembly: GRCh39/mm39
Supplementary files format and content: Txt file contains raw counts for every sample.

source_name: Uterus-draining lymph node

growth_protocol: Foxp3GFPCre.Rosa26RFP female mice were mated to Balb/c males, and uterus-draining lymph nodes were harvested on late gestation day 18.5. A single cell suspension of the lymph node cells was labelled with anti-CD45 and anti-CD4 fluorochrome-conjugated antibodies, and Treg (GFP+RFP+) and exFoxp3 (GFP-RFP+) cells were sorted using a BDFusion cell sorter.

extract_protocol:
RNA was extracted with the Qiagen RNeasy Micro Kit. RNA purity was checked with a Nanodrop and quality was checked with an Agilent Tapestation. RNA from 5 mice with RIN>8.3 were pooled to generate each sample. >6 ng of RNA was sent to Novogene AIT Genomics Singapore Pte Ltd for library construction and sequencing.
Libraries were constructed by Novogene (HK) Company Ltd with the Clontech SMARTer Ultra Low Input mRNA library construction kit. Paired-end 150 bp sequencing was performed on an Illumina Novaseq 6000.

value: Uterus-draining lymph node

value: exFoxp3 (GFP-RFP+)

value: Gestation day 18.5, FACS-isolated


title: p3_PB_M1_VDJ

description:
Library name: p3_PB_M1_VDJ
10x Genomics


title: exFoxp3, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 4

description: Library name: exTreg_4


title: DMSO1

description: Library name: PRCH493

value: hTERT-A41hWAT-SVF CRL-3386


title: DMSO2

description: Library name: PRCH494


title: exFoxp3, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 3

description: Library name: exTreg_3


title: p3_BM_M3_VDJ

description:
Library name: p3_BM_M3_VDJ
10x Genomics

source_name: BM aspirate

value: BM aspirate


title: THP-1 CoCl2 treated 1

description: Library name: THP1 TREAT BioRep1

value: No tissue


title: THP-1 Control Replicate 3

description: Library name: THP1_CTRL_BioRep3

value: THP-1 cell line (ATCC)

value: Untreated Control


title: p3_IP_VDJ

description:
Library name: p3_IP_VDJ
10x Genomics

source_name: Infusion Product

value: Infusion Product

value: CAR T infusion product


title: THP-1 Control Replicate 1

description: Library name: THP1_CTRL_BioRep1

value: Monocytes


title: p2_PB_M1_VDJ

description:
Library name: p2_PB_M1_VDJ
10x Genomics


title: exFoxp3, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 2

description: Library name: exTreg_2


title: p1_IP_VDJ

description:
Library name: p1_IP_VDJ
10x Genomics


title: SKVO3 cells, shNR3C1y - 3D - rep2

city: Baronissi

first: Giovanna

middle: Maria

last: Ventola

state: Salerno

address: Via S. Allende, 43L

country: Italy

institute: Genomix4life s.r.l.

description:
Library name: Sample11
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample11

data_processing:
RNA-seq pipeline: Quality Control of the reads; Remove the adapter and short reads; Alignment and Transcriptome expression quantification analysis; Differentially Expression Analysis (DEA).
FastQC tool was used to Quality Control of all Samples.
The reads were trimmed using cutadapt tool (version 4)
The samples were mapped on reference genome (HG38 of GenCode- Release 37(GRCh38.p13)) using the bioinformatics tool STAR (version 2.7.10b), with the standard parameters for paired reads. The quantification of transcripts expressed for each sequenced sample was performed using featureCount algorithm (version 2.0.3).
The Bioconductor package DESeq2 was used to normalize the data, using the median of ratio, and to perform the differential expression analysis.
Assembly: HG38 - GenCode- Release 37(GRCh38.p13)
Supplementary files format and content: tab-delimited text file includes raw count for all Samples
Supplementary files format and content: tab-delimited text file includes normalized count for all Samples

source_name: cell line

growth_protocol: SK-OV-3 cell line was purchased from ATCC (HTB-77) derived from ascites of HGSOC carcinoma. Cell line was routinely tested for Mycoplasma-free state and used within passage 24. Cell lines were cultured in DMEM/F12 (21331-020, Gibco), 10% FBS (ECS5000L, EuroClone), Penicilin/Streptomycin (15140-122, Gibco) and L-Glutamine (25030-024, Gibco).

extract_protocol:
For RNA Sequencing,  SK-OV-3 cells (NR3C1 KD and CTR cells) were plated at high density (1.2 × 10³ cells/cm²) in 60mm plates and SK-OV-3 spheroids (NR3C1 KD and CTR cells) in ultra low-attachment plates and harvested ay day 6. RNA purification was performed using Trizol.
mRNA liibraries were prepared with Illumina Stranded mRNA Prep (April-2021) following manufacturer's protocol.

value: High grade serous ovarian cancer (HGSOC) cell model

value: short hairpin RNAs (shRNA) targeting NR3C1 gene (shNR3C1)

tag: growth setting


title: exFoxp3, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 1

description: Library name: exTreg_1


title: p2_BM_M1_VDJ

description:
Library name: p2_BM_M1_VDJ
10x Genomics


title: p1_BM_M3_VDJ

description:
Library name: p1_BM_M3_VDJ
10x Genomics


title: THP-1 Control Replicate 2

description: Library name: THP1_CTRL_BioRep2


title: SKVO3 cells, shNR3C1y - 3D - rep3

description:
Library name: Sample12
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample12


title: p1_PB_M1_VDJ

description:
Library name: p1_PB_M1_VDJ
10x Genomics


title: p1_PB_M3_VDJ

description:
Library name: p1_PB_M3_VDJ
10x Genomics


title: p3_BM_M3_sc

description:
Library name: p3_BM_M3_sc
10x Genomics

data_processing:
scRNA-seq and scTCR-seq data were demultiplexed, aligned to the human reference (GRCh38) and the feature-barcode matrix was quantified using Cell Ranger (v6.0.1) from 10X Genomics. Further computational analysis was performed using Seurat (v3.1.5).
Assembly: GRCh38
Supplementary files format and content: CellRanger output files scRNAseq: sample_barcodes.tsv.gz, sample_features.tsv.gz, sample_matrix.mtx.gz
Supplementary files format and content: CellRanger output files scTCRseq: sample_VDJ_filtered_contig_annotations.csv


