title: B6 iNKT1 1 TCR-Seq

description: Library name: B6 iNKT1 1

value: iNKT1 cells


title: B6 iNKT1 4 TCR-Seq

status: Public on Jan 21 2026

type: SRA

city: Chiba

first: Ryo

last: Nasu

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

country: Japan

institute: Chiba University

description: Library name: B6 iNKT1 4

library_source: transcriptomic

data_processing:
Sequencing was performed using the MiSeq platform (Illumina, USA). The acquired sequences were aligned and assembled, and the clonotypes were identified using the MiXCR software program (version 3.0.12) with default parameters.
VDJtools (version 1.2.1) was employed for data format conversion, categorization based on V/D/J segments, and computation of diversity information used to draw rarefaction curve plots for conventional CD4T and CD8T cells.
Diversity calculations for iNKT cell subsets using the Shannon index involved constructing a downsampling series from count tables generated by VDJtools, followed by computation with custom in-house scripts.
Assembly: mm10
Supplementary files format and content: Tab delimeted text files include the TCR clonotype tables in VDJtools output format
Library strategy: TCR-Seq

molecule: total RNA

organism: Mus musculus

source_name: thymus

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
For cDNA library construction, we used the SMARTer Mouse TCR a/b Profiling Kit (Clontech, Takara Bio USA, Inc) following the manufacturer’s protocols.

tag: tissue

value: thymus

tag: cell type

tag: genotype


title: B6 iNKT1 2 TCR-Seq

description: Library name: B6 iNKT1 2


title: 2030R_CSF

city: New Haven

first: Shelli

last: Farhadian

state: CT

address: 135 College St, PO BOX 208022

country: USA

institute: Yale School of Medicine

description:
Library name: 2030R_CSF
final_processed_tpm_values_csf.txt

data_processing:
Reads were trimmed for quality and length using trimmomatic.
Trimmed reads were mapped to hg38 genome using HiSAT2
Per-gene count matrices were geneated using StringTie
Gene count matrices and associated metadata were analyzed using DESeq2 in R, and plotted using appropriate software.
Assembly: hg38
Supplementary files format and content: TPM matrix. Tab separate values file with TPM values for each gene in each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: Cerebrospinal Fluid

extract_protocol:
DNA/RNA was extracted from thawed CSF cells using the AllPrep DNA/RNA Micro Kit (CAT No 80284). DNA/RNA was extracted from thawed PBMC using the AllPrep DNA/RNA/miRNA Universal Kit (CAT No: 80224)
Paired end library preparation

value: Cerebrospinal Fluid

tag: treatment

value: NP-Long COVID


title: B6 iNKT1 3 TCR-Seq

description: Library name: B6 iNKT1 3


title: BALB/c CD8T 1 TCR-Seq

description: Library name: BALB/c CD8T 1

value: CD8T cells

value: BALB/c


title: 2034CA_CSF

description:
Library name: 2034CA_CSF
final_processed_tpm_values_csf.txt


title: Knee joint, LOXL2, Control, Replicate3

city: Boston

first: Manish

middle: V.

last: Bais

state: MA

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

description: Library name: Vehicle_DMM_LOXL2wt_Rep3

data_processing:
In-house perl script developed by NOVOGENE bioinformatics facility.
Reference genome alignment using HISAT2.
Gene expression quantification using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized count for each samples

source_name: Knee joint

extract_protocol:
RNA was isolated using TRIzol and purified with RNeasy Mini kit (Qiagen). Around 400 nanogram of RNA was used for sequencing at NOVOGENE facility.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

value: Knee joint


title: 2025R_CSF

description:
Library name: 2025R_CSF
final_processed_tpm_values_csf.txt


title: 2027R_CSF

description:
Library name: 2027R_CSF
final_processed_tpm_values_csf.txt


title: FAPs, PRP

city: Chengdu City

first: Huizhen

last: Zou

address: No. 270, Tianhui Road, Rongdu Avenue, Jinniu District

country: China

institute: The General Hospital of Western Theater Command PLA

description: Library name: sample1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to mm10 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary fibro-adipogenic progenitors

growth_protocol: FAPs were cultured in growth medium (GM) consisting of Dulbecco’s modified Eagle medium (DMEM) with 20% FBS and 2% penicillin‒streptomycin. For induction of adipogenic differentiation, FAPs were exposed to adipogenic induction medium consisting of DMEM with 20% FBS, 0.5 mM IBMX, 0.25 μM dexamethasone and 10 μg/ml insulin

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

treatment_protocol: FAPs were treated by PRP or vehicle as control.

value: primary fibro-adipogenic progenitors

value: WT

value: adipogenic differentiation


title: FAPs, control

description: Library name: sample2


title: DD2_rDKK3_d3_acinar RNA_20

city: Ulm

first: Alexander

last: Kleger

address: Albert einstein allee 23

department: Institute for Molecular Oncology and Stem Cell biology

country: Germany

institute: Universitaetsklinikum Ulm

description:
Library name: DD2_rDKK3_d3_acinar_RNA_20_S137469
Column name in rnaseq_deseq_batch_counts_raw.tsv: DD2_rDKK3_d3_acinar_RNA_20_S137469

data_processing:
Illumina NovaSeq Control Software (NVCS) 1.8.1 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm39 (UCSC Genome Browser mm39) and GENCODE reference transcriptome M32 (February 2023) with STAR 2.7.9a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.16 package DESeq2 1.38.0, running under R 4.2.2.
Assembly: UCSC mm39 based on GRCm39
Supplementary files format and content: tsv file includes raw counts for each sample

source_name: Pancreas

growth_protocol: Acinar cells were cultures using Waymouth media supplemented with 10% FBS  1% Pencillin/ streptomycin , 0,1mg/ml trypsin inhibitor and 10µg/ml dexamethasone

extract_protocol:
RNA isolation was done using Rneasy Plus Mini kit from Qiagen
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

treatment_protocol: Dkk3 null acinar cells were treated with recombinant form of soluble DKK3 commercially available to rescue the phenotype

value: Pancreas

tag: cell line

value: Primary cells

value: Acinar cells

value: DKK3 knockout

value: recombinant DKK3

tag: Sex

value: Male

tag: age

value: 15 weeks


title: BALB/c iNKT17 4 TCR-Seq

description: Library name: BALB/c iNKT17 4

value: iNKT17 cells


title: BALB/c CD4T 2 TCR-Seq

description: Library name: BALB/c CD4T 2

value: thymus

value: CD4T cells


title: BALB/c CD8T 2 TCR-Seq

description: Library name: BALB/c CD8T 2


title: BALB/c CD4T 3 TCR-Seq

description: Library name: BALB/c CD4T 3


title: BALB/c CD4T 1 TCR-Seq

description: Library name: BALB/c CD4T 1


title: BALB/c iNKT17 1 TCR-Seq

description: Library name: BALB/c iNKT17 1


title: FAPs, control

description: Library name: sample2

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: FAPs were transfection with TGFBR3 overexpressing plasmids or vector as control.


title: VCaP, control, replicate2

city: Chicago

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University

library_source: genomic

data_processing:
Sequencing reads were processed using the  ATAC-Seq workflow available at https://github.com/reskejak/ATAC-seq.
Assembly: hg38
Supplementary files format and content: The bigWig files are coverage tracks.

molecule: genomic DNA

source_name: VCaP

extract_protocol:
DNA was extracted from VCaP cells using Active Motif ATAC-Seq Kit (53150).
Sequencing libraries were constructed using Active Motif ATAC-Seq Kit (53150).

treatment_protocol: For IGF1R-AS1 knockdown, one siRNA were designed targeting IGF1R-AS1 and purchased from Horizon Discovery. VCaP cells in 6 well plate were transfected with 30 pmol siRNAs using Lipofectamine® RNAiMAX (Invitrogen) according to the manufacture instruction, and cells were harvested for analysis 72 h after transfection.

value: VCaP

value: epithelial cell


title: DD2_d3_acinar RNA _16

description:
Library name: DD2_d3_acinar_RNA_16_S137468
Column name in rnaseq_deseq_batch_counts_raw.tsv: DD2_d3_acinar_RNA_16_S137468

value: 13 weeks


title: FAPs, TGFBR3 OE

description: Library name: sample1


title: BALB/c iNKT17 3 TCR-Seq

description: Library name: BALB/c iNKT17 3

value: BALB/c


title: VCaP, control, replicate3


title: BALB/c iNKT2 4 TCR-Seq

description: Library name: BALB/c iNKT2 4

value: iNKT2 cells


title: 2023_CSF

description:
Library name: 2023_CSF
final_processed_tpm_values_csf.txt

value: Cerebrospinal Fluid

value: NP-Long COVID


title: B6 iNKT17 2 TCR-Seq

description: Library name: B6 iNKT17 2


title: BALB/c iNKT17 2 TCR-Seq

description: Library name: BALB/c iNKT17 2


title: VCaP, si025, replicate3

value: IGF1R-AS1 knockdown


title: VCaP, control, replicate1

value: WT


title: BALB/c iNKT2 3 TCR-Seq

description: Library name: BALB/c iNKT2 3


title: WT1_d3_acinar RNA_4

description:
Library name: WT1_d3_acinar_RNA_4_S137464
Column name in rnaseq_deseq_batch_counts_raw.tsv: WT1_d3_acinar_RNA_4_S137464

value: Pancreas

value: Primary cells

value: Acinar cells

value: 10 weeks


title: DD1_rDKK3_d3_acinar RNA_15

description:
Library name: DD1_rDKK3_d3_acinar_RNA_15_S137467
Column name in rnaseq_deseq_batch_counts_raw.tsv: DD1_rDKK3_d3_acinar_RNA_15_S137467

value: DKK3 knockout

value: recombinant DKK3

value: Male

value: 14 weeks


title: BALB/c iNKT2 2 TCR-Seq

description: Library name: BALB/c iNKT2 2

value: thymus


title: DD1_d3_acinar RNA_11

description:
Library name: DD1_d3_acinar_RNA_11_S137465
Column name in rnaseq_deseq_batch_counts_raw.tsv: DD1_d3_acinar_RNA_11_S137465

value: 12 weeks


title: WT2_d3_acinar RNA_6

description:
Library name: WT2_d3_acinar_RNA_6_S137466
Column name in rnaseq_deseq_batch_counts_raw.tsv: WT2_d3_acinar_RNA_6_S137466

