title: Liver Immune cells,  ConA+D8THC, Biological replicate 2

city: COLUMBIA

first: Hamida

last: Hamida

state: SC

address: 6311 Garners Ferry Road

department: Pathology, Microbiology & Immunology

institute: University of South Carolina School of Medicine

description:
Library name: ConA+D8THC2
Column name in miRNA_counts_allSamples.csv: ConA+D8THC2

data_processing:
The sequence reads were processed using the GeneGlobe RNA-seq Analysis Portal (QIAGEN) to perform sequence alignment and generate raw read counts.
Assembly: Mouse mm10
Supplementary files format and content: csv file includes raw counts for all 6 samples

source_name: Liver

extract_protocol:
Liver-infiltrating immune cells were isolated using the Mouse Liver Dissociation Kit and gentleMACS™ Octo Dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Total RNA, including miRNA, was extracted from the isolated liver immune cells using the miRNeasy Mini Kit (QIAGEN) as per the manufacturer’s protocol.
miRNA libraries were generated using the QIAseq miRNA Library Kit (QIAGEN) following manufacturer's protocol.

treatment_protocol: Autoimmune hepatitis was induced by intravenous administration of ConA (Sigma-Aldrich) at 12.5 mg/kg via the retro-orbital sinus under brief isoflurane anesthesia. Δ8-THC (Cayman; 20 mg/kg in DMSO/corn oil; 100 μL) was administered intraperitoneally 15-18 h prior to ConA and again 30 min after ConA challenge; vehicle controls received DMSO in corn oil.

tag: strain

value: Wildtype

value: Female

value: 10 weeks

value: Liver

value: liver immune cells

value: ConA (12.5mg/kg) and D8THC 20mg/kg

tag: disease state

value: ConA-induced autoimmune hepatitis


title: Liver Immune cells,  ConA+D8THC, Biological replicate 1

status: Public on Feb 18 2026

type: SRA

country: USA

description:
Library name: ConA+D8THC1
Column name in miRNA_counts_allSamples.csv: ConA+D8THC1

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

tag: Sex

tag: age

tag: tissue

tag: cell type

tag: treatment


title: Psoriasis_17_NL_88

type: RNA

city: Aarhus N

first: Thomas

last: Emmanuel

state: Midtjylland

address: Palle Juul Jensens Boulevard 99

department: Dermatology

country: Denmark

institute: Aarhus University

hyb_protocol: Following RNA readout, tissues were incubated for 2 h with a cocktail of four fluorophore-conjugated antibodies (DNA, PanCK, CD45, CD68 and a general membrane stain) within the CosMx SMI instrument. After washing away unbound antibodies and DAPI with Reporter Wash Buffer, Imaging Buffer was added, and nine Z-stack images were acquired across the five channels (four antibodies plus DAPI).

scan_protocol: Image processing and feature extraction were performed using the Nanostring analysis pipeline, which first identifies the XYZ coordinates of individual transcripts. Following image registration, feature detection, and localisation, Z-stack images of nuclear and membrane markers were used to define cell boundaries through a machine-learning–based segmentation algorithm. These segmentation boundaries enabled assignment of transcripts to individual cells and subcellular compartments, resulting in the generation of a cell-by-gene count matrix. The pipeline outputs included the cell-by-gene matrix, cell segmentation polygons, and associated cell metadata.

data_processing: Processed files were combined into a seurat object; standard workflow for CosMx data, reflecting the output generated by the AtomX cloud. The processed files uploaded also allow for manual creation of the Seurat object in RStudio, if required.

organism: Homo sapiens

source_name: skin

label_protocol: RNA target readout on the CosMx SMI instrument was performed according to the manufacturer’s workflow. Briefly, the assembled flow cell was loaded onto the instrument, and Reporter Wash Buffer was introduced to remove air bubbles. A preview scan of the full flow cell was acquired, and 9-12 fields of view (FOVs) were positioned on each TMA to correspond to regions of interest identified on an H&E-stained adjacent serial section. RNA readout commenced by introducing 100 μl of Reporter Pool 1 into the flow cell, followed by a 15-min incubation. Unbound reporter probes were removed by washing with 1 mL Reporter Wash Buffer, after which Imaging Buffer was added. For each FoV, nine Z-stack images (0.8 μm step size) were captured. Fluorophores were then photocleaved by UV exposure and removed with Strip Wash Buffer. This fluidic and imaging cycle was performed sequentially for all 16 reporter pools, and the complete 16-cycle hybridization–imaging process was repeated multiple times to enhance RNA detection sensitivity.

extract_protocol: Formalin fixed paraffin embedded tissue tissue microarray cores with a diameter of 1.5 mm were cut in 5 μm thick sections were using a microtome. Slides were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH),  deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes. In situ hybridization was performed according to the manufacturer’s instructions (User Manual: Slide Preparation for RNA Assays, NanoString).

value: skin

tag: lesional/nonlesional

value: NL

tag: characteristics

tag: patient id

value: Male

tag: fields of view (fov)


title: mesc_rad21_depletion_IAA-3h_018, Smart-seq3

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv

library_source: transcriptomic single cell

data_processing:
Smart-seq3 data were processed using zUMIs (https://github.com/sdparekh/zUMIs).
Bulk RNA-seq data were mapped to human reference genome using STAR and RSEM was used to calculate mRNA count for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell and sample
Supplementary files format and content: tab-delimited text files include cell barcode and sample information for Smart-seq3

molecule: polyA RNA

source_name: mouse embryonic stem cell

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq3 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq3 & bulk RNA-seq

value: mouse embryonic stem cell

value: IAA (3h)


title: Liver Immune cells,  Vehicle, Biological replicate 1

description:
Library name: Vehicle1
Column name in miRNA_counts_allSamples.csv: Vehicle1

value: DMSO

value: No disease


title: mesc_rad21_depletion_IAA-3h_013, Smart-seq3


title: Psoriasis_17_NL_92


title: Psoriasis_17_NL_90


title: T_3h-meJA-3

city: Excellent (top 5%)

first: Qifang

last: Pan

address: No 800 Dongchuan Road, Minhang District, Shanghai

institute: Shanghai Jiaotong University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: CRO.fa (We downloaded the assembled sequences from the website: http://datadryad.org/)
Supplementary files format and content: TXT file contain counts for each sample

organism: Catharanthus roseus

source_name: leaf

growth_protocol: Seedlings were transplanted into soil and grown in the greenhouse at 25 ± 2◦C.

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2-week-old seedlings were sprayed with 100μM ethephon (ET) or 100μM MeJA and then sampled at 0, 3 and 24 h for RNA-seq.

value: leaf

tag: cultivar

value: Vitae Rose Red

value: MeJA

tag: time


title: Liver Immune cells,  ConA+Vehicle, Biological replicate 2

description:
Library name: ConA+Vehicle2
Column name in miRNA_counts_allSamples.csv: ConA+Vehicle2

value: Wildtype

value: ConA (12.5mg/kg)


title: mesc_rad21_depletion_IAA-3h_020, Smart-seq3


title: 425 cels, ChIP-Seq, control, irradiation

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

description: Library name: DRIP_C1_IR_YH

library_source: genomic

data_processing:
Reads were alilgned to the human genome sequence (hg38) by Bowtie 2 v2.5.2 with default parameters
aligned reads were sorted by genomic coordinate using samtools v1.19.2
The genome was divided into 500bp bins and bins with read counts >20 in all replicates were kept for DESeq2 differential analysis. Peak calling was performed with MACS2 v2.2.9.1. Peak regions and differential bins were overlapped using bedtools intersect v2.31.1.
Assembly: UCSC Genome hg38
Supplementary files format and content: Peak files for each samples
Supplementary files format and content: Differential peak file

molecule: genomic DNA

growth_protocol: Neuronal progenitor cells were maintained in STEMdiff™ Neural Progenitor Medium (STEMCELL Technologies) at 37°C and 5% CO2

extract_protocol:
Cells were washed once with phosphate-buffered saline (PBS; Thermo Fisher) and then pelleted and suspended in 1.6 mL of Tris-EDTA buffer (TE buffer, 10 mM Tris-HCl pH 8, and 1 mM EDTA). 50 µL of SDS 20% (wt./vol) (Santa Cruz) and 5 µL of Proteinase K (20 mg/mL; Invitrogen) were added. Samples were incubated at 37°C overnight. Samples were transferred to 15 mL high-density Maxtract phase lock gel tubes (Qiagen) and one volume (1.6 mL) of Phenol:Chloroform:Isoamyl alcohol (25:24:1; Sigma-Aldrich) was added to each sample. Samples were centrifuged at 1,500 g for 5 min and the supernatant was transferred to a new 15 mL tube. Nucleic acids were precipitated by adding 1/10 volume of 3 M NaOAc pH 5.2 (160 µL) and 2.5 volumes of 100% ethanol (4 mL). Tubes were gently inverted until DNA fully precipitated and became visible. Precipitate was then transferred to a 1.5 mL tube, washed twice with 80% ethanol, air-dried, and resolved in 100 µL of TE buffer. DNA was then fragmented with restriction enzymes (BsrG I, EcoR I, Hind III, Ssp I, Xba I, 30 units each) (NEB) at 37°C overnight. The digested nucleic acids were then recovered by phenol-chloroform extraction.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer's instructions. 10ng of DNA was used as starting material for input and ip. Libraries were size selected using AMPure XP beads from Beckman Coulter.

treatment_protocol: Cells were either left untreated or irradiated with 10Gy and incubated for 6h at 37°C and 5% CO2

tag: cell line

value: neuronal progenitor cells

value: WT

value: irradiation, 6h recovery time

tag: chip antibody

value: anti-RNA:DNA hybrid S9.6 (Millipore)


title: mesc_rad21_depletion_IAA-3h_017, Smart-seq3


title: Psoriasis_17_NL_91


title: 427 cels, ChIP-Seq, control, no treatment

description: Library name: DRIP_C3_YH

value: no treatment


title: Liver Immune cells,  ConA+Vehicle, Biological replicate 1

description:
Library name: ConA+Vehicle1
Column name in miRNA_counts_allSamples.csv: ConA+Vehicle1

value: Female

value: 10 weeks

value: Liver

value: liver immune cells

value: ConA-induced autoimmune hepatitis


title: mesc_rad21_depletion_IAA-3h_011, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: GM03487 cels, ChIP-Seq, ATM null, no treatment

description: Library name: DRIP_AT1_YH

value: ATM null


title: Psoriasis_17_NL_85

value: skin

value: NL

value: Male


title: Psoriasis_17_NL_86


title: T_3h-ETh-3

value: leaf

value: Vitae Rose Red

value: ethephon


title: 427 cells, control, irradiation

description: Library name: RNA_C3_6hIR

data_processing:
RNA-seq reads were aligned to the human genome (hg38) using TopHat v2.1.0 with default parameters
Aligned reads were sorted by genomic coordinate using samtools v1.19.2
Differential gene expression analysis was conducted using Cuffdiff v2.2.1
Assembly: UCSC Genome hg38
Supplementary files format and content: genes.fpkm
Supplementary files format and content: Differential gene expression file