title: p3_PB_M1_sc

description:
Library name: p3_PB_M1_sc
10x Genomics


title: Treg, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 4

description: Library name: Treg_4

value: Treg (GFP+RFP+)


title: Treg, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 3

description: Library name: Treg_3


title: Treg, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 5

description: Library name: Treg_5


title: SKVO3 cells, shNR3C1y - 3D - rep1

description:
Library name: Sample10
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample10


title: p2_IP_VDJ

description:
Library name: p2_IP_VDJ
10x Genomics


title: Stage 21M, scRNA-seq

city: Harbin

first: li

middle: jia

last: meng

state: Harbin

address: Northeast Forestry University

institute: Northeast Forestry University

description: 10x Genomics

data_processing:
Data was primarily processed by Cellranger software (version 4.0.0) and Seurat (Version 4.3.0.1)
Assembly: T. scripta (GCA_013100865.1)
Supplementary files format and content: Tab-seperated values files and matrix files

organism: Trachemys scripta

source_name: Gonad

extract_protocol:
At each developmental stage, 100 pairs of gonads underwent digestion for 20 minutes at 37°C in a 0.25% trypsin solution. Single-cell suspensions were filtered through a 40 μm cell strainer (431750, Corning) and washed two to three times with PBS. Cell viability was assessed using trypan blue staining with a TC20 automated cell counter (Bio-Rad, Hercules, CA). The viability of gonadal cells in the single-cell suspensions exceeded 85%.
Single-cell suspension concentration was adjusted to between 700 and 1200 cells/μL. Cells from each sample were processed using Chromium Single Cell 3' Reagent Kits (v3 chemistry, CG000183) following the manufacturer's instructions at Novogene Bioinformatics Technology Co., Ltd., Tianjin, China. Input cells were loaded onto the Single Cell B Chip (v3 chemistry, PN-1000153) channels according to expected counts. 10x libraries were constructed using the Chromium Controller and Chromium Single Cell 3’ Reagent Kits (v3 chemistry, CG000183). Briefly, single-cell suspensions were loaded into each channel of a Chromium Controller (10x Genomics, Pleasanton, CA) to generate single-cell gel beads in emulsion (GEMs). Subsequently, 10x libraries for each channel were prepared using the Chromium Single Cell 3’ Gel Bead and Library Kit v3 (PN-1000153, 1000075, 120262; 10x Genomics). Sequencing was performed on an Illumina NovaSeq with 150-bp paired-end reads.

value: Gonad

value: Gonadal cells


title: SKVO3 cells, shEmpty - 3D - rep3

description:
Library name: Sample9
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample9

value: empty vector (shEmpty)


title: Treg, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 2

description: Library name: Treg_2

value: Uterus-draining lymph node


title: SKVO3 cells, shEmpty - 3D - rep1

description:
Library name: Sample7
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample7


title: p2_PB_M1_sc

description:
Library name: p2_PB_M1_sc
10x Genomics

value: PBMC

value: CAR T cell

value: CAR+ fraction


title: p2_BM_M1_sc

description:
Library name: p2_BM_M1_sc
10x Genomics

value: BM aspirate


title: cell, ZA, rep3

city: 南京

first: XINXI

last: YUAN

state: 江苏省

address: 峨嵋岭20号

department: School of Stomatology

institute: Nanjing Medical University

description: Library name: ZA_3

data_processing:
RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The libraries were then sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. The transcriptome sequencing and analysis were conducted by OE Biotech.
Assembly: mm9
Supplementary files format and content: txt files

source_name: BMDMs

extract_protocol:
Total RNA of BMDMs treated with or without ZA was extracted using Trizol reagent (ThermoFisher, 15596018CN) following the manufacturer’s procedure. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The libraries were then sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. The transcriptome sequencing and analysis were conducted by OE Biotech.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocals.

value: BMDMs

value: Macrophage


title: SKVO3 cells, shEmpty - 3D - rep2

description:
Library name: Sample8
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample8


title: p3_IP_sc

description:
Library name: p3_IP_sc
10x Genomics


title: p3_PB_M3_sc

description:
Library name: p3_PB_M3_sc
10x Genomics


title: SKVO3 cells, shNR3C1y - 2D - rep3

description:
Library name: Sample6
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample6


title: cell, ZA, rep2

description: Library name: ZA_2


title: p2_IP_sc

description:
Library name: p2_IP_sc
10x Genomics


title: Stage 15_5M, scRNA-seq

description: 10x Genomics


title: SKVO3 cells, shNR3C1y - 2D - rep2

description:
Library name: Sample5
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample5


title: p1_PB_M3_sc

description:
Library name: p1_PB_M3_sc
10x Genomics


title: cell, ZA rep1

description: Library name: ZA_1


title: Stage 17M, scRNA-seq

description: 10x Genomics


title: SKVO3 cells, shNR3C1y - 2D - rep1

description:
Library name: Sample4
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample4


title: cell, Ctrl, rep3

description: Library name: Ctrl_3


title: SKVO3 cells, shEmpty - 2D - rep3

description:
Library name: Sample3
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample3


title: Stage 21F, scRNA-seq

description: 10x Genomics


title: Stage 17F, scRNA-seq

description: 10x Genomics


title: p1_BM_M3_sc

description:
Library name: p1_BM_M3_sc
10x Genomics


title: p1_PB_M1_sc

description:
Library name: p1_PB_M1_sc
10x Genomics


title: cell, Ctrl, rep2

description: Library name: Ctrl_2


title: Treg, sorted from mouse uterus-draining lymph node gestation day 18.5, replicate 1

description: Library name: Treg_1

value: Gestation day 18.5, FACS-isolated


title: Stage 19M, scRNA-seq

description: 10x Genomics


title: SKVO3 cells, shEmpty - 2D - rep2

description:
Library name: Sample2
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample2


title: p1_IP_sc

description:
Library name: p1_IP_sc
10x Genomics

value: Infusion Product


title: Stage 19F, scRNA-seq

description: 10x Genomics


title: Stage 16_5M, scRNA-seq

description: 10x Genomics


title: cell, Ctrl, rep1

description: Library name: Ctrl_1


title: Stage 16F, scRNA-seq

description: 10x Genomics


title: SKVO3 cells, shEmpty - 2D - rep1

description:
Library name: Sample1
Column names in Rawcount.txt and in Normalizedcount_AllSamples.txt: Sample1


title: 2KOCT20,rep3

description: Library name: Sample18

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1)
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

treatment_protocol: For synchronization, cells were plated in 6-well plates and treated with 200 nM dexamethasone (DEX, Sigma-Aldrich, MO, USA) in PBS for 0.5 hours.

