title: Hs766T, TSA-treated

value: TSA-induced cell death resistant


title: Beta-carotene-producing yeast, YPD, rep2

status: Public on Aug 03 2026

type: SRA

city: Pathumthani

first: Peerapat

last: Khamwachirapithak

address: Phahonyothin Road, Khlong Luang

country: Thailand

institute: Thammasat University

description: Library name: Beta_2

library_source: transcriptomic

data_processing:
FastQC
Reads were align to Saccer3 genome using the Hisat2
Sorting and indexing using Samtools
Duplication was removed by Picard tools
Raw read counts were normalized by DEseq2
Assembly: Saccer3
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Cell pellet

growth_protocol: Cells were cultured in YPD medium at 30°C and 250 rpm for 18 hours

extract_protocol:
RNA was extracted by RNeasy Mini Kit (Qiagen, Germany).
DNBSEQ stranded mRNA library

tag: tissue

value: Cell pellet

tag: cell line

value: betacarotene

tag: cell type

value: Yeast cell

tag: genotype

value: CrtI/E/YB

tag: treatment

value: YPD


title: E16.5_M_WT_2

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

hyb_protocol: Hybridized to Agilent-015087 arrays according to the manufacturer's protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5 um

data_processing: Let x-norm = x - y + mean(y), where x = log10(Cy3), y =log10(Cy5). x-batch = x - median(new data) + median(old data) for every gene. The batched normalized value x-batch is used for the final processed VALUE

organism: Mus musculus

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit according to the manufacturer's instructions

growth_protocol: Placenta from male mice at d.p.c 16.5 and 18.5 were harvested from wild-type (WT) and PLAC1 Knock-out (Plac1 null)

extract_protocol: The samples were dissolved in the well with TRIzol reagent 1/2 mL. They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample. They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 15,300 rpm on an eppendorf centrifuge at 4C. The aqueous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun for 5 minutes, then the ethanol was dumped out. Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer. ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -80C for storage.

tag: strain

value: WT

tag: Sex

value: Male

tag: age

value: Placenta

source_name: Universal probe

tag: sample type

value: Universal probe


title: S1_CD45_VEH

city: Barcelona

first: Lucía

last: Prohens Coll

state: Barcelona

address: Casanova 143, Facultat de Medicina, Dept de Fonamens Clínics, Unitat de Farmacologia, Planta 1, ala Nord

department: Basic Clinical Practice

country: Spain

institute: Universitat de Barcelona

description: Library name: Sample 1

data_processing:
Raw sequencing reads were generated in FASTQ format.
Read quality was assessed using FastQC.
Adapter sequences and low-quality bases were removed from raw reads.
Filtered reads were aligned to the mouse reference genome.
Gene-level read counts were obtained from aligned reads.
Downstream normalization and differential expression analyses were performed in R.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files containing raw gene-level read counts for each individual sample. Each file corresponds to one RNA-seq sample and includes unnormalized count values.
Supplementary files format and content: A supplemental comma-separated values (CSV) file containing the combined raw count matrix (genes × samples), generated by merging individual sample count files, with gene symbols as row identifiers and unnormalized count values.

source_name: Frontal Cortex

growth_protocol: Adult male mice were housed under standard laboratory conditions with controlled temperature and humidity, on a 12 h light/dark cycle, with food and water available ad libitum.

extract_protocol:
Frontal cortices were dissected, pooled (five animals per sample), and dissociated into a single-cell suspension. Microglia, astrocytes and neurons were sequentially isolated using an antibody-based immunopanning protocol involving depletion of endothelial cells, capture of CD45+ microglia, depletion of oligodendrocytes and oligodendrocyte precursor cells, and subsequent isolation of Thy1+ neurons and HepaCAM+ astrocytes. Total RNA was extracted directly from each immunopanned cell fraction using the Total RNA Extraction Miniprep kit (Viogene), following the manufacturer’s instructions.
RNA-seq libraries were prepared from 20 ng of total RNA using the QIAseq FastSelect RNA Library Kit (QIAGEN), including rRNA depletion and cDNA synthesis with random hexamer and oligo-dT primers. Libraries were purified, amplified and quantified, and sequenced as paired-end reads on an Illumina NextSeq 2000 System.

treatment_protocol: Mice were treated once daily from postnatal day 60 to 74 with vehicle, clozapine (10 mg/kg), or risperidone (1 mg/kg) administered intraperitoneally. Animals were sacrificed at postnatal day 75.

value: Frontal Cortex

value: microglia fractions

value: vehicle

tag: batch


title: Hs766T, control

city: Elche

first: Miguel

last: Saceda

state: Valencian Community

address: Unidad de Investigación del Hospital geneCami de la Almazara 11, edificio Anexo II

department: Unidad de Investigación

institute: Fundacion para el Fomento de la Investigacion Sanitaria y Biomédica de la Comunidad Valenciana

hyb_protocol: Once synthesized and purified, 15 µg of cRNA from each preparation were fragmented to prepare the hybridization mixtures. The hybridization procedures were performed by PROGENIKA SA. Quality controls for the hybridizations included the detection of spike-in controls and the assessment of 3'/5' signal ratios for housekeeping genes.

scan_protocol: After hybridization, arrays were washed, stained, and scanned following the standard Affymetrix protocols. The scanned images were processed using the Affymetrix GCOS 1.2 software to generate the corresponding CEL files for subsequent analysis.

data_processing: Prior to array comparison, data from each array were scaled to minimize discrepancies due to variables such as sample preparation, hybridization, and other technical factors. Using the Affymetrix GCOS 1.2 software, all arrays were scaled by setting the target mean intensity to an arbitrary value of 100. GCOS calculates the average intensity of the entire array by averaging the signal values of all probe sets, excluding the highest and lowest 2% of values. This mean intensity is then multiplied by a scaling factor to adjust it to the user-defined target value (in this case, 100). Scaling factors for arrays within the same experiment are expected to be similar and, as far as possible, close to 1. In this study, the scaling factors applied to each sample fell within the acceptable limits established by Affymetrix.

label: biotin

organism: Homo sapiens

source_name: Pancreatic adenocarcinoma, untreated control

label_protocol: Starting from 2 µg of each sample, cDNA was synthesized using the One-Cycle cDNA Synthesis Kit (Affymetrix) following the manufacturer’s Expression Analysis Technical Manual. Subsequently, cRNA was generated from the cDNA using the Affymetrix IVT Labeling Kit according to the provided protocol. The resulting cRNA was purified with the Affymetrix GeneChip Sample Cleanup Module and recovered in a final volume of 22 µL of RNase-free water. The quantity and quality of the biotinylated cRNA were assessed by spectrophotometric measurement using a NanoDrop device and by electrophoresis on an agarose gel.

growth_protocol: Pancreatic cells were cultured at 37°C in a humidified atmosphere containing 5% CO₂ in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Leukemia cell lines were maintained in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol: RNA was isolated using the NZY Total RNA Isolation Kit following manufacturer's instructions.

treatment_protocol: L1210 and L1210R cells were plated at a density of 3×10⁵ cells/mL and treated with 1 µM TSA in the presence or absence of 100 µM AEBSF for 6 hours. Pancreatic cell lines were treated with 1 µM TSA for 6 hours after reaching 80% confluence.


title: S016_CD4_CXCR5hi_PD1hi

status: Public on Aug 02 2026

city: Cambridge

first: Vinay

middle: S

last: Mahajan

state: MA

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

description: Library name: S016_CD4_CXCR5hi_PD1hi

library_source: genomic

data_processing:
Sequencing reads were aligned to hg38 using Bowtie2
Accessible peaks / regions were identified using macs2
Assembly: hg38
Supplementary files format and content: narrowPeak.bed (peak file in bed format)
Supplementary files format and content: bw (bigwig files, fraom ATAC-seq alignment to hg38)

molecule: genomic DNA

source_name: tonsil

extract_protocol:
Cells were FACS-sorted, stored on ice, and prompty processed for ATAC-seq
ATAC-seq: nuclei were isolated and tagmented in 10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630 for 30 min at 37 degrees C as described in Buenrostro et al., 2013 (PMID: 24097267). Tagmented DNA was purified with Qiagen MinElute PCR purification kit, indexed and amplfied for sequencing.

value: tonsil

value: CD4+ CXCR5hi PD1hi


title: Beta-carotene-producing yeast, YPD, rep1

description: Library name: Beta_1


title: E16.5_M_WT_1


title: S013_CD4_CXCR5hi_PD1hi

description: Library name: S013_CD4_CXCR5hi_PD1hi


title: S012_CD4_CXCR5pos_PD1int

description: Library name: S012_CD4_CXCR5pos_PD1int

value: CD4+ CXCR5pos PD1int


title: S011_CD4_CXCR5pos_PD1int

description: Library name: S011_CD4_CXCR5pos_PD1int


title: S009_CD4_CXCR5pos_PD1int

description: Library name: S009_CD4_CXCR5pos_PD1int


title: S007_CD4_CXCR5pos_PD1neg

description: Library name: S007_CD4_CXCR5pos_PD1neg

value: CD4+ CXCR5pos PD1neg


title: S006_CD4_CXCR5pos_PD1neg

description: Library name: S006_CD4_CXCR5pos_PD1neg


title: S005_CD4_CXCR5pos_PD1neg

description: Library name: S005_CD4_CXCR5pos_PD1neg


title: S004_CD4_naive

description: Library name: S004_CD4_naive

value: CD4+ naive


title: S003_CD4_naive

description: Library name: S003_CD4_naive


title: S001_CD4_naive

description: Library name: S001_CD4_naive


title: HUVECs, Ad5-S-3M, 72 h, biol rep 3

city: Kuopio

first: Nihay

last: Laham Karam

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: Library name: HUVEC_AdS-3M_72h_3

data_processing:
RNA-seq data was trimmed using the following tools: Trimmomatic (v.0.36) for quality trimming the reads (LEADING:5 TRAILING:5 MINLEN:36), HOMER (v.4.10) to trim poly-A ends (-3 AAAAAAAA -mis 1 -min 36).
Reads were aligned using STAR (v.2.7.9) to map to the genome (hg38).
DESeq2  was used for differential gene expression analysis using the commands from HOMER. Reads were counted only if their direction matched the transcript (”-strand +”) and only one identical read was accepted (”-pc 1”).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts that have been transformed with DESeq2's rlog

molecule: polyA RNA

source_name: primary HUVEC

growth_protocol: HUVECs were maintained in endothelial cell growth medium (ECGM; PromoCell) with the provided SupplementMix (PromoCell) as well as 30 µg/ml gentamicin and 15 ng/ml amphotericin B antibiotic (Lonza). The plates used for culturing HUVECs were coated with a solution of 10 µg/ml fibronectin (Corning) and 0.05 % gelatin (Sigma Aldrich) in PBS at 37 °C for at least 5 min, before removing the solution and plating the cells. Cells were cultured at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). 5000 ng of RNA was DNase-treated using the TURBO DNA-free kit (Invitrogen) in a total reaction volume of 25 µl. Of Dnase-treated RNA, 500 ng was used for sequencing library construction.
RNA libraries for RNA sequencing were constructed using QuantSeq 3′ mRNA-Seq FWD and Unique Dual Indexing (UDI) 12 nt Kits (Lexogen), according to the manufacturer’s instructions.

treatment_protocol: HUVECs were transduced with multiplicity of infection ratio of 125 viral particles/cell one day after plating, and the Ad5 vectors were incubated on the cells for 4 h, after which the media was changed. RNA extraction followed 72 h after the transduction.

