title: Listeria monocytogenes F2365 delta-buk mutant, biological replicate 2

city: Mississippi State

first: Monzur

last: Chowdhury

state: MS

address: 240 Wise Center Dr

department: Comparative Biomedical Sciences, College of Veterinary Medicine

institute: Mississippi State University

description:
Library name: buk_2
buk deletion mutant of L. monocytogenes F2365 grown to stationary phase in defined minimal media (MM) at 25 degrees C

data_processing:
Quality control: raw reads assessed with FastQC; adapters and low-quality bases trimmed using Novogene in-house QC pipeline.
Read alignment: trimmed reads mapped to L. monocytogenes F2365 reference genome (GenBank AE017262.2) using Bowtie2 with default parameters.
Transcript assembly and quantification: mapped reads assembled using Rockhopper; gene structures compared against reference genome annotation.
Quantification: gene-level read counts extracted using FeatureCounts; normalized expression values (FPKM) calculated per gene per sample.
Differential expression: DESeq2 R package; genes with |log2 fold change| > 0 and Benjamini-Hochberg adjusted p-value < 0.05 considered differentially expressed.
Assembly: Listeria monocytogenes F2365; GenBank accession AE017262.2
Supplementary files format and content: counts_matrix_all_genes.txt: tab-delimited text file containing raw gene counts for all genes across all 4 samples (WT_1, WT_2, buk_1, buk_2). Row identifiers are gene locus tags; column headers match library names.
Supplementary files format and content: FPKM values (Fragments Per Kilobase per Million mapped reads) provided as supplementary normalized expression measure per gene per sample.

organism: Listeria monocytogenes

source_name: Bacteria

growth_protocol: L. monocytogenes strains were grown overnight at 37 degrees C in brain-heart infusion (BHI) broth with shaking. Overnight cultures were normalized to equivalent OD600, washed with sterile PBS, and inoculated into defined minimal media (MM) at 25 degrees C. Bacteria were incubated statically until reaching stationary phase.

extract_protocol:
Total RNA was extracted from two independent biological replicates per condition using the FastRNA spin kit for microbes with the FastPrep-24 instrument (MP Biomedicals, Santa Ana, CA). Genomic DNA contamination was removed by on-column DNase treatment (RNase-free DNase set, Qiagen). RNA quantity and purity were assessed by NanoDrop ND-1000 spectrophotometry. Ribosomal RNAs were depleted using the Ribo-Zero magnetic kit for Gram-positive bacteria (Epicentre), and enriched mRNA was fragmented prior to library preparation.
RNA-seq libraries were constructed and sequenced by Novogene Co. Fragmented, rRNA-depleted RNA was reverse transcribed into cDNA using random hexamer primers. Libraries were prepared following Novogene standard strand-specific library preparation protocols. Sequencing was performed on an Illumina NovaSeq 6000 platform using 150-bp paired-end (PE150) strategy.

treatment_protocol: No chemical or environmental treatment applied. Bacteria were grown under standard low-temperature (25 degrees C) conditions to simulate cold adaptation.

value: Bacteria

value: delta-buk (in-frame deletion of buk, LMOf23651387)


title: HeLa S3 METTL4 KO, rep3

status: Public on Jun 05 2026

type: SRA

city: Pushchino

first: Andrey

middle: Igorevich

last: Buyan

state: Moskovskaya obl.

address: Institutskaya st., 4

country: Russia

institute: Institute of Protein Research

description: Library name: deltaM4_mRNA_3

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for universal illumina adapter and low-quality sequence using cutadapt (parameters -q 20 -a AGATCGGAAGAGC).
Trimmed sequence reads were mapped to GRCh38/hg38 or GRCm38/mm10 using STAR 2-pass mapping with other parameters set according to ENCODE standard long RNA-seq pipeline and STAR-Fusion default parameters.
The resulting bam files were used as input for featureCounts with gencode comprehensive v.42 or v.M20 annotation in order to calculate gene-level coverages. Next, they were used in edgeR for differential expression estimation of 13813 (human data) or 11390 (mouse data) genes with at least 3 cpm in 3 or more samples. For that, counts were normalized with calcNormFactors, followed by estimateDisp, glmQLFit and glmQLFTest.
Alternative splicing events were identified using rMATS with -t single --variable-read-length --readLength 120 options and gencode v.42 (human data) or v.M20 (mouse data) annotation.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample, edgeR differential expression results for METTL4 KO vs WT (control) and the alternative splicing events from rMATS for METTL4 KO (group 2) vs WT (group 1).

molecule: polyA RNA

organism: Homo sapiens

source_name: HeLa S3

growth_protocol: HeLa S3 сells were cultured in DMEM/F12 medium (Gibco™: 11320033), containing 10% FBS (Gibco™: 16000044), 100 U/mL of penicillin and 100 µg/mL of streptomycin (Gibco™: 15140122) with 1% glutaMAX (Gibco™: 35050061) at 37oC, 5% CO2. Animals were kept in individually ventilated cages (IVC system, TECNIPLAST S.p.A., Italy) with free access to food and water purified by reverse osmosis, in an environment free of specific pathogens, with light regime 12/12 (light on at 09:00), in rooms with air exchange rate more than 15 r/h, at 20-24°C, humidity 30-70%. Wood chips with minimal dust formation were used as bedding. Shelters and building materials for nests made of natural materials were used as enrichment of the environment. All materials supplied to the animals were sterilized by autoclaving.

extract_protocol:
RNA was extracted using QIAzol lysis reagent (QIAGEN:79306) following the manufacturer's instructions.
NEB NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770) was used for library preparation. Beads were mixed with first strand buffer, random primer and water according to the protocol provided by the manufacturer and incubated at 94°C for 12 min to get longer RNA fragments. The following steps were performed according to the protocol provided by the manufacturer, the resulting cDNA library was sequenced using HiSeq 1500.

treatment_protocol: Inactivation of METTL4 gene was done by CRISPR/Cas9 system.

tag: cell line

value: HeLa S3

tag: cell type

value: epithelial

tag: genotype

value: METTL4 KO


title: Cite-seq, Young ,HTO 4

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

description:
Library name: Young Arch HT sample 9
sampes are 11,12,13 weeks old with reads spread over HT and GEX fastqs; there are 3 hashtags with each one mapping to one age group
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
feature-ref1.csv

library_source: other

data_processing:
Sequencing was performed on an Illumina HiSeq 4000 platform using 2 × 150 bp paired-end reads with >90% sequencing saturation. Raw sequencing data were processed using Cell Ranger Single Cell Software Suite v3.1 (10x Genomics) for demultiplexing, barcode processing, UMI counting, and generation of gene expression matrices. Downstream analyses were performed using Seurat v4.0.5 in R/RStudio. Quality control, normalization, scaling, batch correction, dimensionality reduction, neighborhood graph construction, and clustering analyses were performed using Seurat. Mitochondrial transcript content was regressed using the SCTransform function, and clustering was performed based on principal component analysis.
Assembly: mm10
Supplementary files format and content: Cellranger filtered barcode output: gene x cell matrix (.mtx.gz); features.tsv.gz; barcodes.tsv.gz
Supplementary files format and content: feature reference CSV
Library strategy: CITE-seq

molecule: protein

organism: Mus musculus

source_name: Ascending thoracic aorta

extract_protocol:
Young ATA tissues were enzymatically digested for 60 min at 37°C in a solution containing type II collagenase (10 mg/mL; Sigma Aldrich, C6885) and elastase (1 mg/mL; Worthington Biochemistry, LS002292). Digested tissues were filtered through a 70 μm cell strainer to obtain single-cell suspensions. Viable cells were enriched using a Dead Cell Removal Kit (Miltenyi Biotech, 130-090-101). Cell viability was assessed by Trypan Blue staining (0.4%; Bio-Rad, 1450013) using a TC20 automated cell counter (Bio-Rad).
Approximately 15,000 viable cells per sample were loaded onto a 10x Genomics Chromium Controller to generate gel beads-in-emulsion (GEMs). Single-cell 3′ gene expression libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v2 (10x Genomics; PN-120237, PN-120236, PN-120262) according to the manufacturer’s instructions.

tag: tissue

value: Ascending thoracic aorta

tag: hto


title: Rep_1_rodo_int

city: Tel Aviv

first: Merav

last: Cohen

address: Chaim Levanon St 55

department: Clinical microbiology and immunology

country: Israel

institute: Tel Aviv University

description: Library name: Rep_1_rodo_int

library_source: genomic

data_processing:
We generated FASTQ files from the raw BCL files using the bcl2fastq software provided by Illumina (v.2.20.0.422) with default parameters.
Next, we perfrormed QC on the fastq files using fastp with --detect-adapter-for-pe
Sequences were mapped to the mouse genome (GRCm39) using STAR (v.2.7.1a).
We processed the resulting BAM files with samtools (v.1.10) to remove duplicate mapping and mappings with low quality, as well as remove mitochondrial reads.
BigWig files were created using the bamCoverage function from deepTools (v.3.3.2)
Using bedtools (v2.27.1) we excluded established blacklist regions of the genome.
Peaks were identified, labelled and quantified using MACS3 (v.3.0.3) and featureCounts (v.2.0.0).
Assembly: GRCm39
Supplementary files format and content: BigWig files containing chromatin accessibility information for each sample.

molecule: genomic DNA

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
B16: To obtain single cell suspensions of B16 tumors, the tumors were removed and weighed using an analytical scale, and then placed in RPMI-1640 supplemented with DNase (28 μg/ml, Sigma-Aldrich) and collagenase IV (1 mg/ml, Worthington). Tissues were incubated at 37 °C for 10 minutes with agitation and then pipetted through 16G, 18G, 19G and 21G needles before they were incubated again at 37 °C for 10 minutes with agitation. Cell suspensions were then washed with cold sorting buffer and pelleted. Finally, cells were bulk sorted into 4 bins according to pHrodo intensity.
The library preparation was performed…

value: Rodo intermediate

tag: batch


title: Listeria monocytogenes F2365 delta-buk mutant, biological replicate 1

description:
Library name: buk_1
buk deletion mutant of L. monocytogenes F2365 grown to stationary phase in defined minimal media (MM) at 25 degrees C

molecule: total RNA


title: Cite-seq, Young ,HTO 3

description:
Library name: Young Arch HT sample 12
sampes are 11,12,13 weeks old with reads spread over HT and GEX fastqs; there are 3 hashtags with each one mapping to one age group
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
feature-ref1.csv


title: Cite-seq, Young ,HTO 2

description:
Library name: Young Arch HT sample 11
sampes are 11,12,13 weeks old with reads spread over HT and GEX fastqs; there are 3 hashtags with each one mapping to one age group
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
feature-ref1.csv


title: HeLa S3 METTL4 KO, rep1

description: Library name: deltaM4_mRNA_1


title: Rep_1_rodo_neg

description: Library name: Rep_1_rodo_neg

value: Rodo negative


title: Listeria monocytogenes F2365 wild-type, biological replicate 1

description:
Library name: WT_1
Wild-type L. monocytogenes F2365 grown to stationary phase in defined minimal media (MM) at 25 degrees C

value: wild-type


title: Cite-seq, Young ,HTO 1

description:
Library name: Young Arch HT sample 10
sampes are 11,12,13 weeks old with reads spread over HT and GEX fastqs; there are 3 hashtags with each one mapping to one age group
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
feature-ref1.csv


title: HGC_NC3

status: Public on Jun 04 2026

city: hefei

first: yan

last: zheng

state: anhui province

address: Anhui Medical University

country: China

institute: Anhui Medical University

description: Library name: sample 12

data_processing:
Paired-end sequencing was performed on the Illumina NovaSeq 6000. Raw reads were filtered using the following quality control steps: removing adapter sequences, trimming bases with Phred quality scores < 20 at the 5' or 3' ends and ambiguous N bases, and discarding reads shorter than 75 bp after trimming. An average of ~44.5 million clean reads were obtained per sample, which were then aligned to the human reference genome (GRCh38/hg38; http://asia.ensembl.org/Homo_sapiens/Info/Annotation/) using HISAT2. Read counts of all annotated genes were quantified using featureCounts, and differentially expressed genes (DEGs) were identified with the DESeq2 R package.
Assembly: GRCh38 (hg38)
Supplementary files format and content: raw data

extract_protocol:
The total RNA of VRTN overexpression in HGC27 cells and MGC803 cells were obtained to isolate total RNA using TRIzol (Cat#15596018, Thermo Fisher, Waltham, MA, USA) according to the manufacturer's instructions.
After assessing the quality of RNA by concentration determination and agarose gel electrophoresis without degradation, 1 μg of total RNA was then used to construct cDNA libraries using the TruSeq RNA Sample Preparation kit (Illumina, Inc, San Diego, California, USA).

