title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 26

description: Library name: Baboon-miRNA-Hugh Taylor_026


title: IFN7-LineC-Dif2-Sample1

status: Public on May 04 2026

type: SRA

city: Stanford

first: Michelle

middle: Katherine

last: Drews

state: CALIFORNIA

address: 318 Campus Drive, W150

department: Biology

country: USA

institute: Stanford University

description:
Library name: Sample 7
Column 9 in Count Table

library_source: transcriptomic

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).

molecule: polyA RNA

organism: Homo sapiens

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.

tag: tissue

value: hCO

tag: cell line

tag: genotype

value: WT

tag: treatment

value: IFNg


title: Micrococcus sp. strain B5738, FeCl3 treated

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: plus_B5738

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

molecule: total RNA

organism: Micrococcus

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: with FeCl3 treatment


title: IFN5-LineC-Dif1-Sample1

description:
Library name: Sample 5
Column 7 in Count Table


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 24

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_024

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: Micrococcus sp. strain B5738, no FeCl3

description: Library name: minus_B5738

value: without FeCl3 treatment


title: cy0975, M1/M1, mRNA

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_cy0975_Pro-inflammatory_mRNA
polyA RNA
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

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

organism: Macaca fascicularis

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.

tag: cell type

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: batch

tag: library type

value: mRNA

tag: cells detected_by_cellranger_multi


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 22

description: Library name: Baboon-miRNA-Hugh Taylor_022


title: IFN4-LineD-Dif3-Sample1

description:
Library name: Sample 4
Column 6 in Count Table


title: IFN3-LineD-Dif1-Sample2

description:
Library name: Sample 3
Column 5 in Count Table


title: IFN6-LineC-Dif1-Sample2

description:
Library name: Sample 6
Column 8 in Count Table


title: Pantoea sp. strain B5559, FeCl3 treated

description: Library name: plus_B5559

organism: Pantoea


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 20

description: Library name: Baboon-miRNA-Hugh Taylor_020


title: Pantoea sp. strain B5559, no FeCl3

description: Library name: minus_B5559


title: IFN2-LineC-Dif3-Sample1

description:
Library name: Sample 2
Column 4 in Count Table


title: IFN1-LineD-Dif1-Sample1

description:
Library name: Sample 1
Column 3 in Count Table


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 18

description: Library name: Baboon-miRNA-Hugh Taylor_018


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 16

description: Library name: Baboon-miRNA-Hugh Taylor_016


title: 4-cell embryo, control rABE, n=3

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

department: BMB

institute: UMass Chan Medical School

description: Library name: rABE-48hpf_NovaSeq

data_processing:
StringTie 2.2.1 for TPM and SAILOR for edits.
Assembly: mm10
Supplementary files format and content: TPM (txt files) and SAILOR edits (bed files).

organism: Mus musculus

source_name: 4-cell embryo

extract_protocol:
Smart-seq3 polyA mRNA with TCL buffer and RNA XP beads.
Smart-seq3 and Nextera XT library prep kit.

value: 4-cell embryo

value: FVB/NJ

value: rABE (control) mRNA microinjection at zygote stage

value: 4-cell stage


title: RPF, TRMT5 KD, replicate 2

city: Cambridge

first: Francisco

middle: Jose

last: Campos-Laborie

address: Tennis Court Rd

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
Library name: RPF_TRMT5_2
Poly RNA, Ribo-protected fragments

data_processing:
Reads were mapped against the reference genome sequence (GRCh38, v98 - longest CDS reference) using bowtie2, where rDNA and mtRNA sequences were previously filtered from FASTA files. Single mapper reads were kept using samtools and duplicates were removed by umi-tools ‘dedup’ tool. Following alignment and filtering, P-site coverage of CDS reads (e.g. for codon occupancy analysis) and whole transcript coverage (e.g. for transcriptional efficiency analysis) were produced using own R scripts. TE efficiency analysis was performed between control (PANC-1 WT cells) and knockdown conditions (PANC-1 TRMT5-KD cells). After filtering transcripts with fewer than 20 reads (n=11596 transcripts), Ribosome Protected Fragments (RPF) and input RNA reads were normalized (median of ratios normalization) and compared using the Xtail R package. Genes with adjusted p-value < 0.05 and absolute TE log2FC > 0 were considered significant. Codon occupancy analysis was performed by comparing observed and expected reads on P-site per codon from every transcript. After summarizing observed count reads per codon, linear regression against expected counts (calculated as described in ‘m1G meRIP codon usage analysis’ section) was performed. Residuals of the linear model were calculated and compared between control and knockdown replicates via t-test. For every codon, t-statistics from all genes were considered to assess significant enrichment/depletion (p-value < 0.001) in a particular subset of genes (i.e. up or down TE).
Assembly: Reads were mapped against the reference genome sequence (GRCh38, v98 - longest CDS reference)
Supplementary files format and content: Bedgraph file per sample (GRCh38, v98)
Library strategy: Ribo-Seq

source_name: Pancreas

growth_protocol: PANC-1 cells were cultured in DMEM medium (Gibco) supplemented with 10% (v/v) FBS (Gibco).

extract_protocol:
Ribosome profiling. Cells were washed briefly with ice-cold PBS (supplemented with 100 µg/ml Cycloheximide (CHX)) and the cell pellet was resuspended in RP-Lysis Buffer (20 mM Tris-HCL pH 7.5, 10 mM MgCl2, 100 mM KCl, 1 % Triton-X 100, 2 mM DTT, 100 µg/ml CHX, 1x EDTA-free Complete Protease Inhibitor Cocktail). After lysis, all samples were centrifuged at 6400 rpm, 5 min, 4 °C. The supernatant was digested with 1 U/µl of RNase I for 45 min at room temperature. Digested lysates were run through a 7 % - 47 % sucrose gradient using a Beckmann Coulter SW41 Ti rotor at 36,000 rpm at 4 °C for 2 h. Monosome fractions were obtained and digested with 1 % SDS and 0,15 µg/µl Proteinase K for 45 min at 45 °C. Resulting footprints were extracted following a standard Trizol-Chloroform extraction protocol and size-selected using a 12 % denaturing gel.
Library construction: Footprint RNA was dephosphorylated using 5 U of T4 PNK for 30 min at 37°C. Subsequently, preadenylated UMI-linkers were ligated to the RNA 3’end using 100 U T4 RNA Ligase. Residual linker was eliminated with 25 U 5’ Deadenylase and 15 U RecJf for 60 min at 30 °C. Ribosomal RNA was depleted using a biotinylated rRNA oligo pool in 1x SSC buffer (3 M NaCl, 300 mM trisodium citrate, pH 7) and pulled down using MyOne Streptavidin C1 DynaBeads. Resulting RNA footprints were reverse transcribed using the SuperScript III First-Strand Synthesis System. Resulting cDNA was size-selected using an 8 % denaturing gel. cDNA was circularized using the CircLigase II Kit from Lucigen. Samples were subjected to PCR to introduce Illumina i7 indexes, followed by size-selection on an 8 % non-denaturing PAGE gel. Resulting sample concentrations were measured with Qubit 3.0 using Qubit DNA HS kit. The final libraries were single-end sequenced with an Illumina NextSeq2000 P2 system.

treatment_protocol: PANC-1 cells were reversed transfected with siRNAs using  DharmaFECT 1 transfection reagent (Horizon) according to the manufacturer’s instructions.

value: Pancreas

value: Pancreatic Ductal Adenocarcinoma

value: TRMT5 KD

value: I


title: RPF, TRMT5 KD, replicate 1

description:
Library name: RPF_TRMT5_1
Poly RNA, Ribo-protected fragments


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 14

description: Library name: Baboon-miRNA-Hugh Taylor_014


title: RNAseq_kdm6bKO_p1_rep3

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

description:
Library name: Sample 9
DGE_emx1_kdm6b_p1.txt

data_processing:
Reads were aligned to the mouse reference genome (UCSC mm9) using HISAT2
The mapped reads were normalized to reads as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
The differential gene expression was calculated by Cuffdiff program and the statistic cutoff for identification of differential gene expression is q < 0.05 and 2-fold RPKM change between samples.
Assembly: mm9
Supplementary files format and content: DGE_emx1_kdm6b_p1.txt
Supplementary files format and content: DGE_emx1_kdm6b_p30.txt

source_name: mouse cortex

extract_protocol:
RNA was extracted and purified from cells using QI shredder (Qiagen) and RNeasy (Qiagen) spin columns.
Total RNA was extracted using per the manufacturer’s instructions. RNA-seq libraries were  repared from total RNA using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). Adapter-ligated cDNA was PCR-amplified and size-selected magnetic beads. DNA was measured by an Invitrogen Qubit fluorometer. Libraries were sequenced on AVITI or NovaSeq 6000 sequencer at the Michigan State University Genomics Core.

value: mouse cortex


title: RNAseq_kdm6bKO_p1_rep6

description:
Library name: Sample 12
DGE_emx1_kdm6b_p1.txt


title: RNAseq_kdm6bKO_p1_rep5

description:
Library name: Sample 11
DGE_emx1_kdm6b_p1.txt


title: 4-cell embryo, Ybx1-rABE, n=5

description: Library name: Ybx1-rABE-48hpf

value: Ybx1-rABE mRNA microinjection at zygote stage


title: DIA WT3

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

description:
Library name: 25L006841
TPMs in column ARG1WT_DIAM_25L006841 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt

data_processing:
NGS data quality was assessed with FastQC (RRID: SCR 014583).
Gene-level quantification was performed with Salmon version 1.9.0 (RRID: SCR_017036). Settings were: -libType A, -gcBias, -biasSpeedSamp 5 using the mm39 (Release 113, GRCm39) reference transcriptome provided by Gencode.
Gene count normalization and differential expression analysis were performed with DESeq2 version 1.46.0 (RRID: SCR_015687) after import of gene-level estimates with ‘tximport’ version 1.34.0 (RRID: SCR_016752) in R (RRID: SCR_001905, R version 4.4.2). For gene annotation, ‘AnnotationHub’ version 3.14.0 (RRID: SCR_0024227), and genome information provided by Ensembl (GRCm39, release 113) was used. Genes with a mean expression higher than the 10th percentile, fold-change of 1.5-fold and Benjamini-Hochberg-adjusted p value < 0.05 were defined as significantly changed.
Assembly: mm39
Supplementary files format and content: “SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt” contains the TPMs of all genes per sample (unfiltered) as well as the log2FoldChange (log2FC), p values (P) and Benjamini-Hochberg-adjusted P-value (Padj) of the DESeq results for the medium effect in WT (“_wt_DIAMvsDMEM”), the ARG1KO effect on DMEM (“_DMEM_Arg1KOvsWT”), the ARG1KO effect on DIAM (“_DIAM_Arg1KOvsWT”) and the ARG1KO-dependent DIAM effect (“_Arg1KOdepDIAM”), besides the baseMean, ENSEMBL and ENTREZ gene IDs and gene symbols as tab-delimited text  file (.txt).

