title: RNAseq data from intratumoral CD45-EPCAM+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 6

data_processing:
Sequencing read alignment and quantification and differential gene expression analysis was performed in the Bluebee Genomics Platform, a cloud-based service provider (www.bluebee.com). Briefly, reads are first trimmed with bbduk from BBTools (Bushnell B., BBMap, https://sourceforge.net/projects/bbmap/) to remove adapter sequences and polyA tails.
Assembly: Trimmed reads are aligned to the GRCm38/mm10 genome assembly with STAR v 2.5.
Supplementary files format and content: Read counting is performed with HTSeq

source_name: Breast tumor

growth_protocol: All animal experiments were performed in the CNIO (Spanish National Cancer Research Centre) in accordance with protocols approved by the Research Ethics and Animal Welfare Committee on Animal Experimentation of the Instituto de Salud Carlos III (PROEX 387/15 and PROEX 206.7/21). Experiments were performed in accordance with the guidelines stated in the International Guiding Principles for Biomedical Research Involving Animals developed by the Council for International Organizations of Medical Sciences. Mice were bred at the CNIO Animal Facility. Mouse strains were maintained under specific pathogen-free conditions at the CNIO Animal Facility. Animals were kept in a climate-controlled environment (22±2ºC) with cycles of 12h light/dark and with ad libitum access to food and water.

extract_protocol:
Tumors were harvested, minced and dissociated with Tumor Dissociation Kit enzymes (Miltenyibiotec, #130-096-730) and incubated in gentleMACS C tubes (Miltenyibiotec, #130-093-237) on gentleMACS™ Octo Dissociator (Miltenyibiotec, #130-095-937) using 37C_m_TDK_1 programme. Then, 10% FBS DMEM medium were added to stop enzyme reaction and cell suspension was passed through a 40µm strainer. Next, centrifugation was performed at 300g, 5min, 4ºC and cell pellet was resuspended in RBC 1X Lysis buffer (eBioscience, #00-4333-57). After washing with 1x PBS, cell suspension was resuspended in Flow cytometry staining (FACS) buffer (PBS, 1% Bovine Serum Albumin, 1% FBS, 0.01% Sodium Azide) and used for cell staining and FACS sorting. CD45-EPCAM+ cells were sorted using BD Influx directly into RLT Lysis buffer. Then, RNA was extracted using RNAeasy Mini Plus Kit (Qiagen, #74134) and quantified in LabChip GX Touch Nucleic Acid Analyzer (PerkinElmer). RNA quality was determined by Agilent's 2100 Bioanalyzer Lab-Chip technology. Only samples with RNA Integrity Number (RIN)>7 was used for sequencing.
Variable amounts of total RNA samples, with RNA Quality score of 7.0 on average (PerkinElmer LabChip analyzer), were analysed. They were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) with a UMI Second Strand Synthesis module. Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Random primers feature a 6 nt long Unique Molecular Identifier 5' tag. Primers from both steps contain, in addition, Illumina-compatible sequences. Libraries are completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.{This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}

treatment_protocol: Anti-VEGFA clone B20-4.1.1 was prepared in 1x PBS and administered at 5 mg/kg intraperitoneally twice per week for 6 weeks.

value: Breast tumor

value: FACS sorted CD45-EPCAM+ cells

value: tumor cells

value: MMTV-PyMT mice (FVB/N-Tg (MMTV-PyVT)634Mul/J)


title: QAG359-QAG360-QAG365, scRNAseq

status: Public on May 05 2026

type: SRA

city: Madrid

first: Jose Luis

last: Ruiz-Sepulveda

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Translational Research

country: Spain

institute: CNIO

description: 10x Genomics; CMO-OLIGOS for each of mouse QAG359:1-2-3-4, QAG360:5-6-7-8, QAG365:9-10-11-12

library_source: transcriptomic single cell

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina RTA software  (RTA v2). Conversion of BCL files to FASTQ format was performed with "cellranger mkfastq" (10xGenomics), a wrapper for "bcl2fastq" (Illumina).
The bollito pipeline (García-Jimeno et al., 2022) was used to perform the initial steps of the single-cell analysis, checking cell-level quality control by removing outlier cells based on read counts, number of expressed genes and the percentage of mitochondrial counts distributions. All of its parameters were set as default (random seed:4848, minimum number of genes detected per cell: 500, maximum number of genes detected per cell: 100000, minimum percentage of reads mapping to mitochondrial gene: 8, minimum percentage of reads mapping to the ribosomal genome: 40).
The samples were merged into a single object.
Seurat v4.3.0 was employed to exclude cells with low quality (those with fewer than 2,500 UMIs) or cells identified as potential multiplets (those with more than 27500 UMIs). Only cells expressing a minimum of 50 house-keeping genes from a curated list specific to quality control (Tirosh et al., 2016) were retained for analysis.
The expression levels were normalized to log transcripts per 10,000 cells (TP10K).
Variable genes were identified with FindVariableFeatures, selecting 2,500 genes using the ‘vst’ method. The data was then  scaled with ScaleData, followed by a PCA conducted with RunPCA. We utilized RunUMAP for the UMAP embedding, opting for 16 dimensions based on an elbow plot, while keeping the remaining parameters at their default settings.
Cell annotation was conducted using SingleR v2.0.0. using as the ImmGen mouse reference dataset obtained from the previously mentioned package with its ImmGenData() function. Cells labels were kept to its general names (i.e., 'T cell (T.4FP3+25+)' to just 'T cell' )
Assembly: mm10
Supplementary files format and content: Samples' cell barcodes, genes/features and  metadata (supplementary) as tab-separated values files
Supplementary files format and content: Samples' expression values as matrix files

molecule: total RNA

organism: Mus musculus

source_name: Breast cancer

growth_protocol: All animal experiments were performed in the CNIO (Spanish National Cancer Research Centre) in accordance with protocols approved by the Research Ethics and Animal Welfare Committee on Animal Experimentation of the Instituto de Salud Carlos III (PROEX 387/15 and PROEX 206.7/21). Experiments were performed in accordance with the guidelines stated in the International Guiding Principles for Biomedical Research Involving Animals developed by the Council for International Organizations of Medical Sciences. MMTV-PyMT mice (FVB/N-Tg (MMTV-PyVT)634Mul/J) and BALB/c were bred at the CNIO Animal Facility. Mouse strains were maintained under specific pathogen-free conditions at the CNIO Animal Facility. Animals were kept in a climate-controlled environment (22±2ºC) with cycles of 12h light/dark and with ad libitum access to food and water.

extract_protocol:
Tumors were extracted from mice and dissagregated using Tumor Dissociation Kit, mouse (Miltenyi, #130-096-730). Single cell tumor cell suspension were stained with DAPI and DAPI- cells were sorted in BD-FACS-ARIA into PBS. After that, three different tumors were multiplexed using oligo labeling was by 3’CellPlex Kit Set A (10xGenomics, cat no. 1000261). Next, a secondary sort of DAPI- cells was executed with the BD FACS ARIA to further enrich for viable cells. Multiplexed-single-cell suspensions sourced from three distinct tumors were processed together into one sample, which was drop encapsulated with Chromium device (10xGenomics). Finally, it was sequenced in Illumina Nextseq 550 (with v2.5 reagent kit)
Cell multiplexed samples were processed with the "Chromium Next GEM Single Cell 3' Kit v3.1" (10xGenomics  PN-1000268). Generation of gel beads in emulsion (GEMs), barcoding, post GEM-RT clean-up, cDNA amplification and both 3’ Gene Expression and Cell Multiplexing library construction were all performed as recommended by the manufacturer.

treatment_protocol: Treatments with the different drugs were started at 7th weeks of age of MMTV-PyMT mouse models. Anti-VEGFA clone B20-4.1.1 or Isotype mouse IgG2a clone C1.18.4 were prepared in 1x PBS and administered at 5 mg/kg intraperitoneally twice per week during 6 weeks

tag: tissue

value: Breast cancer

tag: treatment


title: Patient 2 Healthy

city: Bordeaux

first: Hamid-Reza

last: Rezvani

address: 2 Rue Dr Hoffmann Martinot

country: France

institute: Bordeaux Institute of Oncology (BRIC)

description: Library name: 10-S2203938-SAIN

library_source: transcriptomic

data_processing:
The resulting FASTQ files were processed towards a gene expression count matrix using the HTG EdgeSeq Reveal Software. The quality control (QC) of NGS data was assessed prior analysis to ensure the data robustness.
Assembly: hg38
Supplementary files format and content: File name is "21019221207_HTGseq_rawdata.xlsx". File contains the count matrix. Sample names allow the reconstruction of metadata regarding specimen origin (SAIN = heatlhy skin, PRE = Actinic keratosis/In situ cSCC, TUM = tumor).

organism: Homo sapiens

source_name: Healthy skin

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) skin specimens were obtained from a cohort of eight patients with cutaneous squamous cell carcinoma (cSCC). For each patient, tissue blocks contained histologically distinct regions corresponding to (i) healthy skin, (ii) actinic keratosis (AK) and/or in situ cSCC, and (iii) advanced invasive cSCC. Hematoxylin and eosin–stained sections were reviewed by a board-certified dermatopathologist to confirm diagnoses and to guide region selection. The three regions of interest (healthy, AK/in situ cSCC, and advanced cSCC) were macro-dissected separately from 5-µm FFPE unstained sections using annotated reference slides. Care was taken to minimize cross-contamination between regions. Sections were then subjected to lysis and Proteinase K treatment for 20min at 56°C. After protein inactivation, DNase digestion was performed at 37°C for 30 min and the quantitative nuclease protection assay was run using the HTG EdgeSeq Processors. Adapters and sample tags were finally added in a PCR amplification.
The resulting libraries were sequenced using on an Illumina NextSeq 2000 (Flow cell P2 - 100 cycles).

value: Healthy skin


title: QAG364-QAG397-QAG404, scRNAseq

description: 10x Genomics; CMO-OLIGOS for each of mouse QAG364:1-2-3-4, QAG397:5-6-7-8, QAG404:9-10-11-12

value: IgG2a isotype


title: QAG356-QAG357-QAG348, scRNAseq

description: 10x Genomics; CMO-OLIGOS for each of mouse QAG348:1-2-3-4, QAG356:5-6-7-8, QAG357:9-10-11-12


title: QAG432-QAG452-QAG465, scRNAseq

description: 10x Genomics; CMO-OLIGOS for each of mouse QAG432:1-2-3-4, QAG452:5-6-7-8, QAG465:9-10-11-12


title: RNAseq data from intratumoral CD45-EPCAM+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 4

tag: cell line

tag: cell type

tag: genotype


title: RNAseq data from intratumoral CD45-EPCAM+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 5


title: RNAseq data from intratumoral CD45-EPCAM+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 3


title: RNAseq data from intratumoral CD45-EPCAM+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 2


title: Spleen_FADS3_2

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

country: USA

institute: Dana Farber Cancer Institute

description: Library name: 6AJV_E2

data_processing:
The sequences in raw FASTQ files were aligned to the EMSEMBL GRCm38.p6 mouse reference transcriptome105 and quantified using Kallisto (v0.46.1).
Assembly: GRCm38
Supplementary files format and content: Gzipped kallisto output

source_name: Spleen

growth_protocol: Adult mice were used on a C57Bl/6J background (The Jackson Laboratory, #000664). B6(Cg)-Zbtb46tm2Mnz/J (The Jackson Laboratory, #026850) were bred to AHR-Flox mice to generate Zbtb46CreAHRfl (AHRZBTB) and KLF4-Flox mice to generate Zbtb46CreKLF4fl (KLF4ZBTB). Ahrtm3.1Bra/J (AHR-Flox) mice were purchase from Jackson laboratory (The Jackson Laboratory, #006203)96. KLF4-Flox and FADS3KO mice were kingly donated by Dr. Florent Ginhoux and Dr. J. Thomas Brenna, respectively. C57BL/6-Tg (Tcra2D2, Tcrb2D2)1Kuch/J (The Jackson Laboratory, #006912) were used for co-coculture with BMDCs. B6.D2N-Ahrd/J (The Jackson Laboratory, #002921) were used for in vitro experiments38,39. B6(cg)-Zbtb46tm1(BBEGF)Mnz/J (The Jackson Laboratory, #019506) were used for generate FADS3 chimeras. Tg(CAG-Kaede)15Kgwa mice on a C57Bl/6J background were obtained from RIKEN BRC, Japan. All mice were housed in a conventional, pathogen-free facility at the Brigham and Women’s Hospital (BWH) – Harvard Medical School (HMS) in sterile autoclaved cages with irradiated food and acidified, autoclaved water. Mouse handling and weekly cage changes were performed by investigators or mouse husbandry staff wearing sterile gowns, masks and gloves in a sterile biosafety hood. All experiments were reviewed and approved by Institutional Animal Care and Use Committee (IACUC) at Brigham and Women’s Hospital – Harvard Medical School.