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen). Approximately 1 million cells were lysed by repetitive pipetting in 1 mL of TRIzol. Phase separation was performed by adding 0.2 mL of chloroform (Sigma-Aldrich), followed by centrifugation at 20,000 g for 15 min at 4°C. The top aqueous layer (~500 µL) was transferred to a new tube and the RNA was precipitated overnight at -80°C with an equal volume (500 µL) of 100% isopropanol (Fisher Scientific), 1/10 volume (50 µL) of 3 M sodium acetate (Teknova), and 4 µL of 5 mg/mL glycogen (Thermo). Samples were then centrifuged at 15,000 g for 20 min at 4°C, washed twice with 1 mL of 75% ethanol, and dissolved in 50 µL of nuclease-free water.
RNA libraries for RNA-seq were prepared using the KAPA RNA Hyperprep Kit with RiboErase following the manufacturer's instructions

value: neuronal progenitor cells

value: WT

value: irradiation, 6h recovery time


title: mesc_rad21_depletion_IAA-3h_016, Smart-seq3


title: 426 cels, ChIP-Seq, control, no treatment

description: Library name: DRIP_C2_YH

value: no treatment

value: anti-RNA:DNA hybrid S9.6 (Millipore)


title: Liver Immune cells,  Vehicle, Biological replicate 2

description:
Library name: Vehicle2
Column name in miRNA_counts_allSamples.csv: Vehicle2

value: Wildtype

value: Female

value: 10 weeks

value: Liver

value: DMSO

value: No disease


title: mesc_rad21_depletion_IAA-3h_015, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: 425 cels, ChIP-Seq, control, no treatment

description: Library name: DRIP_C1_YH


title: mesc_rad21_depletion_IAA-3h_008, Smart-seq3


title: Psoriasis_17_NL_89

value: skin

value: NL

value: Male


title: Psoriasis_16_LS_81

value: LS


title: mesc_rad21_depletion_IAA-3h_007, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_014, Smart-seq3


title: GM01526 cels, ChIP-Seq, ATM null, no treatment

description: Library name: DRIP_AT3_YH

value: neuronal progenitor cells

value: ATM null


title: GM08436 cells, ATM null, irradiation

description: Library name: RNA_AT2_6hIR

value: irradiation, 6h recovery time


title: GM03487 cells, ATM null, irradiation

description: Library name: RNA_AT1_6hIR


title: Psoriasis_17_NL_87


title: GM08436 cels, ChIP-Seq, ATM null, no treatment

description: Library name: DRIP_AT2_YH

value: no treatment


title: mesc_rad21_depletion_IAA-3h_012, Smart-seq3


title: T_3h-meJA-2

value: leaf

value: Vitae Rose Red

value: MeJA


title: T_3h-meJA-1


title: mesc_rad21_depletion_IAA-3h_010, Smart-seq3


title: Psoriasis_16_LS_79


title: Psoriasis_16_LS_84


title: T_3h-ETh-2

value: ethephon


title: 426 cells, control, irradiation

description: Library name: RNA_C2_6hIR

value: WT


title: mesc_rad21_depletion_IAA-3h_009, Smart-seq3


title: T_24h-ETh-3


title: 426 cells, control, no treatment

description: Library name: RNA_426_UT_C2


title: 425 cells, control, irradiation

description: Library name: RNA_C1_6hIR


title: Psoriasis_16_LS_83


title: mesc_rad21_depletion_IAA-3h_003, Smart-seq3


title: Psoriasis_16_LS_77


title: T_3h-ETh-1


title: GM01526 cells, ATM null, irradiation

description: Library name: RNA_AT3_6hIR


title: T_24h-meJA-3


title: Psoriasis_16_LS_82


title: Psoriasis_16_LS_80


title: T_24h-meJA-1


title: mesc_rad21_depletion_IAA-3h_005, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_001, Smart-seq3


title: GM08436 cells, ATM null, no treatment

description: Library name: RNA_08436_UT_AT2


title: T_24h-meJA-2


title: mesc_rad21_depletion_IAA-3h_006, Smart-seq3


title: Psoriasis_16_NL_73


title: T_0h_1

value: ck


title: mesc_rpb1-degron_IAA_Rad21_CUTTAG_rep1

description: CUT&TAG

data_processing:
Bulk Micro-C datasets were processed using distiller-nf pipeline.
CUT&TAG data were processed using the CUT&RUN tools 2.0 (https://github.com/XiangYe-Vandy/CUTRUN_tools) by selecting CUT&TAG (default) as the experiment type.
In brief, raw reads were trimmed tro remove sequencing adapters and mapped to the reference genome using bowtie2.
bigWig files were generated using bamCoverage and normalized with CPM.
Heatmaps and metagene plots were generated using Deeptools (v3.5.2).
Assembly: mm10
Supplementary files format and content: tab-delimited text files for contact pairs
Supplementary files format and content: contact matrices (hic and mcool files) for each sample
Supplementary files format and content: bigWig files
Library strategy: CUT&TAG

source_name: mouse embryonic stem cells

extract_protocol:
Harvested cells were crosslinked with freshly made 1% PFA followed by 3 mM DSG, then cells were lysed and titrated to test the appropriate MNase concentration (fig. S2B). Before end repair, we added 50 μL 0.3% SDS and incubated at 62℃ for 10 min, then quenched by 50 μL 3% Triton X-100 and incubated at 37℃ for 15 min. Then nuclei were end repaired and biotin labeled, followed by in situ ligation with T4 ligase. Before DNA extraction, nuclei were incubated with exonuclease III (NEB, #M0206) to remove un-ligated ends (Micro-C). Cells were dissociated with trypsin and wash twice with 1x PBS at RT (CUT&TAG).
Extracted DNA were either sonicated to 300 bp or select di-nucleosome fragments for library preparation (Micro-C). 0.1 million cells were used as input and processed with CUT&Tag kit (Vazyme, TD903) according to the manufacturer’s instructions. RAD21 primary antibody (GeneTex, GTX106012) was used (CUT&TAG).

treatment_protocol: All mESCs were pretreated with 1 μg/mL doxycycline for 12 h to induce the expression of OsTIR1. Pol II depletion was achieved by the addition of 500 μM indole-3-acetic acid (auxin/IAA) and cultured for 4 h.

value: mouse embryonic stem cells

value: IAA (4h)


title: Psoriasis_16_NL_75


title: Psoriasis_16_LS_78


title: Input-repeat3

city: Jinan

first: cong

middle: Tai

last: Tan

state: Shandong

address: Jingshi Street

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description: Library name: Input-repeat3

data_processing:
Raw sequencing reads underwent quality filtering (Q20/Q30 thresholds) using Fastp (0.24.0)
Alignment to the Saccharomyces cerevisiae genome (SacCer3 2011 assembly) was performed with Bowtie2 (v2.5.3), generating sorted BAM files.
Read density normalization (RPKM) and genome-wide fold-enrichment calculations (50-bp bins, ChIP/input ratios) were implemented through deepTools (v3.5.4)
Peak detection employed MACS2 (v2.2.9.1) with parameters: effective genome size 1.21×10⁷ bp, --nomodel --extsize 200 -q 0.05 (FDR-controlled), excluding broad peak calling
Assembly: SacCer3
Supplementary files format and content: bedgraph

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Wild type(UFD2-9MYC) cells were induced to synchronously enter meiosis in SPM.

extract_protocol:
The cells were broken with glass beads in lysis buffer and the chromatin was sheared by sonication.
Library preparation utilized the VAHTS Universal DNA Library Prep Kit for Illumina V4 (Vazyme, Cat# ND610-02) following manufacturer protocols.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 90 min. The reaction was quenched with glycine.

value: yeast cell

value: Wild type(UFD2-9MYC)

value: fixed with 1% formaldehyd


title: T_24h-ETh-2


title: Psoriasis_16_NL_72

value: skin

value: NL

value: Male


title: GM03487 cells, ATM null, no treatment

description: Library name: RNA_03487_UT_AT1

value: neuronal progenitor cells

value: ATM null


title: 427 cells, control, no treatment

description: Library name: RNA_427_UT_C3

value: no treatment


title: Input-repeat2

description: Library name: Input-repeat2


title: 425 cells, control, no treatment

description: Library name: RNA_425_UT_C1


title: mesc_rad21_depletion_IAA-3h_004, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: 3-mono-arsi

city: Bordeaux

first: Laurence

last: Bresson-Bepoldin

address: 146 rue de saignat

country: France

institute: INSERM

description: Library name: Sample 5

data_processing:
FastQC  0.11.9
STAR
Assembly: GENCODE v47 GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Primary human monocytes

growth_protocol: Monocytes were isolated from buffy coat of healthy blood donors. Monocytes were purified from PBMC by magnetic cell sorting using CD14 microbeads, human kit (Miltenyi Biotec, Paris, France) according to the manufacturer’s recommendations. Primary human monocytes were seeded at a density of 1 × 10⁶ cells per well in 12-well plates and maintained in 1 mL of Gibco™ RPMI 1640 with HEPES and GlutaMAX™, supplemented with 10% FBS and 10% human AB serum

extract_protocol:
Qiagen RNeasy Mini Kit was used to perform RNA isolation (RNA concentration > 10 ng/µL and RIN>5
Libraries are prepared with Watchmaker mRNA Library Prep Kit for Illumina  protocol according supplier recommendations. Briefly the key stages of this protocol are successively, the selection of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 100ng total RNA, a fragmentation to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. The sequencing was performed on an Illumina NovaSeq X Plus sequencer as paired end 2x100 bp reads.

treatment_protocol: Monocytes were exposed for 24 hours to one of the following conditions: untreated (control), co-culture with ARSI cell line at 75,000 cells per well, or recombinant human IL-10 at a final concentration of 5 ng/mL. CD14⁺ monocytes were subsequently isolated from all experimental groups using magnetic-activated cell sorting (MACS), according to the manufacturer’s instructions, to ensure consistency across conditions. Only samples achieving a minimum post-sort purity of 99.7% were selected for downstream analysis. Purity was assessed by confirming the absence of contaminating ARSI cells, identified by CD20⁺ or CD19⁺ expression. The purified CD14⁺ cells were then cryopreserved.

value: Primary human monocytes

value: primary cells

value: monocyte-derived macrophages

value: ARSI cells

tag: batch


title: 3-mono-il10

description: Library name: Sample 6

value: WT

value: 5ng/mL IL-10


title: Psoriasis_16_NL_76


title: GM01526 cells, ATM null, no treatment

description: Library name: RNA_01526_UT_AT3


title: T_0h-3

value: leaf

value: Vitae Rose Red

value: ck


title: T_0h-2


title: T_24h-ETh-1

value: ethephon


title: mesc_rad21_depletion_IAA-3h_002, Smart-seq3


title: mesc_rpb1-degron_IAA_Rad21_CUTTAG_rep3

description: CUT&TAG

value: mouse embryonic stem cells

value: IAA (4h)


title: Psoriasis_16_NL_74

value: skin

value: NL

value: Male


title: mesc_rpb1-degron_untreat_Rad21_CUTTAG_rep1

description: CUT&TAG

value: Untreated


title: Ufd2p-ChIP-repeat3

description: Library name: Ufd2p-ChIP-repeat3

value: yeast cell

value: Wild type(UFD2-9MYC)

value: fixed with 1% formaldehyd


title: mesc_rpb1-degron_IAA_Rad21_CUTTAG_rep2

description: CUT&TAG


title: mesc_rpb1-degron_untreat_Rad21_CUTTAG_rep3

description: CUT&TAG


title: Input-repeat1

description: Library name: Input-repeat1


title: Psoriasis_16_NL_71


title: 3-mono

description: Library name: Sample 4

value: Primary human monocytes

value: primary cells

value: monocyte-derived macrophages

value: untreated


title: Hyalomma asiaticum whole body transcriptome, EC treatment, biol rep 3

city: Xinjiang

first: 马祯

last: 祯

state: Xinjiang Uygur  Autonomous Region

address: nongda east road 311

department: College of Veterinary Medicine

institute: Xinjiang Agricultural University

description: Library name: EC3

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated. Then clean and deduplicated data were de novo assembled by Trinity (version 2.15.1) with default parameters (20). Sequencing reads were aligned back to the assembled transcripts for assessing the quality of the transcriptome assembly by using Bowtie2 (21). The longest transcripts of the same genes were screened as unigenes. For functional annotations of the unigenes, protein databases Nr, Uniprot, Pfam, eggNog, GO and KEGG were used. Unigenes differentially expressed between groups (S. aureus、E. coli and PBS) were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. GO analysis and KEGG enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version 2.1.1) with a p-value cutoff of 0.05 to judge statistically significant enrichment.
Assembly: Not applicable; de novo transcriptome assembly was performed.
Supplementary files format and content: Annotation.xlsx；gene_expression.xlsx；Trinity.fasta；Unigene.fasta

organism: Hyalomma asiaticum

source_name: Ticks as a whole

growth_protocol: Unfed female ticks of similar body weight, from the same artificially reared batch at two weeks post-molting, were selected as the target samples for bacterial stress experiments. To minimize the impact of environmental microorganisms on the tick samples, their body surfaces were cleaned thoroughly. Briefly, Each tick was immersed in sterilized PBS and subjected to shaking for 15 seconds, followed by transfer to a 75% ethanol solution for an additional 15 seconds with agitation. Subsequently, the ticks were rinsed three times with ddH2O with agitation applied during each rinse. Finally, the cleaned ticks were placed on sterilized absorbent paper for surface drying. Injections of S. aureus and E. coli into unfed female ticks of Amblyomma americanum are described previously . Briefly, unfed female ticks were injected using a precision microsyringe (Hamilton Bonaduz, Switzerland) with a 10⁷ CFU/ml dilution of S. aureus or E. coli on the right side, between the fourth coxal segments, at a volume of 0.5 µl per tick. Immediately after completing the injection procedure, the injection site was sealed with a minimal amount of sterile Vaseline to prevent hemolymph leakage. After 24 h post-injection, ten individuals were randomly selected from each group to be pooled. The PBS-injected group was designated as the negative control to establish baseline gene expression profiles for comparative analysis. Each treatment group, including the negative control group, comprised 10 unfed female adult ticks. Three biological replicates were included for each group. Ticks were immediately transferred to freezing tubes and immersed in liquid nitrogen for snap-freezing to preserve RNA integrity prior to RNA-Seq.