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line

value: FEN1 konckdown

value: dexamethasone shock for 30 minutes


title: Forebrain organoid

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
The samples were allocated to the plate wells as described below.  The text in brackets reports how each sample is named in the file cell_metadata.csv.gz.
Well A1: Unguided forebrain organoid day 20 replicate 1 (CB01_d200)
Well A2: Unguided forebrain organoid day 20 replicate 2 (CB02_d20)
Well A3: Unguided forebrain organoid day 20 replicate 3 (CB03_d20)
Well A4: Guided forebrain organoid day 20 replicate 1 (FB01_d20)
Well A5: Guided forebrain organoid day 20 replicate 2 (FB02_d20)
Well A6: Guided forebrain organoid day 20 replicate 3 (FB03_d20)
Well A7: Unguided forebrain organoid day 40 replicate 1 (CB01_d40)
Well A8: Unguided forebrain organoid day 40 replicate 2 (CB02_d40)
Well A9: Unguided forebrain organoid day 40 replicate 3 (CB03_d40)
Well A10: Guided forebrain organoid day 40 replicate 1 (FB01_d40)
Well A11: Guided forebrain organoid day 40 replicate 2 (FB02_d40)
Well A12: Guided forebrain organoid day 40 replicate 3 (FB03_d40)

data_processing:
The bioinformatics pipeline split-pipe (version 1.0.6p), produced by Parse Biosciences, was used to process these files. The pipeline performed multiple functions, including identifying barcodes, mapping reads to the human reference genome (GRCh38 / version 102) and quantifying gene expression at the single cell level. The pipeline was run with default parameters for a Parse Mini Kit using Version 2 chemistry.
The filtered digital gene expression (DGE) matrix was analysed in R using Seurat. Only cells with total transcripts >100 and <150,000, unique transcripts <12,000 and mitochondrial transcripts <10% of total were analysed. The full dataset was split into the four conditions, normalising and identifying variable features of each dataset before reintegration based on repeatedly variable features (integration anchors). The integrated dataset was scaled and dimensionality reduction performed using principal component analysis (PCA) and visualised with UMAP generated on the first 15 principle components. K-Nearest Neighbour graph-based clustering, with Louvain algorithm and resolution = 1, resulted in 21 clusters, which upon differential gene expression analysis of known marker genes and literature review were combined and manually annotated to 12 clusters.
Pseudotime analysis was performed using Monocle3 on the data from guided and unguided FOs separately by subsetting and converting the integrated Seurat object. UMAP coordinates and clusters were assigned from Seurat and trajectory analysis performed not considering cluster partitions. Cells were ordered by denoting clusters of mitotic radial glia as starting points.
Assembly: GRCh38 / version 102
Supplementary files format and content: DGE.mtx.gz: filtered count matrix produced by the standard Parse split-pipe bioinformatics pipeline.  The file is in comma-separated values format and reports read count at the gene / cell resolution.
Supplementary files format and content: all_genes.csv.gz: the file is produced by the standard Parse split-pipe bioinformatics pipeline and lists the gene to which each read was aligned.  The file is in comma-separated values format.
Supplementary files format and content: cell_metadata.csv.gz: the file is produced by the standard Parse split-pipe bioinformatics pipeline and lists the barcode information for each putative cell.   The file is in comma-separated values format.

growth_protocol: The human iPSC line IMR90 clone 4 was purchased from WiCell and maintained on growth factor reduced Matrigel-coated plates (Corning) in mTESR1 medium (Stem Cell Technologies). Passaging was performed using Gentle cell dissociation reagent (Stem Cell Technologies). Unguided FOs were generated with the Cerebral Organoid Kit (Stem Cell Technologies) according to manufacturer instructions with the following modifications: On day 0, 600,000 iPSCs per well were seeded in AggrewellTM800 24-well plates (Stem Cell Technologies) pre-treated with Anti-Adherence Rinsing Solution (Stem Cell Technologies) in embryoid body (EB) Seeding medium with 50 μM ROCK inhibitor (Y27632, Stem Cell Technologies). On day 7 EBs were transferred from AggrewellTM800 24-well plates using wide-bore p1000 pipette tips and embedded in Matrigel by gently mixing around 30 EBs in 100 μl Expansion medium with 150 μl cold Matrigel (Corning) using wide-bore p200 tips and plating the mixture in a circle (diameter around 10 mm) in 60 mm (low-binding?) culture dishes. Following 30 min incubation at 37°C to polymerize the Matrigel, 4 ml Expansion medium was added per dish. On day 10 the dishes were moved to an INFORS HT Celltron orbital shaker set to 57 rpm in a 37°C incubator. On day 15, the FOs were released from the Matrigel by gentle pipetting with wide-bore p1000 tips and around 16 FOs per dish cultured in 5 ml medium. Guided FOs were generated using the STEMdiff Dorsal FO Differentiation Kit (Stem Cell Technologies) and maintained with the STEMdiff Neural Organoid Maintenance Kit (Stem Cell Technologies) according to manufacturer protocols with the following modifications: during the expansion period guided FOs were cultured in low-binding 24-well plates with 4-5 FOs per well to minimise fusion of the FOs. At around day 20, the FOs were moved to 60 mm low-binding culture dishes with 16 FOs per dish.  For both FO differentiations 1% Penicillin/Streptomycin (Pen/Strep, Gibco) and 1 μg/ml Amphotericin B (Amp B, Thermo Scientific) was added to the medium from day 10 onwards. The number of FOs per dish was gradually decreased from 16 to 5 with increasing size of the FOs. For both FO differentiations 1% Penicillin/Streptomycin (Pen/Strep, Gibco) and 1 μg/ml Amphotericin B (Amp B, Thermo Scientific) was added to the medium from day 10 onwards. The number of FOs per dish was gradually decreased from 16 to 5 with increasing size of the FOs.

