title: HEK293T cells, ERM, Label_Input, 3G, Rep2


title: WT, RA+, Day 5

status: Public on May 10 2025

type: SRA

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: Salk Institute for Biological Studies

library_source: transcriptomic single cell

data_processing:
For the snRNA-seq libraries, CellRanger (v.2.1.1) was used to perform sample-demultiplexing, barcode processing and single-nuclei gene-UMI counting.
An expression matrix was obtained for each experiment by aligning to the hg19 reference genome using CellRanger with default parameters.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: H1 hESCs

growth_protocol: hESCs were mantained in mTeSR1 media on matrigel-covered plates.

extract_protocol:
GEMx
Chromium single-cell

treatment_protocol: Day 5 samples were untreated or treated with RA 1uM for 24h (from day 4 to day 5). Day 30 samples were untreated or treated with RA 1uM full-treatment of 3 days (From day 4 to day 7).

tag: cell line

value: H1 hESCs

tag: cell type

value: WT hESC-derived CPCs Day 5, RA 1uM 24h

tag: genotype

value: WT

tag: treatment

value: RA 1uM 24h (D4 to D5)


title: KO67

city: Chongqing

first: rui

last: Liu

address: No. 1 Medical College Road, Yuzhong District

country: China

institute: CHONGQING MEDICAL UNIVERSITY

library_source: transcriptomic

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

organism: Mus musculus

source_name: The diethylnitrosamine (DEN)-induced HCC of KO mice

extract_protocol:
Total RNA was extracted from animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse model

value: diethylnitrosamine (DEN)-induced HCC

tag: tissue

value: liver


title: B. velezensis cells, axenic, 13h, biol rep 3, A13_3

city: Cuernavaca

first: Leobardo

last: Serrano Carreón

state: Morelos

address: Av Universidad 2001

department: Ingenieria Celular y Biocatálisis

country: Mexico

institute: Instituto de Biotecnología - UNAM

data_processing:
RNA-seq data was aligned and quantified by Salmon (v0.14.1)
The differential gene expression analysis was performed by edge R (Bioconductor package) using RPM as response variable.
To study the effect of time or microbial interaction, two comparisons were analyzed: 1) Samples from co-culture (treatment) vs axenic (control), regardless of time and 2) Samples from 13 h (treatment) vs 8 h (control), regardless of if it comes from of axenic or co-cultivation.
An orthology assignment was performed by eggNOG-Mapper (Version 4.5)
Assembly: Genome of B. velezensis 83 (NCBI accession No. CP034203) was used as reference.
Supplementary files format and content: Tab-delimited text files include  NumReads values for each sample

organism: Bacillus velezensis

growth_protocol: Axenic (B.velensis 83) and co-cultures (B.velezensis 83 and C.gloeosporioides) were carried out in a stirred tank type bioreactor using potato dextrose mineral medium. 29 °C, pH6.8 and DOT>30%.

extract_protocol:
RNA was isolated by RNeasy Mini Kit (74104, QUIAGEN). Remotion of rRNA was performed by Ribominus™ Transcriptome Isolation Kit.
Hi Seq4000 Sequencing Systems (Ilumina Inc., CA, USA) was used for RNA-seq.

treatment_protocol: Bacterial RNA from axenic and co-cultures was isolated. Sampling (8h and 13h) was done before glucose limitation.

value: vegetative

value: Axenic culture 13 h


title: B. velezensis cells, axenic, 13h, biol rep 2, A13_2


title: miRNC_1

city: shijiazhuang

first: LuSha

address: 12 Jiankang Road

department: Deportment of Gynecology

institute: The Fourth hospital of hebei medical research

data_processing:
The expression levels of genes and transcripts were quantified separately using the software RSEM for subsequent analysis of differential gene/transcript expression among different samples, and the regulatory mechanisms of genes can be revealed by combining sequence function information.
The software used for differential expression was DESeq2 (with biological replicates, used by default) or DEGseq (without biological replicates, used by default), the default screening criteria for significantly differentially expressed genes are: FDR < 0.05 & |log2FC| ≧ 1, and when a gene satisfies both conditions, it will be regarded as a differentially expressed gene (DEG).
This analysis was performed using the software Goatools for enrichment analysis using Fisher's exact test. Four multiple tests (Bonferroni, Holm, Sidak and false discovery rate) were used to correct the p-value to control for the calculated false positive rate, and in general, significant enrichment was considered to exist for this GO function when the corrected p-value (p_fdr) was < 0.05
Assembly: hg38
Supplementary files format and content: gene.count.matrix.annot.xlsx

source_name: Endometrial cancer

extract_protocol:
TOTAL RNA was extracted from the tissue samples, the concentration and purity of the extracted RNA was examined using Nanodrop2000, RNA integrity was examined by agarose gel electrophoresis, and the Agilent5300 determined the RQN values were determined by Agilent5300. For single library construction, the total RNA amount was 1 μg, the concentration was ≥ 30 ng/μL, the RQN was > 6.5, and the OD260/280 was between 1.8 and 2.2.
Total RNA was first extracted and mRNA was enriched by Oligo dT, then fragmented mRNA was synthesized into cDNA by reverse transcription, ligated into adapter, and sequenced by NovaSeq X Plus platform after fragment screening and library enrichment.

value: Endometrial cancer

value: Ishikawa

tag: transfection

value: control mimics-NC


title: miRNC_2


title: HEK293T cells, ERM, Label_Input, 3G, Rep1

city: Beijing

first: Ruixiang

last: Wang

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
Cutadapt (v.1.18) was utilized firstly for adaptor sequence removal.
Then the reads were mapped by hisat2 (v.2.1.0) against the genome assembly downloaded from Ensembl.
Using the gene annotation (v.87) downloaded from Ensembl, the mapped reads were counted by HTSeq (v0.7.2) with the option “–stranded no”.
Then, differential expression analysis was carried out by DESeq2(v.1.16.1).
Assembly: GRCh38 (hg38), GRCm39 (mm39)
Supplementary files format and content: XLSX format includes raw counts for each sample

growth_protocol: HEK293T and MC38 cells were cultured in complete medium consisting of Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum at 37°C with 5% CO2.

extract_protocol:
RNAs were extract following the TRIzol Reagent manufacturer’s instructions, digested with 1-2 μL DNaseI at 37°C for 30 min, and then incubated with click reagents consisting of 0.1 mM biotin-azide, 2 mM THPTA, 0.5 mM CuSO4 and 5 mM sodium ascorbate. After 10 min of CuAAC reaction at room temperature, RNAs were purified with RNA Clean&Concentrator kit and eluted with pre-warmed nuclease-free water. The RNA integrity was detected by Fragment Analyzer. Approximately 1 μg RNA was kept as pre-enrichment samples, while the remaining was purified with streptavidin beads and the post-enrichment samples were purified by TRIzol Reagent.
Total RNAs were used for library construction and libraries were constructed by NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) following the manuyfacturer's instructions.

treatment_protocol: Cells stably expressing ERM located LAP were seeded to 100-mm cell culture dishes, then labeled at around 90% confluence. Cells were incubated with 10 mM PA and 50 μM furimazine in DMEM medium supplemented with 10% fetal bovine serum at 37 °C for 15-60 min. Then, the cells were washed with cold PBS thrice.


title: HEK293T cells, ERM, Label_Enrich, 3G, Rep3


title: KO1354


title: B. velezensis cells, axenic, 13h, biol rep 1, A13_1


title: miRNA-1229-5P-3

value: miR-1229-5p mimics


title: HEK293T cells, ERM, Label_Enrich, 3G, Rep2


title: SY63-BM-1

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description: Library name: SY63-BM-1

data_processing:
RNA-seq raw reads were filtered by fastp (v.0.23.4) to remove low quality reads and adapter. Clean reads were aligned to the MSU7.0 rice reference genome (Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/) by hisat2 (v.2.1.0). FeatureCounts (v.2.0.1) were used for quantitative analysis and the differentially expressed genes were calculated by DESeq2. For the single-cell RNA seq data of hybrid (SY63), fastp (v.0.23.4) was used to remove duplicate and low-quality reads, and then clean reads were matched with the reference genomes of parents ZS97 and MH63 (ZS97RS3 and MH63RS3, Rice Information GateWay [RIGW], http://rice.hzau.edu.cn/rice_rs3/) using hisat2 (v.2.1.0). Further use PP2PG65 software to isolate parental reads through SNPs of ZS97 and MH63.
Fastp (v.0.23.4) was used to remove low-quality reads and adapter from the CUT&Tag raw data. Clean reads were mapped to the MSU7.0 genome by Bowtie2 (v.2.4.1). SAMtools (v.1.20)  is used to convert between SAM and BAM formats, sort and deduplicate BAM files, and merge two biological replicates. MACS2 (v.2.2.7.1) was used to call histone modification peaks with the parameters (-f BAMPE -g 3.8e8 --broad -q 0.01 for H3K27me3, H3K36me3 and H3K9me2; -f BAMPE -g 3.8e8 -q 0.01 for H3K4me3), and H3 sample was used as control. The bigwig files were generated using bamCoverage with the parameters (-bam -binSize 10 –normalize Using BPM) in deepTools (v.2.5.3), which were visualized in the Integrated Genome Browser, draw heatmaps and metaplots.
BS-seq low-quality reads were filtered out from the raw data by TrimGalore (v.0.6.6; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were mapped to the MSU7.0 rice genome. Bismark (v.0.23.1) was used to match, deduplicate and extract methylation sites. To obtain more loci for analysis, we combined the two biological replicates. Duplicates were removed and uniquely mapped reads were retained and each cytosine covered by at least five reads for further analysis. Density plots show the frequency distribution of DNA methylation differences between 50-bp window of two samples with at least 20 informative sequenced cytosines in both samples and 70% CG, 30% CHG, or 10% CHH methylation in either of the samples as previously described.
Assembly: MSU7.0
Supplementary files format and content: bigwig file
Supplementary files format and content: RNA-seq normalized counts file

molecule: polyA RNA

organism: Oryza sativa Indica Group

source_name: Bicellular microspore

growth_protocol: For field cultivation, the plants were grown in Wuhan during summer seasons under standard agricultural practices. Seedlings were transplanted to the field in early May and harvested in October. For greenhouse experiments, germinated rice seedlings were planted in soil-filled containers and grown under controlled conditions with a 14-h light/10-h dark cycle at 32°C (light) and 26°C (dark). Tillers of rice plants at an appropriate developmental stage were harvested for collection of spikelets. The collected spikelets were used for phenotypic analysis and isolation of male germ cells.