value: Female

value: 11 weeks


title: BALB/c iNKT1 3 TCR-Seq

description: Library name: BALB/c iNKT1 3

value: iNKT1 cells

value: BALB/c


title: BALB/c iNKT2 1 TCR-Seq

description: Library name: BALB/c iNKT2 1

value: iNKT2 cells


title: BALB/c iNKT1 4 TCR-Seq

description: Library name: BALB/c iNKT1 4


title: hip osteoarthritis, sample2

city: Los Angel

first: Arijita

last: Sarkar

state: California

address: 1450 Biggy Street

institute: University of Southern California

description: Library name: OA_2

library_source: transcriptomic single cell

data_processing:
Raw fastq files were checked for their quality, trimmed, and reads with an average base quality score per position > 30 was considered for further analysis using Cell Ranger (v7, 10x Genomics). The raw sequencing data were demultiplexed to assign reads to individual cells based on their unique cell barcodes and unique molecular identifiers (UMIs). The reads were then aligned using STAR aligner (v2.7.3) to the reference human genome (GRCh38), and a gene expression matrix was generated, quantifying the number of transcripts detected for each gene in each cell. Quality control measures were implemented using the DropletUtils package (v1.16.0) to assess the quality of the cells. Cells with greater than 10% mitochondrial content were excluded from further analysis. To identify and remove doublets, Doubletfinder (v2.0.3) was employed. Cells predicted to be doublets were filtered out to enhance the quality of the dataset. To refine the gene expression data further, Soupx (v1.6.2) was used to perform noise correction. The filtered gene expression matrix was imported into R using the Seurat package (v5). Thereafter, data were downsampled and normalized, and dimensionality reduction was performed using Principal Component Analysis (PCA), and the first 30 principal components were selected for downstream analysis. Clustering was conducted using the Louvain algorithm with a resolution parameter set to 0.5, enabling the identification of distinct cell populations. Cell types were annotated using the ‘FindAllMarkers’ function to identify genes significantly expressed in each cluster, applying a significance threshold of adjusted p-value < 0.05. Uniform Manifold Approximation and Projection (UMAP) and other visualizations were generated using Seurat and ggplot2 functions, to depict the clustering of cells and highlight the expression of key marker genes.
Assembly: Homo sapiens hg38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Femoral head

extract_protocol:
Each femoral head was washed once with PBS and cut into quarters to facilitate mechanical digestion. Approximately 20-25g (wet weight) of processed tissue was divided into 4-5 tubes (5g per tube) for enzymatic digestion. Tissue fragments were digested in a solution containing 0.2% collagenase type II (Sigma-Aldrich) and 0.2% dispase II (Sigma-Aldrich) in serum-free Dulbecco's Modified Eagle Medium (DMEM) at 37°C for 4 hours with continuous agitation. The digested suspension was then filtered through a 70-μm strainer, and the resulting filtrate was centrifuged at 400 × g for 5 minutes. The cell pellet was resuspended in 20 ml of serum-free DMEM. To remove bone debris and enrich for nucleated cells, the cell suspension was subjected to density gradient centrifugation using a Percoll solution (Sigma-Aldrich). RBC lysis was performed using a commercial buffer (Lonza, Basel, CH). Cells were then stained with anti-RBC antibody according to manufacturer’s protocol (BioLegend, San Diego, CA, USA), washed, and resuspended in PBS with 1% FBS containing DAPI. Fluorescence-activated cell sorting (FACS) analysis was performed to identify and sort live cells using a BD LSR II flow cytometer (BD Biosciences, Franklin Lakes, NJ, USA).
Single-cell samples were prepared using the Chromium Next GEM Single Cell 3/ Reagent Kits v3 and Chip Kits (10x Genomics, Pleasanton, CA, USA), following the manufacturer’s protocol. In brief, FACS-sorted live cells were resuspended in 0.04% BSA-PBS solution. Approximately 700–1000 cells/μL were added to each chip well, aiming for a target cell recovery of 5000–9000 cells. Gel bead-in emulsions (GEMs) were generated using the Chromium controller (10x Genomics). GEMs underwent reverse transcription, the droplets were broken, and single-stranded cDNA was isolated. The cDNA was cleaned using DynaBeads and amplified. After amplification, adapters were ligated to the cDNA, followed by further amplification and cleanup with SPRIselect. The quality of the purified libraries was checked using Agilent Tapestation D1000 (Agilent, Santa Clara, CA, USA) and their concentration was quantified by dsDNA high-sensitivity kit using Qubit fluorometer (Thermo Fisher Scientific, MA, USA). Equimolar concentration of the libraries was pooled and sequenced on Illumina NextSeq platform (Illumina, San Diego, CA, USA).

value: Femoral head


title: BALB/c iNKT1 2 TCR-Seq

description: Library name: BALB/c iNKT1 2


title: VCaP, si025, replicate2

value: VCaP

value: epithelial cell

value: IGF1R-AS1 knockdown


title: BALB/c iNKT1 1 TCR-Seq

description: Library name: BALB/c iNKT1 1


title: Gut_TCR_KO_rep6

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Reads were processed using the publicly available nf-core rnseq pipeline v3.15.1 (https://nf-co.re/rnaseq/3.15.1/) with the STAR /RSEM option against mouse genome assembly GRCm38 and Ensembl release 95 transcript annotations. Other options were left as default.
Gene-level RSEM abundance estimates were imported into R using the Bioconductor package tximport’s tximport function for further analysis using DESeq2
Normalisation factors were calculated per gene using the default DESeq2 function, correcting for library size and feature length.
Variance-stabilised abundance estimates were calculated using the VST function. PCA analysis was performed on the variance stabilised values using all available genes
Assembly: mm10
Supplementary files format and content: RSEM normalised counts, in .genes.results files output from nf-core/rnaseq pipeline run

source_name: Gut IEL (Vγ7+) γδ T cells

growth_protocol: Mouse colony

extract_protocol:
RNA extraction using RNeasy® Plus Micro Kit - QIAGEN
NEBNext_Low_Input_w_NEB_Ultra_II_FS

treatment_protocol: Tamoxifen

value: Gut

tag: strain of_mouse

value: TCR KO


title: steroid-induced osteonecrosis of the femoral head, sample2

description: Library name: ONFH_2


title: Gut_TCR_KO_rep5


title: VCaP, si025, replicate1


title: steroid-induced osteonecrosis of the femoral head, sample1

description: Library name: ONFH_1


title: Gut_TCR_KO_rep4


title: hip osteoarthritis, sample3

description: Library name: OA_3


title: HIV_1_Tat_3

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

description: Library name: H_HIV1_ Tat_3

data_processing:
Reads were aligned to the hg38 human genome using STAR.
Aligned read files were analyzed using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph

source_name: brain

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Poly-A mRNA was extracted from total RNA using Oligo-dT beads in a NEBNext Poly (A) RNA Magnetic Isolation Module (New England Biolabs), after which RNA-seq libraries are prepared using a RNA-Seq library preparation kit for Illumina (New England Biolabs) according to the manufacturer’s protocols.

value: brain

value: primary cell

value: microvascular endothelial cells

value: Tat


title: Gut_TCR_KO_rep3


title: HIV_1_Tat_2

description: Library name: H_HIV1_ Tat_2


title: HDM  – Ear - Mouse 8

type: RNA

city: Cambridge

first: Xin

last: Chen

state: Massachusetts

address: 200 Sidney St

institute: AbbVie

description: gene expression from HDM  – Ear - Mouse 8

hyb_protocol: Prepared target samples were hybridized to the Clariom S Mouse HT 24 sample array.

scan_protocol: Clariom S Mouse HT arrays were scanned using the GeneTitan MC instrument.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) using SST-RMA to get summarized gene expression matrix.

label: biotin

source_name: HDM  – Ear - Mouse 8

label_protocol: 100ng of mouse RNA samples were processed using the Affymetrix GeneChip WT PLUS Reagent kit

growth_protocol: HDM-treated NC/Nga mice were maintained under SPF condition. 8 mm punches were obtained from back skin and ears for gene analysis.

extract_protocol: Total RNA was isolated from the homogenates via the automated QIAcube Workstation, utilizing the Qiagen RNeasy Fibrous Tissue Mini Kit with DNAse I Digest.

treatment_protocol: RNA within ear and dorsal skin was stabilized by immersion of the samples in Invitrogen RNAlater at 4°C for a minimum of 18 hours, before the samples were stored at -80°C. Thawed samples were disrupted and homogenized in Qiagen RLT lysis buffer utilizing the Qiagen TissueRuptor II (Germantown, Maryland).

value: Ear

tag: agent

value: HDM Treated


title: HIV_1_Tat_1

description: Library name: H_HIV1_ Tat_1


title: Ctrl_3

description: Library name: H_Ctrl_3

value: control


title: HDM  – Ear - Mouse 7

description: gene expression from HDM  – Ear - Mouse 7

source_name: HDM  – Ear - Mouse 7


title: Gut_TCR_KO_rep1


title: HDM  – Ear - Mouse 6

description: gene expression from HDM  – Ear - Mouse 6

source_name: HDM  – Ear - Mouse 6


title: Ctrl_2

description: Library name: H_Ctrl_2


title: hip osteoarthritis, sample1

description: Library name: OA_1


title: Gut_TCR_KO_rep2


title: Ctrl_1

description: Library name: H_Ctrl_1


title: patientID=LC5, sampleOrigin=TISSUE

city: Brno

first: Robin

last: Jugas

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

description:
Library name: METSEQ-T90
column name in raw_miRNA_counts.tsv=METSEQ-T90

data_processing:
The pre-alignment quality control (QC) of the sequencing data was done using FastQC. Adaptors present within sequenced reads were trimmed off with cutadapt. Adapter-trimmed small RNA sequencing reads were collapsed exploiting unique molecular identifiers (UMIs) with FASTX-Toolkit Subsequently, reads were quality trimmed using cutadapt and reads shorter than 15 bp were removed from the dataset. The remaining reads were mapped against the database miRBase (version 21) using the miraligner tool.
Assembly: GRCh38 / miRBase v21
Supplementary files format and content: Tab-delimited text file containg raw miRNA counts

source_name: BRAIN TISSUE

extract_protocol:
Fresh-frozen tissue: RNA was isolated using mirVana miRNA Isolation Kit (Thermo Fisher Scientific). Plasma: After thawing plasma samples on ice, 250 µl of the sample were transferred to a clean tube and centrifuged (1000 × g, 5 min, 4˚C). Subsequently, 200 µl of supernatant were used for isolation of small RNA species using the miRNeasy Serum/Plasma Kit (Qiagen). CSF: After thawing CSF on ice, 1 ml of sample was used for isolation and purification of small RNA  using the Urine microRNA Purification Kit (Norgen Biotek). Purified RNA was then frozen at −80˚C until further use.
Small RNA libraries were constructed using QIAseq miRNA Library Kit (Qiagen). The RNA input was 100 ng for tissue and 5 µl for plasma and CSF. Libraries were normalized and pooled in equimolar ratio using online weight to molar quantity converter. Library pools (24 libraries in each pool) were then processed according to the NextSeq System Denature and Dilute Libraries Guide. Denatured and diluted PhiX Control v3 was added at 1% to all pools as an internal standard and single-read sequencing with 75 bp read length was performed using NextSeq 500 Sequencing System and NextSeq 500/550 High Output v2 kit (75 cycles) (Illumina). Approximately 16.7 M sequencing reads per library were expected.

