title: Donor12, SIC, scRNA-seq, T3

city: wuhan

first: Mingjie

address: union hospital

institute: Huazhong University of Science and Technology

description: Library name: Donor12, SIC, scRNA-seq, T3

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10x Genomics CellRanger pipeline (https://support.10xgenomics.com/ single-cell-geneexpression/ software/ pipelines/latest/what-is-cell-ranger) using default parameters. For each gene and each cell barcode filtered by CellRanger, unique molecule identifiers (UMIs) were counted to construct digital expression matrices.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: locally advanced rectal cancer

extract_protocol:
Single-cell suspensions were generated using the Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s protocol. A Dead Cell Removal Kit (Miltenyi Biotec) was applied to eliminate dead cells from the single-cell suspensions. Cell viability in single-cell suspensions was >90%. The concentration of single-cell suspension was adjusted to 700-1200 cells/uL. The cell suspension was loaded into Chromium microfluidic chips to establish single-cell gel beads in emulsion (GEMs) for the directed retrieval of approximately 5000 cells and barcoded with the Chromium Controller (10x Genomics).
RNA from the barcoded cells was subsequently reverse transcribed, and sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) according to the manufacturer’s instructions. Sequencing was performed with the Illumina sequencing platform (NovaSeq) in Novogene.

value: locally advanced rectal cancer

value: stromal and immune cells


title: TGF-beta stimulated epicardial cell EVs, TGFb-EVs, rep 1

status: Public on Jun 03 2026

type: SRA

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

description: Library name: TGFb1

library_source: transcriptomic

data_processing:
Libraries were sequenced using a NovaSeq 6000 S4 (Illumina) at  2× 150 (bp) and an average depth of 12 million reads.
R1 reads were trimmed to 75 bp before analysis and these were the files used for further analyses.
The Qiagen RNA- seq Analysis Portal 3.0 (workflow version 1.2) was used to align trimmed R1 sequencing data to the human genome (GRCh38.103) via the miRbase v22 database and generate raw miRNA count files for each sample (see EpiEV_rawcounts.txt).
Biological replicates with fewer than 100 total aligned miRNA counts were considered to have failed sequencing and not included in further analyses (NT2, FGF1).
Publicly available ComBat-seq R code was used to perform batch effect adjustment of raw miRNA count data based on RNA extraction cell culture batches according to a published protocol: https://doi.org/10.1093/nargab/lqaa078 (see EpiEV_Adjustedcounts.txt). RNA extraction batches: 1 (all groups reps 1 and 2), 2 (all groups reps 3 and 4); Culture batches = biological replicate numbers (1 to 4, for each group)
Assembly: GRCh38.103/miRbase v22
Supplementary files format and content: EpiEV_rawcounts.txt: tab-delimited text file including raw counts for each sample
Supplementary files format and content: EpiEV_Adjustedcounts.txt: tab-delimited text file including ComBat-seq adjusted counts for each sample along with calculated counts per million (CPM) mapped miRNA transcripts for each sample and average CPM for each group.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
miRNA was isolated from lysed EV pellets using the miRNeasy Micro Kit (Qiagen, 217084) according to the manufaturer's protocol.
Library preparation was performed using the QIAseq miRNA Library Kit (Qiagen, catalog no. 331502).

treatment_protocol: To prepare epicardial cells for EV isolation, cryopreserved non-GFP pro-epicardial cells were seeded on 6 well plates using the same density and protocol as described above. Four different culture stimulation conditions were applied to different subsets of pro-epicardial cells. The ‘SB’ epicardial cell group was cultured in the same supplemented StemPro media formulation as outlined above from the time of plating (day 0) for the full duration of culture. Cells in the ‘TGF-b’ stimulation group were grown in the same supplemented StemPro media, but with no SB-431542 and with the addition of 5 ng/ml TGF-b1 (PeproTech, 100-21-10UG) starting one day after plating (considered day 0) for 4 days total. The ‘FGF’ stimulation group was grown in supplemented StemPro media with no SB-431542 and with the addition of 10 ng/ml bFGF (R&D Systems, 233-FB-025) starting one day after plating (day 0) for the full duration of culture. ‘No treatment’ (NT) cells were cultured in supplemented StemPro media with no SB-431542 and no other additives from the time of plating (day 0) for the full duration of culture. Culture media was changed every 2 days. On day 4, culture media (following the formulations specified above for each stimulation group) was ultrafiltered via centrifugation in Amicon Ultra-15 100kDa centrifugal filters (MilliporeSigma, UFC910024) at 4000g for 30 minutes at room temperature to deplete supplemented media of background EVs. Cells from each stimulation group were cultured in their respective formulations of ultrafiltered media for two 48-hour periods (day 4 to day 6 and day 6 to day 8). Conditioned media collected from cells on days 6 and 8 was frozen at -20C until EV isolation. Thawed conditioned media was centrifuged at 3200g for 10min to pellet cell debris. Supernatant was collected. The PEG-based miRCURY exosome isolation kit (Qiagen, 76743) was utilized for EV isolation.  PEG-media solutions were rotated overnight at 4C then centrifuged for 30min at 3200g and 21C to pellet EVs. Pellets were rinsed superficially with PBS without resuspension. EV pellets were resuspended directly in Qiazol lysis buffer for total RNA extraction.

tag: cell line

tag: cell type

value: epicardial-derived cell

tag: treatment

value: 5 ng/ml TGF-b1, 4 days; no treatment, 4 days


title: primary rat astrocytes, H2O2 3

city: Charlestown

first: Kazuhide

last: Hayakawa

state: Massachusetts

address: MGH149 13th street, Room 2401

department: Radiology

country: USA

institute: Massachusetts General Hospital

description: Library name: Stress 3

data_processing:
by GENEWIZ (New Jersey, USA).
Assembly: Alignment files (BAM) were generated for downstream analysis. Gene-level counts were quantified using featureCounts from the Subread package (v1.5.2), counting uniquely mapped reads overlapping annotated exons (strand-specific when applicable).