value: siNC

tag: treatment

value: total RNA

value: paired-end


title: HGC_NC2

description: Library name: sample 11


title: HGC_NC1

description: Library name: sample 10


title: HGC_si2

description: Library name: sample 8


title: AGS_NC3

description: Library name: sample 6

source_name: AGS

value: AGS


title: AGS_NC1

description: Library name: sample 4


title: AGS_si3

description: Library name: sample 3


title: AGS_si2

description: Library name: sample 2


title: AGS_si1

description: Library name: sample 1


title: Normal-5

city: Hefei

first: Jingjing

last: Hu

address: NO.117 Meishan Road

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

description: Library name: CL21000575meR-IP

data_processing:
Cutadapt (v2.5 ) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”.
m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.
m6A peak were identified using exomePeak R package under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200” . GO and KEGG analysis were performed using clusterprofile R package (v3.6.0).
m6A-RNA-related genomic features were visualized using Guitar R package (v1.16.0).Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Assembly: GRXh38
Supplementary files format and content: excel
Supplementary files format and content: diff_peak
Library strategy: MeRIP-Seq

source_name: blood

growth_protocol: Total RNAs were extracted from   Blood

extract_protocol:
Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc., Cyberjaya, Malaysia) by following the manufacturer's instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation.
The library quality was evaluated with Bioptic Qsep100 Analyzer(Bioptic lnc.,Taiwan,China). Library sequencing was performed on an illumina NovaSeq instrument with 150bp paired-end reads.

treatment_protocol: an m6A-specific antibody(（Sigma-Aldrich, cat. no ABE572）) was used to immunoprecipitate RNA.

value: blood

tag: disease

value: Normal


title: Normal-4

description: Library name: CL21000574meR-IP


title: ATDC5 Day 21 rep2

city: Freiburg

first: Anna

last: Klawonn

address: Hugstetter Str. 55

country: Germany

institute: University Hospital Freiburg

description: Library name: D212

data_processing:
Raw data were processed on Galaxy platform (usegalaxy.eu). Quality control was performed using FastQC (version 0.74+galaxy1)
Adapter trimming with Trim Galore! (version 0.6.7+galaxy0)
Mapping of trimmed reads to mouse genome mm39 with RNA STAR (version 2.7.11a+galaxy1) as paired end data and “length of the genomic sequence around annotated junctions” set to 149
Read counts per gene were quantified using featureCounts (version 2.0.6+galaxy0)
Assembly: mm39
Supplementary files format and content: tabular file containing read counts gene for each sample (feature counts output)

growth_protocol: Up to day 0 ATDC5 cells were maintained in growth medium composed of Dulbecco’s modified eagle medium and Ham´s F-12 in a ratio of 1:1, supplemented with 10 % fetal calf serum, 1% Sodium Pyruvate, 100 U/ml penicillin and 100 µg/ml streptomycin at 37°C and 5% CO2. After day 0 cells were maintained in differentiation medium, similar to growth medium but with 5% FCS and supplemented with 10µg/ml insulin, 30nM sodium selenite, 50µg/ml ascorbic acid and 10µg/ml transferrin. The medium was changed every other day.

extract_protocol:
RNA was extracted with Qiagen Rneasy Fibrous Tissue Kit according to manufacturers instruction
Novogene in house protocol: Purification: mRNA was isolated from total RNA using poly‑T oligo‑attached magnetic beads. cDNA synthesis: Fragmented mRNA was reverse transcribed using random hexamer primers to generate first-strand cDNA, followed by second-strand synthesis. Library construction: Libraries were prepared by end repair, A‑tailing, adapter ligation, size selection, amplification, and purification. Quality control: Libraries were quantified using Qubit and qPCR; size distribution was assessed with a Bioanalyzer.

value: wild type

tag: time

value: day 21


title: Normal-input-3

description: Library name: CL21000572meR-input


title: Normal-3

description: Library name: CL21000572meR-IP


title: Normal-2

description: Library name: CL21000570meR-IP


title: Cite-seq, old ,GEX 3

description:
Library name: Old Arch mRNA sample 3
samples are 81,84, and 88 weeks old with reads split across fastqs
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

extract_protocol:
Aged ATA tissues were enzymatically digested for 60 min at 37°C in a solution containing type II collagenase (10 mg/mL; Sigma Aldrich, C6885) and elastase (1 mg/mL; Worthington Biochemistry, LS002292). Digested tissues were filtered through a 70 μm cell strainer to obtain single-cell suspensions. Viable cells were enriched using a Dead Cell Removal Kit (Miltenyi Biotech, 130-090-101). Cell viability was assessed by Trypan Blue staining (0.4%; Bio-Rad, 1450013) using a TC20 automated cell counter (Bio-Rad).
Approximately 15,000 viable cells per sample were loaded onto a 10x Genomics Chromium Controller to generate gel beads-in-emulsion (GEMs). Single-cell 3′ gene expression libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v2 (10x Genomics; PN-120237, PN-120236, PN-120262) according to the manufacturer’s instructions.


title: XX at D5 under ovarian condition

city: Suita

first: Katsuhiko

last: Hayashi

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

country: Japan

institute: The University of Osaka

description: Library name: D5 XX/Ova

library_source: transcriptomic single cell

data_processing:
Transcriptome reads from 10x Genomics were mapped to the mouse genome (GRCm38) using CellRanger v6.0.1 with the --exclude-introns option. The mapped reads were then summarized into raw UMI count matrices. For quality control, cells were filtered using the following thresholds: more than 8,000 total UMIs, more than 2,000 detected genes, and less than 20% of UMIs mapped to mitochondrial genes (percentMT < 0.2). In addition, potential multiplets were removed based on predictions by Scrublet v0.2.3 (Wolock et al., 2019, doi:10.1016/j.cels.2018.11.005). Datasets were applied to RECODE v0.2.1 (Imoto et al., 2022; Life Science Alliance, DOI: 10.26508/lsa.202201591), implemented in Python (https://github.com/yusuke-imoto-lab/RECODE). UMI counts were normalized by the total UMI count per cell, scaled to 100,000, and log₂-transformed with a pseudo-count of 1 [log₂(ss100k + 1)]. To account for technical variation across batches, we then applied fastMNN implemented in batchelor v1.20.0　(Haghverdi et al., 2018; doi:10.1038/nbt.4091), using the following options: cos.norm = FALSE, correct.all = TRUE, and d = 200.
Assembly: GRCm38
Supplementary files format and content: Comma-separated value files and matrix files

organism: Mus

source_name: Mouse ES cells

extract_protocol:
Differentiated cells cultured under each condition were dissociated by incubation with 0.05% trypsin/EDTA for 7 minutes at 37 °C, followed by gentle pipetting with an equal volume of DMEM supplemented with 10% FBS, 2 mM glutamine, and 1× penicillin-streptomycin. The resulting single-cell suspension was incubated with BV421-conjugated anti-hCD271 antibody, and hCD271-positive cells were subsequently sorted using a BD FACSAria Fusion. The sorted cells were centrifuged and resuspended in XXXXX buffer.
cDNA libraries were constructed using the Chromium Single Cell 3ʹ v3 Reagent Kits (10x Genomics). FACS-sorted cells were mixed with the Single Cell Master Mix to generate gel bead-in-emulsions (GEMs). Within each GEM, RNA was reverse-transcribed, and the resulting cDNAs were amplified by PCR. Sequencing libraries, adapted for the Illumina platform, were then prepared from the amplified cDNAs. The single-cell RNA-seq libraries were sequenced using paired-end reads on an Illumina HiSeq X Ten platform.

value: Induced cells

value: ES cell-derived gonadal cells

value: Female


title: Normal-input-2

description: Library name: CL21000570meR-input


title: AL_020

city: Pittsburgh

first: Neil

last: Carleton

state: PA

address: 5051 Centre Ave

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh

data_processing:
For processing, we used Rsubread (Bioconductor release 2.16) to align sequence reads to reference genome and used edgeR and limma R packages (Bioconductor release 4.0 and 3.58 respectively) to normalize gene expression level to log2 transcripts per million (TPM)
Assembly: We aligned sequence reads to GRCh38 release 14 human genome reference sequence and mapped the aligned sequences to Entrez Genes
Supplementary files format and content: After normalization, we removed genes of which expression level is zero across all samples to get 39,404 genes for further pathway analysis.

extract_protocol:
We used the standard procedure of RNeasy kit to extract total RNA from ER+ breast cancer samples of 83 tumor or 85 tumor-adjacent normal tissue obtained from Pitt Biospecimen Core (PBC) and grouped them by chronological age.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
Library size and quality were checked using Fragment Analyzer (Agilent) and fluorescent quantification on the Infinite F Nano + (Tecan). The libraries were normalized and pooled, and then sequenced using the NovaSeq 6000 Platform (Illumina) to an average of 25M 101 PE reads. Sequencing data was given as raw data with a Phred Q30 score of 80 or better.