value: BRAIN TISSUE

value: human brain tissue

value: LC

tag: batch


title: Gut_WT_rep3

value: WT


title: HDM  – Ear - Mouse 5

description: gene expression from HDM  – Ear - Mouse 5

source_name: HDM  – Ear - Mouse 5


title: HDM  – Ear - Mouse 4

description: gene expression from HDM  – Ear - Mouse 4

source_name: HDM  – Ear - Mouse 4


title: patientID=BC4, sampleOrigin=TISSUE

description:
Library name: METSEQ-T53
column name in raw_miRNA_counts.tsv=METSEQ-T53

value: BC


title: patientID=RCC3, sampleOrigin=TISSUE

description:
Library name: METSEQ-T89
column name in raw_miRNA_counts.tsv=METSEQ-T89

value: RCC


title: patientID=MEL2, sampleOrigin=TISSUE

description:
Library name: METSEQ-T57
column name in raw_miRNA_counts.tsv=METSEQ-T57

value: MEL


title: patientID=MEL3, sampleOrigin=TISSUE

description:
Library name: METSEQ-T59
column name in raw_miRNA_counts.tsv=METSEQ-T59


title: patientID=BC2, sampleOrigin=TISSUE

description:
Library name: METSEQ-T83
column name in raw_miRNA_counts.tsv=METSEQ-T83


title: patientID=LC4, sampleOrigin=TISSUE

description:
Library name: METSEQ-T60
column name in raw_miRNA_counts.tsv=METSEQ-T60


title: Gut_WT_rep1


title: patientID=BC3, sampleOrigin=TISSUE

description:
Library name: METSEQ-T88
column name in raw_miRNA_counts.tsv=METSEQ-T88


title: Dermis_TCR_KO_rep4

source_name: Dermal (Vγ4+ & Vγ6+) γδ T cells

value: Dermis


title: HDM  – Ear - Mouse 1

description: gene expression from HDM  – Ear - Mouse 1

source_name: HDM  – Ear - Mouse 1


title: Dermis_TCR_KO_rep3


title: patientID=CRC2, sampleOrigin=TISSUE

description:
Library name: METSEQ-T13
column name in raw_miRNA_counts.tsv=METSEQ-T13

value: CRC


title: HDM  – Ear - Mouse 3

description: gene expression from HDM  – Ear - Mouse 3

source_name: HDM  – Ear - Mouse 3


title: Dermis_TCR_KO_rep2

value: TCR KO


title: patientID=LC3, sampleOrigin=TISSUE

description:
Library name: METSEQ-T48
column name in raw_miRNA_counts.tsv=METSEQ-T48


title: HDM  – Ear - Mouse 2

description: gene expression from HDM  – Ear - Mouse 2

source_name: HDM  – Ear - Mouse 2


title: patientID=RCC6, sampleOrigin=TISSUE

description:
Library name: METSEQ-T122
column name in raw_miRNA_counts.tsv=METSEQ-T122

value: runB


title: patientID=BC6, sampleOrigin=TISSUE

description:
Library name: METSEQ-T121
column name in raw_miRNA_counts.tsv=METSEQ-T121


title: Dermis_WT_rep4


title: patientID=MEL6, sampleOrigin=TISSUE

description:
Library name: METSEQ-T119
column name in raw_miRNA_counts.tsv=METSEQ-T119


title: Dermis_TCR_KO_rep1


title: Sham – Ear - Mouse 6

description: gene expression from Sham – Ear - Mouse 6

source_name: Sham – Ear - Mouse 6

value: Sham


title: patientID=MEL5, sampleOrigin=TISSUE

description:
Library name: METSEQ-T118
column name in raw_miRNA_counts.tsv=METSEQ-T118


title: patientID=BC1, sampleOrigin=TISSUE

description:
Library name: METSEQ-T52
column name in raw_miRNA_counts.tsv=METSEQ-T52


title: patientID=CRC6, sampleOrigin=TISSUE

description:
Library name: METSEQ-T117
column name in raw_miRNA_counts.tsv=METSEQ-T117


title: patientID=BC5, sampleOrigin=TISSUE

description:
Library name: METSEQ-T120
column name in raw_miRNA_counts.tsv=METSEQ-T120


title: Sham – Ear - Mouse 5

description: gene expression from Sham – Ear - Mouse 5

source_name: Sham – Ear - Mouse 5


title: Sham – Ear - Mouse 7

description: gene expression from Sham – Ear - Mouse 7

source_name: Sham – Ear - Mouse 7


title: Gut_WT_rep2

value: Gut


title: Sham – Ear - Mouse 8

description: gene expression from Sham – Ear - Mouse 8

source_name: Sham – Ear - Mouse 8


title: patientID=CRC4, sampleOrigin=TISSUE

description:
Library name: METSEQ-T115
column name in raw_miRNA_counts.tsv=METSEQ-T115


title: patientID=CRC3, sampleOrigin=TISSUE

description:
Library name: METSEQ-T114
column name in raw_miRNA_counts.tsv=METSEQ-T114


title: Sham – Ear - Mouse 4

description: gene expression from Sham – Ear - Mouse 4

source_name: Sham – Ear - Mouse 4


title: patientID=LC6, sampleOrigin=TISSUE

description:
Library name: METSEQ-T111
column name in raw_miRNA_counts.tsv=METSEQ-T111


title: Sham – Ear - Mouse 2

description: gene expression from Sham – Ear - Mouse 2

source_name: Sham – Ear - Mouse 2


title: Epidermis_TCR_KO_rep4

source_name: DETC (Vγ5+) γδ T cells

value: Epidermis


title: patientID=MEL4, sampleOrigin=TISSUE

description:
Library name: METSEQ-T110
column name in raw_miRNA_counts.tsv=METSEQ-T110


title: patientID=RCC5, sampleOrigin=TISSUE

description:
Library name: METSEQ-T11
column name in raw_miRNA_counts.tsv=METSEQ-T11


title: Dermis_WT_rep2


title: patientID=CRC1, sampleOrigin=TISSUE

description:
Library name: METSEQ-T109
column name in raw_miRNA_counts.tsv=METSEQ-T109


title: patientID=CRC5, sampleOrigin=TISSUE

description:
Library name: METSEQ-T116
column name in raw_miRNA_counts.tsv=METSEQ-T116


title: patientID=RCC4, sampleOrigin=TISSUE

description:
Library name: METSEQ-T09
column name in raw_miRNA_counts.tsv=METSEQ-T09


title: Epidermis_TCR_KO_rep3


title: Epidermis_TCR_KO_rep1


title: patientID=MEL1, sampleOrigin=TISSUE

description:
Library name: METSEQ-T08
column name in raw_miRNA_counts.tsv=METSEQ-T08


title: Epidermis_TCR_KO_rep2


title: patientID=LC2, sampleOrigin=TISSUE

description:
Library name: METSEQ-T06
column name in raw_miRNA_counts.tsv=METSEQ-T06


title: patientID=RCC2, sampleOrigin=TISSUE

description:
Library name: METSEQ-T03
column name in raw_miRNA_counts.tsv=METSEQ-T03


title: Sham – Ear - Mouse 1

description: gene expression from Sham – Ear - Mouse 1

source_name: Sham – Ear - Mouse 1

value: Ear


title: patientID=LC1, sampleOrigin=TISSUE

description:
Library name: METSEQ-T05
column name in raw_miRNA_counts.tsv=METSEQ-T05


title: patientID=RCC6, sampleOrigin=PLASMA

description:
Library name: METSEQ-P47
column name in raw_miRNA_counts.tsv=METSEQ-P47

source_name: PLASMA

value: PLASMA

value: human blood plasma


title: patientID=BC5, sampleOrigin=PLASMA

description:
Library name: METSEQ-P45
column name in raw_miRNA_counts.tsv=METSEQ-P45


title: Epidermis_WT_rep4


title: patientID=BC6, sampleOrigin=PLASMA

description:
Library name: METSEQ-P46
column name in raw_miRNA_counts.tsv=METSEQ-P46


title: HDM – Back skin - Mouse 7

description: gene expression from HDM – Back skin - Mouse 7

source_name: HDM – Back skin - Mouse 7

value: Back skin_Dorsal

value: HDM Treated


title: Epidermis_WT_rep2


title: patientID=LC6, sampleOrigin=PLASMA

description:
Library name: METSEQ-P44
column name in raw_miRNA_counts.tsv=METSEQ-P44

value: LC


title: patientID=MEL5, sampleOrigin=PLASMA

description:
Library name: METSEQ-P42
column name in raw_miRNA_counts.tsv=METSEQ-P42


title: patientID=MEL6, sampleOrigin=PLASMA

description:
Library name: METSEQ-P43
column name in raw_miRNA_counts.tsv=METSEQ-P43


title: Epidermis_WT_rep1

value: WT


title: HDM – Back skin - Mouse 5

description: gene expression from HDM – Back skin - Mouse 5

source_name: HDM – Back skin - Mouse 5


title: HET_Gut_REP5

library_source: other

data_processing:
Reads were processed using the publicly available nf-core atacseq pipeline v1.2.1  (https://nf-co.re/atacseq/2.1.2) against the mouse genome assembly GRCm38
using Nextflow v22.04.0 and Singularity v3.6.4, with the following settings:
--deseq2_vst, --min_reps_consensus ,--macs_gsize 2600000000
A peak was only considered to be genuine if present in at least 3 biological replicates for each treatment group.
A consensus peak set was then constructed by combining the peak calls from the individual genotype x organ groups into a set of non-overlapping intervals.
Assembly: Mm10 / GRCm38 (release 95)
Supplementary files format and content: bigWig files, output from nf-core/atacseq pipeline

molecule: other

source_name: Gut IEL (Vγ7+) γδ T cells

extract_protocol:
Tn5 Tagmentation was performed using ATAC-Seq Kit from Active Motif
ATAC-Seq Kit from Active Motif