extract_protocol:
Total RNA was extracted from tick samples using TRIzol Reagent (Invitrogen, California, USA) according to the manufacturer's instructions. Following RNA extraction, DNA digestion was performed using DNase I (Thermo Fisher Scientific, Waltham, MA, USA) to eliminate any residual genomic DNA. The quality of the extracted RNAs was assessed by measuring the A260/A280 ratio with a NanodropTM OneC spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Additionally, RNA integrity was verified using either a Qsep 100 (BIOptic, New Taipei City, Taiwan, China) or an Agilent 2100 (Agilent Technologies, Santa Clara, CA, USA) instrument, ensuring the high-quality and integrity of the RNA samples for downstream applications.
For the preparation of stranded RNA sequencing libraries, 1 μg of total RNAs was utilized following the manufacturer's instructions for the KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Wuhan Seqhealth, China). This kit incorporates a unique molecular identifier (UMI) consisting of 8 random bases to label pre-amplified cDNA molecules, effectively eliminating duplication bias during the PCR and sequencing steps. Library products within the size range of 200-500 bps were enriched, accurately quantified, and subsequently sequenced on a NovaSeq 6000 (Illumina, San Diego, CA, USA) in PE150 mode, ensuring high-throughput and accurate sequencing results.

value: Ticks as a whole

value: female


title: 5. GM0402 (Hachiman)T4 phage DNA

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

description: Library name: 5. GM0402 (Hachiman)T4 phage DNA

data_processing:
Paired-end reads were quality and adapter trimmed using Cutadapt to remove adapter sequences, poly-A/T, and low-quality bases (Q<30), retaining only reads ≥20 nt in length.
Cutom genome indices were built from FASTA files using bowtie2-build. Reads were aligned to either pGEM9z plasmid or T4 phage reference genomes using Bowtie2 to produce SAM alignment files.
SAM files were converted to sorted and indexed BAM format using Samtools (1.21)
Fragment lengths and strand-specific 5 prime end counts were extracted using the Bioconductor Rsamtools package in R (4.3.1).
The top 100 5 prime ends were used to extract ±10 nucleotide windows from the reference genome using Bsgenome and GenomicRanges R packages. Fasta sequences were saved for downstream WebLogo motif analysis.
Assembly: pGEM9z plasmid
Assembly: T4 phage
Supplementary files format and content: BigWig (.bw) files for each sample contain read coverage tracks generated from BAM files.

organism: Bacillus toyonensis

source_name: bacteria

extract_protocol:
1 M Tris-HCl pH 8.0, 10% SDS, and 0.5 M EDTA pH 8.0 were added to the cleavage reaction followed by 10% SDS to reach 500 µL total volume. 500 µL of Phenol:Chlorofom:Isoamyl Alchol 25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA (Sigma Aldrich) was added, vortexed, centrifuged, and the resulting aqueous phage was added to 50 µL 3M NaOAc and 1 µL 20 mg mL−1 glycogen. 1 mL of 100% ethanol was added, vortexed, and samples were stored at −20°C overnight. The following day, samples were pelleted and washed with 70% ethanol three times before resuspension in RNase-free dH2O.
Sequencing libraries were made from single stranded DNA fragments using a xGEN kit (IDT) and sequenced on a NextSeq500

treatment_protocol: Nuclease-NTPase protein concentrations were optimized to generate 100–600 bp DNA fragments required for DNA sequencing. 25 nM PaAbpAB, 75 nM BtHachiman, 1 µM EcPD-T4-8 were individually incubated with 400 ng pGEM9Z plasmid in a 40 µL reactions with DNA cleavage buffer (20 mM Tris-HCl pH 7.5, 150 mM KCl, 5 mM MgCl2, 1 mM MnCl2, 1 mM DTT). 25 nM PaAbpAB, 1 µM BmAzaca, 25 nM BtHachiman, and 1 µM EcPD-T4-8 were individually incubated with 400 ng phage T4 DNA in 40 µL reactions with DNA cleavage buffer. Proteins were diluted in gel filtration buffer supplemented with 10% glycerol. Reactions were incubated at 37°C for 30 min followed by 100 µg mL−1 Proteinase K treatment at 50°C for 30 min.

tag: strain

value: bacteria


title: 2-mono-il10

description: Library name: Sample 3

value: WT

value: 5ng/mL IL-10


title: mesc_rpb1-degron_untreat_microc_rep2

description:
Micro-C
rpb1-untreat.mm10.mapq_20.1000.mcool
rpb1-untreat.mm10.nodups.pairs.gz

data_processing:
Bulk Micro-C datasets were processed using distiller-nf pipeline.
CUT&TAG data were processed using the CUT&RUN tools 2.0 (https://github.com/XiangYe-Vandy/CUTRUN_tools) by selecting CUT&TAG (default) as the experiment type.
In brief, raw reads were trimmed tro remove sequencing adapters and mapped to the reference genome using bowtie2.
bigWig files were generated using bamCoverage and normalized with CPM.
Heatmaps and metagene plots were generated using Deeptools (v3.5.2).
Assembly: mm10
Supplementary files format and content: tab-delimited text files for contact pairs
Supplementary files format and content: contact matrices (hic and mcool files) for each sample
Supplementary files format and content: bigWig files
Library strategy: Micro-C

value: mouse embryonic stem cells


title: Psoriasis_16_NL_70

value: skin


title: mesc_rpb1-degron_untreat_Rad21_CUTTAG_rep2

description: CUT&TAG


title: Ufd2p-ChIP-repeat2

description: Library name: Ufd2p-ChIP-repeat2


title: mesc_rpb1-degron_untreat_microc_rep1


title: Psoriasis_21_LS_64

value: LS

value: Female


title: mesc_rpb1-degron_IAA_microc_rep2

description:
Micro-C
rpb1-iaa4h.mm10.mapq_20.1000.mcool
rpb1-iaa4h.mm10.nodups.pairs.gz

value: IAA (4h)


title: 2-mono-arsi

description: Library name: Sample 2

value: ARSI cells


title: Psoriasis_16_NL_69

value: NL

value: Male


title: Hepatopancreas, infected, VP-AHPND3

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

description: Library name: V3

data_processing:
Alignment with Cell Ranger (v8.0.1) to reference assembly; top 10,000 UMIs selected.
Assembly: ASM4276789v1, GCF_042767895.1
Supplementary files format and content: h5

organism: Penaeus vannamei

source_name: Hepatopancreas, reverse gavage, bacteria

extract_protocol:
Hepatopancreas was removed from shrimp, gently chopped into pieces, and placed into 2 mL of dispase for 15 min at 37°C. After treatment, 10 mL of phosphate buffered saline (PBS) was added, and the tissue was gently passed through a 70 μm and then 40 μm cell sieve to create single-cell suspensions.
10x Genomics 3' GEM-X kit (v4) and Chromium X Instrument following manufacterer protocol

treatment_protocol: H1-3: no treatments; C1-2: mock treatment with media via reverse gavage; V1-3: infected with AHPND causing Vibrio parahaemolyticus

value: Hepatopancreas

value: Infected


title: Psoriasis_21_LS_63


title: Hepatopancreas, infected, VP-AHPND2

description: Library name: V2


title: Hyalomma asiaticum whole body transcriptome, PBS control, biol rep 2

description: Library name: PBS2


title: Hepatopancreas, infected, VP-AHPND1

description: Library name: V1


title: 2-mono

description: Library name: Sample 1

value: Primary human monocytes

value: primary cells

value: monocyte-derived macrophages


title: Ufd2p-ChIP-repeat1

description: Library name: Ufd2p-ChIP-repeat1

value: yeast cell

value: Wild type(UFD2-9MYC)

value: fixed with 1% formaldehyd


title: Psoriasis_21_LS_62


title: Psoriasis_21_LS_67


title: mesc_rpb1-degron_IAA_microc_rep1


title: Psoriasis_21_LS_61


title: Psoriasis_21_LS_66


title: Psoriasis_21_LS_68


title: Psoriasis_21_LS_65


title: 4. GM0402 (Hachiman) pGEM9z

description: Library name: 4. GM0402 (Hachiman) pGEM9z

library_source: other

molecule: other

value: bacteria


title: Hyalomma asiaticum whole body transcriptome, EC treatment, biol rep 2

description: Library name: EC2

value: Ticks as a whole

value: female


title: Hyalomma asiaticum whole body transcriptome, PBS control, biol rep 3

description: Library name: PBS3


title: 3. GM0202 (Azaca) T4 phage DNA

description: Library name: 3. GM0202 (Azaca) T4 phage DNA

organism: Bacillus massilioanorexius


title: mesc_tpt_treat_rep2, bulk RNA-seq

description:
Bulk RNA-seq
TPT_2
mesc_topo_inhibition_gene_counts.tsv

value: mouse embryonic stem cell

value: Wild type

value: TPT


title: mesc_tpt_treat_rep1, bulk RNA-seq

description:
Bulk RNA-seq
TPT_1
mesc_topo_inhibition_gene_counts.tsv


title: Hyalomma asiaticum whole body transcriptome, EC treatment, biol rep 1

description: Library name: EC1


title: Hepatopancreas, healthy, mock1

description: Library name: C1

source_name: Hepatopancreas, reverse gavage, media

value: Healthy, mock


title: Hyalomma asiaticum whole body transcriptome, SA treatment, biol rep 3

description: Library name: SA3


title: Hyalomma asiaticum whole body transcriptome, PBS control, biol rep 1

description: Library name: PBS1


title: Hyalomma asiaticum whole body transcriptome, SA treatment, biol rep 1

description: Library name: SA1


title: mesc_eto_treat_rep1, bulk RNA-seq

description:
Bulk RNA-seq
ETO_10_1
mesc_topo_inhibition_gene_counts.tsv

value: ETO


title: Psoriasis_21_LS_60

value: skin

value: LS

value: Female


title: mesc_eto_treat_rep2, bulk RNA-seq

description:
Bulk RNA-seq
ETO_10_2
mesc_topo_inhibition_gene_counts.tsv


title: UPS04_BO112

city: Stanford

first: Anusha

last: Kalbasi

state: CA

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

description:
Library name: UPS04_BO112
Bulk RNAseq

data_processing:
Reads were aligned to the human reference genome using HISAT2 (v.2.0.4)
Gene expression was quantified using HTSeq-counts (v.0.6.1)
Differential expression analysis was performed using DESeq2
Assembly: GRCh38.
Supplementary files format and content: Tab-delimited text files with raw counts for each sample.