extract_protocol:
Single-cell dissociation was performed on a total of 7-8 FOs (day 20) or 2-3 FOs (day 40) in triplicates. FOs were collected and incubated in 1 ml of Accumax (Sigma, A7089) at 37°C for 20 min with gentle agitation. At 5 min intervals, the sample tubes were flicked, and after 15 min pipetted 1 time, followed by a final pipetting of 7 times at 20 min. Clumps were allowed to settle and the supernatant passed through a 70 µm strainer (Fisherbrand, 11597522). Cells were counted (CountessII, Invitrogen) and at least 1x106 viable cells were collected for the following EvercodeTM Cell fixation (Parse Biosciences, ECF2001) according to manufacturer instructions omitting bovine serum albumin in the pre-fixation buffer.
The 12 samples were barcoded and sequencing libraries prepared using the Evercode™ WT Mini v2 kit (Parse Biosciences) according to the manufacturer's protocol. The libraries were then sequenced on NextSeq 2000 (Illumina) using a P2 flowcell (Illumina) for 200 cycles.


title: Mu_E_3_ATAC

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

description: Library name: Mu_E_3_ATAC

data_processing:
For ATAC-seq, Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). Q20 and Q30 of the raw data and clean data were calculated. These reads were aligned to a reference genome downloaded from NCBI BioProject database (accession number PRJNA555707) using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥ 13), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt). All peak calling was performed with MACS2 using ‘MACS2 call-peak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
For RNA-seq, The original image data were transferred into sequencing data by base calling, which were defined as raw reads. Clean data (clean reads) were obtained by removing reads containing an adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, and GC contents of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Then, E. sinensis genome was downloaded from NCBI BioProject database (accession number PRJNA555707) and used as reference genome. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: accession number reference genome is PRJNA555707
Supplementary files format and content: .narrowPeak files inlcude peak information
Supplementary files format and content: excel file include FPKM of genes

organism: Eriocheir sinensis

source_name: muscle

growth_protocol: The healthy river crabs obtained from aquatic farm were cultured in a plastic incubator (70×40×50 cm) at 20±1◦C with natural light.

extract_protocol:
nuclei were extracted from muscle samples for ATAC-seq anlysis. The total RNA was extracted using the TRIzol method (Invitrogen) for RNA-seq analysis.
For ATAC-seq analysis, the nuclei pellet was re-suspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition. PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated. For RNA-seq analysis, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations. Library quality was assessed on the Agilent Bioanalyzer 2100 system and 150 bp paired-end reads were generated.

treatment_protocol: During collection of the samples, crabs with average weight of 8.41±1.47 g were put on the ice plate for low-temperature anesthesia. Muscle of each crab were quickly collected and put in liquid nitrogen immediately, and then transferred to −80◦C refrigerator for preservation.

value: muscle

value: WT

value: untreated


title: Lungs from mice with a high metastatic burden

city: Aurora

first: Jessica

last: Christenson

state: CO

department: Pathology

description:
Library name: High
10x Genomics

data_processing:
FASTQ files for each sample were processed using Cell Ranger 2.0.2. (10x Genomics) using a modified version (PYMT was appended) of the mm10 reference genome. The resulting data was then aggregated using the Cell Ranger aggr pipeline. A total of 5,765 cells (high-burden n=3,121; low-burden n=2,644) remained following aggregation. Expression data for high-burden and low-burden cells was imported into an R environment; the data was filtered and analyzed using the R packages Seurat and Monocle. Filtering based on unique gene counts less than 1,000 or greater than 7,000, or mitochondrial percentages greater than 10% resulted in 5,504 cells in the final analysis, with an average of 11,764 unique molecular identifier (UMI) counts per cell and a median of 2,487 genes per cell. Principal Component Analysis (PCA) was then performed, and the top 10 principal components (PC) were selected for subsequent use. The dimensionality was reduced to two dimensions using t-stochastic neighbor embedding (t-SNE), with the 10 PCs being used as input. Cell clusters were demarcated via fast search and find of density peaks [23]. Differentially expressed genes were identified for each cluster using the two-sided Student's t-test provided by the Seurat FindMarkers function. Normalized gene expression within cells from a particular cluster was compared to expression within cells from all other clusters. Genes with less than a 25% change or those expressed in less than 10 percent of cells in both populations being compared were excluded from analysis. Following cluster designation, a likelihood ratio test using a generalized linear model was performed to identify genes that vary by cluster.
Assembly: Mouse mm10 (with PYMT appended)
Supplementary files format and content: Tab-separated values

source_name: Lung

extract_protocol:
Mice were perfused with 10mL 1X Hank’s balanced salt solution (HBSS; Corning CellGro, No. 21-023-CV). Lungs were collected and rinsed in chilled 1X PBS. The tissue was cut into small pieces with a razor blade and incubated in 5mg/mL type 2 collagenase (Worthington Biochemical Corporation, No. LS004174) in phenol-red free DMEM for 10min at 37ºC on a benchtop shaker. Enzyme A/Buffer Y mix from the Neural Tissue Dissociation Kit P from Miltenyi Biotec (No. 130-092-628) was added to the collagenase-tissue mixture and incubated for another 15min at 37ºC on a benchtop shaker. Pipetting periodically during this incubation was used to dissociate the tissue. Ice cold PBS/bovine serum albumin (BSA) cell buffer (1X PBS with 0.5% 50mg/mL BSA; ThermoFisher Scientific, No. AM26160) was used to halt the dissociation enzymatic reaction. Cells were passed through a 100μm mesh filter and centrifuged at 300 xg for 5min at 4ºC. Cells were then resuspended in ammonium-chloride-potassium (ACK) buffer for 1min at 20ºC to lyse any remaining red blood cells. Cold PBS/BSA cell buffer was added and cells centrifuged at 300 xg for 10min at 4ºC. Cells were resuspended in cold 1X PBS and debris was removed using cold Debris Removal Solution (Miltenyi Biotech, No. 130-109-398) according to the manufacturer’s instructions. Cells were washed again with PBS/BSA cell buffer and centrifuged at 300 xg for 5min at 4ºC. Finally, cells were resuspended in 500μL-1mL PBS/BSA cell buffer and filtered through a 40μm Flowmi cell strainer (Millipore Sigma, No. BAH136800040).
Approximately 10,000 cells were used to generate libraries and sequenced by the Genomics Shared Resource (RRID:SCR_021984) at the University of Colorado Anschutz Medical Campus.