organism: Rattus norvegicus

source_name: Primary

growth_protocol: Astrocytes were plated in poly-D-lysine-coated 75-cm2 flasks, and maintained in Dulbecco’s Modified Eagle’s medium containing 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA, including mitochondrial mRNA, was extracted from mitochondria-enriched fractions using the RNeasy Micro Kit (QIAGEN) according to the manufacturer’s protocol.
Library preparation and sequencing were performed by GENEWIZ (New Jersey, USA). Raw reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic (v0.36) and aligned to the Rattus norvegicus reference genome (Rnor6.0, Ensembl annotation) using the splice-aware aligner STAR aligner (v2.5.2b).

treatment_protocol: Cells were treated with H₂O₂ at a final concentration of 100 µM for 30 min at 37 °C in a humidified 5% CO₂ incubator by adding plate-specific volumes of the 10 mM H₂O₂ stock (1 µL, 10 µL, and 20 µL to 96-well, 12-well, and 6-well plates, respectively), while vehicle control wells received the same volume of sterile distilled water.

tag: tissue

value: Primary

value: astrocyte

value: WT

tag: genotype

value: ATP restoration

tag: batch

value: polyA RNA


title: Donor12, SIC, scRNA-seq, T2

last: Li

country: China

description: Library name: Donor12, SIC, scRNA-seq, T2

library_source: transcriptomic single cell


title: Untreated pro-epicardial cell EVs, NT-EVs, rep 4

description: Library name: NT4

value: No treatment


title: primary rat astrocytes, H2O2 2

description: Library name: Stress 2


title: Donor12, SIC, scRNA-seq, T1

description: Library name: Donor12, SIC, scRNA-seq, T1


title: Untreated pro-epicardial cell EVs, NT-EVs, rep 3

description: Library name: NT3


title: 25-VP-015-01, lesional skin biopsy

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description: Library name: 25_VP_015_01_lesioneel_A4

data_processing:
Raw read QC was done using FastQC (v0.12.1)
Adapter and quality trimming was done using cutadapt (v5.0)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.11b)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.6)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.1)
Assembly: Homo sapiens  GRCh38 (Ensembl release 112)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

source_name: skin

extract_protocol:
The sampled tissue was lysed mechanically using a 1000 µL pipette tip, followed by shearing through a syringe (Terumo Corporation, Tokyo, Japan) fitted with a 20Gx1½ needle (Terumo Corporation). Total RNA was extracted using the conventional TriReagent/chloroform method and subsequently purified with the Direct-zol Microprep RNA Kit (Zymo Research), including on-column DNase I treatment, according to the manufacturer’s instructions. As residual genomic DNA was detected in some samples, an additional DNase treatment was performed using the TURBO DNA-free™ Kit (Invitrogen, Thermo Fisher Scientific) on all RNA extracts.
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen)

value: skin


title: Donor11, SIC, scRNA-seq, T2

description: Library name: Donor11, SIC, scRNA-seq, T2


title: Untreated pro-epicardial cell EVs, NT-EVs, rep 1

description: Library name: NT1


title: primary rat astrocytes, H2O2 1

description: Library name: Stress 1


title: HYP.IP.4

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Library name: Pool2_38

data_processing:
The reads were trimmed for adapter "AGATCGGAAGAGCACACGTCT" and polyX tails by using fastp.
Adapter-trimmed reads were aligned to mouse genome (mm10) by using STAR.
featureCounts was used to assign mapped sequencing reads to genomic features. For reads mapped to multiple features, it assigns fractions (1/number of features).
Assembly: mm10
Supplementary files format and content: miRNA_count_table.csv, CSV file

organism: Mus musculus

source_name: Hypothalamus

growth_protocol: Male mice (8-12 weeks old, fed standard chow) were used.

extract_protocol:
RNA was extracted by Trizol-chloroform.
Libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep Kit for Illumina® (Index Primers 1-48) Cat#E7560S, per manufacturer's instructions.

treatment_protocol: 4-thiouracil was injected intraperitoneally (50mg/kg) 4 times every 48hrs to label BAT-miRNAs.

value: Hypothalamus

tag: type

value: IP

tag: mouse id


title: primary rat astrocytes, control 3

description: Library name: Control 3


title: Donor11, SIC, scRNA-seq, T1

description: Library name: Donor11, SIC, scRNA-seq, T1


title: Mature epicardial cell EVs, SB-EVs, rep 4

description: Library name: SB4


title: Donor10, SIC, scRNA-seq, T2

description: Library name: Donor10, SIC, scRNA-seq, T2


title: primary rat astrocytes, control 2

description: Library name: Control 2


title: Mature epicardial cell EVs, SB-EVs, rep 3

description: Library name: SB3


title: primary rat astrocytes, control 1

description: Library name: Control 1


title: Donor10, SIC, scRNA-seq, T1

description: Library name: Donor10, SIC, scRNA-seq, T1


title: Mature epicardial cell EVs, SB-EVs, rep 2

description: Library name: SB2


title: Mature epicardial cell EVs, SB-EVs, rep 1

description: Library name: SB1


title: Donor9, SIC, scRNA-seq, T2

description: Library name: Donor9, SIC, scRNA-seq, T2


title: Control 15, skin biopsy

description: Library name: 23_Controle_15_gezond_G3


title: JEG-3_MEL_1000nM_rep5

city: Atlanta

first: Erica

middle: L

last: Johnson

state: GA

address: 720 Westview Dr SW

department: Department of Microbiology, Biochemistry, and Immunology

institute: Morehouse School of Medicine

description:
Library name: J20
Trophoblast-like cell (JEG-3) with 1000 nM melatonin, biological replicate 5.