extract_protocol:
Bulk RNA was isolated using Qiagen Rneasy Kit
RNA-seq libraries were prepared using the KAPA mRNA stranded library preparation kit, according to the manufacturer’s recommendations.

value: Sarcoma cell line

tag: timepoint

value: 6 hours


title: mesc_dmso_treat_rep2, bulk RNA-seq

description:
Bulk RNA-seq
DMSO_2
mesc_topo_inhibition_gene_counts.tsv

tag: genotype

value: DMSO


title: Hepatopancreas, healthy, mock2

description: Library name: C2

value: Hepatopancreas


title: UPS04_media

description:
Library name: UPS04_media
Bulk RNAseq

value: vehicle control


title: mesc_dmso_treat_rep1, bulk RNA-seq

description:
Bulk RNA-seq
DMSO_1
mesc_topo_inhibition_gene_counts.tsv


title: Psoriasis_21_NL_59

value: NL

tag: Sex


title: Hyalomma asiaticum whole body transcriptome, SA treatment, biol rep 2

description: Library name: SA2


title: Hepatopancreas, healthy, atlas1

description: Library name: H1

source_name: Hepatopancreas, no treatment

value: Healthy


title: MF, PBMC, infected

city: Changsha

first: Nouhoum

last: Dibo

state: Hunan

address: No. South Lushan Road

institute: Central South University

description:
Library name: Sample 2
Singleron

data_processing:
Cutadapt v1.17 was used to remove low-quality reads, trim poly-A tails, and adapter sequences. Raw reads from scRNA-seq were processed to generate a gene expression matrix using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline.
Assembly: mouse reference genome GRCm38 (Ensembl version 92 annotation)
Supplementary files format and content: Sparse Matrix Market(MTX), Gene Count Matrix

organism: Alexandromys fortis

source_name: Blood

extract_protocol:
The Isolated cells were washed with Ca/Mg-free PBS before adding 2 mL GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) at 25°C for 10 minutes to remove the red blood cells (RBCs). After removing the RBCs, the cells were washed with PBS, and the PBMCs were isolated by centrifugation. The PBMCs were stained with Trypan Blue, and the cell viability was evaluated microscopically.
Single-cell suspensions were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads were subsequently collected from the microwell chip, followed by reverse transcription of the mRNA and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina Novaseq 6000 with 150 bp paired-end reads.

value: Blood

value: Microtus fortis

value: Peripheral blood mononuclear cells

value: S. japonicum


title: Psoriasis_21_NL_57

tag: age


title: UPS03_BO112

description:
Library name: UPS03_BO112
Bulk RNAseq


title: S. lacustris, DMSO, 4 h, rep 3

city: New Haven

first: Jacob

middle: M.

last: Musser

state: CT

address: 260 Whitney Avenue YSB 223D

department: MCDB

institute: Yale University

description:
Library name: Sample 17
Column name in counts_allSamples.txt: star_trans_clean_out/17_R3D_T4_W_Aligned.sortedByCoord.out.bam

data_processing:
Reads were trimmed using fastP to remove polyG regions. Reads were mapped to Trinity transcriptome of Spongilla using STAR and gene counts were quantified using featuresCount.
Assembly: Trinity transcriptome of Spongilla lacustris (Musser et al. 2021)
Supplementary files format and content: Tab-delimited txt file containing raw counts for each Sample

organism: Spongilla lacustris

source_name: Whole body

growth_protocol: S. lacustris was grown in M-medium at 18 C for 9 days before treatment and RNA extraction.

extract_protocol:
RNA was extracted using Qiagen AllPrep Kit according to manufacturer's instructions.
RNA polyA library preparation was performed using the Watchmaker mRNA Library Prep Kit following manufacturer's instructions.

treatment_protocol: S. lacustrist were treated with 37.5 uM tryptamine for 1 h, 4 h, or 4 h followed by washout and a 24 hour recovery peroid..

tag: tissue

value: Whole body

value: WT

value: 0.03% DMSO 4 hours


title: UPS02_BO112

description:
Library name: UPS02_BO112
Bulk RNAseq

tag: cell type


title: S. lacustris, DMSO, 4 h recovery, rep 3

description:
Library name: Sample 18
Column name in counts_allSamples.txt: star_trans_clean_out/18_R3D_T4_W24_Aligned.sortedByCoord.out.bam

tag: treatment

value: 0.03% DMSO 4 hours washout recovery 24 hours


title: CSN8-BAT-KO-5

city: Augusta

first: Weiqin

last: Chen

state: GA

address: 1462 Laney Walker Blvd

department: Physiology

institute: Augusta University

description: Library name: Sample 18

data_processing:
Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
Assembly: RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: Brown adipose tissue

extract_protocol:
Tissues were homogenized in Trizol for the extraction of total RNA according to the manufacture's instructions. Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: Brown adipose tissue

value: male

value: Csn8A KO


title: CSN8-BAT-KO-4

description: Library name: Sample 17


title: MF, PBMC, control

description:
Library name: Sample 1
Singleron

value: uninfected


title: UPS03_media

description:
Library name: UPS03_media
Bulk RNAseq

value: Sarcoma cell line

value: 6 hours


title: Psoriasis_21_NL_56

value: skin

tag: lesional/nonlesional

value: Female


title: Psoriasis_21_NL_55

value: NL

tag: characteristics


title: Psoriasis_21_NL_54

tag: patient id


title: Psoriasis_21_NL_58

tag: fields of view (fov)


title: Hepatopancreas, healthy, atlas3

description: Library name: H3

value: Hepatopancreas

value: Healthy


title: Hepatopancreas, healthy, atlas2

description: Library name: H2


title: S. lacustris, DMSO, 1 h, rep 3

description:
Library name: Sample 16
Column name in counts_allSamples.txt: star_trans_clean_out/16_R3D_T1_W_Aligned.sortedByCoord.out.bam

value: 0.03% DMSO 1 hour


title: CSN8-BAT-KO-3

description: Library name: Sample 16


title: S. lacustris, tryptamine, 4 h, rep 3

description:
Library name: Sample 14
Column name in counts_allSamples.txt: star_trans_clean_out/14_R3T_T4_W_Aligned.sortedByCoord.out.bam

value: 37.5 µM tryptamine 4 hours


title: CSN8-BAT-KO-2

description: Library name: Sample 15


title: UPS02_media

description:
Library name: UPS02_media
Bulk RNAseq

value: vehicle control


title: Psoriasis_21_NL_52


title: CSN8-BAT-KO-1

description: Library name: Sample 14


title: Psoriasis_21_NL_53


title: Psoriasis_21_NL_51


title: S. lacustris, tryptamine, 1 h, rep 3

description:
Library name: Sample 13
Column name in counts_allSamples.txt: star_trans_clean_out/13_R3T_T1_W_Aligned.sortedByCoord.out.bam

value: Whole body

value: WT

value: 37.5 µM tryptamine 1 hour


title: UPS01_media

description:
Library name: UPS01_media
Bulk RNAseq


title: S. lacustris, tryptamine, 4 h recovery, rep 3

description:
Library name: Sample 15
Column name in counts_allSamples.txt: star_trans_clean_out/15_R3T_T4_W24_Aligned.sortedByCoord.out.bam

value: 37.5 µM tryptamine 4 hours washout recovery 24 hours


title: Psoriasis_22_NL_50

value: Male


title: S. lacustris, DMSO, 4 h recovery, rep 2

description:
Library name: Sample 12
Column name in counts_allSamples.txt: star_trans_clean_out/12_R2D_T4_W24_Aligned.sortedByCoord.out.bam

value: 0.03% DMSO 4 hours washout recovery 24 hours


title: CSN8-BAT-WT-5

description: Library name: Sample 13

value: Brown adipose tissue

value: male


title: S. lacustris, DMSO, 4 h, rep 2

description:
Library name: Sample 11
Column name in counts_allSamples.txt: star_trans_clean_out/11_R2D_T4_W_Aligned.sortedByCoord.out.bam

value: 0.03% DMSO 4 hours


title: CSN8-BAT-WT-4

description: Library name: Sample 12


title: I5-Input

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: Tongwei Road

institute: Nanjing agricultural university

description:
Library name: sample15
input

data_processing:
Reads were quality controlled using FastQC (v0.11.5) and TrimGalore (v0.6.0).
rRNA sequence were removed by using bowtie2(v2.3.4.1) with --ungz or --un-conc-gz parameter.
The retained reads were aligned to GRCm38/mm10 by HISAT2 (v2.2.1) with default parameters.
Bigwig files were obtained by using bamCoverage function in deepTools (v3.5.1) and visualized in IGV (v11.0.19).
Read counts were quantified by using featureCounts (v1.6.0).
Assembly: Sus_scrofa.Sscrofa11.1
Supplementary files format and content: bigwig
Library strategy: MeRIP-Seq

organism: Sus scrofa

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent. RNA quality and integrity were assessed by NanoDrop ND 1000 spectrophotometry and agarose gel electrophoresis. Dynabeads Oligo (dT)25 was employed to isolate the mRNA containing PolyA in total RNA pool. The isolated mRNA was then sonicated into fragments of 150-200 bp through 30 cycle of ultrasound, with each cycle comprising 30 s on and 30 s off.  A total of 50 ng of fragmented mRNA was used as input. In the immunoprecipitation (IP) process, 25 μL of protein G beads (NEB, Cat. S1430) were pre-incubated with 1 μL of anti-m6Aantibody (NEB, Cat. E1610S) in reaction buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40) at 4°C for 30 min. Following this, a 250 μL mixture containing 950 ng of mRNA, 50 μL IP buffer (750 mM NaCl, 50 mM Tris-HCl, 0.5% NP-40), and 5 μL RNA inhibitor was added to antibody and incubated for 1 h at 4℃. Subsequently, beads were washed sequentially in the following solutions: twice in reaction buffer, twice in low salt buffer (50 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40), and twice in high salt buffer (500 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40). RNA was then eluted from beads with 100 μL of buffer RLT (QIAGEN, Cat. 1015762) by incubation for 1 min and then purified using a clean and concentrate RNA kit according to the manufacturer’s protocol. (Zymo research, Cat. R1017).
Library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian (Takara), according to the manufacturer’s protocol.

value: liver

tag: breed

value: (Durocx [Landrace x Yorkshire])

tag: group

value: iron deficiency


title: Psoriasis_22_NL_48

data_processing: Processed files were combined into a seurat object; standard workflow for CosMx data, reflecting the output generated by the AtomX cloud. The processed files uploaded also allow for manual creation of the Seurat object in RStudio, if required.