extract_protocol:
Sorted cells were lysed on extraction buffer and RNA was isolated using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific, #KIT0204).
RNA was suspended in 10 µL of nuclease free water at a concentration of 0.5-1 ng/µL and sequenced using or SMARTSeq2104 at the Broad Institute.

value: Spleen

value: Dendritic Cells

value: FADS3 Knockout


title: Spleen_WT_4

description: Library name: 6AJV_D12

value: WT


title: Spleen_WT_2

description: Library name: 6AJV_D10


title: Spleen_WT_3

description: Library name: 6AJV_D11


title: Spleen_FADS3_3

description: Library name: 6AJV_E3


title: Spleen_FADS3_4

description: Library name: 6AJV_E4


title: Spleen_FADS3_1

description: Library name: 6AJV_E1


title: Spleen_WT_1

description: Library name: 6AJV_D9


title: CNS_FADS3_4

description: Library name: 6AJV_D8

source_name: CNS

value: CNS


title: CNS_FADS3_3

description: Library name: 6AJV_D7


title: RNAseq data from intratumoral CD45-EPCAM+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 1


title: RNAseq data from intratumoral CD45+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 7

extract_protocol:
Tumors were harvested, minced and dissociated with Tumor Dissociation Kit enzymes (Miltenyibiotec, #130-096-730) and incubated in gentleMACS C tubes (Miltenyibiotec, #130-093-237) on gentleMACS™ Octo Dissociator (Miltenyibiotec, #130-095-937) using 37C_m_TDK_1 programme. Then, 10% FBS DMEM medium were added to stop enzyme reaction and cell suspension was passed through a 40µm strainer. Next, centrifugation was performed at 300g, 5min, 4ºC and cell pellet was resuspended in RBC 1X Lysis buffer (eBioscience, #00-4333-57). After washing with 1x PBS, cell suspension was resuspended in Flow cytometry staining (FACS) buffer (PBS, 1% Bovine Serum Albumin, 1% FBS, 0.01% Sodium Azide) and used for cell staining and FACS sorting. CD45+ cells were sorted using BD Influx directly into RLT Lysis buffer. Then, RNA was extracted using RNAeasy Mini Plus Kit (Qiagen, #74134) and quantified in LabChip GX Touch Nucleic Acid Analyzer (PerkinElmer). RNA quality was determined by Agilent's 2100 Bioanalyzer Lab-Chip technology. Only samples with RNA Integrity Number (RIN)>7 was used for sequencing.
Variable amounts of total RNA samples, with RNA Quality score of 7.0 on average (PerkinElmer LabChip analyzer), were analysed. They were processed into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) with a UMI Second Strand Synthesis module. Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Random primers feature a 6 nt long Unique Molecular Identifier 5' tag. Primers from both steps contain, in addition, Illumina-compatible sequences. Libraries are completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.{This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}

tag: population

value: FACS sorted CD45+ cells

value: Immune cells


title: CNS_FADS3_2

description: Library name: 6AJV_D6


title: RNAseq data from intratumoral CD45+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 6


title: dissected zebrafish intestines, WT+het from meis1b whole gene deletion heterozygous incross

city: Bethesda

first: Jeffrey

middle: Allen

last: Farrell

state: MD

address: 6 Center Drive (6A/1A06)

department: Division of Developmental Biology

institute: National Institute of Child Health and Human Development

description:
Library name: Sample 1_meis1b WT+het
10x Genomics

data_processing:
Alignment of sequencing reads and processing into a digital gene expression matrix was performed using Cell Ranger version 9.0.1, including the aligner STAR version 2.5.1b, with standard parameters. The data was aligned and quantitated against a custom reference index using Ensembl GRCz11 release 99 (January 2020) genomic FASTA, and using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2, published in Lawson et al. eLife 2020.
Assembly: Ensembl GRCz11 release 99 (January 2020)
Supplementary files format and content: Tab separated values files and matrix files

organism: Danio rerio

source_name: dissected intestines

extract_protocol:
Dissected intestinal tissues were collected in 400 µL of sterile Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES, pH 7.0) in 1.5 mL Eppendorf tubes. For each scRNA-seq experiment, protease solution (0.25% trypsin, 1 mM EDTA in 1× PBS, pH 8.0; Sigma-Aldrich T4549) was prepared fresh, and collagenase P (100 mg/mL in Hank’s Balanced Salt Solution; Sigma-Aldrich H9269 and 11213865001) was thawed on ice. For each sample, 1.2 mL of protease solution was added to a well of a 24-well plate, which was then incubated at 28 °C to equilibrate. The Ringer’s solution from each dissected sample (WT and mutant) was reduced to 100 µL, and the intestines were gently abraded by pipetting five times with a P200 set to 80 µL. Samples were rinsed by adding 1 mL fresh Ringer’s solution, allowing tissue to settle, and removing all but 100 µL. The intestines, along with the remaining Ringer’s, were then transferred into the equilibrated protease solution, followed by addition of 30 µL collagenase P per well. After swirling to mix (final volume 1.33 mL per well), plates were incubated at 28 °C and dissociation was monitored under a stereomicroscope. Every 5 minutes, samples were pipetted slowly 20 times with a P1000. After 10 minutes, each sample was passed once through a P200 by transferring from one well to another. Digestion was stopped after 20–25 minutes by adding 270 µL of 6× STOP solution (30% calf serum, 6 mM CaCl₂ in 1× PBS) and gently swirling (final volume 1.5 mL). Some small tissue fragments typically remained, but over-digestion usually reduced cell viability significantly and was avoided. Cell suspensions were then passed through a 40 µm cell strainer into 1.5 mL tubes, and each tube was flicked vigorously 20 times. Cells were spun down at 300 x g for 3 minutes at 4°C. Supernatant was removed (leaving ~ 100 L) and cells were resuspended in 1 mL chilled DMEM/F12 (0% BSA; Gibco 12500062). Cells were washed by spinning at 300 x g for 3 minutes at 4°C, removing supernatant, and resuspending cells in 1 mL chilled DMEM/F12 (0% BSA). The single cell suspension was then filtered once again through a 40 µm cell strainer into clean tube, centrifuged at 300 x g for 3 minutes at 4°C. Supernatant was removed leaving ~50 L in which the cell suspension was resuspended.
Droplet emulsions of single cell capture were generated using the 10X Genomics Chromium controller with Single Cell 3’ v3.1 consumable reagents for pbx3ay731 mutant samples, and the 10X Genomics Chromium GEM–X platform with Single Cell 3’ v4 reagents for the meis1by730 mutant samples. Single-cell suspensions were stained with acridine orange / propidium iodide (10 mL of cells + 1 mL of Logos F23001 Acridine Orange/Propidium Iodide Stain) and then examined and quantified on a Logos Luna FL automated cell counter. Samples with sufficient concentration, low multiplet rate (<5% to proceed, <4.2% on average), and high viability (>85% to proceed, >90% on average) were then loaded into the instrument. WT and mutant samples for each mutant were then loaded into two channels at normal concentrations (pbx3ay731: 18,000 cells loaded, targeting 10,000 cells recovered; meis1by730: 15,000 –18,000 cells loaded, targeting 11,000 – 13,000 cells recovered). Downstream reactions were performed in Eppendorf MasterCycler x50s Thermal cyclers. 10–12 cycles were used for cDNA amplification, and the result was inspected using Agilent D5000 ScreenTape Tapestation Assay. The remaining steps were performed according to the 10X 3’ v3.1 and 3’ v4 protocols, with 8–12 cycles used for sample index PCR, based on the concentration of amplified cDNA in the previous step. Final libraries were evaluated using Agilent D5000 ScreenTape Tapestation Assay and quantitated using a ThermoFisher Qubit 4 with dsDNA High Sensitivity (HS) reagents. Average fragment length from the Bioanalyzer and concentrations obtained from the Qubit were used to pool the WT and mutant libraries in equimolar concentrations. Libraries were then sequenced on a Novaseq 6000 Sequencing System (Illumina) using SP100-cycle full flowcells with 28 bases for Read 1, 10 bases for i7 index, 10 bases for i5 index, and 90 bases for Read 2. PhiX control library was spiked in at 1%. Reads obtained from these runs were used for downstream analyses.

value: dissected intestines

value: intestinal cells, smooth muscle, enteric neurons, immune cells, progenitors


title: dissected zebrafish intestines, WT from pbx3a whole gene deletion heterozygous incross

description:
Library name: Sample 3_pbx3a WT
10x Genomics


title: dissected zebrafish intestines, homozygote mutants from pbx3a whole gene deletion heterozygous incross

description:
Library name: Sample 3_pbx3a_mutant
10x Genomics

value: mutant


title: CNS_FADS3_1

description: Library name: 6AJV_D5


title: RNAseq data from intratumoral CD45+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 5

value: Breast tumor


title: CNS_WT_4

description: Library name: 6AJV_D4


title: RNAseq data from intratumoral CD45+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 4


title: dissected zebrafish intestines, homozygote mutants from meis1b whole gene deletion heterozygous incross

description:
Library name: Sample 2_meis1b mutant
10x Genomics


title: CNS_WT_3

description: Library name: 6AJV_D3


title: RNAseq data from intratumoral CD45+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 3


title: Low-P-B

city: Tucson

first: ALBA

last: FILELLA FILELLA LOPEZ DE LAMADRID

state: Arizona

address: 1007 E Lowell St.

department: MCB

institute: The University of Arizona

description: Library name: EFB_3-B

data_processing:
Raw FASTQ reads (paired-end, R1/R2) were quality-checked using FastQC and adapter- and quality-trimmed with Trimmomatic. Reads were aligned to the Synechococcus sp. WH8102 reference genome (NCBI RefSeq NC_009481.1) using Bowtie2, with alignment metrics assessed for concordant, discordant, and unaligned reads. Gene-level counts were generated using featureCounts from the Rsubread Bioconductor package, and counts were subsequently normalized for downstream analysis and quality-checked across replicates.
Assembly: Synechococcus sp. WH8102 reference genome, NCBI RefSeq accession NC_009481.1.
Supplementary files format and content: Processed data files include tab-delimited gene-level count tables, normalized expression values (TPM/FPKM), and metadata linking samples to phosphate treatment conditions and biological replicates.
Supplementary files format and content: Syn_EFB_deseq2_normalized_counts_annotated.xlsx: Normalized gene-level counts were generated using DESeq2. Raw counts obtained from featureCounts were normalized using DESeq2’s median-of-ratios method (size factor normalization) to account for differences in sequencing depth and RNA composition across samples. The dataset includes gene annotations (locus_tag, gene_name, product, GO terms) alongside normalized expression values for each sample (High-P, Mid-P, Low-P conditions with biological replicates). These normalized counts are suitable for downstream exploratory analyses such as visualization, clustering, and principal component analysis, but should not be used directly for statistical testing of differential expression, which requires raw counts within the DESeq2 framework.
Supplementary files format and content: Log2 fold change (log2FC) and statistical results for pairwise comparisons of gene expression across phosphorus treatments (Low-P, Mid-P, High-P), including functional annotation and expression patterns.