title: HDM – Back skin - Mouse 4

description: gene expression from HDM – Back skin - Mouse 4

source_name: HDM – Back skin - Mouse 4


title: HET_Gut_REP4


title: HDM – Back skin - Mouse 8

description: gene expression from HDM – Back skin - Mouse 8

source_name: HDM – Back skin - Mouse 8


title: patientID=CRC5, sampleOrigin=PLASMA

description:
Library name: METSEQ-P39
column name in raw_miRNA_counts.tsv=METSEQ-P39


title: patientID=CRC4, sampleOrigin=PLASMA

description:
Library name: METSEQ-P38
column name in raw_miRNA_counts.tsv=METSEQ-P38


title: patientID=CRC3, sampleOrigin=PLASMA

description:
Library name: METSEQ-P37
column name in raw_miRNA_counts.tsv=METSEQ-P37


title: HDM – Back skin - Mouse 1

description: gene expression from HDM – Back skin - Mouse 1

source_name: HDM – Back skin - Mouse 1


title: patientID=MEL4, sampleOrigin=PLASMA

description:
Library name: METSEQ-P41
column name in raw_miRNA_counts.tsv=METSEQ-P41


title: HET_Gut_REP3


title: HDM – Back skin - Mouse 2

description: gene expression from HDM – Back skin - Mouse 2

source_name: HDM – Back skin - Mouse 2


title: patientID=LC4, sampleOrigin=PLASMA

description:
Library name: METSEQ-P35
column name in raw_miRNA_counts.tsv=METSEQ-P35


title: patientID=CRC6, sampleOrigin=PLASMA

description:
Library name: METSEQ-P40
column name in raw_miRNA_counts.tsv=METSEQ-P40


title: HDM – Back skin - Mouse 6

description: gene expression from HDM – Back skin - Mouse 6

source_name: HDM – Back skin - Mouse 6


title: patientID=MEL2, sampleOrigin=PLASMA

description:
Library name: METSEQ-P33
column name in raw_miRNA_counts.tsv=METSEQ-P33


title: HET_Gut_REP2_a


title: HET_Gut_REP2_b


title: HDM – Back skin - Mouse 3

description: gene expression from HDM – Back skin - Mouse 3

source_name: HDM – Back skin - Mouse 3


title: patientID=LC5, sampleOrigin=PLASMA

description:
Library name: METSEQ-P32
column name in raw_miRNA_counts.tsv=METSEQ-P32


title: Sham – Back skin - Mouse 6

description: gene expression from Sham – Back skin - Mouse 6

source_name: Sham – Back skin - Mouse 6


title: patientID=MEL3, sampleOrigin=PLASMA

description:
Library name: METSEQ-P34
column name in raw_miRNA_counts.tsv=METSEQ-P34


title: patientID=BC3, sampleOrigin=PLASMA

description:
Library name: METSEQ-P30
column name in raw_miRNA_counts.tsv=METSEQ-P30

value: BC


title: patientID=RCC3, sampleOrigin=PLASMA

description:
Library name: METSEQ-P31
column name in raw_miRNA_counts.tsv=METSEQ-P31

value: RCC


title: Dermis_WT_rep1

source_name: Dermal (Vγ4+ & Vγ6+) γδ T cells


title: WT_Gut_REP2_b


title: Sham – Back skin - Mouse 7

description: gene expression from Sham – Back skin - Mouse 7

source_name: Sham – Back skin - Mouse 7


title: patientID=LC3, sampleOrigin=PLASMA

description:
Library name: METSEQ-P29
column name in raw_miRNA_counts.tsv=METSEQ-P29


title: WT_Gut_REP2_a


title: Sham – Back skin - Mouse 5

description: gene expression from Sham – Back skin - Mouse 5

source_name: Sham – Back skin - Mouse 5


title: Sham – Back skin - Mouse 8

description: gene expression from Sham – Back skin - Mouse 8

source_name: Sham – Back skin - Mouse 8


title: HET_Gut_REP1


title: patientID=CRC1, sampleOrigin=PLASMA

description:
Library name: METSEQ-P15
column name in raw_miRNA_counts.tsv=METSEQ-P15


title: patientID=BC1, sampleOrigin=PLASMA

description:
Library name: METSEQ-P25
column name in raw_miRNA_counts.tsv=METSEQ-P25


title: WT_Gut_REP1_b


title: patientID=BC2, sampleOrigin=PLASMA

description:
Library name: METSEQ-P17
column name in raw_miRNA_counts.tsv=METSEQ-P17


title: patientID=RCC5, sampleOrigin=PLASMA

description:
Library name: METSEQ-P11
column name in raw_miRNA_counts.tsv=METSEQ-P11


title: Sham – Back skin - Mouse 4

description: gene expression from Sham – Back skin - Mouse 4

source_name: Sham – Back skin - Mouse 4


title: WT_Gut_REP1_a


title: DU145, GC7 3

city: Nice

first: Michel

last: KAHI

address: 151 Route Saint Antoine

country: France

institute: INSERM U1065

description:
Library name: Sample 6
Column name in raw_count: GC7 3

data_processing:
RNA-seq Preprocessing: Raw sequencing reads were aligned on the human genome (GRCh38) using STAR (v2.7.8a), with the annotation of known genes from gencode v37. Gene expression levels were then quantified using Salmon (1.4.0) and the annotation of protein coding genes from gencode v37.
Assembly: the human genome (GRCh38) using STAR (v2.7.8a)
Supplementary files format and content: excel files containing processed data

source_name: Prostate

growth_protocol: DU145 prostate cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, in a humidified incubator at 37°C with 5% CO₂.

extract_protocol:
DU145 Cells were seeded at 106 cells/10cm dish, treated with 40µM CG7 48h later (D0) during 24h. At the end of this treatment, cells were treated 10min with emetin (Sigma-Aldrich) 25µg/ml, washed twice with PBS, and harvested by trypsination. Cytoplasmic lysates were prepared by incubation of cells 10min in hypotonic buffer (10mM Tris-HCl pH 7.4, 0.5mM MgCl2, 10mM KCl, 1X CompleteTM EDTA free protease inhibitor (Roche) and 10U/mL RNAseOutTM (Invitrogen). Cells are disrupted by shaking in presence of ceramic beads (10sec at 4500rpm in a Precellys Evolution homogenizer). Nuclei were pelleted by centrifugation at 750 g for 5min at 4°C, and mitochondria were pelleted by centrifugation at 12,000 g for 10min at 4°C. The protein content of the cytosolic extract was measured by Bradford assay and samples containing 2mg protein were loaded on top of 15–50% sucrose gradients poured using the Gradient Master (Serlabo Technologies). After ultracentrifugation at 250 000g during 105min at 4°C on a SW41 Beckman rotor, fractions of 700µl each were collected from each gradient while 254nm absorbance profiles were generated using an ISCO UA-6 detector.
the human genome (GRCh38) using STAR (v2.7.8a)

treatment_protocol: Cells were treated with GC7 (N¹-guanyl-1,7-diaminheptane) at the indicated concentration for 24 h, Control samples (Ctl) were treated with vehicle only.

value: Prostate

value: metastatic prostate carcinoma


title: Sham – Back skin - Mouse 3

description: gene expression from Sham – Back skin - Mouse 3

source_name: Sham – Back skin - Mouse 3


title: Sham – Back skin - Mouse 1

description: gene expression from Sham – Back skin - Mouse 1

source_name: Sham – Back skin - Mouse 1


title: patientID=LC2, sampleOrigin=PLASMA

description:
Library name: METSEQ-P06
column name in raw_miRNA_counts.tsv=METSEQ-P06

source_name: PLASMA


title: patientID=BC4, sampleOrigin=PLASMA

description:
Library name: METSEQ-P26
column name in raw_miRNA_counts.tsv=METSEQ-P26


title: HET_Skin_REP4

source_name: DETC (Vγ5+) γδ T cells


title: Sham – Back skin - Mouse 2

description: gene expression from Sham – Back skin - Mouse 2

source_name: Sham – Back skin - Mouse 2


title: patientID=CRC2, sampleOrigin=PLASMA

description:
Library name: METSEQ-P13
column name in raw_miRNA_counts.tsv=METSEQ-P13

value: CRC


title: patientID=RCC4, sampleOrigin=PLASMA

description:
Library name: METSEQ-P09
column name in raw_miRNA_counts.tsv=METSEQ-P09


title: patientID=MEL1, sampleOrigin=PLASMA

description:
Library name: METSEQ-P08
column name in raw_miRNA_counts.tsv=METSEQ-P08

value: MEL


title: HET_Skin_REP3

value: TCR KO


title: patientID=RCC2, sampleOrigin=PLASMA

description:
Library name: METSEQ-P03
column name in raw_miRNA_counts.tsv=METSEQ-P03


title: DU145, GC7 2

description:
Library name: Sample 5
Column name in raw_count: GC7 2


title: patientID=LC1, sampleOrigin=PLASMA

description:
Library name: METSEQ-P05
column name in raw_miRNA_counts.tsv=METSEQ-P05


title: patientID=RCC3, sampleOrigin=CSF

description:
Library name: METSEQ-C27
column name in raw_miRNA_counts.tsv=METSEQ-C27

source_name: CSF

value: CSF

value: human cerebrospinal fluid


title: HET_Skin_REP2

value: Epidermis


title: patientID=RCC1, sampleOrigin=PLASMA

description:
Library name: METSEQ-P01
column name in raw_miRNA_counts.tsv=METSEQ-P01


title: patientID=RCC1, sampleOrigin=CSF

description:
Library name: METSEQ-C25
column name in raw_miRNA_counts.tsv=METSEQ-C25


title: DU145, GC7 1

description:
Library name: Sample 4
Column name in raw_count: GC7 1


title: patientID=BC6, sampleOrigin=CSF

description:
Library name: METSEQ-C24
column name in raw_miRNA_counts.tsv=METSEQ-C24


title: DU145, Ctl 1

description:
Library name: Sample 1
Column name in raw_count: Ctl 1

value: Ctl


title: HET_Skin_REP1


title: patientID=BC5, sampleOrigin=CSF

description:
Library name: METSEQ-C23
column name in raw_miRNA_counts.tsv=METSEQ-C23


title: WT_Gut_REP3

source_name: Gut IEL (Vγ7+) γδ T cells

value: Gut


title: patientID=RCC2, sampleOrigin=CSF

description:
Library name: METSEQ-C26
column name in raw_miRNA_counts.tsv=METSEQ-C26


title: WT_Skin_REP3


title: WT_Skin_REP2


title: patientID=BC4, sampleOrigin=CSF

description:
Library name: METSEQ-C22
column name in raw_miRNA_counts.tsv=METSEQ-C22


title: patientID=BC3, sampleOrigin=CSF

description:
Library name: METSEQ-C21
column name in raw_miRNA_counts.tsv=METSEQ-C21


title: patientID=LC3, sampleOrigin=CSF

description:
Library name: METSEQ-C15
column name in raw_miRNA_counts.tsv=METSEQ-C15


title: WT_Skin_REP1


title: DAY5_2_Input

city: hangzhou

first: huan

last: chen

state: Zhejiang

address: Hangzhou, Zhejiang Province, China

institute: Zhejiang Chinese Medical University

data_processing:
*library strategy: MeRIP-Seq
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost 3length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited txst files include count values for each Sample

source_name: BMDM

growth_protocol: BMDMs were maintained in DMEM supplementred with 10%fetal bovine serum (FBS) under conditions of 37℃ in an atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construstion of sequencing livraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufactruer's protocols

treatment_protocol: GMCSF 20ng/ml

value: BMDM

value: GMCSF


title: DU145, Ctl 3

description:
Library name: Sample 3
Column name in raw_count: Ctl 3


title: DAY5_1_IP


title: patientID=BC2, sampleOrigin=CSF

description:
Library name: METSEQ-C20
column name in raw_miRNA_counts.tsv=METSEQ-C20