value: skin

value: NL


title: Psoriasis_22_NL_49


title: I5-IP

description:
Library name: sample29
immunoprecipitation


title: CSN8-BAT-WT-3

description: Library name: Sample 11


title: UPS01_BO112

description:
Library name: UPS01_BO112
Bulk RNAseq

tag: cell line

value: Sarcoma cell line

value: 6 hours


title: S. lacustris, DMSO, 1 h, rep 2

description:
Library name: Sample 10
Column name in counts_allSamples.txt: star_trans_clean_out/10_R2D_T1_W_Aligned.sortedByCoord.out.bam

value: 0.03% DMSO 1 hour


title: Psoriasis_22_NL_47


title: CSN8-BAT-WT-1

description: Library name: Sample 9


title: I2-IP

description:
Library name: sample25
immunoprecipitation


title: I4-Input

description:
Library name: sample13
input


title: I4-IP

description:
Library name: sample27
immunoprecipitation


title: S. lacustris, tryptamine, 4 h recovery, rep 2

description:
Library name: Sample 9
Column name in counts_allSamples.txt: star_trans_clean_out/9_R2T_T4_W24_Aligned.sortedByCoord.out.bam

value: Whole body


title: Psoriasis_22_NL_46


title: S. lacustris, tryptamine, 1 h, rep 2

description:
Library name: Sample 7
Column name in counts_allSamples.txt: star_trans_clean_out/7_R2T_T1_W_Aligned.sortedByCoord.out.bam

value: WT


title: Psoriasis_22_NL_45


title: CSN8-SF-KO-3

description: Library name: Sample 7

source_name: Subcutaneous adipose tissue

value: Subcutaneous adipose tissue

value: Csn8A KO


title: S. lacustris, DMSO, 4 h recovery, rep 1

description:
Library name: Sample 6
Column name in counts_allSamples.txt: star_trans_clean_out/6_R1D_T4_W24_Aligned.sortedByCoord.out.bam


title: N6-IP

description:
Library name: sample23
immunoprecipitation

value: negative control


title: CSN8-BAT-WT-2

description: Library name: Sample 10


title: S. lacustris, tryptamine, 4 h, rep 2

description:
Library name: Sample 8
Column name in counts_allSamples.txt: star_trans_clean_out/8_R2T_T4_W_Aligned.sortedByCoord.out.bam

value: 37.5 µM tryptamine 4 hours


title: Psoriasis_22_NL_44

value: Male


title: CSN8-SF-KO-2

description: Library name: Sample 6

value: male


title: CSN8-SF-KO-4

description: Library name: Sample 8


title: N6-Input

description:
Library name: sample7
input


title: Psoriasis_22_NL_42


title: CSN8-SF-KO-1

description: Library name: Sample 5


title: S. lacustris, DMSO, 1 h, rep 1

description:
Library name: Sample 4
Column name in counts_allSamples.txt: star_trans_clean_out/4_R1D_T1_W_Aligned.sortedByCoord.out.bam


title: S. lacustris, DMSO, 4 h, rep 1

description:
Library name: Sample 5
Column name in counts_allSamples.txt: star_trans_clean_out/5_R1D_T4_W_Aligned.sortedByCoord.out.bam

value: 0.03% DMSO 4 hours


title: Psoriasis_22_LS_41

value: LS


title: N5-IP

description:
Library name: sample19
immunoprecipitation

value: liver

value: (Durocx [Landrace x Yorkshire])


title: S. lacustris, tryptamine, 4 h recovery, rep 1

description:
Library name: Sample 3
Column name in counts_allSamples.txt: star_trans_clean_out/3_R1T_T4_W24_Aligned.sortedByCoord.out.bam

value: 37.5 µM tryptamine 4 hours washout recovery 24 hours


title: CSN8-SF-WT-3

description: Library name: Sample 3


title: CSN8-SF-WT-4

description: Library name: Sample 4


title: Psoriasis_22_NL_43

value: skin

value: NL


title: N5-Input

description:
Library name: sample3
input


title: S. lacustris, tryptamine, 4 h, rep 1

description:
Library name: Sample 2
Column name in counts_allSamples.txt: star_trans_clean_out/2_R1T_T4_W_Aligned.sortedByCoord.out.bam


title: N3-IP

description:
Library name: sample17
immunoprecipitation


title: Psoriasis_22_LS_40


title: Psoriasis_22_LS_38


title: Tendon tissues, Lysm-Cre; Ampkα1fl/fl mice，rep3

city: shanghai

first: lisha

last: zhu

address: yanchangzhonglu street

institute: tongji university

description: Library name: SAMPLES6

data_processing:
data obtained from sequencing were filtered using SOAPnuke (v1.5.6).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Tendon tissue

growth_protocol: All animals were housed in ventilated cages under a 12/12-h light/dark cycle with ad libitum access to food and water.

extract_protocol:
The total RNA of tissues was extracted using TRIzol reagent (Thermo Fisher Scientific).Total RNA concentration and purity were detected with Agilent 2100. cDNA libraries were sequenced to RNA-Seq using the BGISEQ platform .
cDNA library construction, library purification, and transcriptome sequencing were performed according to the instructions of the Wuhan Huada Sequencing Company

treatment_protocol: For tendon transection, mice were intraperitoneally injected with 1% pentobarbital (0.1 mL per 100 g). After complete anesthesia, the Achilles tendon was exposed through lateral transection. A transverse incision of the Achilles tendon was made on each leg using microsurgical instruments. The wound was irrigated, and the skin was closed with sutures. Subsequently, the mice were euthanized at planned postoperative time points with an overdose of anesthesia, and the repair tissues were collected.

value: Tendon tissue

value: myeloid specific AMPK knockout

value: tendon transection


title: X.laevis NF57-58 spinal cord replicate 6

city: Klosterneuburg

first: Yuri

last: Ignatyev

address: Am Campus

country: Austria

institute: ISTA Austria

description:
Library name: 322197
10x Genomics

data_processing:
10X CellRanger v5.0.0 was used for gene alignment to obtain gene-barcode matrices. The genome used for the reference was Xenla 9.2 (X. laevis v9). For stages NF37-38, NF47-48 and NF54-55 samples were aggregated with the cellranger function aggr
Ambient RNA was removed with CellBender v0.3.2 with 150 epochs and fpr of 0.01 from the raw features matrices produced by the cellranger function count.
Assembly: Xenla 9.2 (X. laevis v9)
Supplementary files format and content: raw feature matrices in h5 format after the cellranger function count
Supplementary files format and content: filtered features matrices in h5 format after cellbender

organism: Xenopus laevis

source_name: spinal cord

extract_protocol:
For all stages, acquired tissue was dissociated with liberase to obtain single-cell suspension according to previously published methods, and FACS-sorted for the presence of GFP using a BD FACS Aria III Cell Sorter.  All animals, except for one replicate from NF57-58 batch, were transgenic Xla.Tg(tubb2b:maptGFP)Amaya (EXRC), expressing GFP under neuron-specific tubb2b transcriptional control, enabling us to enrich neuronal cells.
Cells were processed following the Chromium Single Cell 3’ v3.1 protocol and Chromium Reagent Kits were used to prepare single-cell libraries (10X Genomics). Sequencing was performed on a NovaSeq (Illumina).

value: spinal cord

tag: developmental stage


title: Three 3-week-old offspring from dams exposed to 1.5% DSS from E13 to E19 3

city: Daegu

first: Ji-Min

address: 680, Gukchaebosang-ro

department: Cell & Matrix Research Institute

country: South Korea

institute: Kyungpook National University

description: Library name: Test_3

data_processing:
Raw reads were quality-checked using FastQC v0.11.7,
Trimmed with Trimmomatic v0.38, and mapped to the mm10 reference genome using HISAT2 v2.1.0.
Transcript assembly and quantification were performed using StringTie v2.1.3b, and gene-level counts were generated
Differentially expressed genes were identified using DESeq2
Assembly: mm10/NCBI_108
Supplementary files format and content: Processed data includes a tab-delimited matrix file containing gene symbols as row names and FPKM values across samples

source_name: colon

extract_protocol:
Total RNA was extracted from colon tissue using QIAzol Lysis Reagent followed by purification with the RNeasy Lipid Tissue Mini Kit (Qiagen, Cat# 74804), according to the manufacturer's instructions
TruSeq Stranded mRNA Reference Guide #1000000040498v00

value: colon

value: 1.5% DSS from E13 to E19


title: Psoriasis_22_LS_39

city: Aarhus N

first: Thomas

address: Palle Juul Jensens Boulevard 99

institute: Aarhus University

source_name: skin

extract_protocol: Formalin fixed paraffin embedded tissue tissue microarray cores with a diameter of 1.5 mm were cut in 5 μm thick sections were using a microtome. Slides were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH),  deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes. In situ hybridization was performed according to the manufacturer’s instructions (User Manual: Slide Preparation for RNA Assays, NanoString).


title: S. lacustris, tryptamine, 1 h, rep 1

description:
Library name: Sample 1
Column name in counts_allSamples.txt: star_trans_clean_out/1_R1T_T1_W_Aligned.sortedByCoord.out.bam

value: Whole body

value: WT

value: 37.5 µM tryptamine 1 hour


title: X.laevis NF57-58 spinal cord replicate 5

description:
Library name: 322196
10x Genomics


title: CSN8-SF-WT-2

description: Library name: Sample 2

value: Subcutaneous adipose tissue

value: male


title: N3-Input

description:
Library name: sample1
input

value: negative control


title: Psoriasis_22_LS_37

value: LS

value: Male


title: Three 3-week-old offspring from dams exposed to 1.5% DSS from E13 to E19 2

description: Library name: Test_2


title: Tendon tissues, Lysm-Cre; Ampkα1fl/fl mice，rep2

description: Library name: SAMPLES5


title: Psoriasis_22_LS_36


title: Tendon tissues, Lysm-Cre; Ampkα1fl/fl mice，rep1

description: Library name: SAMPLES4


title: Three 3-week-old offspring from dams exposed to 1.5% DSS from E13 to E19 1

description: Library name: Test_1


title: CSN8-SF-WT-1

description: Library name: Sample 1


title: Tendon tissues,control group，rep2

description: Library name: SAMPLES2

value: littermates


title: Tendon tissues,control group，rep3

description: Library name: SAMPLES3


title: I2-Input

description:
Library name: sample11
input

value: liver

value: (Durocx [Landrace x Yorkshire])

value: iron deficiency


title: X.laevis NF57-58 spinal cord replicate 2

description:
Library name: 319739
10x Genomics


title: X.laevis NF57-58 spinal cord replicate 4

description:
Library name: 319064
10x Genomics


title: X.laevis NF57-58 spinal cord replicate 1

description:
Library name: 286435
10x Genomics

value: wild type


title: Psoriasis_22_LS_34

value: skin


title: Psoriasis_22_LS_35


title: Tendon tissues,control group，rep1

description: Library name: SAMPLES1

value: Tendon tissue

value: tendon transection


title: Three 3-week-old offspring from dams exposed to 0% DSS from E13 to E19 3

description: Library name: Con_3

value: colon

value: 0% DSS from E13 to E19


title: X.laevis NF57-58 spinal cord replicate 3

description:
Library name: 319740
10x Genomics

value: spinal cord


title: iKAP cells, Untreated_biol rep 3

status: Public on Feb 17 2026

city: Austin

first: Jonathan

last: Sessler

state: Texas

address: 100 E 24th St, Austin, TX

institute: University of Texas Austin

description:
Library name: Sample 12
A23

data_processing:
The NextSeq RTA (version 2.4.11.0) was used for base calling. Bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files. Fastq files were aligned to the mouse reference genome (mm10) using HISAT2 software and assembled using StringTie. R package DESeq2 was used for data normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: raw counts

source_name: iKAP

growth_protocol: iKAP cells were maintained with DMEM supplemented with 10% FBS and 1 μg/ml doxycycline in humidified atmostphere with 5% CO2 at 37ºC

extract_protocol:
RNA was harvested using the QIAGEN RNeasy Plus Universal Mini Total RNA protocol
Libraries were generated using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit following manufacturers protocol.

treatment_protocol: iKAP cells were seeded in 10 mm plate. After a 3-day incubation (60-70% confluency) the media was removed and treated media with either compound 1, oxaliplatin, or auranofin was added. For the control group only, fresh media was added. After 4-hour incubation at 37ºC in the presence of 5% CO2., the media was removed from each flask and the cells were washed with warm PBS and then treated with trypsin. The trypsin was quenched with media and cells were transferred to 15 mL centrifuge tubes where they were pelleted. The media was discarded, and the cell pellet was washed 3x with PBS. Cells were then re-suspended in PBS and treated with the QIAzol Lysis Reagent and homogenized by vigorous vortexing and shaking.

value: iKAP

value: colorectal cancer

value: KRASG12D,  APC-/- and TRP53-/-


title: iKAP cells, Untreated_biol rep 2

description:
Library name: Sample 11
A22


title: Psoriasis_22_LS_33

last: Emmanuel


title: Three 3-week-old offspring from dams exposed to 0% DSS from E13 to E19 1

description: Library name: Con_1


title: iKAP cells, Oxaliplatin_biol rep 3

description:
Library name: Sample 6
J23


title: RNA enriched from tau fibrils from seeded AD brain tau fibrils

city: Los Angeles

first: David

middle: S.