organism: Parasynechococcus marenigrum WH 8102

source_name: cyanobacteria, whole cell

growth_protocol: Synechococcus sp. WH8102 cultures were grown in SN medium under controlled laboratory conditions (26°C, 12/12-h light/dark cycle at 250 μE m⁻² s⁻¹) using exponentially fed-batch (EFB) cultures. Continuous phosphate treatments were applied at three concentrations (High-P 36 µM, Mid-P 5 µM, Low-P 1 µM) with culture volumes ranging from 500–850 mL and a daily sample collection of ~100–200 mL. Culture aeration, mixing, and medium flow were maintained using peristaltic pumps controlled by a programmable microcontroller to ensure steady-state growth.

extract_protocol:
Filters containing Synechococcus sp. WH8102 cells (~700 mL culture per sample) were processed using TRIzol reagent. Cells were lysed with lysozyme and mechanically disrupted with 0.1 mm beads. RNA was extracted via phase separation with chloroform, precipitated with isopropanol, washed with 70% ethanol, and resuspended in nuclease-free water. Residual genomic DNA was removed by TURBO DNase treatment, and RNA was further purified with phenol-chloroform. RNA integrity and concentration were assessed using Nanodrop and Qubit instruments.
RNA libraries were prepared from ribosomal RNA-depleted RNA using standard protocols and sequenced by SeqCoast Genomics. Libraries were sequenced as paired-end 2 × 150 bp reads, generating approximately 12 million reads per sample on an Illumina platform.

treatment_protocol: Cultures were exposed to three steady-state phosphate regimes (High-P, Mid-P, Low-P) throughout exponential growth in EFB cultures. Samples for RNA extraction were collected at the end of the experiment, after cells had adapted to their respective phosphate conditions, with three biological replicates per treatment.

value: cyanobacteria, whole cell

value: 1 uM P


title: Mid-P-C

description: Library name: EFB_2-C

value: 5 uM P


title: Low-P-C

description: Library name: EFB_3-C


title: Mid-P-A

description: Library name: EFB_2-A


title: Low-P-A

description: Library name: EFB_3-A


title: High-P-A

description: Library name: EFB_1-A

value: 36 uM P


title: Mid-P-B

description: Library name: EFB_2-B


title: High-P-C

description: Library name: EFB_1-C


title: High-P-B

description: Library name: EFB_1-B


title: RNAseq data from intratumoral CD45+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 2

value: MMTV-PyMT mice (FVB/N-Tg (MMTV-PyVT)634Mul/J)


title: CNS_WT_1

description: Library name: 6AJV_D1


title: RNAseq data from intratumoral CD45+ cells from B20-4.1.1 treated MMTV-PyMT breast tumors sample 1


title: CNS_WT_2

description: Library name: 6AJV_D2


title: Eco RNAP on Eco Genome R3

status: Public on May 04 2026

city: Dallas

first: Ping

last: Shen

state: Texas

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

description:
Library name: Nova-Eco-on-Eco-2-ERCC
E. coli RNA polymerase on E. coli genome template, replicate 3

data_processing:
Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases. cutadapt -g ^TCCGACGATCATTGATGGTGCCTACAG  --match-read-wildcards --discard-untrimmed -l 15
Processed reads were aligned to the reference genome using a standard aligner to generate strand-specific coverage profiles.
Transcriptional pausing sites were identified using a multi-round Z-score–based approach applied to strand-specific coverage data.
Terminator-associated sites were defined based on proximity to in vivo transcription termination sites.
Assembly: Escherichia coli MG1655 (NC_000913.3) and Clostridioides difficile 630 (CP010905.2)
Supplementary files format and content: not included

organism: Escherichia coli

source_name: in vitro transcription system

growth_protocol: Not applicable. In vitro transcription assays were performed using purified RNA polymerases.

extract_protocol:
RNA transcripts generated from in vitro transcription reactions were purified using standard phenol-chloroform extraction followed by ethanol precipitation.
RNA libraries were prepared using a 3′ adapter ligation-based protocol. Briefly, RNA fragments were ligated to a pre-adenylated DNA adapter using T4 RNA ligase 2 (truncated), followed by reverse transcription, circularization, and PCR amplification. Libraries were sequenced on an Illumina platform.

treatment_protocol: Purified RNA polymerases from Escherichia coli or Clostridioides difficile were incubated with DNA templates under defined in vitro transcription conditions. Where indicated, NusG was added to the reaction.

value: in vitro transcription system

value: wild type


title: Eco RNAP on Eco Genome R2

description:
Library name: Nova-Eco-on-Eco-1-ERCC
E. coli RNA polymerase on E. coli genome template, replicate 2


title: Eco RNAP on Eco Genome R1

description:
Library name: 4-Eco-on-Eco
E. coli RNA polymerase on E. coli genome template, replicate 1


title: Cdf RNAP on Eco Genome R3

description:
Library name: Nova-Cdf-on-Eco-2-ERCC
Clostridioides difficile RNA polymerase on E. coli genome template, replicate 3


title: Cdf RNAP on Eco Genome R1

description:
Library name: 2-Cdf-on-Eco
Clostridioides difficile RNA polymerase on E. coli genome template, replicate 1


title: Cdf RNAP on Eco Genome R2

description:
Library name: Nova-Cdf-on-Eco-1-ERCC
Clostridioides difficile RNA polymerase on E. coli genome template, replicate 2


title: Tibialis anterior muscle, KPC tumor-bearing, rep4

city: Gainesville

first: Andrew

middle: R

last: Judge

state: FL

address: 1275 Center Drive, Biomedical Sciences Building RM J303

institute: University of Florida

description:
Library name: K8
KPC v Sham Differential_expression_analysis_table.xlsx
KPC Differential_expression_analysis_table.xlsx

data_processing:
RNA-Seq libraries were prepared from mRNA enriched using Oligo(dT) beads with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA). Enriched mRNA was fragmented (15 min, 94 °C), and first- and second-strand cDNA synthesis was performed. cDNA fragments were end-repaired, adenylated at the 3' ends, ligated to universal adapters, indexed, and PCR-enriched. Libraries were validated on the Agilent TapeStation 4200 and quantified using a Qubit 2.0 Fluorometer and qPCR (KAPA Biosystems, Wilmington, MA). Sequencing libraries were clustered on two flowcell lanes and sequenced on an Illumina HiSeq 2000 using a 2×150 bp paired-end configuration. Image analysis and base calling were performed with Illumina Control Software, and raw .bcl files were converted to FASTQ and de-multiplexed using bcl2fastq (v2.17).  Unique gene counts were obtained with FeatureCounts from the Subread package (v1.5.2), considering only reads uniquely mapped to exons.
Assembly: GRCm38
Supplementary files format and content: xlsx files include log2 fold changes, readcounts, and padj values

source_name: Tibialis anterior muscle

growth_protocol: Pancreases of C57Bl/6J mice were surgically exposed and injected with 50 μL sterile saline containing 1.5×105 KPC cells.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal mini kit (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA)
RNA-seq

treatment_protocol: Mouse tibialis anterior skeletal muscles were dissected and immediately placed in liquid nitrogen and stored at −80 °C, then shipped as frozen samples on dry ice to Azenta Life Sciences (South Plainfield, NJ) for RNA extraction, library preparation, and RNA sequencing (RNA-Seq).

value: Tibialis anterior muscle

value: KPC tumor bearing + standard chow


title: Tibialis anterior muscle, KPC tumor-bearing, rep1

description:
Library name: K5
KPC v Sham Differential_expression_analysis_table.xlsx
KPC Differential_expression_analysis_table.xlsx


title: Tibialis anterior muscle, KPC tumor-bearing + ursolic acid, rep3

description:
Library name: K11
KPC UA Differential_expression_analysis_table.xlsx
KPC Differential_expression_analysis_table.xlsx

value: KPC tumor bearing + ursolic acid-supplemented chow


title: Tibialis anterior muscle, KPC tumor-bearing + ursolic acid, rep4

description:
Library name: K12
KPC UA Differential_expression_analysis_table.xlsx
KPC Differential_expression_analysis_table.xlsx


title: Tibialis anterior muscle, KPC tumor-bearing, rep3

description:
Library name: K7
KPC v Sham Differential_expression_analysis_table.xlsx
KPC Differential_expression_analysis_table.xlsx


title: Tibialis anterior muscle, KPC tumor-bearing + ursolic acid, rep2

description:
Library name: K10
KPC UA Differential_expression_analysis_table.xlsx
KPC Differential_expression_analysis_table.xlsx


title: Tibialis anterior muscle, Sham, non-tumor bearing, rep2

description:
Library name: K2
KPC v Sham Differential_expression_analysis_table.xlsx
KPC UA Differential_expression_analysis_table.xlsx

value: non-tumor bearing + standard chow


title: PSO-D5

city: 长沙

first: 烁琦

last: 张

address: 解放中路199号湘雅二医院有色院研究生宿舍

country: China

institute: 中南大学

description: Library name: Sample 7

data_processing:
Raw sequencing data were processed using fastp v0.23.2: adapter trimming and removal of reads <100 bp, reads with >10 N bases, or reads with >40% of bases having Q≤30.
Clean reads were aligned to the Mus musculus reference genome GRCm39 using HISAT2 v2.2.1 with default parameters (alignment rates: 97.11%-97.49%).
Gene-level raw counts were generated using featureCounts v2.0.3 from the Subread package.
Transcript abundance was quantified as TPM using StringTie v2.2.1.
Differential expression analysis was performed using DESeq2 v1.38.3 with |log2FC| ≥ 1 and p < 0.05.
Assembly: GRCm39

source_name: spleen

growth_protocol: Female BALB/c mice (6-8 weeks old) were housed under specific pathogen-free conditions with standard chow and water ad libitum, 12h light/dark cycle.

extract_protocol:
Total RNA was extracted from spleen tissue using TRIzol reagent (Invitrogen) following manufacturer's instructions. Genomic DNA was removed by DNase I treatment. RNA purity and concentration were assessed by NanoDrop 2000, and RNA integrity was verified by 1% agarose gel electrophoresis.
Poly(A)-tailed mRNA was enriched from total RNA using oligo(dT) magnetic beads. Libraries were constructed using NEBNext Ultra II RNA Library Prep Kit (NEB). The libraries are non-strand-specific (stranded: false). Paired-end sequencing (150 bp) was performed on an Illumina HiSeq platform.

treatment_protocol: For control group (Con): vehicle (petrolatum) was applied to dorsal skin and ears. For PSO-D group: imiquimod (5% cream) was applied topically to dorsal skin once daily for 5 days. For PSO-E group: imiquimod (5% cream) was applied to the ear once daily for 5 days. For IL-23 group: recombinant mouse IL-23 (1 μg per ear) was intradermally injected into the ear every other day for 7 consecutive days (total of 4 injections).