extract_protocol:
For collection of tetrads and microspores, when tillers flag leaf collar and penultimate leaf collar aligned spikelets of 0.4-0.6 cm length were taken. Like extracting meiocytes, anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with tetrad shapes were collected as tetrads. Cells with single, free-floating state and have not formed cell walls were collected as microspores.For collection of mature unicellular microspores, when tillers flag leaf auricle was about 5 cm above the auricle of the penultimate leaf, fresh spikelets > 0.6 cm were collected. At this stage the color of the spikelets is still white. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct germination pores and having formed cell walls are collected as unicellular microspores.For collection of bicellular microspores, spikelets turning greener in color were taken. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. Cells with distinct large vacuoles, two nuclei, and thickened pollen walls are collected as bicellular microspores.For collection of mature pollen, tillers green spikelets were taken. At this point, the anthers have developed into yellow color. Anthers were dissected out and gentle pressure was applied to allow the release of germ cells. The cells that are distinctly filled with starch are collected as pollen.A differential centrifugation isolation method was used to separate sperm from whole rice anthers.
Isolation and purification of mRNA from different types of cells were performed using the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat. # N712). The RNA-seq libraries were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat. # TD502) and sequenced on Illumina HiSeq 6000. For rice in SY63 backgrounds, we used single male germ cell to construct the transcriptome library. We used approximately 100-200 male germ cells to construct the transcriptome library.BS-seq libraries were constructed using reported protocol Clark et al (2017). About 400–500 male germ cells were pooled for each replicate bisulfite seq library construction.The CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat. # TD903) and sequenced on Illumina HiSeq 6000. We used approximately 10,000 male germ cells to construct the CUT&Tag library by male germ cell isolation technology. The male germ cells were lysed with 200 µL Nuclear extraction buffer 2 (NEB2) (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100, 1× protease inhibitor), and the nuclei pellet was resuspended in 100 µL wash buffer (from the TD903 kit) for library construction. About 100,000 sperm cells were pooled for each replicate CUT&Tag library construction. About 100,000–200,000 seedling cell nuclei were pooled for each replicate CUT&Tag library construction.For ATAC-seq library construction, the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, Cat. # TD711) was used to prepare libraries for different types of cells. Using the same number of cells as for CUT&Tag, we isolated approximately 10,000 male germ cells to construct the ATAC-seq library. Approximately 100,000 sperm cells and 100,000–200,000 seedling cell nuclei were pooled for each replicate ATAC-seq library construction.

value: Bicellular microspore


title: B. velezensis cells, axenic, 8h, biol rep 3, A8_3

value: Axenic culture 8 h


title: miRNA-1229-5P-2


title: HEK293T cells, ERM, Label_Enrich, 3G, Rep1


title: B. velezensis cells, axenic, 8h, biol rep 1, A8_1


title: B. velezensis cells, axenic, 8h, biol rep 2, A8_2


title: S coelicolor mRNA day 8_rep2

status: Public on May 09 2025

city: Minneapolis

first: Erin

middle: E

last: Carlson

state: MN

address: 207 Pleasant St. SE

department: Chemsitry

institute: University of Minnesota

description: Log 2 transformed of expression output

data_processing:
alignment and prcoessing performed by Rockhopper
expression values are RPKM values normalized by the upper quartile of gene expression
values were then log2(x+1) transformed
Genome_build: NC_003888
Supplementary_files_format_and_content: .csv file with locus tag identifiers and log2 transformed expression values for each time point and biological replicate

organism: Streptomyces coelicolor

source_name: bacterial cells

growth_protocol: S coelicolor grown on solid mannitol-soya for 3 days at 27 C, a single colony transferred to 30 mL of ISP2 and shaken at 275 rm at 27 C, after 36 hours 5 mL of starter culture was transferred to 1L of ISP2 media

extract_protocol:
cells were collected every 24 hours for 8 days after initial transfer to 1L cultures, quiagen RNAeasy kit was used. Cells were resuspended in RLT buffer with ten 3mm glass beads and then vortexed, followed by an additional equal volume of acid phenol chloroform. Samples were then vortexed and centrifuged at 15,000 rpm (10,000 x g) for 10 min at RT. The aqueous was isolated and diluted with an equal volume of 70 % (V/V) ethanol followed by purification with the RNAeasy column according to manufacturer’s instructions. To remove gDNA contaminants an on column digestion was performed with 2 µL of TurboDNase. An Agilent 2100 Bioanalyzer was used to confirm the integrity of the RNA by assessing the 23s and 16s RNA bands.
After ribozero treatment and library creation, sequencing was performed on an Illumina HiSeq 2500 system in high-output mode with 50 bp single-reads.

treatment_protocol: no treatment

tag: time

value: day 8

tag: strain


title: miRNA-1229-5P-1


title: S coelicolor mRNA day 6_rep1

description: Log 2 transformed of expression output

value: day 6


title: S coelicolor mRNA day 6_rep3

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 6_rep2

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 7_rep3

description: Log 2 transformed of expression output

value: day 7


title: S coelicolor mRNA day 7_rep1

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 5_rep3

description: Log 2 transformed of expression output

value: day 5


title: S coelicolor mRNA day 7_rep2

description: Log 2 transformed of expression output


title: C. elegans-1 N2 worms Control, 5 days

city: Changchun

first: Anran

last: Li

state: Jilin

address: Qianjin Street

institute: Jilin University

description:
Library name: Sample1
column A1 in ref_trans_full_table.txt

data_processing:
Use the specified genome as a reference for the analysis, the download address was: https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6 (WBcel235, accessed on: 19 October 2019). Quantification of gene expression levels: Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Assembly: Use the specified genome as a reference for the analysis, the download address was: https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6 (WBcel235, accessed on: 19 October 2019). Quantification of gene expression levels: Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Supplementary files format and content: Differential expression analysis of two samples was performed using the edgeR. The FDR < 0.01 and Fold Change ≥ 2 was set as the threshold for significantly differential expression.
Supplementary files format and content: Differential expression analysis of two samples was performed using the edgeR. The FDR < 0.01 and Fold Change ≥ 2 was set as the threshold for significantly differential expression.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Ellagic Acid (EA, 96%, Aladdin, Shanghai, China) was dissolved in dimethyl sulfoxide (DMSO), and finally prepare it as a stock solution containing 2% dimethyl sulfoxide and 200 mM ellagic acid. The stock solution was sterilized by filtration through 0.2 µm pore size membranes. Mix the stock solution with E. coli OP50 bacterial solution and compound them separately to contain 0.2% DMSO and 50 μM ,100 μM ,200 μM ellagic acid, which is the working solution of EA.

extract_protocol:
Gene expression in N2 worms treated with 100 µM EA or vehicle control, at days 5, was assessed by Biomarker Technology Company (Beijing, China). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Use the specified genome as a reference for the analysis, the download address was: https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6 (WBcel235, accessed on: 19 October 2019). Quantification of gene expression levels: Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

value: whole animal


title: KO1361


title: S coelicolor mRNA day 5_rep1

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 5_rep2

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 4_rep1

description: Log 2 transformed of expression output

value: day 4


title: S coelicolor mRNA day 4_rep2

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 4_rep3

description: Log 2 transformed of expression output


title: C. elegans-1 N2 worms treated with 100 µM EA, 5 days

description:
Library name: Sample2
column B1 in ref_trans_full_table.txt

treatment_protocol: Ellagic Acid (EA, 96%, Aladdin, Shanghai, China) was dissolved in dimethyl sulfoxide (DMSO), and finally prepare it as a stock solution containing 2% dimethyl sulfoxide and 200 mM ellagic acid. The stock solution was sterilized by filtration through 0.2 µm pore size membranes. Mix the stock solution with E. coli OP50 bacterial solution and compound them separately to contain 0.2% DMSO and 50 μM ,100 μM ,200 μM ellagic acid, which is the working solution of EA.


title: S coelicolor mRNA day 3_rep1

description: Log 2 transformed of expression output

value: day 3


title: S coelicolor mRNA day 3_rep3

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 3_rep2

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 2_rep3

description: Log 2 transformed of expression output

value: day 2


title: S coelicolor mRNA day 8_rep3

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 2_rep2

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 1_rep3

description: Log 2 transformed of expression output

value: day 1


title: S coelicolor mRNA day 2_rep1

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 1_rep1

description: Log 2 transformed of expression output


title: S coelicolor mRNA day 1_rep2

description: Log 2 transformed of expression output


title: abh1, Cytoplasmic RNA, replicate 2

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

description: Library name: S33_9C

data_processing:
Raw read quality was diagnosed using FastQC.
Trim Galore (Babraham Bioinformatics) was used for adapter and low-quality read trimming with PHRED score < 20.
Reads were aligned to the TAIR10 genome assembly using STAR (Dobin et al 2014).
FeatureCounts (Liao et al 2014) was used for determine transcript abundance on gene-level features extracted from the TAIR10 annotation retrived from EnsemblPlants (Kersey et al 2016).
Bedtools (genomecov -bga -split -scale -5) was used to generate a bedGraph file from the BAM files. The flag -5 was included to only consider read depth at the first nucleotide of the read for GMUCT libraries. A per-million scaling factor was provided to the -scale flag, determined by 1,000,000/total fragments (total fragments = [samtools view -F 260 -c]/2).
bedGraphToBigWig (kentUtils) was used to generate bigWig files (using the .bed files) for visualizing read depth across TAIR10 features.
Assembly: TAIR10
Supplementary files format and content: .bg: bedgraph file of scaled counts (RPM) across TAIR10 genome coordinates for each sample.
Supplementary files format and content: .bigWig: files for visualizing read coverage (scaled to reads per million, RPM) in a genome browser (e.g. IGV) for each sample.
Supplementary files format and content: .counts: raw counts for gene-level featres in each sample computed by FeatureCounts
Library strategy: GMUCT

molecule: cytoplasmic RNA

organism: Arabidopsis thaliana

source_name: Early-stage flower bud

growth_protocol: Seeds were sown onto moist soil (treated overnight with diatomaceous earth), supplemented with 10 g/L Jack’s Professional 15-16-17 Peat-Lite water-soluble fertilizer (JR Peters, Allentown, PA, USA) and NemAttack (Arbico Organics, Tucson, AZ, USA), and stratified in the dark for 48 h at 4 °C. Plants were grown at 22 °C under a 16-h-light (100-150 µmol m-2 s-1)/8-h-dark photoperiod. Approximately 20-30 mg of early-stage flower buds (stages 1-1235) were harvested from 10-week old plants. Early-stage flower buds were used owing to their numerosity, ability to produce a large number of small RNAs, and being cell dense structures. Excised buds were immediately frozen in liquid nitrogen and stored at -80 °C. Biological replicates represent pooled flower buds collected from independently grown plants.