data_processing:
Raw reads were provided in FASTQ format. Adapter sequences and low-quality bases were removed using vendor quality-control pipelines. Clean reads were aligned to the human reference genome GRCh38 (NCBI GCF_000001405.39, GRCh38.p13) using STAR (v2.7). Only uniquely mapped, properly paired reads were retained. Gene-level counts were generated using featureCounts. Downstream differential expression analysis was performed in DESeq2 using the median-ratio normalization method and a negative binomial model. Wald tests were used to estimate log₂ fold changes and Benjamini–Hochberg adjusted p-values. Log₂ fold changes were shrunk with the apeglm method. Variance-stabilizing transformation (VST) was applied for clustering and visualization. Gene set enrichment used fgsea with MSigDB Hallmark gene sets.
Assembly: Homo sapiens GRCh38 (NCBI GCF_000001405.39, GRCh38.p13)
Supplementary files format and content: Processed data are provided as a gene-by-sample matrix text file (melatonin_counts_raw.txt). Rows correspond to individual genes (gene identifiers), and columns correspond to RNA-seq libraries (JEG-3 and decidual macrophage samples across all treatments). Each cell contains the raw count of reads assigned to that gene in that sample, as generated by featureCounts after alignment to GRCh38.

growth_protocol: Term placentas (>37 weeks’ gestation) were obtained from healthy pregnant individuals (>18 years old, HIV-1 and hepatitis B seronegative) undergoing cesarean delivery at Grady Memorial Hospital (Atlanta, GA, USA) after written informed consent. Maternal decidua basalis was dissected, washed extensively in ice-cold PBS, and enzymatically digested. Mononuclear cells were isolated by Ficoll-Paque density gradient centrifugation and CD14⁺ decidual macrophages were enriched using magnetic microbeads and cultured in complete RPMI (10% FBS, 1% penicillin–streptomycin, 2 mM L-glutamine, HEPES) at 37 °C, 5% CO₂. The human JEG-3 trophoblast-like cell line (ATCC HTB-36) was maintained in EMEM supplemented with 10% FBS and 1% penicillin–streptomycin at 37 °C with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions, including on-column DNase digestion when applicable. RNA concentration and purity were assessed by NanoDrop spectrophotometry, and RNA integrity was evaluated using an Agilent Bioanalyzer. Only samples with RNA integrity number (RIN) ≥ 7 were used for library preparation.
mRNA libraries were prepared using the MGIEasy RNA Directional Library Prep Kit (MGI/BGI). Briefly, polyadenylated RNA was enriched using oligo(dT) beads, fragmented, and reverse-transcribed to generate first-strand cDNA. Second-strand synthesis incorporated dUTP for strand specificity, followed by end repair, A-tailing, adapter ligation, and PCR amplification. Libraries were quantified and pooled according to manufacturer’s recommendations and sequenced on a BGISEQ/DNBSEQ platform with paired-end reads.

treatment_protocol: Decidual macrophages and JEG-3 cells were seeded at defined densities and allowed to adhere. Cells were assigned to one of four conditions: No Treatment, Vehicle (diluent control), 1 nM melatonin, or 1000 nM melatonin. For these RNA-seq samples, cells were incubated for 24 h under the indicated melatonin or vehicle conditions. In the broader experimental study, additional conditions included LPS stimulation and melatonin pretreatment or post-treatment, but only the basal melatonin conditions are included in this dataset.

value: trophoblast-like cell

value: 1000 nM melatonin


title: JEG-3_MEL_1nM_rep5

description:
Library name: J19
Trophoblast-like cell (JEG-3) with 1 nM melatonin, biological replicate 5.

value: 1 nM melatonin


title: LC_wtHSV1_female_rep3

type: RNA

city: Stillwater

first: Clinton

last: Jones

state: Oklahoma

address: 250 McElroy Hall

department: Veterinary Pathobiology

institute: Oklahoma State University

hyb_protocol: Samples were submitted to NanoString Technologies for RNA isolation and subsequent sample processing

data_processing: Quality control, normalization, and between-group comparisons for differential gene expression were done using the nSolver Analysis Software from NanoString Technologies

label: NanoString target-specific fluorescent barcodes

source_name: LC, wt HSV-1

extract_protocol: Serial coronal sections (60 µm thick) of brainstem were obtained on super frost plus slides using a cryostat (Leica CM3050S). The principal sensory nucleus (Pr5) of the spinal trigeminal tract and locus coeruleus (LC) were microdissected by Palkovit’s punch technique, using a mouse brain stereotaxic atlas as a reference (Paxinos and Franklin, 2019). Bilateral micropunches were collected from 60-µm thick coronal sections based on stereotaxic coordinates. Punches collected from Pr5 and LC were preserved in RNAlater at -20°C until shipped.

tag: Sex

value: female

value: LC

tag: infection


title: AngII+MOTS-c4

city: Shanghai

first: Ying

middle: ying

last: Liao

address: 150 Jimo Road，Pudongxin,Shanghai

institute: Shanghai East Hospital

description: Library name: NGS20250703-021-00006_M4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Alignment files were sorted and duplicates removed using Picard tools (v1.41) and SAMtools (v0.1.18).
Supplementary files format and content: csv files include Reads count for each Sample

source_name: atrial

extract_protocol:
After 48 h of treatment, total RNA was extracted using Trizol and subjected to RNA sequencing.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

value: atrial

value: Primary atrial  fibroblasts


title: Donor9, SIC, scRNA-seq, T1

description: Library name: Donor9, SIC, scRNA-seq, T1

value: locally advanced rectal cancer

value: stromal and immune cells


title: NK-92 cells, shADAR1-1

city: Guangzhou

first: Rukang

last: Liang

state: Guangdong

address: Shipai Street, Tianhe district

department: Biotherapy Center

institute: The Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
fastp (version 0.18.0)
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 fastp (version 0.18.0).
Assembly: Ensembl release106
Supplementary files format and content: tab-delimited text fle includes raw counts and FPKM values for each Sample

growth_protocol: NK-92 cells were cultured in RPMI 1640 medium supplemented with 12.5% FBS, 50 μM β-mercaptoethanol, 100 IU/ml recombinant human IL-2 and 1% Penicillin-Streptomycin solution.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA).
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.     The ligation reaction was purified with the AMPure XP Beads(1.0X).