tag: strain

value: BALB/c

value: spleen

tag: Sex

value: female

value: imiquimod dorsal application

tag: batch


title: Tibialis anterior muscle, KPC tumor-bearing + ursolic acid, rep1

description:
Library name: K9
KPC UA Differential_expression_analysis_table.xlsx
KPC Differential_expression_analysis_table.xlsx


title: Tibialis anterior muscle, Sham, non-tumor bearing, rep1

description:
Library name: K1
KPC v Sham Differential_expression_analysis_table.xlsx
KPC UA Differential_expression_analysis_table.xlsx


title: Tibialis anterior muscle, Sham, non-tumor bearing, rep3

description:
Library name: K3
KPC v Sham Differential_expression_analysis_table.xlsx
KPC UA Differential_expression_analysis_table.xlsx


title: Tibialis anterior muscle, Sham, non-tumor bearing, rep4

description:
Library name: K4
KPC v Sham Differential_expression_analysis_table.xlsx
KPC UA Differential_expression_analysis_table.xlsx


title: PSO-D2

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 4


title: Con-2

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 1

value: vehicle control


title: Con-5

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 3


title: PSO-D4

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 6


title: PSO-E1

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 8

value: imiquimod ear application


title: Con-4

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 2


title: PSO-D3

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 5


title: IL23-2

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 13

value: IL-23 intradermal injection (ear)


title: PS0-E3

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 9


title: Tibialis anterior muscle, KPC tumor-bearing, rep2

description:
Library name: K6
KPC v Sham Differential_expression_analysis_table.xlsx
KPC Differential_expression_analysis_table.xlsx


title: IL23-3

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 14


title: PS0-E4

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 10


title: IL23-1

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 12


title: PS0-E5

address: 解放中路199号湘雅二医院有色院研究生宿舍

description: Library name: Sample 11


title: genomic DNA from saliva sample H167_44

type: genomic

city: University Park

first: Laura

last: Etzel

address: Health and Human Development Building

institute: Penn State

hyb_protocol: Five hundred nanograms of genomic DNA per sample was treated with sodium bisulfite using the Zymo EZ-96 DNA Methylation Kit™ (Zymo Research) following the manufacturer’s instructions. Two hundred nanograms of bisulfite-converted DNA was amplified, fragmented, and hybridized to the Illumina Infinium MethylationEPIC v2.0 BeadChip according to the manufacturer’s standard protocol.

scan_protocol: BeadChips were scanned using an Illumina iScan system following the manufacturer’s recommended scanning procedures.

data_processing: Raw Illumina IDAT files were imported into R using the Bioconductor package minfi. Detection p-values were calculated from raw red and green channel intensities using minfi::detectionP. Background correction and control-based normalization were performed using Illumina’s recommended method as implemented in minfi::preprocessIllumina (background correction enabled, control normalization). Processed beta values (proportion methylated) were extracted using minfi::getBeta. A processed data table was generated containing, for each probe (ID_REF), the processed beta value and the corresponding detection p-value for each sample.

label: cy3, cy5

molecule: genomic DNA

label_protocol: Not applicable. DNA labeling is performed enzymatically as part of the Infinium assay workflow according to the manufacturer’s protocol; no external labeling step was performed by the investigators.

extract_protocol: Saliva samples were collected via passive drool and stored according to standardized protocols. Genomic DNA was extracted from saliva using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s instructions. DNA quantity and purity were assessed using spectrophotometric methods prior to downstream processing.

value: saliva


title: genomic DNA from saliva sample H167_63


title: genomic DNA from saliva sample H167_51


title: genomic DNA from saliva sample H167_42


title: genomic DNA from saliva sample H167_61


title: genomic DNA from saliva sample H167_56


title: genomic DNA from saliva sample H167_57


title: genomic DNA from saliva sample H167_47


title: genomic DNA from saliva sample H167_52


title: genomic DNA from saliva sample H167_41


title: genomic DNA from saliva sample H167_38


title: genomic DNA from saliva sample H167_49

source_name: prenatal


title: genomic DNA from saliva sample H167_53


title: genomic DNA from saliva sample H167_35


title: genomic DNA from saliva sample H167_46


title: genomic DNA from saliva sample H167_37


title: genomic DNA from saliva sample H167_64


title: genomic DNA from saliva sample H167_58


title: genomic DNA from saliva sample H167_60


title: genomic DNA from saliva sample H167_43


title: genomic DNA from saliva sample H167_48


title: genomic DNA from saliva sample H167_55


title: genomic DNA from saliva sample H167_40


title: genomic DNA from saliva sample H167_34


title: genomic DNA from saliva sample H167_27


title: genomic DNA from saliva sample H167_29


title: genomic DNA from saliva sample H167_33


title: genomic DNA from saliva sample H167_16


title: genomic DNA from saliva sample H167_30


title: genomic DNA from saliva sample H167_15


title: genomic DNA from saliva sample H167_32


title: genomic DNA from saliva sample H167_26


title: genomic DNA from saliva sample H167_8


title: genomic DNA from saliva sample H167_21


title: genomic DNA from saliva sample H167_28


title: genomic DNA from saliva sample H167_24


title: genomic DNA from saliva sample H167_18


title: genomic DNA from saliva sample H167_20


title: genomic DNA from saliva sample H167_14


title: genomic DNA from saliva sample H167_11


title: genomic DNA from saliva sample H167_9


title: genomic DNA from saliva sample H167_19


title: genomic DNA from saliva sample H167_22


title: genomic DNA from saliva sample H167_23


title: genomic DNA from saliva sample H167_5


title: genomic DNA from saliva sample H167_6


title: genomic DNA from saliva sample H167_7


title: genomic DNA from saliva sample H167_10


title: genomic DNA from saliva sample H167_17


title: genomic DNA from saliva sample H167_3


title: genomic DNA from saliva sample H167_2


title: genomic DNA from saliva sample H85_159


title: genomic DNA from saliva sample H167_31


title: genomic DNA from saliva sample H85_154


title: genomic DNA from saliva sample H85_153


title: genomic DNA from saliva sample H85_158


title: genomic DNA from saliva sample H85_157


title: genomic DNA from saliva sample H85_156


title: genomic DNA from saliva sample H167_13


title: genomic DNA from saliva sample H85_151


title: genomic DNA from saliva sample H85_148


title: genomic DNA from saliva sample H85_152


title: genomic DNA from saliva sample H85_138


title: genomic DNA from saliva sample H85_149


title: genomic DNA from saliva sample H85_160


title: genomic DNA from saliva sample H85_146


title: genomic DNA from saliva sample H85_145


title: genomic DNA from saliva sample H167_12


title: genomic DNA from saliva sample H85_144


title: genomic DNA from saliva sample H85_139


title: genomic DNA from saliva sample H85_147


title: genomic DNA from saliva sample H85_150


title: genomic DNA from saliva sample H85_140


title: genomic DNA from saliva sample H85_155


title: genomic DNA from saliva sample H85_135


title: genomic DNA from saliva sample H85_136


title: genomic DNA from saliva sample H85_142


title: genomic DNA from saliva sample H85_134


title: genomic DNA from saliva sample H85_137


title: genomic DNA from saliva sample H85_131


title: genomic DNA from saliva sample H85_141


title: genomic DNA from saliva sample H85_128


title: genomic DNA from saliva sample H85_127


title: genomic DNA from saliva sample H85_129


title: genomic DNA from saliva sample H85_132


title: genomic DNA from saliva sample H85_130


title: genomic DNA from saliva sample H85_124


title: genomic DNA from saliva sample H85_122


title: genomic DNA from saliva sample H85_126


title: genomic DNA from saliva sample H85_123


title: genomic DNA from saliva sample H85_116


title: genomic DNA from saliva sample H85_113


title: genomic DNA from saliva sample H85_109


title: genomic DNA from saliva sample H85_119


title: genomic DNA from saliva sample H85_114


title: genomic DNA from saliva sample H85_117


title: genomic DNA from saliva sample H85_112


title: genomic DNA from saliva sample H85_118


title: genomic DNA from saliva sample H85_107


title: genomic DNA from saliva sample H85_110


title: genomic DNA from saliva sample H85_111


title: genomic DNA from saliva sample H85_108


title: genomic DNA from saliva sample H85_133


title: genomic DNA from saliva sample H85_104


title: genomic DNA from saliva sample H85_106


title: genomic DNA from saliva sample H85_125


title: genomic DNA from saliva sample H85_105


title: genomic DNA from saliva sample H85_115


title: genomic DNA from saliva sample H85_101


title: genomic DNA from saliva sample H85_99


title: genomic DNA from saliva sample H85_98


title: genomic DNA from saliva sample H85_102


title: genomic DNA from saliva sample H85_103


title: genomic DNA from saliva sample H85_100


title: genomic DNA from saliva sample H85_97


title: genomic DNA from saliva sample H85_95


title: genomic DNA from saliva sample H85_91


title: genomic DNA from saliva sample H85_90


title: genomic DNA from saliva sample H85_92


title: genomic DNA from saliva sample H85_96


title: genomic DNA from saliva sample H85_87


title: genomic DNA from saliva sample H85_93


title: genomic DNA from saliva sample H85_85


title: genomic DNA from saliva sample H85_79


title: genomic DNA from saliva sample H85_86


title: genomic DNA from saliva sample H85_83


title: genomic DNA from saliva sample H85_82


title: genomic DNA from saliva sample H85_89


title: genomic DNA from saliva sample H85_78


title: genomic DNA from saliva sample H85_81


title: genomic DNA from saliva sample H85_88


title: Pseudomonas sp. strain B13192, no FeCl3

city: Gunsan

first: Sang Eun

last: Jeong

state: Jeonbuk (Jeollabuk-do)

address: 558 Daehak-ro

country: South Korea

institute: Kunsan National University

description: Library name: minus_B13192

data_processing:
Raw sequencing reads were quality assessed using FastQC v0.11.7.
Low-quality reads and adapter sequences were removed using Trimmomatic v0.38.
Filtered reads were aligned to strain-specific reference genomes using a Bowtie2-based alignment workflow.
Gene expression levels were quantified and summarized as FPKM values.
Assembly: Strain-specific reference genomes of Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738 were used for read alignment.
Supplementary files format and content: tab-delimited text file includes normalized values for each Sample

organism: Pseudomonas

source_name: strain

growth_protocol: Bacterial strains were initially cultured in appropriate growth media and harvested by centrifugation. Cells were washed twice with M9 minimal medium and then incubated in M9 medium prior to RNA extraction.

extract_protocol:
Total RNA was extracted from harvested bacterial cells using a standard RNA extraction protocol. RNA quality was assessed prior to library preparation.
RNA-seq libraries were constructed from total RNA after mRNA enrichment. Libraries were prepared using a standard cDNA library preparation protocol and sequenced using an Illumina paired-end platform.

treatment_protocol: Cells were incubated for 12 h in M9 minimal medium under two conditions: iron-replete medium supplemented with 100 uM FeCl3 and iron-limited medium without FeCl3.