tag: tumor or adjacent

tag: agerange

value: Young

tag: chronologicalage

tag: read length


title: Normal-1

description: Library name: CL21000568meR-IP


title: SLE-4

description: Library name: CL2100056meR-IP

value: SLE


title: Normal-input-1

description: Library name: CL21000568meR-input


title: SLE-input-4

description: Library name: CL21000567meR-input


title: Rep_3_rodo_neg

description: Library name: Rep_3_rodo_neg


title: SLE-5

description: Library name: CL21000565meR-IP


title: SLE-input-5

description: Library name: CL21000565meR-input


title: SLE-3

description: Library name: CL21000564meR-IP


title: SLE-input-3

description: Library name: CL21000564meR-input


title: wt rep 1

city: Eugene

first: Samuel

last: Bertrand

state: OR

address: 1318 Franklin Blvd

department: IMB

institute: University of Oregon

description: Library name: abc-1

data_processing:
Trimming of adaptors and low-quality reads was performed by Cutadapt
Alignment, quantification, and analysis of RNA sequencing data was performed using the Rsubread
Reads were aligned to a comprehensive transcript annotation for zebrafish in R (Lawson et al., 2020)
Read counts and differential gene expression analysis were performed using the Deseq2 Bioconductor R package
Assembly: Lawson lab transcriptome assembly (Lawson et al., 2020) and GRCz11 [danRer11.primary.fa.txt]
Supplementary files format and content: tab delimited file with all BAM files

organism: Danio rerio

source_name: whole body

extract_protocol:
Total RNA extraction was performed using a DirectZol RNA kit following manufacturer instructions for n = 5 controls and n = 5 mutants for RNA seq and n = 1 control and mutant for whole genome sequencing
Libraries were sequenced on a HiSeq 2500 using a P3 flow cell according to the manufacturer’s instructions for paired end reads.

value: whole body


title: SLE-2

description: Library name: CL21000563meR-IP


title: SLE-input-2

description: Library name: CL21000563meR-input


title: SLE-1

description: Library name: CL21000562meR-IP


title: HeLa S3 WT METTL4 rep2

description:
Library name: WT_mRNA_2
Processed data on this series is identical to GSE299981.

value: HeLa S3

value: epithelial

value: WT


title: SLE-input-1

description: Library name: CL21000562meR-input


title: Cite-seq, Young ,GEX 1

description:
Library name: Young Arch mRNA sample 13
sampes are 11,12,13 weeks old with reads spread over HT and GEX fastqs; there are 3 hashtags with each one mapping to one age group
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

value: Ascending thoracic aorta


title: Paracancerous

city: Guangzhou

first: Shanrong

last: Shu

address: 613 West Huangpu Avenue, Tianhe District

institute: The First Affiliated Hospital of Jinan University

description:
Library name: Paracancerous
Paracancerous tissue

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count and fpkm value for each Sample

source_name: Paracancerous tissue

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

value: Paracancerous tissue

value: Paracancerous


title: Cancer

description:
Library name: Cancer
Cancer tissue

source_name: cancer tissue

value: cancer tissue

value: Cancer


title: si-NC

description:
Library name: si-NC
si-NC cell culture

source_name: cell culture

value: cell culture

value: si-NC


title: si-IGF2BP3

description:
Library name: si-IGF2BP3
si-IGF2BP3 cell culture


title: Placental tissue miRNA-Seq sample S24, transmitting

city: Lima

first: Carla

middle: Angelica

last: Apaza-Quiroz

address: Honorio Delgado 430 San Martin de Porres

country: Peru

institute: Universidad Peruana Cayetano Heredia

description:
Library name: S24
Column name in RawCounts_AllSamples.txt: S24

data_processing:
Raw sequencing reads were processed using the Galaxy Europe platform.
Read quality was assessed using FastQC and summarized with MultiQC.
Adapter sequences were removed and reads were filtered by length prior to downstream analysis.
Processed reads were prepared using miRDeep2 Mapper.
Known human mature miRNAs were quantified using miRDeep2 Quantifier with reference sequences from miRBase v22.1.
The resulting raw count matrix was used for downstream differential expression analysis in R.
Assembly: GRCh38/hg38; miRBase v22.1
Supplementary files format and content: RawCounts_AllSamples.txt: tab-delimited matrix containing raw miRNA counts for all samples.

source_name: placental tissue

extract_protocol:
Total RNA was extracted from placental tissue using the mirVana miRNA Isolation Kit (Invitrogen) according to the manufacturer’s instructions. RNA concentration was measured using a Qubit 4 Fluorometer (Thermo Fisher Scientific), and RNA integrity was assessed using an Agilent 2100 TapeStation. Samples with RINe ≥ 7.0 were included in downstream analyses.
Small RNA libraries were prepared from total RNA using the QIAseq miRNA Library Kit (QIAGEN) following the manufacturer’s instructions. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Placental tissue samples were obtained at delivery from women enrolled in prospective cohorts at Hospital de la Mujer “Dr. Percy Boland” (Santa Cruz, Bolivia). Maternal Trypanosoma cruzi infection was confirmed during pregnancy by serological testing. Samples were classified according to neonatal qPCR results as transmitting (newborn qPCR-positive) or non-transmitting (newborn qPCR-negative).

value: placental tissue


title: Placental tissue miRNA-Seq sample S22, transmitting

description:
Library name: S22
Column name in RawCounts_AllSamples.txt: S22


title: Placental tissue miRNA-Seq sample S18, transmitting

description:
Library name: S18
Column name in RawCounts_AllSamples.txt: S18


title: Placental tissue miRNA-Seq sample S20, transmitting

description:
Library name: S20
Column name in RawCounts_AllSamples.txt: S20


title: HeLa S3 METTL4 KO, rep2

description: Library name: deltaM4_mRNA_2

value: METTL4 KO


title: Rep_1_rodo_low

description: Library name: Rep_1_rodo_low

value: Rodo low


title: Placental tissue miRNA-Seq sample S15, transmitting

description:
Library name: S15
Column name in RawCounts_AllSamples.txt: S15


title: Placental tissue miRNA-Seq sample S14, transmitting

description:
Library name: S14
Column name in RawCounts_AllSamples.txt: S14


title: Placental tissue miRNA-Seq sample S13, transmitting

description:
Library name: S13
Column name in RawCounts_AllSamples.txt: S13


title: Placental tissue miRNA-Seq sample S12, transmitting

description:
Library name: S12
Column name in RawCounts_AllSamples.txt: S12


title: Placental tissue miRNA-Seq sample S09, transmitting

description:
Library name: S09
Column name in RawCounts_AllSamples.txt: S09


title: Placental tissue miRNA-Seq sample S23, non-transmitting

description:
Library name: S23
Column name in RawCounts_AllSamples.txt: S23


title: Placental tissue miRNA-Seq sample S21, non-transmitting

description:
Library name: S21
Column name in RawCounts_AllSamples.txt: S21


title: Placental tissue miRNA-Seq sample S19, non-transmitting

description:
Library name: S19
Column name in RawCounts_AllSamples.txt: S19


title: Placental tissue miRNA-Seq sample S17, non-transmitting

description:
Library name: S17
Column name in RawCounts_AllSamples.txt: S17


title: Listeria monocytogenes F2365 wild-type, biological replicate 2

description:
Library name: WT_2
Wild-type L. monocytogenes F2365 grown to stationary phase in defined minimal media (MM) at 25 degrees C