value: primary HUVEC

value: endothelial cell

value: Ad5-S-3M transduction


title: HUVECs, Ad5-S-3M, 72 h, biol rep 2

description: Library name: HUVEC_AdS-3M_72h_2


title: HUVECs, Ad5-RBD-3M, 72 h, biol rep 2

description: Library name: HUVEC_AdRBD-3M_72h_2

value: Ad5-RBD-3M transduction


title: HUVECs, Ad5-RBD-3M, 72 h, biol rep 1

description: Library name: HUVEC_AdRBD-3M_72h_1


title: HUVECs, Ad5-CMV, 72 h, biol rep 3

description: Library name: HUVEC_AdCMV_72h_3

value: Ad5-CMV transduction


title: HUVECs, Ad5-CMV, 72 h, biol rep 2

description: Library name: HUVEC_AdCMV_72h_2

value: WT


title: HUVECs, Ad5-CMV, 72 h, biol rep 1

description: Library name: HUVEC_AdCMV_72h_1


title: Tumor, H3K27ac, CUT&RUN

city: Durham

first: Arum

last: Kim

state: NC

address: Medical Sciences Research Building III  3 Genome Ct

institute: Duke University

data_processing:
All reads were mapped to the human genome (hg19), then the non-primary alignment and PCR duplicates were removed from aligned data using the Picard, Samtools and bedtools.
Bigwig files, heatmaps and averaged plotting of CUT&RUN signals were generated using Deeptools.
Profiles of CUT&RUN read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters.
Assembly: hg19
Supplementary files format and content: Bigwig files
Library strategy: CUT&RUN

source_name: Hepatocellular carcinoma

growth_protocol: HepG2 cells were grown in RPMI1640 medium plus 10% FBS and 1% antibiotics. Huh7 cells were grown in DMEM medium plus 10% FBS and 1% antibiotics.

extract_protocol:
Cells were trypsinized with 0.05% of trypsin and pellets were collected for CUT&RUN. CUT&RUN was performed according to manufacturer’s instructions (CUTANA™ pAG-MNase for ChIC/CUT&RUN, EpiCypher, Cat# 15-1116).
1-10 ng of the purified CUT&RUN-enriched DNA was used for preparation of multiplexed sequencing libraries with the NEB Ultra II DNA Library Prep Kit per manufacturer's instructions (NEB #E7645). Libraries were subject to pair-end sequencing using an Illumina Nextseq.

treatment_protocol: no treatment

value: Hepatocellular carcinoma


title: Tumor, H3K27me3, CUT&RUN


title: Tumor, EZH2, CUT&RUN


title: Huh7, H3K4me3, CUT&RUN


title: HUVECs, Ad5-RBD-3M, 72 h, biol rep 3

description: Library name: HUVEC_AdRBD-3M_72h_3


title: Huh7, H3K27ac, CUT&RUN


title: Huh7, H3K27me3, CUT&RUN, abcam


title: Huh7, H3K27me3, CUT&RUN, CST


title: Huh7, EZH2, CUT&RUN, HA


title: Huh7, EZH2, CUT&RUN, CST


title: Damaraland mole-rat, liver, DMR2

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

description: Library name: Fdam_Liver_Rep1

data_processing:
Sequencing adaptors and low-quality reads were removed using Cutadapt with the following parameters: a minimum read length of 25 bp after trimming (-m 25), a minimum sequence quality score of 30 (-q 30), and the removal of any reads containing more than one N base (--max-n 1).
Trimmed reads from each species were pseudo-aligned and quantified to their respective reference transcriptome using Salmon v.013.1, with a decoy-aware index. The pseudo-mapping process included corrections for GC content bias (--gcBias) and sequence-specific biases (--seqBias). Quantification was performed at the transcript level.
For each species, we summarised transcript-level abundance estimates generated by Salmon to the gene level using the tximport v1.24 R package, with counts corrected for effective transcript length via the lengthScaledTPM method. To enable cross-species comparisons, we retained only one-to-one orthologous genes. We then merged gene-level count matrices across species and imported them into DESeq2. We normalised the combined dataset across all samples using the median-of-ratios method implemented in DESeq2, which adjusts for library size by computing sample-specific size factors as the median of ratios of observed counts to a pseudo-reference (the geometric mean across samples for each gene). To account for technical variation introduced by different data sources, we included a batch term in the DESeq2 model (~species + data source). Finally, we applied the variance-stabilising transformation (VST) to the normalised counts, which were then used for downstream analyses.
Assembly: The reference genome and transcriptomes for naked mole-rat (HetGla1.0), Damara mole-rat (DMRv1.0), guinea pig (Cavpor3.0) and mouse (GRCm38) were downloaded from Ensembl v102
Supplementary files format and content: Vst-normalised counts across 13,929 one-to-one orthologous for each sample in the study

organism: Fukomys damarensis

source_name: liver

extract_protocol:
Total RNA was extracted from 10-50 mg of tissue samples, previously flash-frozen in dry ice and kept at -80C. Briefly, frozen tissue samples were homogenised in lysis buffer (RNAEasy, Qiagen) using homogenisation beads (Precellys hard tissue homogenising tubes CK28) in a FastPrep-24 tissue homogeniser (MP Biosciences) with three 20 s pulses at a speed of 4.5 m/s. Homogenised tissue lysates were used directly for RNA extraction using a commercial RNA extraction kit (RNEasy, Qiagen).
500 ng of total RNA from each sample were used for preparation of total RNA-sequencing libraries with NEBNext UltraTM II RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, total RNA was depleted of ribosomal RNA (rRNA) with rRNA Depletion Kit v2 (New England Biolabs) and RNA sample purification beads. rRNA-depleted RNA was used for preparation of cDNA and RNA-sequencing libraries following manufacturer specifications, with 12-15 minutes of RNA fragmentation at 94C and 10 cycles of PCR amplification. RNA-sequencing libraries were quantified by quantitative PCR with Kapa Illumina library quantification kit (Roche diagnostics) in a Roche LC480 instrument. RNA-seq libraries were then pooled in equimolar concentrations and sequenced in an Illumina NovaSeq instrument by commercial supplier Novogene UK.

value: liver

value: male

tag: age (months)

tag: individual


title: S11_HEPA_RIS

description: Library name: Sample 11

value: Frontal Cortex

value: astrocyte fractions

value: risperidone


title: S10_HEPA_CLZ

description: Library name: Sample 10

value: clozapine


title: HepG2, SREBP2, CUT&RUN


title: S8_HEPA_VEH

description: Library name: Sample 8

value: vehicle


title: E16.5_F_Plac1 KO_1

data_processing: Let x-norm = x - y + mean(y), where x = log10(Cy3), y =log10(Cy5). x-batch = x - median(new data) + median(old data) for every gene. The batched normalized value x-batch is used for the final processed VALUE using EX-Atlas program.

source_name: Placenta_E16.5_F_Plac1 null

treatment_protocol: Placentas (d.p.c 16.5 or 18.5) were harvested from wild-type (WT) and PLAC1 Knock-out (Plac1 null) mice

value: C57/Bl6_Plac1 null

value: Female

value: Placenta


title: C17 baseline

city: Heidelberg

first: Fabienne Dorothea

last: Lusky

address: Röntgenstr. 1

country: Germany

institute: Thoraxklinik at Heidelberg University Hospital

hyb_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website

data_processing: For statistical analysis we used R and the bioconductor package simpleaffy and affy, we transformed our data using RMA Algorithm

source_name: Whole blood

extract_protocol: We used the  PAXgene Blood RNA Kit according to the manufacturer’s instructions (PreAnalytiX, Hombrechtikon, CH)

treatment_protocol: Whole blood RNA was collected in PAXGene blood RNA tubes and incubated at room temperature for 2 hours to maximize cell lysis. Samples were stored frozen at  -80°C until processing

value: baseline

tag: group


title: HepG2, H3K4me3, CUT&RUN


title: E18.5_M_Plac1 KO_2

source_name: Placenta_E18.5_M_Plac1 null

value: Male

value: Universal probe


title: S7_HEPA_VEH

description: Library name: Sample 7


title: HepG2, H3K27ac, CUT&RUN


title: HepG2, H3K27me3, CUT&RUN, abcam


title: HepG2, H3K27me3, CUT&RUN, CST


title: HepG2, EZH2, CUT&RUN, HA


title: HepG2, EZH2, CUT&RUN, CST


title: Huh7, SREBP2, CUT&RUN


title: Huh7_shEZH2_2

data_processing:
The fastq files were aligned to the GRCh38 human genome (GRCh38.d1.vd1.fa) using STAR v2.4.2 with the following parameters: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM.
The transcript abundance for each sample was estimated with salmon to quantify the transcriptome defined by Ensembl annotation.
Gene level counts were summed across isoforms and genes with low counts (maximum expression < 10) were filtered out for the downstream analyses.
Assembly: GRCh38
Supplementary files format and content: tab delimited matrix of gene level count estimates

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit (Qiagen, #74134).
For the construction of multiplexed RNA-sequencing libraries, 1 ug of total RNA per sample was processed by using either Illumina Truseq sample prep kit v2 or NEBNext Ultra II RNA library Prep kit (NEB, #E7770) following the instructions of the manufacture’s product manual.

treatment_protocol:
HepG2 cells were treated with 5uM of DMSO, MS7126, C24, MS7126N1 or MS7126N2 for 48h.
Huh7 cells were treated with 5uM of DMSO, MS7126, C24, MS7126N1 or MS7126N2 for 24h.
Cells were infected with the pLKO.1-puro lentivirus containing either EZH2-targeting shRNA (shEZH2) or empty vector (shEV), followed by puromycin selection.
Cells were infected with the pLKO.1-puro lentivirus containing either SREBP2-targeting shRNA (shSREBP2) or empty vector (shEV), followed by puromycin selection.


title: C7 baseline

scan_protocol: We used the excellent Expression Profiling services of the Microarray Core Facility, German Cancer Research Center (DKFZ), all information can be found on their website


title: Huh7_shEZH2_1


title: Huh7_shControl_1


title: Huh7_shControl_2


title: S4_CD45_CLZ

description: Library name: Sample 4

value: microglia fractions


title: RNA-Seq mpkDCT4a cells rep3

city: Nijmegen

first: Lotte

last: Tholen

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Physiology

country: Netherlands

institute: Radboudumc

data_processing:
Reads were trimmed, aligned, bam sieved, and peak called using seq2science:
Low quality reads, short reads, and adapter sequences were trimmed using Fastp.
Reads were quantified using htseq.
Alignment was performed using STAR.
After, uniquely mapped reads with MAPQ > 255 scores were kept.
Assembly: mm10
Supplementary files format and content: tab-delimited value file include raw counts for each sample

source_name: Kidney

growth_protocol: mpkDCT 4a cells were grown in DMEM/F-12 containing 2% (v/v) fetal calf serum, 90 nm sodium selenate; 5 μg/ml transferrin; 2 mM glutamine; 50 nM dexamethasone; 1 nM triiodothyronine; 10 ng/ml epidermal growth factor; 5 μg/ml insulin; 20 mM d-glucose; and 20 mM HEPES, pH 7.4. Cells were grown at 37 °C in a humidity-controlled incubator with 5% (v/v) CO2.

extract_protocol:
RNA was isolated using the NucleoSpin RNA plus kit (Macherey Nagel) 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) with RNA fragmentation of approximately 300 bp fragments.