treatment_protocol: For transduction, lentivirus was added to NK-92 cells in the presence of 8 μg/mL polybrene. Then, the samples were centrifuged at the speed of 1800 g for 60 mins at 32 ℃ and incubated overnight in a humidified incubator at 37 ℃ with 5% CO2 before replacing the medium with a regular growth medium


title: Donor8, SIC, scRNA-seq, T3

description: Library name: Donor8, SIC, scRNA-seq, T3


title: JEG-3_No_Treatment_rep5

description:
Library name: J17
Trophoblast-like cell (JEG-3) with no treatment, biological replicate 5.

value: no treatment


title: MUS.IP.4

description: Library name: Pool2_28

source_name: Muscle (gastrocnemius)

value: Muscle (gastrocnemius)


title: LC_uninfected_female_rep1

description:
OCJ4140_Female_LC_HSVvsControl.txt
OCJ4140_Female_LC_dLATvsControl.txt

scan_protocol: Samples were submitted to NanoString Technologies for RNA isolation and subsequent sample processing

source_name: LC, uninfected

value: uninfected


title: LC_uninfected_male_rep2

description:
OCJ4140_Male_LC_HSVvsControl.txt
OCJ4140_Male_LC_dLATvsControl.txt

label_protocol: Samples were submitted to NanoString Technologies for RNA isolation and subsequent sample processing

value: male


title: LC_dLAT2903_female_rep2

source_name: LC, dLAT2903


title: LC_uninfected_male_rep1


title: LC_dLAT2903_male_rep1


title: LC_dLAT2903_female_rep1


title: BoMacWT,Input

city: Yinchuan

first: Gang

last: Zhao

address: 489 Helan West Road, Xixia District

institute: ningxia university

library_source: genomic

data_processing:
The reads were trimmed from 3' end until the final base had a quality score>30, using Trim-glore, discarding reads left with <20bp.
The reads were aligned to ARS-UCD1.2 genome using bwa-mem version 0.7.17 with default settings (BWA-MEM).
Peaks were called using MACS2 v2.2.6 with f = BAMPE; nomodel; shift = 0; extsize = 200; q = 0.05; keep-dup all
Assembly: ARS-UCD1.2
Supplementary files format and content: bigWig, Peak (except for Input sample)

molecule: genomic DNA

organism: Bos taurus

source_name: BoMac

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator.
ChIP-Seq libraries were prepared by ChIP-IT ChIP-Seq Kit (Active Motif).

value: BoMac

value: BoMacWT

tag: antibody

value: Input


title: LC_dLAT2903_male_rep2


title: NK-92 cells, shscramble-2

value: shscramble


title: JEG-3_MEL_1000nM_rep4

description:
Library name: J16
Trophoblast-like cell (JEG-3) with 1000 nM melatonin, biological replicate 4.

value: trophoblast-like cell


title: Donor8, SIC, scRNA-seq, T2

description: Library name: Donor8, SIC, scRNA-seq, T2


title: LC_wtHSV1_male_rep2


title: Donor8, SIC, scRNA-seq, T1

description: Library name: Donor8, SIC, scRNA-seq, T1


title: GDM_12, 20-GDM-8

city: DAEJEON

first: SEONG EUN

last: LEE

address: 282 MUNHWA-RO

country: South Korea

institute: CHUNGNAM NATIONAL UNIVERSITY

data_processing:
FastQC(v0.11.7) software used for quality check
Trimmomatic(0.38) performs trimming with various parameters for illumina paired-end or single-end.
HISAT2(v2.1.0) quickly and accurately maps high-throughput sequencing data to the reference genome to produce aligned reads.
The transcript assembly through the StringTie(v2.1.3b) program is performed using the information of the aligned reads based on the reference.
The expression profile obtained by transcript quantification of each sample is extracted with FPKM or RPKM, which is the normalization value considering read count and transcript length and depth of coverage.
Assembly: UCSC hg38
Supplementary files format and content: Microsoft excel files include raw count for each Sample

source_name: placenta

extract_protocol:
RNA was harvested using Trizol reagent. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SureSelectXT RNA Direct Reagent Kit following manufacturer's protocols.

value: placenta

tag: disease state

value: GDM


title: Donor7, SIC, scRNA-seq, T3

description: Library name: Donor7, SIC, scRNA-seq, T3


title: GDM_11, 20-GDM-7


title: JEG-3_MEL_1nM_rep4

description:
Library name: J15
Trophoblast-like cell (JEG-3) with 1 nM melatonin, biological replicate 4.

value: 1 nM melatonin


title: LC_wtHSV1_male_rep1

value: LC


title: LC_wtHSV1_female_rep2

value: female


title: JEG-3_No_Treatment_rep4

description:
Library name: J13
Trophoblast-like cell (JEG-3) with no treatment, biological replicate 4.


title: Donor7, SIC, scRNA-seq, T1

description: Library name: Donor7, SIC, scRNA-seq, T1


title: Arhgef11Sglt2_DOCA,rep3

city: Jackson

first: Bioinformatics

last: Core

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

description: Library name: A2299_Arhgef11Sglt2_DOCA_S18

data_processing:
The reads were then quantified using Salmon (v1.10.0; Patro et al., 2017) against the Ensembl GRCm39 release 113 reference transcriptome. Transcript annotations were obtained from the corresponding Ensembl GTF file.
The differential expression analysis was conducted using the DESeq2 package in R (4.4.1)
Assembly: GRCm39 release 113
Supplementary files format and content: Zipped Salmon quant files

source_name: Kidney

extract_protocol:
RNA was isolated from mouse kidney samples from Studies 2 and 3 using phenol: chloroform extraction and PureLink RNA Mini Kit (Invitrogen) per the manufacturer’s instructions. RNA quantity (Qubit BR RNA Assay Kit; Invitrogen) and quality measures (RIN >8) (QIAxcel Advanced Bioanalyzer; Qiagen) were validated to confirm intact 18S/28S ribosomal RNA.
Samples were then prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) per the manufacturer’s instructions. Samples were pooled into a single library and sequenced on the Illumina NextSeq 2000 platform using NextSeq™ 2000 P3 Reagent Kit (200 Cycles)

value: Kidney


title: GDM_10, 20-GDM-4


title: GDM_9, 20-GDM-3


title: Sglt2Cre_DOCA,rep5

description: Library name: A2291_Sglt2Cre_DOCA_S11


title: AngII+HNG1

description: Library name: NGS20250703-021-00006_H1

value: atrial

value: Primary atrial  fibroblasts


title: Donor6, SIC, scRNA-seq, T3

description: Library name: Donor6, SIC, scRNA-seq, T3

value: locally advanced rectal cancer

value: stromal and immune cells


title: JEG-3_MEL_1nM_rep3

description:
Library name: J11
Trophoblast-like cell (JEG-3) with 1 nM melatonin, biological replicate 3.