value: Lung

value: FVB/NJ

value: IV Met-1 mouse mammary carcinoma cells, 3 week


title: PFC Scramble Control Pooled Sample #2a

city: New York

first: Priya

last: Rajasethupathy

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
Library name: CTRL_2a
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the seqc software (https://github.com/dpeerlab/seqc)
Assembly: mm10
Supplementary files format and content: csv file (cells along rows, genes along columns)

source_name: Brain - PFC

extract_protocol:
Briefly, mice were sacrificed with an overdose of isoflurane, followed by transcardial perfusion with carbonated (95% O2, 5% CO2) Hanks' Balanced Salt Solution (HBSS) containing small-molecule cocktail consisting of 1 μM TTX (Sigma), 100 μM AP-V (Thermo Fisher Scientific), 5 μg actinomycin D (Sigma) per milliliter and 10 μM triptolide (Sigma) to optimize for preserving transcriptional state. Brains were removed, 500μm sections were collected, and the region of interest was dissected (ANT or ACC). The tissue was dissociated using papain (Worthington, cat. no. LS003124) dissolved in Hibernate A buffer (Fisher Scientific, cat. no. NC1787837) containing 1 μM TTX, 100 μM AP-V (Thermo Fisher Scientific), 5 μg actinomycin D (Sigma) per milliliter, 10 μM triptolide (Sigma), and 10 μg anisomycin (Sigma) per milliliter, and incubated for 25-30 min at 37C, followed by manual trituration using fire polished Pasteur pipettes and filtering through a 40μm cell strainer (Millipore Sigma, cat. no. BAH136800040). Cells were washed with a wash buffer (PBS + 1% BSA) and centrifuged at 500 g for 5 min, the supernatant was carefully removed, and cells were resuspended in ~500ul wash buffer and 10% DAPI.
Single cell RNA- sequencing was carried out with the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, cat. no. 1000268). Manufacturer’s instructions were followed for downstream cDNA synthesis (12-14 PCR cycles) and library preparation.

value: Brain - PFC

value: All Brain Cell Type

tag: Sex

value: male

tag: strain/line

value: Scramble shRNA Control

value: day 1


title: 2KOCT20,rep2

city: Suzhou

first: Tao

last: Zhang

institute: Suzhou Vocational Health College

description: Library name: Sample17

source_name: HEK 293T

extract_protocol:
RNA was harvested using Magzol Reagent (Magen，R4801-02). 1.4ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS mRNA Capture Beads（N401）+ VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605-02 following manufacturer's protocols.


title: Lungs from mice with a low metastatic burden

institute: University of Colorado Anschutz Medical Campus

description:
Library name: Low
10x Genomics

value: IV Met-1 mouse mammary carcinoma cells, 1 week


title: Mouse heart, 3, T497A, 1 weeks after TAC surgery, 11 weeks old, rep3

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description: Library name: T497A-TAC-1w-3

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the human genome (GRCH38) or mouse genome (mm10) using STAR (2.7.3a). Gene expression was quantified using featureCounts of the Subread (v1.6.3) package. Low-expressed genes (genes with the expression value of 0 in more than 30% of samples) were removed before any subsequent analysis. Gene expression was normalized using the Voom method from the R package limma (v3.50.3). Differentially expressed genes were identified using the same package. Gene Set Enrichment Analysis (GSEA) for the DEGs was performed using R package clusterProfiler (v4.2.2).
Assembly: mm10
Supplementary files format and content: counts_raw.tsv

source_name: left ventricle

extract_protocol:
Total RNA was extracted from murine cardiac tissue using the RNeasy Mini Kit  (74104, Qiagen, Hilden, Germany) following the manufacturer's instructions. RNA integrity was assessed using Agilent 2200 Tapestation and RNA Screentape (5067-5576, Agilent Technologies).
RNA-seq libraries were generated from total RNA using the KAPA  mRNA HyperPrep Kit (KK8581, Roche) according to the manufacturer's protocol.  Libraries were sequenced on an Illumina NextSeq2000 platform using  single-end 50-cycle high-output mode.

treatment_protocol: WT and Prkca T497A mice were subjected to Sham or transverse aortic constriction (TAC) surgery using a 27-gauge needle at the age of 10 weeks .