value: Bacteria

value: wild-type


title: Placental tissue miRNA-Seq sample S06, non-transmitting

description:
Library name: S06
Column name in RawCounts_AllSamples.txt: S06


title: Placental tissue miRNA-Seq sample S11, non-transmitting

description:
Library name: S11
Column name in RawCounts_AllSamples.txt: S11


title: Placental tissue miRNA-Seq sample S10, non-transmitting

description:
Library name: S10
Column name in RawCounts_AllSamples.txt: S10


title: Placental tissue miRNA-Seq sample S05, non-transmitting

description:
Library name: S05
Column name in RawCounts_AllSamples.txt: S05


title: Placental tissue miRNA-Seq sample S04, non-transmitting

description:
Library name: S04
Column name in RawCounts_AllSamples.txt: S04


title: Placental tissue miRNA-Seq sample S819, non-transmitting

description:
Library name: S819
Column name in RawCounts_AllSamples.txt: S819


title: Placental tissue miRNA-Seq sample S872, transmitting

description:
Library name: S872
Column name in RawCounts_AllSamples.txt: S872


title: Placental tissue miRNA-Seq sample S775, non-transmitting

description:
Library name: S775
Column name in RawCounts_AllSamples.txt: S775


title: Placental tissue miRNA-Seq sample S753, non-transmitting

description:
Library name: S753
Column name in RawCounts_AllSamples.txt: S753


title: HGC_si1

description: Library name: sample 7

value: total RNA

value: paired-end


title: Placental tissue miRNA-Seq sample S729, non-transmitting

description:
Library name: S729
Column name in RawCounts_AllSamples.txt: S729


title: HGC_si3

description: Library name: sample 9


title: Placental tissue miRNA-Seq sample S725, non-transmitting

description:
Library name: S725
Column name in RawCounts_AllSamples.txt: S725


title: Placental tissue miRNA-Seq sample S705, non-transmitting

description:
Library name: S705
Column name in RawCounts_AllSamples.txt: S705


title: Placental tissue miRNA-Seq sample S668, non-transmitting

description:
Library name: S668
Column name in RawCounts_AllSamples.txt: S668


title: Placental tissue miRNA-Seq sample S675, transmitting

description:
Library name: S675
Column name in RawCounts_AllSamples.txt: S675


title: Placental tissue miRNA-Seq sample S399, non-transmitting

description:
Library name: S399
Column name in RawCounts_AllSamples.txt: S399


title: Placental tissue miRNA-Seq sample S294, non-transmitting

description:
Library name: S294
Column name in RawCounts_AllSamples.txt: S294


title: Placental tissue miRNA-Seq sample S439, transmitting

description:
Library name: S439
Column name in RawCounts_AllSamples.txt: S439


title: MASH-HCC, tumor 6, transcriptome

city: New Haven

first: Xiaolong

last: Tian

state: CT

address: 55 Prospect St Rm 103

institute: yale university

description:
Library name: MASH_HCC_6T_transcripts
PE150

data_processing:
Barcode positions within the read are detailed in the file barcode_position_image.png.
Read 1 (sample_1.fq.gz): contains the glycan/protein barcode sequence or cDNA sequence.
Read 2 (sample_2.fq.gz): contains spatial Barcode A, spatial Barcode B, and the UMI.
For Read 2, we use the following positions to specify the barcodes and UMI:
Barcode B: positions 22 - 30
Barcode A: positions 60 - 68
UMI: positions 98 - 108
The *'barcode.xls'* file contains the 50 barcode sequences used in our study. The *'spatial_barcode_50x50.xls'* file contains the 2,500 combinations of Barcode A and Barcode B used to define the spatial coordinates.
The image files ('roi.jpg') and associated position files ('postion.txt') required for data analysis have been included. The spatial coordinates were extracted based on the ROI covered by our microfluidic device.
LDT and ADT UMI counts were quantified at each spatial pixel using CITE-seq-Count version 1.4.5 with default settings. A whole-transcriptome count matrix was additionally generated using the recommended parameters in ASTRO version 1.0. An independent spatial gene-level transcript count matrix was generated using ST Pipeline version 1.8.2, separately from the whole-transcriptome count matrix generated by ASTRO.
DBiT-GPT glycan, protein, and transcript count matrices were processed in Seurat using modality-specific SCT normalization, PCA, graph-based clustering, UMAP visualization, and differential feature analysis to identify spatially heterogeneous pixel clusters.
Assembly: GRCh38
Supplementary files format and content: ROI_jpg: use Adobe Photoshop to crop the microscope image into exactly the size of the DBiT-GPT covering region of interest area (ROI).
Supplementary files format and content: position_txt: convert the cropped image into a binary tissue mask, with tissue shown in black and background in white, and then run the MATLAB script `pixel_identification.m` to generate a `position.txt` file containing the coordinates of tissue-covered pixels for downstream analysis.
Supplementary files format and content: glycans_proteins.tsv: the resulting combined glycan and protein expression matrix contained the spatial coordinates (barcode A × barcode B) together with the corresponding glycan and protein expression levels. Columns 164-194 correspond to glycans, and columns 1-163 correspond to proteins.
Supplementary files format and content: transcripts.tsv: the resulting whole-transcripts expression matrix contained spatial coordinates (barcode A × barcode B) and corresponding total RNAs expression level.
Supplementary files format and content: mRNA.tsv: an classical exon-mapped spatial gene-level expression matrix containing spatial coordinates (barcode A × barcode B) and gene-level counts assigned to annotated exonic features of coding genes and annotated long non-coding RNAs. Short non-coding RNA and intronic features are not included in this matrix.
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
Archival FFPE tissue blocks were sectioned at 10 μm thickness and mounted onto Poly-L-lysine–coated slides. Sections were deparaffinized, rehydrated, and subjected to on-tissue polyadenylation. DNA-barcoded lectin staining was then performed to profile glycans, followed by a sugar-blocking. Sections were subsequently stained with DNA-barcoded antibodies for protein profiling. Transcripts and DNA-barcoded lectin/antibody tags were captured in situ, followed by on-tissue reverse transcription and library preparation of spatially barcoded cDNA and tag-derived products for sequencing.
Spatial glycomics and protein libraries, corresponding to DNA-barcoded lectin-derived tags and antibody-derived tags (LDTs and ADTs), were prepared following the spatial CITE-seq library preparation protocol. Whole-transcript libraries were prepared following the Patho-DBiT protocol.

value: Liver


title: AGS_NC2

description: Library name: sample 5

value: AGS

value: siNC


title: MASH-HCC, tumor 6, glycome, proteome

description:
Library name: MASH_HCC_6T_glycans_proteins
PE150

data_processing:
Barcode positions within the read are detailed in the file barcode_position_image.png.
Read 1 (sample_1.fq.gz): contains the glycan/protein barcode sequence or cDNA sequence.
Read 2 (sample_2.fq.gz): contains spatial Barcode A, spatial Barcode B, and the UMI.
For Read 2, we use the following positions to specify the barcodes and UMI:
Barcode B: positions 22 - 30
Barcode A: positions 60 - 68
UMI: positions 98 - 108
The *'barcode.xls'* file contains the 50 barcode sequences used in our study. The *'spatial_barcode_50x50.xls'* file contains the 2,500 combinations of Barcode A and Barcode B used to define the spatial coordinates.
The image files ('roi.jpg') and associated position files ('postion.txt') required for data analysis have been included. The spatial coordinates were extracted based on the ROI covered by our microfluidic device.
LDT and ADT UMI counts were quantified at each spatial pixel using CITE-seq-Count version 1.4.5 with default settings. A whole-transcriptome count matrix was additionally generated using the recommended parameters in ASTRO version 1.0. An independent spatial gene-level transcript count matrix was generated using ST Pipeline version 1.8.2, separately from the whole-transcriptome count matrix generated by ASTRO.
DBiT-GPT glycan, protein, and transcript count matrices were processed in Seurat using modality-specific SCT normalization, PCA, graph-based clustering, UMAP visualization, and differential feature analysis to identify spatially heterogeneous pixel clusters.
Assembly: GRCh38
Supplementary files format and content: ROI_jpg: use Adobe Photoshop to crop the microscope image into exactly the size of the DBiT-GPT covering region of interest area (ROI).
Supplementary files format and content: position_txt: convert the cropped image into a binary tissue mask, with tissue shown in black and background in white, and then run the MATLAB script `pixel_identification.m` to generate a `position.txt` file containing the coordinates of tissue-covered pixels for downstream analysis.
Supplementary files format and content: glycans_proteins.tsv: the resulting combined glycan and protein expression matrix contained the spatial coordinates (barcode A × barcode B) together with the corresponding glycan and protein expression levels. Columns 164-194 correspond to glycans, and columns 1-163 correspond to proteins.
Supplementary files format and content: transcripts.tsv: the resulting whole-transcripts expression matrix contained spatial coordinates (barcode A × barcode B) and corresponding total RNAs expression level.
Supplementary files format and content: mRNA.tsv: an classical exon-mapped spatial gene-level expression matrix containing spatial coordinates (barcode A × barcode B) and gene-level counts assigned to annotated exonic features of coding genes and annotated long non-coding RNAs. Short non-coding RNA and intronic features are not included in this matrix.
Library strategy: CITE-seq

molecule: other


title: Placental tissue miRNA-Seq sample S643, transmitting

description:
Library name: S643
Column name in RawCounts_AllSamples.txt: S643


title: MASH-HCC, tumor 5, transcriptome

description:
Library name: MASH_HCC_5T_transcripts
PE150


title: MASH-HCC, tumor 5, glycome, proteome

description:
Library name: MASH_HCC_5T_glycans_proteins
PE150


title: MASH-HCC, tumor 4, transcriptome

description:
Library name: MASH_HCC_4T_transcripts
PE150


title: MASH-HCC, tumor 4, glycome, proteome

description:
Library name: MASH_HCC_4T_glycans_proteins
PE150


title: MASH-HCC, tumor 3, transcriptome

description:
Library name: MASH_HCC_3T_transcripts
PE150


title: MASH-HCC, tumor 3, glycome, proteome

description:
Library name: MASH_HCC_3T_glycans_proteins
PE150


title: MASH-HCC, tumor 2, glycome, proteome

description:
Library name: MASH_HCC_2T_glycans_proteins
PE150


title: MASH-HCC, tumor 1, transcriptome

description:
Library name: MASH_HCC_1T_transcripts
PE150


title: MASH-HCC, tumor 2, transcriptome

description:
Library name: MASH_HCC_2T_transcripts
PE150


title: MASH-HCC, tumor 1, glycome, proteome

description:
Library name: MASH_HCC_1T_glycans_proteins
PE150


title: non-tumor background, non-tumor 6, transcriptome

description:
Library name: HCC_6N_transcripts
PE150


title: non-tumor background, non-tumor 6, glycome, proteome

description:
Library name: HCC_6N_glycans_proteins
PE150


title: non-MASH-HCC, tumor 6, glycome, proteome

description:
Library name: HCC_6T_glycans_proteins
PE150


title: non-MASH-HCC, tumor 6, transcriptome

description:
Library name: HCC_6T_transcripts
PE150


title: non-tumor background, non-tumor 5, transcriptome

description:
Library name: HCC_5N_transcripts
PE150


title: non-tumor background, non-tumor 5, glycome, proteome

description:
Library name: HCC_5N_glycans_proteins
PE150


title: non-MASH-HCC, tumor 5, transcriptome

description:
Library name: HCC_5T_transcripts
PE150


title: Normal-input-5

description: Library name: CL21000575meR-input

value: blood

value: Normal


title: non-MASH-HCC, tumor 5, glycome, proteome

description:
Library name: HCC_5T_glycans_proteins
PE150


title: non-MASH-HCC, tumor 4, glycome, proteome

description:
Library name: HCC_4T_glycans_proteins
PE150


title: non-MASH-HCC, tumor 4, transcriptome

description:
Library name: HCC_4T_transcripts
PE150


title: non-MASH-HCC, tumor 3, transcriptome

description:
Library name: HCC_3T_transcripts
PE150


title: non-tumor background, non-tumor 2, transcriptome

description:
Library name: HCC_2N_transcripts
PE150


title: non-MASH-HCC, tumor 3, glycome, proteome

description:
Library name: HCC_3T_glycans_proteins
PE150


title: non-tumor background, non-tumor 2, glycome, proteome

description:
Library name: HCC_2N_glycans_proteins
PE150


title: non-MASH-HCC, tumor 2, transcriptome

description:
Library name: HCC_2T_transcripts
PE150


title: non-MASH-HCC, tumor 2, glycome, proteome

description:
Library name: HCC_2T_glycans_proteins
PE150


title: non-tumor background, non-tumor 1, transcriptome

description:
Library name: HCC_1N_transcripts
PE150


title: non-tumor background, non-tumor 1, glycome, proteome

description:
Library name: HCC_1N_glycans_proteins
PE150


title: non-MASH-HCC, tumor 1, transcriptome

description:
Library name: HCC_1T_transcripts
PE150


title: non-MASH-HCC, tumor 1, glycome, proteome

description:
Library name: HCC_1T_glycans_proteins
PE150


title: Normal-input-4

description: Library name: CL21000574meR-input


title: A549 cells, Palboclib 5 umol/L, day 7, DUL, rep2

city: Salt

first: Javier

middle: Abel

last: Menendez

state: Girona

address: Dr Castany s/n. Parc hospitalari Marti i Julia

country: Spain

institute: Girona Biomedical Research Institute

description:
Library name: A549_D7_DUL_PALBO_5_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_PALBO_5_R2_Read_Count

data_processing:
BCL/cBCL (base call) binary files are converted into FASTQ files using bcl2fastq
Trimmed reads are mapped to reference genome with HISAT2
Stringtie was used for transcript assembly
read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes read counts for each sample

extract_protocol:
Total RNA was extracted from cells using the NucleoSpin RNA Plus kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit acording to standard Illumina protocols. Reference Guide # 1000000040498 v00

value: Lung cells

value: Day 7

value: Palboclib 5 umol/L


title: A549 cells, Palboclib 5 umol/L, day 7, DUL, rep1

description:
Library name: A549_D7_DUL_PALBO_5_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_PALBO_5_R1_Read_Count


title: A549 cells, Palboclib 1 umol/L, day 7, DUL, rep2

description:
Library name: A549_D7_DUL_PALBO_1_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_PALBO_1_R2_Read_Count

value: Palboclib 1 umol/L


title: A549 cells, proliferative control, day 7, DUL, rep2

description:
Library name: A549_D7_DUL_CT_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_CT_R2_Read_Count

value: no treatment


title: A549 cells, Palboclib 1 umol/L, day 7, DUL, rep1

description:
Library name: A549_D7_DUL_PALBO_1_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_PALBO_1_R1_Read_Count


title: A549 cells, proliferative control, day 7, DUL, rep1

description:
Library name: A549_D7_DUL_CT_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_CT_R1_Read_Count


title: A549 cells, bleomycin 5 umol/L, day 7, DUL, rep1

description:
Library name: A549_D7_DUL_BLEO_5_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_BLEO_5_R1_Read_Count

value: bleomycin 5 umol/L


title: A549 cells, bleomycin 20 umol/L, day 7, DUL, rep2

description:
Library name: A549_D7_DUL_BLEO_20_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_BLEO_20_R2_Read_Count

value: bleomycin 20 umol/L


title: LG815_TDI_205

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description:
Library name: Sample 44
mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes.
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v4 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: hippocampus