title: GDM_8, 20-GDM-2


title: Sglt2Cre_DOCA,rep4

description: Library name: A2287_Sglt2Cre_DOCA_S9


title: GDM_7, 20-GDM-1


title: JEG-3_Vehicle_rep3

description:
Library name: J10
Trophoblast-like cell (JEG-3) with vehicle control, biological replicate 3.

value: vehicle control


title: Donor5, SIC, scRNA-seq, T3

description: Library name: Donor5, SIC, scRNA-seq, T3


title: JEG-3_No_Treatment_rep3

description:
Library name: J9
Trophoblast-like cell (JEG-3) with no treatment, biological replicate 3.

value: no treatment


title: GDM_6, 4511698


title: Arhgef11Sglt2_DOCA,rep1

description: Library name: A2255_Arhgef11Sglt2_DOCA_S5


title: JEG-3_MEL_1000nM_rep2

description:
Library name: J8
Trophoblast-like cell (JEG-3) with 1000 nM melatonin, biological replicate 2.

value: 1000 nM melatonin


title: Donor5, SIC, scRNA-seq, T1

description: Library name: Donor5, SIC, scRNA-seq, T1


title: JEG-3_MEL_1nM_rep2

description:
Library name: J7
Trophoblast-like cell (JEG-3) with 1 nM melatonin, biological replicate 2.


title: Sglt2Cre_DOCA,rep3

description: Library name: A2252_Sglt2Cre_DOCA_S7


title: GDM_5, 4465211


title: GDM_4, 4162589


title: Sglt2Cre_DOCA,rep2

description: Library name: A2246_Sglt2Cre_DOCA_S4


title: Donor4, SIC, scRNA-seq, T3

description: Library name: Donor4, SIC, scRNA-seq, T3


title: JEG-3_Vehicle_rep2

description:
Library name: J6
Trophoblast-like cell (JEG-3) with vehicle control, biological replicate 2.


title: GDM_3, 4433712


title: Sglt2Cre_DOCA,rep1

description: Library name: A2244_Sglt2Cre_DOCA_S3


title: Donor4, SIC, scRNA-seq, T1

description: Library name: Donor4, SIC, scRNA-seq, T1


title: JEG-3_No_Treatment_rep2

description:
Library name: J5
Trophoblast-like cell (JEG-3) with no treatment, biological replicate 2.


title: GDM_2, 4062342


title: BV-2 cells, SF8628 exposed, 6h, N3

city: Stockholm

first: Martin

last: Skandik

address: Nobels vag 13

country: Sweden

institute: Karolinska Institutet

description: Library name: bv2_SF8628_6h_N3

data_processing:
Basecalling and demultiplexing were performed using Illumina bcl2fastq (v2.20.0).
Sequence data quality was assessed using FastQC (v0.11.8).
Counts for each gene were estimated using featureCounts (v1.5.1).
Reads were aligned to the Ensembl GRCm38 reference genome using STAR (v2.7.9a).
Assembly: mm10/ GRCm38
Supplementary files format and content: Tab-delimited text file contains raw counts for each sample.

source_name: brain

growth_protocol: BV-2 microglia (RRID: CVCL_0182), primary patient-derived SF188 pHGG cells (RRID: CVCL_6948), primary patient-derived SF8628 DIPG cells (RRID: CVCL_IT46) have been used in this study. BV-2, SF188, and SF8628 cells were cultured in high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with penicillin (100 μg/ml), streptomycin (100 μg/ml) and 10% foetal bovine serum (FBS) at 37°C and 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini kit (Qiagen) with an additional step of Dnase treatment. The yield and quality of the isolated RNA were analysed using NanoDrop spectrophotometer. Total RNA samples were subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions.
The 200 ng of total RNA was subjected to Illumina sequencing and libraries were prepared with the Illumina TruSeq Stranded mRNA kit which includes cDNA synthesis, ligation of adaptors and amplification of indexed libraries. The yield and quality of the amplified libraries was analysed using Qubit by Thermo Fisher and the Agilent Tapestation. The indexed cDNA libraries were normalized and combined, and the pools were sequenced on the Illumina Hiseq 2000 generating 50 bp single-end reads.

treatment_protocol: Segregated co-cultures were performed whereby 2x106 SF8628 DMG cells or SF188 pHGG cells were plated in 10 cm culture dishes and 120,000 BV-2 microglia cells were plated on coverslip. Cells were plated in complete DMEM medium containing 10% FBS overnight. The next day the media was removed from the SF8628 DMG/SF188 pHGG cell culture dishes and replaced with DMEM containing 5% FBS, 4 coverslips containing BV2-microglia were transferred to each 10 cm dish in transwell inserts and left for 3 or 6 hours.

value: brain

value: microglia

value: WT


title: JEG-3_MEL_1000nM_rep1

description:
Library name: J4
Trophoblast-like cell (JEG-3) with 1000 nM melatonin, biological replicate 1.

value: trophoblast-like cell


title: BV-2 cells, SF188 exposed, 6h, N3

description: Library name: bv2_SF188_6h_N3


title: JEG-3_MEL_1nM_rep1

description:
Library name: J3
Trophoblast-like cell (JEG-3) with 1 nM melatonin, biological replicate 1.


title: JEG-3_Vehicle_rep1

description:
Library name: J2
Trophoblast-like cell (JEG-3) with vehicle control, biological replicate 1.