value: Kidney

value: DCT


title: RNA-Seq mpkDCT4a cells rep2


title: RNA-Seq mpkDCT4a cells rep1


title: ChIP-Seq mpkDCT4a cells

data_processing:
Reads were trimmed, aligned, bam sieved, and peak called using seq2science:
Low quality reads, short reads, and adapter sequences were trimmed using Fastp.
Alignment was performed using bwa-mem2.
After, uniquely mapped reads with MAPQ > 30 scores were kept.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Chromatin was isolated from mpkDCT4a cells (15.106 cells per sample) by fixing with 1% (v/v) formaldehyde (Ultra-Pure) (Thermo scientific) for 8 minutes at RT and quenched with 1/10 volume 1.25 M glycine. Cells were washed twice with PBS and permeabilized in 1% SDS. Samples were sonicated in a Bioruptor pico (Diagenode, Ougrée, Belgium), 12 times 30 seconds on 30 seconds off at normal intensity. Chromatin samples were then immunoprecipitated with Protein A/G beads with anti-H3K27ac for 1 hours at 4 °C. Samples were de-crosslinked in 5 M NaCl at 65 °C overnight and DNA was purified using QIAquick MinElute PCR Purification Kit (Qiagen, 28006) following the manufacturer’s protocol.
Libraries for histone ChIP-seq were prepared using using KAPA HyperPrep Kit  (Kapa Biosystems). Adaptor sequences were linked to the generated ChIP samples. The library was size selected (150–300 bp) and amplified by PCR. Sequencing was completed on an Illumina NextSeq 500.

tag: chip antibody

value: H3K27ac (Diagenoide, C15410196)


title: BxPC-3, control

value: TSA-induced cell death sensitive


title: ATAC-Seq mpkDCT4a cells

data_processing:
Reads were trimmed, aligned, bam sieved, and peak called using seq2science:
Low quality reads, short reads, and adapter sequences were trimmed using Fastp.
Alignment was performed using bwa-mem2.
After, uniquely mapped reads with MAPQ > 30 scores and reads with lenth < 150 were kept.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01. MACS2 was run with nomodel False, a shiftsize of 200 bp, and peak width extended to 200 bp.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
50.000 mpkDCT4a cells were collected and lysed in 2 mL lysis buffer (10 mM Tris/HCl (Ph 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1% NP40). Nuclei were pelleted at 500 x g for 30 minutes at 4 °C and resuspended in 24 μL of the tagment DNA buffer and 1 μL Tn5 transposase (In-house generated) to tagment the DNA. The samples were incubated at 37 °C for 6 minutes while shaking at 650 RPM. After tagmentation, 9 μL of clean-up buffer (1% SDS, 2 mg/mL Proteinase K, 0.45 M NaCl, 0.15 M EDTA in nuclease-free water) was added to the samples and incubated for 30 minutes at 40 °C while shaking at 650 RPM.
DNA was purified by AMPure XP beads and amplified with Nextera primers and Kapa High-Fidelity 2× PCR Master Mix (Roche, KK2601) using 5 PCR cycles. Libraries were purified by AMPure XP beads and a final amplification of the library was performed using the 5 PCR cycles. Subsequently, DNA was purified using AMPure XP beads and quality control for constructed libraries were performed by Agilent Bioanalyzer High Sensitivity DNA kit and libraries were sequenced with a NextSeq 500 system (Illumina).


title: HiC macrophages siCTCF unstimulated rep C

city: Parkville

first: Hannah

middle: D

last: Coughlan

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

description: Library name: OV_siCTCF_Unst_C

data_processing:
The HiC libraries were processed as previously described with changes in parameters (doi: 10.1038/s41590-018-0234-8). Libraries were aligned to the mm39 genome with the diffHic package v1.38.0
The FixMateInformation command from the Picard suite v1.117 (https://broadinstitute.github.io/picard/) was applied to synchronize mate information for each read pair. Duplicates were marked with MarkDuplicates from Picard and sorted by name with samtools
Each BAM file was processed to identify alignments for each read to a specific MboI restriction fragment with the preparePairs function in diffHic. Duplicate reads and those with mapping quality scores below 10 were discarded. Read pairs were determined to be dangling ends and removed if the pairs of inward-facing reads or outward-facing reads on the same chromosome were separated by less than 1000 bp for inward-facing and outward-facing reads. Read pairs with fragment sizes above 1000 bp were removed. Biological replicates were summed with the mergePairs function.
HDF files of read pairs were converted to the Juicer format .hic with juicer tools v1.22.01.
Assembly: mm39
Supplementary files format and content: .hic file, a highly compressed binary file storing sparse contact matrices from multiple resolutions (20000,50000,100000,200000,1000000 bp) into a single file

source_name: bone marrow

growth_protocol: Bone marrow cells from the femur and tibia of mice were maintained in media containing 50 ng/ml M-CSF for 7 days to allow for macrophage differentiation.

extract_protocol:
Adherent cells were lifted using Accutase and pelleted. Pelleted cells were washed in PBS and treated with 1% v/v formaldehyde (1 ml per 1E6 cells) for 10 minutes at room temperature with rotation. This reaction was quenched by treated cells with 0.6 ml of 1M Tris HCL pH 7.5 for 5 minutes with rotation. Cells were spun and supernatant was discarded. Pelleted cells were flash frozen in dry ice/ ethanol and stored at -80C.
In situ HiC protocol was performed as in Rao et al. Cell (2014) (PMID: 25497547) with library preparation performed using the NEB library preparation kit (E7645), following the manufacturer's instructions.

treatment_protocol: Differentiated macrophages were transfected siRNA targeting Ctcf using Lipofectamine RNAiMax (thermofisher) following manufacter's protocol. One day later, cells were treated with PBS or 100 ng/ml LPS for 6 hours.

value: bone marrow

value: macrophages

value: Unstimulated and transfections with siRNA targeting Ctcf


title: S2_CD45_VEH

description: Library name: Sample 2

value: Frontal Cortex


title: HiC macrophages siNeg LPS stimulated rep C

description: Library name: OV_siNeg_LPS_C

value: LPS stimulated and transfections with scramble siRNA


title: HiC macrophages siCTCF LPS stimulated rep C

description: Library name: OV_siCTCF_LPS_C

value: LPS stimulated and transfections with siRNA targeting Ctcf


title: HiC macrophages siNeg unstimulated rep C

description: Library name: OV_siNeg_Unst_C

value: Unstimulated and transfections with scramble siRNA


title: HiC macrophages siCTCF LPS stimulated rep B

description: Library name: OV_siCTCF_LPS_B


title: HiC macrophages siCTCF LPS stimulated rep A

description: Library name: OV_siCTCF_LPS_A


title: HiC macrophages siCTCF unstimulated rep A

description: Library name: OV_siCTCF_Unst_A


title: HiC macrophages siCTCF unstimulated rep B

description: Library name: OV_siCTCF_Unst_B


title: HiC macrophages siNeg LPS stimulated rep B

description: Library name: OV_siNeg_LPS_B


title: HepG2_shSREBP2 #667_2


title: HepG2_shSREBP2 #667_1


title: HepG2_shSREBP2 #665_2


title: HiC macrophages siNeg LPS stimulated rep A

description: Library name: OV_siNeg_LPS_A


title: HiC macrophages siNeg unstimulated rep B

description: Library name: OV_siNeg_Unst_B


title: HiC macrophages siNeg unstimulated rep A

description: Library name: OV_siNeg_Unst_A


title: HepG2_shSREBP2 #665_1


title: HepG2_shSREBP2 #664_2


title: Ribo AML GC7 rep 3

city: Cincinnati

first: Courtney

last: Jones

state: OH

address: 3333 Burnet Ave MLC 7013

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Ribo_9

library_source: other

data_processing:
Ribo-Seq FASTQ files were processed using the nf-core/riboseq pipeline (version 1.2.0) executed with Nextflow on the Cincinnati Children’s Hospital research high performance LSF computing cluster using Singularity containers. Quality control was performed using FastQC version 0.12.1 and validated using fq version 0.12.0. Illumina small-RNA adapters were removed using Trim Galore! version 0.6.10 and Cutadapt version 4.9, with a Phred quality threshold of 20, maximum error rate of 0.1, minimum adapter overlap of 1 nucleotide, and minimum retained read length of 18 nucleotides. Ribosomal RNA reads were depleted using SortMeRNA version 4.3.7 in paired-read mode against the eight default nf-core Rfam and SILVA default ribosomal RNA reference databases. Remaining ribosome-protected fragments were aligned using STAR version 2.7.11b to the Illumina iGenomes UCSC hg38 human reference genome and corresponding gene annotation. The STAR genome index was generated with annotated splice junctions and an sjdbOverhang of 100. Alignment was performed in basic two-pass mode with end-to-end alignment, a minimum annotated splice-junction overhang of 1 nucleotide, and a maximum of 20 reported alignments per read.  Matched paired-end bulk RNA-sequencing libraries were aligned to the human GRCh38 reference genome using STAR version 2.4.0h in a two-pass, sample-specific alignment. During the first pass, splice-junction evidence was collected using a maximum intron length of 500 kb, maximum mate gap of 1 Mb, and a maximum of 20 reported alignments per read. The resulting splice-junction coordinates were used to construct a sample-specific STAR genome index, followed by a second alignment to produce coordinate-sorted BAM files. Alignments retained standard mapping, mismatch, alignment-score, and splice-strand attributes.
Assembly: hg38 human reference genome
Supplementary files format and content: FASTQ
Library strategy: Ribo-Seq

molecule: other

source_name: Hematopoietic Cells

growth_protocol: PDX cells were cultured in IMDM medium (Gibco, 12440061) supplemented with 20% heat inactivated fetal bovine serum (FBS; Corning, 35011CV), 100 U/mL penicillin-streptomycin (Gibco, 15140163), 10 ng/mL SCF (PeproTech, 300-07), 10 ng/mL Flt-3 ligand (PeproTech, 300-19), 10 ng/mL TPO (PeproTech, 300-18), 10 ng/mL IL-3 (PeproTech, 200-03), and 10 ng/mL IL-6 (PeproTech, 200-06).