tag: Sex

value: Female

tag: age

value: Scn1a +/+

value: TDI


title: A549 cells, bleomycin 20 umol/L, day 7, DUL, rep1

description:
Library name: A549_D7_DUL_BLEO_20_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_BLEO_20_R1_Read_Count


title: LG815_TDI_204

description:
Library name: Sample 43
mRNA expression in mouse hippocampus

value: Male


title: A549 cells, alisertib 500 nmol/L, day 7, DUL, rep2

description:
Library name: A549_D7_DUL_ALI_500_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_ALI_500_R2_Read_Count

value: alisertib 500 nmol/L


title: A549 cells, bleomycin 5 umol/L, day 7, DUL, rep2

description:
Library name: A549_D7_DUL_BLEO_5_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_BLEO_5_R2_Read_Count


title: LG815_TDI_199

description:
Library name: Sample 42
mRNA expression in mouse hippocampus

value: Scn1a +/-


title: A549 cells, alisertib 500 nmol/L, day 7, DUL, rep1

description:
Library name: A549_D7_DUL_ALI_500_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_ALI_500_R1_Read_Count


title: LG815_TDI_160

description:
Library name: Sample 40
mRNA expression in mouse hippocampus


title: LG815_TDI_163

description:
Library name: Sample 41
mRNA expression in mouse hippocampus


title: A549 cells, alisertib 100 nmol/L, day 7, DUL, rep1

description:
Library name: A549_D7_DUL_ALI_100_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_ALI_100_R1_Read_Count

value: alisertib 100 nmol/L


title: LG815_TDI_152

description:
Library name: Sample 39
mRNA expression in mouse hippocampus

value: Scn1a  +/-


title: A549 cells, Palboclib 5 umol/L, day 7, AGL, rep1

description:
Library name: A549_D7_AGL_PALBO_5_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_PALBO_5_R1_Read_Count


title: LG815_TDI_149

description:
Library name: Sample 38
mRNA expression in mouse hippocampus


title: LG815_TDI_141

description:
Library name: Sample 37
mRNA expression in mouse hippocampus


title: LG815_Ctrl_216

description:
Library name: Sample 36
mRNA expression in mouse hippocampus

value: Ctrl


title: LG815_Ctrl_195

description:
Library name: Sample 35
mRNA expression in mouse hippocampus


title: A549 cells, proliferative control, day 7, AGL, rep2

description:
Library name: A549_D7_AGL_CT_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_CT_R2_Read_Count

value: Lung cells


title: A549 cells, bleomycin 5 umol/L, day 7, AGL, rep2

description:
Library name: A549_D7_AGL_BLEO_5_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_BLEO_5_R2_Read_Count

value: Day 7


title: LG815_Ctrl_174

description:
Library name: Sample 33
mRNA expression in mouse hippocampus


title: LG815_Ctrl_169

description:
Library name: Sample 32
mRNA expression in mouse hippocampus


title: A549 cells, bleomycin 5 umol/L, day 7, AGL, rep1

description:
Library name: A549_D7_AGL_BLEO_5_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_BLEO_5_R1_Read_Count


title: A549 cells, bleomycin 20 umol/L, day 7, AGL, rep2

description:
Library name: A549_D7_AGL_BLEO_20_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_BLEO_20_R2_Read_Count


title: A549 cells, bleomycin 20 umol/L, day 7, AGL, rep1

description:
Library name: A549_D7_AGL_BLEO_20_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_BLEO_20_R1_Read_Count


title: LG815_Ctrl_162

description:
Library name: Sample 30
mRNA expression in mouse hippocampus


title: A549 cells, alisertib 500 nmol/L, day 7, AGL, rep2

description:
Library name: A549_D7_AGL_ALI_500_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_ALI_500_R2_Read_Count


title: LG815_C_95

description:
Library name: Sample 28
mRNA expression in mouse hippocampus

value: Scn1a +/-; cGAS +/+


title: A549 cells, alisertib 500 nmol/L, day 7, AGL, rep1

description:
Library name: A549_D7_AGL_ALI_500_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_ALI_500_R1_Read_Count


title: LG815_C_35

description:
Library name: Sample 26
mRNA expression in mouse hippocampus

value: Scn1a +/+; cGAS +/+


title: A549 cells, alisertib 100 nmol/L, day 7, AGL, rep2

description:
Library name: A549_D7_AGL_ALI_100_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_ALI_100_R2_Read_Count


title: A549 cells, alisertib 100 nmol/L, day 7, AGL, rep1

description:
Library name: A549_D7_AGL_ALI_100_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_ALI_100_R1_Read_Count


title: LG815_C_33

description:
Library name: Sample 25
mRNA expression in mouse hippocampus

value: Scn1a +/+; cGAS +/-


title: A549 cells, Palboclib 5 umol/L, day 3, DUL, rep2

description:
Library name: A549_D3_DUL_PALBO_5_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_PALBO_5_R2_Read_Count

value: Day 3

value: Palboclib 5 umol/L


title: LG815_C_64

description:
Library name: Sample 27
mRNA expression in mouse hippocampus

value: hippocampus


title: A549 cells, Palboclib 5 umol/L, day 3, DUL, rep1

description:
Library name: A549_D3_DUL_PALBO_5_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_PALBO_5_R1_Read_Count


title: LG815_C_31

description:
Library name: Sample 24
mRNA expression in mouse hippocampus

value: Female


title: LG815_C_30

description:
Library name: Sample 23
mRNA expression in mouse hippocampus


title: LG815_C_29

description:
Library name: Sample 22
mRNA expression in mouse hippocampus


title: A549 cells, Palboclib 1 umol/L, day 3, DUL, rep1

description:
Library name: A549_D3_DUL_PALBO_1_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_PALBO_1_R1_Read_Count

value: Palboclib 1 umol/L


title: LG815_C_172

description:
Library name: Sample 21
mRNA expression in mouse hippocampus


title: A549 cells, proliferative control, day 3, DUL, rep2

description:
Library name: A549_D3_DUL_CT_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_CT_R2_Read_Count

value: no treatment


title: LG815_C_164

description:
Library name: Sample 20
mRNA expression in mouse hippocampus


title: LG815_C_159

description:
Library name: Sample 19
mRNA expression in mouse hippocampus

value: Scn1a +/-; cGAS +/-


title: A549 cells, proliferative control, day 3, DUL, rep1

description:
Library name: A549_D3_DUL_CT_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_CT_R1_Read_Count


title: LG815_C_153

description:
Library name: Sample 18
mRNA expression in mouse hippocampus


title: A549 cells, bleomycin 5 umol/L, day 3, DUL, rep1

description:
Library name: A549_D3_DUL_BLEO_5_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_BLEO_5_R1_Read_Count

value: bleomycin 5 umol/L


title: LG815_C_139

description:
Library name: Sample 17
mRNA expression in mouse hippocampus


title: A549 cells, bleomycin 20 umol/L, day 3, DUL, rep2

description:
Library name: A549_D3_DUL_BLEO_20_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_BLEO_20_R2_Read_Count

value: bleomycin 20 umol/L


title: A549 cells, bleomycin 20 umol/L, day 3, DUL, rep1

description:
Library name: A549_D3_DUL_BLEO_20_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_BLEO_20_R1_Read_Count


title: LG815_C_122

description:
Library name: Sample 15
mRNA expression in mouse hippocampus

value: Male

value: Scn1a +/-; cGAS  +/-


title: A549 cells, alisertib 500 nmol/L, day 3, DUL, rep2

description:
Library name: A549_D3_DUL_ALI_500_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_ALI_500_R2_Read_Count

value: alisertib 500 nmol/L


title: LG815_C_121

description:
Library name: Sample 14
mRNA expression in mouse hippocampus


title: LG815_C_106

description:
Library name: Sample 13
mRNA expression in mouse hippocampus


title: A549 cells, alisertib 100 nmol/L, day 3, DUL, rep2

description:
Library name: A549_D3_DUL_ALI_100_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_ALI_100_R2_Read_Count

value: Lung cells

value: alisertib 100 nmol/L


title: DVPV_Hipp_333

description:
Library name: Sample 12
mRNA expression in mouse hippocampus

value: PV Cre/+, Scn1a +/+


title: A549 cells, alisertib 100 nmol/L, day 3, DUL, rep1

description:
Library name: A549_D3_DUL_ALI_100_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_ALI_100_R1_Read_Count


title: A549 cells, Palboclib 5 umol/L, day 3, AGL, rep2

description:
Library name: A549_D3_AGL_PALBO_5_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_PALBO_5_R2_Read_Count


title: DVPV_Hipp_327

description:
Library name: Sample 9
mRNA expression in mouse hippocampus

value: PV Cre/+, Scn1a F/+


title: A549 cells, Palboclib 1 umol/L, day 3, AGL, rep2

description:
Library name: A549_D3_AGL_PALBO_1_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_PALBO_1_R2_Read_Count


title: DVPV_Hipp_330

description:
Library name: Sample 11
mRNA expression in mouse hippocampus


title: A549 cells, Palboclib 5 umol/L, day 3, AGL, rep1

description:
Library name: A549_D3_AGL_PALBO_5_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_PALBO_5_R1_Read_Count


title: DVPV_Hipp_329

description:
Library name: Sample 10
mRNA expression in mouse hippocampus


title: DVPV_Hipp_311

description:
Library name: Sample 7
mRNA expression in mouse hippocampus


title: A549 cells, proliferative control, day 3, AGL, rep2

description:
Library name: A549_D3_AGL_CT_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_CT_R2_Read_Count


title: DVPV_CTX_333

description:
Library name: Sample 6
mRNA expression in mouse hippocampus

source_name: cortex

value: cortex


title: DVPV_Hipp_324

description:
Library name: Sample 8
mRNA expression in mouse hippocampus


title: A549 cells, proliferative control, day 3, AGL, rep1

description:
Library name: A549_D3_AGL_CT_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_CT_R1_Read_Count

value: Day 3


title: A549 cells, Palboclib 1 umol/L, day 3, AGL, rep1

description:
Library name: A549_D3_AGL_PALBO_1_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_PALBO_1_R1_Read_Count


title: DVPV_CTX_330

description:
Library name: Sample 5
mRNA expression in mouse hippocampus


title: A549 cells, bleomycin 5 umol/L, day 3, AGL, rep2

description:
Library name: A549_D3_AGL_BLEO_5_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_BLEO_5_R2_Read_Count


title: DVPV_CTX_329

description:
Library name: Sample 4
mRNA expression in mouse hippocampus


title: DVPV_CTX_327

description:
Library name: Sample 3
mRNA expression in mouse hippocampus


title: A549 cells, bleomycin 20 umol/L, day 3, AGL, rep2

description:
Library name: A549_D3_AGL_BLEO_20_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_BLEO_20_R2_Read_Count


title: DVPV_CTX_324

description:
Library name: Sample 2
mRNA expression in mouse hippocampus


title: A549 cells, alisertib 100 nmol/L, day 7, DUL, rep2

description:
Library name: A549_D7_DUL_ALI_100_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_DUL_ALI_100_R2_Read_Count

value: Day 7


title: A549 cells, bleomycin 20 umol/L, day 3, AGL, rep1

description:
Library name: A549_D3_AGL_BLEO_20_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_BLEO_20_R1_Read_Count