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Far-Red light - bio rep #2

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Far-Red_light_timepoint_12_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)

data_processing:
.Mapping and counting of transcripts were performed using the nf-core RNA-seq pipeline v3.14.0 (Di Tommaso et al., 2017; Harshil et al., 2024) on the VBC CLIP Batch Environment (CBE) cluster. Raw reads were mapped to the M. polymorpha Tak-1 reference genome assembly MpTak1_v5.1 and its corresponding gene annotation version MpTak1_v5.1_r1 (marchantia.info) using STAR (Dobin., et al., 2013). Reads were normalized by the sequencing depth of each library. After confirming low variability among biological replicates, the average expression value of each gene in each treatment was computed and used for downstream analyses
Assembly: Marchantia polymorpha Takaragaike-1 (MpTak1_v5.1)
Supplementary files format and content: Combined_marchantia_light_transcroptomes_matrix_averaged3replicates.csv; Comma-separated File; A matrix containing gene expression counts normalized by sampling depth (reads per 1 million reads); Each column shows the average computed out of three replicates for each treatment - for particular wavelength (Dark / White / Blue/ Red / Far-Red) for particular time point (0 / 30m / 60m / 180m / 720m-12h / 1440m-24h)
Supplementary files format and content: Combined_marchantia_light_transcroptomes_matrix_3replicates.csv; Comma-separated File; A matrix containing gene expression counts normalized by sampling depth (reads per 1 million reads); Each column indicating one of three replicates for each wavelength (Dark / White / Blue/ Red / Far-Red) for particular time point (0 / 30m / 60m / 180m / 720m-12h / 1440m-24h)

organism: Marchantia polymorpha

source_name: Marchantia polymorpha Thallus

growth_protocol: Wild type Tak-1 gemmae were transferred onto medium plates (½ Gamborg, MES, 1% sucrose, and 1% agar), each plate containing three biological replicates. Gemmae were cultured under continuous white light at 23°C for eight days, followed by a 24-hour dark incubation.

extract_protocol:
For each condition, three biological replicates - each containing three individual Tak-1 plants - were collected in 2 mL Eppendorf tubes containing a stainless-steel bead (5 mm) and immediately frozen in liquid nitrogen at the defined timepoints of 0 min, 30 min, 60 min, 180 min, 12 hours, and 24 hours in dark, white light, blue light, red, far-red light, respectively. All samples were stored at -70°C until the full set was collected. Tissue from the samples was disrupted using a mixer mill (RETSCH MM 400) for 4 minutes at 30 Hz, with nitrogen-based cooling breaks during the process. Total RNA was extracted using the High-Performance RNA Bead Isolation kit from the Molecular Biology Service facility at the Vienna BioCenter. The kit employs a guanidine thiocyanate-based lysis method adapted from (Boom et al., 1990), and utilizes carboxylate-modified Sera-Mag Speed beads, with processing done on the KingFisher instrument (Thermo).
mRNA library preparation, including poly(A) capture and NovaSeq S4 PE150 XP RNA sequencing, was performed by the Next Generation Sequencing (NGS) VBC Core Facility. The 78 cDNA libraries, corresponding to 26 treatments with three biological replicates each.

treatment_protocol: After this dark period, the plates were either kept in darkness (control) or exposed to different light conditions: broad white light (WL), monochromatic blue light (BL, λmax = 430 nm), monochromatic red light (RL, λmax = 660 nm), or monochromatic far-red light (FRL, λmax = 730 nm). The light intensity in the monochromatic light treatments was increased by a factor of four, relative to the intensity of the respective wavelength in the standard white light condition.

value: Marchantia polymorpha Thallus

value: Takaragaike-1 (Tak-1, male)

value: Far_Red-light 720 minutes / 12 hours


title: DU145, Ctl 2

description:
Library name: Sample 2
Column name in raw_count: Ctl 2


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Far-Red light - bio rep #3

description:
Library name: Far-Red_light_timepoint_24_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)

value: Far_Red-light 1440 minutes / 24 hours


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Far-Red light - bio rep #3

description:
Library name: Far-Red_light_timepoint_12_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)


title: DAY5_1_Input

value: WT


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Far-Red light - bio rep #2

description:
Library name: Far-Red_light_timepoint_24_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)


title: patientID=LC2, sampleOrigin=CSF

description:
Library name: METSEQ-C14
column name in raw_miRNA_counts.tsv=METSEQ-C14

value: LC


title: patientID=LC4, sampleOrigin=CSF

description:
Library name: METSEQ-C16
column name in raw_miRNA_counts.tsv=METSEQ-C16


title: patientID=BC1, sampleOrigin=CSF

description:
Library name: METSEQ-C19
column name in raw_miRNA_counts.tsv=METSEQ-C19

value: BC


title: patientID=LC6, sampleOrigin=CSF

description:
Library name: METSEQ-C18
column name in raw_miRNA_counts.tsv=METSEQ-C18


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Far-Red light - bio rep #1

description:
Library name: Far-Red_light_timepoint_12_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Far-Red light - bio rep #1

description:
Library name: Far-Red_light_timepoint_24_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)


title: DAY5_2_IP


title: patientID=LC1, sampleOrigin=CSF

description:
Library name: METSEQ-C13
column name in raw_miRNA_counts.tsv=METSEQ-C13


title: patientID=MEL5, sampleOrigin=CSF

description:
Library name: METSEQ-C11
column name in raw_miRNA_counts.tsv=METSEQ-C11


title: patientID=MEL2, sampleOrigin=CSF

description:
Library name: METSEQ-C08
column name in raw_miRNA_counts.tsv=METSEQ-C08


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Far-Red light - bio rep #2

description:
Library name: Far-Red_light_timepoint_180_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)

value: Far_Red-light 180 minutes


title: patientID=CRC5, sampleOrigin=CSF

description:
Library name: METSEQ-C05
column name in raw_miRNA_counts.tsv=METSEQ-C05

value: CRC


title: DAY3_2_IP


title: DAY3_1_IP


title: patientID=MEL6, sampleOrigin=CSF

description:
Library name: METSEQ-C12
column name in raw_miRNA_counts.tsv=METSEQ-C12

value: MEL


title: patientID=MEL3, sampleOrigin=CSF

description:
Library name: METSEQ-C09
column name in raw_miRNA_counts.tsv=METSEQ-C09

value: CSF


title: patientID=MEL4, sampleOrigin=CSF

description:
Library name: METSEQ-C10
column name in raw_miRNA_counts.tsv=METSEQ-C10

value: human cerebrospinal fluid


title: patientID=CRC6, sampleOrigin=CSF

description:
Library name: METSEQ-C06
column name in raw_miRNA_counts.tsv=METSEQ-C06


title: patientID=MEL1, sampleOrigin=CSF

description:
Library name: METSEQ-C07
column name in raw_miRNA_counts.tsv=METSEQ-C07


title: patientID=CRC4, sampleOrigin=CSF

description:
Library name: METSEQ-C04
column name in raw_miRNA_counts.tsv=METSEQ-C04


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Far-Red light - bio rep #3

description:
Library name: Far-Red_light_timepoint_180_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)


title: DAY3_2_Input


title: patientID=CRC2, sampleOrigin=CSF

description:
Library name: METSEQ-C02
column name in raw_miRNA_counts.tsv=METSEQ-C02


title: patientID=LC5, sampleOrigin=CSF

description:
Library name: METSEQ-C17
column name in raw_miRNA_counts.tsv=METSEQ-C17


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Far-Red light - bio rep #2

description:
Library name: Far-Red_light_timepoint_60_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)

value: Far_Red-light 60 minutes


title: 18)  ARPE-19 NRF2-edited NACET-treated replicate 3 (C1_NACET_rep3)

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: Library name: C1_NACET_rep3

data_processing:
Fastq files quality check was performed using FastQC
The fastq files were mapped to the hg19 genome using TopHat v2.1.0 with the following parameters –bowtie1 –no-coverage-search -a 5
The number of reads covered by each gene was calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Assembly: hg19
Supplementary files format and content: HTSeq-Count txt files

source_name: eye-etinal pigment epithelium

growth_protocol: Cells were cultured in DMEM/F12 1% FCS

extract_protocol:
total RNA was purified using EuroGOLD TriFast™ (Euroclone, Milan, Italy). RNA quantity and quality were evaluated by Nanodrop 8000 (Thermo Fisher Scientific, Waltham, MA, USA) and Fragment Analyzer (Advanced Analytical Technologies, Heidelberg, Germany) using the DNF-471 Standard Sensitivity RNA Analysis Kit (15nt) (Agilent Technologies, Santa Clara, CA, USA).
RNA samples were  processed for mRNA-seq library preparation using the TruSeq RNA Sample preparation v2 kit according to the manufacturer’s instructions (Illumina, San Diego, CA, USA).

treatment_protocol: Confluent cells were cultured in DMEM/F12 1% FCS for 22 hours and then treated with 1 mM NACET or 0.2 mM H2O2 for 2 hours.

value: eye-etinal pigment epithelium

value: human retinal pigment epithelial (RPE) cell line

value: 1 mM NACET

value: Advanced ChemBloks, #O32426, Lot#:AC99952A


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Far-Red light - bio rep #1

description:
Library name: Far-Red_light_timepoint_180_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)

value: Marchantia polymorpha Thallus


title: 16)  ARPE-19 NRF2-edited NACET-treated replicate 1 (C1_NACET_rep1)

description: Library name: C1_NACET_rep1


title: patientID=CRC3, sampleOrigin=CSF

description:
Library name: METSEQ-C03
column name in raw_miRNA_counts.tsv=METSEQ-C03