last: Eisenberg

address: 611 Charles E. Young Dr. East

institute: University of California, Los Angeles

description: Library name: Sample 1

data_processing:
The reads were mapped by STAR 2.7.9a under default parameters and read counts per gene/transcript were quantified using the mouse genome mm39 in Partek Flow.
Assembly: mouse genome mm39
Supplementary files format and content: all gene counts are in a csv file

source_name: mouse liver

extract_protocol:
100 mg of liver tissues from C57BL/6J mice was homogenized in 1 mL TRIzol Regent, with an RNA extraction of 0.2 mL chloroform. Recombinant tau40 was incubated with extracted mouse liver RNA with AD tau fibrils and shaken at 37C for 2 days. Finally, AD-seeded fibrils were centrifuged for 1 hour and washed twice with RNase-free water, where sample was sent for sequencing.
The library was synthesized using the KAPA mRNA HyperPrep Kit with RiboErase rRNA depletion.

value: mouse liver


title: iKAP cells, Oxaliplatin_biol rep 1

description:
Library name: Sample 4
J21


title: iKAP cells, Compound 1_biol rep 3

description:
Library name: Sample 3
E23


title: iKAP cells, Compound 1_biol rep 1

description:
Library name: Sample 1
E21


title: iKAP cells, Untreated_biol rep 1

description:
Library name: Sample 10
A21


title: iKAP cells, Auranofin_biol rep 3

description:
Library name: Sample 9
K23


title: iKAP cells, Auranofin_biol rep 1

description:
Library name: Sample 7
K21


title: Three 3-week-old offspring from dams exposed to 0% DSS from E13 to E19 2

description: Library name: Con_2


title: iKAP cells, Auranofin_biol rep 2

description:
Library name: Sample 8
K22


title: iKAP cells, Oxaliplatin_biol rep 2

description:
Library name: Sample 5
J22


title: Brain Tissue_Control group_Male 1

city: Middle Village

first: Teeshavi

middle: D

last: Acosta

state: NY

address: 61-53 78th street

institute: St Johns University

description: Library name: Male_1

data_processing:
Raw FASTQ reads were quality-checked and trimmed using fastp to remove adapter sequences and low-quality bases.Cleaned reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2 (v2.2.1) with splice-aware alignment. Gene-level read counts were generated using featureCounts (v2.0.6).Expression levels were normalized to FPKM (Fragments Per Kilobase of transcript per Million mapped reads)Differential expression analysis was performed with DESeq2 (v1.42.0) (for samples with biological replicates) or edgeR (v4.0.16) (for samples without replicates).GO, KEGG, GSEA enrichment, and alternative splicing analyses were performed using clusterProfiler, rMATS, and related R packages. SNP and fusion gene analyses were conducted with GATK and STAR_fusion, respectively.
Assembly: GRCm39
Supplementary files format and content: .txt  --  This file contains normalized gene expression values (FPKM) for all RNA-seq samples included in the study. Each row represents a gene (annotated with Ensembl gene ID, gene name, chromosome location, start and end coordinates, strand, gene length, biotype, and description). Each column represents an individual mouse brain sample (Female and Male, across control, disease, and treatment groups). Values are fragments per kilobase of transcript per million mapped reads (FPKM).

source_name: Brain

extract_protocol:
Whole brain tissue was rapidly dissected from each mouse, immediately snap-frozen in liquid nitrogen, and stored at -80°C until processing .Total RNA was extracted using Trizol and followed by purfication with the Qiagen RNeasy mini kit to remove contaminants.
Non strand specific library Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Strand specific library Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and and bioanalyzer for size distribution detection.

treatment_protocol: Adult C57BL/6 mice were administered lipopolysaccharide (LPS) intraperitoneally at a dose of 0.5 mg/kg once daily for 7 consecutive days to induce chronic neuroinflammation.  Treatment groups received N,N-dimethylacetamide (DMA) concurrently via intraperitoneal injection once daily for 7 days following the first LPS dose.  Control animals were injected with sterile phosphate-buffered saline (PBS) using the same schedule.  Mice were euthanized on Day 7, and whole brain tissue was collected for RNA extraction and sequencing.

value: Brain

value: PBS treated Day 7


title: Brain Tissue_ Treatment Group_Male 2

description: Library name: Male_6

value: Male

value: LPS + DMA treated Day 7


title: Brain Tissue_Disease Group_Male 2

description: Library name: Male_4

value: LPS treated Day 7


title: Brain Tissue_ Treatment Group_Male 1

description: Library name: Male_5


title: iKAP cells, Compound 1_biol rep 2

description:
Library name: Sample 2
E22


title: Brain Tissue_Control group_Male 2

description: Library name: Male_2


title: Brain Tissue_Control group_Female 2

description: Library name: Female_2

value: Female


title: Brain Tissue_ Treatment Group_Female 1

description: Library name: Female_5


title: Brain Tissue_ Treatment Group_Female 2

description: Library name: Female_6


title: IM-FEN cells treated with 10% BSA for 24 h_rep6

city: Decatur

first: Shanthi

last: Srinivasan

state: Georgia

address: 5A137-1670 Clairmont Rd,

department: Division of Digestive Diseases

institute: Emory University

description:
Library name: P10_Veh06
RNA-seq from Vehicle-treated IM-FEN cells

data_processing:
Raw FASTQ files were quality-checked using FastQC and aligned to the mouse genome (mm10) using STAR aligner.
Gene-level counts were generated using featureCounts (Subread v2.0). Differential expression was performed using DESeq2 in R. Log2 fold changes and p-values were calculated.
Assembly: GRCm38/mm10 (GENCODE M25 annotation)
Supplementary files format and content: Excel spreadsheet with gene IDs as rows and expression values (TPM) per sample as columns. DEG metrics (log2FC, p-value, padj) included.
Supplementary files format and content: PA_treatmentvsPA_control_deg_processed_file.xlsx

source_name: IM-FEN

growth_protocol: IM-FEN cells were seeded in modified N2 medium supplemented with 10% fetal bovine serum (FBS), 20 U/mL recombinant mouse interferon-γ, and glial cell line-derived neurotrophic factor (GDNF). Cells were maintained at 33°C in a humidified incubator with 5% CO₂. After 24 h, media were replaced with Neurobasal-A medium containing B-27 Plus, 1 mM L-glutamine, 1% FBS, and GDNF. Cells were transferred to 39°C to induce differentiation.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit following the manufacturer’s protocol.
mRNA library preparation (poly A selection)

treatment_protocol: Cells were treated with 0.5 mM palmitic acid (PA) or vehicle (10% BSA) for 24 hours prior to RNA extraction.

value: IM-FEN

value: Immortalized Mouse-Fetal Enteric Neurons

value: wild type


title: Brain Tissue_Disease Group_Female 2

description: Library name: Female_4


title: IM-FEN cells treated with 10% BSA for 24 h_rep5

description:
Library name: P10_Veh05
RNA-seq from Vehicle-treated IM-FEN cells


title: IM-FEN cells treated with 10% BSA for 24 h_rep3

description:
Library name: P10_Veh03
RNA-seq from Vehicle-treated IM-FEN cells


title: Brain Tissue_Disease Group_Male 1

description: Library name: Male_3


title: IM-FEN cells treated with 10% BSA for 24 h_rep2

description:
Library name: P10_Veh02
RNA-seq from Vehicle-treated IM-FEN cells


title: Brain Tissue_Disease Group_Female 1

description: Library name: Female_3


title: Brain Tissue_Control group_Female 1

description: Library name: Female_1


title: IM-FEN cells treated with palmitic acid (0.5 mM) for 24 h_rep1

description:
Library name: P10_PA01
RNA-seq from palmitate-treated IM-FEN cells

value: Palmitic acid- 0.5 mM


title: IM-FEN cells treated with 10% BSA for 24 h_rep4

description:
Library name: P10_Veh04
RNA-seq from Vehicle-treated IM-FEN cells


title: IM-FEN cells treated with palmitic acid (0.5 mM) for 24 h_rep6

description:
Library name: P10_PA06
RNA-seq from palmitate-treated IM-FEN cells


title: IM-FEN cells treated with 10% BSA for 24 h_rep1

description:
Library name: P10_Veh01
RNA-seq from Vehicle-treated IM-FEN cells


title: IM-FEN cells treated with palmitic acid (0.5 mM) for 24 h_rep5

description:
Library name: P10_PA05
RNA-seq from palmitate-treated IM-FEN cells


title: IM-FEN cells treated with palmitic acid (0.5 mM) for 24 h_rep3

description:
Library name: P10_PA03
RNA-seq from palmitate-treated IM-FEN cells


title: IM-FEN cells treated with palmitic acid (0.5 mM) for 24 h_rep2

description:
Library name: P10_PA02
RNA-seq from palmitate-treated IM-FEN cells


title: 4-MGT_2

city: London

first: Mariia

last: Yuneva

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: PAN4777A14

data_processing:
The demultiplexing, barcoded processing and gene counting was performed using Cell Ranger software v7.1.0 and 10X mouse transcript reference refdata-gex-mm10-2020-A. https://www.10xgenomics.com/support/software/cell-ranger/latest
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated filtered barcode, features and matrix files output from Cell Ranger per sample.

source_name: Mammary gland tumour

growth_protocol: MMTV-MYC mammary gland tumour-derived cells (LM1) were maintained in DMEM/F12 supplemented with 10% FBS, 10mM HEPES, 2 mM glutamine, 5ug/ml insulin, 1 ug/ml hydrocortisone, 10 ng/ml EGF, 100 ug/ml penicillin/streptomycin and kept in humidified atmosphere with 5% CO2 at 37 0C. 50,000 LM1 cells were injected into the fat pads of healthy 6–8-week-old female FVB/NJ mice, and 28 days later,  primary tumours and lungs from tumour-bearing and control mice were collected for single-cell RNA seq sample preparation. Additionally, LM1 cells were also collected and submitted for the sequencing.

extract_protocol:
The concentration and viability of the single cell suspension was measured using acridine orange (AO) and propidium iodide (PI) and the Luna-FX7 Automatic Cell Counter. Approximately (10,000 cells were loaded on Chromium Chip and partitioned in nanolitre scale droplets using the Chromium Controller and Chromium (4)Next GEM Single Cell Reagents (CG000315 Chromium Single Cell 3' Reagent Kits User Guide (v3.1 - Dual Index)). Within each droplet the cells were lysed, and the RNA was reverse transcribed. All of the resulting cDNA within a droplet shared the same cell barcode.
Illumina compatible libraries were generated from the cDNA using Chromium Next GEM Single Cell library reagents in accordance with the manufacturer’s instructions (10x Genomics, CG000315 Chromium Single Cell 3' Reagent Kits User Guide (v3.1 - Dual Index)). Final libraries are QC’d using the Agilent TapeStation and sequenced using the Illumina  NovaSeq 6000. Sequencing read configuration: 28-10-10-90.

value: Mammary gland tumour

value: cells isolated from mammary gland tumours

value: FVB/N


title: RORgt_2

city: Beijing

first: Hao

last: Zhang

address: Haidian  District

institute: Tsinghua University

description: Library name: RORgt_2

data_processing:
The CUT&Tag reads were aligned to mouse mm10 genome by using bowtie2. Subsequent preprocessing steps included the removal of low-quality mapped reads, mitochondrial reads, and PCR duplicates using Picard MarkDuplicates. Peak calling was performed using Macs2 with the parameters “-f BAM -B --nomodel --keep-dup all”. To assess differential signal intensity between experimental and control groups, Macs2 bdgcmp was employed to generate bedGraph files using the setting “-m logLR -p 0.00001”. Deeptools was utilized to generate coverage track file (bigWig) which can be visualized in IGV.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: small intestine

extract_protocol:
The CUT&Tag experiments were performed as previously described(Vazyme TD904 kit) to generate DNA libraries derived from cells
The CUT&Tag experiments were performed as previously described(Vazyme TD904 kit) to generate DNA libraries derived from cells. Every sample has two replicates.