extract_protocol:
Nucleoplasmic- and cytoplasmic-enriched RNA fractions were isolated using the Cytoplasmic and Nuclear RNA Purification Kit (Norgen Biotek, Thorold, ON, CAN) following manufacturer’s instructions, including on-column DNA nuclease treatment of the nuclear RNA fraction (RNase-Free DNase I Kit, Norgen Biotek, Thorold, ON, CAN). A detailed protocol is available on Protocols.io (dx.doi.org/10.17504/protocols.io.kqdg3x2nqg25/v1).
GMUCT libraries were constructed using an adapted protocol (Willmann et al., 2014). Details are described on Protocols.io (dx.doi.org/10.17504/protocols.io.yxmvm2jjbg3p/v1).

value: Early-stage flower bud

tag: ecotype


title: abh1, Cytoplasmic RNA, replicate 3

description: Library name: S35_11C


title: Liver from aged mice following HBO treatment, 21-month-old, biol rep 4

city: Shanghai

first: Qiaoyu

last: Fu

address: 639 Zhizaoju Road

department: Depart of Plastic & Reconstructive Surgery

institute: Shanghai 9th People’s Hospital  School of Medicine  Shanghai Jiao Tong University

description:
Library name: Sample 36
Column name in Liver_gene_count.txt: OH4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Clean reads were aligned to the reference genome GRCh38 or GRCm39 using Hisat2
Supplementary files format and content: The .txt files include gene counts for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from frozen tissues or cultured cells using TriZol.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

value: WT

value: HBO treatment


title: Liver from aged mice, 21-month-old, biol rep 3

description:
Library name: Sample 31
Column name in Liver_gene_count.txt: OLD3


title: Liver from aged mice, 21-month-old, biol rep 2

description:
Library name: Sample 30
Column name in Liver_gene_count.txt: OLD2


title: Liver from aged mice following HBO treatment, 21-month-old, biol rep 3

description:
Library name: Sample 35
Column name in Liver_gene_count.txt: OH3


title: Liver from aged mice following HBO treatment, 21-month-old, biol rep 2

description:
Library name: Sample 34
Column name in Liver_gene_count.txt: OH2


title: abh1, Nucleoplasmic RNA, replicate 3

description: Library name: S34_11N

molecule: nuclear RNA


title: Liver from aged mice following HBO treatment, 21-month-old, biol rep 1

description:
Library name: Sample 33
Column name in Liver_gene_count.txt: OH1


title: Liver from aged mice, 21-month-old, biol rep 4

description:
Library name: Sample 32
Column name in Liver_gene_count.txt: OLD4


title: Liver  from young mice, 2-month-old, biol rep 4

description:
Library name: Sample 28
Column name in Liver_gene_count.txt: YNG4


title: Liver  from young mice, 2-month-old, biol rep 3

description:
Library name: Sample 27
Column name in Liver_gene_count.txt: YNG3


title: Liver from aged mice, 21-month-old, biol rep 1

description:
Library name: Sample 29
Column name in Liver_gene_count.txt: OLD1


title: Liver  from young mice, 2-month-old, biol rep 2

description:
Library name: Sample 26
Column name in Liver_gene_count.txt: YNG2


title: Liver from young mice, 2-month-old, biol rep 1

description:
Library name: Sample 25
Column name in Liver_gene_count.txt: YNG1


title: Kidney from aged mice, 21-month-old, biol rep 4

description:
Library name: Sample 20
Column name in Kidney_gene_count.txt: OLD4

source_name: Kidney

value: Kidney


title: Kidney from aged mice following HBO treatment, 21-month-old, biol rep 2

description:
Library name: Sample 22
Column name in Kidney_gene_count.txt: OH2


title: Kidney from aged mice following HBO treatment, 21-month-old, biol rep 3

description:
Library name: Sample 23
Column name in Kidney_gene_count.txt: OH3


title: Kidney from aged mice, 21-month-old, biol rep 1

description:
Library name: Sample 17
Column name in Kidney_gene_count.txt: OLD1


title: Kidney from aged mice, 21-month-old, biol rep 3

description:
Library name: Sample 19
Column name in Kidney_gene_count.txt: OLD3


title: Kidney from aged mice following HBO treatment, 21-month-old, biol rep 4

description:
Library name: Sample 24
Column name in Kidney_gene_count.txt: OH4


title: Kidney from aged mice following HBO treatment, 21-month-old, biol rep 1

description:
Library name: Sample 21
Column name in Kidney_gene_count.txt: OH1


title: Kidney from aged mice, 21-month-old, biol rep 2

description:
Library name: Sample 18
Column name in Kidney_gene_count.txt: OLD2


title: Kidney from young mice, 2-month-old, biol rep 3

description:
Library name: Sample 15
Column name in Kidney_gene_count.txt: YNG3


title: Kidney from young mice, 2-month-old, biol rep 1

description:
Library name: Sample 13
Column name in Kidney_gene_count.txt: YNG1


title: Kidney from young mice, 2-month-old, biol rep 4

description:
Library name: Sample 16
Column name in Kidney_gene_count.txt: YNG4


title: Skin from aged mice following HBO treatment, 21-month-old, biol rep 4

description:
Library name: Sample 12
Column name in Skin_gene_count.txt: OH4

source_name: Skin

value: Skin


title: Kidney from young mice, 2-month-old, biol rep 2

description:
Library name: Sample 14
Column name in Kidney_gene_count.txt: YNG2


title: Skin from aged mice following HBO treatment, 21-month-old, biol rep 3

description:
Library name: Sample 11
Column name in Skin_gene_count.txt: OH3


title: abh1, Nucleoplasmic RNA, replicate 2

description: Library name: S32_9N


title: Skin from aged mice following HBO treatment, 21-month-old, biol rep 1

description:
Library name: Sample 9
Column name in Skin_gene_count.txt: OH1


title: Skin from aged mice following HBO treatment, 21-month-old, biol rep 2

description:
Library name: Sample 10
Column name in Skin_gene_count.txt: OH2


title: Skin from aged mice, 21-month-old, biol rep 1

description:
Library name: Sample 5
Column name in Skin_gene_count.txt: OLD1


title: Skin from aged mice, 21-month-old, biol rep 2

description:
Library name: Sample 6
Column name in Skin_gene_count.txt: OLD2


title: Skin from aged mice, 21-month-old, biol rep 4

description:
Library name: Sample 8
Column name in Skin_gene_count.txt: OLD4


title: Skin from young mice, 2-month-old, biol rep 4

description:
Library name: Sample 4
Column name in Skin_gene_count.txt: YNG4


title: Skin from young mice, 2-month-old, biol rep 3

description:
Library name: Sample 3
Column name in Skin_gene_count.txt: YNG3


title: Skin from young mice, 2-month-old, biol rep 1

description:
Library name: Sample 1
Column name in Skin_gene_count.txt: YNG1


title: Skin from young mice, 2-month-old, biol rep 2

description:
Library name: Sample 2
Column name in Skin_gene_count.txt: YNG2


title: Hippocampus_WT_430

city: New York

first: Scott

middle: Ian

last: Adamson

state: New York

address: 101 6th Ave

institute: New York Genome Center

data_processing:
Adapters were trimmed from read pairs using cutadapt  version 4.4 using parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT and -m 40
Trimmed reads were used to quantify expression with kallisto version 0.48.0by pseudo-aligning to a Gencode version M35 reference transcriptome (with --bias parameter set).
Transcript abundance estimates were imported into R using tximport for differential expression analysis using DESeq2 version 1.38.3.
Assembly: GRCm39/Gencode vM35
Supplementary files format and content: Gene_counts.tsv is a tab delmited file with gene_id, gene_name, and counts for each sample after importing into DESeq2 using tximport.
Supplementary files format and content: kallisto_estimated_transcript_counts.tsv is a tab delimited file with transcript_id, gene_id, gene_name, and estimated counts from kallisto for each sample.

source_name: Hippocampus

extract_protocol:
Animals were euthanized by CO2 asphyxiation and tissues were harvested, frozen on dry-ice, and stored in -80°C freezer until use. The RNA was isolated using RNeasy Mini Kit and DNAse-treated following the manufacturer’s protocol (Qiagen).
Libraries were prepared from DNase-treated total RNA using the KAPA mRNA HyperPrep Kit. Briefly, the protocol includes isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.