title: A549 cells, bleomycin 5 umol/L, day 3, AGL, rep1

description:
Library name: A549_D3_AGL_BLEO_5_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_BLEO_5_R1_Read_Count


title: A549 cells, Palboclib 5 umol/L, day 7, AGL, rep2

description:
Library name: A549_D7_AGL_PALBO_5_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_PALBO_5_R2_Read_Count

value: Palboclib 5 umol/L


title: A549 cells, Palboclib 1 umol/L, day 7, AGL, rep1

description:
Library name: A549_D7_AGL_PALBO_1_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_PALBO_1_R1_Read_Count


title: A549 cells, Palboclib 1 umol/L, day 7, AGL, rep2

description:
Library name: A549_D7_AGL_PALBO_1_R2_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_PALBO_1_R2_Read_Count


title: DVPV_CTX_311

description:
Library name: Sample 1
mRNA expression in mouse hippocampus


title: A549 cells, alisertib 500 nmol/L, day 3, AGL, rep2

description:
Library name: A549_D3_AGL_ALI_500_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_ALI_500_R2_Read_Count


title: LLC Sildenafil-3

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

description:
Library name: RNA_18
Illumina TruSeq stranded mRNA libraries

data_processing:
Illumina RTA v4.12.2software was used fro base calling, Bcl2fastq v2.17 was used for sample demultiplexing
Adapters from the samples were trimmed using Cutadapt 1.18 software
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome mm10 and gencode M21
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: gene count matrix in csv format

source_name: LLC Lung tumor

growth_protocol: 4T1 cells were cultured in RPMI 1640 medium, while MC38 and LLC cells were cultured in Dulbecco's Modified Eagle Medium (DMEM). All media were supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 1% penicillin-streptomycin. Cells were maintained in a humidified incubator at 37°C with 5% CO2

extract_protocol:
Following their respective treatment durations, cells were washed with phosphate-buffered saline (PBS) and lysed using RLT buffer. Total RNA was subsequently isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions
mRNA library preparation, we used the Illumina TruSeq stranded mRNA ligation kit. We use between 100ng to 1ug of total RNA as the input to an mRNA capture with oligo-dT coated magnetic beads. The mRNA is fragmented, and then a random-primed cDNA synthesis is performed. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a sequencing ready library. The final purified product is then quantitated by qPCR before cluster generation and paired end ( 2x100 cycle) sequencing on NovaSeq.

treatment_protocol: Cells were treated with either DMSO (Control) or 100uM Sildenafil Citrate. The treatment duration was 24 hours for 4T1 and MC38 cells, and 48 hours for LLC cells

value: LLC Lung tumor

value: LLC

value: Lewis Lung Carcinoma

value: Sildenafil Citrate-treated


title: A549 cells, proliferative control, day 7, AGL, rep1

description:
Library name: A549_D7_AGL_CT_R1_1
colum name in Read_counts_ALL_samples:  A549_D7_AGL_CT_R1_Read_Count

value: no treatment


title: LG815_Ctrl_180

description:
Library name: Sample 34
mRNA expression in mouse hippocampus

value: hippocampus

value: Female

value: Scn1a +/+

value: Ctrl


title: A549 cells, alisertib 500 nmol/L, day 3, AGL, rep1

description:
Library name: A549_D3_AGL_ALI_500_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_ALI_500_R1_Read_Count

value: Lung cells

value: alisertib 500 nmol/L


title: A549 cells, alisertib 100 nmol/L, day 3, AGL, rep2

description:
Library name: A549_D3_AGL_ALI_100_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_ALI_100_R2_Read_Count

value: alisertib 100 nmol/L


title: LLC Sildenafil-2

description:
Library name: RNA_17
Illumina TruSeq stranded mRNA libraries


title: LG815_Ctrl_168

description:
Library name: Sample 31
mRNA expression in mouse hippocampus


title: LLC Sildenafil-1

description:
Library name: RNA_16
Illumina TruSeq stranded mRNA libraries


title: LG815_Ctrl_160

description:
Library name: Sample 29
mRNA expression in mouse hippocampus

value: Male


title: A549 cells, alisertib 100 nmol/L, day 3, AGL, rep1

description:
Library name: A549_D3_AGL_ALI_100_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_AGL_ALI_100_R1_Read_Count


title: LLC Control-3

description:
Library name: RNA_15
Illumina TruSeq stranded mRNA libraries

value: Control


title: A549 cells, proliferative control, day 1, DUL, rep2

description:
Library name: A549_D1_DUL_CT_R2_1
colum name in Read_counts_ALL_samples:  A549_D1_DUL_CT_R2_Read_Count

value: Day 1


title: LLC Control-2

description:
Library name: RNA_14
Illumina TruSeq stranded mRNA libraries


title: A549 cells, proliferative control, day 1, AGL, rep2

description:
Library name: A549_D1_AGL_CT_R2_1
colum name in Read_counts_ALL_samples:  A549_D1_AGL_CT_R2_Read_Count


title: LLC Control-1

description:
Library name: RNA_13
Illumina TruSeq stranded mRNA libraries


title: A549 cells, proliferative control, day 1, DUL, rep1

description:
Library name: A549_D1_DUL_CT_R1_1
colum name in Read_counts_ALL_samples:  A549_D1_DUL_CT_R1_Read_Count


title: MC38 Sildenafil-3

description:
Library name: RNA_12
Illumina TruSeq stranded mRNA libraries

source_name: MC38 Colon tumor

value: MC38 Colon tumor

value: Colon Adenocarcinoma


title: A549 cells, proliferative control, day 1, AGL, rep1

description:
Library name: A549_D1_AGL_CT_R1_1
colum name in Read_counts_ALL_samples:  A549_D1_AGL_CT_R1_Read_Count


title: MC38 Sildenafil-2

description:
Library name: RNA_11
Illumina TruSeq stranded mRNA libraries


title: MC38 Sildenafil-1

description:
Library name: RNA_10
Illumina TruSeq stranded mRNA libraries


title: shPML_r2

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

description: Library name: shPML_c

data_processing:
Raw FASTQ files were aligned to the human genome assembly hs1 using Bismark (v0.24.2) with bisulfite-specific indexes generated via HISAT2.
Assembly: hs1
Supplementary files format and content: Methylation calls were extracted using the bismark_methylation_extractor tool and to produce cytosine report and coverage files.

source_name: breast

growth_protocol: MDA-MB-231 cells were cultured in DMEM (Euroclone) supplemented with 10% fetal bovine serum (FBS; Euroclone) and 1% Penicillin/Streptomycin (Lonza).

extract_protocol:
DNA was extracted from MDA-MB-231 cells stably expressing shCTRL or shPML using the QIAamp DNA Mini Kit (QIAGEN) according to the manufacturer’s instructions. The concentration and quality of the extracted DNA were assessed using a NanoDrop spectrophotometer.
RRBS libraries were prepared from 250 ng of gDNA using Zymo-Seq RRBS Library Kit (Zymo Research) following manufacturer’s instruction with minor modifications. Specifically, the column-based purification steps were replaced with 1x AMPure beads (Beckman Coulter) purification. After the bisulfite conversion step, DNA was purified using Zymo MagBinding Beads following EZ-96 DNA Methylation-Lightning MagPrep protocol (Zymo Research). Final libraries were quality controlled using Qubit fluorimeter (Thermo Fisher) for concentration and Tapestation (Agilent) for size distribution.

treatment_protocol: Constitutive PML knockdown was performed with pLKO.1-puro vectors expressing human shPML and shRNA control were purchased from SIGMA (MISSION®). Cell transduced with shRNA control (shC) were treated with 100nM decitabin for 72hrs.

value: breast

value: TNBC

value: shPML


title: MC38 Control-3

description:
Library name: RNA_9
Illumina TruSeq stranded mRNA libraries


title: shPML_r1

description: Library name: shPML_b


title: shC_r2

description: Library name: shC_NT_c

value: shC


title: MC38 Control-2

description:
Library name: RNA_8
Illumina TruSeq stranded mRNA libraries


title: shC_r1

description: Library name: shC_NT_b


title: MC38 Control-1

description:
Library name: RNA_7
Illumina TruSeq stranded mRNA libraries


title: 4T1 Sildenafil-3

description:
Library name: RNA_6
Illumina TruSeq stranded mRNA libraries

source_name: 4T1 breast tumor

value: 4T1 breast tumor

value: Breast Carcinoma

value: Sildenafil Citrate-treated


title: shC_dec_r2

description: Library name: shC_100nMdecitabina_72h_c


title: shC_dec_r1

description: Library name: shC_100nMdecitabina_72h_b


title: A549 cells, Palboclib 1 umol/L, day 3, DUL, rep2

description:
Library name: A549_D3_DUL_PALBO_1_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_PALBO_1_R2_Read_Count

value: Day 3

value: Palboclib 1 umol/L


title: 4T1 Sildenafil-2

description:
Library name: RNA_5
Illumina TruSeq stranded mRNA libraries


title: LMS12

city: Zurich

first: Lara

last: Planas-Paz

address: Schmelzbergstrasse 12

department: Pathology and Molecular Pathology

country: Switzerland

institute: University Hospital Zurich

description: Library name: LR2022_195

data_processing:
Dragen RNA
Assembly: Homo_sapiens_assembly38.fasta.gz, hg38.ncbiRefSeq.gtf.gz
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample

source_name: leiomyosarcoma

growth_protocol: Cells were maintained in advanced Dulbecco’s modified Eagle medium (DMEM; Gibco, 12634028) supplemented with 10% heat-inactivated horse serum (Gibco, 260500888), 1x Glutamax (Gibco 35050038) and 0.2 % Primocin (InvivoGen, ant-pm-2). For cell expansion, the previous media was mixed 1:1 with DMEM containing 1 mM N-acetylcyteine (Sigma-Aldrich, A9165), 50 ng/ml recombinant human epidermal growth factor (Sigma-Aldrich, E9644), 100 ng/ml recombinant human fibroblast growth factor 10 (PeproTech, 100-26), 10 µM Y-27632 (Sellekchem, S1049), 5 µM A-83-01 (Sigma-Aldrich, SLM0788), 10 mM nicotinamide (Sigma-Aldrich, N0636), 10 % R-Spondin conditioned media (self-produced), B27 supplement (Gibco, 17504001), 10 mM HEPES (Gibco, 15630-080), 36 ng/ml hydrocortisone (Sigma-Aldrich, H6909) and 500 ng/ml epinephrine (Sigma-Aldrich, E4250). All cells were passaged when subconfluent  conditions were reached in cell culture‐treated flasks, incubated at 37°C in a humidified atmosphere with 5% CO2, and routinely tested for Mycoplasma.