source_name: aortic smooth muscle cells

growth_protocol: Primary SMCs were isolated from the aorta of RBC.ARG1 wildtype (WT) and RBC.ARG1 knockout (KO) mice, cut into small pieces and digested in Dulbecco Modified Eagle Medium (DMEM; GlutaAX-I; Gibco) containing collagenase II (5 mg/mL; Gibco). Cells were resuspended in DMEM containing 10% fetal bovine serum (FBS; Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco), and seeded onto 0.2% gelatin-coated 6-well plates. Cells were cultivated in a humidified 5% CO2 atmosphere at 37℃.

extract_protocol:
Total RNA was isolated from primary murine SMCs using TRI Reagent (Thermo Fisher Scientific). The quantity and quality of the isolated RNA was verified using spectrophotometry (Nanodrop; Thermo Scientific) and validated on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano kit (for RNA-sequencing), following the manufacturer’s instructions.
Library preparation and rRNA depletion were conducted using the TruSeq unstranded mRNA Library Prep kit (Illumina) starting with 500 ng of DNAse-depleted total RNA for each biological triplicate.

treatment_protocol: To promote lipid accumulation, SMCs (at 80% confluency) were switched to DMEM supplemented with dexamethasone (0.1 µM; Sigma), insulin (1 µM; Sigma) and L-ascorbic acid (50 µg/mL; Sigma) for 10 days. Controls were maintained in DMEM with 10% FBS.

tag: strain

tag: Sex

value: male

value: aortic smooth muscle cells

value: DIAM


title: Sample1

type: RNA

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

description: Mouse 5k Panel

hyb_protocol: Xenium Prime 5K Mouse Pan Tissue and Pathways Assay Kit was used according to manufacturer's instructions

scan_protocol: Spatial transcriptomics was performed using fully automated Xenium Analyzer instrument.

data_processing: Xenium Onboard Analysis v4.0.1

label: Xenium probe set

source_name: liver

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Five-micron tissue sections were cut from FFPE tissue blocks using a microtome and adhered to Xenium slides (10x Genomics).

treatment_protocol: Mice were fed high cholesterol diet with 20% alcohol in drinking water for 10 weeks.

value: liver

tag: tissue preservation method

value: FFPE

value: high cholesterol diet, alcohol

value: WT, Kdm5b KO

tag: cell_id for treatment groups

tag: file description

value: cell id for each treatment group


title: RNAseq_kdm6bKO_p1_rep4

description:
Library name: Sample 10
DGE_emx1_kdm6b_p1.txt


title: Murine Splenic CD45+ cells

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: Murine Splenic CD45+ cells
sequencing instrument: BD Rhapsody

library_source: transcriptomic single cell

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's RhapRef_Mouse_WTA_2025-03
Supplementary files format and content: 10X-like feature, barcode and matrix files.

source_name: male (n=8)

extract_protocol:
Spleen mononuclear cells were isolated from intact mice by tissue disaggregation and density gradient centrifugation using Ficoll. CD45+ cells were isolated from spleen mononuclear cells using magnetic sorting.
Library was performed according to the manufacter’s instructions (mRNA Whole Transcriptome Analysis (WTA) Library Preparation Protocol).

value: CD45+ cells

value: Spleen

tag: age

value: 3-6 month


title: DIA WT2

description:
Library name: 25L006839
TPMs in column ARG1WT_DIAM_25L006839 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt

tag: tissue


title: DIA WT4

description:
Library name: 25L006842
TPMs in column ARG1WT_DIAM_25L006842 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: DIA KO4

description:
Library name: 25L006840
TPMs in column ARG1KO_DIAM_25L006840 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: DIA KO3

description:
Library name: 25L006838
TPMs in column ARG1KO_DIAM_25L006838 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 12

description: Library name: Baboon-miRNA-Hugh Taylor_012

value: Plasma

value: No treatment


title: RPF, WT control, replicate 2

description:
Library name: RPF_Ctrl_2
Poly RNA, Ribo-protected fragments

value: Pancreas

tag: cell line

value: Pancreatic Ductal Adenocarcinoma


title: RNAseq_kdm6bKO_p1_rep2

description:
Library name: Sample 8
DGE_emx1_kdm6b_p1.txt

value: mouse cortex

tag: genotype


title: RNAseq_kdm6bKO_p1_rep1

description:
Library name: Sample 7
DGE_emx1_kdm6b_p1.txt

tag: treatment


title: DIA KO2

description:
Library name: 25L006837
TPMs in column ARG1KO_DIAM_25L006837 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 10

description: Library name: Baboon-miRNA-Hugh Taylor_010

tag: timepoint (months)


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 8

description: Library name: Baboon-miRNA-Hugh Taylor_008

tag: baboon number


title: RPF, WT control, replicate 1

description:
Library name: RPF_Ctrl_1
Poly RNA, Ribo-protected fragments

value: I


title: Input RNA, TRMT5 KD, replicate 2

description:
Library name: Input_TRMT5_2
Poly RNA, input

value: TRMT5 KD


title: DIA WT1

description:
Library name: 25L006836
TPMs in column ARG1WT_DIAM_25L006836 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt

value: male

value: aortic smooth muscle cells


title: DIA KO1

description:
Library name: 25L006835
TPMs in column ARG1KO_DIAM_25L00683 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt

value: DIAM


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 6

description: Library name: Baboon-miRNA-Hugh Taylor_006

tag: plasma volume


title: RNAseq_kdm6bWT_p1_rep6

description:
Library name: Sample 6
DGE_emx1_kdm6b_p1.txt

value: wild-type


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 4

description: Library name: Baboon-miRNA-Hugh Taylor_004


title: DMEM WT4

description:
Library name: 25L006834
TPMs in column ARG1WT_DMEM_25L006834 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt

tag: cell type

value: DMEM


title: RNAseq_kdm6bWT_p1_rep5

description:
Library name: Sample 5
DGE_emx1_kdm6b_p1.txt


title: Input RNA, TRMT5 KD, replicate 1

description:
Library name: Input_TRMT5_1
Poly RNA, input

tag: batch


title: Input RNA, WT control, replicate 2

description:
Library name: Input_Ctrl_2
Poly RNA, input


title: RNAseq_kdm6bWT_p1_rep4

description:
Library name: Sample 4
DGE_emx1_kdm6b_p1.txt


title: RNAseq_kdm6bWT_p1_rep2

description:
Library name: Sample 2
DGE_emx1_kdm6b_p1.txt


title: m1G precipitated RNA, TRMT5 KD, experiment 2, replicate 3

description: Library name: m1G_TRMT5_e2_s3

data_processing:
Reads from both RNA and RNA-IP samples were sequenced using HiSeq4000 and mapped against the reference genome sequence (GRCh38, v98) using STAR aligner (v2.7.1). Single mapper reads were kept using samtools and PCR duplicates were removed by Picard Markduplicates [“Picard Toolkit.” 2018. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute]. ‘bedtools’ and ‘bigWigToBedGraph’ were used to generate bigWig and bedGraph tracks of all samples for visualization purposes. Using all biological replicates per condition and RNA input samples as control, MACS2 (v2.2.5) was used to roughly estimate peak size (300bp) before peak calling. Significant called peaks between IP and input samples (control and TRMT5 KD) by MACS2 (--nomodel --extsize 300bp) were kept for subsequent analyses. In parallel, the MetDiff R package was also used to call peaks following the same experimental design. Significant summits from MACS2 were kept with a fixed window of +/- 150bp, and they were overlapped and merged with MetDiff peaks using ‘findOverlapPairs’ and ‘punion’ functions from GenomicRanges R package in a single bed file for reference. Counts under peaks per replicate were obtained with the ‘featureCounts’ function (Rsubread suite) the edgeR and DESeq2 R packages were used to filter (min. 20 reads along all samples) and to normalise read counts per peak. Wald test from DESeq2 R package was used to detect differential binding between control vs KD conditions considering input and IP samples (FDR < 0.10), as well as controlling the variance between the two independent RIP-seq experiments. Peaks were annotated to CDS location using ensembldb and ChIPseeker R packages against the reference genome sequence (GRCh38, v98).
Assembly: Reads from both RNA and RNA-IP samples were sequenced using HiSeq4000 and mapped against the reference genome sequence (GRCh38, v98) using STAR aligner (v2.7.1).
Supplementary files format and content: BED files containing detected peaks (GRCh38)

extract_protocol:
5-10μg polyA+ enriched RNA of control and TRMT5 KD transfected PANC-1 cells was fragmented to 100-200nt average size using RNA fragmentation reagents following the manufacturer’s instructions (ThermoFisher Scientific). The fragment sizes were confirmed using an Agilent Tapestation 2200 with RNA screentape (Agilent).  Fragmented RNA was diluted with RNAse free water to 755μl and heated at 75ºC for 5 minutes to disrupt secondary structures, before being immediately placed on ice for >1 minute. 200U RNAseOUT (Life Technologies), 10μg anti-m1G antibody (ab208199) or GFP antibody and 200μl 5X IP buffer (50mM Tris-HCl pH7.4, 750mM NaCl, 0.5% Igepal CA-630) were then mixed with the RNA in nonstick, RNase-free tubes (ThermoFisher Scientific). The reaction was incubated overnight at 4ºC on a rotating mixer to allow the antibody to bind to the modification of interest. Protein A Dynabeads (Life Technologies) and Protein G Dynabeads (Life Technologies Ltd) were combined at a 1:1 ratio (allowing for 50μl per reaction) and washed with 1X IP buffer (10mM Tris-HCl pH7.4, 150mM, 0.1% IGEPAL CA-630) and then resuspended in 1ml 1X IP buffer containing 0.5mg/ml bovine serum albumin (BSA) to block non-specific binding to the beads. The beads were then incubated for 2 hours at 4ºC with rotation. The beads were then washed three times with 1X IP buffer and resuspended in the original volume. 50μl of blocked beads were used for each IP reaction. The pre-blocked beads were then added directly to the fragmented RNA/antibody complex prepared previously. The reactions were then incubated for 2 hours at 4ºC with rotation. The following wash steps were then used to reduce non-specific binding: low salt buffer (10mM Tris pH7.4, 75mM NaCl, 0.1% IGEPAL CA-630), high salt buffer (10mM Tris pH7.4, 200mM NaCl, 0.1% IGEPAL CA-630) and TEN buffer (10mM Tris-HCl pH7.4, 1mM EDTA, 0.05% IGEPAL CA-630). The immunoprecipitated RNA was eluted by competition with free modified nucleoside. Each IP reaction was eluted with 450μl competition elution buffer (90μl 1X IP buffer, 6mM free nucleoside, 7μl RNAseOUT and RNAse free water up to 450μl), then incubated at 4ºC for 2h with shaking. Eluted RNA was recovered using Trizol LS reagent (ThermoFisher Scientific), followed by isopropanol precipitation and precipitated overnight at -80ºC.
The immunoprecipitated RNA was used for sequencing using NEXTflex Rapid Directional sequencing kit (PerkinElmer), adjusting the ratio of AMPure XP beads (Beckman Coulter) for the desired size selection.