value: small intestine

value: Rag1 knockout


title: RORgt_1

description: Library name: RORgt_1


title: 2-MGT_1

description: Library name: PAN4777A12


title: IgG_Rabbit

description: Library name: IgG_Rabbit


title: IM-FEN cells treated with palmitic acid (0.5 mM) for 24 h_rep4

description:
Library name: P10_PA04
RNA-seq from palmitate-treated IM-FEN cells


title: RUNX3_2

description: Library name: RUNX3_2


title: 1-MetLung_1

description: Library name: PAN4777A11

source_name: Lung

value: Lung

value: Isolated lung cells

value: WT

value: Mammary fat pad tumour cell injection


title: 4C-CNS11

description: Library name: 4C-CNS11

data_processing:
4C-seq data were analyzed using the pipe4C pipeline to map, normalize, and visualize interactions. Raw sequencing reads were preprocessed to remove adapters and low-quality bases using fastp (version 0.19.5). The processed reads were aligned to the reference genome (mm10) with Bowtie2, followed by selection of reads mapping to the bait region and removal of low-quality or duplicate reads. Using pipe4C, aligned reads were assigned to restriction fragments and normalized for coverage. Fragment counts were smoothed and visualized to reveal contact frequency along the genome using WashU Epigenome Browser (http://epigenomegateway.wustl.edu/browser/, with parameters: aggregate method-MEAN, Smooth-7). All analyses were conducted with pipe4C (version 1.1) with default parameters.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: 4C-Seq

extract_protocol:
4C-seq were performed as previously described with slight modifications(Krijger et al., 2020). In brief, 3*106 ILC3s were crosslinked with 1% formaldehyde. Cells were lysed in lysis buffer containing 10mM Tris-HCl (pH8.0), 10mM NaCl, 0.2% Igepal CA630 and protease inhibitors on ice for 50 min. Crosslinked DNA was digested with MboI (NEB) overnight at 37°C, ligated by T4 DNA ligase (NEB), and de-crosslinked with Proteinase K. After DNA purification using the ChIP DNA Clean & Concentrator kit (ZYMO, D5205), a secondary digestion was performed using NlaIII (NEB) at 37°C for 5h, followed by ligation and a final round of DNA purification.
The 4C library was amplified using CNS11 specific primers (5'-AGATGGAAATGCTGGTGGAACC-3' and 5'-CCCCTTTGCACCCCTGCATG-3') by Expand Long Template PCR System (Roche, 11681834001).


title: IgG_Rat

description: Library name: IgG_Rat


title: 7-MGT_3

description: Library name: PAN4777A17


title: 3-MetLung_2

description: Library name: PAN4777A13


title: 6-MetLung_3

description: Library name: PAN4777A16


title: LM1_cells

description: Library name: PAN4777A20

value: MMTV-MYC tumour-derived cells


title: mESC ,WT ,Replicate 1

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

institute: Sylvester Comprehensive Cancer Center

description:
Library name: ESC_WT_REP1
Raw counts for all samples and replicates

data_processing:
Data was processed using nf-core/rnaseq v3.10.1 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020).  The pipeline was executed with Nextflow v22.10.7 (Di Tommaso et al., 2017)
trimGalore! 0.6.7
salmon  1.9.0
STAR 2.7.9a
Assembly: mm10
Supplementary files format and content: tab-delimited text files inclues raw counts for each sample

source_name: Mouse embryonic stem cells (mESCs)

extract_protocol: Please check manuscript

treatment_protocol: NPCs and differentiated NPCs were generated following the protocol from Bibel and colleagues (https://www.nature.com/articles/nprot.2007.147). Rescue experiments were performed by adding 3µg of CHIR99021 at day 6 of ESC differentiation with retinoic acid and 10%

value: Mouse embryonic stem cells (mESCs)


title: 8-WtLung_2

description: Library name: PAN4777A18

value: Control


title: RUNX3_1

description: Library name: RUNX3_1


title: 5-WtLung_1

description: Library name: PAN4777A15


title: mESC ,Clone R70H 282 ,Replicate 2

description: Library name: ESC_Clone_282_REP2


title: mESC ,WT ,Replicate 2

description: Library name: ESC_WT_REP2


title: MBD_Water

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

description:
Library name: Sample3
10x Genomics

data_processing:
Using Cellranger (Ver: 7.1.0) the fastq files were aligned to the mouse reference genome and feature counts were generated. Cluster analysis was performed using Seurat (4.0) and cluster identities were classified using cell type specific markers
Assembly: Mouse mm10
Supplementary files format and content: tsv and matrix
Supplementary files format and content: tsv and features
Supplementary files format and content: tsv and barcodes

source_name: Colon

growth_protocol: 3 weeks old mice were fed on either recular chow diet (RCD) or a milk-based diet (Lactogen 2, Nestle) until 8 weeks.

extract_protocol:
The mice were euthanized, and the colon was carefully dissected and cut open longitudinally. The tissue was washed three times with PBS, cut into small pieces, and incubated in a pre-digestion buffer (1X PBS with 25 mM HEPES, 10 mM EDTA, 0.5 mM DTT) at 37°C with shaking at 200 RPM for 15 minutes. The mixture was centrifuged to remove the pre-digestion buffer, and wash media (RPMI + 5% FBS) was added. The sample was vortexed, and the epithelial cells were collected from the supernatant. The supernatant was then filtered through a nylon cell strainer with a 70-μm pore size, followed by a second filtration with a 40-μm pore size. The remaining tissue was treated with digestion buffer (RPMI with 10% FBS, 25 mM HEPES, 0.5 mg/ml Collagenase IV, 0.5 mg/ml Dispase) for 45 minutes at 37°C, with shaking at 200 RPM. The mixture was centrifuged at 1500 RPM for 5 minutes at room temperature, and the supernatant was discarded. Pre-warmed wash media was added, and the sample was vortexed. The supernatant was then filtered through a nylon cell strainer with a 70-μm pore size, followed by a 40-μm pore size, and the cells were counted.The epithelial cells were pooled with immune cells and counted the number of live cells using Luna- II Automated Cell Counter. We pooled three mice from each group of Chow water, Chow with 1.5% DSS; MBD water and MBD 1.5% DSS in equal numbers. The cells were sorted into four group Epithelial (+EPICAM, -DAPI), B cells ( -DAPI, +CD45, +CD19), T cells ( -DAPI, +CD45, +CD3), myeloid cells (-DAPI, +CD45, -CD3, -CD19) using BD-FACS Aria sorter. In each group we pooled 6000 epithelial, 2000 B, 4000 T and 8000 myeloid cells
Pooled single cells were used to prepare single cell transcriptome sequencing libraries using the Single Cell 3’ v3.1 Gel Beads kit (cat no 2000164) from 10X genomics. Libraries were sequenced using Novaseq 6000 machine (Illumina).

treatment_protocol: 1.5 % DSS or water (control) were given ad libitum to the mice for one week.

value: Colon

value: Male

value: Epitheilial, B cell, T cell and myeloid cell

value: Water

value: 8 weeks


title: mESC ,Clone R70H 112 ,Replicate 2

description: Library name: ESC_Clone_112_REP2


title: 9-WtLung_3

description: Library name: PAN4777A19


title: mESC ,Clone R70H 112 ,Replicate 1

description:
Library name: ESC_Clone_112_REP1
deseq2 RDS object to be loaded in R


title: mESC ,Clone R70H 282 ,Replicate 1

description:
Library name: ESC_Clone_282_REP1
Normalized (median of ratios ) counts for all samples and replicates


title: RCD_DSS

description:
Library name: Sample2
10x Genomics


title: mouse liver, D5-DT

city: Würzburg

first: Stefan

last: Thomann

address: Versbacher Strasse 9

country: Germany

institute: Würzburg Systems Immunology

data_processing:
FASTQ files were mapped to a reference using kallisto (Bray et al., 2016) and the GRCm38.99 cDNA reference.
Assembly: GRCm38.99 cDNA
Supplementary files format and content: Matrix, gene and barcode files

growth_protocol: All animal experiments were authorized by the German Regional Council of Baden-Württemberg and Bavaria (Regierungspräsidium Freiburg and Würzburg, Regierung Unterfranken. C57BL/6J mice were bred in a 12 hour light/dark cycle with free access to water and food and kept under defined pathogen free conditions, while tolerating commensal and non-pathogenic opportunistic bacteria. Treatment and termination criteria were defined based on the ATBW criteria and reevaluated at defined time intervals based on the severity of burden.

extract_protocol:
For each timepoint, two independent isolation protocols were used for D0, D3, D5, D9, D19 and D25. A gradient centrifugation was used to enrich cell types of interest and cells were magnetically enriched when feasible. In protocol A the following cell types were FACS sorted at equal ratios: alive singlet, Cd45+, Lyve-1+, Pdpn+, Epcam+, Cd31+ Lyve-1-, retinoid-autofluorescent cells (405 nm excitation, 450/40 emission, according to Mederacke et al. Nat. Methods (2015). For protocol B the following cell types were FACS sorted at equal ratios: alive cells from HSC prep, Cd45+ Itgax+ Cd64-, Epcam+, Cd3e+ Lyve-1-.  For the diet stop condition and Mgl2-DTR cell depletion protocol B was used and compared with protocol B data of the respective timepoint.
Libraries from protocol A derived data were generated using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Single Index), while libraries from protocol B data were generated using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index).

treatment_protocol: Mice were fed with chow supplemented with 0.1% 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine (DDC) for time periods of 0 - 25 days or a combination of prolonged diet (DDC D18) in combination with a subsequent recovery period of 7 days. For Mgl2-DTR depletion experiments, Mgl2-DTR mice were used (Kumamoto et al. Immunity (2013)). For depletion, mice were injected DT at day -1 and day 2 and mice were fed DDC for 5 days.

value: liver


title: mouse, liver, D19, protocol B


title: mouse, liver, D25, protocol B


title: mouse liver STOP


title: MBD_DSS

description:
Library name: Sample4
10x Genomics


title: mouse, liver, D9, protocol B


title: mouse, liver, D19, protocol A


title: mouse, liver, D25, protocol A


title: mouse, liver, D0, protocol B


title: RCD_Water

description:
Library name: Sample1
10x Genomics


title: mouse, liver, D3, protocol A


title: mouse, liver, D0, protocol A


title: mouse, liver, D5, protocol A


title: mouse, liver, D5, protocol B


title: Th1_WT_IgG_CUTnTag

city: Bethesda

first: Behdad (Ben)

last: Afzali Khoshkbijari

state: MD

address: 10 Center Drive, 10/8D03

department: Kidney Diseases Branch

institute: National Institutes of Diabetes, Digestive, and Kidney Diseases

data_processing:
Raw reads were processed using CutRunTools/20200629 [21] with the mm10 mouse genome as reference. CTCF CUT&Tag signal data was RPKM normalized using deepTools/3.5.5 with extendReads enabled. Peak calling for CTCF was performed using SEACR/v1.3 with stringent settings and all fragment sizes incorporated. Peaks were further filtered by disassociation of peak summits belonging to the mm10 blacklist (CutRunTools) using bedtools/2.30.0 intersect. Peak signals were recalculated using deepTools computeMatrix +/- 200bp and further filtered by at least 2-fold signal change over cell-type summed IgG signal. Differential CTCF peaks from either genotype were at least +/- 4-fold change in signal between respective genotypes. CTCF motif scoring was evaluated by HOMER/4.11.1 findMotifsGenome.pl with option -size 200. Pik3cdE1020K/+ induced and repressed CTCF peaks were visualized using deepTools and mapped to nearest gene using HOMER annotatePeaks default settings.
Assembly: mm10
Supplementary files format and content: bigwig coverage tracks of CUT&Tag signal data.
Library strategy: CUT&Tag

source_name: Sorted CD4 T Cells

growth_protocol: Sorted naïve CD4 T cells were activated and expanded using anti-CD3 (1ug/mL) and anti-CD28 (3ug/mL) in complete IMDM media in presence of antigen presenting cells (mitomycin C treated T-cell depleted splenocytes)

extract_protocol:
Tagmentation
CUT&Tag/v3
Naïve (liveTCRb+CD4+CD8-CD44-CD62L+CD25-), in vitro Th1 polarized (liveCD4+) and Th2 polarized (liveCD4+) CD4 T cells from WT and Pik3cdE1020K/+ mice were sorted using an Aria Fusion Sorter (BD), as previously described and then subjected to CUT&Tag using the CUT&Tag/v3 protocol (dx.doi.org/10.17504/protocols.io.bcuhiwt6) [20] as indicated on isolated nuclei from naïve CD4 T cells and in vitro polarized Th1 and Th2 cells from WT and Pik3cdE1020K/+ mice. CUT&Tag utilized primary antibodies against CTCF (D31H2, Cell Signaling) and Rabbit mAB IgG XP Isotype Control (DA1E, Cell Signaling). All primary antibodies were diluted 1:50 with the corresponding guinea-pig anti-rabbit secondary diluted 1:100 accordingly. pA-Tn5 was sourced pre-loaded (C01070001, Diagenode). Primary antibody incubation occurred for 1 hr at RT with nutation and all other protocol steps as indicated in the native CUT&Tag protocol. Prepared libraries were normalized and pooled and prepared for sequencing via NovaSeq SP (Illumina) at the NHLBI Genomics Core.