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Far-Red light - bio rep #3

description:
Library name: Far-Red_light_timepoint_60_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)

value: Takaragaike-1 (Tak-1, male)


title: DAY0_2_Input

value: BMDM


title: patientID=CRC1, sampleOrigin=CSF

description:
Library name: METSEQ-C01
column name in raw_miRNA_counts.tsv=METSEQ-C01


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Far-Red light - bio rep #1

description:
Library name: Far-Red_light_timepoint_60_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Far-Red light - bio rep #3

description:
Library name: Far-Red_light_timepoint_30_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)

value: Far_Red-light 30 minutes


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Far-Red light - bio rep #2

description:
Library name: Far-Red_light_timepoint_30_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)


title: 14)  ARPE-19 NRF2-edited H2O2-treated replicate 2 (C1_H2O2_rep2)

description: Library name: C1_H2O2_rep2


title: 13)  ARPE-19 NRF2-edited H2O2-treated replicate 1 (C1_H2O2_rep1)

description: Library name: C1_H2O2_rep1


title: DAY0_1_Input

value: WT


title: 17)  ARPE-19 NRF2-edited NACET-treated replicate 2 (C1_NACET_rep2)

description: Library name: C1_NACET_rep2


title: 15)  ARPE-19 NRF2-edited H2O2-treated replicate 3 (C1_H2O2_rep3)

description: Library name: C1_H2O2_rep3


title: DAY0_1_IP


title: 11)  ARPE-19 NRF2-edited untreated replicate 2 (C1_Ctrl _rep2)

description: Library name: C1_Ctrl_rep2

value: Milli-Q H2O


title: DAY0_2_IP


title: DAY3_1_Input

value: GMCSF


title: 7)      ARPE-19 control NACET-treated replicate 1 (ARPE_ NACET_rep1)

description: Library name: ARPE_NACET_rep1


title: 8)      ARPE-19 control NACET-treated replicate 2 (ARPE_ NACET_rep2)

description: Library name: ARPE_NACET_rep2


title: Heart, 8wks, AAV9.Cpt1a TAC4

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

data_processing:
Raw fastq files were aligned to mouse reference genome GRCm38 with hisat2 v2.1.0
Gene wise counts were generated with featureCounts from the subread package v1.5.1 for genes annotated by ensembl Mus_musculus.GRCm38.102, counting the primary alignment in the case of multimapped reads
Assembly: GRCm38
Supplementary files format and content: tsv file

source_name: Heart

growth_protocol: Animals underwent TAC or sham surgery and hearts were collected 8 wks after surgery

extract_protocol:
Hearts were collected and flash frozen in liquid nitrogren
The RNA Integrity Number (RIN) for DNase-treated total RNA was assessed using Agilent BioAnalyzer RNA Nano Kit (#5067-1511; Agilent Technologies, Inc., Santa Clara, CA) and the RNA amount was assayed with the Invitrogen Qubit RNA HS Assay Kit (#Q32852; Therma Fisher Scientific, Waltham, MA). Samples with RIN > 7 were used in mRNA-seq library generation using the NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit (#E7760L; Ipswich, MA) plus the NEBNext Poly (A) mRNA Magnetic Isolation Module (#E7490). Briefly, 200 ng total RNA was used as input. RNA fragmentation was set at 10 minutes for 12 PCR cycles and were used in final library generation. Library quantification and characterization was assessed with Agilent BioAnalyzer HS DNA Kit (#5067-4626) and the Invitrogen Qubit DNA HS Assay Kit (#Q32854). Libraries were pooled together with other index – compatible RNA-seq libraries for sequencing on Illumina NovaSeq 6000 (San Diego, CA) paired-end 100bp flow cell to a minimum depth of 20 million clusters per sample.

treatment_protocol: Trasnverse aoritc constriction was performed by placing a 0.016 inch or 0.018 inch microclip across the transverse aorta

value: Heart

value: AAV9.Cpt1a and transverse aortic constriction


title: 12)  ARPE-19 NRF2-edited untreated replicate 3 (C1_Ctrl_rep3)

description: Library name: C1_Ctrl_rep3


title: 5)      ARPE-19 control H2O2-treated replicate 2 (ARPE_ H2O2_rep2)

description: Library name: ARPE_H2O2_rep2


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Red light - bio rep #2

description:
Library name: Red_light_timepoint_24_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)

value: Red-light 1440 minutes / 24 hours


title: 10)  ARPE-19 NRF2-edited untreated replicate 1 (C1_Ctrl_rep1)

description: Library name: C1_Ctrl_rep1


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Red light - bio rep #3

description:
Library name: Red_light_timepoint_24_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Red light - bio rep #1

description:
Library name: Red_light_timepoint_24_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)


title: 9)      ARPE-19 control NACET-treated replicate 3 (ARPE_ NACET_rep3)

description: Library name: ARPE_NACET_rep3


title: Heart, 8wks, AAV9.Cpt1a TAC1


title: Heart, 8wks, AAV9.Cpt1a TAC3


title: 6)      ARPE-19 control H2O2-treated replicate 3 (ARPE_ H2O2_rep3)

description: Library name: ARPE_H2O2_rep3


title: Heart, 8wks, AAV9.Cpt1a TAC2


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Red light - bio rep #3

description:
Library name: Red_light_timepoint_12_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)

value: Red-light 720 minutes / 12 hours


title: 4)      ARPE-19 control H2O2-treated replicate 1 (ARPE_ H2O2_rep1)

description: Library name: ARPE_H2O2_rep1


title: 2)      ARPE-19 control untreated replicate 2 (ARPE_Ctrl_rep2)

description: Library name: ARPE_Ctrl_rep2


title: 3)      ARPE-19 control untreated replicate 3 (ARPE_Ctrl_rep3)

description: Library name: ARPE_Ctrl_rep3


title: Heart, 8wks, AAV9.Cpt1a Sham1

value: AAV9.Cpt1a and sham surgery


title: ARPE-19 in DMEM/F12 with 10% FBS treated with vehicle (H2O)

description: Library name: 10Percent_FBS_CTR

treatment_protocol: confluent retinal pigment epithelial cell line (ARPE-19) treated with N-acetilcysteine (NAC) or N-acetilcysteine ethyl ester (NACET) in 1% or 10% FCS. Confluent ARPE-19 cells were cultured for 44 hours in DMEM/F12 with 1% or 10% FBS and treated chronically with NAC, NACET or H2O (as a negative control). 0.4 mM NAC or NACET were added at 0, 24, and 40 hours after medium change with DMEM/F12 with 1% or 10% FBS.

value: normal eyes of a 19-year-old male who died from head trauma


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Red light - bio rep #3

description:
Library name: Red_light_timepoint_180_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)

value: Red-light 180 minutes


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Red light - bio rep #2

description:
Library name: Red_light_timepoint_12_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)


title: Heart, 8wks, AAV9.Cpt1a Sham2


title: Heart, 8wks, AAV9.Cpt1a Sham3


title: Heart, 8wks, AAV9.Cpt1a Sham4


title: ARPE-19 in DMEM/F12 with 1% FBS treated with vehicle (H2O)

description: Library name: 1Percent_FBS_CTR

growth_protocol: Confluent ARPE-19 cells were cultured for 44 hours in DMEM/F12 with 1% or 10% FBS

value: eye-etinal pigment epithelium

value: human retinal pigment epithelial (RPE) cell line

value: ARPE-19 in DMEM/F12 with 10% FBS treated with vehicle (H2O)


title: ARPE-19 in DMEM/F12 with 1% FBS treated with NACET

description: Library name: 1Percent_FBS_NACET

value: ARPE-19 in DMEM/F12 with 10% FBS treated with N-acetylcysteine ethyl ester (NACET)

value: Advanced ChemBloks, #O32426, Lot#:AC99952A


title: Heart, 8wks, PBS TAC2

value: PBS and transverse aortic constriction


title: ARPE-19 in DMEM/F12 with 1% FBS treated with NAC

description: Library name: 1Percent_FBS_NAC

value: ARPE-19 in DMEM/F12 with 10% FBS treated with N-acetylcysteine (NAC).


title: ARPE-19 in DMEM/F12 with 10% FBS treated with NAC

description: Library name: 10Percent_FBS_NAC


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Red light - bio rep #1

description:
Library name: Red_light_timepoint_12_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)

value: Marchantia polymorpha Thallus

value: Takaragaike-1 (Tak-1, male)


title: patientID=RCC1, sampleOrigin=TISSUE

description:
Library name: METSEQ-T01
column name in raw_miRNA_counts.tsv=METSEQ-T01

source_name: BRAIN TISSUE

value: BRAIN TISSUE

value: human brain tissue

value: RCC


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Red light - bio rep #2

description:
Library name: Red_light_timepoint_180_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)


title: Heart, 8wks, PBS TAC3

value: Heart


title: COLO320 DM, H3K56ac (ChIP-Seq)

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

description: Library name: COLO320 DM, H3K56ac (ChIP-Seq)

data_processing:
ChIP-seq Data Processing and Alignment: Raw sequencing read quality was assessed using FastQC (v0.11.9). Adapter sequences and low-quality bases (Phred score < 20) were trimmed using Cutadapt (v3.4). Filtered reads were aligned to the human reference genome (GRCh38/hg38) using BWA-MEM (v0.7.17) with default parameters. SAMtools (v1.13) was used for sorting and indexing aligned reads in BAM format. PCR duplicates were identified and removed using Picard MarkDuplicates (Broad Institute).
Peak Calling and Signal Normalization: Peak calling was performed for BRD4 and H3K56ac datasets against their respective IgG control inputs using MACS2 (v2.2.7.1) with parameters -g hs -q 0.05. To generate signal tracks for visualization, BAM files were converted to bigWig format using the bamCoverage function in deepTools (v3.5.1), normalizing for sequencing depth using CPM. Input-normalized log2 fold change signal tracks were subsequently generated using the bigwigCompare function in deepTools, comparing ChIP signals to their corresponding input tracks.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: Colon

growth_protocol: PC3 DM cells (a prostate cancer cell line) and COLO320 DM (a colorectal cancer cell line) were purchased from the Bioresource Collection and Research Center (BCRC, Hsinchu, Taiwan). The cell line was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 1 mM sodium pyruvate, and 1× Antibiotic-Antimycotic (Gibco), under the conditions of 5% CO2 at 37°C. The mycoplasma absence was tested by Mycoplasma PCR Detection Kit (abm) before the experiments.