treatment_protocol: PANC-1 were reversed transfected with siRNAs using DharmaFECT 1 transfection reagent (Horizon) according to the manufacturer’s instructions.

value: m1G precipitation + TRMT5 KD

value: II


title: DMEM WT3

description:
Library name: 25L006833
TPMs in column ARG1WT_DMEM_25L006833 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: RNAseq_kdm6bWT_p1_rep3

description:
Library name: Sample 3
DGE_emx1_kdm6b_p1.txt


title: WT GFP 2

city: Lucknow

first: Dr Satish

last: Mishra

state: Uttar Pradesh

address: Sector 10 jankipuram extension

department: Molecular Microbiology and Immunology

country: India

institute: CSIR- Central Drug Research Institute Lucknow

description:
Library name: Sample 2
Column name in read_all_Sample.txt: WT_gfp2

data_processing:
The Illumina-compatible sequencing libraries were quantified via a Qubit fluorometer, and the fragment size distribution was analyzed using an Agilent 2200 TapeStation. The libraries were paired-end sequenced on an Illumina NovaSeq 6000 sequencer for 150 cycles (Illumina, San Diego, USA).
Assembly: Ensemble
Supplementary files format and content: CSV
Supplementary files format and content: READ COUNT MATRIX AND NORMALISED COUNT (Gene verification can be done by using https://plasmodb.org/plasmo/app/record/dataset/NCBITAXON_5823 )

organism: Plasmodium berghei

source_name: Gametocytes

extract_protocol:
To enrich the gametocytes, mice were pretreated with 50 mg/kg phenylhydrazine were injected with WT GFP and MTP KO parasites. Further, mice were given 2 mg/L sulfadiazine in the drinking water to remove the asexual blood stage of the parasite. Mice with high gametocytemia were sacrificed, and blood was collected. The gametocytes were purified using the nycodenz-density gradient centrifugation. RNA was isolated using Qiagen RNeasy micro kit and treated with DNase I in the column as per manufacturer’s instructions.
RNA sequencing libraries were prepared with an Illumina-compatible NEBNext® Ultra™ II Directional RNA Library Prep Kit.

value: Gametocytes

tag: host cell_type

value: Infected Erythrocytes (mouse)

value: Wild Type

value: gene deletion


title: Input RNA, WT control, replicate 1

description:
Library name: Input_Ctrl_1
Poly RNA, input


title: m1G precipitated RNA, TRMT5 KD, experiment 2, replicate 2

description: Library name: m1G_TRMT5_e2_s2


title: UNKGKO 1

description:
Library name: Sample 3
Column name in read_all_Sample.txt: UNKGKO1

value: PFTP KO


title: RNAseq_kdm6bWT_p1_rep1

description:
Library name: Sample 1
DGE_emx1_kdm6b_p1.txt


title: DMEM KO4

description:
Library name: 25L006832
TPMs in column ARG1KO_DMEM_25L006832 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: UNKGKO 2

description:
Library name: Sample 4
Column name in read_all_Sample.txt: UNKGKO2


title: Differential expression of microRNAs in early-stage endometriosis in baboons, Sample 2

description: Library name: Baboon-miRNA-Hugh Taylor_002

value: Plasma

value: No treatment


title: DMEM KO3

description:
Library name: 25L006830
TPMs in column ARG1KO_DMEM_25L006830 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: DMEM WT2

description:
Library name: 25L006831
TPMs in column ARG1WT_DMEM_25L006831 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: m1G precipitated RNA, TRMT5 KD, experiment 2, replicate 1

description: Library name: m1G_TRMT5_e2_s1

value: Pancreas

value: Pancreatic Ductal Adenocarcinoma


title: DMEM KO2

description:
Library name: 25L006829
TPMs in column ARG1KO_DMEM_25L006829 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: DMEM WT1

description:
Library name: 25L006828
TPMs in column ARG1WT_DMEM_25L006828 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt


title: WT GFP 1

description:
Library name: Sample 1
Column name in read_all_Sample.txt: WT_gfp1


title: Monocyte native long-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 3

city: Utrecht

first: Jorg

last: van Loosdregt

address: Lundlaan 6

country: Netherlands

institute: UMC Utrecht

description: Library name: HC3LPS_Nanopore

data_processing:
For short-read RNA-Seq, libraries were sequenced at the Utrecht Sequencing Facility using the Nextseq500 platform (Illumina), which produced single end reads of 75 bp. For Native RNA-Seq, Raw data was interpreted by Nanopore Technologies sequencing base calling software (basecRAWller) and reads that passed minimum quality were kept for the analysis.
Short-reads were trimmed using Trim Galore and aligned and counted to the reference genome using STAR. Long-reads aligned to the reference genome using minimap2 and were quantified using flair. Both data were also quantified using salmon.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts per gene/isoform (STAR and flair)
Supplementary files format and content: tab-delimited tekt file including raw abundances per isoform (salmon)

source_name: PBMC

extract_protocol:
Monocytes were lysed in TRIzol LS reagent (Thermo Fisher) directly or after LPS activation. RNA was isolated using the Dynabead mRNA Purification Kit (Thermo Fisher) according to the manufacturer's protocol. For short-read RNA-Seq, the concentration of RNA was quantified using a Qubit RNA HS assay and Qubit fluorometer (Thermo Fisher). For Native RNA-Seq, 1 μM mRNA per sample was loaded on MinION flowcells and ran for approximately two hours at the Utrecht Sequencing Facility.
For short-read RNA-Seq, polyadenylated messenger RNA was isolated using Poly(A) beads (NEXTflex), and sequencing libraries were made using the Rapid Directional RNA-seq kit (NEXTflex).

treatment_protocol: Human peripheral blood mononuclear cells (PBMCs) were obtained from healthy donor blood in sodium heparin tubes and isolated using Ficoll-paque plus (Cytiva, Marlborough, MA, USA) density gradient media. Primary human CD14+ monocytes were isolated from PBMC using automatic magnetic-activated cell sorting (MACS, Miltenyi Biotech, Bergisch Gladbach, Germany) using human CD14+ monocyte isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturers protocol. Ex vivo samples were collected at this stage, to avoid any stimulation from in vitro culture. Primary monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Thermo Fisher, Hampton, NH, USA) supplemented with 10% heat-inactivated fetal calf serum (Sigma-Aldrich, St. Louis, MI, USA), 1% L-glutamine (Life Technologies, Carlsbad, CA, USA), 100 U/mL of penicillin and 100 mg/mL of streptomycin (Gibco, New York, NY, USA). Cells were cultured at 37 °C in 5% CO2m and stimulated with 100 ng/ml LPS (Sigma-Aldrich) for 3 hours in culture medium.

value: PBMC

value: Human monocytes (CD14 +)

value: LPS


title: Input RNA, TRMT5 KD, experiment 2, replicate 3

description: Library name: Input_TRMT5_e2_s3

value: none + TRMT5 KD


title: Input RNA, TRMT5 KD, experiment 2, replicate 2

description: Library name: Input_TRMT5_e2_s2


title: CLP, KO, replicate 2

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description:
Library name: Sample 11
KO_CLP-2

data_processing:
Reads were quality checked with fastQC and preprocessed (adapter removal) with TRIMMOMATIC v0.34 (ILLUMINACLIP & MINLEN filters)
Reads were mapped to the mm39 reference genome with STAR (2.7.10b) and the gencode M30 and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differnatial gene expression was determined using DESeq2
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

growth_protocol: Male C57BL/6J mice were purchased from Janvier. All mice were housed in individually ventilated cages at standard housing conditions (22 °C, 14/10 h light/dark cycle) with food (chow diet consisting of 18% proteins, 4.5% fibers, 4.5% fat, 6.3% ashes, Provimi Kliba SA) and water ad libitum in a specific pathogen free facility.

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a Cloudbreak sequencing kit on the element AVITI according the the manufacturer's instructions

treatment_protocol: The inducubile RXRa KO was acivated by treating the mice with tamoxifen for a 5 days and then waiting for 9 days t allow the recombination to take place as well as reduces the direct tamoxifen effects.  Mice were then subjected to Sham or CLP and livers were isolated in RNA later 24h after the procedure

value: liver

value: male

value: Rxra KO

value: CLP

tag: treatment time


title: CLP, KO, replicate 3

description:
Library name: Sample 12
KO_CLP-3

tag: strain


title: RCC1-8-3-4

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

description: Library name: RCC1-8-3-4

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: DMEM KO1

description:
Library name: 25L006827
TPMs in column ARG1KO_DMEM_25L006827 of SMCs_Arg1KOvsWT_DIAMvsDMEM_unfilteredDESeqResults.txt

tag: Sex

value: aortic smooth muscle cells

value: DMEM


title: Monocyte native long-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 1

description: Library name: HC1LPS_Nanopore


title: Input RNA, TRMT5 KD, experiment 2, replicate 1

description: Library name: Input_TRMT5_e2_s1

value: II


title: Monocyte native long-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 2

description: Library name: HC2LPS_Nanopore


title: Sham, KO, replicate 3

description:
Library name: Sample 9
KO_SHAM-3

value: SHAM


title: CLP, KO, replicate 1

description:
Library name: Sample 10
KO_CLP-1


title: Sham, KO, replicate 2

description:
Library name: Sample 8
KO_SHAM-2


title: m1G precipitated RNA, WT control, experiment 2, replicate 3

description: Library name: m1G_Ctrl_e2_s3

value: m1G precipitation


title: Monocyte native long-read RNA-Seq, Ex vivo, healthy volunteer 3

description: Library name: HC3exvivo_Nanopore

value: ex vivo


title: CLP, WT, replicate 2

description:
Library name: Sample 5
WT_CLP-2

value: Rxra WT


title: Roots, LjUBI:LSH1_immunoprecipitation_rep4

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

institute: Max Planck Institute for Plant Breeding Research

description:
LjUBI-LSH1_rep4_bamCompare.bw
LjUBI-LSH1_rep4_q0.05_narrowPeak.bed

library_source: genomic

data_processing:
Raw reads were quality-controlled, and mapped to the M. truncatula reference genome version 5.0 (A17 r5.0, annotation version 1.9) (Pecrix et al., 2018) (https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/) using bowtie2.
Duplicate reads were removed from the aligned reads with Picard MarkDuplicates (http://broadinstitute.github.io/picard)
The peaks were called by macs2 (Zhang et al., 2008) with the pooled control samples and the immunoprecipitated samples as input. The initial p-value threshold for peak calling was p < 0.01. Then they were subsequently filtered by the q-value threshold of q < 0.05 to correct for false discovery rate.
The called peaks were annotated by the ChIPseeker R package (Yu et al., 2015). Peaks that were called in > 50% of replicates (3 out of 4 replicates in LjUBI:LSH1, 2 out of 3 replicates in LjUBI:NIN)) were merged using BEDToolsbedtools (Quinlan and Hall, 2010) merge and are considered as high confidence peaks.
The bigwig files were generated by deepTools2 bamCompare  (Ramírez et al., 2016) and were visualized in Medicago genome browser (https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/)
Assembly: M. truncatula reference genome version 5.0 (A17 r5.0, annotation version 1.9)
Supplementary files format and content: .narrowPeaks.bed
Supplementary files format and content: .bw file genetated to highlight differential read alignment of control and immunoprecipitations