extract_protocol:
Total RNA Extraction Using the Trizol Method 1) Thoroughly grind an appropriate amount of tissue in liquid nitrogen, transfer it to a 1.5 mL centrifuge tube, add 1 mL of Trizol, and mix thoroughly immediately. 2) Incubate the mixture at room temperature for 10 minutes to ensure complete lysis. 3) Add 200 μL of chloroform, shake vigorously to mix, and centrifuge at 12,000 rpm and 4C for 10 minutes. 4) Collect the upper aqueous phase, add an equal volume of phenol: chloroform (25:24), mix thoroughly, and centrifuge at 12,000 rpm and 4ÅãC for 10 minutes. 5) Collect the upper aqueous phase, add an equal volume of chloroform, mix thoroughly, and centrifuge at 12,000 rpm and 4ÅãC for 10 minutes. 6) Collect the upper aqueous phase, add an equal volume of isopropanol, incubate at -20ÅãC for 1 hour, and centrifuge at 12,000 rpm and 4ÅãC for 10 minutes. 7) Discard the supernatant, add 1 mL of 75% ethanol to wash the pellet, centrifuge at 8,000 rpm and 4ÅãC for 5 minutes, and discard the supernatant. 8) Repeat the previous step. 9) Briefly centrifuge, remove residual ethanol with a pipette, and vacuum-dry for 2–4 minutes. 10) Add 20–50 μL of RNase-free water, dissolve at room temperature for 10 minutes, mix, and briefly centrifuge. 11) Store at -80C.  For Ribosome Sequencing 1. Cell Fixation • Add harringtonine to the cell culture medium to a final concentration of 2 μg/ml and incubate at room temperature for 2 minutes. • Then, add cycloheximide to a final concentration of 100 μg/ml and incubate at room temperature for 1 minute. 2. Cell Washing • Remove culture medium and wash cells with PBS. 3. Cell Collection • Scrape the cells from the culture dish. • Collect the cells into a 1.5 mL Eppendorf tube. • Centrifuge at 500 g for 5 minutes at 4ÅãC. • Carefully discard the supernatant and collect the cell pellet. 4. Cell Lysis • Add cell lysis buffer to the cell sample. • Vortex to mix thoroughly. • Incubate on ice for 10 minutes. • Centrifuge at 17,000 g for 10 minutes at 4ÅãC. • Discard the pellet and collect the supernatant. 5. DNA and RNA Digestion • Take 400 μl of the cell supernatant. • Add 10 μl of RNase I and 6 μl of DNase I. • Incubate at room temperature for 45 minutes. 6. Ribosome Separation • Gently invert the MicroSpin S-400 Column to mix the resin and tap the walls of the tube to remove any bubbles. • Open both ends of the column to allow the liquid within the resin to naturally flow out. • Add 3 ml of 1Å~ Mammalian Polysome Buffer to the column and let it flow through by gravity. • Once the buffer has drained, place a 1.5 ml centrifuge tube under the column. • Centrifuge at 600 g for 4 minutes at room temperature. • Discard the flow-through liquid. • Place the column into a new 1.5 ml centrifuge tube. • Add the product from the previous step to the column, centrifuge again at 600 g for 2 minutes, and collect the flow-through. 7. RPF (Ribosome Protected Fragment) extraction • Add 700 μl of Lysis Reagent and incubate at room temperature for 8 minutes. • Add 140 μl of chloroform and mix thoroughly. • Incubate at room temperature for 5 minutes. • Centrifuge at 12,000 g for 15 minutes at 4ÅãC. • Transfer 350 μl of the supernatant to a new Eppendorf tube, add 525 μl of absolute ethanol, and mix well. • Load 700 μl of the sample onto a spin column and centrifuge at 10,000 rpm for 15 seconds at room temperature; discard the flow-through. • Repeat the above step. • Add 700 μl of Buffer RWT, centrifuge at 10,000 rpm for 15 seconds at room temperature, and discard the flow-through. • Add 500 μl of Buffer RPE, centrifuge at 10,000 rpm for 15 seconds at room temperature, and discard the flow-through. • Repeat the above step. • Transfer the spin column to a new 1.5 ml Eppendorf tube and add 30 μl of RNase-free water. 8. Removal of ribosomal RNA (rRNA) • Prepare a reaction for the removal of rRNA and perform PCR at 68°C for 10 minutes. Reagent Volume Ribo-Zero rRNA Reaction Buffer 4 μl Ribo-Zero Removal Solution 8 μl RNA sample（RPF） 28 μl Total 40 μl • Add the solution from the previous step to Magnetic Beads, and let it stand at room temperature for 10 minutes, followed by incubation at 50ÅãC for 5 minutes. • Purify the product from the previous step using Agencourt RNA Clean XP Beads. 9. 5’ phosphorylation reaction • Prepare the reaction system according to the table (not provided here). • Perform the reaction using PCR at 37°C for 30 minutes. Reagent Volume RNA 11 μl 10ÅBuffer 1.5 μl T4 Polynucleotide Kinase 1 μl ddH2O 1.5 μl total 15 ul
Library preparation 1) 3’ Adapter Ligation • Prepare the 3’ adapter ligation mixture. Reagent Volume Input RNA 6 μl 3ÅL SR Adaptor 1 μl 3ÅL Ligation Reaction Buffer (2X) 10 μl 3ÅL Ligation Enzyme Mix 3 μl Total 20 μl • Mix thoroughly and perform a brief centrifugation. • Incubate the reaction in a PCR machine at 25ÅãC for 1 hour. • Hold the reaction at 4ÅãC. 2) Reverse Transcription Primer Annealing • Add 1 μl of the SR RT primer specific for Illumina sequencing. • Add 4.5 μl of nuclease-free water. • Incubate in a PCR machine at 75ÅãC for 5 minutes, followed by 37ÅãC for 15 minutes, then 25ÅãC for 15 minutes. • Hold the reaction at 4ÅãC. 3) 5’ Adapter Ligation • Prepare the 5’ adapter ligation mixture. Reagent Volume Product from last step 25.5μl 5ÅL SR Adaptor 1 μl 5ÅL Ligation Reaction Buffer (10X) 1 μl 5ÅL Ligation Enzyme Mix 2.5 μl Total 30 μl • Mix thoroughly and perform a brief centrifugation. • Incubate the reaction in a PCR machine at 25C for 1 hour. • Hold the reaction at 4C. 4) Reverse Transcription Setup • Prepare the reverse transcription reaction mixture. Reagent Volume Adaptor Ligated RNA 30 μl First Strand Synthesis Reaction Buffer 8 μl Murine RNase Inhibitor 1 μl ProtoScript II Reverse Transcriptase 1 μl Total 40 μl • Incubate the reaction in a PCR machine at 50ÅãC for 1 hour to reverse transcribe the ligated RNA products into double-stranded cDNA. 5) PCR Reaction Setup: • Prepare the PCR reaction mixture as per your specific requirements or protocol. Reagent Volume LongAmp Taq 2X Master Mix 50 μl SR Primer for Illumina 2.5 μl Index (X) Primer 2.5 μl Nuclease free water 5 μl Product from last step 40 μl Total 100 μl • PCR (94C 15s，62C 30s，70C 5 min，4C hold) 6) Purification using PAGE Gel • Recover and purify DNA fragments of approximately 140 bp using a PAGE (Polyacrylamide Gel Electrophoresis) gel. • Dissolve the purified DNA fragments in 20 μl of EB (Elution Buffer) solution to complete the library construction. 7) DNA Quality and Concentration Analysis • Use the DNA 1000 Assay Kit (Agilent Technologies, Part No. 5067-1504) or the High Sensitivity DNA Assay Kit (Agilent Technologies, Part No. 5067- 4626) for analysis. • The DNA 1000 Assay Kit detects DNA fragment sizes ranging from 25 to 1000 base pairs, with concentration ranges from 0.1 to 50 ng/μL. • The High Sensitivity DNA Assay Kit allows for precise quantification of samples at picogram levels, often used as a quantification standard before sequencing, detecting fragment sizes from 50 to 7000 base pairs and concentration ranges from 5 to 500 pg/μL.

treatment_protocol: Cells were treated with 10uM DENSpm or 50uM GC7 for 24 hours.

value: Hematopoietic Cells

value: PDX Model

value: AML


title: Ribo AML GC7 rep 2

description: Library name: Ribo_8


title: S015_CD4_CXCR5hi_PD1hi

description: Library name: S015_CD4_CXCR5hi_PD1hi

value: tonsil

value: CD4+ CXCR5hi PD1hi


title: HepG2_shSREBP2 #664_1


title: Ribo AML GC7 rep 1

description: Library name: Ribo_7


title: HepG2_shEZH2_2


title: Ribo AML DENSpm rep 3

description: Library name: Ribo_6

value: DENSpm


title: HepG2_shEZH2_1


title: S014_CD4_CXCR5hi_PD1hi

description: Library name: S014_CD4_CXCR5hi_PD1hi


title: HepG2_shControl_2


title: Ribo AML DENSpm rep 1

description: Library name: Ribo_4


title: HepG2_shControl_1


title: Ribo AML vehicle rep 3

description: Library name: Ribo_3

value: Vehicle


title: N-9Gm

city: Mayaguez

first: Maribella

last: Domenech

state: PR

address: PO Box 9000

country: Puerto Rico

institute: Universidad de Puerto Rico

description: Library name: 31470-047.R1

data_processing:
All primary analysis is carried out using CLC Genomics Server 25.0. The workflow “QIAseq miRNA Quantification” of CLC Genomics Server with standard parameters is used to map the reads to miRBase version 22. In short, the reads are processed by (1) trimming of the common sequence, UMI and adapters, and (2) filtering of reads with length < 15 nt or length > 55 nt. They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated , (2) are from the same strand, and (3) have identical UMIs. Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton’s UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen).
All reads that don’t map to miRBase, neither with perfect matches nor as isomiRs (maximum 2 mismatches and/or alternative start/end position of 2 nt), are mapped to the human genome hg38 with ENSEMBL GRCh38 version 98 annotation. This is carried out using the “RNA-Seq Analysis” workflow of CLC Genomics Server with standard parameters.
Assembly: hg38 with ENSEMBL GRCh38 version 98 annotation.
Supplementary files format and content: microsoft excel comma separated values file containing CPM per sample

extract_protocol:
RNA was isolated from using the exoRNeasy Midi (QIAGEN) according to manufacturer’s instructions with an elution volume of 14 uL
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 10 ng total RNA was converted into miRNA NGS libraries. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (19 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation was quality controlled using capillary electrophoresis (Tape D1000). Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pool(s) were quantified using qPCR. The library pool(s) were then sequenced on a AVITI (Element Biosciences, San Diego, CA, USA) sequencing instrument according to the manufacturer instructions (1x76, 2x10). Raw data was de-multiplexed and FASTQ files for each sample were generated using Element Biosciences bases2fastq version 00.000.000.4.2.4.

value: mesenchymal stem cells

value: WT

tag: time

value: Day 9

value: Ground (mG)

tag: culture

value: Suspension


title: Ribo AML vehicle rep 1

description: Library name: Ribo_1


title: NC-9Gm

description: Library name: 31470-045.R1

value: bone marrow

value: COL


title: MV4;11, control, CUT&Tag

description: Library name: MV4;11_control_CT

data_processing:
All reads were mapped to the human genome (hg38), and then the non-primary alignment and PCR duplicates were removed from aligned data respectively using the Picard, Samtools and bedtools.
Bigwig files, heatmaps and averaged plotting of CUT&Tag signals were generated using Deeptools.
Profiles of CUT&Tag read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters.
Assembly: hg38
Supplementary files format and content: BW files
Library strategy: CUT&Tag

growth_protocol: MV4;11 cells were grown in RPMI1640 medium supplemented with 10% of FBS and 1% of antibiotics.

extract_protocol:
Cell pellets were collected for CUT&Tag. CUT&Tag was performed according to manufacturer’s instructions (CUTANA™ CUT&Tag Assays, EpiCypher).
N/A. By adding sequencing adapters at antibody-bound target sites, CUT&Tag can skip traditional library prep steps. The samples were subject to pair-end sequencing using an Illumina Nextseq.


title: BC-9Gm

description: Library name: 31470-044.R1


title: AC-9Gm

description: Library name: 31470-043.R1

source_name: adipose

value: adipose


title: MV4;11, H3K27me3, CUT&Tag

description: Library name: MV4;11_H3K27me3

tag: cut&run antibody

value: H3K27me3 (Millipore)


title: MV4;11, H3K27ac, CUT&Tag

description: Library name: MV4;11_H3K27ac

value: H3K27ac (abcam)


title: 8h UV post UVsample, Rpb1 NTD (ChIP) Replicate 3

city: Stockholm

first: Neus

last: Visa

address: Svante Arrhenius väg 20c

country: Sweden

institute: Stockholm University

description: Library name: INPUT_8hUV_Rep3

data_processing:
Samples were sequenced on NovaSeqXPlus (control-software 1.1.0.18335) with a 151nt(Read1)-19nt(Index1)-10nt(Index2)-151nt(Read2) setup using '10B' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
nf-core/ChIP-seq Workflow
Assembly: GRCh38
Supplementary files format and content: bigWig; output from nf-core pipeline

source_name: Cell line

growth_protocol: DMEM High Glucose, w/o puruvate, +10% Fetal Calf Serum + Penicillin and Streptomycin, Blasticidin HCl (4 μg/ml ) and Hygromycin (100 μg/mL). Cells were cultred at 37°C with 5% CO2.