extract_protocol:
RNA from fresh frozen sarcoma patient samples or patient-derived cells was extracted using the Maxwell RSC simplyRNA Tissue kit (Promega AS1340). The extracted RNA was quantified with a Nanodrop (ThermoFisher Scientific) and the High Sensitivity RNA ScreenTape Assay for TapeStation systems (Agilent 5067).
RNA sequencing libraries were prepared using the Illumina Stranded mRNA sample preparation protocol

value: leiomyosarcoma


title: 4T1 Sildenafil-1

description:
Library name: RNA_4
Illumina TruSeq stranded mRNA libraries


title: LMS11

description: Library name: LR2022_194


title: 4T1 Control-3

description:
Library name: RNA_3
Illumina TruSeq stranded mRNA libraries


title: LMS10

description: Library name: LR2022_188


title: 4T1 Control-2

description:
Library name: RNA_2
Illumina TruSeq stranded mRNA libraries


title: LMS09

description: Library name: LR2022_187


title: 4T1 Control-1

description:
Library name: RNA_1
Illumina TruSeq stranded mRNA libraries


title: LMS08

description: Library name: LR2022_183


title: LMS07

description: Library name: LR2022_182


title: mus, ketogenic diet+radiation, rep3

city: Yangzhou

first: Yefei

last: Zhu

address: No. 45, Taizhou Road

institute: Yangzhou University

description:
Library name: SAMPLE9
After 16 weeks of intervention with ketogenic diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.

data_processing:
RNA Sequencing and Differentially Expressed Genes Analysis The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.  Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq25. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar .
Based on the hypergeometric distribution, GO6, KEGG7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: mmu10
Supplementary files format and content: tab-delimited text file include FPKM value for each sample.

source_name: colon

growth_protocol: All mice were grown under SPF condition

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: After 16 weeks of intervention with ketogenic diet, high-fat diet, and normal diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing. Each group consisted of 3 mice.

value: colon

value: not applied

value: male


title: mus, ketogenic diet+radiation, rep2

description:
Library name: SAMPLE8
After 16 weeks of intervention with ketogenic diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.


title: A549 cells, bleomycin 5 umol/L, day 3, DUL, rep2

description:
Library name: A549_D3_DUL_BLEO_5_R2_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_BLEO_5_R2_Read_Count

value: Lung cells

value: bleomycin 5 umol/L


title: LMS06

description: Library name: LR2022_175


title: LMS05

description: Library name: LR2022_169


title: mus, ketogenic diet+radiation, rep1

description:
Library name: SAMPLE7
After 16 weeks of intervention with ketogenic diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.


title: mus, normal diet+radiation, rep3

description:
Library name: SAMPLE6
After 16 weeks of intervention with normal diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.


title: LMS04

description: Library name: LR2022_158


title: mus, normal diet+radiation, rep2

description:
Library name: SAMPLE5
After 16 weeks of intervention with normal diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.


title: LMS03

description: Library name: LR2022_61


title: mus, normal diet+radiation, rep1

description:
Library name: SAMPLE4
After 16 weeks of intervention with normal diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.


title: mus, high-salt diet+radiation, rep3

description:
Library name: SAMPLE3
After 16 weeks of intervention withhigh-fat diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.

value: After 16 weeks of intervention with high-salt diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.


title: LMS02

description: Library name: LR2022_60


title: LMS01

description: Library name: LR2022_59


title: MPNST11

description: Library name: LR2022_178

source_name: malignant peripheral nerve sheath tumor

value: malignant peripheral nerve sheath tumor


title: mus, high-salt diet+radiation, rep2

description:
Library name: SAMPLE2
After 16 weeks of intervention withhigh-fat diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.


title: mus, high-salt diet+radiation, rep1

description:
Library name: SAMPLE1
After 16 weeks of intervention withhigh-fat diet on mice, a single radiation was administered to establish the RIII mouse model. One week later, the mice were sacrificed and the colon tissues were collected for RNAseq sequencing.


title: Prostate, Toxoplasma infected, sample 5

city: Indianapolis

first: Oliver

last: Strobel

state: IN

address: A418 VanNuys Medical Sciences Building, 635 Barnhill Drive

department: Biochemistry and Molecular Pharmacology

institute: Indiana University School of Medicine

description:
Library name: Infected Sample 5 (E5)
Processed with C5

data_processing:
Seurat v5 (Satija Lab) was utilized for downstream analysis. The Single-cell best practices publication was used as a guide for the analysis35. Cells were retained if they contained at least 200 detected genes (nFeature) and were present in three or more cells. Two samples (C0 and E0), which comprised an experimental pair, were removed as they exhibited consistently reduced per-cell RNA content relative to the remaining samples (Supplemental Figure S1). Additional quality control filtering was performed per sample using a 3 median absolute deviation (MAD) threshold for mitochondrial gene percentage (cells with more than 3 MAD mitochondrial counts were removed), total transcript counts (nCount), and number of detected genes (nFeature). Cells with greater than 10% hemoglobin gene expression were excluded, and putative doublets were removed using scDblFinder36.
Filtered objects were normalized using SCTransform with ncells=5000 and flavor="v2". To correct for batch effects across biological replicates, datasets were integrated using Harmony37. Principal component analysis (PCA) was performed, and the first 30 principle components were used for downstream analysis. Shared nearest neighbor (SNN) graphs were constructed with FindNeighbors, followed by graph-based clustering using FindClusters at a resolution of 0.4. Two-dimensional embeddings were generated with RunUMAP using the top 30 principal components. The full workflow for preprocessing, quality control, normalization, and clustering is summarized in Figure S2.
Fibroblast subset analysis: To focus on stromal fibroblast populations, clusters 0, 1, 5, 12, 16, 20, 22, and 23 were subset from the integrated object (see Figure S4). The resulting stromal subset was re-processed in Seurat v5 using SCTransform (ncells=5000, flavor="v2"). Dimensionality reduction was performed with principal component analysis (PCA), and the top 30 principal components were used for downstream steps. Two-dimensional embeddings were generated with RunUMAP, and shared nearest neighbor (SNN) graphs were constructed with FindNeighbors. Graph-based clustering was performed with FindClusters at a resolution of 0.1 to define stromal subpopulations. For fibroblast subsets, pseudobulk expression matrices were generated using the AggregateExpression function in Seurat v5, grouping cells by biological replicate (orig.ident), experimental condition, and Seurat cluster. This produced a cluster-level pseudobulk object in which each sample × cluster × condition was represented as a single aggregated profile. Differential expression analysis was performed using DESeq2 implemented within Seurat (FindMarkers, test.use="DESeq2"), with comparisons run independently for each fibroblast cluster between experimental and control conditions. To benchmark pseudobulk results against single-cell data, we also performed Wilcoxon rank-sum testing (FindMarkers, test.use="wilcox") on the original single-cell object. For each cluster, differential expression outputs from single-cell and pseudobulk analyses were merged. Results were exported and saved.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5 contains the Cell Ranger filtered gene-by-cell UMI count matrix for each sample. cell_metadata_allcells_with_fib.tsv.gz is a tab-delimited table with one row per cell barcode containing sample/condition, clusters, and UMAP coordinates; fibroblast-only annotations are filled only for fibroblast barcodes

source_name: Prostate

growth_protocol: Parasite culture: Toxoplasma gondii parasites of the PruΔhxprt ldh2GFP (PruΔC32) strain29 were grown on human foreskin fibroblasts (HFFs). The HFFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin and cultures were maintained at 37 °C with 5% CO2. Parasite isolation and preparation: Parasites were harvested from infected HFF cultures containing a mixture of parasites still within host cells and egressed parasites. Cultures were scraped off their flasks, passed through a 27-gauge needle to release intracellular parasites, and pelleted at 800 × g for 5 minutes at 4 °C. The parasites were washed in PBS, then pelleted again (800 × g for 5 minutes at 4 °C). The pellet was again resuspended in PBS, and the parasite concentration was determined using a hemocytometer. The parasites were prepared for infection at a concentration of 40,000 parasites/100 µL in PBS. The parasite suspension was kept on ice to maintain their viability until injection. The time from intracellular parasite release to infection was kept under 45 minutes.

extract_protocol:
Tissue harvest and preparation for single-cell sequencing: 28 DPI mouse prostates were harvested en bloc and placed immediately into ice-cold PBS31. Under a dissecting microscope, individual lobes were isolated as close to the urethra as possible and minced into ~1 mm² pieces in Dulbecco’s Modified Eagle Medium (DMEM). Minced tissue was incubated in 5 mL of DMEM containing collagenase type IV (final concentration: 5000 U/mL) at 37 °C with rotation for 45 min. To maximize viability of cells through the digestion process, cells were collected by centrifugation every 15 min, in which buffer was collected, centrifuged at 500 × g for 5 min at 4 °C, and the resulting pellet was resuspended in 1 mL DMEM supplemented with 1% GlutaMAX and 10% fetal bovine serum (FBS), then held on ice; this mid digestion harvest was implemented to improved cell viability. The remaining tissue fragments were gently triturated five times using a wide-bore pipette tip, replenished with warm digestion medium, and returned to 37 °C. After 45 min of digestion, the supernatant was again collected, pelleted, and processed as above. Residual tissue was treated with 1 mL of dispase (5 U/mL), triturated for 2 min, and transferred into 5 mL DMEM with 1% GlutaMAX and 10% FBS. Cells were pelleted (500 × g, 5 min, 4 °C), resuspended in 1 mL of ice-cold red blood cell (RBC) lysis buffer (Roche), gently triturated, and incubated for 2 min on ice. The suspension was filtered through a pre-wetted 40 µm cell strainer and rinsed with DMEM containing 1% GlutaMAX and 10% FBS. Cells were again centrifuged (500 × g, 5 min, 4 °C) and resuspended in 100 µL of microbeads for dead cell removal (Dead Cell Removal Kit, Miltenyi Biotec). Manufacturer’s instructions were followed: briefly, cells were incubated with microbeads for 15 min at room temperature, applied to magnetic LS columns, and viable cells were collected from the flow-through eluted into PBS.
The resulting single-cell suspensions were diluted in DMEM with 1% GlutaMAX and 10% FBS to a final target concentration of 400–800 live cells/µL and a total of ~16,000 cells were processed to create the gel bead-in-emulsion (GEM) utilizing the 10X Genomics Chromium GEM-X Technology. The average time from prostate harvest to GEM generation and cell lysis was ~2.5 h. Libraries were prepared using the 10x Genomics Chromium platform according to the manufacturer’s instructions and sequenced on an Illuminal Novaseq 6000. Raw sequencing data were processed using Cell Ranger (v7.0.1, 10x Genomics). Briefly, raw base call (BCL) files generated by the Illumina Novaseq 6000 platform were demultiplexed into sample-specific FASTQ files using Cell Ranger mkfastq. Reads were then aligned to the mm10 reference genome (GRCm38, Ensembl version M36) using the STAR aligner as implemented within Cell Ranger33. The Cell Ranger count pipeline was used to trace aligned reads back to individual cell barcodes, collapse unique molecular identifiers (UMIs), and generate gene-by-cell expression matrices. Only barcodes passing default Cell Ranger quality filters (filtered feature–barcode matrices) were retained for downstream analysis.

treatment_protocol: Animal care and infection: CBA/J mice, aged 8–12 weeks, were housed in accordance with Institutional Biosafety Committee (IBC) protocols at Indiana University School of Medicine. All experiments were conducted following approved animal care guidelines. Mice were infected by injecting 100 µL of PBS containing 40,000 PruΔC32 Toxoplasma gondii parasites intraperitonially, while control animals were injected with 100 µL of sterile PBS. A 27-gauge needle was used for all injections. Mice were monitored daily for signs of infection. Surviving mice were then sacrificed at 28 DPI or 60 DPI for prostate harvest.