molecule: genomic DNA

organism: Medicago truncatula

source_name: transformed roots

growth_protocol: Seeds were scarified, surface sterilized with 10 % (v/v) bleach solution, stratified for 3 days at 4 °C and germinated on water agar plates. Plants were grown in sterile conditions in controlled environment rooms at 22 °C (80 % humidity, 16 h light/8 h dark, 300 μmol m2 s-1 light intensity) on filter paper-lined agar media in sealed plates unless otherwise specified. For Chromatin-Immunoprecipitation, hairy roots were grown on modified Fahraeus medium supplemented with 0.5 mM NH4NO3 (Boisson-Dernier et al., 2001)  for 3 weeks.

extract_protocol:
ChiP was performed using a combination of two protocols described in (Schiessl et al., 2014) and (Cortijo et al., 2018). Transiently transformed 3-week old M. truncatula hairy roots in the ecotype jemalong expressing pLjUBI:GFP-LSH1, pLjUBI:GFP-NIN or control pLjUBI:NLS-GPF grown under non-symbiotic conditions were used. Root tissue [2000–3000 mg (fresh weight) per sample] were fixed in 35 mL of fixation buffer [NaHPO4 (100 mM) buffer, 1% formaldehyde, 100 μM PMSF] under vacuum for 20 min on ice. Cross-linking was stopped with 100 μM glycine for 10 min on ice. Tissue was washed twice with water, frozen in liquid nitrogen and stored at -80°C. Ground tissue was resuspended in 25 ml extraction buffer 1 (10 mM Tris-HCl pH 8, 10 mM MgCl2, 0.4 M sucrose, 100 μM PMSF, 10 mM ß-mercaptoethanol, 1 tablet (per 50 ml of buffer) of protease inhibitor cocktail complete Mini, EDTA-free (11836170001, Roche)), filtered through miracloth and centrifuged at 1800 x g for 20 min at 4°C. The pellet was resuspended in 10 ml extraction buffer 2 (10 mM Tris-HCl pH 8, 10 mM MgCl2, 0.24 M sucrose, 100 μM PMSF, 10 mM ß-mercaptoethanol, 1% Triton, 1 tablet (per 50 ml of buffer)  of protease inhibitor cocktail complete Mini, EDTA-free (11836170001, Roche)) and centrifuged at 1800 x g for 10 min at 4°C. This washing step was repeated twice, followed by three washes with extraction buffer 3 (10 mM Tris-HCl pH 8, 10 mM MgCl2, 1.70 M sucrose, 100 μM PMSF, 10 mM ß-mercaptoethanol, 0.15% Triton, 1 tablet (per 50 ml of buffer) of protease inhibitor cocktail complete Mini, EDTA-free (11836170001, Roche)) as described in Cortijo et al. 2018. Purified nuclei pellets were resuspended in 1 mL of sonication buffer containing 500 mM Hepes, 150 mM NaCl, 5 mM MgCl2, 10% (vol/vol) TRITON X-100, and one-half of a tablet of protease inhibitor mixture complete Mini, EDTA-free (Roche). Sonication was performed in a Bioruptor water bath sonicator at 4 °C (3 × 6 min high-power level with 30 s on/30 s off cycles), resulting in an average fragment size of 300-500 bp. After centrifugation, the supernatant was mixed with 500 μL of immunoprecipitation buffer containing 0.5 M Hepes, 150 mM NaCl, 5 mM MgCl2, 10% (vol/vol) TRITON X-100, 1 mg/mL BSA, and 25 μL of anti-GFP μMACS Microbeads (Miltenyi Biotec); incubated on ice for 30 min; and loaded on a μ Column (Miltenyi Biotec) that had been equilibrated with 200 μL of immunoprecipitation buffer and placed into a magnetic μMACS separator (Miltenyi Biotec). After washing four times with 200 - 400 μL of immunoprecipitation buffer and twice with 200 μL of TE buffer [100 mM Tris (pH 8), 10 mM EDTA (pH 8)], DNA was eluted once with 20 μL and twice with 50 μL of preheated (96 °C) elution buffer containing 50 mM Tris (pH 8), 10 mM EDTA, 50 mM DTT, and 1% SDS. One hundred microliters of TE buffer and 9 μL of 25 mg/mL Proteinase K (Sigma) were added to the eluted samples and to the input control samples. Cross-linking was reverted in eluted and input samples at 37 °C overnight, followed by addition of 9 μL of 25 mg/mL Proteinase K and 8 h of incubation at 65 °C, phenol-chloroform extraction, and precipitation with ethanol overnight at −20 °C. After washing in 70% (vol/vol) EtOH, the air-dried DNA was resuspended in 100 μL of PCR-grade water (Roche), purified using a PCR purification Kit (catalog no. 18104; Qiagen), and stored at −80 °C.
ChIP-Seq libraries were prepared with the Illumina TruSeq® ChiP-Seq library kit

value: transformed roots

value: LSH1 overexpression

tag: ecotype

value: jemalong

tag: cultivar

value: Jester


title: m1G precipitated RNA, WT control, experiment 2, replicate 2

description: Library name: m1G_Ctrl_e2_s2

value: Pancreas

value: Pancreatic Ductal Adenocarcinoma


title: Input RNA, WT control, experiment 2, replicate 2

description: Library name: Input_Ctrl_e2_s2


title: Input RNA, WT control, experiment 2, replicate 3

description: Library name: Input_Ctrl_e2_s3


title: Monocyte native long-read RNA-Seq, Ex vivo, healthy volunteer 1

description: Library name: HC1exvivo_Nanopore

value: PBMC

value: Human monocytes (CD14 +)


title: Sham, KO, replicate 1

description:
Library name: Sample 7
KO_SHAM-1

value: liver

value: male

value: Rxra KO


title: CLP, WT, replicate 1

description:
Library name: Sample 4
WT_CLP-1

value: CLP


title: Roots, LjUBI:LSH1_immunoprecipitation_rep2

description:
LjUBI-LSH1_rep2_bamCompare.bw
LjUBI-LSH1_rep2_q0.05_narrowPeak.bed


title: Pb_W_M_7_2

first: Ralph

last: Hückelhoven

address: Emil-Ramann-Str. 2

department: Chair of Phytopathology

institute: Technische Universität München

description: Library name: 206_S119_R1_001

data_processing:
nf‐core/rnaseq (v3.17.0) using Nextflow  (v24.04.4) for processing the raw reads
3’UTR regions of the last exon extended either by 3 kb or until the following gene
FastQC (v0.12.1) for raw read quality control
Trim Galore (v0.6.10) with Cutadapt (v4.9) for adapter trimming and filtering
STAR (v2.7.11b) was used for read alignment
Salmon (v1.10.3) for transcript quantification
Assembly: The Morex V3 genome (Mascher et al., 2021) was merged with the F. culmorum genome FusCulm_01 (GenBank assembly GCA_003033665.1) to improve mapping accuracy and count Fusarium RNA read counts.
Supplementary files format and content: The HordeumVulgareV3.salmon.gene-counts.csv is a comma-separated table containing the mapped salmon gene-counts for Hordeum vulgare after running the nf-core/rnaseq pipeline.
Supplementary files format and content: The sampleInformation.csv is a comma-separated table explaining the the abbreviations used for the sample names.

organism: Hordeum vulgare

source_name: spike tissue

growth_protocol: The plants were grown under controlled conditions in a greenhouse cabin on flooding tables at the Plant Technology Center of the Technical University of Munich. 3-litre pots with a peat substrate (Einheitserde C700, Stender, Germany) were used to grow five seeds each at a temperature of 18/16 °C day/night, with additional lighting for 16 hours per day and a relative air humidity of 60%.

extract_protocol:
Spike material was ground in liquid nitrogen, and extraction of total RNA was performed with 100 mg of each sample using the GeneMATRIX Universal RNA Purification Kit (EURx Molecular Biology Products), following the manufacturer’s instructions.
Libraries for 3’-RNA-sequencing (Moll et al., 2014) were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen, Austria) according to the manufacturer’s instructions. Library sizes were quantified with a Qubit Fluorometer 2.0 and a Qubit DNA High Sensitivity Assay Kit. Ready-to-load pools of cDNA libraries were determined with qPCR. An Agilent 2010 Electrophoresis Bioanalyzer with the High Sensitivity DNA Assay was used to check the integrity and mRNA fragment size distribution of each library.

treatment_protocol: For artificial infection, three isolates of F. culmorum, Fc002, Fc03, and Fc06 from the fungal culture collection of the Chair of Phytopathology, Technical University of Munich (Hofer et al., 2016; Hoheneder et al., 2022; Linkmeyer et al., 2013) were used. The fungi were grown on potato dextrose agar at 21°C, 60% relative humidity, and a 12 h cycle of UV plus white light and darkness. Fungal inoculum in the form of a spore solution was prepared in autoclaved tap water containing 1 ml/l Tween 80® and was adjusted to a spore concentration of 50,000 conidia/ml containing equal amounts of spores from each strain. Mock treatment consisted of autoclaved tap water and 1 ml/l Tween 80. Barley spikes were sprayed with either F. culmorum spore solution or mock solution until run-off around mid-flowering (GS 65) and afterwards covered and sealed in plastic bags for 2 days to ensure 99% relative air humidity. Treated spikes were sampled 4 and 7 days post inoculation and immediately frozen in liquid nitrogen. For each cultivar, treatment, and time point, four replicates were collected, each consisting of four pooled spikes.