extract_protocol:
Cells were plated and grown to ~90% confluency, collected using trypsinization and  crosslinked with 1 % PFA/PBS for 10 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.125 M for 5 minutes at room temperature. Cells were washed with cold PBS and lysed  in a buffer containing 1% SDS, 10mM EDTA, 50mM Tris-HCl (pH 8.0) and protease inhibitors. Chromatin was sonicated using a Bioruptor apparatus (Diagenode) at 4 °C (settings: 30 s “ON” / 30 s “OFF”; power: “High”; time: 20 min).
SMARTer ThruPLEX DNA-seq (ChIP)

treatment_protocol: To induce exogenous DIS3- HA expression cells were treated with 0.5ug/ml Doxycyline Hyclate for 48h. DNA damage was induced by irradiating cells with 20J/m2 UV-C,  samples were collected at different time points after UV treatment as indicated per sample.

value: U2OS Flp-In/T-REx

value: Human osteosarcoma

tag: treatment (uv-c_dose)

tag: treatment (_time_after_uv)

tag: chip-antbody


title: Ribo AML DENSpm rep 2

description: Library name: Ribo_5

tag: tissue

value: Hematopoietic Cells

tag: cell line

value: PDX Model

tag: cell type

value: AML


title: 3h UV post UVsample, Rpb1 NTD (ChIP) Replicate 3

description: Library name: INPUT_3hUV_Rep3


title: B29-9Gm

description: Library name: 31470-041.R1

tag: genotype

tag: treatment


title: kidney_scRNA-seq_CMO

city: Wuerzburg

first: Matthias

last: Becker

state: Bavaria

address: Am Hubland

department: Biochemistry and RNA-Biology

institute: University Wuerzburg

description:
Library name: kidney_scRNA-seq_CMO
10x Genomics

data_processing:
Bulk RNA-seq: Initial quality assessment was conducted using FastQC version 0.11.8 (Andrews). Adapter and read trimming were carried out with TrimGalore version 0.6.1 (Galore., 2015), utilizing Cutadapt version 2.3 (Martin, 2011). The trimmed reads were then mapped to the ENSEMBL mouse reference genome scRNA-seq:Raw sequencing data were processed using the cellRanger v6.0.0 (10x Genomics) workflow. Downstream quality control and analysis were carried out in R v4.1.0 using Seurat v4.0. Cells were filtered based on standard quality metrics: those with fewer than 200 detected genes or more than 10% mitochondrial gene content were excluded.
Assembly: Bulk RNA-seq: GRCm38.99 scRNA-seq: Mouse mm10
Supplementary files format and content: Bulk RNA-seq: xlsx files contain FPKM values for each sample
Supplementary files format and content: scRNA-seq: Tab-seperated values files and matrix files

source_name: kidney

extract_protocol:
Bulk RNA-seq: Total RNA was isolated from flash frozen kidney tissue using TRIzol reagent (Invitrogen/ Thermo Fisher Scientific). scRNA-seq: Pregnant female mice were euthanized on embryonic day 17.5 (E17.5) by CO₂ inhalation followed by cervical dislocation. After laparotomy, embryos were harvested, euthanized, and kidneys were dissected. To minimize stress-induced transcriptional artifacts, a cold dissociation protocol was applied using Bacillus licheniformis cold-active protease (CAP).
Bulk RNA-seq: Library preparation and total polyA RNA-sequencing (150 bp paired-end, average of 57.6 mio reads) was performed by Novogene Corporation Inc (Planegg/Martinsried, Germany)  as described by the company: After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.  scRNA-seq: Single-cell suspensions were processed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for cell multiplexing, according to the manufacturer’s instructions (10x Genomics, CG000390 Rev B). Cells from different mice were labeled with cell multiplexing oligonucleotides (CMOs) following the protocol (10x Genomics, CG000391) and loaded onto the Chromium Controller for Gel Beads-in-Emulsion (GEM) generation. Reverse transcription and barcoding were carried out within the GEMs. Aiming for a cell concentration of 1400 cells/μl, approximately 40,000 cells were loaded, resulting in a final recovery of ~24,000 cells. After cDNA amplification, separate libraries were prepared for gene expression and CMOs. Libraries were pooled and sequenced on an NovaSeq 6000 S2 flow cell (Illumina).

value: kidney

tag: developmental stage

value: Trim28f/f, Trim28delta/delta

tag: Sex

value: male


title: Pre UV sample, Rpb1 NTD  (ChIP) Replicate 3

description: Library name: INPUT_Pre_Rep3

value: none 20J/m2 20J/m2

value: Pre


title: A29-9Gm

description: Library name: 31470-040.R1

value: mesenchymal stem cells

value: WT

value: Day 9

value: Ground (mG)


title: 8h UV post UVsample, DIS3-HA (ChIP) Replicate 3

description: Library name: HA_8hUV_Rep3

value: HA ab9110 Abcam


title: 3h UV post UVsample, DIS3-HA (ChIP) Replicate 3

description: Library name: HA_3hUV_Rep3


title: kidney_scRNA-seq_Gex

description:
Library name: kidney_scRNA-seq_Gex
10x Genomics

library_source: transcriptomic single cell


title: N01-9Gm

description: Library name: 31470-039.R1

value: bone marrow


title: Bulk RNA_seq Cntrl_kidney_biol rep_3

description:
Library name: T2874_5
bulk


title: 8h UV post UVsample, Input, Replicate 2

description: Library name: INPUT_8hUV_Rep2


title: 3h UV post UVsample, Input,  Replicate 2

description: Library name: INPUT_3hUV_Rep2


title: Bulk RNA_seq KO_kidney_biol rep_3

description:
Library name: T2874_4
bulk


title: Pre UV sample, Input, Replicate 2

description: Library name: INPUT_Pre_Rep2


title: A01-9Gm

description: Library name: 31470-037.R1

value: adipose


title: 8h UV post UVsample, Rpb1 NTD (ChIP) Replicate 2

description: Library name: NTD_8hUV_Rep2

value: U2OS Flp-In/T-REx

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958  Cell Signaling


title: 3h UV post UVsample, Rpb1 NTD (ChIP) Replicate 2

description: Library name: NTD_3hUV_Rep2

value: Human osteosarcoma


title: Pre UV sample, Rpb1 NTD  (ChIP) Replicate 2

description: Library name: NTD_Pre_Rep2


title: N-6Gm

description: Library name: 31470-036.R1

value: Day 6

value: Suspension


title: Bulk RNA_seq KO_kidney_biol rep_2

description:
Library name: T2932_4
bulk

value: kidney

value: female


title: 8h UV post UVsample, Input, Replicate 1

description: Library name: INPUT_8hUV_Rep1


title: B-6Gm

description: Library name: 31470-035.R1


title: 3h UV post UVsample, Input,  Replicate 1

description: Library name: INPUT_3hUV_Rep1


title: A-6Gm

description: Library name: 31470-034.R1


title: Bulk RNA_seq Cntrl_kidney_biol rep_1

description:
Library name: T2932_3
bulk

value: male


title: Pre UV sample, Input, Replicate 1

description: Library name: INPUT_Pre_Rep1


title: Bulk RNA_seq KO_kidney_biol rep_1

description:
Library name: T2932_2
bulk


title: 3h UV post UVsample, Rpb1 NTD (ChIP) Replicate 1

description: Library name: NTD_3hUV_Rep1


title: NC-6Gm

description: Library name: 31470-033.R1

value: COL


title: Pre UV sample, Rpb1 NTD  (ChIP) Replicate 1

description: Library name: NTD_Pre_Rep1

value: Pre


title: BC-6Gm

description: Library name: 31470-032.R1

value: mesenchymal stem cells


title: 3h UV post UVsample, DIS3-HA (ChIP) Replicate 1

description: Library name: HA_3hUV_Rep1


title: Pre UV sample, DIS3-HA (ChIP) Replicate 1

description: Library name: HA_Pre_Rep1


title: Tissue_Reparative_R3

city: Boston

first: Ruaidhrí

last: Jackson

address: New Research Building, 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard Medical School

description:
Library name: TRA00226646_Tissue_Reparative
Bulk_M2_3

data_processing:
Demultiplexed FASTQ files were mapped to the reference transcriptome using Salmon.
Quant.sf files were read into R using tximport.
Differential gene expression analysis was performed using DESeq2.
Log2(normalized counts per million + 1) gene expression data were generated using EdgeR.
Assembly: GRCm39 (Gencode M28)
Supplementary files format and content: Excel file containing log2(normalized counts per million + 1) of gene expression with samples as columns (log_cpm_pseudocounts.xlsx).
Supplementary files format and content: Salmon quant.sf pseudocount files for each sample.

source_name: Bone Marrow

growth_protocol: Bone marrow was extracted from male C57BL/6J mice aged 8-10 weeks. Bone marrow was flushed using PBS, filtered through a 70µm cell strainer, and plated in 150mm plastic tissue culture plates. Cells were cultured for 6 days in complete Dulbecco's Modified Eagle Medium supplemented with 4.5g/L D-Glucose, 110mg/L sodium pyruvate, 10% fetal bovine serum, 1% Penicillin-Streptomycin, and 50ng/mL macrophage colony-stimulating factor (MCSF) to generate BMDMs.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions. PolyA RNA selection was performed using the Poly(A)Purist™ MAG Kit (Invitrogen) according to the manufacturer’s instructions.
Total-RNA samples were quantified using an Agilent 4200 TapeStation instrument, with a corresponding Agilent TapeStation RNA assay. RIN (RNA Integrity Number) scores and concentrations were taken into account for qualifying samples to proceed. Samples were normalized to 200ng of input in 50uL (4ng/uL), and the mRNA was captured using oligo-dT beads as part of the KAPA mRNA HyperPrep workflow. cDNA synthesis, adapter ligation, and amplification were conducted subsequently as part of the same workflow. Following amplification, residual primers were eluted away using KAPA Pure Beads in a 0.63x SPRI-based cleanup. The resulting purified libraries were run on an Agilent 4200 Tapestation instrument, with a corresponding Agilent High Sensitivity D1000 ScreenTape assay to visualize the libraries and check that the size and concentrations of the libraries matched the expected product. qPCR with the KAPA Library Quantification kit, which uses primers complementary to the sequencing flowcell oligos, was run to confirm the functional concentration. Molarity values obtained from this assay were used to normalize all samples in equimolar ratio for one final pool.

treatment_protocol: BMDMs were treated with 100ng/mL lipopolysaccharide (LPS) and 20ng/mL IFNγ for 24 hours, to generate inflammatory macrophages, or 20ng/mL IL-4 and 20ng/mL IL-13 for 24 hours, to generate tissue reparative macrophages. Steady state macrophages received no additional treatment.

value: Bone Marrow

value: Bone Marrow Derived Macrophages


title: AC-6Gm

description: Library name: 31470-031.R1

value: WT

value: Ground (mG)


title: Tissue_Reparative_R2

description:
Library name: TRA00226645_Tissue_Reparative
Bulk_M2_2


title: WEHI-231, H3K27ac, CUT&Tag

description: Library name: WEHI-231_H3K27ac

data_processing:
All reads were mapped to the mouse genome (mm10), and then the non-primary alignment and PCR duplicates were removed from aligned data respectively using the Picard, Samtools and bedtools.
Bigwig files, heatmaps and averaged plotting of CUT&Tag signals were generated using Deeptools.
Profiles of CUT&Tag read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters.
Assembly: mm10
Supplementary files format and content: BW files
Library strategy: CUT&Tag

growth_protocol: WEHI-231 cells were grown in DMEM medium supplemented with 10% of FBS, 1% of antibiotics, and 55uM of 2-mercaptoethanol.