value: Hippocampus

tag: Sex

value: female


title: Hippocampus_WT_434

value: male


title: Hippocampus_WT_550


title: Hippocampus_WT_561


title: Hippocampus_E815K_558


title: Hippocampus_E815K_557


title: Hippocampus_D801N_439


title: Hippocampus_D801N_440


title: Hippocampus_D801N_442


title: Hippocampus_E815K_555


title: Cortex_WT_434

source_name: Cortex

value: Cortex


title: Hippocampus_D801N_436


title: Hippocampus_E815K_556


title: Cortex_WT_550


title: Cortex_WT_561


title: Cortex_E815K_557


title: Cortex_E815K_558


title: Cortex_E815K_555


title: Cortex_D801N_442


title: Cortex_E815K_556


title: Skin from aged mice, 21-month-old, biol rep 3

description:
Library name: Sample 7
Column name in Skin_gene_count.txt: OLD3


title: Cortex_D801N_440


title: Cortex_D801N_439


title: Cerebellum_WT_561

source_name: Cerebellum

value: Cerebellum


title: Cerebellum_WT_434


title: Cerebellum_WT_550


title: Cerebellum_WT_430


title: Cerebellum_E815K_557


title: Cerebellum_E815K_556


title: Cerebellum_D801N_436


title: Cerebellum_E815K_555


title: Cerebellum_D801N_442


title: Cerebellum_D801N_440


title: Cortex_WT_430


title: Brainstem_WT_430

source_name: Brainstem

value: Brainstem


title: Brainstem_WT_561


title: Brainstem_WT_550


title: Cerebellum_D801N_439


title: Brainstem_WT_434


title: Brainstem_E815K_555


title: Brainstem_E815K_556


title: Brainstem_D801N_436


title: Brainstem_E815K_558


title: Brainstem_D801N_442


title: Brainstem_D801N_439


title: Brainstem_D801N_440


title: Brainstem_E815K_557


title: Cortex_D801N_436


title: MuSC, H3K27ac

city: Shatin, NT

first: CHUHAN

last: LI

state: shatin

address: The Chinese University of Hong Kong, Central Ave

country: Hong Kong

institute: CUHK

library_source: genomic

data_processing:
The raw data were first pre-processed by initial quality assessment, adapters trimming, and low-quality filtering and then mapped to the mouse reference genome (mm10) using bowtie2, and only the non-redundant reads were kept.
The protein DNA-binding peaks (sites) were identified using MACS2. During the peak calling, candidate peaks were compared with the background, dynamic programming was used to determine λ of Poisson distribution, and the P-value cutoff was set to 0.001 for JunB ChIP-Seq experiment.
Assembly: mm10
Supplementary files format and content: *.bedGraph
Supplementary files format and content: *.narrowPeak
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: Muscle

extract_protocol:
CUT&RUN assay was conducted according to the manufacturer’s instructions. (Cell Signaling Technology, 86652)
Library construction was according to the manufacturer’s instructions(NEB, E7645S).

value: Muscle

value: MuSC

tag: chip antibody

value: H3K27ac antibody (CST, #8173)


title: Cerebellum_E815K_558


title: MVC, biol rep2

data_processing:
Briefly, the adapter and low-quality sequences were trimmed from 3’ to 5’ ends by Trimmomatic and the reads shorter than 36 bp were discarded
Subsequently, the preprocessed reads were aligned to the mouse genome (mm10) using STAR. The aligned reads were then converted to bam format using samtools.
The aligned RNA-Seq reads were accepted  and assembled into a parsimonious set of transcripts.  These transcripts were then estimated the relative abundances by Cufflinks.
Assembly: mm10
Supplementary files format and content: indexed binary file for display of track dense

extract_protocol:
Total RNAs from cells or tissues were extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions.
cDNAs were synthesized under the manufacturer’s instructions of HiScript® II Reverse Transcriptase Kit with gDNA wiper (Vazyme, R223-01). Real-time PCR was performed to quantify the expression level of mRNAs by Luna® Universal qPCR Master Mix (NEB, M3003E) and LightCycler ®480 Real-Time PCR System (Roche). GAPDH (glyceraldehydes 3-phosphate dehydrogenase) or 18s RNA were used as internal controls for normalization.

value: MVC


title: MVC, biol rep3


title: MVC, biol rep1


title: DMSO, biol rep3

value: DMSO


title: DMSO, biol rep2


title: Donor K202 - sorted kidney B cells

city: Cambridge

first: Ondrej

last: Suchanek

address: Francis Crick Avenue

department: Department of Medicine, Molecular Immunity Unit

country: United Kingdom

institute: University of Cambridge

description: Library name: K202_Cortex

data_processing:
Raw MiSeq reads were filtered for base quality (median Phred score > 32) using QUASR 6.X.
Universal barcoded regions were identified in reads and orientated to read from V-primer to constant region primer. The barcoded region within each primer was identified and checked for conserved bases (i.e. the T’s in NNNNTNNNNTNNNNT). Primers and constant regions were trimmed from each sequence, and sequences were retained only if there was >80% sequence certainty between all sequences obtained with the same barcode, otherwise discarded. The constant region allele with highest sequence similarity was identified by 10-mer matching to the reference constant region genes from the IMGT database (v3.1.24), and sequences were trimmed to give only the region of the sequence corresponding to the variable (V–D–J) regions.
Isotype usage information for each IGH was retained throughout the analysis hereafter. Sequences without complete reading frames and non-immunoglobulin sequences were removed and only reads with significant similarity to reference Ighv and Ighj genes from the IMGT database were retained using BLAST (v2.7.1).
Only sequences with more than one read were retained for further downstream analysis. IGHV and IGHJ genes and mutational status were determined for each BCR using IMGT/V-QUEST (v3.4.9).
Assembly: IMGT/V-QUEST (v3.4.9)
Supplementary files format and content: tab limited text files are  IMGT/V-QUEST output and contain filtered (productive-only) nt BCR sequences with isotype information. These files were subsequently used as source (input) data for VDJ tools.
Library strategy: BCR-seq

source_name: kidney

extract_protocol:
RNA was extracted from sorted B cell lysates using the RNeasy plus micro kit (QIAGEN) as per manufacturer’s instructions.
Reverse transcription (RT) was performed in two steps:  First, 1uL barcoded reverse primer mix (10uM per each primer), 1uL dNTP (10mM) and 14uL RNA template (up to 500ng) were mixed and heated to 65°C for 5 mins followed by an immediate transfer to ice for at least one minute. Second, mixture 2 including 4uL 5X First-Strand Buffer, 1uL DTT (0.1M), 1uL RNaseOUTTM (Thermo Scientific) and 1uL SuperScript®III (Life Technologies) was added and incubated at 50 °C for 60 min followed by 15 min inactivation at 70 °C. cDNA was cleaned-up with Agencourt AMPure XP beads and PCR amplified with V-gene multiplex primer mix (10 μM each forward primer) and 3′ universal reverse primer (10 μM) using KAPA protocol (KAPA Biosystems) and the thermal cycling conditions: 1 cycle (95 °C—5 min); 5 cycles (98 °C—5 s, 72 °C—2 min); 5 cycles (98°C—5 s, 65 °C—10 s, 72 °C—2 min); 30 cycles (98 °C—20 s, 60 °C—1 min, 72 °C—2 min) and 1 step (72 °C—7 min). Primers are provided in Supplementary Information (Table 2).

value: kidney

value: B cell

value: Transplant organ donor


title: Donor K202 - sorted splenic B cells

description: Library name: K202_Spleen

source_name: spleen

value: spleen


title: MuSC, Aged

data_processing:
The raw data were first pre-processed by initial quality assessment, adapters trimming, and low-quality filtering and then mapped to the mouse reference genome (mm10) using bowtie2, and only the non-redundant reads were kept.
The protein DNA-binding peaks (sites) were identified using MACS2. During the peak calling, candidate peaks were compared with the background, dynamic programming was used to determine λ of Poisson distribution, and the P-value cutoff was set to 0.001 for JunB ChIP-Seq experiment.
Assembly: mm10
Supplementary files format and content: *.bedGraph/*.bw
Supplementary files format and content: *.narrowPeak
Library strategy: CUT&RUN

value: JunB antibody (CST, #3753)

tag: group

value: Aged


title: Donor K198 - sorted splenic B cells

description: Library name: K198_Spleen


title: Donor K159 - sorted kidney B cells

description: Library name: K159_Cortex


title: MuSC, Young, biol rep3

value: Young


title: MuSC, Young, biol rep2


title: MuSC, Young, biol rep1


title: Donor K154 - sorted kidney B cells

description: Library name: K154_Cortex


title: Donor K159 - sorted splenic B cells

description: Library name: K159_Spleen


title: MVC, scRNAseq

description: 10x Genomics

data_processing:
The orginal FASTQ files were processed by CellRanger 7.0.0 to produce outputs including feature-barcode matrices.
Subsequently, the processed matices were read in by Seurat 5.0.1 for following analysis.
Assembly: mm10
Supplementary files format and content: CellRanger output files: Tab-separated values files and matrix files

source_name: limb muscle

extract_protocol:
Whole live muscle cells were freshly isolated by FACs sorting
Sequential crosslinking was performed with the following steps: Whole muscle cells were isolated  with an additional step of viability validation by PI staining. Red blood cells were also eliminated by ACK buffers (150M NH4Cl, 100mM KHCO3, 10mM EDTA-2Na) before sorting. After sorting, live cells were washed with 0.04% BSA in PBS for twice and resuspended in the BSA solution at an appropriate concentration (300-1200 cells/μl). Suspended cells were counted under a microscope and Typan blue was used to examine the cell viability. After the confirmation of cell number and viability, following the 10x manufacturer’s instructions for generation of Gel Bead-In Emulsions (GEMs) using the 10X Chromium system. Next GEMs were proceeded with in-GEM reverse transcription (RT) under manufacturer’s instructions. After RT, two steps of DNA cleaning up and purification were performed to obtain the purified cDNA sample for further library construction with the manufacturer's protocols. Bioanalyzer analysis and qPCR were used to measure the quality of DNA libraries including the DNA size and purity. Finally, DNA libraries were sequenced on the Illumina Illumina HiSeq X ten platform.