value: spike tissue

value: Palmella Blue

value: watered+mock


title: Roots, LjUBI:LSH1_immunoprecipitation_rep1

description:
LjUBI-LSH1_rep1_bamCompare.bw
LjUBI-LSH1_rep1_q0.05_narrowPeak.bed


title: CLP, WT, replicate 3

description:
Library name: Sample 6
WT_CLP-3


title: Pb_W_M_7_1

description: Library name: 205_S118_R1_001


title: Roots, LjUBI:LSH1_immunoprecipitation_rep3

description:
LjUBI-LSH1_rep3_bamCompare.bw
LjUBI-LSH1_rep3_q0.05_narrowPeak.bed


title: Pb_W_M_4_3

description: Library name: 156_S84_R1_001


title: Sham, WT, replicate 2

description:
Library name: Sample 2
WT_SHAM-2

value: SHAM


title: Pb_W_M_7_3

description: Library name: 207_S120_R1_001


title: Pb_W_M_4_4

description: Library name: 161_S85_R1_001


title: Input RNA, WT control, experiment 2, replicate 1

description: Library name: Input_Ctrl_e2_s1

value: II


title: Pb_W_M_4_1

description: Library name: 145_S77_R1_001


title: Pb_W_M_4_2

description: Library name: 152_S81_R1_001


title: Sham, WT, replicate 3

description:
Library name: Sample 3
WT_SHAM-3

value: Rxra WT


title: Pb_W_Fc_7_4

description: Library name: 203_S116_R1_001

value: watered+inoculated


title: Pb_W_M_7_4

description: Library name: 208_S121_R1_001


title: m1G precipitated RNA, TRMT5 KD, experiment 1, replicate 2

description: Library name: m1G_TRMT5_e1_s2

value: m1G precipitation + TRMT5 KD

value: I


title: m1G precipitated RNA, WT control, experiment 2, replicate 1

description: Library name: m1G_Ctrl_e2_s1

value: Pancreas

value: m1G precipitation


title: m1G precipitated RNA, TRMT5 KD, experiment 1, replicate 1

description: Library name: m1G_TRMT5_e1_s1

value: Pancreatic Ductal Adenocarcinoma


title: Input RNA, TRMT5 KD, experiment 1, replicate 1

description: Library name: Input_TRMT5_e1_s1

value: none + TRMT5 KD


title: Roots, LjUBI:LSH1_control_rep4

value: transformed roots

value: LSH1 overexpression

value: jemalong

value: Jester


title: Roots, LjUBI:LSH1_control_rep3


title: Pb_W_Fc_7_3

description: Library name: 202_S115_R1_001

value: spike tissue


title: Roots, LjUBI:LSH1_control_rep1


title: Sham, WT, replicate 1

description:
Library name: Sample 1
WT_SHAM-1

value: liver

value: male


title: Roots, LjUBI:NIN_immunoprecipitation_rep3

description:
LjUBI-NIN_rep3_bamCompare.bw
LjUBI-NIN_rep3_q0.05_narrowPeak.bed

value: NIN overexpression


title: Pb_W_Fc_4_3

description: Library name: 168_S89_R1_001

value: Palmella Blue


title: m1G precipitated RNA, WT control, experiment 1, replicate 1

description: Library name: m1G_Ctrl_e1_s1


title: m1G precipitated RNA, WT control, experiment 1, replicate 2

description: Library name: m1G_Ctrl_e1_s2


title: Pb_W_Fc_7_2

description: Library name: 200_S113_R1_001


title: Input RNA, WT control, experiment 1, replicate 1

description: Library name: Input_Ctrl_e1_s1


title: Roots, LjUBI:NIN_immunoprecipitation_rep2

description:
LjUBI-NIN_rep2_bamCompare.bw
LjUBI-NIN_rep2_q0.05_narrowPeak.bed


title: Roots, LjUBI:LSH1_control_rep2


title: Pb_W_Fc_7_1

description: Library name: 199_S112_R1_001


title: 1DPA, mouse limb cultured in air liquid interface - replicate 2

city: Tübingen

first: Can

last: Aztekin

address: Max-Planck-Ring 9

department: TheFriedrich Miescher Laboratory

institute: The Max Planck Society for Biology

description: Library name: ALI-2

data_processing:
Paired-end ATAC-seq reads were trimmed for adapter sequences and low-quality bases using Trim Galore (version 0.6.10). Trimmed reads were aligned to the Mus musculus reference genome (GRCm39) using Bowtie2 (version 2.5.1) with local and very sensitive settings, allowing partial matches at read ends. Only concordant, properly paired read, with a maximum insert size of 1000 bp were retained. Alignments were filtered with samtools (version 1.16.1, using htslib 1.20) to retain only non-mitochondrial, high-confidence, properly paired reads with a mapping quality ≥10. Duplicate reads were removed using Picard MarkDuplicates (version 2.27.5) and mate information was corrected with samtools fixmate to ensure consistency across the remaining paired-end reads.
Normalized genome-wide coverage tracks were generated from final deduplicated BAM files using deepTools bamCoverage (v3.5.1) in 10 bp bins. Reads were extended to estimated fragment length, and coverage was normalized using the Reads Per Genomic Content (RPGC) method, excluding chrX, and accounting for the effective genome size of Mus musculus (GRCm39). --binSize 10  --normalizeUsing RPGC --ignoreForNormalization chrX chrM --effectiveGenomeSize $genomeSize --extendReads
Coverage tracks were subsequently used for computing signal matrices around TSS using deepTools computeMatrix (v3.5.1), with 20 bp bins and ±1 kb flanking regions, excluding regions with zero coverage.
Assembly: Mus musculus reference genome (GRCm39)
Supplementary files format and content: Normalized genome-wide coverage tracks in bigWig format

source_name: limb explants

extract_protocol:
For bulk ATAC sequencing, 4 mouse limbs each from ALI and 96-well cultures were collected at 1 dpa in 1.5 ml Protein LoBind Tubes (Eppendorf 0030108442) and washed in 1 ml of PBS 1x at room temperature. Limbs were dissociated by incubation in 200 µl of 0.25% Trypsin-EDTA (Gibco 25200-072) for 6 min at 37 °C, followed by gentle pipetting. The enzymatic reaction was stopped by the addition of 400 µl DMEM base, and diluted with 800 µl of PBS 1x. The cells were pelleted by centrifugation for 5 min at 400 rcf. Nuclei extraction was performed using the Diagenode ATAC-seq kit (Diagenode C01080002)
Sequencing libraries were generated using the Diagenode ATAC-seq kit (Diagenode C01080002) and i7 and i5 index primers described previously (Zenk et al., 2023). Quality control of sequencing libraries was performed using the Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit (Agilent 5067-4626) on the Agilent 2100 Bioanalyzer system. A 15 nM equimolar pool of samples was submitted to GENEWIZ for sequencing. The sequencing libraries, bearing dual combinatorial indices and with a 5% PhiX spike-in, were loaded on a 25B flow cell on the Illumina NovaSeq X Plus instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.8.1 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.

value: limb explants

value: WT CD-1 mice


title: 1DPA, mouse limb cultured in air liquid interface - replicate 1

description: Library name: ALI-1


title: 1DPA, mouse limb cultured in 96 well plate - replicate 2

description: Library name: 96w-2


title: 1DPA, mouse limb cultured in 96 well plate - replicate 3

description: Library name: 96w-3


title: 1DPA, mouse limb cultured in air liquid interface - replicate 3

description: Library name: ALI-3


title: Roots, LjUBI:NIN_immunoprecipitation_rep1

description:
LjUBI-NIN_rep1_bamCompare.bw
LjUBI-NIN_rep1_q0.05_narrowPeak.bed


title: Roots, LjUBI:NIN_control_rep3


title: 1DPA, mouse limb cultured in 96 well plate - replicate 1

description: Library name: 96w-1


title: Pb_W_Fc_4_4

description: Library name: 174_S91_R1_001

value: watered+inoculated


title: Pb_W_Fc_4_1

description: Library name: 151_S80_R1_001


title: Pb_W_Fc_4_2

description: Library name: 166_S87_R1_001


title: LENG8_aux_2

description: Library name: LENG8_aux_2

tag: condition


title: LENG8_aux_1

description: Library name: LENG8_aux_1


title: LENG8_aux_3

description: Library name: LENG8_aux_3


title: Roots, LjUBI:NIN_control_rep2


title: LENG8_control_3

description: Library name: LENG8_control_3


title: Gdf9-cre Nat10 cKO_3

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

country: China

institute: Life Sciences  Institute

data_processing:
The raw reads were first cleaned with Trim Galore v0.6.7, and the cleaned reads were further mapped to mm10 genome by using STAR v2.7.10a. Uniquely mapped reads were applied for gene expression quantification by using FeatureCounts b2.0.2. The trimmed reads were also mapped to the ERCC genome for gaining the percentage of ERCC.
Assembly: mm10
Supplementary files format and content: The count list calibrated by ERCC.

extract_protocol:
The fully growing oocytes (FGO) were harvested from WT and Gdf9-cre Nat10 conditional knockout female mice 36-48h after PMSG injection, then after washing by PBS with 0.2% containing, the oocytes were lysed with lysis buffer containing 0.2% Triton X-100 and RRI.
The library construction were standard Smart-seq2 protocol. Briefly, polyA RNA in cell lysis were first hybrided with Oligo-dT primer, then reverse transcripted by the PrimeScript Ⅱ RTase and TSO primer. The producted cDNA were pre-amplified with KAPA HiFi HotStart Ready Mix (2×) & TSO-PCR primer. Purified intact cDNA were then fragmented and amplified with barcodes adding by using TruePrep DNA Lybrary Prep Kit V2 for Illumina (cat.#TD502, Vazyme).

value: oocyte

value: Gdf9-cre Nat10 cKO


title: Gdf9-cre Nat10 cKO_2


title: Pb_D_M_7_4

description: Library name: 212_S125_R1_001

value: drought+mock


title: LENG8_control_2

description: Library name: LENG8_control_2


title: Pb_D_M_7_3

description: Library name: 211_S124_R1_001


title: Gdf9-cre Nat10 cKO_1


title: Wildtype_FGO_3

value: WT


title: LENG8_control_1

description: Library name: LENG8_control_1


title: Roots, LjUBI:NIN_control_rep1


title: Pb_D_M_7_2

description: Library name: 210_S123_R1_001


title: Eco RNAP on Cdf Genome R2

city: Dallas

first: Ping

last: Shen

state: Texas

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

description:
Library name: 1-Nova-EcoonCdf-ERCC_S520_L004_R1
E. coli RNA polymerase on C. difficile genome template, replicate 2