title: BV-2 cells, unexposed, 6h, N3

description: Library name: bv2_unexp_6h_N3


title: control_9, 20-control-7

value: placenta

value: control


title: BV-2 cells, SF8628 exposed, 3h, N3

description: Library name: bv2_SF8628_3h_N3


title: Donor6, SIC, scRNA-seq, T2

description: Library name: Donor6, SIC, scRNA-seq, T2


title: Donor2, SIC, scRNA-seq, T3

description: Library name: Donor2, SIC, scRNA-seq, T3


title: control_8, 20-control-5


title: Donor4, SIC, scRNA-seq, T2

description: Library name: Donor4, SIC, scRNA-seq, T2


title: BV-2 cells, SF188 exposed, 3h, N3

description: Library name: bv2_SF188_3h_N3


title: Decidual_Macro_MEL_1000nM_rep4

description:
Library name: M16
Decidual macrophage (Decidual_Macro) with 1000 nM melatonin, biological replicate 4.

source_name: decidua basalis of placenta

value: decidua basalis of placenta

value: decidual macrophage


title: Donor2, SIC, scRNA-seq, T2

description: Library name: Donor2, SIC, scRNA-seq, T2


title: Donor3, SIC, scRNA-seq, T3

description: Library name: Donor3, SIC, scRNA-seq, T3


title: Donor3, SIC, scRNA-seq, T2

description: Library name: Donor3, SIC, scRNA-seq, T2


title: GDM_1, 4767893

value: GDM


title: control_7, 20-control-4


title: BV-2 cells, unexposed, 3h, N3

description: Library name: bv2_unexp_3h_N3


title: control_10, 20-GDM-5


title: Decidual_Macro_MEL_1nM_rep4

description:
Library name: M15
Decidual macrophage (Decidual_Macro) with 1 nM melatonin, biological replicate 4.

value: 1 nM melatonin


title: control_6, 20-control-3


title: BV-2 cells, SF8628 exposed, 6h, N2

description: Library name: bv2_SF8628_6h_N2


title: Donor2, SIC, scRNA-seq, T1

description: Library name: Donor2, SIC, scRNA-seq, T1


title: Decidual_Macro_Vehicle_rep4

description:
Library name: M14
Decidual macrophage (Decidual_Macro) with vehicle control, biological replicate 4.


title: Donor1, SIC, scRNA-seq, T3

description: Library name: Donor1, SIC, scRNA-seq, T3


title: Donor3, SIC, scRNA-seq, T1

description: Library name: Donor3, SIC, scRNA-seq, T1


title: control_5, 20-control-2


title: BV-2 cells, SF188 exposed, 6h, N2

description: Library name: bv2_SF188_6h_N2


title: Decidual_Macro_No_Treatment_rep4

description:
Library name: M13
Decidual macrophage (Decidual_Macro) with no treatment, biological replicate 4.


title: control_4, 20-control-1


title: Donor1, SIC, scRNA-seq, T2

description: Library name: Donor1, SIC, scRNA-seq, T2


title: BV-2 cells, unexposed, 6h, N2

description: Library name: bv2_unexp_6h_N2


title: Decidual_Macro_MEL_1000nM_rep3

description:
Library name: M12
Decidual macrophage (Decidual_Macro) with 1000 nM melatonin, biological replicate 3.


title: Donor1, SIC, scRNA-seq, T1

description: Library name: Donor1, SIC, scRNA-seq, T1


title: control_3, 4280660


title: BV-2 cells, SF8628 exposed, 3h, N2

description: Library name: bv2_SF8628_3h_N2


title: Decidual_Macro_MEL_1nM_rep3

description:
Library name: M11
Decidual macrophage (Decidual_Macro) with 1 nM melatonin, biological replicate 3.


title: control_2, 4586347


title: BV-2 cells, SF188 exposed, 3h, N2

description: Library name: bv2_SF188_3h_N2


title: RHH9016: ArteryTL:short, BloodTL:long

city: Singapore

first: ZHI CHNG

last: LAU

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Library name: RHH9016

data_processing:
FASTQC was utilized to inspect raw sequencing data.
Spliced Transcripts Alignment to a Reference (STAR) (ver2.7.11b) was used to align reads to GRCh38 reference genome.
Estimation for gene level abundance was performed using RSEM software (ver1.3.0).
Gene level count data was processed, normalized, and between group analyses were performed using DESeq2 (ver1.44.0), with adjustment for age and the first surrogate variable using the R package svaseq to estimate for potential confounding factors.
Assembly: GRCh38
Supplementary files format and content: raw gene counts for each Sample

source_name: Arterial wall

extract_protocol:
Arterial wall tissues obtained from 34 patients during their CABG surgery were processed for total RNA extractions using RNeasy® Fibrous Tissue Mini Kit (Qiagen, Germany).
RNA-sequencing libraries were generated using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, USA).

value: Arterial wall

tag: age


title: Decidual_Macro_Vehicle_rep3

description:
Library name: M10
Decidual macrophage (Decidual_Macro) with vehicle control, biological replicate 3.


title: RHH9015: ArteryTL:long, BloodTL:short

description: Library name: RHH9015


title: control_1, 4510389


title: BV-2 cells, unexposed, 3h, N2

description: Library name: bv2_unexp_3h_N2


title: JEG-3_No_Treatment_rep1

description:
Library name: J1
Trophoblast-like cell (JEG-3) with no treatment, biological replicate 1.


title: Decidual_Macro_No_Treatment_rep3

description:
Library name: M9
Decidual macrophage (Decidual_Macro) with no treatment, biological replicate 3.


title: RHH9014: ArteryTL:long, BloodTL:short

description: Library name: RHH9014


title: BV-2 cells, SF8628 exposed, 6h, N1

description: Library name: bv2_SF8628_6h_N1


title: Decidual_Macro_MEL_1000nM_rep2

description:
Library name: M8
Decidual macrophage (Decidual_Macro) with 1000 nM melatonin, biological replicate 2.