extract_protocol:
Approximately 1 × 10⁷ PC3 DM or COLO320 DM cells per assay were crosslinked with 1% formaldehyde for 10 minutes at room temperature, followed by quenching with 125 mM glycine. Cells were lysed, and nuclei were isolated. Chromatin was sheared to an average fragment size of 200–700 bp using a Bioruptor Pico sonicator (Diagenode). Immunoprecipitation was performed overnight at 4°C using 2 µg of antibodies specific for BRD4 (CST-13440 (E2A7X), Cell Signaling Technology) or H3K56ac (PA5-40101, Invitrogen), along with Protein A/G magnetic beads (Thermo Fisher Scientific). An equivalent amount of IgG antibody (12-371, Sigma) was used as a negative control. After washing, chromatin was eluted, reverse-crosslinked, and treated with RNase A and Proteinase K. ChIP DNA was purified using DNA Clean & Concentrator-5 columns (Zymo Research, Irvine, CA, USA).
Libraries were prepared using the KAPA HyperPrep Kit (Roche, Basel, Switzerland) following the manufacturer’s protocol. Libraries were size-selected using AMPure XP beads (Beckman Coulter, Brea, CA, USA). Library quality and concentration were assessed using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA). Sequencing was performed on an Illumina NextSeq 550 platform (Illumina, San Diego, CA, USA) generating 151-bp paired-end reads.

value: Colon

value: COLO320 DM

value: Human Colorectal Adenocarcinoma

value: Double Minutes

tag: chip antibody

value: H3K56ac (PA5-40101, Invitrogen)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Red light - bio rep #1

description:
Library name: Red_light_timepoint_180_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)

value: Red-light 180 minutes


title: PC3 DM, H3K56ac (ChIP-Seq)

description: Library name: PC3 DM, H3K56ac (ChIP-Seq)

value: Prostate

value: PC3 DM

value: Human Prostate Adenocarcinoma


title: 1)      ARPE-19 control untreated replicate 1 (ARPE_Ctrl_rep1)

description: Library name: ARPE_Ctrl_rep1

value: eye-etinal pigment epithelium

value: human retinal pigment epithelial (RPE) cell line

value: WT

value: Milli-Q H2O


title: COLO320 DM, BRD4 (ChIP-Seq)

description: Library name: COLO320 DM, BRD4 (ChIP-Seq)


title: Heart, 8wks, PBS TAC1

value: PBS and transverse aortic constriction


title: ARPE-19 in DMEM/F12 with 10% FBS treated with NACET

description: Library name: 10Percent_FBS_NACET

value: normal eyes of a 19-year-old male who died from head trauma

value: ARPE-19 in DMEM/F12 with 10% FBS treated with N-acetylcysteine ethyl ester (NACET)

value: Advanced ChemBloks, #O32426, Lot#:AC99952A


title: Heart, 8wks, PBS Sham3

value: Heart

value: PBS and sham surgery


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Red light - bio rep #3

description:
Library name: Red_light_timepoint_60_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)

value: Marchantia polymorpha Thallus

value: Takaragaike-1 (Tak-1, male)

value: Red-light 60 minutes


title: PC3 DM, BRD4 (ChIP-Seq)

description: Library name: PC3 DM, BRD4 (ChIP-Seq)

value: Double Minutes


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Red light - bio rep #2

description:
Library name: Red_light_timepoint_60_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Far-Red light - bio rep #1

description:
Library name: Far-Red_light_timepoint_30_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Far-Red Light (30-40 µmol m⁻² s⁻¹, λmax = 730 nm)

value: Far_Red-light 30 minutes


title: Heart, 8wks, PBS Sham2


title: HL-60, wildtype, untreated, HiC

city: PHILADELPHIA

first: Sandra

last: Deliard

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description: Library name: HL60_Wildtype_NT_HiC

data_processing:
Fastq files were processed using the HiC-Pro pipeline.  Processing with the HiC-Pro pipeline includes read alignment, filtering, quality control checks, building contact maps and running iterative correction (ICE) normalization on the contact maps. Significant chromatin interactions were identified by implementing the FitHiC2 tool. Output bias files from HiC-Pro were converted to FitHiC format, then run the FitHiC2 program using the 10kb resolution option and an upper and lower distance limit of 300kb and 20kb, respectively. Overlapping interactions were merged then filtered by a q-value less than 0.01. TADs were determined using the TopDom R tool with a window size of 5 on 40kb resolution data.
Assembly: hg19
Supplementary files format and content: raw contact matrix files

extract_protocol:
In situ Hi-C in monocytes and HL60 cells was performed using the Arima HiC kit (Arima Genomics), following the user guide for mammalian cell lines. For the crosslinking step, according to the standard input protocol, 5 million cells were crosslinked then flash-frozen in aliquots of 1 million cells. After estimating the DNA input from crosslinked cells, one aliquot of cells (~2 ug of DNA) per condition was sufficient to proceed with the Hi-C protocol. Digestion and proximity ligation steps were done according to the kit protocol. Proximally ligated DNA underwent quality control checks for ligation, sonicated with the Covaris ME220 sonicator, then purified and size selected with AMPure XP Beads (Beckman Coulter) to obtain a fragment size distribution of 200-600bp prior to the biotin enrichment step.
For library preparation, end repair, dA-tailing, and adaptor ligation were performed using the NEB Next Ultra II DNA Library Prep kit for Illumina, following a protocol tailored for Arima Hi-C DNA. The Hi-C libraries were sequenced at a depth of at least 300 million 50bp paired-end reads on the Illumina NextSeq 500 Sequencer.

value: wildtype

value: untreated


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Red light - bio rep #1

description:
Library name: Red_light_timepoint_60_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)


title: Macrophage, HiC, rep3

description: Library name: MACRO_HiC_rep3

source_name: macrophage

value: macrophage


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Red light - bio rep #3

description:
Library name: Red_light_timepoint_30_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)

value: Red-light 30 minutes


title: HL-60, mutant, PMA treated, HiC

description: Library name: HL60_Mutant2_PMA_HiC

value: FIRE mutant

value: PMA


title: Heart, 8wks, PBS Sham1


title: HL-60, mutant, untreated, HiC

description: Library name: HL60_Mutant2_NT_HiC


title: Heart, 8wks, TAC Sham3

value: cardiac specific CPT1a knockout

value: transverse aortic constriction


title: Macrophage, HiC,rep1

description: Library name: MACRO_HiC_rep1


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Red light - bio rep #2

description:
Library name: Red_light_timepoint_30_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)


title: Heart, 8wks, TAC Sham4


title: Monocyte, HiC, rep3

description: Library name: MONO_HiC_rep3

source_name: monocyte

value: monocyte


title: Monocyte,HiC, rep2

description: Library name: MONO_HiC_rep2


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Red light - bio rep #1

description:
Library name: Red_light_timepoint_30_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Red Light (80-90 µmol m⁻² s⁻¹, λmax = 660 nm)


title: HL60, wildtype, untreated, Input

description: Library name: HL60_NT_Input

data_processing:
For data processing and analysis, sequencing files were demultiplexed (Bcl2fastq, v2.17.1.14) and quality control (QC) was performed on FASTQ files using FASTQC (v0.11.5). Adaptors were trimmed from sequencing reads with TrimGalore (version 0.6.10), which were then aligned to the human genome (hg19) with Burrows-Wheeler Aligner (BWA), specifically the BWA-MEM algorithm. Alignment files were sorted, filtered for a mapping quality > 10, then had duplicate reads removed with Samtools (version 1.15.1). Peak calling was done using Model-based Analysis of ChIP-seq (MACS2). Input samples were used as controls for peak calling.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
ChIP-seq with antibodies for EGR1 (Bethyl), H3K27ac (Abcam), and H3K4me1 (Abcam) were done in HL-60 cells.  For each experiment, 10 million cells were collected and crosslinked in growth medium containing 1% formaldehyde for 5 minutes then quenched in 0.125M Glycine. Cells were then washed twice with PBS then flash frozen. Cell pellets were lysed in ChIP buffer (150mM NaCl, 1% TritonX-100, 5mM EDTA, 10mM TrisCl, 0.5mM dithiothreitol (DTT), and 0.7% SDS) plus protease inhibitors on ice for 10 minutes.  Sonication was performed using the Covaris ME220 Focused-ultrasonicator to reach an average chromatin fragment length of 200-400bp. Sheared chromatin was cleared by centrifugation at 13,000 RPM for 10 minutes. Prior to adding antibody, 5% of the sample was collected as an input control. For 10 million cells, 10ug of antibody (3ug for H3K27ac) and protein A or G Dynabeads (Invitrogen) were added to chromatin. For RNAPII ChIP-seq, a custom rabbit polyclonal antibody raised against the N-terminal domain was used. On Day 2, beads were washed with twice with Mixed Micelle Wash Buffer (150mM NaCl, 20mM Tris-HCl, 5mM EDTA, 5.2% sucrose, 1% Triton X-100, 0.2% SDS), Buffer 500 (500mM NaCl, 25 mM HEPES, 10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate), LiCl/detergent Wash (250 mM LiCl, 10 mM Tris-HCl, 1 mM EDTA, 0.5% Na deoxycholate, 0.5% NP-40) and once with 1× Tris-EDTA (TE) buffer. Samples were then incubated in TE plus 1% SDS at 65°C for 10 minutes, rotating at 1200 RPM. Elution was repeated twice, and the eluates were further incubated overnight at 65°C to reverse cross-linking, along with the untreated input. On Day 3, proteinase K (0.5mg/mL final concentration) was added to the samples and they were incubated for 1 hour at 65°C. The Zymo ChIP DNA Clear Concentrator Kit (Zymo research) was used for the final DNA extraction.
Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).