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: Clostridioides difficile

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: Pb_D_M_7_1

description: Library name: 209_S122_R1_001


title: Pb_D_M_4_4

description: Library name: 176_S92_R1_001


title: Cdf RNAP on Cdf Genome plus Cdf NusG R2

description:
Library name: 4-Nova-spikein-Cdf-on-Cdf-NusG-rep2
Clostridioides difficile RNA polymerase on C. difficile genome template + Cdf NusG, replicate 2


title: SAC3D1_aux_3

description: Library name: SAC3D1_aux_3


title: Wildtype_FGO_2


title: SAC3D1_aux_2

description: Library name: SAC3D1_aux_2


title: Cdf RNAP on Cdf Genome plus Cdf NusG R1

description:
Library name: 3-Nova-spikein-Cdf-on-Cdf-NusG-rep1
Clostridioides difficile RNA polymerase on C. difficile genome template + Cdf NusG, replicate 1


title: WT-3.IP

data_processing:
The raw reads were first cleaned with Trim Galore v0.6.7, and the cleaned reads were further mapped to mm10 genome by using STAR v2.7.10a. Uniquely mapped reads were applied for gene expression quantification by using FeatureCounts b2.0.2. The trimmed reads were also mapped to the ERCC genome for gaining the percentage of ERCC.
Assembly: mm10
Supplementary files format and content: Table_S3_ac4C_RIP-Seq_acetylated_RNA_sites.mRNA.xlsx

source_name: ovary

extract_protocol:
Total RNA from ovaries and sorted oocytes was isolated using the NucleoZOL reagent (Macherey Nagel, 740404.200) and RNeasy Mini kit,according to the manufacturers’ instructions.Polyadenylated RNA was isolated by two rounds of purification using the Dynabeads® mRNA Purification Kit (Thermo Fisher Scientific, 61006) according to the manufacturer’s protocol. ac4C-RIP-seq was performed as described previously (Daniel Arango et al., 2018), with minor modifications.
The library construction were standard Smart-seq2 protocol. Briefly, polyA RNA in cell lysis were first hybrided with Oligo-dT primer, then reverse transcripted by the PrimeScript Ⅱ RTase and TSO primer. The producted cDNA were pre-amplified with KAPA HiFi HotStart Ready Mix (2×) & TSO-PCR primer. Purified intact cDNA were then fragmented and amplified with barcodes adding by using TruePrep DNA Lybrary Prep Kit V2 for Illumina (cat.#TD502, Vazyme).

value: ovary


title: Pb_D_M_4_2

description: Library name: 163_S86_R1_001


title: SAC3D1_control_3

description: Library name: SAC3D1_control_3


title: Pb_D_M_4_3

description: Library name: 167_S88_R1_001


title: Monocyte native long-read RNA-Seq, Ex vivo, healthy volunteer 2

description: Library name: HC2exvivo_Nanopore

value: PBMC

value: Human monocytes (CD14 +)

value: ex vivo


title: SAC3D1_control_2

description: Library name: SAC3D1_control_2


title: SAC3D1_aux_1

description: Library name: SAC3D1_aux_1


title: WT.IGG


title: WT-3.Input


title: Cdf RNAP on Cdf Genome R3

description:
Library name: 2-Nova-spikein-Cdf-on-Cdf-rep2
Clostridioides difficile RNA polymerase on C. difficile genome template, replicate 3


title: Cdf RNAP on Cdf Genome R2

description:
Library name: 1-Nova-spikein-Cdf-on-Cdf-rep1
Clostridioides difficile RNA polymerase on C. difficile genome template, replicate 2


title: Pb_D_M_4_1

description: Library name: 154_S83_R1_001

value: spike tissue


title: SAC3D1_control_1

description: Library name: SAC3D1_control_1


title: WT-2.IP


title: Eco RNAP on Cdf Genome R3

description:
Library name: 2-Nova-EcoonCdf-ERCC_S521_L004_R1
E. coli RNA polymerase on C. difficile genome template, replicate 3


title: Pb_D_Fc_7_4

description: Library name: 204_S117_R1_001

value: drought+inoculated


title: DLDPh_aux_3

description: Library name: DLDPh_aux_3


title: Cdf RNAP on Cdf Genome R1

description:
Library name: 1-Cdf-on-Cdf
Clostridioides difficile RNA polymerase on C. difficile genome template, replicate 1


title: Pb_D_Fc_7_2

description: Library name: 198_S111_R1_001


title: Kang4_020_013

city: Austin

first: Ningling

last: Kang

state: Minnesota

address: 801 16th AVE NE

department: tumor microenvironment and metastasis

institute: the Hormel Institute

description: Library name: DSP_1001660015949_H_B01_S13_L001

data_processing:
*library strategy: GeoMx DSP
FASTQ files were processed using the NanoString GeoMx NGS Pipeline v2.0 or v2.2. Briefly, reads were trimmed to remove low quality bases and adapter sequences. Paired end reads were stitched and aligned, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum one mismatch allowed. Reads matching the same barcode were deduplicated by UMI. The number of raw reads was highly linearly correlated with the number of unique UMIs at all AOI sizes, suggesting largely uniform library amplification. However, to correct for any PCR amplification bias, all analyses in this study use UMI deduplicated counts. Data were exported to Excel for further analysis.
Supplementary files format and content: xlsx

source_name: CCA

extract_protocol:
Frozen sections of murine CCA were fixed with formalin overnight, and sent to the University of Minnesota Genomics Center for probe hybridization, immunofluorescence staining, and selection of ROIs for analysis. 1x Tris_EDTA (pH9.0) solution and steaming the solution to 95⁰C method were used for antigen retrieval followed by Proteinase K digestion at 37⁰C for 5 minutes (1 µg/mL) to expose RNA targets.
Library preparation was performed according to the NanoString GeoMx_NGS Readout Library Prep manual. The DSP aspirate was dried and resuspended in 10 μL DEPC_treated water, and 4 μL was used in a PCR reaction. NanoString SeqCode primers were used to amplify the tags and add Illumina adaptor sequences and sample demultiplexing barcodes. PCR products were pooled either in equal volumes or in proportion relative to AOI size, depending on the experiment, and purified with two rounds of AMPure XP beads (Beckman Coulter). Libraries were sequenced on an Illumina NextSeq 2000, according to the manufacturer’s instructions, with at least 27 × 27 paired end reads.

value: CCA

value: SB murine CCA cell line

value: CAFs of CCA


title: Kang4_020_012

description: Library name: DSP_1001660015949_H_A12_S12_L001


title: DLDPh_aux_2

description: Library name: DLDPh_aux_2


title: Eco RNAP on Cdf Genome R1

description:
Library name: 3-Eco-on-Cdf
E. coli RNA polymerase on C. difficile genome template, replicate 1


title: WT-2.Input


title: Pb_D_Fc_7_1

description: Library name: 197_S110_R1_001

value: Palmella Blue


title: WT-1.IP


title: WT-1.Input


title: Pb_D_Fc_7_3

description: Library name: 201_S114_R1_001


title: Kang4_020_011

description: Library name: DSP_1001660015949_H_A11_S11_L001


title: DLDPh_aux_1

description: Library name: DLDPh_aux_1


title: DLDPh_control_2

description: Library name: DLDPh_control_2


title: Pb_D_Fc_4_3

description: Library name: 170_S90_R1_001


title: DLDPh_control_3

description: Library name: DLDPh_control_3


title: DLDPh_control_1

description: Library name: DLDPh_control_1


title: Murine intracranial vascular endothelial cells, Sham_Cells_Set2

city: St. Louis

first: Jason

middle: P

last: Wong

state: MO

address: Neuroscience Research Building

department: Neurosurgery

institute: Washington University in St. Louis

description: Library name: Sham_Set2

data_processing:
Transcripts run through the SMART-seq-2 protocol were aligned to the mm39 transcriptome with Salmon, and a gene-level count matrix from TPM-scaled transcript abundance data was created within R using the tximport package.
Assembly: mm39
Supplementary files format and content: csv file and matrix

source_name: Brain vessels

extract_protocol:
CD31⁺CD11b⁻CD45⁻ brain endothelial cells were FACS-sorted directly into 96-well lysis buffer (Bio-Rad) supplemented with RNase inhibitor, oligo(dT), dNTPs, and ERCC spike-in controls. Sorted samples were stored at −80 °C until use.
Sequencing libraries were generated with the Illumina Nextera XT kit and pooled for sequencing on the NovaSeq 6000 platform. Sequencing was performed in 2 × 100 bp paired-end mode with dual 8 bp indexes (200-cycle kit). On average, 7.5 million paired-end reads were obtained per single cell.

value: Brain vessels

value: CD31+ sorted cells


title: Murine intracranial vascular endothelial cells, Sham_Cells_Set1

description: Library name: Sham_Set1


title: Murine intracranial vascular endothelial cells, LITT_Cells_Set1

description: Library name: LITT_Set1


title: PCID2_aux_3

description: Library name: PCID2_aux_3


title: Pb_D_Fc_4_4

description: Library name: 177_S93_R1_001


title: Kang4_020_016

description: Library name: DSP_1001660015949_H_B04_S16_L001


title: PCID2_aux_2

description: Library name: PCID2_aux_2


title: Pb_D_Fc_4_2

description: Library name: 153_S82_R1_001


title: Pb_D_Fc_4_1

description: Library name: 147_S78_R1_001


title: Murine intracranial vascular endothelial cells, LITT_Cells_Set2

description: Library name: LITT_Set2


title: 2259_Braak_II

city: Watertown

first: Mahlon

last: Collins

address: 490 Arsenal Way Suite 110

institute: Parallel Squared Technology Institute

description: Library name: sample_2259

data_processing:
fastp (default options; trim adapters and generate QC report): ‘fastp’
salmon (read mapping and quantification): salmon index -t gentrome.fa.gz -d decoys.txt -p 4 -i salmon_index --gencode
DESeq2 (differential abundance testing)
Assembly: GRCh38 (Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz)
Supplementary files format and content: .sf quantification files from Salmon

source_name: brain

extract_protocol:
total RNA extraction of Brodmann area 9 dorsolateral prefrontal cortex (approx. 50 mg; Monarch Total RNA miniprep kit [NEB #T2010]) according to manufacturer’s instructions
mRNA library preparation (poly A enrichment)

value: brain


title: PCID2_aux_1

description: Library name: PCID2_aux_1


title: Kang4_020_014

description: Library name: DSP_1001660015949_H_B02_S14_L001


title: 2233_Braak_VI

description: Library name: sample_2233


title: Mo_W_M_7_2

description: Library name: 190_S103_R1_001

value: Morex

value: watered+mock


title: B16.F10 melanoma cells, Simvastatin 3.5 uM, 24h_replicate3

city: Cluj-Napoca

first: Giorgiana

last: Negrea

state: Cluj

address: Clinicilor street

country: Romania

institute: Babes-Bolyai University

description:
Library name: Sample 6
treatment biological replicate

data_processing:
The clean obtained sequencing data were mapped to the mouse reference transcriptome by HISAT2 software (v2.0.5).
For the estimation of transcript abundance of coding genes as Fragments Per Kilobase of transcript per Million mapped reads (FPKM), StringTie-eB software (v1.3.1)  was used.
The differential expressed transcripts were identified by Ballgown package 2.22.0.
To measure the level of expression of each gene in SIM-treated group in comparison with its expression in control group, fold regulation (FR) values were calculated. Benjamini-Hochberg method was applied to adjust p-values for multiple testing.
Assembly: Mus musculus reference genome GRCm38 (mm10)
Supplementary files format and content: Sample Raw data are provided in compressed FASTQ (.fastq.gz) format
Supplementary files format and content: csv file - Differentially expressed genes (DEGs): gene identifiers (gene_symbol), fold regulation, p-values, and adjusted p-values (FDR), with indication of up- or downregulation.
Supplementary files format and content: csv file - Functional enrichment analysis: Gene Ontology (GO) and KEGG pathway results including term identifiers, term names, gene counts, and statistical significance values.
Supplementary files format and content: csv file - Protein–protein interaction (PPI) data: interaction pairs of genes/proteins
Supplementary files format and content: csv file - DEGs associated with cancer aggressiveness in cells treated with SIM compared to control
Supplementary files format and content: csv file - In silico analysis results: cross-species comparison with human A375 simvastatin-treated melanoma cell line transcriptional signatures from the LINCS L1000 dataset (CLUE platform)

growth_protocol: B16.F10 murine melanoma cells (ATCC, CRL-6457; RRID: CVCL_0159) were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Lonza Group, Basel, Switzerland) supplemented with 10% fetal bovine serum (FBS), 1% penicillin–streptomycin, and 2 mM L-glutamine. Cells were maintained as a monolayer at 37°C in a humidified atmosphere with 5% CO₂ and 20% O₂.