value: left ventricle

value: cardiomyocyte

value: Prkca T497A

value: TAC surgery


title: PFC Scramble Control Pooled Sample #2b

description:
Library name: CTRL_2b
10x Genomics

value: day 2


title: Mu_E_1_ATAC

description: Library name: Mu_E_1_ATAC

value: muscle


title: Mu_E_2_ATAC

description: Library name: Mu_E_2_ATAC

value: WT


title: Mu_E_3_RNA

description: Library name: Mu_E_3_RNA

value: untreated


title: 2KOCT16,rep1

address: No.28 Kehua Road

description: Library name: Sample13

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line

value: FEN1 konckdown

value: dexamethasone shock for 30 minutes


title: Stage 15, scRNA-seq

description: 10x Genomics

value: Gonad

value: Gonadal cells


title: 2KOCT16,rep2

description: Library name: Sample14


title: PFC Scramble Control Pooled Sample #1

description:
Library name: CTRL_1
10x Genomics

value: Brain - PFC

value: All Brain Cell Type

value: male

value: Scramble shRNA Control


title: PFC Homer1a/Ania3 Developmental Knockdown Pooled Sample #2a

description:
Library name: KD_2a
10x Genomics

value: Homer1a/Ania3 Developmental shRNA Knockdown

value: day 1


title: Mouse heart, 2, T497A, 1 weeks after TAC surgery, 11 weeks old, rep3

description: Library name: T497A-TAC-1w-2

value: left ventricle

value: cardiomyocyte

value: Prkca T497A

value: TAC surgery


title: PFC Homer1a/Ania3 Developmental Knockdown Pooled Sample #1

description:
Library name: KD_1
10x Genomics


title: Mouse heart, 3, WT, 1 weeks after TAC surgery, 11 weeks old, rep3

description: Library name: WT-TAC-1w-3

value: WT


title: PFC Homer1a/Ania3 Developmental Knockdown Pooled Sample #2b

description:
Library name: KD_2b
10x Genomics

value: day 2


title: 2KOCT20,rep1

description: Library name: Sample16

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line


title: Mu_E_1_RNA

description: Library name: Mu_E_1_RNA

value: muscle

value: untreated


title: Mu_E_2_RNA

description: Library name: Mu_E_2_RNA


title: 2KOCT12,rep3

description: Library name: Sample12

value: FEN1 konckdown

value: dexamethasone shock for 30 minutes


title: PFC CC025 Pooled Sample #2

description:
Library name: CC025_2
10x Genomics

value: Brain - PFC

value: All Brain Cell Type


title: Mouse heart, 2, WT, 1 weeks after TAC surgery, 11 weeks old, rep3

description: Library name: WT-TAC-1w-2


title: Mouse heart, 1, WT, 1 weeks after TAC surgery, 11 weeks old, rep3

description: Library name: WT-TAC-1w-1


title: 2KOCT16,rep3

description: Library name: Sample15


title: PFC CC083 Pooled Sample #2

description:
Library name: CC083_2
10x Genomics

value: male


title: PFC CC083 Pooled Sample #1

description:
Library name: CC083_1
10x Genomics


title: BS3

city: Changchun

first: Xiaohui

last: Dong

address: No. 1363, Shengtai Street, Jingyue High-tech Industrial Development Zone

department: Institute of Plant Protection

institute: Jilin Academy of Agricultural Sciences

description:
Library name: DM3
BS group, replicate bisoample 3

data_processing:
Raw sequencing reads were assembled to generate transcript sequences, which were hierarchically clustered using the Corset program to produce a unified reference transcript set for downstream analyses. Differential gene expression analysis was performed using DESeq2 (version 1.20.0). Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted based on the identified differentially expressed genes using the clusterProfiler R package (version 3.8.1).
Assembly: GCF_020709855.1
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

organism: Ostrinia furnacalis

source_name: gut tissues

extract_protocol:
Total RNA was extracted from gut tissues, and RNA integrity was assessed prior to library construction.
RNA sequencing libraries were prepared and sequenced on an Illumina HiSeq platform by Novogene Co., Ltd. (Beijing, China). Three biological replicates were included for each treatment. After quality control, library concentrations were measured using a Qubit 2.0 Fluorometer (hermo Fisher Scientific, Waltham, MA, USA), and samples were diluted to 1.5 ng/μL. Insert sizes were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and effective library concentrations were accurately quantified by qRT-PCR. Libraries were pooled according to effective concentration and target sequencing depth and subsequently subjected to Illumina sequencing.

value: gut tissues


title: Mouse heart, 1, T497A, 1 weeks after TAC surgery, 11 weeks old, rep3

description: Library name: T497A-TAC-1w-1


title: BS2

description:
Library name: DM2
BS group, replicate bisoample 2


title: BS1

description:
Library name: DM1
BS group, replicate bisoample 1


title: Mouse heart, 3, T497A, 1 weeks after sham surgery, 11 weeks old, rep3

description: Library name: T497A-Sham-1w-3

value: Sham surgery


title: PFC CC025 Pooled Sample #1

description:
Library name: CC025_1
10x Genomics


title: Mouse heart, 1, T497A, 1 weeks after sham surgery, 11 weeks old, rep3

description: Library name: T497A-Sham-1w-1

value: left ventricle


title: Mouse heart, 2, T497A, 1 weeks after sham surgery, 11 weeks old, rep3

description: Library name: T497A-Sham-1w-2

value: cardiomyocyte


title: 2KOCT12,rep1

description: Library name: Sample10


title: PFC CC083 #3

description:
Library name: 83E_S9
CC_PFC_DESeq_normalized_counts.csv

data_processing:
Sequencing reads were aligned to the mouse genome using STAR (v2.4.2a), quantified using Salmon (v0.8.2), and normalized counts were determined using DESeq2.
For differential expression analysis, different batches of RNAseq were included as a covariate in the DESeq2 model.
Assembly: mm10
Supplementary files format and content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

extract_protocol:
Mice were sacrificed by cervical dislocation and immediately decapitated. The targeted brain regions were harvested from 1 mm brain slices, obtained by brain matrices (ZIVIC) using 1.0 mm tissue punches and transferred to a tube containing 300 µL of ice-cold lysis buffer and 3 µL ß-mercaptoethanol (Total RNA Purification kit, NORGEN; following the manufacturer’s protocol). Samples were then homogenized by passing a 25G insulin syringe six times and left on ice. For RNA extraction, the total RNA Purification kit was used according to the manufacturer’s instructions (NORGEN).
RNA libraries were prepared from 100ng of total RNA per sample using the TruSeq stranded mRNA LT kit (Cat# RS-122-2101, Illumina).

tag: mouse group

value: CC High Performing Line


title: 2KOCT8,rep2

description: Library name: Sample8


title: PFC CC083 #2

description:
Library name: 83B_S8
CC_PFC_DESeq_normalized_counts.csv


title: 2KOCT8,rep3

description: Library name: Sample9


title: 2KOCT8,rep1

description: Library name: Sample7


title: C3

description:
Library name: C3
control group, replciate biosample 3


title: Mouse heart, 3, WT, 1 weeks after sham surgery, 11 weeks old, rep3

description: Library name: WT-Sham-1w-3


title: Mouse heart, 2, WT, 1 weeks after sham surgery, 11 weeks old, rep3

description: Library name: WT-Sham-1w-2


title: 2KOCT4,rep3

description: Library name: Sample6


title: C1

description:
Library name: C1
control group, replciate biosample 1


title: PFC CC083 #1

description:
Library name: 83A_S7
CC_PFC_DESeq_normalized_counts.csv


title: 2KOCT12,rep2

description: Library name: Sample11


title: C2

description:
Library name: C2
control group, replciate biosample 2


title: 2KOCT4,rep2

description: Library name: Sample5


title: PFC CC025 #2

description:
Library name: 25C_S11
CC_PFC_DESeq_normalized_counts.csv

value: CC Low Performing Line


title: 18-months3

city: Bunkyo-ku

first: Masanari

last: Ikeda

state: Tokyo

address: Yayoi 1-1-1

country: Japan

institute: the University of Tokyo

description: Library name: Sample18

data_processing:
The sequenced reads were preprocessed using Trimmomatic (version 0.39-1b), followed by quality control using FastQC. The reads were then mapped to the mRatBN7.2 using STAR (version 2.7.10b). Gene expression levels were quantified using RSEM (version 1.3.3).
Assembly: mRatBN7.2
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes TPM for each Sample