value: limb muscle

value: muscle mononuclear cell


title: h83C_P

city: West Hollywood

first: Simon

last: Knott

state: California

address: 8687 Melrose Ave

department: BFG

institute: Cedars Sinai

description: Library name: h83C_P

data_processing:
fastqs were processed via cellranger to produce count matrices and then merged for scanpy analysis
Assembly: hg38
Supplementary files format and content: h5ad files processed with scanpy pipeline

source_name: breast

extract_protocol:
Core biopsies were obtained under local anesthesia using a 12G core needle apparatus (Bard Magnum). Biopsies were placed immediately into a 50 mL conical tube containing ice-cold DMEM and transferred on ice from the clinic to the laboratory (generally within 30 min of the procedure). A portion of the biopsy was immediately placed into formalin for subsequent paraffin embedding. The remainder of the biopsy was minced with a sterile scalpel into 2 mm pieces and placed in a gentleMACS™ C- tube (Miltenyi Biotech) containing 4.7 mL of ice-cold DMEM. Enzymes from the Human Tumor Dissociation Kit (Miltenyi Biotech) were added to the sample according to the manufacturer's protocol for dissociation of tough tumors. After the enzymes were added, the C-tube was placed onto a gentleMACS Octo Dissociator (Miltenyi Biotech), the heating element was placed over the tube, and the 37C_h_TDK_3 program was initiated. Prior to completion of the dissociation protocol, two 70 μm cell strainers were each placed onto a 50 mL conical tube on ice and pre-wetted with 3 mL of heat inactivated FBS. Upon completion of the dissociation protocol, the sample was poured through the first 70 μm cell strainer and the strainer was washed with 5 mL of heat inactivated FBS. The filtrate was then poured through the second 70 μm cell strainer and the strainer was washed with 5 mL of heat inactivated FBS. The sample was centrifuged at 300 g for 7 min at 4 ºC. The supernatant was removed, and the sample was resuspended in 2 mL of DMEM and transferred to a microcentrifuge tube on ice. An aliquot of the sample was taken for cell counting via a hemocytometer and the remaining sample was centrifuged at 300 g for 10 min at 4 ºC. The supernatant was removed, and the sample was resuspended in 80 μL FACS buffer (10 μM pH 8 EDTA + 5% H.I. FBS + 0.001% m/v NaN3 in PBS, sterile filtered) per 107 cells. Miltenyi anti-human CD45 microbeads were added to cells), and the sample was incubated at 4 ºC covered with foil for 15 min. After incubation, 1 mL FACS buffer per 107 cells was added to the sample and pipet mixed. The sample was centrifuged at 300 g for 10 min at 4 ºC. The supernatant was removed, and the sample was resuspended with 500 μL FACS buffer and transferred to a 15 mL conical. The sample was placed in a pre-cooled AutoMACS tube holder and the Miltenyi AutoMACS Possel_S program was initiated. At this time, 10X Genomics reagents required for running the Single Cell 5' v1 Assay were removed from their storage conditions to equilibrate at room temperature for 30 min. Upon completion of the AutoMACS program, the CD45-positive fraction was centrifuged at 300 g for 7 min at 4 ºC. The sample was resuspended in 50 μL of DMEM and a cell count was performed via a hemocytometer. If possible, the sample was diluted to 103 cells/μL and the sample was processed according to the 10X Genomics protocol for the Single Cell 5' v1 assay with a targeted 10,000 cell recovery (or maximum recovery possible with the number of cells in the sample).
Subsequent gene expression libraries were prepared according to the 10X Genomics Single Cell 5' v1 protocol. Gene expression libraries were sequenced using paired end 150bp reads to an average 60-70% sequencing saturation (as calculated by 10X Genomics Cellranger v4.0.0) on an Illumina Novaseq. Demultiplexed fastq files for gene expression libraries were processed using Cellranger (v4.0.0, GRCh38-3.0.0 transcriptome reference, read 1 and read 2 set to 100bp). Doublet cells were identified using Scrublet95 from the filtered feature barcode matrices produced by Cellranger." Singlets were further filtered to express at least 250 unique genes, contain less than 30 X 105 total UMIs, and have ≤10% total UMIs associated with mitochondrial genes.

value: breast

value: Radiation therapy + PD1

tag: batch


title: DMSO, scRNAseq

description: 10x Genomics


title: Donor K149 - sorted kidney B cells

description: Library name: K149_Cortex


title: Donor K149 - sorted splenic B cells

description: Library name: K149_Spleen


title: 20231230-FT-5_BC16

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

data_processing:
After mapping to human transcriptome using bowtie2 and peak calling by RNA peak caller (cfPeak), count matrix was created by merge 3 pairs of samples. EV-sorting small RNA sites in normal human plasma total RNA-seq were annotated by comparing differentially expressed peaks (EV vs. EV-depleted Plasma).
Assembly: human transcriptome
Supplementary files format and content: bed; bigwig

source_name: plasma

extract_protocol:
Peripheral whole blood samples were collected from individuals before therapy or surgery using EDTA-coated vacutainer tubes. Plasma was separated within 2 hr after collection by centrifuge at 1,900 g for 10 min at 4 ℃. All plasma samples were aliquoted and stored at -80°C. Plasma EV were purified by a membrane-affinity approach using exoRNeasy Midi Kit(Qiagen, 77144) following the manufacturer’s instructions. Plasma-nonEV (EV-depleted Plasma) component were collected from flow through part of MinElute spin column from kit. Both plasma EV RNA and Plasma nonEV RNA were extracted using QIAzol Lysis Reagent (QIAGEN, Beijing, China)
DNA contamination was removed by Recombinant DNase I (RNase-free) (TAKARA, Beijing, China). End repair and polyadenylation were performed using E. coli Poly(A) Polymerase (NEB, Beijing, China), and T4 Polynucleotide Kinase (NEB, Beijing, China). Reverse transcription and libraries were prepared according to DETECTOR-seq protocol with minor modifications by replacing original TSO with uracil-containing TSO and digestion with Uracil-DNA Glycosylase (NEB, Beijing, China) after reverse transcription. Library quantification was performed by Qubit dsDNA HS Kit and fragment size was checked by Agilent 2100 Bioanalyzer. Libraries were sequenced on MGI Tech DNBSEQ-T7 with PE150.

value: plasma

tag: gender

value: F

tag: age

tag: patient

tag: condition

value: Healthy

value: EV-depleted plasma


title: 20231230-FT-5_BC18


title: h83B_P

description: Library name: h83B_P


title: 20231215-EV-5_BC18

value: plasma EV


title: h83A_P

description: Library name: h83A_P

value: Baseline


title: 20231215-EV-3_BC16


title: 20231230-FT-5_BC15

value: not collected


title: 20231215-EV-1_BC15


title: h82C_P

description: Library name: h82C_P


title: h82C_N

description: Library name: h82C_N


title: A740003 [GA43161]

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: colon

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: colon

tag: cell type

value: PDGFRalpha+ Ly6Chigh fibroblasts

value: wild-type


title: DCPIB [GA43160]

tag: genotype

value: cGAMP + DCPIB


title: DMSO, biol rep1

value: Muscle

value: MuSC

tag: treatment

value: DMSO


title: h82B_P

description: Library name: h82B_P


title: cGAMP [GA43159]

value: cGAMP


title: Donor K198 - sorted kidney B cells

description: Library name: K198_Cortex

value: kidney

value: B cell

value: Transplant organ donor


title: control [GA43158]


title: Donor K154 - sorted splenic B cells

description: Library name: K154_Spleen

value: spleen


title: h82B_N

description: Library name: h82B_N

value: breast


title: h83C_N

description: Library name: h83C_N

value: Radiation therapy + PD1


title: sulfasalazine [GA30576]

value: cGAMP + sulfasalazine


title: DCPIB [GA30575]


title: h72C_N

description: Library name: h72C_N


title: cGAMP [GA30574]


title: control [GA30573]


title: h72B_N

description: Library name: h72B_N


title: Control, replicate 1, snRNAseq

city: Houston

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cardiac tissue

extract_protocol:
Single nuclei were isolated according to methods described in publication (PMID:35471998)
The snRNA-Seq libraries were generated using the 10x Genomics Chromium Single Cell 3’ v3 reagent kit and the sequencing was performed by Novogene.

value: cardiac tissue

value: Male

value: 3.5 month old

value: Tamoxifen injections


title: CF-KI, replicate 1, snRNAseq

description: 10X genomics


title: h72A_P

description: Library name: h72A_P

value: Baseline


title: h72B_P

description: Library name: h72B_P


title: h72A_N

description: Library name: h72A_N


title: 10Gyx3-566

description: Library name: 10Gyx3-566

data_processing:
All further data processing steps were performed using scripts in the Python 3.8 environment. Cells classified as multiplets by GMM-Demux were further screened by assessing the ratio of the counts for the highest to second-highest expressed HTO tags. Cells where this ratio was greater than a factor of 5 (i.e,. the highest expressed tag had more than 5x the number of counts than the second-highest expressed tag) were re-classified as singlets. All remaining multiplets and non-classified cells were removed from further analysis. Singlets were further filtered to express at least 250 unique genes, contain less than 30,000 total UMIs, and have less than or equal to 10% of total UMIs associated with mitochondrial genes. Dimensional reduction and clustering were performed on total count-normalized, log-transformed counts using Scanpy's (v1.5.1) implementation of the self-assembling manifold (SAM) method (k = 30, distance = euclidean, standardization = Normalizer) and Leiden clustering (resolution = 0.8), respectively73,74. Differential gene expression analysis (DGEA) was performed using sc.tl.rank_genes_groups (method = wilcoxon) and gene signature scores were generated using sc.tl.score_genes on total count-normalized, log-transformed counts.
Assembly: mm10
Supplementary files format and content: All vdjca files contain aligned TCR sequences ran using mixcr qiagen mouse pipeline. Single-cell rna seq data was processed using Python and stored as an h5ad file.
Library strategy: TCR-Seq

extract_protocol:
Cryopreserved cells were gently thawed using a 37C water bath and washed with pre-warmed growth media (10% FBS in DMEM). Cells were washed twice with FACS buffer (10 μM pH 8 EDTA + 5% H.I. FBS + 0.001% m/v NaN3 in PBS) and stained with Biolegend HTO antibodies, following standard manufacturer procedures, and counted with a hemocytometer. Cells from ~8 samples were then pooled in equal proportions and the sample processed according to the 10X Genomics protocol for the Single Cell 3' v2 assay with a targeted 10,000 cell recovery. Subsequent gene expression and HTO libraries were prepared according to the 10X Genomics Single Cell 3' v2 protocol. Demultiplexed fastqs for the gene expression libraries were processed with CellRanger (v4.0).
Total RNA was isolated using the RNeasy mini kit (#74104, Qiagen) from M/D-driven tumors left untreated or treated with P+T as described in the treatment's section and harvested at end point. Libraries were prepared using the Qiaseq Targeted RNA Panel Mouse TCR kit (#334671, Qiagen). Demultiplexed fastqs were deduplicated and aligned using MiXCR with the Qiaseq preset and the following tag pattern flag: --tag-pattern "^(R1:*) ^(UMI:N{12:18})N{12}(R2:*)".

tag: cell line


title: splenic slices transplant

first: Yuan

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

institute: Beijing Proteome Research Center

description: 10 × Genomics

data_processing:
Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38, using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v2.3.0) R toolkit for quality control and downstream analysis of our single cell RNAseq data. All functions were run with default parameters, unless specified otherwise. We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package. To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded. The normalized data (NormalizeData function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package. Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts and transcript counts for every gene and every sample.