value: strain

value: without FeCl3 treatment


title: Pseudomonas sp. strain B13192, FeCl3 treated

description: Library name: plus_B13192

value: with FeCl3 treatment


title: genomic DNA from saliva sample H85_77


title: genomic DNA from saliva sample H85_94


title: IPO323_earlyH2O2_GPL_1

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

description: Library name: Unknown_BW591-001U0024

data_processing:
Sequencing adapters and reads shorter than 50 bp were trimmed using Trimmomatic v.0.38 (Bolger et al. 2014) with the following parameters: ILLUMINACLIP:${adapters}:2:30:10 LEADING:15 TRAILING:15 SLIDINGWINDOW:5:15 MINLEN:50. The trimmed reads were aligned to the Z. tritici IPO323 transcriptome reference (Lapalu et al. 2023), and transcript abundances were quantified using Kallisto v0.46.1 (Bray et al. 2016) with default parameters for paired-end reads. Read counts were summarized using tximport v1.32.0 (Soneson et al. 2016). Differential gene expression analysis was conducted using the R package DESeq2 (Love et al. 2014). Principal component analysis (PCA) was performed on the DESeq2 r-log transformed normalized counts. Genes were considered differentially expressed if the adjusted p-value was < 0.05 and the log2 fold change was > 1.5 (upregulated) or < -1.5 (downregulated)(Love et al. 2014).
Assembly: Zymoseptoria tritici IPO323
Supplementary files format and content: Tab separated file of DESeq2 differential expression analysis

molecule: nuclear RNA

organism: Zymoseptoria tritici

source_name: Spores

growth_protocol: The pre-culture of the reference strain IPO323 (Goodwin et al. 2011) was pre-cultured by transferring 150 µL of glycerol stock into 50 mL of yeast extract peptone dextrose (YPD) medium (10 g/L yeast extract, 20 g/L bactopeptone, 20 g/L dextrose, and 50 mg/L kanamycin). Cultures were incubated at 18°C in the dark with shaking at 120 rpm for seven days. After incubation, cultures were filtered through two layers of gauze to isolate blastospores (yeast-like asexual spores). The filtrate was centrifuged at 3,273 × g for 10 minutes at 4°C, and the resulting spore pellets were resuspended in ~20 mL of glucose peptone liquid (GPL) medium (14.3 g/L dextrose, 7.1 g/L bactopeptone, 1.4 g/L yeast extract, and 50 mg/L kanamycin). To assess the transcriptomic response, we prepared 25 mL spore suspensions (2.5 x 105 spores/mL) for each treatment, maintaining the same environmental conditions used for the phenotyping. These suspensions were incubated for 90 hours at 18°C in the dark, with three biological replicates per condition. For hydrogen peroxide, due to its rapid degradation, a spore suspension of the hydrogen peroxide treatment and another spore suspension for the control were prepared and incubated for only 15 hours at 18°C.

extract_protocol:
Spore pellets were immediately flash-frozen and stored at -80°C. Frozen samples were sent to Biomarker Technologies GmbH (BMKgene, Münster, Germany) for RNA extraction and sequencing
Sequencing was performed using Illumina NovaSeq X, with paired-end 150 bp reads.

treatment_protocol: Treatment media with different environments simulating host-defense responses: salicylic acid (SA) was added to a final concentration of 2 mM in GPL medium (adjusted to pH 5 with HCl); gibberellic acid (GA) was also prepared at 2 mM in GPL medium (pH 5); hydrogen peroxide (H2O2) was used at 1 mM in GPL medium (pH 7); low pH treatment consisted of GPL medium (adjusted to pH 5 with HCl); and control conditions consisted of GPL medium (pH 7).

value: Spores

value: Glucose peptone liquid  media 15h pH7, hydrogen peroxide 1mM


title: genomic DNA from saliva sample H85_76


title: IPO323_earlyH2O2_GPL_3

description: Library name: Unknown_BW591-001U0076


title: genomic DNA from saliva sample H85_84


title: IPO323_pH_GPL_2

description: Library name: Unknown_BW591-001U0046

value: Glucose peptone liquid media 90h pH5


title: genomic DNA from saliva sample H85_74


title: IPO323_pH_GPL_1

description: Library name: Unknown_BW591-001U0020


title: genomic DNA from saliva sample H85_121


title: IPO323_H2O2_GPL_3

description: Library name: Unknown_BW591-001U0071

value: Glucose peptone liquid media 90h pH7, hydrogen peroxide 1mM


title: IPO323_earlyH2O2_GPL_2

description: Library name: Unknown_BW591-001U0050


title: IPO323_pH_GPL_3

description: Library name: Unknown_BW591-001U0072


title: genomic DNA from saliva sample H85_73


title: genomic DNA from saliva sample H85_72


title: genomic DNA from saliva sample H85_71


title: genomic DNA from saliva sample H85_70


title: IPO323_H2O2_GPL_2

description: Library name: Unknown_BW591-001U0045


title: IPO323_SA_GPL_2

description: Library name: Unknown_BW591-001U0039

value: Glucose peptone liquid media 90h pH5, salicylic acid 2mM


title: IPO323_SA_GPL_1

description: Library name: Unknown_BW591-001U0013


title: genomic DNA from saliva sample H85_75


title: genomic DNA from saliva sample H85_120


title: IPO323_H2O2_GPL_1

description: Library name: Unknown_BW591-001U0019


title: IPO323_GA_GPL_3

description: Library name: Unknown_BW591-001U0064

value: Glucose peptone liquid media 90h pH5, gibberrellic acid 2mM


title: genomic DNA from saliva sample H85_65


title: IPO323_SA_GPL_3

description: Library name: Unknown_BW591-001U0065


title: genomic DNA from saliva sample H85_67


title: genomic DNA from saliva sample H85_69


title: genomic DNA from saliva sample H85_66


title: IPO323_GA_GPL_1

description: Library name: Unknown_BW591-001U0012


title: genomic DNA from saliva sample H85_64


title: genomic DNA from saliva sample H85_80


title: IPO323_S18C_GPL_1

description: Library name: Unknown_BW591-001U0008

value: Glucose peptone liquid  media 15h pH7


title: genomic DNA from saliva sample H85_63


title: IPO323_S18C_GPL_3

description: Library name: Unknown_BW591-001U0060


title: genomic DNA from saliva sample H85_62


title: IPO323_S18C_GPL_2

description: Library name: Unknown_BW591-001U0034


title: IPO323_GA_GPL_2

description: Library name: Unknown_BW591-001U0038


title: genomic DNA from saliva sample H167_1


title: genomic DNA from saliva sample H85_61


title: IPO323_18C_GPL_3

description: Library name: Unknown_BW591-001U0053

value: Glucose peptone liquid media 90h pH7


title: genomic DNA from saliva sample H85_68

value: female


title: genomic DNA from saliva sample H85_60


title: genomic DNA from saliva sample H85_59


title: IPO323_18C_GPL_1

description: Library name: Unknown_BW591-001U0001


title: genomic DNA from saliva sample H85_56


title: IPO323_18C_GPL_2

description: Library name: Unknown_BW591-001U0027


title: genomic DNA from saliva sample H85_57


title: rh2808, A004.01/A019.02/B012.03/B015.03/DR04.01/DR03.01, ADT

city: Madison

first: David

middle: H

last: O'Connor

state: WI

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

description:
Library name: M008656_rh2808_Pro-inflammatory_ADT
Antibody-derived oligonucleotide
Mmul10_rh2808.fa
Mmul10_rh2808.gtf.gz
rh2808_expression_results.xlsx
rh2808_seurat_object.Rds
rh2808_raw_feature_bc_matrix.h5
rh2808_assignment_confidence_table.csv

library_source: other

data_processing:
Data were processed using Cell Ranger 9.0.0 using the multi subcommand to demultiplex hashtagged samples.
To optimize hash tagged sample demultiplexing, raw multiplexed feature barcode matrices for each pool were loaded into Seurat and subset to those barcodes that were identified as cells by cell ranger (based on the pool assignment_confidence_table.csv). Antibody-derived tag (ADT) counts including both hashtag oligos (HTOs) and surface antigen tags were normalized using the CLR method. Samples were demultiplexed using HTOs with the HTODemux command from Seurat v5. Seurat objects were subset to those cells identified as singlets by HTODemux. The metadata column "HTO_classification" contains the called sample for each cell.
Gene expression data were normalized, variable features were identified, data was scaled, and PCA was run. Individual hash tagged samples (pro-inflammatory, anti-inflammatory, t-cell activation, and untreated control) were integrated for each pool using RPCAIntegration.
Neighbors and clusters were identified using FindNeighbors and FindClusters respectively. UMAP generation was accomplished for the RNA assay using the RunUMAP function. A UMAP embedding based only on surface antigen counts was also created.
Seurat objects were saved as Rds files.
Raw data note: Multiplexed reads are provided as per-library FASTQ files. To re-process, users must download both mRNA and ADT FASTQ files, then run 'cellranger multi' using the provided feature_reference.csv file to separate hashtags using HT1-HT4 antibody tags.
Assembly: Mmul_10 + custom sequences
Supplementary files format and content: Gzipped GTF and FASTA files of the reference genome used to process samples with Cell Ranger
Supplementary files format and content: H5 files containing raw gene count matrices for each pool
Supplementary files format and content: CSV files (assignment_confidence_table.csv) containing cell ranger demultiplexing and cell calls for each barcode
Supplementary files format and content: CSV file (feature_reference.csv) formatted for cell ranger input indicating ADT barcode sequences.
Supplementary files format and content: Excel files with cell-level wilcoxon rank sum test differential for each sample vs. all others.
Supplementary files format and content: Rds files containing Seurat objects with sample demultiplexing for each pool.
Library strategy: CITE-seq

molecule: protein

organism: Macaca mulatta

source_name: peripheral blood mononuclear

extract_protocol:
Single cells were barcoded and extracted using the 10X Genomics 5' single cell RNA-seq GEM-X v3 kit according to the manufacturer instructions.
scRNA-seq and antibody-derived-tag libraries were prepared using the 10X Genomics 5' single cell RNA-seq GEM-X v3 kit according to the manufacturer instructions.

value: peripheral blood mononuclear

value: Pro-inflammatory:IFN-gamma, TNF-alpha, IL-1beta; Anti-inflammtory:IL-10, TGF-beta; T-Cell_Activation:CD3/CD298_beads; Untreated_control:N/A

tag: library type

value: ADT

tag: adt

value: TotalSeq-C0045 anti-human CD4, TotalSeq-C0080 anti-human CD8a, TotalSeq-C0161 anti-human CD11b, TotalSeq-C0081 anti-human CD14, TotalSeq-C0083 anti-human CD16,  TotalSeq-C0100 anti-human CD20, TotalSeq-C0006 anti-human CD86

tag: cells detected_by_cellranger_multi


title: rh2808, A004.01/A019.02/B012.03/B015.03/DR04.01/DR03.01, mRNA

description:
Library name: M008656_rh2808_Pro-inflammatory_mRNA
polyA RNA
Mmul10_rh2808.fa
Mmul10_rh2808.gtf.gz
rh2808_expression_results.xlsx
rh2808_seurat_object.Rds
rh2808_raw_feature_bc_matrix.h5
rh2808_assignment_confidence_table.csv

molecule: polyA RNA

value: mRNA


title: r22016, A004.01/A004.01/B048.01/B048.01/DR06.01/DR01.01, ADT

description:
Library name: M008656_r22016_Pro-inflammatory_ADT
Antibody-derived oligonucleotide
Mmul10_r22016.fa
Mmul10_r22016.gtf.gz
r22016_expression_results.xlsx
r22016_seurat_object.Rds
r22016_raw_feature_bc_matrix.h5
r22016_assignment_confidence_table.csv


title: genomic DNA from saliva sample H85_55

value: saliva


title: genomic DNA from saliva sample H85_54


title: genomic DNA from saliva sample H85_53


title: r22016, A004.01/A004.01/B048.01/B048.01/DR06.01/DR01.01, mRNA

description:
Library name: M008656_r22016_Pro-inflammatory_mRNA
polyA RNA
Mmul10_r22016.fa
Mmul10_r22016.gtf.gz
r22016_expression_results.xlsx
r22016_seurat_object.Rds
r22016_raw_feature_bc_matrix.h5
r22016_assignment_confidence_table.csv


title: genomic DNA from saliva sample H85_52


title: genomic DNA from saliva sample H85_143


title: genomic DNA from saliva sample H85_51


title: IN2045 HK2KD biol rep 1

city: Wolverhampton

first: Christopher

last: Edwards

address: Wulfruna Street

country: United Kingdom

institute: University of Wolverhampton

description: Library name: Sample 11

data_processing:
Sequencing and data processing was carried out by BMKGENE (https://www.bmkgene.com/)
Raw sequencing data of each sample underwent QC, with adapter sequences and low-quality reads removed using Perl.
Clean reads were mapped to the Ensembl 95 human GRCh38 reference genome using HISAT2. StringTie was employed to assemble mapped reads into transcripts.
Read count and normalisation to gene length (FPKM) was perfomed using StringTie.
Differentially expressed genes between sample groups were determined and counted using DESeq2.
Assembly: Ensembl 95 human GRCh38
Supplementary files format and content: Tab delimited text files including raw and FKPM-normalised counts for HK2-targeted or non-targeting negative-control siRNA transfected U87-MG samples
Supplementary files format and content: Tab delimited text files including raw and FKPM-normalised counts for HK2-targeted or non-targeting negative-control siRNA transfected IN859 samples
Supplementary files format and content: Tab delimited text files including raw and FKPM-normalised counts for HK2-targeted or non-targeting negative-control siRNA transfected IN2045 samples

growth_protocol: Human glioblastoma cell lines and patient derived cell cultures were grown in ‘growth medium’ comprised of HAM’s F10 nutrient mixture with 25 mM HEPES and 1 mM glutamine (Gibco) supplemented with 10% FBS (Gibco). Cell cultures were incubated under normoxic conditions at 37ºC in a standard incubator without carbon dioxide. Growth medium replacement or passaging was performed every 2-3 days in accordance with cell confluency.