title: N29-6Gm

description: Library name: 31470-030.R1

value: bone marrow


title: WEHI-231, H3K27me3, CUT&Tag

description: Library name: WEHI-231_H3K27me3


title: Tissue_Reparative_R1

description:
Library name: TRA00226644_Tissue_Reparative
Bulk_M2_1


title: WEHI-231, Ezh2, CUT&Tag

description: Library name: WEHI-231_Ezh2


title: B29-6Gm

description: Library name: 31470-029.R1


title: WEHI-231, control, CUT&Tag

description: Library name: WEHI-231_control


title: Inflammatory_R4

description:
Library name: TRA00226643_Inflammatory
Bulk_M1_4

value: LPS + IFNγ


title: S48_CD4_CXCR5hi_PD1hi_H3K27Ac

description: Library name: S48

data_processing:
Sequencing reads were aligned to hg38 using Bowtie2.
CUT&RUN peaks were identified using macs2
Assembly: hg38
Supplementary files format and content: broadPeak.bed (macs2 format)
Library strategy: CUT&Run

extract_protocol:
Cells were FACS-sorted, stored on ice, and prompty processed for CUT&RUN
CUT&RUN was performed with 25-50 thousand cells as described by Skene et al, 2018 (PMID: 29651053). Briefly, nuclei were immobilized and permeabilized with digitonin on ConA beads, incubated with specific antibodies against H3K4me1, H3K4me3 or H3K27ac.  pA-MNase was used to cleave and release antibody-bound chromatin. Released chromatin DNA was purified and indexed libraries were prepared for sequencing.

value: tonsil

tag: histone mark


title: S47_CD4_CXCR5hi_PD1hi_H3K27Ac

description: Library name: S47


title: S46_CD4_CXCR5hi_PD1hi_H3K27Ac

description: Library name: S46


title: Inflammatory_R3

description:
Library name: TRA00226642_Inflammatory
Bulk_M1_3


title: N01-6Gm

description: Library name: 31470-027.R1


title: S45_CD4_CXCR5hi_PD1hi_H3K27Ac

description: Library name: S45


title: Inflammatory_R2

description:
Library name: TRA00226641_Inflammatory
Bulk_M1_2


title: S44_CD4_CXCR5pos_PD1int_H3K27Ac

description: Library name: S44


title: B01-6Gm

description: Library name: 31470-026.R1


title: S43_CD4_CXCR5pos_PD1int_H3K27Ac

description: Library name: S43


title: Inflammatory_R1

description:
Library name: TRA00226640_Inflammatory
Bulk_M1_1


title: S42_CD4_CXCR5pos_PD1int_H3K27Ac

description: Library name: S42


title: A01-6Gm

description: Library name: 31470-025.R1

value: adipose


title: S41_CD4_CXCR5pos_PD1int_H3K27Ac

description: Library name: S41


title: S40_CD4_CXCR5hi_PD1hi_H3K4me3

description: Library name: S40


title: Control_R4

description:
Library name: TRA00226639_Control
Bulk_NT_4


title: N-9m

description: Library name: 31470-024.R1

value: Day 9

value: Microgravity (m)


title: S39_CD4_CXCR5hi_PD1hi_H3K4me3

description: Library name: S39


title: Control_R3

description:
Library name: TRA00226638_Control
Bulk_NT_3


title: S38_CD4_CXCR5hi_PD1hi_H3K4me3

description: Library name: S38


title: S37_CD4_CXCR5hi_PD1hi_H3K4me3

description: Library name: S37


title: B-9m

description: Library name: 31470-023.R1

value: Suspension


title: Control_R2

description:
Library name: TRA00226637_Control
Bulk_NT_2


title: S36_CD4_CXCR5pos_PD1int_H3K4me3

description: Library name: S36


title: A-9m

description: Library name: 31470-022.R1


title: S35_CD4_CXCR5pos_PD1int_H3K4me3

description: Library name: S35


title: Control_R1

description:
Library name: TRA00226636_Control
Bulk_NT_1


title: NC-9m

description: Library name: 31470-021.R1


title: S34_CD4_CXCR5pos_PD1int_H3K4me3

description: Library name: S34


title: S33_CD4_CXCR5pos_PD1int_H3K4me3

description: Library name: S33


city: Seodaemun-gu,

first: Ga YOung

last: Heo

state: seoul

address: 50-1 Yonsei-ro, Sinchon-dong,

country: South Korea

institute: yonsei university

description:
Library name: Sample_12
Adenine-induced CKD with colchicine treatment mouse kidney tissue, biological replicate 4

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform to generate 101 bp paired-end reads.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39(NCBI) whole genome using STAR
Calculation mapped reads using salmon
TMM + CPM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files contain Read count values for each sample.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

value: kidney

value: Colchicine 0.3mg/kg/day IP, 5% adenine diet

tag: batch


title: A29-6Gm

description: Library name: 31470-028.R1

value: Day 6


title: S32_CD4_CXCR5hi_PD1hi_H3K4me1

description: Library name: S32


title: BC-9m

description: Library name: 31470-020.R1

value: COL


description:
Library name: Sample_11
Adenine-induced CKD with colchicine treatment mouse kidney tissue, biological replicate 3

value: Colchicine 0.3mg/kg/day IP, 4% adenine diet


title: S30_CD4_CXCR5hi_PD1hi_H3K4me1

description: Library name: S30


title: S31_CD4_CXCR5hi_PD1hi_H3K4me1

description: Library name: S31


title: S29_CD4_CXCR5hi_PD1hi_H3K4me1

description: Library name: S29


title: S28_CD4_CXCR5pos_PD1int_H3K4me1

description: Library name: S28


description:
Library name: Sample_10
Adenine-induced CKD with colchicine treatment mouse kidney tissue, biological replicate 2

value: Colchicine 0.3mg/kg/day IP, 3% adenine diet


title: N29-9m

description: Library name: 31470-018.R1

value: mesenchymal stem cells


title: S27_CD4_CXCR5pos_PD1int_H3K4me1

description: Library name: S27


description:
Library name: Sample_9
Adenine-induced CKD with colchicine treatment mouse kidney tissue, biological replicate 1

value: Colchicine 0.3mg/kg/day IP, 2% adenine diet


title: S26_CD4_CXCR5pos_PD1int_H3K4me1

description: Library name: S26


title: B29-9m

description: Library name: 31470-017.R1

value: WT


title: S25_CD4_CXCR5pos_PD1int_H3K4me1

description: Library name: S25


title: S24_CD4_CXCR5pos_PD1neg_H3K27Ac

description: Library name: S24


title: Adenine-induced CKD kidney tissue replicate 4

description:
Library name: Sample_8
Adenine-induced CKD mouse kidney tissue, biological replicate 4

value: Saline IP, 2% adenine diet


title: A29-9m

description: Library name: 31470-016.R1


title: S23_CD4_CXCR5pos_PD1neg_H3K27Ac

description: Library name: S23


title: Adenine-induced CKD kidney tissue replicate 3

description:
Library name: Sample_7
Adenine-induced CKD mouse kidney tissue, biological replicate 3


title: N01-9m

description: Library name: 31470-015.R1

value: bone marrow


title: S21_CD4_CXCR5pos_PD1neg_H3K27Ac

description: Library name: S21


title: S22_CD4_CXCR5pos_PD1neg_H3K27Ac

description: Library name: S22


title: Adenine-induced CKD kidney tissue replicate 2

description:
Library name: Sample_6
Adenine-induced CKD mouse kidney tissue, biological replicate 2


title: Ribo AML vehicle rep 2

description: Library name: Ribo_2

value: Hematopoietic Cells

value: PDX Model

value: AML

value: Vehicle


title: B-9Gm

description: Library name: 31470-046.R1

value: Day 9

value: Ground (mG)


title: Steady_State_replicate_3

description: Long read direct RNA-sequencing

data_processing:
Basecalling was performed using Bream v7.0.9 and Guppy v6.0.7.
Passing individual fastq files from the same sample were merged to generate a single fastq file per sample.
FASTQ files were aligned to the reference transcriptome using minimap2 v2.24 with the parameters “-ax splice -uf -k14”.
Salmon pseudocount files were generated using the parameters “quant –ont -lU -a --numBootstraps 30" with Salmon v1.10.2.
Assembly: GRCh38.p13 (Gencode 43)
Supplementary files format and content: Salmon quant.sf pseudocount files for each sample.

source_name: Peripheral Blood

growth_protocol: Anonymous peripheral blood samples were collected from the Mississippi Valley Regional Blood Center as waste cellular products. Human CD14+ cells were isolated using MojoSort™ Human CD14 Selection Kit (Biolegend #480026). To generate human monocyte-derived macrophages (MDMs), purified monocytes were stimulated with 50 ng/mL M-CSF (Biolegend #574806) and 50 ng/mL GM-CSF (Biolegend #572904) in RPMI 1640 Medium containing 10% fetal bovine serum and Penicillin-Streptomycin for 6 days.

extract_protocol:
Treated cells were washed with PBS and lysed with 1ml of TRIzol (Invitrogen #15596026) to extract RNA according to the manufacturer’s instructions. PolyA RNA selection was performed using the Poly(A)Purist™ MAG Kit (Invitrogen) according to the manufacturer’s instructions.
Libraries were prepared using the Direct RNA Sequencing kit SQK-RNA002 (Oxford Nanopore Technologies) according to the manufacturer’s instructions. 50ng of polyA selected RNA was used as input for each sample.

treatment_protocol: On day 6, MDMs were treated with Accutase (Biolegend #423201) and re-plated 5 million per 10 cm dish and rested overnight before treatment with PBS, or different cytokine combinations including 100 ng/ml IFN-γ (Biolegend #570204) plus 100 ng/ml LPS (InvivoGen #tlrl-eblps) for 24 hours. Treated cells were washed with PBS and lysed with 1ml of TRIzol (Invitrogen #15596026) before total RNA extraction.