value: Prostate

value: 8-12 weeks old

tag: strain

value: CBA/J

value: Toxoplasma gondii

value: 28 days post infection


title: Prostate, Toxoplasma infected, sample 3

description:
Library name: Infected Sample 3 (E3)
Processed with C3


title: MPNST09

description: Library name: LR2022_176


title: Prostate, Toxoplasma infected, sample 4

description:
Library name: Infected Sample 4 (E4)
Processed with C4


title: MPNST07

description: Library name: LR2022_173


title: Prostate, Toxoplasma infected, sample 2

description:
Library name: Infected Sample 2 (E2)
Processed with C2


title: Prostate, uninfencted, sample 5

description:
Library name: Control Sample 5 (C5)
Processed with E5

value: uninfected


title: MPNST03

description: Library name: LR2022_168


title: Prostate, uninfencted, sample 3

description:
Library name: Control Sample 3 (C3)
Processed with E3


title: MPNST04

description: Library name: LR2022_170


title: Prostate, uninfencted, sample 4

description:
Library name: Control Sample 4 (C4)
Processed with E4


title: Prostate, uninfencted, sample 2

description:
Library name: Control Sample 2 (C2)
Processed with E2


title: B.sub_TST2

status: Public on Jun 06 2026

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

institute: Engelhardt Molecular Biology Institute

description: Library name: TST_2

data_processing:
read trimming with Trimmomatic
read alignment with STAR
read couning with featureCounts
Assembly: Drosophila melanogaster BDGP6.54
Supplementary files format and content: Tab-separated files, with 1st column – Flybase gene identifier, and 2nd – number of reads spanning into exonic regions of genome

organism: Drosophila melanogaster

growth_protocol: D.melanogaster flies were maintained on standard yeast-agar medium, at 24 Celsius temperature, with 12/12 light/dark incubator.

extract_protocol:
Total RNA was isolated using RNAzol RT reagent (Molecular Research Center, USA). Briefly, 10–20 flies were homogenized in 200 μL of RNAzol reagent, after which 80 μL of dH₂O was added, and the mixture was incubated on ice for 10 minutes. The homogenate was then centrifuged at 15,000×g for 10 minutes at 4°C. The resulting supernatant was collected and transferred to a new sterile 1.5-mL tube. An additional purification step was performed by adding 1 μL of 4-bromoanisole (MRC, BN 191). The mixture was incubated at room temperature for 3 minutes and centrifuged again at 15,000×g for 10 minutes at +4°C. The supernatant was transferred to a new sterile tube, and 200 μL of isopropyl alcohol was added to precipitate the RNA. The mixture was incubated on ice for 30 min and then centrifuged at 20,000×g for 20 min at +4°C. The RNA pellet was washed twice with chilled 75% ethanol and dissolved in RNase-free water.
RNA-seq libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (cat# NR605-01, Vazyme Biotech, China) according to the manufacturer’s protocol. Sequencing was performed on an Illumina NextSeq 500 platform

treatment_protocol: 5 day old flies were infected with bacteria (Bacillus subtilis) by needle pricking method. Gram-positive bacterium Bacillus Subtilis with a (DAP)-type peptidoglycan  at a concentration of 5 OD was used.

value: whole body

value: TST1 deletion

value: B.subtilis inoculated


title: RNAseq of TCM6

description: Library name: TCM6

data_processing:
Clean reads were aligned to the mouse reference genome (GRCm39) using HISAT2, and gene-level counts were obtained with featureCounts. Differential expression analysis was performed with DESeq2, defining differentially expressed genes as those with Benjamini–Hochberg–adjusted p < 0.05 and absolute log2(fold change) ≥ 0.585. Functional enrichment of differentially expressed genes for Gene Ontology and KEGG pathways was carried out with the clusterProfiler package. Gene set enrichment analysis (GSEA) using MSigDB c2 (curated) and c5 (GO) gene sets with 1,000 permutations was also performed; pathways with |normalised enrichment score (NES)| > 1.5 and FDR q < 0.25 were regarded as significantly enriched, whereas those with 0.25 ≤ FDR q < 0.40 were considered to show a suggestive trend and are reported as exploratory findings.
Assembly: GRCm39
Supplementary files format and content: txt file including Reads count for each sample

source_name: kidney

extract_protocol:
Total RNA was isolated from kidney tissue with TRIzol reagent (Invitrogen, USA) and treated with DNase I; RNA integrity was verified by Bioanalyzer 2100.
Libraries were prepared using the VAHTS mRNA-seq V3 kit (Vazyme, China) and sequenced as 150-bp paired-end reads on an Illumina NovaSeq 6000 platform.

value: kidney


title: MPNST01

description: Library name: LR2022_58


title: RNAseq of TCM5

description: Library name: TCM5


title: Dmd wt/wt-EGFP

city: paris

first: gaspard

last: macaux

address: 24, rue du Faubourg Saint-Jacques

country: France

institute: INSERM

description:
Library name: Dmd-htz-Egfp
polyA RNA

data_processing:
The sequencing data were processed into transcript count tables using Cell Ranger Single Cell Software Suite 1.3.1 (10x Genomics). Raw base call files from the Nextseq 500 system (Illumina, San Diego, CA, USA) were demultiplexed using the Cell Ranger mkfastq pipeline into library-specific FASTQ files. The FASTQ files for each library were then processed independently with the Cell Ranger pipeline. Once aligned, barcodes associated with these reads, namely cell identifiers and Unique Molecular Identifiers, were subjected to filtering and correction. Reads associated with retained barcodes were quantified and used to build a transcript count table. The resulting data for each sample were then aggregated using the Cell Ranger aggr pipeline, which performed a between-sample normalization step and concatenated the two transcript count tables.
Assembly: Mus Musculus transcriptome (sequence: GRCm39, Annotation: Gencode v25)
Supplementary files format and content: CellRanger output file: barcodes.tsv.gz features.tsv.gz, matrix.tsv.gz

source_name: Tibialis anterior

extract_protocol:
Nuclei were isolated using the Chromium protocol kit (CG000505, Rev A, 10X Genomics, Pleasanton, CA, USA) from the TA muscles of DmdEGFP/wt heterozygous mice using a previously reported protocol with modifications [29]. A filtration step was added to the protocol using 70-µm filters immediately after tissue lysis. Single-nuclei gel bead-in-emulsions (GEMs) were produced using a Chromium Controller (10X Genomics). Sequencing libraries were created using Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Nuclei were hybridized with probe barcodes and then partitioned into nanoliter-scale GEMs using a microfluidic chip in the iX Chromium (10X Genomics) to target 20,000 nuclei.
After a cleanup with SPRIselect Reagent Kit and fragment size estimation with High Sensitivity™ HS DNA kit runned on 2100 Bioanalyzer (Agilent), the libraries were constructed by performing the following steps: fragmentation, end-repair, A-tailing, SPRIselect cleanup, adaptor ligation, SPRIselect cleanup, sample index PCR, and SPRIselect size selection. The fragment size estimation of the resulting libraries were assessed with High Sensitivity™ HS DNA kit runned on 2100 Bioanalyzer (Agilent) and quantified using the Qubit™ dsDNA High Sensitivity HS assay (ThermoFisher Scientific). Libraries were then sequenced by pair with a HighOutput flowcel using an Illumina Nextseq 500 with the following mode : 28 bp (10X Index + UMI), 10 bp (i7 Index), 10 bp (i5 Index), and 90 bp (Read 2).

value: Tibialis anterior

value: myonuclei

value: no treatment


title: UPS13

description: Library name: LR2022_199

source_name: undifferentiated pleomorphic sarcoma

value: undifferentiated pleomorphic sarcoma


title: RNAseq of TCM4

city: Hefei

first: Jingjing

last: Hu

address: NO.117 Meishan Road

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

description: Library name: TCM4


title: 3rd non-stressed wild-type mouse

city: Jerusalem

first: Tamir

last: Ben-Hur

address: Hadassah Hospital

department: Department of Neurology

institute: Hadassah – Hebrew University Medical Center

description:
Library name: Wt Control 3
column O in the processed data file

data_processing:
Raw reads in FASTQ format were generated using bcl2fastq v2.20.0.422, with default parameters. Adapter sequences, polyA tails, and low-quality regions were removed using cutadapt v3.5, keeping reads of length 15 and above after trimming. Subsequently, low-quality reads were filtered out with the fastq_quality_filter tool from the FASTX package, v0.0.14, applying a quality threshold of 20 for at least 90% of the read positions. Processed reads were aligned to the mouse genome with STAR(35), using genome version GRCm39 with annotations from Ensembl release 106. Raw counts per gene per sample were obtained with htseq-count, using the parameter --stranded=reverse.
Assembly: GRCm39
Supplementary files format and content: DESeq2_final.xlsx- normalized counts, Log 2fold changes, p values and adjusted p values for differential expression

source_name: Brain

extract_protocol:
ice were terminally anesthetized and decapitated, and the brains were excised into Earl’s based salt solution. The brains were dissociated to a single-cell suspension using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, 130–092–628) according to the manufacturer’s protocol. For myelin removal, Percoll (Cytiva) protocol was performed. CNS myeloid cells were isolated from myelin-free single-cell suspension using CD11b-conjugated beads (Miltenyi Biotec, 130–093-634) according to the manufacturer’s protocol followed by depletion with MS columns (Miltenyi Biotec, 130-042-201). The procedure resulted in > 90% CD11b + cells.RNA was produced immediately from isolated brain microglia of 5XFAD and wt mice using RNeasy Mini Kit 50 (Qiagen) according to the manufacturer's instructions. High quality RNA (RNA integrity number [RIN] > 9.3) was extracted from all groups.
Libraries were prepared by the Center for Genomic Technologies at the Hebrew University of Jerusalem, using the KAPA Stranded mRNA-Seq Kit (KR0960, Roche) with poly-A selection, according to the manufacturer's protocol. Single-end sequencing was conducted on an Illumina NextSeq 500 machine using 76 cycles. Sequencing depth ranged between 32 and 40 million reads, with an average of 36 million reads per sample.

treatment_protocol: stressed and non-stressed wt (C57Bl) and 5xFAD mice

value: Brain

value: CD11b+ cells

value: CNS myeloid cell

value: wildtype

value: Control


title: 5th stressed 5xFAD mouse

description:
Library name: 5xFAD CMS 5
column Z in the processed data file

value: Chronic Mild Stress (CMS)


title: UPS12

description: Library name: LR2022_198


title: RNAseq of TCM3

description: Library name: TCM3


title: 3rd stressed wild- type mouse

description:
Library name: Wt CMS 3
column U in the processed data file


title: UPS11

description: Library name: LR2022_167


title: RNAseq of TCM2

description: Library name: TCM2


title: 3rd stressed 5xFAD mouse

description:
Library name: 5xFAD CMS 3
column X in the processed data file


title: 3rd non-stressed 5xFAD mouse

description:
Library name: 5xFAD Control 3
column R in the processed data file


title: UPS10

description: Library name: LR2022_166