source_name: liver

extract_protocol:
Mice were perfused through portal vein cannulation by normal saline solution. Liver tissues were removed and minced with ophthalmic scissors in DMEM medium, and enzymatically digested using the liver dissociation kit (Miltenyi Biotech , 130-105-807). Cell suspensions were filtered through a 100 μm nylon mesh, centrifuged at 50 g for 3 min  at 4 ºC, and the supernatants were further centrifuged at 320 g for 8 min to obtain non-parenchymal liver cells. Isolation of hepatic immune cells were performed through a 30% Percoll (GE Healthcare, 17-0891-01) . Primary CD45+ non-parenchymal liver cells  were further sorted by staining with antibodies antibody  for mouse CD45 (Biolegend, 103112). Cells were sorted using FACSAria (Becton, Dickinson).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

tag: tissue

value: liver


title: h71C_N

description: Library name: h71C_N


title: P-P-TAM-278

description: Library name: P-P-TAM-278


title: h71B_P

description: Library name: h71B_P


title: 10Gyx3-669

description: Library name: 10Gyx3-669


title: P-P-TAM-288

description: Library name: P-P-TAM-288


title: h82A_P

description: Library name: h82A_P


title: h71A_P

description: Library name: h71A_P


title: h71B_N

description: Library name: h71B_N


title: Control-671

description: Library name: Control-671


title: h82A_N

description: Library name: h82A_N


title: h71A_N

description: Library name: h71A_N


title: h72C_P

description: Library name: h72C_P


title: h68C_P

description: Library name: h68C_P


title: P-P-TAM-687

description: Library name: P-P-TAM-687


title: h68B_P

description: Library name: h68B_P


title: Control-647

description: Library name: Control-647


title: h68B_N

description: Library name: h68B_N


title: 10Gyx3-685

description: Library name: 10Gyx3-685


title: h71C_P

description: Library name: h71C_P


title: P-P-TAM-467

description: Library name: P-P-TAM-467


title: h68A_N

description: Library name: h68A_N


title: P-P-TAM-274

description: Library name: P-P-TAM-274


title: 10Gyx3-670

description: Library name: 10Gyx3-670


title: P-P-TAM-273

description: Library name: P-P-TAM-273


title: h59B_P

description: Library name: h59B_P


title: h59A_P

description: Library name: h59A_P


title: 10Gyx3-102

description: Library name: 10Gyx3-102


title: h59A_N

description: Library name: h59A_N


title: h55C_P

description: Library name: h55C_P


title: P-P-TAM-487

description: Library name: P-P-TAM-487


title: h55C_N

description: Library name: h55C_N


title: 10Gyx3-269

description: Library name: 10Gyx3-269


title: h55B_P

description: Library name: h55B_P


title: Control-170

description: Library name: Control-170


title: h55B_N

description: Library name: h55B_N


title: h55A_P

description: Library name: h55A_P


title: T3B_HTO

description: Library name: T3B_HTO

data_processing:
All further data processing steps were performed using scripts in the Python 3.8 environment. Cells classified as multiplets by GMM-Demux were further screened by assessing the ratio of the counts for the highest to second-highest expressed HTO tags. Cells where this ratio was greater than a factor of 5 (i.e,. the highest expressed tag had more than 5x the number of counts than the second-highest expressed tag) were re-classified as singlets. All remaining multiplets and non-classified cells were removed from further analysis. Singlets were further filtered to express at least 250 unique genes, contain less than 30,000 total UMIs, and have less than or equal to 10% of total UMIs associated with mitochondrial genes. Dimensional reduction and clustering were performed on total count-normalized, log-transformed counts using Scanpy's (v1.5.1) implementation of the self-assembling manifold (SAM) method (k = 30, distance = euclidean, standardization = Normalizer) and Leiden clustering (resolution = 0.8), respectively73,74. Differential gene expression analysis (DGEA) was performed using sc.tl.rank_genes_groups (method = wilcoxon) and gene signature scores were generated using sc.tl.score_genes on total count-normalized, log-transformed counts.
Assembly: mm10
Supplementary files format and content: All vdjca files contain aligned TCR sequences ran using mixcr qiagen mouse pipeline. Single-cell rna seq data was processed using Python and stored as an h5ad file.


title: T3B_GEX

description: Library name: T3B_GEX


title: h55A_N

description: Library name: h55A_N


title: T3A_HTO

description: Library name: T3A_HTO


title: h68A_P

description: Library name: h68A_P


title: Control-171

description: Library name: Control-171


title: h59C_P

description: Library name: h59C_P


title: T3A_GEX

description: Library name: T3A_GEX


title: h35B

description: Library name: h35B


title: h59C_N

description: Library name: h59C_N


title: T2C_HTO

description: Library name: T2C_HTO


title: T2C_GEX

description: Library name: T2C_GEX


title: T2B_HTO

description: Library name: T2B_HTO


title: h34C

description: Library name: h34C


title: h34A

description: Library name: h34A


title: h34B

description: Library name: h34B


title: 10Gyx3-305

description: Library name: 10Gyx3-305


title: Control-819

description: Library name: Control-819


title: T2B_GEX

description: Library name: T2B_GEX


title: T2A_HTO

description: Library name: T2A_HTO


title: T2A_GEX

description: Library name: T2A_GEX


title: h33B

description: Library name: h33B


title: h33A

description: Library name: h33A


title: T1B_HTO

description: Library name: T1B_HTO


title: T1B_GEX

description: Library name: T1B_GEX


title: h32A

description: Library name: h32A


title: T1A_HTO

description: Library name: T1A_HTO


title: h31B

description: Library name: h31B


title: h31C

description: Library name: h31C


title: h31A

description: Library name: h31A


title: S3A_HTO

description: Library name: S3A_HTO


title: S3B_GEX

description: Library name: S3B_GEX


title: S3B_HTO

description: Library name: S3B_HTO


title: h35A

description: Library name: h35A


title: MCD, replicate 3, 5prime, cohort 3

first: david

last: smith

state: Pennsylvania

address: 3501 Civic Center Blvd

institute: CHOP

description: Library name: cohort3_MCD3

data_processing:
Reads were processed using CellRanger Single-Cell Software Suite (v6.1.1 and v7.0.0) from 10x Genomics, more details on the associated publication.
Assembly: Reads were aligned to the human reference genome GRCh38. Custom references were also prepared to include Epstein-Barr virus (NCBI:txid10376), human herpesvirus 8 (NCBI:txid37296), and human immunodeficiency virus 1 (NCBI:txid11676).
Supplementary files format and content: filtered h5 files, output from CellRanger pipeline

source_name: Lymph node

extract_protocol:
Lymph node resections with clinicopathological diagnoses of UCD, MCD, and non-malignant non-infectious reactive lymph nodes (RLN) were identified from the institutional archives. We identified cases where rapid intraoperative frozen section diagnosis was conducted on whole lymph node resections. Upon removal from the patient, lymph node sections were embedded in Optimal Cutting Temperature (OCT) compound and frozen within a 10-minute window per clinical intraoperative diagnostic requirements that also ensured high-quality RNA reflecting the in-vivo state. The lymph node was bisected along its long axis. One-half of the bisected lymph node was frozen, while the other half was fixed in formalin and subsequently embedded in paraffin (FFPE). The OCT-frozen half was used for single-nuclei transcriptomic analysis, while the corresponding FFPE half was used for single-cell proteomic imaging (Supplemental Figure 1). Frozen tissue was used for DNA sequencing and SNP array analysis
Single nuclei RNA was processed for sequencing by constructing gene expression (GEX) libraries (Chromium Next GEM Single Cell 3ʹ Kit v3.1, PN-1000268) or gene expression and V(D)J immune profiling libraries (Chromium Next GEM Single Cell 5' Kit v2, PN-1000263; Chromium Single Cell Human TCR Amplification Kit , PN-1000252; Chromium Single Cell Human BCR Amplification Kit, PN-1000253). Briefly, the single nuclei suspension was mixed with RT Master Mix and loaded with barcoded single-cell 3’ or 5′ gel beads and partitioning oil onto microfluidic chips to encapsulate 5000 nuclei per sample using Chromium Controller. After reverse transcription and cleanup, cDNA libraries were generated according to manufacturer instructions with one additional cycle of PCR amplification to account for the relatively lower amount of RNA in nuclei than in whole cells. cDNA was fragmented and end-repaired, size-selected and PCR amplified to generate a 3’ or 5′ gene expression library. For VDJ library construction, full-length TCR or BCR transcripts were enriched from 4μL of amplified cDNA, and 50 ng of enrichment product was used for library construction.

value: Lymph node

tag: diagnosis

value: MCD

tag: library type

value: gene expression


title: S3A_GEX

description: Library name: S3A_GEX


title: KFD, replicate 1, TCR, cohort 3

description: Library name: cohort3_KFD1_TCR

data_processing:
Reads were processed using CellRanger Single-Cell Software Suite (v6.1.1 and v7.0.0) from 10x Genomics, more details on the associated publication.
Assembly: Reads were aligned to the human reference genome GRCh38. Custom references were also prepared to include Epstein-Barr virus (NCBI:txid10376), human herpesvirus 8 (NCBI:txid37296), and human immunodeficiency virus 1 (NCBI:txid11676).
Supplementary files format and content: filtered h5 files, output from CellRanger pipeline
Library strategy: TCR-Seq