value: Peripheral Blood

value: Monocyte Derived Macrophages


title: N29-9Gm

description: Library name: 31470-042.R1


title: B01-9m

description: Library name: 31470-014.R1

value: Microgravity (m)


title: S20_CD4_naive_H3K27Ac

description: Library name: S20

value: tonsil


title: Adenine-induced CKD kidney tissue replicate 1

description:
Library name: Sample_5
Adenine-induced CKD mouse kidney tissue, biological replicate 1

value: kidney


title: Inflammatory_replicate_3

description: Long read direct RNA-sequencing

value: LPS + IFNγ


title: A01-9m

description: Library name: 31470-013.R1

value: adipose

value: mesenchymal stem cells


title: S19_CD4_naive_H3K27Ac

description: Library name: S19


title: Control kidney tissue replicate 4

description:
Library name: Sample_4
Control group mouse kidney tissue, biological replicate 4

value: Saline IP, Normal diet


title: Steady_State_replicate_2

description: Long read direct RNA-sequencing


title: Pre UV sample, DIS3-HA (ChIP) Replicate 3

description: Library name: HA_Pre_Rep3

value: U2OS Flp-In/T-REx

value: Human osteosarcoma

value: Pre

value: HA ab9110 Abcam


title: N-6m

description: Library name: 31470-012.R1

value: bone marrow

value: WT

value: Day 6

value: Suspension


title: S18_CD4_naive_H3K27Ac

description: Library name: S18


title: B01-9Gm

description: Library name: 31470-038.R1

value: Day 9

value: Ground (mG)


title: Control kidney tissue replicate 3

description:
Library name: Sample_3
Control group mouse kidney tissue, biological replicate 3


title: Inflammatory_replicate_2

description: Long read direct RNA-sequencing

value: Peripheral Blood

value: Monocyte Derived Macrophages


title: Bulk RNA_seq Cntrl_kidney_biol rep_2

description:
Library name: T2932_6
bulk

value: kidney

value: female


title: B-6m

description: Library name: 31470-011.R1

value: Microgravity (m)


title: S17_CD4_naive_H3K27Ac

description: Library name: S17

value: tonsil


title: A-6m

description: Library name: 31470-010.R1

value: adipose

value: mesenchymal stem cells


title: Control kidney tissue replicate 2

description:
Library name: Sample_2
Control group mouse kidney tissue, biological replicate 2

value: Saline IP, Normal diet


title: S16_CD4_CXCR5pos_PD1neg_H3K4me3

description: Library name: S16


title: Steady_State_replicate_1

description: Long read direct RNA-sequencing


title: Control kidney tissue replicate 1

description:
Library name: Sample_1
Control group mouse kidney tissue, biological replicate 1


title: Inflammatory_replicate_1

description: Long read direct RNA-sequencing

value: LPS + IFNγ


title: NC-6m

description: Library name: 31470-009.R1

value: COL


title: S15_CD4_CXCR5pos_PD1neg_H3K4me3

description: Library name: S15


title: ovarian cells, 100nm PS-MPs (1 mg per 100 µL per mouse), 35d

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

description: Library name: sample2

data_processing:
Raw sequencing reads of the cDNA library were processed through the BD Rhapsody Sequence Analysis Pipeline Version 2.0. Reads were aligned to mouse genome assembly GRCm39. For downstream analysis, Matrix of UMI counts for each gene per cell among all the output files was used. We utilized Seurat for clustering analysis and data visualization. Gene expression matrices were processed into Seurat objects. Cells containing over 25% mitochondrial UMI, fewer than 500 UMI or less than 200 genes were filtered out. Following log-normalization based on total UMI counts, principal component analysis (PCA) was conducted on the top 2,000 highly variable features after data scaling. Clustering was performed at a resolution of 0.6, followed by Uniform Manifold Approximation and Projection (UMAP) visualization. Differentially expressed genes (DEGs) and cluster markers were identified using Seurat function 'FindAllMarkers' with the Wilcoxon Test under (logFC threshold 0.25, adjusted p-value <0.05, minimum detection fraction 0.25). Cell type annotation was performed using R package SingleR (v1.4.1). Pseudotime trajectories were constructed with Monocle2 employing DDR-Tree reduction method, maintaining default analysis parameters. To assess cell-to-cell interactions between different ovarian cell types, we used CellChat (v2.1.2) to define these ligand-receptor pairs across cell types with prior ligand-receptor interaction database CellChatDB.
Assembly: Ensembl 108
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mouse ovary

extract_protocol:
Ovary samples from different mice in control and 0.1-H PS-MP-treated group (n = 16) were collected for the scRNA-seq assay. After removing fat and other adherent tissues using a dissection microscope, single-cell suspensions were prepared through enzymatic digestion and filtered with 40 μm cell strainer.
Cell viability (>85%) and concentration were quantified via BD Rhapsody™ Scanner (BD Biosciences). The BD Rhapsody™ Single-Cell Analysis System was employed for microbeads-captured single-cell library construction, involving microfluidic partitioning of individual cells, mRNA capture using magnetic beads, and subsequent reverse transcription. The resulting cDNA was amplified using BD Rhapsody cDNA Kit (BD Biosciences, 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, 633801) to generate the final cDNA library, which were ultimately sequenced on Illumina Novaseq platform with the PE150 mode.

treatment_protocol: Post-weaning (three-week-old) female ICR mice were randomly assigned to 5 groups (n >15 per group): Control (ddH2O), 0.1 µm PS-MPs low-dose (0.1-L; 0.1 mg per 100 µL per mouse), and 0.1 µm PS-MPs high-dose (0.1-H, 1 mg per 100 µL per mouse), 5 µm PS-MPs low-dose (5-L, 0.1 mg per 100 µL per mouse), and 5 µm PS-MPs high-dose (5-H, 1 mg per 100 µL per mouse). Mice received daily oral gavage administrations for 35 days. Terminal sacrifices were performed 24 h post-final administration, with subsequent collection of organs for scRNA-seq.

value: mouse ovary

tag: age

value: pubertal PS-MPs exposure


title: BC-6m

description: Library name: 31470-008.R1

value: bone marrow

value: WT

value: Day 6


title: lcat OE-3

city: Jinan

first: Yuanyuan

last: Fu

address: No. 44, West Wenhua Road

institute: Shandong University

description:
Library name: Lcat_3
Column name in gene_expression.csv: fpkm_Lcat_3, tpm_Lcat_3, read_count_Lcat_3

data_processing:
Data Filtering: The raw data obtained from sequencing were filtered using SOAPnuke to remove: 1. Reads containing adapters (adapter contamination); 2. Reads with an unknown base 'N' content greater than 0.1%; 3. Low-quality reads (reads with a percentage of bases with a quality value less than 15 exceeding 20% of the total bases in the read). The filtered data, referred to as clean data, were subsequently analyzed, visualized, and mined using Online Multi-Omics Data Mining System.
Reference Genome Alignment: HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) is a software used for aligning RNA-seq reads to a reference genome. Compared to other software, HISAT has advantages such as fast speed, high sensitivity and accuracy, and low memory consumption. HISAT utilizes two types of indexing: global genome indexing and local genome indexing, based on Burrows-Wheeler transform and Ferragina-Manzini (FM) index. For detailed alignment schematic, refer to the HISAT alignment schematic. Genome alignment result statistics. Firstly, HISAT anchors partial sequences of each read to the genome using global FM indexing; then, it utilizes local indexing of these alignment positions to align the remaining sequences of each read to extend the alignment region.
Differential Gene Analysis: Clean data was aligned to the reference gene set using Bowtie2 (v2.3.4.3). Gene expression quantification was performed using RSEM (v1.3.1) software, and gene expression clustering heatmaps across different samples were generated using pheatmap (v1.0.8). DESeq2 (v1.4.5) (or DEGseq or PoissonDis) was employed for differential gene detection, with criteria set as Q value≤ 0.05 or FDR ≤ 0.001.
KEGG and GO Enrichment Analysis: To further explore gene functions related to phenotypic changes, we conducted GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis on differential genes using the hypergeometric test implemented in Phyper, with a threshold of Q value ≤ 0.05. Genes meeting this criterion were considered significantly enriched in the candidate gene set.
Variant Detection: Clean data was aligned to the reference genome using HISTA2 (v2.1.0) software. Subsequently, gene fusion detection was performed using Ericscript (v0.5.5), and alternative splicing and differential alternative splicing were detected using rMATS (V3.2.5).
Assembly: Danio_rerio_7955.NCBI.GCF_000002035.6_GRCz11.v2201
Supplementary files format and content: csv files include FPKM, TPM and read counts for each sample

organism: Danio rerio

extract_protocol:
using RNeasy Micro kit (Qiagen, 217084)
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. Theenriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reversetranscription using random N6 primers to synthesize cDNA double strands. The synthesized doublestrandedDNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' endforming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3'end. The ligation products were PCR amplified using specific primers. The PCR products weredenatured to single strands, and then single-stranded circular DNA libraries were generated using abridged primer. The constructed libraries were quality-checked and sequenced after passing thequality control.

value: liver

value: hepatocytes

value: epithelial cells

value: lcat OE


title: S14_CD4_CXCR5pos_PD1neg_H3K4me3

description: Library name: S14


title: ovarian cells, ddH2O, 35d

description: Library name: sample1

value: female


title: 8h UV post UVsample, Rpb1 NTD (ChIP) Replicate 1

description: Library name: NTD_8hUV_Rep1

value: U2OS Flp-In/T-REx

value: Human osteosarcoma

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958  Cell Signaling


title: AC-6m

description: Library name: 31470-007.R1

value: adipose

value: mesenchymal stem cells

value: Microgravity (m)


title: lcat OE-2

description:
Library name: Lcat_2
Column name in gene_expression.csv: fpkm_Lcat_2, tpm_Lcat_2, read_count_Lcat_2


title: S13_CD4_CXCR5pos_PD1neg_H3K4me3

description: Library name: S13

value: tonsil


title: Granulosa cells,PS-MPs treatment, ATAC-seq, biol rep 2

description: Library name: sample4

data_processing:
In ATAC-seq analysis, quality control, genome alignment, peak calling, differential peak analysis, and subsequent functional analyses are crucial steps. First, the quality control step removes low-quality reads, adapter sequences, and short fragments to ensure the accuracy and reliability of the data, resulting in high-quality clean data. Genome alignment is performed using Bowtie2 (v2.5.0) to map short reads to the reference genome and determine the exact positions of each read. Next, peak calling is done using MACS2 (v2.2.9.1) to identify open chromatin regions, providing data support for downstream analyses. The IDR (v2.0.3) method is used to extract highly consistent peak regions from multiple biological replicates, ensuring the reliability of the results. For differential peak analysis, DiffBind (v3.8.4) is employed to detect differential binding regions under different experimental conditions. Motif analysis is performed using HOMER (v4.11) to scan the sequences of the peak regions and identify shared motif regions. Footprint analysis of transcription factor binding sites is carried out using TOBIAS (v0.16.1), which helps reveal the binding states of transcription factors. Finally, HMMRATAC (v1.2.10) is used for nucleosome positioning analysis, shedding light on the organization of nucleosomes and their relationship to gene regulation.
Assembly: Ensenbl_110
Supplementary files format and content: bigwig, narrowPick

source_name: mouse ovarian granulosa cells

growth_protocol: The isolated GCs were (passages 0-5) cultured in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F-12) (Gibco, USA) supplemented with 10% fetal bovine serum (FBS), 100 IU/mL penicillin-streptomycin, 10 ng/mL basic fibroblast growth factor (bFGF), 1 × ITS Liquid Media Supplement, 0.2 ng/mL Recombinant Human FSH alpha/beta Protein and 500 ng/mL Testosterone at 37°C with 5% CO2.

extract_protocol:
Cells were collected and counted at room temperature using the Countstar Rigel S2(Shanghai Ruiyu,FL20447,CHINA). The requisite number of cells for the experiment was lysed for 5 minutes to extract the nuclei.
The nuclei were then suspended in a transposition reaction system containing Tn5 transposase. This was followed by incubation and DNA purification. The resulting product was subjected to polymerase chain reaction (PCR) amplification with the introduction of specific indexes. The PCR amplification conditions were as follows: incubation at 72° C for 3 minutes, pre-denaturation at 98 ° C for 1 minute, denaturation at 98 ° C for 10 seconds, annealing at 60° C for 25 seconds, and extension at 72° C for 25 seconds, for a total of 13 to 15 cycles, with a final extension at 72° C for 5 minutes. Library fragments of approximately 200-700 bp were obtained through bead selection. The concentration of the library was measured using Qubit(Thermo， Qubit3.0， USA) and the integrity of the fragments was assessed using a Bioanalyzer 2100(Agilent, CA, USA)

treatment_protocol: GCs (2 × 104 cells/ 0.15 mL/well) were seeded in 96-well plates, adhered for 12 h, then treated with sonicated PS-MPs (100 nm; 0,750μg/mL) for 24h.