treatment_protocol: Naïve cells were sorted and used directly for analysis. Th1 polarized cells were differentiated in presence of IL-12 and anti-IL-4. Th2 polarized cells were differentiated in the presence of IL-4 and anti-IL12.

value: Sorted CD4 T Cells


title: Th1_Pik3cdE1020K_IgG_CUTnTag


title: Th2_Pik3cdE1020K_IgG_CUTnTag


title: Naïve_Pik3cdE1020K_IgG_CUTnTag


title: Th2_WT_CTCF_CUTnTag


title: mouse, liver, D9, protocol A


title: Th2_Pik3cdE1020K_CTCF_CUTnTag


title: Naïve_WT_CTCF_CUTnTag


title: FXS;Smad4cKO4

city: La Jolla

first: James

last: Deng

address: 1 Miramar St, 929133

department: Molecular Neurobiology

institute: Salk Institute

description: from FACS-sorted SOX9+NEUN- nuclei

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using bcl2fastq v2.20 Conversion Software, and quality tested with MultiQC v1.0.dev0 (Ewels et al., 2016)
Alignment to the mm10 genome was performed using the STAR aligner version 2.5.3a (Dobin et al., 2013). Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 10 multi-mapping locations per read).
Raw and normalized (TPM) gene expression was quantified across all genes (RNAseq) using the top-expressed isoform as proxy for gene expression using HOMER v4.10.4 (Heinz et al., 2010), resulting in 17-35 million uniquely mapped reads per sample.
Assembly: mm10
Supplementary files format and content: Excel Table with normalized gene counts for each sample

molecule: nuclear RNA

source_name: cortex

growth_protocol:
Normal 12h:12h light/ dark rearing
ad lib access to standard mouse chow

extract_protocol:
Freshly dissected mouse cortex in cold physiological buffer, then homogenized to single nuclei and sorted for astrocytes by SOX9 (Abcam AB185966) and NEUN (Millipore #MAB377X) immunostaining as in the protocol from Labarta-Bajo et al., 2023. Sorted SOX9+NEUN- nuclei were lysed, and all RNA extracted with Qiagen RNeasy Micro kit with DNase step.
Illumina Ribo-Zero Plus rRNA Depletion Kit with IDT for Illumina RNA UD Indexes, following manufacturer instructions

treatment_protocol: normal rearing of the mouse strains: Fmr1 (Jax #003025), Gfap-Cre73.12 (Jax #012886), Smad4 floxed (Jax #017462)

value: cortex

value: post natal day 27

tag: manipulation

value: normal rearing

value: Fmr1 -/y x Smad4 fl/fl x GFAP-cre+


title: Th2_WT_IgG_CUTnTag


title: Th1_Pik3cdE1020K_CTCF_CUTnTag


title: Th1_WT_CTCF_CUTnTag


title: Naïve_Pik3cdE1020K_CTCF_CUTnTag


title: Naïve_WT_IgG_CUTnTag


title: FXS5

description: from FACS-sorted SOX9+NEUN- nuclei

tag: strain

value: Fmr1 -/y x Smad4 fl/fl x GFAP-cre-


title: FXS;Smad4cKO2

description: from FACS-sorted SOX9+NEUN- nuclei

value: post natal day 26


title: FXS;Smad4cKO1

description: from FACS-sorted SOX9+NEUN- nuclei


title: mouse, liver, D3, protocol B

source_name: liver


title: WT;Smad4cKO6

description: from FACS-sorted SOX9+NEUN- nuclei

value: Fmr1 +/y x Smad4 fl/fl x GFAP-cre+


title: WT;Smad4cKO4

description: from FACS-sorted SOX9+NEUN- nuclei

value: post natal day 28


title: WT;Smad4cKO5

description: from FACS-sorted SOX9+NEUN- nuclei


title: WT;Smad4cKO2

description: from FACS-sorted SOX9+NEUN- nuclei


title: WT;Smad4cKO1

description: from FACS-sorted SOX9+NEUN- nuclei


title: FXS4

description: from FACS-sorted SOX9+NEUN- nuclei


title: FXS1

description: from FACS-sorted SOX9+NEUN- nuclei


title: FXS3

description: from FACS-sorted SOX9+NEUN- nuclei


title: FXS2

description: from FACS-sorted SOX9+NEUN- nuclei


title: FXS;Smad4cKO3

description: from FACS-sorted SOX9+NEUN- nuclei


title: WT;Smad4cKO3

description: from FACS-sorted SOX9+NEUN- nuclei


title: WT1

description: from FACS-sorted SOX9+NEUN- nuclei

value: Fmr1 +/y x Smad4 fl/fl x GFAP-cre-


title: WT4

description: from FACS-sorted SOX9+NEUN- nuclei


title: WT3

description: from FACS-sorted SOX9+NEUN- nuclei


title: WT2

description: from FACS-sorted SOX9+NEUN- nuclei


title: HSF1 knock-down treated with 17-AAG 48 hours replicate 3

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

institute: The Institute of Cancer Research

hyb_protocol: The resulting cRNA was co-hybridised with Cy5 labelled Universal Human Reference RNA (Stratagene, CA) to the 4x44K Agilent human gene expression array (G4112F-014850, Agilent).

scan_protocol: Scanned on a Agilent Technologies Scanner G2505C US84300231

data_processing: The images were feature-extracted to generate raw data files using Agilent feature extraction version 10.5.1.1 and extraction protocol GE2_105_Jan09 and grid file 014850_D_F_20090416. Background subtracted data for sample and reference were entered in the Genespring analysis software (Agilent) and Lowess normalization was applied to the samples.

label_protocol: The Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol v 5.7 was used. Briefly, 1 microgram of RNA was labelled with Cy3 using the Agilent Quick Amp kit according to manufacturer’s instructions.

growth_protocol: U2-OS cells were obtained from the ATCC. Cells were cultured in DMEM supplemented with 10% FCS, 2 mM glutamine and non-essential amino acids. All cell lines were maintained at 37 °C, 5% CO2 and tested negative for mycoplasma

extract_protocol: RNA was extracted using the ABI PRISM 6100 Nucleic Acid PrepStation (Applied Biosystems, CA) according to the manufacturer’s instructions, from at least three independent cell cultures. RNA quality was assessed using the bioanalyzer (Agilent, CA).

treatment_protocol: The HiPerFect (Qiagen) reverse transfection protocol was used as standard for U2OS transfection using 50 nM siRNA for 48 or 72h. 250 nM17-AAG, or the equivalent volume of DMSO, was added on the final day of the experiment so a 6h treatment would coincide with either 48 or 72h siRNA knock-down

tag: sirna

value: Osteosarcoma

tag: time (hours)

source_name: Universal Human Reference RNA (Stratagene)

tag: sample type

value: Reference sample


title: Brangus whole blood under heat stress, biological replicate 2

city: Zuru

first: Akeem

middle: Babatunde

last: Sikiru

state: Kebbi

address: Department of Animal Science, College of Agriculture, FUAZ, Zuru, Nigeria.

department: Animal Science

country: Nigeria

institute: Federal University of Agriculture Zuru

description:
Library name: Brangus2_L1_1.fq.gz
Female, non-pregnant, non-lactating, age 4.5±1.2 years, body weight 450±15 kg. Sample collected from jugular vein during peak heat load.

data_processing:
Libraries constructed using Illumina Stranded mRNA Prep kit. mRNA enriched by poly-A selection, fragmented, reverse-transcribed. Libraries end-repaired, A-tailed, ligated with indexed adapters, amplified by PCR. Quality assessed using Agilent 2100 Bioanalyzer. Sequenced on Illumina NovaSeq 6000 (paired-end, 2 × 150 bp).
Raw reads quality assessed with FastQC v0.11.9. Adapter trimming and quality filtering with Trimmomatic v0.39.
Reads aligned to Bos taurus reference genome (ARS-UCD1.2) using HISAT2 v2.2.1.
Gene counts quantified using featureCounts v2.0.1. Expression normalized as FPKM.
Assembly: Differential expression analysis using DESeq2 v1.38.0. Genes with adjusted p < 0.05 and log2FC > 1 considered differentially expressed.
Supplementary files format and content: ARS-UCD1.2
Supplementary files format and content: raw_counts.txt: Tab-delimited gene count matrix. FPKM_normalized_expression.txt: FPKM-normalized values. differential_expression_results.txt: DESeq2 results with gene symbols, log2FC, p-values, adjusted p-values.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Bos indicus x Bos taurus

source_name: whole blood

growth_protocol: Clinically healthy, non-pregnant, non-lactating adult female cows (mean age: 4.50 ± 1.20 years; mean body weight: 450.00 ± 15.00 kg) were maintained at Universiti Putra Malaysia Teaching and Research Farm, Serdang, Selangor, Malaysia (2°59'24"N, 101°42'32"E, elevation 68 m). The farm is characterized by a humid tropical climate with minimal seasonal temperature variation, mean annual temperature of 27.5°C, and relative humidity of 70-90%.

extract_protocol:
Animals were sampled during peak heat load conditions with Temperature-Humidity Index (THI) of 44.68. All experimental procedures were approved by IACUC (UPM/IACUC/AUP-R055/2025) and conducted in accordance with Malaysian Codes of Practice for Care and Use of Animals for Scientific Purposes and ARRIVE guidelines.
Total RNA was extracted from whole blood using PrimeZOL reagent (Canvax Biotech, Spain). RNA was precipitated with isopropanol, washed with 75% ethanol, and resuspended in nuclease-free water. RNA concentration and purity assessed by NanoDrop. RNA integrity evaluated with RIN > 7.0 required.

treatment_protocol: Heat stress (Temperature-Humidity Index: 44.68)

value: whole blood

tag: genotype

value: Brangus (intermediate composite breed)

value: heat stress (Temperature-Humidity Index:44.68)


title: Brangus whole blood under heat stress, biological replicate 1

description:
Library name: Brangus1_L1_1.fq.gz
Female, non-pregnant, non-lactating, age 4.5±1.2 years, body weight 450±15 kg. Sample collected from jugular vein during peak heat load.

tag: tissue


title: DHX8 knock-down treated with 17-AAG 72 hours replicate 3


title: All Stars siRNA negative control DMSO vehicle control 72 hours replicate 2

value: All Stars

value: DMSO