value: KFD

value: TCR library


title: S2A_GEX

description: Library name: S2A_GEX


title: KFD, replicate 1, 5prime, cohort 3

description: Library name: cohort3_KFD1


title: h33C

description: Library name: h33C


title: S2A_HTO

description: Library name: S2A_HTO


title: KFD, replicate 2, TCR, cohort 2

description: Library name: cohort2_KFD2_TCR


title: S1B_HTO

description: Library name: S1B_HTO


title: S1B_GEX

description: Library name: S1B_GEX


title: RLN, replicate 2, TCR, cohort 2

description: Library name: cohort2_RLN2_TCR

value: RLN


title: S1A_HTO

description: Library name: S1A_HTO


title: UCD, replicate 3, 5prime, cohort 2

description: Library name: cohort2_UCD3

value: UCD


title: UCD, replicate 2, 5prime, cohort 2

description: Library name: cohort2_UCD2


title: L3B_HTO

description: Library name: L3B_HTO


title: S1A_GEX

description: Library name: S1A_GEX


title: KFD, replicate 3, 5prime, cohort 2

description: Library name: cohort2_KFD3


title: T1A_GEX

description: Library name: T1A_GEX


title: L3B_GEX

description: Library name: L3B_GEX


title: KFD, replicate 2, 5prime, cohort 2

description: Library name: cohort2_KFD2


title: L3A_HTO

description: Library name: L3A_HTO


title: MCD, replicate 4, 5prime, cohort 2

description: Library name: cohort2_MCD4


title: L3A_GEX

description: Library name: L3A_GEX


title: MCD, replicate 3, 3prime, cohort 1

description: Library name: cohort1_MCD3


title: L2B_HTO

description: Library name: L2B_HTO


title: L2B_GEX

description: Library name: L2B_GEX


title: KFD, replicate 3, TCR, cohort 2

description: Library name: cohort2_KFD3_TCR


title: L2A_HTO

description: Library name: L2A_HTO


title: L2A_GEX

description: Library name: L2A_GEX


title: MCD, replicate 2, 3prime, cohort 1

description: Library name: cohort1_MCD2


title: KFD, replicate 1, 3prime, cohort 1

description: Library name: cohort1_KFD1


title: MCD, replicate 1, 3prime, cohort 1

description: Library name: cohort1_MCD1


title: Bleomycin-induced senescent human primary stromal cells with single-session HBO, biol rep 3

description:
Library name: Sample 45
Column name in PSC27_gene_count.txt: BLEO-HBO-3

value: Primary normal human prostate stromal cell

value: WT

value: HBO treatment


title: L1B_GEX

description: Library name: L1B_GEX

value: breast


title: RLN, replicate 1, 3prime, cohort 1

description: Library name: cohort1_RLN1


title: L1A_HTO

description: Library name: L1A_HTO


title: L1A_GEX

description: Library name: L1A_GEX


title: UCD, replicate 1, 3prime, cohort 1

description: Library name: cohort1_UCD1


title: Bleomycin-induced senescent human primary stromal cells with single-session HBO, biol rep 1

description:
Library name: Sample 43
Column name in PSC27_gene_count.txt: BLEO-HBO-1


title: L1B_HTO

description: Library name: L1B_HTO


title: Retina, 4 weeks AVI group, ATAC

description:
Library name: WIF1-4w_snATAC
10x Genomics

library_source: genomic single cell

data_processing:
Cell Ranger ARC v2.0.1 count functions to aggregate reads across sequencing lanes into a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz
Subsequently, the processed matices were read in by Seurat 5.0.1 and Signac 1.12.0 for following analysis.
Assembly: mm10
Supplementary files format and content: CellRanger ARC output files: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Whole live retinal cells were freshly isolated with papain enzyme and the nuclei extraction with lysis buffer.
Library construction was performed according to the standard 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow.

value: Retina

value: All retinal cell types

tag: strain


title: Bleomycin-induced senescent human primary stromal cells with single-session HBO, biol rep 2

description:
Library name: Sample 44
Column name in PSC27_gene_count.txt: BLEO-HBO-2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Clean reads were aligned to the reference genome GRCh38 or GRCm39 using Hisat2
Supplementary files format and content: The .txt files include gene counts for each sample


title: Retina, 4 weeks AVI group, GEX

description:
Library name: WIF1-4w_snRNA
10x Genomics


title: Retina, 2 weeks AVI group, ATAC

description:
Library name: WIF1-2w_snATAC
10x Genomics


title: Retina, 2 weeks AVI group, GEX

description:
Library name: WIF1-2w_snRNA
10x Genomics


title: Bleomycin-induced senescent human primary stromal cells, biol rep 2

description:
Library name: Sample 41
Column name in PSC27_gene_count.txt: BLEO-2


title: RLN, replicate 2, 5prime, cohort 2

description: Library name: cohort2_RLN2


title: Proliferative human primary stromal cells, biol rep 3

description:
Library name: Sample 39
Column name in PSC27_gene_count.txt: CTRL-3


title: Retina, Control group, ATAC

description:
Library name: Ctrl_snATAC
10x Genomics

value: Naïve


title: Proliferative human primary stromal cells, biol rep 2

description:
Library name: Sample 38
Column name in PSC27_gene_count.txt: CTRL-2


title: Bleomycin-induced senescent human primary stromal cells, biol rep 1

description:
Library name: Sample 40
Column name in PSC27_gene_count.txt: BLEO-1


title: Proliferative human primary stromal cells, biol rep 1

description:
Library name: Sample 37
Column name in PSC27_gene_count.txt: CTRL-1


title: Retina, Control group, GEX

description:
Library name: Ctrl_snRNA
10x Genomics


title: ROI.065.CD45

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description:
Library name: DSP-1001660011191-D-H01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 065 | CD45

data_processing:
Raw count data were processed and normalized using the R package GeoMxTools (GeoMx_NGS_Pipeline_2.3.3.10). Details on thresholds, settings, and normalization are provided in Supplementary Table 11 of the original article.
Assembly: GRCh38.p13
Supplementary files format and content: Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: normalized gene counts
Library strategy: Spatial Transcriptomics

source_name: HGSOC, FFPE

growth_protocol: A tissue microarray (TMA) comprising 55 cores (2 mm diameter each) from non-tumorous adjacent stroma (n = 10), ovarian cancer (n = 29), and omental metastases (n = 16) was constructed using samples from 30 patients with high-grade serous ovarian cancer (HGSOC).

extract_protocol:
mRNA expression in FFPE tissues was measured using the GeoMx Human Whole Transcriptome Atlas (NanoString, GMX-RNA-NGS HuWTA-4), which targets 18,000 protein-coding genes via UV-cleavable oligonucleotide barcodes. Probe hybridization and immunofluorescent staining were performed according to the GeoMx FFPE slide preparation protocol. Briefly, the slide was baked overnight at 37°C, followed by deparaffinization, rehydration, target retrieval, and proteinase K (0.1 μg/mL) treatment. After post-fixation, in situ probe hybridization was performed overnight. Morphology markers used for immunofluorescent staining included: pan-cytokeratin (pan-CK; Novus Biologicals, NBP2-33200AF532, AF532, 1:40), CD45 (NBP2-34528AF594, AF594, 1:20), CD163 (Abcam, ab218294, AF647, 1:100), and SYTO 13 nuclear stain (NanoString, 121300303, FITC, 1:10). Slides were scanned at 20x magnification using the GeoMx Digital Spatial Profiler. Regions of interest (ROIs) were selected by a pathologist based on morphology marker staining, guided by H&E staining to exclude necrotic areas and big vessels. ROIs were subdivided into areas of interest (AOIs), and only those containing ≥50 cells based on manual counting were included. Four AOI types were collected: (1) panCK+ cancer epithelium, (2) CD163+ monocytes/macrophages, (3) CD45+ CD163- immune cells, and (4) stroma (panCK- CD163- CD45-). Oligonucleotide barcodes from AOIs were collected into 96-well plates via UV ablation.
Subsequent PCR amplification, pooling, quality control, and sequencing were conducted following the GeoMx DSP-NGS protocol. Libraries were purified using two rounds of Ampure XP magnetic beads (1.2:1 bead-to-library ratio) with the HighPrep PCR Clean-up System (MAGBIO, AC-60500), then sequenced on an Illumina NovaSeq PE50 flow cell at a depth of 100x/μm².

treatment_protocol: All included patients were treatment naiive.

value: HGSOC, FFPE

value: chemotherapy-naïve

tag: roi

tag: nanostring id

tag: sample location

value: omentum


title: Retina, ST, bio rep3, frame3

description:
Library name: TX001-3
10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm 10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: layer.tif: image of tisse and spots
Supplementary files format and content: json: scalefactors in json format
Supplementary files format and content: Spatial Ranger output files: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

extract_protocol:
The fresh frozen posterior eyes were embedded in the OCT compound, the tissues were cryosectioned and placed on the Visium Spatial Slides.
Library construction was performed according to the standard Visium workflow.


title: ROI.064.CD45

description:
Library name: DSP-1001660011191-D-G12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 064 | CD45


title: Retina, ST, bio rep2, frame2

description:
Library name: TX001-2
10x Genomics


title: Retina, ST, bio rep1, frame1

description:
Library name: TX001-1
10x Genomics


title: ROI.063.Cancer Cells

description:
Library name: DSP-1001660011191-D-G10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 063 | Cancer Cells

value: Cancer Cells


title: ROI.063.Stroma

description:
Library name: DSP-1001660011191-D-G11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 063 | Stroma

value: Stroma


title: Retina, ST, bio rep4, frame4

description:
Library name: TX001-4
10x Genomics


title: ROI.063.CD45

description:
Library name: DSP-1001660011191-D-G09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 063 | CD45


title: ROI.063.CD163

description:
Library name: DSP-1001660011191-D-G08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 063 | CD163


title: Bleomycin-induced senescent human primary stromal cells, biol rep 3

description:
Library name: Sample 42
Column name in PSC27_gene_count.txt: BLEO-3


title: UL1

city: Oklahoma City

first: Jie

last: Wu

state: OK

address: 975 NE 10th Street

department: Stephenson Cancer Center

institute: University of Oklahoma Health Sciences Center

data_processing:
Sample QC
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by 2nd strand cDNA synthesis.
Library was checked with Qubit and real-time PCR for quantification and bioanalyzer
Sequencing using  Illumina platform (NoveSeq PE150 (6 G raw data per sample)
Bioinformatics analysis pipeline: data quality control (perl scripts), readsmapping to reference genome (Hisat2 v2.05), quantification of gene expression level (featureCounts v1.5.0-p3), differential expression analysis (DESeq2)
Assembly: mm10
Supplementary files format and content: a tab-delimited text file include FPKM values for all samples

source_name: gastrocnemius

growth_protocol: Mice with or without HT1080 tumors

extract_protocol:
Female ICR SCID mice with or without s.c. HT1080 tumors were treated with vehicle while female ICR SCID mice with s.c. HT1080 tumors were treated with selpercatinib (30 mg/kg, once a day, oral gavage) for 19 days. Total RNA was isolated from hindlimb gastrocnemius muscle and processed for RNA-seq
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by 2nd strand cDNA synthesis, end repair and A-tailing, adapter ligation, size selection, PCR amplification, and purification.