value: mouse ovarian granulosa cells

value: 100nm PS-MPs, 750 μg/mL,24h


title: 8h UV post UVsample, DIS3-HA (ChIP) Replicate 1

description: Library name: HA_8hUV_Rep1

value: HA ab9110 Abcam


title: lcat OE-1

description:
Library name: Lcat_1
Column name in gene_expression.csv: fpkm_Lcat_1, tpm_Lcat_1, read_count_Lcat_1


title: Tissue_Reparative_R4

description:
Library name: TRA00226647_Tissue_Reparative
Bulk_M2_4

value: Bone Marrow

value: Bone Marrow Derived Macrophages


title: N29-6m

description: Library name: 31470-006.R1

value: bone marrow

value: WT

value: Day 6


title: S12_CD4_naive_H3K4me3

description: Library name: S12

source_name: tonsil


title: Granulosa cells,PS-MPs treatment, ATAC-seq, biol rep 1

description: Library name: sample3


title: CTL-3

description:
Library name: CTL_3
Column name in gene_expression.csv: fpkm_CTL_3, tpm_CTL_3, read_count_CTL_3

value: liver

value: hepatocytes

value: epithelial cells

value: CTL


title: B29-6m

description: Library name: 31470-005.R1


title: S11_CD4_naive_H3K4me3

description: Library name: S11


title: WEHI-231, Srebp2, CUT&Tag

description: Library name: WEHI-231_Srebp2


title: Granulosa cells,Control, ATAC-seq, biol rep 2

description: Library name: sample2


title: CTL-2

description:
Library name: CTL_2
Column name in gene_expression.csv: fpkm_CTL_2, tpm_CTL_2, read_count_CTL_2


title: CTL-1

description:
Library name: CTL_1
Column name in gene_expression.csv: fpkm_CTL_1, tpm_CTL_1, read_count_CTL_1


title: A29-6m

description: Library name: 31470-004.R1


title: Granulosa cells,Control, ATAC-seq, biol rep 1

description: Library name: sample1


title: S10_CD4_naive_H3K4me3

description: Library name: S10


title: S09_CD4_naive_H3K4me3

description: Library name: S09


title: N01-6m

description: Library name: 31470-003.R1


title: Granulosa cells,PS-MPs treatment,biol rep 3

description: Library name: Sample6

data_processing:
1_Filtering of Clean Reads
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). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9), including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
2_Alignment with Reference Genome
We aligned reads of all samples to the GRCm39 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. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
3_Quantification of Gene Abundance
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.
Assembly: Ensenbl_110
Supplementary files format and content: gene_id: unique gene identifier
Supplementary files format and content: chr: chromosome name
Supplementary files format and content: start: starting point of transcripts or genes on a chromosomes.
Supplementary files format and content: end: trmination site of transcripts or genes on chromosomes
Supplementary files format and content: strand: sense strand“+” or antisense strand“-”
Supplementary files format and content: gene_name: abbreviations or short forms of gene names
Supplementary files format and content: EntrezID: entrez gene ID, which refers to the NCBI gene ID.
Supplementary files format and content: transcript_id: transcript ID, due to alternative splicing, a single gene can be transcribed and spliced to generate multiple transcripts.
Supplementary files format and content: GO: Gene Ontology annotation
Supplementary files format and content: KEGG: Kyoto Encyclopedia of Genes and Genomes pathway name, used to indicate a specific biological pathway
Supplementary files format and content: KO_ENTRY: indicating similar results or functions across all species.
Supplementary files format and content: EC: Enzyme number
Supplementary files format and content: TF_Family: annotation of transcription factor families,“NA” means no information available.
Supplementary files format and content: Description: specific description of transcripts or genes
Supplementary files format and content: trans_type: types of transcripts corresponding to genes
Supplementary files format and content: DO: DO comment, human only
Supplementary files format and content: Reactome: reactome annotations, limited to a few species such as humans, mice, and rats
Supplementary files format and content: FPKM.A: gene expression level (FPKM value) of sample A
Supplementary files format and content: count.A: reads count of gene A in sample A

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.
After total RNA was extracted, 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.


title: Tissue_Reparative_replicate_3

data_processing:
Basecalling was performed using Bream v7.0.9 and Guppy v6.0.7.
Passing individual fastq files from the same sample were merged to generate a single fastq file per sample.
FASTQ files were aligned to the reference transcriptome using minimap2 v2.24 with the parameters “-ax splice -uf -k14”.
Salmon pseudocount files were generated using the parameters “quant –ont -lU -a --numBootstraps 30" with Salmon v1.10.2.
Log2(normalized counts per million + 1) summary gene quantification data was produced using edgeR v4.2.0.
Assembly: GRCm39 (Gencode M28)
Supplementary files format and content: Excel file containing log2(normalized counts per million + 1) of gene expression with samples as columns (LCPM_expression_estimate_prior_count_1.xlsx).
Supplementary files format and content: Salmon quant.sf pseudocount files for each sample.

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions. PolyA RNA selection was performed using the Poly(A)Purist™ MAG Kit (Invitrogen) according to the manufacturer’s instructions.
Libraries were prepared using the Direct RNA Sequencing kit SQK-RNA002 (Oxford Nanopore Technologies) according to the manufacturer’s instructions. 500ng of polyA selected RNA was used as input for each sample.
Long read direct RNA-sequencing


title: S008_CD4_CXCR5pos_PD1neg

description: Library name: S008_CD4_CXCR5pos_PD1neg

data_processing:
Sequencing reads were aligned to hg38 using Bowtie2
Accessible peaks / regions were identified using macs2
Assembly: hg38
Supplementary files format and content: narrowPeak.bed (peak file in bed format)
Supplementary files format and content: bw (bigwig files, fraom ATAC-seq alignment to hg38)

extract_protocol:
Cells were FACS-sorted, stored on ice, and prompty processed for ATAC-seq
ATAC-seq: nuclei were isolated and tagmented in 10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630 for 30 min at 37 degrees C as described in Buenrostro et al., 2013 (PMID: 24097267). Tagmented DNA was purified with Qiagen MinElute PCR purification kit, indexed and amplfied for sequencing.

value: CD4+ CXCR5pos PD1neg


title: B01-6m

description: Library name: 31470-002.R1


title: S08_CD4_CXCR5pos_PD1neg_H3K4me1

description: Library name: S08


title: Granulosa cells,PS-MPs treatment,biol rep 2

description: Library name: Sample5


title: Inflammatory_replicate_4

value: LPS + IFNγ


title: A01-6m

description: Library name: 31470-001.R1

value: adipose

value: mesenchymal stem cells


title: S07_CD4_CXCR5pos_PD1neg_H3K4me1

description: Library name: S07

value: tonsil


title: Granulosa cells,PS-MPs treatment,biol rep 1

description: Library name: Sample4

value: mouse ovarian granulosa cells


title: Steady_State_replicate_3


title: S06_CD4_CXCR5pos_PD1neg_H3K4me1

description: Library name: S06


title: Tissue_Reparative_replicate_2


title: Granulosa cells,Control,biol rep 2

description: Library name: Sample2


title: Granny Val - Rep 2 - Layer 2

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

institute: UNIVERSITY OF FLORIDA

description: Library name: G-2-2

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program (Martin 2011) to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis.
Reads were aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference; v2.7.9a) and the Muscadinia rotundifolia ‘Noble’ genome (NCBI accession: PRJNA738474; Park et al., 2022) was used as the reference genome.
Mapped reads were processed with HTSeq (v0.11.2) (Anders et al., 2015), SAMtools, and in-house scripts developed by the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida to remove PCR duplicates and count uniquely mapped reads.
Differential expression analysis was conducted using the R package, DESeq2 (Love et al., 2014). Differentially expressed genes (DEGs) were identified with a log₂ fold change threshold of  ≥ 2 or ≤ –2 and adjusted p-values ≤ 0.05. KEGG enrichment analysis was performed using ShinyGO (Version 0.82, https://bioinformatics.sdstate.edu/go/). Transcription factor analysis was performed using the Plant Transcription Factor Database (PlantTFDB v5.0, https://planttfdb.gao-lab.org/). GO enrichment for candidate gene identification was performed using Panther’s Gene Ontology Resource (http://geneontology.org/). Predicted expression localization of candidates was performed using the University of Toronto’s eFP browser (https://bar.utoronto.ca/). All tools previously mentioned used the Vitis vinifera genome as a reference.
Assembly: Muscadinia rotundifolia ‘Noble’ genome (NCBI accession: PRJNA738474)
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

organism: Vitis rotundifolia

source_name: peel

extract_protocol:
Mature berries of ‘Alachua’, ‘Granny Val’, and ‘Supreme’ cultivars were harvested, and tissues were separated into four layers: epidermis/cuticle, hypodermis, mesocarp, and endocarp. Tissues were frozen in liquid nitrogen and stored at –80°C until further processing. Total RNA was isolated using the NucleoSpin RNA Plant and Fungi Kit (Macherey-Nagel, Hawthorne, NJ, USA), with a modified grinding step: 100–300 mg tissue was ground in 2 mL tubes with four 5-mm zirconia beads (Inframat Advanced Materials, Manchester, CT, USA) using a Mini-Beadbeater-96 (BioSpec Products, Bartlesville, OK, USA). RNA samples were treated with DNase using the PureLink™ DNase Kit (Invitrogen™, CA, USA) to remove residual DNA.
Total RNA  quality of sample was assessed using the Agilent TapeStation 4200 (Agilent Technologies, Inc). 250 ng of total RNA was used for library construction using NEB Ultra II Directional RNA-seq library preparation kit for Illumina according to manufacturer's protocol. First, 300 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then followed by RNA library construction with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) according to the manufacturer's user guide.

treatment_protocol: To assess relative skin thickness across muscadine cultivars, mature berries were harvested from 6 muscadine cultivars, 3 purple (‘Alachua’, ‘Paulk’, ‘Supreme’) and 3 green (‘Granny Val’, ‘Hall’, ‘Triumph’) from a research plot at the University of Florida Plant Science Research and Education Unit vineyard in Citra, Florida. Thirty berries per genotype were collected and transported to the postharvest laboratory in an icebox for dissection. Berry diameter was measured using ImageJ software.

value: peel

value: Exocarp


title: S05_CD4_CXCR5pos_PD1neg_H3K4me1

description: Library name: S05


title: Granulosa cells,Control,biol rep 3

description: Library name: Sample3


title: Steady_State_replicate_2

value: Bone Marrow


title: 3dpf-gut-1_S4

first: Daniel

last: Levic

address: 307 Research Drive

department: Cell Biology

description: Library name: Sample 4

data_processing:
Trimmomatic(v0.38) was used to trim sequencing adapters
Reads were aligned to the zebrafish genome (GRCz11)  using STAR 2.7.11.a
Reads were counted using featureCounts in the Subread package (v1.6.3)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files includes counts for each sample

source_name: Intestine

extract_protocol:
Total RNA from FACS-isolated intestinal epithelial cells was extracted using the Monarch Total RNA Miniprep Kit (NEB, T2010S) according to the manufacturer’s instructions.
RNA-sequencing libraries were made from ≥150ng of total RNA purified from zebrafish intestinal cells using the KAPA HyperPrep kit.

value: Intestine

value: cldn15 positive cells

value: Intestinal epithelial cell

value: TgKI - cldn15la-tdTomato

value: 3 dpf


title: Granulosa cells,Control,biol rep 1

description: Library name: Sample1

value: WT


title: S04_CD4_naive_H3K4me1

first: Vinay

last: Mahajan

address: 65 Landsdowne Street

description: Library name: S04


title: 5dpf-gut-3_S3

description: Library name: Sample 3

value: 5 dpf


title: Inflammatory_replicate_3

value: Bone Marrow Derived Macrophages