extract_protocol:
B16.F10 cells were seeded as 1x10^6 cells/flask and treated with 3.5 µM SIM for 24h at 37°C. Then, the RNA isolation was performed using peqGOLD Total RNA isolation kit (PeqLab, Erlangen, DE), including the DNase digestion treatment of the lysates (peqGOLD DNase I Digest Kit, PeqLab, Erlangen, DE), to avoid DNA contamination, according to the manufacturer’s instructions [160]. The RNA was eluted with 50 μl of RNase-free water.
To generate strand-specific cDNA libraries, TruSeq Stranded Total RNA (Illumina, Inc.) was used followed by quality control procedure (Qubit 2.0 Fluorometer, Thermo Scientific, USA; Agilent 2100 bioanalyzer, Argilent Technologies, USA).

treatment_protocol: Simvastatin (SIM)  was purchased from Sigma-Aldrich Chemie GmbH, Germany. SIM IC50 (3.5 µM), as determined in our previous study was prepared from the stock solution of 24 mM SIM into the culture medium shortly before use. Cells were incubated with 3.5 µM SIM for 24h.

value: malignant melanocytic cells

value: WT

value: Simvastatin 3.5 uM


title: B16.F10 melanoma cells, Simvastatin 3.5 uM, 24h_replicate2

description:
Library name: Sample 5
treatment biological replicate


title: Mo_W_M_7_3

description: Library name: 191_S104_R1_001


title: B16.F10 melanoma cells, Simvastatin 3.5 uM, 24h_replicate1

description:
Library name: Sample 4
treatment biological replicate


title: PCID2_control_2

description: Library name: PCID2_control_2

value: untreated


title: 2232_Braak_V

description: Library name: sample_2232


title: PCID2_control_3

description: Library name: PCID2_control_3


title: CETN2_3_aux_3

description: Library name: CETN2_3_aux_3


title: 2225_Braak_V

description: Library name: sample_2225


title: 2223_Braak_VI

description: Library name: sample_2223


title: Mo_W_M_7_1

description: Library name: 189_S102_R1_001


title: B16.F10 melanoma cells, control, 24h_replicate1

description:
Library name: Sample 1
control biological replicate

value: no treatment


title: B16.F10 melanoma cells, control, 24h_replicate3

description:
Library name: Sample 3
control biological replicate


title: PCID2_control_1

description: Library name: PCID2_control_1


title: Mo_W_M_7_4

description: Library name: 192_S105_R1_001


title: Mo_W_M_4_4

description: Library name: 136_S72_R1_001


title: Wildtype_FGO_1

value: oocyte


title: CETN2_3_aux_2

description: Library name: CETN2_3_aux_2


title: Resveratrol Treated Visceral Adipose Tissue 2

city: Chilpancingo de los Bravo

first: Mónica

last: Espinoza-Rojo

state: Guerrero

address: Av. Lazaro Cardenas SN

department: Facultad de Ciencias Químico Biológicas

country: Mexico

institute: Universidad Autónoma de Guerrero

description: Library name: VOBRSV2

data_processing:
Quality control of raw FASTQ files was performed using FastQC.
Read alignment to the Mus musculus reference genome (GRCm39) was performed using the Rsubread package (v2.12.3) with the align function.
Gene-level quantification was performed using featureCounts against the Ensembl GRCm39.115 annotation (GTF).
Assembly: GRCm39 (Ensembl release 115)
Supplementary files format and content: csv file include raw read counts per gene

source_name: Visceral adipose tissue

growth_protocol: Male C57BL/6 mice (8 weeks of age) were fed a High-Fat Diet (60% kcal from fat) for 8 weeks. Control animals received standard chow. Mice were housed under controlled conditions (22 ± 2°C, 12h light/dark cycle).

extract_protocol:
Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (74804, Quiagen) protocol. RNA concentration and purity were determined using NanoDrop, and integrity was confirmed using an Agilent 2100 Bioanalyzer (RIN values > 7.0 for all samples).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit (Poly-A enrichment). High-throughput sequencing was performed on an Illumina NovaSeq 6000 platform (Novogene Co., Ltd.) generating paired-end 150 bp (PE150) reads with an average depth of 20-30 million reads per sample.

treatment_protocol: Treatments were administered daily via gastric tube for 28 days, following 8 weeks of HFD (16 weeks of age). Dose: Resveratrol (2.25 mg/kg). Untreated groups received only the vehicle.

value: Visceral adipose tissue

value: resveratrol


title: B16.F10 melanoma cells, control, 24h_replicate2

description:
Library name: Sample 2
control biological replicate


title: Kang4_020_015

description: Library name: DSP_1001660015949_H_B03_S15_L001

value: CCA


title: 2203_Braak_VI

description: Library name: sample_2203


title: Resveratrol Treated Visceral Adipose Tissue 1

description: Library name: VOBRSV1


title: 2191_Braak_II

description: Library name: sample_2191


title: Mo_W_M_4_3

description: Library name: 127_S70_R1_001

value: spike tissue


title: CETN2_3_aux_1

description: Library name: CETN2_3_aux_1


title: 2132_Braak_V

description: Library name: sample_2132


title: Mo_W_M_4_1

description: Library name: 115_S65_R1_001


title: 2112_Braak_VI

description: Library name: sample_2112


title: CETN2_3_control_3

description: Library name: CETN2_3_control_3


title: Mo_W_M_4_2

description: Library name: 119_S67_R1_001


title: 2068_Braak_II

description: Library name: sample_2068


title: CETN2_3_control_2

description: Library name: CETN2_3_control_2


title: Mo_W_Fc_7_4

description: Library name: 188_S101_R1_001

value: watered+inoculated


title: Obesity Visceral Adipose Tissue 1

description: Library name: VOB1

value: vehicle


title: Obesity Visceral Adipose Tissue 2

description: Library name: VOB2


title: CETN2_3_control_1

description: Library name: CETN2_3_control_1


title: Mo_W_Fc_7_3

description: Library name: 185_S98_R1_001


title: Control Visceral Adipose Tissue, vehicle 1

description: Library name: VC1


title: 2015_Braak_III

description: Library name: sample_2015


title: 1926_Braak_V

description: Library name: sample_1926


title: 2018_Braak_II

description: Library name: sample_2018


title: DLD_aux_2

description: Library name: DLD_aux_2


title: Mo_W_Fc_7_1

description: Library name: 182_S95_R1_001


title: Mo_W_Fc_7_2

description: Library name: 183_S96_R1_001


title: DLD_aux_3

description: Library name: DLD_aux_3


title: Curcumin Treated Visceral Adipose Tissue 1

description: Library name: VDMCUR1

growth_protocol: Male C57BL/6 mice were used. Diabetes was induced with a single dose of Streptozotocin (70 mg/kg, i.p.) at 2 days of age. At 3 weeks of age, mice began a High-Fat Diet (60% kcal from fat) for 8 weeks. Control mice were fed standard laboratory chow. Animals were housed under controlled temperature and a 12h light/dark cycle.

treatment_protocol: Curcumin (50 mg/kg) was administered daily via oral gavage for 28 days, starting at week 8 of the HFD protocol (11 weeks of age). Control and untreated DM groups received the vehicle only.

value: curcumin


title: Diabetic Visceral Adipose Tissue 2

description: Library name: VDM2


title: Curcumin Treated Visceral Adipose Tissue 2

description: Library name: VDMCUR2


title: Mo_W_Fc_4_4

description: Library name: 140_S74_R1_001


title: 1907_Braak_III

description: Library name: sample_1907


title: DLD_aux_1

description: Library name: DLD_aux_1


title: Mo_W_Fc_4_2

description: Library name: 120_S68_R1_001


title: Diabetic Visceral Adipose Tissue 1

description: Library name: VDM1


title: Mo_W_Fc_4_3

description: Library name: 125_S69_R1_001


title: 1906_Braak_III

description: Library name: sample_1906


title: DLD_control_2

description: Library name: DLD_control_2


title: Mo_W_Fc_4_1

description: Library name: 117_S66_R1_001


title: Mo_D_M_7_4

description: Library name: 196_S109_R1_001

value: drought+mock


title: 1854_Braak_III

description: Library name: sample_1854

value: brain


title: Control Visceral Adipose Tissue 1

description: Library name: VC1


title: TPR_4h_aux_3

description:
Library name: TPR_74_4G_4h_aux_3
Ribo-Zero-depleted

library_source: other

molecule: other


title: DLD_control_3

description: Library name: DLD_control_3


title: 1886_Braak_0

description: Library name: sample_1886


title: Aged garlic extract Treated Hypothalamus 1

description: Library name: DMEAE1

data_processing:
Quality control of raw FASTQ files was performed using FastQC.
Sequence alignment to the Mus musculus reference genome (GRCm39) was executed using the Rsubread package (v2.12.3) with the align function in R environment.
Gene-level quantification was performed using featureCounts against the Ensembl GRCm39.115 annotation (GTF).
Assembly: GRCm39 (Ensembl release 115)
Supplementary files format and content: csv file include raw read counts per gene

source_name: Hypothalamus

growth_protocol: Male C57BL/6 mice were used. Diabetes was induced via a single intraperitoneal injection of Streptozotocin (70 mg/kg) at postnatal day 2. At 3 weeks of age, mice were transitioned to a High-Fat Diet (60% kcal from fat) for 8 weeks. Control animals received a standard laboratory diet. All mice were maintained under a 12h light/dark cycle with ad libitum access to water.