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from rat frozen tibialis anterior muscle sections using Rneasy mini kit (Qiagen).
Qualified libraries were constructed by BGI (Shenzhen, China) using TruSeq RNA Library Prep Kit -Set A- (Illumina).

value: skeletal muscle

value: WT

tag: age


title: PFC CC025 #3

description:
Library name: 25E_S12
CC_PFC_DESeq_normalized_counts.csv


title: 18-months2

description: Library name: Sample17


title: 2Bm-MphKO

city: Charlottesville

first: Vikram

last: Sabapathy

state: Virginia

address: 1340 Jefferson Park Ave., Pinn Hall, Room No: 4043

department: Center for Immunity, Inflammation and Regenerative Medicine

institute: University of Virginia

description: Library name: Sample3

data_processing:
The quality of the library preparation was checked using FASTQC to evaluate the quality of the sequencing quality.
The fastq files were trimmed to remove the Illumina adapter sequences, and low-quality sequencing reads using cutadapt with a phred quality cutoff of 20, then reassessed using FastQC.
The trimmed sequencing reads were aligned to the mouse reference genome mm10 using HISAT2
FeatureCounts was used to count the number of reads mapped to genes, creating a count matrix.
Differential gene expression was analyzed using DESeq2
Assembly: mm10
Supplementary files format and content: Count Matrix as .csv file, which is the output of FeatureCounts.

source_name: Bone Marrow

extract_protocol:
The RNA was extracted from cells using the RNeasy Plus mini kit (Qiagen).
The ribosomal RNA (rRNA) was then removed from the total RNA before preparing the transcriptome library.

value: Bone Marrow

value: Macrophages

value: ST2 Knockout


title: VTA DO Low Performer #3

description:
Library name: 104-EH-VTA
PPI-VTA-PFC_normalized_counts.csv

source_name: Brain - VTA

value: Brain - VTA

value: DO Low Performing Mouse

value: Diversity Outbred


title: 2Bm-MphWT

description: Library name: Sample4


title: PFC CC025 #1

description:
Library name: 25A_S10
CC_PFC_DESeq_normalized_counts.csv

value: Brain - PFC


title: 2KOCT0,rep3

description: Library name: Sample3

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line

value: FEN1 konckdown

value: dexamethasone shock for 30 minutes


title: 3-months3

description: Library name: Sample15


title: 2KOCT4,rep1

description: Library name: Sample4


title: 18-months1

description: Library name: Sample16


title: Mouse heart, 1, WT, 1 weeks after sham surgery, 11 weeks old, rep3

description: Library name: WT-Sham-1w-1

value: left ventricle

value: Sham surgery


title: 2KOCT0,rep2

description: Library name: Sample2


title: VTA DO Low Performer #2

description:
Library name: 83-CH-VTA
PPI-VTA-PFC_normalized_counts.csv

value: male


title: 2KOCT0,rep1

description: Library name: Sample1


title: 3-months2

description: Library name: Sample14


title: 1Bm-MphWT

description: Library name: Sample2


title: 2WTCT20,rep3

description: Library name: Sample18

value: Wildtype


title: VTA DO High Performer #1

description:
Library name: 73-BD-VTA
PPI-VTA-PFC_normalized_counts.csv

value: DO High Performing Mouse


title: 1Bm-MphKO

description: Library name: Sample1


title: PT7

city: Columbus

first: Andrew

last: Gunderson

state: OH

address: 460 W. 10th Avenue

department: Department of Surgery

institute: The Ohio State University

description:
Library name: PT7
11x11mm FFPE Visium Cytassist

data_processing:
Raw sequencing fastq files were processed using SpaceRanger v2.1.1, to raw gene counts.
Output processed files were opened and analyzed in Seurat v5. Raw counts were normalized and transformed using SCTransform.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain raw counts, SCTransformed gene expression, and an aligned H&E image as a Seurat v5 object, saved as a .RDS R data object.
Library strategy: Spatial Transcriptomics

source_name: Pancreas-PDAC tumor

extract_protocol:
FFPE tumor sections were cut into 10um sections with a microtome
Spatial gene expression libraries were generated using 10x Genomics Visium CytAssist for FFPE Spatial Gene Expression 11mm Kit.

value: Pancreas-PDAC tumor

value: Female

tag: diagnosis

value: PDAC


title: dKO6

description: Library name: Sample12

value: skeletal muscle

value: p16-null DMD


title: VTA DO Low Performer #1

description:
Library name: 64-FH-VTA
PPI-VTA-PFC_normalized_counts.csv

value: Brain - VTA

value: DO Low Performing Mouse


title: 2WTCT20,rep2

description: Library name: Sample17


title: PT4

description:
Library name: PT4
11x11mm FFPE Visium Cytassist


title: VTA DO High Performer #3

description:
Library name: 97-BD-VTA
PPI-VTA-PFC_normalized_counts.csv

value: Diversity Outbred


title: 3-months1

description: Library name: Sample13

value: WT


title: dKO5

description: Library name: Sample11


title: 2WTCT16,rep3

description: Library name: Sample15

value: HEK 293T

value: human embryonic kidney (HEK) derived cell line


title: PFC DO Low Performer #3

description:
Library name: 104-EH-PFC
PPI-VTA-PFC_normalized_counts.csv

value: Brain - PFC


title: dKO4

description: Library name: Sample10


title: 2WTCT20,rep1

description: Library name: Sample16

value: dexamethasone shock for 30 minutes


title: PT2

description:
Library name: PT2
11x11mm FFPE Visium Cytassist


title: PFC DO Low Performer #2

description:
Library name: 83-CH-PFC
PPI-VTA-PFC_normalized_counts.csv


title: PFC DO Low Performer #1

description:
Library name: 64-FH-PFC
PPI-VTA-PFC_normalized_counts.csv


title: HUVEC, Senescence+C3N QDs+Irradiation, 3

city: Shanghai

first: xuelian

last: wang

address: Ruijin er road No.197

institute: Ruijin hospital

description: Library name: S+C+I -3

data_processing:
Reads were aligned to the human genome, and gene expression levels were quantified. Differential expression analysis was performed using the DESeq2 R package with an FDR threshold of < 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values

source_name: umbilical vein

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Invitrogen) according to standard protocols.
Poly(A) RNA was selected from 1 μg total RNA and libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following the manufacturer’s instructions.