title: R1 cell, Usb1-KO, Day 3 repeat 3

city: Chengdu

first: chao

last: yang

state: Sichuan

address: No.20, Section 3, Renmin South Road

department: West China Second University Hospital

institute: Sichuan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmotatic v0.39.
Trimmed sequence reads were mapped to GRCm38 using hisat2 v2.1.0.
TPM expression were performed using stringtie v1.3.6.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample.

extract_protocol:
RNA were harvested using RNeasy mini plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: mouse embryo stem cell

value: Usb1 knockout

value: Retinoic acid differentiation

tag: time point

value: Day 3


title: R1 cell, Usb1-KO, Day 3 repeat 2


title: RHH9013: ArteryTL:long, BloodTL:long

description: Library name: RHH9013


title: Pr5_wtHSV1_male_rep3

source_name: Pr5, wt HSV-1

value: male


title: BV-2 cells, SF188 exposed, 6h, N1

description: Library name: bv2_SF188_6h_N1


title: Decidual_Macro_MEL_1nM_rep2

description:
Library name: M7
Decidual macrophage (Decidual_Macro) with 1 nM melatonin, biological replicate 2.


title: RHH9012: ArteryTL:long, BloodTL:long

description: Library name: RHH9012


title: R1 cell, Usb1-KO, Day 3 repeat 1


title: BV-2 cells, unexposed, 6h, N1

description: Library name: bv2_unexp_6h_N1


title: Decidual_Macro_Vehicle_rep2

description:
Library name: M6
Decidual macrophage (Decidual_Macro) with vehicle control, biological replicate 2.

value: vehicle control


title: RHH9010: ArteryTL:short, BloodTL:short

description: Library name: RHH9010


title: R1 cell, WT, Day 3 repeat 3


title: BV-2 cells, SF8628 exposed, 3h, N1

description: Library name: bv2_SF8628_3h_N1

value: brain


title: Decidual_Macro_No_Treatment_rep2

description:
Library name: M5
Decidual macrophage (Decidual_Macro) with no treatment, biological replicate 2.

value: no treatment


title: Tomato mutant Beta, B (cv AC)  biological replicate 3 Full Ripe or Breaker+10 stage

city: rome

first: SARAH

last: FRUSCIANTE

state: Roma

address: via anguillarese 301

department: SSPT (Department for Sustainability)

country: Italy

institute: ENEA -  Italian National Agency for new Technologies, Energy and Sustainable Economic Development

description: not applicable

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Eu-TOM3 (custom exon) was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0001 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 72 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: Image acquisition, processing: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner3000 7G using default parameters.

data_processing:
Data were processed using RobiNA v2.0 software. Normalization method: rma; P-value correction method: fdr; Multiple testing strategy: global; P-value cut-off value for significant differential expression: 0.05; Genes that showed a log2-fold change smaller than two ignored: yes
eutom3gene_v2_ucprobes
EUTOM3_funcion_GO.tsv

label: Biotin

organism: Solanum lycopersicum

source_name: mutant immature fruit

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). The sense strand cDNA was synthesized with the same kit, then it was fragmented and labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown in a greenhouse under a long photoperiod (16-h light/24°C and 8-h dark/20°C) and irradiance (150 mmol m22 s21). Fruit were labeled at the Mature Green stage of ripening and collected at Mature Green, Breaker and 10 days later Breaker. Pericarps was frozen in liquid nitrogen and stored at -80°C for subsequent analyses.

extract_protocol: Briefly, total RNA isolation was performed using a Tris-Borate/phenol-chloroformisoamyl alcohol 25:24:1-based extraction followed by Potassium Acetate/Lithium Chloride/Sodium Chloride precipitation steps (Lopez-Gomez and Gomez-Lim, 1992) and DNAse I purification at 37°C for 20’. RNA quality was determined by using a Nanodrop ND-1000 (NanoDrop Technologies) and an Agilent 2100 Bioanalyzer: only RNAs showing A260/A280 and A260/230 ratios between, respectively, 1.8-2.0 and 2.0-2.2 and with a 28S/18S ratio between 1.5 and 2.0 were selected.

treatment_protocol: not applicable

value: pericarp


title: RHH9009: ArteryTL:short, BloodTL:long

description: Library name: RHH9009


title: R1 cell, WT, Day 3 repeat 2

value: WT


title: BV-2 cells, SF188 exposed, 3h, N1

description: Library name: bv2_SF188_3h_N1

value: microglia


title: Decidual_Macro_MEL_1000nM_rep1

description:
Library name: M4
Decidual macrophage (Decidual_Macro) with 1000 nM melatonin, biological replicate 1.

value: 1000 nM melatonin


title: RHH9008: ArteryTL:long, BloodTL:long

description: Library name: RHH9008


title: R1 cell, WT, Day 3 repeat 1


title: BV-2 cells, unexposed, 3h, N1

description: Library name: bv2_unexp_3h_N1


title: primary rat astrocytes, H2O2, Mitochondria treatment 3

description: Library name: Stress-mito3

value: Primary

value: astrocyte

value: ATP restoration

value: polyA RNA


title: Decidual_Macro_MEL_1nM_rep1

description:
Library name: M3
Decidual macrophage (Decidual_Macro) with 1 nM melatonin, biological replicate 1.

value: decidua basalis of placenta

value: decidual macrophage

value: 1 nM melatonin


title: R1 cell, Usb1-KO, Day 1 repeat 3

value: mouse embryo stem cell

value: Usb1 knockout

value: Retinoic acid differentiation

value: Day 1


title: RHH9007: ArteryTL:short, BloodTL:short

description: Library name: RHH9007

value: Arterial wall


title: IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) rep 8

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

description: Library name: NKHV23

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Alignment: STAR v2.5.3a
Counting: htseq-count v0.6.1p1
Differential expression analysis: DESeq2 v1.16.1
Assembly: mm10
Supplementary files format and content: 2 csv files include raw counts for each sample for naive mice & sham/cuff mice, respectively.