title: Monocyte, HiC, rep1

description: Library name: MONO_HiC_rep1


title: HL60, wildtype, PMA untreated, Input

description: Library name: HL60_PMA_Input


title: Heart, 8wks, TAC Sham2


title: Macrophage, HiC, rep2

description: Library name: MACRO_HiC_rep2


title: PC3 DM, IgG Control (ChIP-Seq)

description: Library name: PC3 DM, IgG Control (ChIP-Seq)

value: Prostate

value: PC3 DM

value: Human Prostate Adenocarcinoma

value: IgG antibody (12-371, Sigma)


title: COLO320 DM, IgG Control (ChIP-Seq)

description: Library name: COLO320 DM, IgG Control (ChIP-Seq)

value: Colon

value: COLO320 DM

value: Human Colorectal Adenocarcinoma


title: Heart, 8wks, TAC Sham1

value: Heart


title: HL-60, wildtype, PMA treated, HiC

description: Library name: HL60_Wildtype_PMA_HiC

value: wildtype


title: HL60, Mutant2, PMA treated, H3K4me1 (ChIP)

description: Library name: HL60_Mutant2_PMA_H3K4me1_ChIP


title: Heart, 8wks, KO Sham3

value: sham surgery


title: Heart, 8wks, KO Sham4


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Blue light - bio rep #2

description:
Library name: Blue_light_timepoint_24_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)

value: Marchantia polymorpha Thallus

value: Takaragaike-1 (Tak-1, male)

value: Blue-light 1440 minutes / 24 hours


title: HL60, Mutant2, untreated, Pol2 (ChIP)

description: Library name: HL60_Mutant2_NT_Pol2_ChIP

value: FIRE mutant

value: untreated


title: HL60, Mutant2, PMA treated, H3K27ac (ChIP)

description: Library name: HL60_Mutant2_PMA_H3K27ac_ChIP

value: PMA


title: HL60, Mutant2, PMA treated, EGR1 (ChIP)

description: Library name: HL60_Mutant2_PMA_EGR1_ChIP


title: HL60, Mutant2, untreated, H3K27ac (ChIP)

description: Library name: HL60_Mutant2_NT_H3K27ac_ChIP


title: Heart, 8wks, KO Sham2

value: cardiac specific CPT1a knockout


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Blue light - bio rep #1

description:
Library name: Blue_light_timepoint_24_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Blue light - bio rep #3

description:
Library name: Blue_light_timepoint_12_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)

value: Blue-light 720 minutes / 12 hours


title: HL60, Mutant2, untreated, H3K4me1 (ChIP)

description: Library name: HL60_Mutant2_NT_H3K4me1_ChIP


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Blue light - bio rep #2

description:
Library name: Blue_light_timepoint_12_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: Heart, 8wks, KO Sham1


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  Blue light - bio rep #3

description:
Library name: Blue_light_timepoint_24_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: HL60, Mutant1, PMA treated, H3K27ac (ChIP)

description: Library name: HL60_Mutant1_PMA_H3K27ac_ChIP


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  Blue light - bio rep #1

description:
Library name: Blue_light_timepoint_12_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: HL60, Mutant2, untreated, EGR1 (ChIP)

description: Library name: HL60_Mutant2_NT_EGR1_ChIP


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Blue light - bio rep #2

description:
Library name: Blue_light_timepoint_180_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)

value: Blue-light 180 minutes


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Blue light - bio rep #3

description:
Library name: Blue_light_timepoint_180_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: HL60, Mutant1, untreated, Pol2 (ChIP)

description: Library name: HL60_Mutant1_NT_Pol2_ChIP


title: HL60, Mutant1, PMA treated, Pol2 (ChIP)

description: Library name: HL60_Mutant1_PMA_Pol2_ChIP


title: Heart, 8wks, FF TAC3

value: CPT1a floxed

value: transverse aortic constriction


title: HL60, Mutant1, PMA treated, H3K4me1 (ChIP)

description: Library name: HL60_Mutant1_PMA_H3K4me1_ChIP


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  Blue light - bio rep #1

description:
Library name: Blue_light_timepoint_180_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: HL60, Mutant1, untreated, H3K4me1 (ChIP)

description: Library name: HL60_Mutant1_NT_H3K4me1_ChIP


title: HL60, wildtype, PMA treated, Pol2 (ChIP)

description: Library name: HL60_Wildtype_PMA_Pol2_ChIP


title: Heart, 8wks, FF TAC2


title: HL60, Mutant2, PMA treated, Pol2 (ChIP)

description: Library name: HL60_Mutant2_PMA_Pol2_ChIP


title: Heart, 8wks, FF TAC4


title: Heart, 8wks, FF TAC1


title: HL60, wildtype, PMA treated, H3K27ac (ChIP)

description: Library name: HL60_Wildtype_PMA_H3K27ac_ChIP


title: HL60, Mutant1, PMA treated, EGR1 (ChIP)

description: Library name: HL60_Mutant1_PMA_EGR1_ChIP


title: HL60, Mutant1, untreated, H3K27ac (ChIP)

description: Library name: HL60_Mutant1_NT_H3K27ac_ChIP


title: Heart, 8wks, FF Sham4


title: HL60, Mutant1, untreated, EGR1 (ChIP)

description: Library name: HL60_Mutant1_NT_EGR1_ChIP


title: HL60, wildtype, PMA treated, EGR1 (ChIP)

description: Library name: HL60_Wildtype_PMA_EGR1_ChIP


title: Heart, 8wks, FF Sham3


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Blue light - bio rep #1

description:
Library name: Blue_light_timepoint_60_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)

value: Blue-light 60 minutes


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Blue light - bio rep #2

description:
Library name: Blue_light_timepoint_60_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: HL60, wildtype, untreated, Pol2 (ChIP)

description: Library name: HL60_Wildtype_NT_Pol2_ChIP


title: HL60, wildtype, PMA treated, H3K4me1 (ChIP)

description: Library name: HL60_Wildtype_PMA_H3K4me1_ChIP


title: HL60, wildtype, untreated, H3K4me1 (ChIP)

description: Library name: HL60_Wildtype_NT_H3K4me1_ChIP


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  Blue light - bio rep #3

description:
Library name: Blue_light_timepoint_60_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: Heart, 8wks, FF Sham2


title: HL60, wildtype, untreated, EGR1 (ChIP)

description: Library name: HL60_Wildtype_NT_EGR1_ChIP


title: Heart, 8wks, FF Sham1


title: HL60, wildtype, untreated, H3K27ac (ChIP)

description: Library name: HL60_Wildtype_NT_H3K27ac_ChIP


title: MACRO, PU.1 (CUT&RUN)

description: Library name: MACRO_PU1_CR

data_processing:
For analysis, sequencing files were demultiplexed and QC was performed on FASTQ files with FASTQC. Adaptors were trimmed from sequencing reads with TrimGalore, which were then aligned to the human genome (hg19) with BWA-MEM. Alignment files were sorted, filtered for a mapping quality > 10. Peak calling was done with MACS2. Motif analysis on peaks was done using MEME-ChIP
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed according to the published protocol by Skene and Henikoff with some modifications. Experiments were performed with primary monocytes and macrophages using antibodies for CTCF (Cell Signaling), SMC1 (Bethyl), PU.1 (Santa Cruz), and EGR1 (Bethyl). Approximately 250-500, 000 cells were used. For digestion, 1.5uL of pAG-mnase (Cell Signaling) was used. The alternative DNA extraction method was used to extract the final DNA product.
Sequencing libraries were generated with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

value: macrophage


title: MACRO, IgG (CUT&RUN)

description: Library name: MACRO_IgG_CR


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  White light - bio rep #3

description:
Library name: White_light_timepoint_24_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

value: White-light 1440 minutes / 24 hours


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Blue light - bio rep #1

description:
Library name: Blue_light_timepoint_30_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)

value: Blue-light 30 minutes


title: MACRO, SMC1 (CUT&RUN)

description: Library name: MACRO_SMC1_CR


title: Testis_8Month_scRNA

city: Guangzhou

first: Jia

middle: Xiao

last: Huang

state: Guangdong

address: Zhongshan 2rd

institute: GDPH

description: 10x Genomics

data_processing:
Single-cell RNA sequencing data of testicular samples was aligned and quantified using the Cell Ranger Software Suite (v3.0.2, 10X Genomics).
We captured approximately 7,000 to 120,000 cells each sample. The reads were aligned to the Mus musculus reference genome mm10, and after alignment, filtering, barcode counting, and UMI counting using the cell count pipeline provided by Cell Ranger, feature-barcode matrices were generated.
We performed quality control using the Seurat R package. Single cells that expressed less than 300 genes and more than 5,000 genes were excluded in case of the potential empty droplets and doublets, and genes expressed in fewer than 20 cells were excluded from further analysis. Individual cells that had less than 25% mitochondrial gene content were retained to remove the dead cells. Only eligible cells will be processed for downstream analysis.
We use the Functions built into Seurat (v4.0) packages to correct for batching effects and merge data sets.
Assembly: mm10
Supplementary files format and content: features.tsv, a file with the gene IDs; representing all genes quantified, barcodes.tsv, a file with the cell IDs, representing all cells quantified; matrix.mtx, a matrix of counts per gene for every cell.

source_name: Testis

extract_protocol:
Testis samples from C57BL/6j mice were dissected aseptically using sterilized scissors. The samples were washed three times with DPBS (Thermo Fisher Scientific, 14190-144), and the tunica albuginea was carefully removed using sterilized tweezers to isolate the interstitial cells as our previous reported13, 14. The interstitial cells were then digested with 1 mg/ml collagenase type IV (Thermo Fisher Scientific, 17104019) in DMEM-F12 (phenol red-free) (Thermo Fisher Scientific, 21041025) at 37 °C for 10 minutes. During the digestion process, the tissues were gently pipetted up and down. The digestion process was halted by adding 2% FBS, and the resulting cell suspension was filtered through a 40-μm nylon mesh. The cells were then centrifuged at 350 rcf for 5 minutes at room temperature and suspended in DPBS or 2% FBS in DPBS for subsequent fluorescence-activated cell sorting analysis (FACSAria III, BD Bioscience). For the 10x Genomics platform, the cell count for each sample was determined using the Biorad Automated Cell Counter. After GEM generation and barcoding utilizing the Chromium Single Cell Library & Gel Bead Kit v3.1 (10x Genomics) according to User Guide, approximately 20,000 single cells per sample were captured by Chromium Controller (10x Genomics).
For library construction, utilizing the Chromium Single Cell Library & Gel Bead Kit v3.1 (10x Genomics) according to User Guide.

value: Testis

value: Interstitial cell

value: 8-Months old

value: Wild type


title: MONO, IgG (CUT&RUN)

description: Library name: MONO_IgG_CR

value: monocyte


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  White light - bio rep #2

description:
Library name: White_light_timepoint_24_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

value: Marchantia polymorpha Thallus

value: Takaragaike-1 (Tak-1, male)


title: MONO, SMC1 (CUT&RUN)

description: Library name: MONO_SMC1_CR


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Blue light - bio rep #3

description:
Library name: Blue_light_timepoint_30_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  Blue light - bio rep #2

description:
Library name: Blue_light_timepoint_30_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in monochromatic Blue Light (30-40 µmol m⁻² s⁻¹, λmax = 430 nm)


title: MACRO, CTCF (CUT&RUN), rep 2

description: Library name: MACRO_CTCF_CR_rep2


title: Testis_24Month_scRNA

description: 10x Genomics

value: 24-Months old


title: MACRO, CTCF (CUT&RUN), rep 3

description: Library name: MACRO_CTCF_CR_rep3


title: MONO, PU.1 (CUT&RUN)

description: Library name: MONO_PU1_CR


title: Testis_1week_scRNA

description: 10x Genomics

value: 1-Week old