value: umbilical vein

value: HUVEC

value: endothelial cell

value: wild-type

value: S+C+I


title: 2WTCT16,rep2

description: Library name: Sample14

value: Wildtype


title: HUVEC, Senescence+C3N QDs+Irradiation, 2

description: Library name: S+C+I -2


title: dKO3

description: Library name: Sample9


title: PFC DO High Performer #3

description:
Library name: 97-BD-PFC
PPI-VTA-PFC_normalized_counts.csv

value: DO High Performing Mouse

value: male


title: dKO1

description: Library name: Sample7

value: skeletal muscle

value: p16-null DMD


title: 2WTCT16,rep1

description: Library name: Sample13


title: dKO2

description: Library name: Sample8


title: PT3

description:
Library name: PT3
11x11mm FFPE Visium Cytassist

value: Pancreas-PDAC tumor

value: Male

value: PDAC


title: HUVEC, Senescence+C3N QDs+Irradiation, 1

description: Library name: S+C+I -1


title: 2WTCT12,rep3

description: Library name: Sample12

value: HEK 293T


title: PFC DO High Performer #1

description:
Library name: 73-BD-PFC
PPI-VTA-PFC_normalized_counts.csv

value: Diversity Outbred


title: HUVEC, Senescence+C3N QDs, 3

description: Library name: S+C -3

value: S+C


title: DMD2

description: Library name: Sample5

value: DMD


title: mdTH DO Low Performer #3

description:
Library name: 104-EH-mdTH
DESeq_PPI-mdTH_normalized_counts.csv

source_name: Brain - MDTh

value: Brain - MDTh

value: DO Low Performing Mouse


title: 2WTCT12,rep1

description: Library name: Sample10

value: human embryonic kidney (HEK) derived cell line

value: dexamethasone shock for 30 minutes


title: DMD1

description: Library name: Sample4


title: HUVEC, Senescence+C3N QDs, 2

description: Library name: S+C -2

value: umbilical vein

value: HUVEC

value: endothelial cell

value: wild-type


title: 2WTCT12,rep2

description: Library name: Sample11

value: Wildtype


title: mdTH DO Low Performer #2

description:
Library name: 83-CH-mdTH
DESeq_PPI-mdTH_normalized_counts.csv

value: male


title: mdTH DO Low Performer #1

description:
Library name: 64-FH-mdTH
DESeq_PPI-mdTH_normalized_counts.csv


title: mdTH DO High Performer #3

description:
Library name: 97-BD-mdTH
DESeq_PPI-mdTH_normalized_counts.csv

value: DO High Performing Mouse


title: HUVEC, Senescence, 3

description: Library name: S -3

value: S


title: HUVEC, Senescence+C3N QDs, 1

description: Library name: S+C -1


title: 2WTCT8,rep2

description: Library name: Sample8


title: WT3

description: Library name: Sample3

value: skeletal muscle

value: WT


title: WT2

description: Library name: Sample2


title: 2WTCT8,rep1

description: Library name: Sample7

value: HEK 293T


title: WT1

description: Library name: Sample1


title: HUVEC, Senescence, 1

description: Library name: S -1


title: Male DOCA+Salt CSF Sample

city: NEW ORLEANS

first: Vahideh

last: Tarhriz

state: LA

address: Perdido,

department: Cardiovascular Research Center of Excellence

institute: Louisiana State University Health Science Center

description:
Library name: MD-CSF
CSF-derived exosomal RNA from male DOCA+Salt mouse

data_processing:
Reads with short or missing UMIs filtered using Perl5 v26. Reads were aligned to miRBase, piRNABank, and Rfam using Bowtie v1.3.0. UMI counts were summarized and normalized using edgeR and converted to CPM (Counts per million). Expression matrices were created for differential expression, PCA, and GO/KEGG pathway analysis using R clusterProfiler. Mouse genome: mm10 (GRCm38) was used for alignment and annotation. The processed data includes expression matrices in .xlsx/.txt format, including CPM and log2-transformed counts for miRNAs, piRNAs, and other ncRNAs.
Assembly: Differential expression results and pathway enrichment results provided in Excel format (.xlsx), grouped by condition (e.g., FD vs FB, MD vs MB).
Supplementary files format and content: Raw-data.xlsx

source_name: CSF

growth_protocol: Not applicable – exosomes were isolated from adult mouse plasma and CSF (not cultured).

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy Micro Kit according to the manufacturer’s instructions.
Libraries were prepared using the QIAseq miRNA Library Kit with UMIs for unique molecular tagging, avoiding PCR duplication. Adapters and low-quality reads removed using Cutadapt v2.7.

treatment_protocol: DOCA-salt treatment was applied to hypertensive groups; baseline mice received no treatment.

value: CSF

value: Male

value: Wild-type

value: DOCA+Salt


title: mdTH DO High Performer #1

description:
Library name: 73-BD-mdTH
DESeq_PPI-mdTH_normalized_counts.csv

value: Brain - MDTh

value: Diversity Outbred


title: 2WTCT8,rep3

state: Jiangsu

description: Library name: Sample9

value: human embryonic kidney (HEK) derived cell line

value: dexamethasone shock for 30 minutes


title: DMD3

description: Library name: Sample6

value: DMD


title: 2WTCT4,rep2

description: Library name: Sample5


title: 2WTCT4,rep3

description: Library name: Sample6


title: Male Baseline CSF Sample

description:
Library name: MB-CSF
CSF-derived exosomal RNA from male baseline mouse

value: Baseline


title: SMG22_T

city: Beijing

first: Zhigang

last: Cai

address: No.22 Zhongguancun South Avenue, Haidian Disrict

institute: Peking University

description: Library name: Sample 12

data_processing:
featureCounts v 2.0.6
Assembly: GRCh38
Supplementary files format and content: tab-delimited format includes fpkm counts for each Sample

source_name: Human Submandibular gland Tissue

extract_protocol:
RNA was extacted from TRNzol Universal Reagent (DP424).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Human Submandibular gland Tissue


title: SMG22_O

description: Library name: Sample 11

source_name: Human Submandibular gland Organoids

value: Human Submandibular gland Organoids


title: 2WTCT0,rep3

description: Library name: Sample3

value: Wildtype