extract_protocol:
Total RNA was isolated from glioblastoma cell cultures using a RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
Library preparation was performed using a NEBNext UltraTM RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s recommendations

treatment_protocol: Glioblastoma cell lines (U87-MG) and glioblastoma patient derived cell cultures (IN859, IN2045) were transfected with either HK2 Ambion Silencer Select (s6562, Ambion Life Technologies) or non-targeting Silencer Select Negative Control No. 1 siRNA (Ambion Life Technologies) at a final concentration of 25 pmol for 48 hours. Transfection was performed with Opti-MEM serum-free medium (Gibco) and Lipofectamine 3000 (Invitrogen). HK2KD in HK2-targeted siRNA transfected cultures was confirmed prior to RNAseq by RT-qPCR.

value: Human glioblastoma patient-derived short-term cell culture

value: HK2-targeted siRNA


title: IN859 HK2KD biol rep 2

description: Library name: Sample 8


title: genomic DNA from saliva sample H85_50


title: IN2045 HK2KD biol rep 2

description: Library name: Sample 12


title: IN2045 Non targeting control biol rep 2

description: Library name: Sample 10

value: WT

value: Non-targeting negative control siRNA


title: IN2045 Non targeting control biol rep 1

description: Library name: Sample 9


title: genomic DNA from saliva sample H85_48


title: BT84_H3K4me3

city: Charlestown

first: Gian Paolo

last: Dotto

state: MA

address: 149 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hsopital

description: Library name: HDF BT84, H3K4me3

library_source: genomic

data_processing:
Raw paired-end reads were trimmed using fastp to remove adapter sequences and low-quality bases. Trimmed reads were aligned to the human reference genome (GRCh38) using Bowtie2 (--local --very-sensitive --no-mixed --no-discordant). Duplicate reads were marked and removed using samtools markdup. Reads overlapping ENCODE blacklist regions were excluded. CPM-normalised BigWig tracks were generated using deepTools bamCoverage for visualisation.
Assembly: GRCh38/hg38
Supplementary files format and content: cpm_bigwig

source_name: skin

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic

extract_protocol:
Human primary fibroblasts were crosslinked in situ by addition of formaldehyde directly to the culture medium to a final concentration of 1% and incubated for 8 minutes at room temperature with gentle agitation. Crosslinking was quenched by addition of glycine to a final concentration of 125 mM and incubated for 10 minutes at room temperature. Cells were washed twice with ice-cold 1X PBS supplemented with 1 mM PMSF and collected by scraping. Nuclei were extracted by hypotonic lysis and chromatin was sheared by sonication using a QSonica sonicator (30 seconds on / 30 seconds off cycles for a total of 25 minutes at 60% amplitude). Shearing efficiency was verified by agarose gel electrophoresis to confirm a fragment size distribution of approximately 150–500 bp. Sheared chromatin was pre-cleared and subjected to overnight immunoprecipitation at 4°C with an anti-H3K4me3 antibody (Active Motif, cat. #39159, rabbit polyclonal). Antibody-chromatin complexes were captured using protein A/G magnetic beads, washed, and retained on a magnetic rack.
Library Construction Protocol Immunoprecipitated chromatin on beads was subjected to tagmentation using Tn5 transposase in Illumina Tagment DNA (TD) buffer for 5 minutes at 37°C. Tagmented DNA was purified using Qiagen MinElute columns. Libraries were amplified using Diagenode Dual Index UDI primers. Final libraries were size-selected using a twosided AMPure XP bead cleanup (0.5X followed by 1.8X bead ratios) to remove primer dimers and large fragments. Library quality and size distribution were assessed using a TapeStation prior to paired-end sequencing on an Illumina NovaSeq X (sequencing performed by BMKGene, Muenster, Germany)

treatment_protocol: Cells were transduced with shCTRL vector and collected 7 days after transduction for chromatin profiling using ChIPmentation protocol.

value: skin

value: primary dermal fibroblasts

value: fibroblast

value: shCTRL

tag: chip antibody


title: genomic DNA from saliva sample H85_45


title: genomic DNA from saliva sample H85_47


title: IN859 Non targeting control biol rep 1

description: Library name: Sample 5


title: IN859 HK2KD biol rep 1

description:
Library name: Sample 7
IN859 HK2KD biol rep 1 submitted as single read due to corruption of '2' paired end file.


title: IN859 Non targeting control biol rep 2

description: Library name: Sample 6


title: genomic DNA from saliva sample H85_46


title: U87 HK2KD biol rep 2

description: Library name: Sample 4

value: Human glioblastoma cell line


title: U87 HK2KD biol rep 1

description: Library name: Sample 3


title: genomic DNA from saliva sample H167_4


title: genomic DNA from saliva sample H85_44


title: U87 Non targeting control biol rep 2

description: Library name: Sample 2


title: genomic DNA from saliva sample H85_58


title: genomic DNA from saliva sample H85_41


title: genomic DNA from saliva sample H85_40


title: U87 Non targeting control biol rep 1

description: Library name: Sample 1


title: T-cells from healty donors

city: Yerevan

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Yerevan

address: Khorenatsi 1

department: Research and Development

country: Armenia

institute: PerikLab

description:
Library name: S15177Nr2
BD Rhapsody

data_processing:
Barcode processing, gene UMI counting and aggregation were made using the BD Rhapsody pipeline v2.2 (https://bd-rhapsody-bioinfo-docs.genomics.bd.com/release_notes.html).
Assembly: BD Rhapsody™ T Cell Expression Panel Hs (https://scomix.bd.com/hc/en-us/article_attachments/360059289712)
Supplementary files format and content: Sample-demultiplexed (via SampleTag HTOs) 10X-like feature, barcode and matrix files containing RNA and ADT data.
Library strategy: CITE-seq

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral blood by centrifugation using Ficoll. T cells were isolated from PBMCs using negative magnetic selection.
Library was performed according to the manufacter’s instructions (BD Rhapsody™ System mRNA Targeted, Sample Tag, and BD® AbSeq Library Preparation Protocol).

treatment_protocol: T cells were activated using anti-CD3/28 microbeads and transduced using anti-Her2:neu lentiviral constructs.

value: T-cells

value: Blood

tag: age


title: genomic DNA from saliva sample H85_43

value: female


title: genomic DNA from saliva sample H85_37


title: genomic DNA from saliva sample H85_39


title: genomic DNA from saliva sample H85_36


title: genomic DNA from saliva sample H85_33


title: genomic DNA from saliva sample H85_42


title: genomic DNA from saliva sample H85_34


title: C4hiPSC

city: London

first: Fiona

last: Lewis-McDougall

address: Charterhouse Square

institute: Queen Mary University of London

description:
Library name: C4hiPSC
RNA-seq

data_processing:
Data processing was performed by Novogene Ltd.
Assembly: hg38
Supplementary files format and content: Raw gene counts for all samples generated by Novogene.

source_name: Patient-derived

growth_protocol: eCPCs and iPSC-CPCs were cultured on CELLstart™ (Thermo Fisher Scientific)-coated cultureware in growth medium, which is composed of (1:1) Dulbecco’s MEM/Ham’s F12 (DMEM/F12; Sigma-Aldrich) and Neurobasal A medium (Thermo Fisher Scientific) containing 10% Stemulate® pooled human platelet lysate (Cook medical, USA), 2mM L-alanyl-L-glutamine (Thermo Fisher Scientific), B27 and N2 supplements (Thermo Fisher Scientific), leukemia inhibitory factor (LIF) (10ng/ml; Millipore), bFGF (10ng/ml; Peprotech), EGF (20ng/ml; Peprotech), insulin-transferrin-selenite (ITS; Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), 0.1% gentamicin (Thermo Fisher Scientific), and 0.1% Fungizone™ (Thermo Fisher Scientific) in a humidified hypoxic incubator at 37°C, 5% CO2, 2% O2.

extract_protocol:
RNA was extracted by directly lysing cells on the inserts using RLT lysis buffer from the Qiagen RNeasy Mini Kit, according to the manufacturer’s instructions.
Library preparation and paired-end 150 bp sequencing (PE150) were performed by Novogene Ltd.

treatment_protocol: CPCs were compared to 1) Human iPSCs, which were cultured in on recombinant human vitronectin and maintained in feeder-free, serum-free E8 Flex medium and 2) Human  iPSC-derived cardiomyocytes (hiPSC-CMs) generated using a protocol adapted from Burridge et al. (2015). Briefly, hiPSC-CMs were generated in CDM3 medium consisting of RPMI 1640 supplemented with 75 mg/mL recombinant human albumin (Merck) and 64 mg/mL L-ascorbic acid 2-phosphate (Merck). Differentiation was induced by treating cells with 6 μM CHIR99021 (Cambridge Bioscience) for 48 hours. On day 2, the medium was replaced with CDM3 containing 2 μM Wnt-C59, and from day 4 onward, cells were maintained in CDM3 alone, with media changes performed every two days.

value: human induced pluripotent stem cell


title: genomic DNA from saliva sample H85_38


title: C2hiPSC

description:
Library name: C2hiPSC
RNA-seq


title: C1hiPSC_CPC

description:
Library name: C1hiPSC_CPC
RNA-seq

value: human induced pluripotent stem cell-derived cardiac progenitor cells

value: CPC differentiation


title: genomic DNA from saliva sample H85_32


title: genomic DNA from saliva sample H85_29


title: genomic DNA from saliva sample H85_35


title: genomic DNA from saliva sample H85_30


title: HepG2_PC041_CAF20_4

city: Taipei City

first: Li-Wen

last: Chiou

address: Chung Shan S. Rd.