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen) protocol. RNA concentration and purity were determined using NanoDrop, and integrity was confirmed using an Agilent 2100 Bioanalyzer (RIN values > 7.0 for all samples).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit (Poly-A enrichment). High-throughput sequencing was performed on an Illumina NovaSeq 6000 platform (Novogene Co., Ltd.) generating paired-end 150 bp (PE150) reads with an average depth of 20-30 million reads per sample.

treatment_protocol: Treatments were administered daily for 28 days starting at week 7 of the HFD protocol. Groups received either Curcumin (50 mg/kg) or Aged Garlic Extract (200 mg/kg) prepared in a suitable vehicle and delivered via oral gavage. The control and untreated DM groups received the vehicle only.

value: Hypothalamus

value: aged garlic extract


title: 1845_Braak_VI

description: Library name: sample_1845


title: Aged garlic extract Treated Hypothalamus 2

description: Library name: DMEAE2


title: Curcumin Treated Hypothalamus 3

description: Library name: DMCUR3


title: Mo_D_M_7_3

description: Library name: 195_S108_R1_001

value: Morex


title: TPR_4h_aux_2

description:
Library name: TPR_74_4G_4h_aux_2
Ribo-Zero-depleted


title: Curcumin Treated Hypothalamus 2

description: Library name: DMCUR2


title: Mo_D_M_7_2

description: Library name: 194_S107_R1_001


title: 1837_Braak_I

description: Library name: sample_1837


title: 1703_Braak_0

description: Library name: sample_1703


title: Mo_D_M_7_1

description: Library name: 193_S106_R1_001


title: TPR_untreated_2

description:
Library name: TPR_74_4G_untreated_2
Ribo-Zero-depleted


title: Mo_D_M_4_3

description: Library name: 129_S71_R1_001


title: Mo_D_M_4_4

description: Library name: 144_S76_R1_001


title: TPR_untreated_3

description:
Library name: TPR_74_4G_untreated_3
Ribo-Zero-depleted


title: Diabetic Hypothalamus 3

description: Library name: DM3


title: TPR_untreated_1

description:
Library name: TPR_74_4G_untreated_1
Ribo-Zero-depleted


title: Curcumin Treated Hypothalamus 1

description: Library name: DMCUR1


title: Mo_D_M_4_2

description: Library name: 111_S63_R1_001


title: TPR_4h_aux_1

description:
Library name: TPR_74_4G_4h_aux_1
Ribo-Zero-depleted


title: 1636_Braak_VI

description: Library name: sample_1636


title: GANP_4h_aux_3

description:
Library name: GANP_4h_aux_3
Ribo-Zero-depleted

value: GANP-AID


title: 1669_Braak_I

description: Library name: sample_1669


title: GANP_4h_aux_2

description:
Library name: GANP_4h_aux_2
Ribo-Zero-depleted


title: Mo_D_M_4_1

description: Library name: 110_S62_R1_001


title: GANP_4h_aux_1

description:
Library name: GANP_4h_aux_1
Ribo-Zero-depleted


title: Diabetic Hypothalamus 1

description: Library name: DM1


title: sample33, HIV negative, invasive cervical carcinoma

city: Accra

first: Charles

middle: Ochieng'

last: Olwal

address: WACCBIP, Volta Road, University Of Ghana

department: Department of Biochemistry, Cell and Molecular Biology

country: Ghana

institute: West African Centre for Cell Biology of Infectious Pathogens

description:
Library name: Sample 33
Column name in raw_counts.txt: CK-21-12

data_processing:
Raw fastq files were subjected to quality control using the FastQC and trimmed using Cutadapt to filter out poor-quality reads and adapters. After trimming, we mapped the reads to the human reference genome (hg38) using STAR package. We counted the reads per transcript using featureCount of the Subread package to generate a count matrix data.
Assembly: Reads were mapped to human reference genome (hg38) curated by the University of California, Santa Cruz
Supplementary files format and content: The processed data included a count matrix data in text format

source_name: Cervical

extract_protocol:
RNA was extracted using an automated nucleic acid extraction system (TANBead maelstrom 9600) and TANBead® Nucleic Acid Extraction Kit (Ref #W665S66) following manufacturers instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® together with the NEBNext rRNA Depletion Kit version 2 following manufacturers protocols.

value: Cervical

value: Epithelial cells


title: sample35, HIV negative, invasive cervical carcinoma

description:
Library name: Sample 35
Column name in raw_counts.txt: CK-21-14


title: Mo_D_Fc_7_4

city: Freising

description: Library name: 187_S100_R1_001

value: drought+inoculated


title: Mo_D_Fc_7_3

description: Library name: 186_S99_R1_001


title: sample34, HIV negative, invasive cervical carcinoma

description:
Library name: Sample 34
Column name in raw_counts.txt: CK-21-13


title: sample32, HIV negative, precancerous cervical lesion

description:
Library name: Sample 32
Column name in raw_counts.txt: CK-21-11


title: Mo_D_Fc_7_2

description: Library name: 184_S97_R1_001


title: sample31, HIV negative, invasive cervical carcinoma

description:
Library name: Sample 31
Column name in raw_counts.txt: CK-21-10


title: GANP_untreated_3

description:
Library name: GANP_untreated_3
Ribo-Zero-depleted

value: untreated


title: GANP_untreated_2

description:
Library name: GANP_untreated_2
Ribo-Zero-depleted


title: Mo_D_Fc_7_1

description: Library name: 181_S94_R1_001


title: PCID2_4h_aux_3

description:
Library name: PCID2_4h_aux_3
Ribo-Zero-depleted


title: DLD_control_1

description: Library name: DLD_control_1


title: 1628_Braak_VI

description: Library name: sample_1628


title: RNAseq_kdm6bKO_p30_rep6

city: East Lansing

first: Jin

last: He

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

description:
Library name: Sample 24
DGE_emx1_kdm6b_p30.txt

data_processing:
Reads were aligned to the mouse reference genome (UCSC mm9) using HISAT2
The mapped reads were normalized to reads as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
The differential gene expression was calculated by Cuffdiff program and the statistic cutoff for identification of differential gene expression is q < 0.05 and 2-fold RPKM change between samples.
Assembly: mm9
Supplementary files format and content: DGE_emx1_kdm6b_p1.txt
Supplementary files format and content: DGE_emx1_kdm6b_p30.txt

source_name: mouse cortex

extract_protocol:
RNA was extracted and purified from cells using QI shredder (Qiagen) and RNeasy (Qiagen) spin columns.
Total RNA was extracted using per the manufacturer’s instructions. RNA-seq libraries were  repared from total RNA using the VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). Adapter-ligated cDNA was PCR-amplified and size-selected magnetic beads. DNA was measured by an Invitrogen Qubit fluorometer. Libraries were sequenced on AVITI or NovaSeq 6000 sequencer at the Michigan State University Genomics Core.

value: mouse cortex


title: GANP_untreated_1

description:
Library name: GANP_untreated_1
Ribo-Zero-depleted


title: sample30, HIV negative, invasive cervical carcinoma

description:
Library name: Sample 30
Column name in raw_counts.txt: CK-21-09


title: Mo_D_Fc_4_4

description: Library name: 142_S75_R1_001


title: Mo_D_Fc_4_3

description: Library name: 137_S73_R1_001


title: sample29, HIV negative, precancerous cervical lesion

description:
Library name: Sample 29
Column name in raw_counts.txt: CK-21-08


title: RNAseq_kdm6bKO_p30_rep5

description:
Library name: Sample 23
DGE_emx1_kdm6b_p30.txt


title: Control Hypothalamus 1

description: Library name: C1


title: RNAseq_kdm6bKO_p30_rep2

description:
Library name: Sample 20
DGE_emx1_kdm6b_p30.txt


title: Mo_D_Fc_4_1

description: Library name: 109_S61_R1_001


title: sample27, HIV negative, invasive cervical carcinoma

description:
Library name: Sample 27
Column name in raw_counts.txt: CK-21-06


title: RNAseq_kdm6bKO_p30_rep4

description:
Library name: Sample 22
DGE_emx1_kdm6b_p30.txt


title: Diabetic Hypothalamus 4

description: Library name: DM4


title: PCID2_4h_aux_2

description:
Library name: PCID2_4h_aux_2
Ribo-Zero-depleted


title: Mo_D_Fc_4_2

description: Library name: 112_S64_R1_001


title: RNAseq_kdm6bKO_p30_rep1

description:
Library name: Sample 19
DGE_emx1_kdm6b_p30.txt


title: PCID2_4h_aux_1

description:
Library name: PCID2_4h_aux_1
Ribo-Zero-depleted


title: Control Hypothalamus 3

description: Library name: C3


title: PCID2_untreated_1

description:
Library name: PCID2_untreated_1
Ribo-Zero-depleted


title: sample25, HIV negative, invasive cervical carcinoma

description:
Library name: Sample 25
Column name in raw_counts.txt: CK-21-04


title: RNAseq_kdm6bKO_p30_rep3

description:
Library name: Sample 21
DGE_emx1_kdm6b_p30.txt


title: B_W_M_7_2

description: Library name: 91_S47_R1_001

value: Barke

value: watered+mock


title: RNAseq_Kdm6bWT_p30_rep6

description:
Library name: Sample 18
DGE_emx1_kdm6b_p30.txt

value: wild-type


title: Control Hypothalamus 2

description: Library name: C2


title: B_W_M_7_4

description: Library name: 97_S53_R1_001

value: spike tissue


title: PCID2_untreated_2

description:
Library name: PCID2_untreated_2
Ribo-Zero-depleted


title: sample24, HIV negative, invasive cervical carcinoma

description:
Library name: Sample 24
Column name in raw_counts.txt: CK-21-03


title: sample28, HIV positive, invasive cervical carcinoma

description:
Library name: Sample 28
Column name in raw_counts.txt: CK-21-07


title: sample26, HIV negative, precancerous cervical lesion

description:
Library name: Sample 26
Column name in raw_counts.txt: CK-21-05


title: ENY2_6h_aux_2

description:
Library name: ENY2_6h_aux_2
Ribo-Zero-depleted


title: B_W_M_7_3

description: Library name: 94_S50_R1_001


title: B_W_M_7_1

description: Library name: 89_S45_R1_001


title: ENY2_6h_aux_3

description:
Library name: ENY2_6h_aux_3
Ribo-Zero-depleted


title: sample, 23, HIV negative, invasive cervical carcinoma

description:
Library name: Sample 23
Column name in raw_counts.txt: CK-21-02


title: RNAseq_Kdm6bWT_p30_rep5

description:
Library name: Sample 17
DGE_emx1_kdm6b_p30.txt


title: Diabetic Hypothalamus 2

description: Library name: DM2

value: vehicle