treatment_protocol: tumor-free mice or tumor-bearing mice treated with vehicle, tumor-bearing mice treated with selpercatinib

value: gastrocnemius

value: skeletal muscle

tag: group

value: TL

value: tumor/selpercatinib


title: UL4


title: ROI.062.Cancer Cells

description:
Library name: DSP-1001660011191-D-G06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 062 | Cancer Cells


title: ROI.062.Stroma

description:
Library name: DSP-1001660011191-D-G07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 062 | Stroma


title: UV8

value: TV

value: tumor/vehicle


title: ROI.062.CD45

description:
Library name: DSP-1001660011191-D-G05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 062 | CD45


title: UL5


title: UV4


title: ROI.061.Stroma

description:
Library name: DSP-1001660011191-D-G03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 061 | Stroma


title: ROI.062.CD163

description:
Library name: DSP-1001660011191-D-G04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 062 | CD163


title: ROI.061.Cancer Cells

description:
Library name: DSP-1001660011191-D-G02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 061 | Cancer Cells


title: UV3


title: UN6

value: NTV

value: vehicle


title: ROI.061.CD45

description:
Library name: DSP-1001660011191-D-G01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 061 | CD45


title: UN5


title: ROI.061.CD163

description:
Library name: DSP-1001660011191-D-F12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 061 | CD163


title: UN3


title: ROI.060.Stroma

description:
Library name: DSP-1001660011191-D-F11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 060 | Stroma

value: ovary


title: UN2


title: ROI.060.Cancer Cells

description:
Library name: DSP-1001660011191-D-F10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 060 | Cancer Cells


title: ko_starv3

first: Samie

last: Jaffrey

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
Library quality was first analyzed using MultiQC 1.14. Adaptors were trimmed using TrimGalore-0.6.9 with --stringency 3 and library quality was again assessed using MultiQC 1.14. The data was then analyzed using the slamdunk all function of the analytical suite SLAM-DUNK 0.4.3 with the default parameters for mapping, quality filtering, and single nucleotide polymorphism identification. The reference genome hg38 and mm10 was used for mapping and the subsequent analysis. PCR duplicates in the quality filtered reads were collapsed using alleyoop collapse function of SLAM-DUNK 0.4.3. The 4sU conversion was further assessed using alleyoop rates, alleyoop tccontext, and alleyoop snpeval functions with the default parameters. alleyoop utrrates was used with a bed file of all exons of each mRNA to analyzed 4sU conversion rates per mRNA. The quality filtered and PCR duplicate-collapsed mapped reads were further analyzed using GRAND-SLAM 2.0.7b with the default parameters to quantify read counts and perform statistical analysis to infer the ratio of transcripts for each gene that originate from pre-4sU labeling and post labeling. The results from GRAND-SLAM 2.0.7b was used to calculate mRNA half-life using grandR 0.2.2.
Assembly: mm10
Supplementary files format and content: The processed data file contains the half-life measurement for each gene.

source_name: MEF

growth_protocol: MEFs were grown at 37°C in 5% CO2 using DMEM (ThermoFisher, 11995065) supplemented with 10% FBS and 10 U/mL penicillin-streptomycin (ThermoFisher, 15140122).  Cells were passaged every 3-4 days using with TrypLE Express (ThermoFisuer, 12604039) according to the manufacturer’s instructions.

extract_protocol:
Total RNA was collected using Qiagen RNeasy Mini kit RLT buffer (Qiagen, 74104) supplemented with 1% 𝛽-mercaptoethanol (BME).  Cells were lysed by passing through a 22-gauge needle, and RNA was isolated following the manufacturer’s instruction with RPE buffer supplemented with 1% BME.
10 µg total RNA was treated with 2,2,2-trifluoroethylamine (TFEE) and sodium periodate (NaIO4) at 45 °C for 1 h to convert 4sU to N4-trifluoroethylcytosine.  RNA was then purified twice using RNAClean beads (Beckman Coulter, A63987). 1 µg of treated RNA was used for RNA-seq library preparation using NEBNext®rRNA Depletion Kit(NEB, E6310X) and NEBNext®Ultra™II Directional RNA Library Prep Kit (NEB, E7760L).  Library quality was assessed on Agilent TapeStation4200 using High Sensitivity DNA ScreenTape (Agilent, 5067-5584).  Library was quantified on Qubit4 Fluorometer using Qubit 1X dsDNA HS Assay Kit (ThermoFisher, Q33231).

treatment_protocol: Cells were washed with PBS for three times, and then incubated in amino acid replete or amino acid-depleted media for 3 h with 500 µM 4-thiouridine (4sU, SigmaAldrich, T4509).

value: MEF

value: Mettl3 knockout

value: amino acid-depleted media with 4sU


title: UL7


title: ROI.060.CD45

description:
Library name: DSP-1001660011191-D-F09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 060 | CD45

value: HGSOC, FFPE


title: ROI.060.CD163

description:
Library name: DSP-1001660011191-D-F08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 060 | CD163

value: chemotherapy-naïve


title: ROI.059.Stroma

description:
Library name: DSP-1001660011191-D-F07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 059 | Stroma

value: omentum


title: ko_ctrl3

value: complete media with 4sU


title: ko_starv1


title: UV6


title: ROI.059.CD163

description:
Library name: DSP-1001660011191-D-F05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 059 | CD163


title: ko_ctrl2


title: wt_starv3

value: wild-type


title: ROI.059.Cancer Cells

description:
Library name: DSP-1001660011191-D-F06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 059 | Cancer Cells

value: Cancer Cells


title: ko_ctrl1


title: ROI.058.Cancer Cells

description:
Library name: DSP-1001660011191-D-F03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 058 | Cancer Cells


title: ROI.058.Stroma

description:
Library name: DSP-1001660011191-D-F04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 058 | Stroma

value: Stroma


title: ROI.057.Stroma

description:
Library name: DSP-1001660011191-D-F02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 057 | Stroma


title: wt_starv1


title: ROI.057.Cancer Cells

description:
Library name: DSP-1001660011191-D-F01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 057 | Cancer Cells


title: ROI.057.CD45

description:
Library name: DSP-1001660011191-D-E12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 057 | CD45


title: wt_ctrl3


title: wt_ctrl1


title: wt_ctrl2


title: ROI.057.CD163

description:
Library name: DSP-1001660011191-D-E11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 057 | CD163


title: ROI.056.Stroma

description:
Library name: DSP-1001660011191-D-E10
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 056 | Stroma


title: cKO_DSS [GA40621 scRNA-seq]

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 50+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene - cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: colon

value: 7AAD-EpCAM- lamina propria cells

value: Pdgfra-cre; Otud3 f/f


title: ROI.056.Cancer Cells

description:
Library name: DSP-1001660011191-D-E09
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 056 | Cancer Cells


title: ko_starv2


title: Otud3_ff_DSS [GA40620 scRNA-seq]

value: Otud3 f/f


title: ROI.055.Stroma

description:
Library name: DSP-1001660011191-D-E07
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 055 | Stroma


title: ROI.056.CD163

description:
Library name: DSP-1001660011191-D-E08
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 056 | CD163


title: ROI.055.Cancer Cells

description:
Library name: DSP-1001660011191-D-E06
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 055 | Cancer Cells


title: T727_nhr-66_No_traps_30min_rep3

city: Nankang, Taipei

first: Hung-Che

last: Lin

address: 128 Academia Road, Section 2

country: Taiwan

institute: Academia sinica

description: Library name: Sample6

data_processing:
we conducted quality control using FastQC
The STAR was employed for alignment of sequencing reads to the reference genome, C. elegans (PRJNA13758) from WormBase WS273, and subsequent mapping
RSEM facilitated accurate quantification of gene and isoform abundances.
For normalization of gene counts, we employed edgeR (3), implementing a sophisticated procedure involving DGEList object creation, stringent filtering based on count and repeat thresholds, and subsequent normalization.
Assembly: PRJNA13758
Supplementary files format and content: tsv files with all the counts for all samples

source_name: whole organism

growth_protocol: C. elegans (wild-type N2 and nhr-66 STOP-IN mutants) were cultured to the late L4 stage under standard conditions with OP50 E. coli as the food source. Arthrobotrys oligospora was grown on 9-cm agar plates for 5 days to establish non-trapping cultures.

extract_protocol:
Total RNA was extracted from lyophilized samples via a Trizol-chloroform based protocol
Library preparation for total RNA samples (Genomic Core Facility, Institute of Molecular Biology, Academia Sinica) were carried out using the Illumina TruSeq stranded mRNA library preparation kit.

treatment_protocol: Late L4 nematodes were transferred to A. oligospora plates and exposed for 30 minutes under non-trapping conditions. After exposure, nematodes were washed twice in M9 buffer to remove residual fungi and bacteria.

value: whole organism


title: ROI.055.CD163

description:
Library name: DSP-1001660011191-D-E05
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 055 | CD163


title: wt_starv2


title: 1_ff [GA35464 scRNA-seq]

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene - cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 3' Reagent Kits User Guide.

value: EpCAM-CD45-CD31-gp38+ stromal cells


title: T727_nhr-66_No_traps_30min_rep1

description: Library name: Sample4


title: 2_ff_cre [GA35465 scRNA-seq]


title: T727_nhr-66_No_traps_30min_rep2

description: Library name: Sample5


title: ROI.053.Stroma

description:
Library name: DSP-1001660011191-D-E02
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 053 | Stroma

value: ovary


title: ROI.054.Stroma

description:
Library name: DSP-1001660011191-D-E04
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 054 | Stroma


title: ROI.054.Cancer Cells

description:
Library name: DSP-1001660011191-D-E03
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 054 | Cancer Cells


title: ROI.053.Cancer Cells

description:
Library name: DSP-1001660011191-D-E01
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 053 | Cancer Cells


title: notrap_30m_rep3

description: Library name: Sample3

value: Bristol


title: ROI.053.CD45

description:
Library name: DSP-1001660011191-D-D12
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 053 | CD45


title: notrap_30m_rep1

description: Library name: Sample1


title: ROI.053.CD163

description:
Library name: DSP-1001660011191-D-D11
Column name in Heide_et_al_2025_BioQC_Norm_Negative_control_Q3.xlsx: 20230424-EL-Janna-1S-MTA-2023-02 | 053 | CD163