department: Pathology

country: Taiwan

institute: National Taiwan University

description: Library name: HepG2_PC041_CAF20_4

data_processing:
The obtained library was sequenced on an Illumina NovaSeq 6000 sequencer. The adaptor sequences were trimmed using Cutadapt (v3.5).
The trimmed reads were aligned to the human reference genome (GRCh38) using STAR (v 2.7.8a) with two-pass mode, and then gene counts were generated (--quantMode GeneCounts) based on the annotation of Gencode (v35).
Normalization was performed using the Trimmed Mean of M values (TMM) method to ensure comparable distributions across samples, and Transcript Per Million (TPM) values were calculated for subsequent analyses.
Differential expression analysis was performed using the limma R package.
Over-representation analysis of genes with differentially accessible ATAC peaks and differential expression was performed using the clusterProfiler R package with gene sets from MSigDB (v7.4).
Assembly: GRCm38.p6
Supplementary files format and content: tab-separated matrix file includes TPM values and scale expression for each sample and GSEA results

source_name: liver

extract_protocol:
Total RNA was extracted from cultured cells after indicated treatment using Trizol reagent.
RNA was ligated to adapters for further amplification using a TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: HepG2 were cultured on collagen I–coated plates or treated with conditioned medium derived from cancer-associated fibroblasts (CAFs)

value: liver

value: cultured with 20% conditioned medium from CAF PC041 for 2 days


title: HepG2_Collagen_5

description: Library name: HepG2_Collagen_5

value: cultured on 5 μg/cm^2 collagen for 2 days


title: HepG2_4

description: Library name: HepG2_4

value: cultured in complete DMEM


title: HepG2_5

description: Library name: HepG2_5

value: WT


title: HepG2_PC041_CAF20_5

description: Library name: HepG2_PC041_CAF20_5


title: genomic DNA from saliva sample H85_28

value: saliva


title: C1hiPSC

description:
Library name: C1hiPSC
RNA-seq


title: RCC1-8-3-2

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

description: Library name: RCC1-8-3-2

data_processing:
Raw fastq files were processed through lcdb-wf v1.10.3rc (https://github.com/lcdb/lcdb-wf) for QC filtering, adapter trimming, mapping and quantification in genes. Briefly, fastq files were trimmed from adapters with cutadapt v4.4; trimmed reads were mapped to hg38 with hisat2 v2.2.1 with parameter --no-unal then sorted with samtools sort v1.16.1; duplicate reads were marked with picard MarkDuplicates v2.27.5; reads in genes were quantified with subread featurecounts v2.0.3.
Assembly: hg38
Supplementary files format and content: featurecounts_set*.txt files contain raw counts in genes.

growth_protocol: The human colorectal cancer cell line DLD-1 was cultured in DMEM (Life Technologies) supplemented with heat-inactivated 10% FBS (Atlanta Biologicals), antibiotics (100 IU/ml penicillin and 100 μg/ml streptomycin), and 2 mM GlutaMAX (Life Technologies) in 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was extracted with Qiagen RNAeasy Plus Mini Kit. Extracted RNA was analyzed for 260/280 and RIN value was assessed on Bioanalyzer 2100 (Agilent), samples with RIN value more than 9 were proceeded for the library construction using Illumina TruSeq Stranded Total RNA Library Preparation Kit (Illumina) according to manufacturer’s instructions.
1-4 ug of total RNA samples  were depleted for ribosomal RNA (Set 2021) before library construction using Ribo-Zero™ Gold Kit H/M/R Kit (Illumina) or purified with PolyA extraction (Set 2024), and then purified mRNAs were constructed to RNA-Seq libraries with specific barcodes using illumina TruSeq Stranded mRNA Library Prep Kit. All the RNA-Seq libraries were pooled together and sequenced using illumina NovaSeq 6000 to generate approximately ~40 million 2x100 paired-end reads for each sample.

treatment_protocol: AID-GANP, AID-ENY2, AID-PCID2, AID-CETN2, AID-CETN2_3 cells were untreated or treated with 1 mM IAA, Sigma, I5148-10G. AID-SAC3D1 and AID-LENG8 cells were treated with DMSO (1:1000) or 1 uM 5-Ph-IAA, BioAcademia.

value: controls set


title: RCC1-8-3-3

description: Library name: RCC1-8-3-3


title: RCC1-8-3-1

description: Library name: RCC1-8-3-1


title: HepG2_Collagen_4

description: Library name: HepG2_Collagen_4


title: RCC1-8-2-4

description: Library name: RCC1-8-2-4


title: genomic DNA from saliva sample H85_27


title: genomic DNA from saliva sample H85_25


title: genomic DNA from saliva sample H85_26


title: genomic DNA from saliva sample H85_24


title: RCC1-8-2-3

description: Library name: RCC1-8-2-3


title: RCC1-8-2-2

description: Library name: RCC1-8-2-2


title: genomic DNA from saliva sample H85_23


title: genomic DNA from saliva sample H85_49


title: RCC1-8-2-1

description: Library name: RCC1-8-2-1


title: genomic DNA from saliva sample H85_21


title: genomic DNA from saliva sample H85_31


title: B_2: I/R model rat kidney RNA-seq Rep2

city: Kunming

first: bo

last: yuan

address: No. 295 Xichang Road, Wuhua District

institute: The First Affiliated Hospital of Kunming Medical University

description:
Library name: B_2
Kidney from renal I/R injury rat

data_processing:
Raw sequencing reads were trimmed and filtered using Cutadapt to remove adapter sequences, low-quality bases and contaminated reads.
Clean high-quality reads were aligned to the rat reference genome using HISAT2 software with default parameters.
Mapped reads were assembled into transcripts and quantified using StringTie to generate FPKM values for gene expression analysis.
Differentially expressed genes were identified using the DESeq2 R package with |fold change| > 1 and p < 0.05 as significance thresholds.
All downstream bioinformatics analyses including GO and KEGG enrichment were performed using standard packages in R and Python.
Assembly: Rattus norvegicus Rnor_6.0 (GCA_000001895.4)
Supplementary files format and content: Tab-delimited text files containing raw gene count matrices and FPKM expression values of all samples for downstream bioinformatics analysis.

organism: Rattus norvegicus

source_name: Kidney

growth_protocol: Male and female Sprague-Dawley rats (6–8 weeks old, 200–220 g) were housed under standard laboratory conditions (22 ± 2 °C, 55 ± 10% humidity, 12-h light/dark cycle) with free access to food and water for 3 days of acclimation prior to experimentation.

extract_protocol:
Total RNA was extracted from rat kidney tissues using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA concentration and purity were determined using a NanoDrop ND-1000 spectrophotometer. RNA integrity (RIN > 7.0) was verified using an Agilent Bioanalyzer 2100.
Poly(A) mRNA was purified from total RNA using Dynabeads Oligo(dT)25. Purified mRNA was fragmented and reverse-transcribed into cDNA. RNA-seq libraries were constructed using standard Illumina library preparation protocols. The final libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 2×150 bp paired-end reads.

treatment_protocol: Rats were randomly divided into six groups: sham, I/R, I/R + low-dose rapamycin (1 mg/kg/day) for 3 days, I/R + low-dose rapamycin for 7 days, I/R + high-dose rapamycin (2 mg/kg/day) for 3 days, I/R + high-dose rapamycin for 7 days. Rapamycin was administered by oral gavage starting 1 day before surgery. Renal ischemia was induced for 45 min followed by 3 or 7 days of reperfusion. *extract protocol

value: Kidney

value: Renal tubular cell

value: Wild-type

value: I/R injury


title: C_3: Sham-operated rat kidney RNA-seq Rep3

description:
Library name: C_3
Kidney from sham-operated rat

value: Sham operation


title: C_1: Sham-operated rat kidney RNA-seq Rep1

description:
Library name: C_1
Kidney from sham-operated rat


title: B_3: I/R model rat kidney RNA-seq Rep3

description:
Library name: B_3
Kidney from renal I/R injury rat


title: genomic DNA from saliva sample H85_22


title: B_1: I/R model rat kidney RNA-seq Rep1

description:
Library name: B_1
Kidney from renal I/R injury rat


title: RCC1-8-1-3

description: Library name: RCC1-8-1-3


title: C_2: Sham-operated rat kidney RNA-seq Rep2

description:
Library name: C_2
Kidney from sham-operated rat


title: RCC1-8-1-4

description: Library name: RCC1-8-1-4


title: RCC1-8-1-2

description: Library name: RCC1-8-1-2


title: A_3: Rapamycin-treated rat kidney RNA-seq Rep3

description:
Library name: A_3
Kidney from I/R rat treated with rapamycin

value: I/R + Rapamycin


title: genomic DNA from saliva sample H85_18

value: female


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 74

city: New Haven

first: Ramanaiah

last: Mamillapalli

state: CT

address: 310 Cedar Street

department: OBGYN

institute: Yale University

description: Library name: Baboon-miRNA-Hugh Taylor_074

data_processing:
The differential analysis was performed using R (R version 4.5.0 (2025-04-11), RRID:SCR_001905). Raw miRNA count data from serum samples were filtered to retain tRFs with a counts-per-million >1 in at least one sample. The raw count data were normalized using the trimmed mean of M-values (TMM) method implemented in edgeR (RRID:SCR_012802) to account for sequencing depth and compositional bias. Because repeated measurements were collected from the same animals, individual baboon identity was modeled as a fixed effect to adjust for individual baseline variation. Normalized counts were then transformed to log₂ counts per million and assigned precision weights using the voom method from the limma package (RRID:SCR_010943). A linear model was applied to the transformed dataset, and each post-induction timepoint (3, 6, 9, and 15 months) was statistically compared with the pre-induction baseline. Statistical comparisons were performed using limma's empirical Bayes moderated t-tests on voom-transformed expression values. Multiple testing correction was performed using the Benjamini-Hochberg procedure, with significance defined as FDR < 0.05. To assess robustness to within-animal correlation, we additionally re-estimated models using limma’s duplicateCorrelation framework, treating animal identity as a blocking factor. Internal validation was performed using leave-one-animal-out analyses restricted to candidate miRNAs, assessing stability of effect sizes across folds. A fully annotated R script reproducing all preprocessing steps, statistical analyses, and figures is provided as Supplementary Material.
Supplementary files format and content: Xslx file that summarizes aligned counts for the miRNAs.

organism: Papio anubis

source_name: Plasma

extract_protocol:
RNAs were extracted using the MagMAX™ total RNA Isolation Kit. Total RNA quality was determined by estimating the A260/A280 and A260/A230 ratios by nanodrop. RNA integrity was determined by running Agilent Fragment Analyzer, which measures  the ratio of the ribosomal peaks.  Samples with RIN values of 7 or greater are used for library prep. RNA was normalized to a starting input between 1ng-500ng. Adapters were ligated sequentially to the 3’ and 5’ ends of miRNAs prior to cDNA synthesis with UMI assignment, cDNA cleanup, amplification, and final library cleanup
The library was run on the Agilent Tapestation and size selection was performed if there was excess adapter dimer. The library was then quantified by qRT-PCR using a commercially available kit (KAPA Biosystems). Sample concentrations were normalized to 2 nM and loaded onto an Illumina NovaSeq X flow cell at a concentration that yields 10-25 million passing filter clusters per sample.

value: Plasma

value: No treatment

tag: timepoint (months)

tag: baboon number

tag: plasma volume


title: genomic DNA from saliva sample H85_20

tag: tissue


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 72

description: Library name: Baboon-miRNA-Hugh Taylor_072

tag: treatment


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 76

description: Library name: Baboon-miRNA-Hugh Taylor_076


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 80

description: Library name: Baboon-miRNA-Hugh Taylor_080


title: RCC1-8-1-1

description: Library name: RCC1-8-1-1

tag: cell line


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 70

description: Library name: Baboon-miRNA-Hugh Taylor_070


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 78

description: Library name: Baboon-miRNA-Hugh Taylor_078


title: genomic DNA from saliva sample H85_19


title: A_1: Rapamycin-treated rat kidney RNA-seq Rep1

description:
Library name: A_1
Kidney from I/R rat treated with rapamycin

tag: cell type


title: RCC1-0-3-4

description: Library name: RCC1-0-3-4

tag: genotype

value: untreated


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 68

description: Library name: Baboon-miRNA-Hugh Taylor_068


title: genomic DNA from saliva sample H85_17


title: T47D siELF5 rep3

city: Philadelphia

first: Alekh

last: Paranjapye

state: Pennsylvania

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using gProfiler.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include normalized count values for each Sample

source_name: T47D siELF5

growth_protocol: Cells were grown in indicated medias using standard methods.

extract_protocol:
T47D cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

treatment_protocol: T47D cells were transfected with either siNC or siELF5. RNA collected 48 hr post-transfection

value: Human luminal A breast epithelial cells

tag: genotype/variation

value: Ambion AM16708 siRNA


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 64

description: Library name: Baboon-miRNA-Hugh Taylor_064


title: RCC1-0-3-3

city: Bethesda

description: Library name: RCC1-0-3-3


title: RCC1-0-3-2

description: Library name: RCC1-0-3-2


title: genomic DNA from saliva sample H85_16


title: A_2: Rapamycin-treated rat kidney RNA-seq Rep2

description:
Library name: A_2
Kidney from I/R rat treated with rapamycin


title: T47D siNC rep3

source_name: T47D siNC

value: Ambion 4390846 siRNA


title: RCC1-0-3-1

description: Library name: RCC1-0-3-1


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 62

description: Library name: Baboon-miRNA-Hugh Taylor_062


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 66

description: Library name: Baboon-miRNA-Hugh Taylor_066


title: genomic DNA from saliva sample H85_15


title: T47D siELF5 rep1


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 58

description: Library name: Baboon-miRNA-Hugh Taylor_058


title: T47D siNC rep2


title: RCC1-0-2-4

description: Library name: RCC1-0-2-4


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 56

description: Library name: Baboon-miRNA-Hugh Taylor_056


title: genomic DNA from saliva sample H85_13


title: T47D siELF5 rep2


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 60

description: Library name: Baboon-miRNA-Hugh Taylor_060


title: genomic DNA from saliva sample H85_12


title: RCC1-0-2-3

description: Library name: RCC1-0-2-3


title: T47D siNC rep1


title: genomic DNA from saliva sample H85_11


title: RCC1-0-2-2

description: Library name: RCC1-0-2-2


title: Herbaspirillum sp. strain B12834, FeCl3 treated

description: Library name: plus_B12834

organism: Herbaspirillum

value: strain

value: with FeCl3 treatment


title: RCC1-0-2-1

description: Library name: RCC1-0-2-1


title: RCC1-0-1-4

description: Library name: RCC1-0-1-4


title: Herbaspirillum sp. strain B12834, no FeCl3

description: Library name: minus_B12834

value: without FeCl3 treatment


title: genomic DNA from saliva sample H85_9

value: saliva


title: genomic DNA from saliva sample H85_10


title: genomic DNA from saliva sample H85_14


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 52

description: Library name: Baboon-miRNA-Hugh Taylor_052


title: RCC1-0-1-2

description: Library name: RCC1-0-1-2

value: controls set


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 48

description: Library name: Baboon-miRNA-Hugh Taylor_048


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 50

description: Library name: Baboon-miRNA-Hugh Taylor_050


title: MLE-15, Pam2+ODN, MHV, 24hpi, Rep 2

type: RNA

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 6565 MD Anderson Blvd, Unit 1059

department: Pulmonary Medicine

institute: University of Texas MD Anderson Cancer Center

data_processing: Gene expression was assessed using the nCounter Mouse Host Response Panel (NanoString Technologies) according to the manufacturer’s instructions. Data were analyzed using nSolver 4.0 Advanced Analysis 2.0 software, with normalization across all experimental groups including PBS-treated controls, and differential expression and pathway enrichment analyses performed using the Omics-Based Interaction Framework (OBIF) and QIAGEN’s Ingenuity Pathway Analysis (IPA) software.

source_name: Distal respiratory epithelium

growth_protocol: Cell lines were maintained in DMEM-based growth media supplemented with 2 percent volume/volume (% v/v) of fetal bovine serum and 1 % v/v antibiotic-antimycotic (100X).

extract_protocol: t 24 hours post-infection, total RNA was isolated, quantified, and three independent biological replicates per condition were submitted to the MD Anderson Cancer Center Advanced Technology Genomics Core for gene expression profiling using the nCounter Mouse Host Response Panel (NanoString).

treatment_protocol: MLE-15 cells at 70–80% confluence were treated with fresh media containing either PBS or Pam2+ODN (4 μM Pam2CSK4 and 1 μM ODN M362) for 4 hours prior to infection, followed by addition of virus at a multiplicity of infection of 0.1 plaque forming units per cell.

value: Lung, Distal respiratory epithelium

value: Epithelial cell

tag: time

value: 24h post infection (hpi)

tag: infection

value: MHV


title: MLE-15, Pam2+ODN, MHV, 24hpi, Rep 3


title: MLE-15, Pam2+ODN, MHV, 24hpi, Rep 1


title: RCC1-0-1-1

description: Library name: RCC1-0-1-1

tag: batch


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 54

description: Library name: Baboon-miRNA-Hugh Taylor_054


title: genomic DNA from saliva sample H85_6

tag: Sex


title: RCC1-0-1-3

description: Library name: RCC1-0-1-3


title: genomic DNA from saliva sample H85_8


title: genomic DNA from saliva sample H85_5


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 46

description: Library name: Baboon-miRNA-Hugh Taylor_046


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 44

description: Library name: Baboon-miRNA-Hugh Taylor_044


title: MLE-15, PBS, MHV, 24hpi, Rep 2

value: PBS


title: MLE-15, PBS, MHV, 24hpi, Rep 3


title: genomic DNA from saliva sample H85_4

value: female


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 40

description: Library name: Baboon-miRNA-Hugh Taylor_040

value: Plasma


title: CTRL7-LineD-Dif2-Sample1

city: Stanford

first: Michelle

middle: Katherine

last: Drews

state: CALIFORNIA

address: 318 Campus Drive, W150

department: Biology

institute: Stanford University

description:
Library name: Sample 15
Column 17 in Count Table

data_processing:
Reads trimmed to remove adapters and low quality sequences with cutadapt (3.4), trim_galore (0.5.0) and trimmomatic (v0.39)
Reads mapped to Homo sapiens reference genome GRCh38p13 with GENCODE annotation using STAR (2.5.4b, Dobin et al 2013)
Reads were counted using HTSeq-Count (0.11.1, Anders et al 2014) in default mode
Differential expression analysis was performed using DESeq2 (1.32.0, Love et al 2014)
Ontology analysis was performed using Enrichr (Chen et al 2013, Kuleshov et al 2016, Xie et al 2021)
Assembly: GRCh38.p13 - GENCODE
Supplementary files format and content: bulkOR_merged_counts.txt: comma separated text file containing raw read counts produced by HT-seq Counts.  The first two columns in the file are ENSEMBL ID and Gene Name respectively.  The subsequent columns are individual samples in the order specified in the sample description field
Supplementary files format and content: Final_Full_ORBulk_Results.csv: comma separated csv file containing differential expression analysis output from DESeq2, with control condition used as reference (ie positive values indicate increased in IFN samples relative to control, negative values indicated increased in CTRL samples relative to IFN).

source_name: hCO

growth_protocol: Human cortical organoids (hCOs) were generated from human induced pluripotent stem-cells (hiPS cells) as previously described (Pasca et al 2015; Yoon et al 2019) and maintained after full differentation in Neurobasal A media with B27 supplement without vitamin A.

extract_protocol:
RNA was extracted with TRIzol per manufacturers instructions and further purified by Qiagen Rneasy Plus system.  3 spheres were pooled and harvested together to form a single biological replicate which are reported here as a single sample.  5 ng of total RNA was used as input for library preparation.
Libraries were prepared for sequencing from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and amplified 16 cycles by PCR.  A Nextera XT DNA Library Preparation Kit (Illumina) with size selection by AMPure XP beads was used to obtain libraries with a mean size of approximately 500 bp.  Libraries were evaluated for quality on an Aligent 2100 Bioanalyzer and were pooled for sequencing.  Samples were sequenced on an Illumina NovaSeq 6000 via a single lane SP100 Cycle.

treatment_protocol: hCOs were treated with either 100 ng/mL Interferon Gamma for 48 hours or an equivalent volume of 0.1% BSA control in Neurobasal A media with B27 supplemet without vitamin A.

value: hCO

value: WT

value: CTRL (BSA)


title: CTRL5-LineC-Dif1-Sample2

description:
Library name: Sample 13
Column 15 in Count Table


title: CTRL6-LineC-Dif2-Sample1

description:
Library name: Sample 14
Column 16 in Count Table


title: MLE-15, Pam2+ODN, PBS, 24hpi, Rep 3

value: Uninfected


title: MLE-15, PBS, MHV, 24hpi, Rep 1


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 42

description: Library name: Baboon-miRNA-Hugh Taylor_042

value: No treatment


title: genomic DNA from saliva sample H85_7


title: genomic DNA from saliva sample H85_3


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 38

description: Library name: Baboon-miRNA-Hugh Taylor_038


title: CTRL4-LineC-Dif1-Sample1

description:
Library name: Sample 12
Column 14 in Count Table


title: MLE-15, Pam2+ODN, PBS, 24hpi, Rep 2


title: genomic DNA from saliva sample H85_1


title: MLE-15, Pam2+ODN, PBS, 24hpi, Rep 1


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 36

description: Library name: Baboon-miRNA-Hugh Taylor_036


title: CTRL3-LineD-Dif1-Sample2

description:
Library name: Sample 11
Column 13 in Count Table


title: MLE-15, PBS, PBS, 24hpi, Rep 3


title: CTRL2-LineD-Dif3-Sample1

description:
Library name: Sample 10
Column 12 in Count Table


title: genomic DNA from saliva sample H85_2


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 32

description: Library name: Baboon-miRNA-Hugh Taylor_032


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 34

description: Library name: Baboon-miRNA-Hugh Taylor_034


title: c20006, M3/M3, mRNA

description:
Library name: M008656_c20006_Pro-inflammatory_mRNA
polyA RNA
Mmul10_M3M3.fa
Mmul10_M3M3.gtf.gz
c20006_expression_results.xlsx
c20006_seurat_object.Rds
c20006_raw_feature_bc_matrix.h5
c20006_assignment_confidence_table.csv

organism: Macaca fascicularis

value: peripheral blood mononuclear

value: Pro-inflammatory:IFN-gamma, TNF-alpha, IL-1beta; Anti-inflammtory:IL-10, TGF-beta; T-Cell_Activation:CD3/CD298_beads; Untreated_control:N/A

tag: library type

value: mRNA


title: IFN8-LineD-Dif2-Sample1

description:
Library name: Sample 8
Column 10 in Count Table

value: IFNg


title: MLE-15, PBS, PBS, 24hpi, Rep 1


title: MLE-15, PBS, PBS, 24hpi, Rep 2


title: cy0975, M1/M1, ADT

description:
Library name: M008656_cy0975_Pro-inflammatory_ADT
Antibody-derived oligonucleotide
Mmul10_M1M1.fa
Mmul10_M1M1.gtf.gz
cy0975_expression_results.xlsx
cy0975_seurat_object.Rds
cy0975_raw_feature_bc_matrix.h5
cy0975_assignment_confidence_table.csv

value: ADT

tag: adt

value: TotalSeq-C0045 anti-human CD4, TotalSeq-C0080 anti-human CD8a, TotalSeq-C0161 anti-human CD11b, TotalSeq-C0081 anti-human CD14, TotalSeq-C0083 anti-human CD16,  TotalSeq-C0100 anti-human CD20, TotalSeq-C0006 anti-human CD86

tag: cells detected_by_cellranger_multi


title: c20006, M3/M3, ADT

description:
Library name: M008656_c20006_Pro-inflammatory_ADT
Antibody-derived oligonucleotide
Mmul10_M3M3.fa
Mmul10_M3M3.gtf.gz
c20006_expression_results.xlsx
c20006_seurat_object.Rds
c20006_raw_feature_bc_matrix.h5
c20006_assignment_confidence_table.csv


title: CTRL1-LineD-Dif1-Sample1

description:
Library name: Sample 9
Column 11 in Count Table


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 28

description: Library name: Baboon-miRNA-Hugh Taylor_028


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 30

description: Library name: Baboon-miRNA-Hugh Taylor_030