molecule: polyA RNA

source_name: Anterior Cingulate Cortex

extract_protocol:
P2836
Absolutely Nanoprep kit (Agilent),with DNase treatment
P2695 : Full length cDNA were generated from 1 ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.
P2836 : Full length cDNA were generated from 1ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: Anterior Cingulate Cortex

value: wildtype, C57BL6/J, injected in the Habenula with an AAVrg-CaMKIIa-m.Cherry-RPL10a-WPRE-SV40

value: Cuff


title: Decidual_Macro_Vehicle_rep1

description:
Library name: M2
Decidual macrophage (Decidual_Macro) with vehicle control, biological replicate 1.

value: vehicle control


title: RHH9006: ArteryTL:short, BloodTL:short

description: Library name: RHH9006


title: R1 cell, Usb1-KO, Day 1 repeat 2


title: RHH9005: ArteryTL:short, BloodTL:long

description: Library name: RHH9005


title: IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) rep 7

description: Library name: NKHV22


title: Decidual_Macro_No_Treatment_rep1

description:
Library name: M1
Decidual macrophage (Decidual_Macro) with no treatment, biological replicate 1.

value: no treatment


title: R1 cell, Usb1-KO, Day 1 repeat 1


title: LC_wtHSV1_male_rep3

value: male

value: LC


title: IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) rep 6

description: Library name: NKHV21


title: RHH9004: ArteryTL:short, BloodTL:long

description: Library name: RHH9004


title: ATAC-seq_HLF_BAF155-WT_rep3

city: Chapel Hill

first: Jesse

last: Raab

state: NC

address: Rm 5028 Genetic Medicine Building

institute: UNC Chapel Hill - Raab Lab

description:
Library name: JR808
ATAC-seq

data_processing:
All data processing was done using github.com/raab-lab/cut-n-run --mode atac
bowtie2 alignment
picard markDuplicate
macs2 peak calling
deeptools bamCoverage using csaw to calculate normalization factors for IGV tracks
Assembly: hg38
Supplementary files format and content: Scaled Bigwig files for visualization

source_name: HLF

growth_protocol: 10% FBS DMEM + p/s

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol [48]. Briefly, 50,000 viable cells per sample were pelleted at 500 × g for 5 minutes at 4°C. Cell pellets were resuspended in 50 μL of cold ATAC-Resuspension Buffer (RSB) containing 0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% digitonin, then pipetted up and down three times and incubated on ice for 3 minutes. Lysis buffer was washed out with 1 mL of cold ATAC-RSB containing 0.1% Tween-20 (without IPEGAL or digitonin), and nuclei were pelleted at 500 xg for 10 minutes at 4°C. Nuclei were resuspended in 50 μL of transposition mix containing 25 μL of 2x TD buffer (Diagenode), 0.05% digitonin, 0.1% Tween-20, and 200 nM Tn5 transposase (custom-loaded, diluted from a 37.5 μM stock). Transposition was carried out at 37°C for 30 minutes in a thermomixer at 1000 RPM. Reactions were cleaned up using the Zymo DNA Clean & Concentrator-5 kit (D4014, Zymo Research) and eluted in 21 μL Elution Buffer.
Libraries were pre-amplified using NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0530) with indexed primers under the following conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by 5 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. To determine the optimal number of additional cycles, 10% of the pre-amplified material was subjected to a qPCR side reaction following the method described by [49]. Final amplification was performed accordingly, and libraries were purified using a two-sided bead cleanup (KAPA Pure Beads, Roche) with 0.6x and 1.2x ratios to remove large fragments and unincorporated adapters. Library concentration and quality were assessed using the Agilent TapeStation with High Sensitivity D1000 ScreenTape. Libraries were pooled and sequenced on an Illumina NextSeq 1000 platform with 2x50 bp paired-end reads

treatment_protocol: CRISPR/CAS9 Knockout with re-expression of BAF155 WT or R1064K Mutant by Lentivirus

value: HLF

value: Liver Cancer


title: R1 cell, WT, Day 1 repeat 3

value: WT


title: IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) rep 5

description: Library name: NKHV20


title: ATAC-seq_HLF_BAF155-R1064K_rep3

description:
Library name: JR807
ATAC-seq


title: RHH9003: ArteryTL:short, BloodTL:short

description: Library name: RHH9003


title: R1 cell, WT, Day 1 repeat 2


title: IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) rep 4

description: Library name: NKHV19


title: ATAC-seq_HLF_BAF155-KO_rep3

description:
Library name: JR806
ATAC-seq


title: R1 cell, WT, Day 1 repeat 1


title: RHH9002: ArteryTL:short, BloodTL:short

description: Library name: RHH9002


title: IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) rep 3

description: Library name: NKHV18


title: RHH9001: ArteryTL:long, BloodTL:long

description: Library name: RHH9001


title: ATAC-seq_HLF_BAF155-WT_rep2

description:
Library name: JR805
ATAC-seq


title: R1 cell, Usb1-KO, Day 0 repeat 3

value: Day 0


title: IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) rep 2

description: Library name: NKHV17


title: ATAC-seq_HLF_BAF155-R1064K_rep2

description:
Library name: JR804
ATAC-seq


title: R1 cell, Usb1-KO, Day 0 repeat 2


title: IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) rep 1

description: Library name: NKHV15


title: RHH8999: ArteryTL:long, BloodTL:short

description: Library name: RHH8999


title: ATAC-seq_HLF_BAF155-KO_rep2

description:
Library name: JR803
ATAC-seq


title: R1 cell, Usb1-KO, Day 0 repeat 1


title: RHH8997: ArteryTL:short, BloodTL:long

description: Library name: RHH8997


title: ATAC-seq_HLF_BAF155-WT_rep1

description:
Library name: JR802
ATAC-seq


title: RHH8996: ArteryTL:short, BloodTL:short

description: Library name: RHH8996


title: IP Sham (Immunoprecipitated RNA fraction from the Sham control group) rep 8

description: Library name: NKHV14

value: Sham


title: R1 cell, WT, Day 0 repeat 2

value: mouse embryo stem cell


title: IP Sham (Immunoprecipitated RNA fraction from the Sham control group) rep 7

description: Library name: NKHV13


title: ATAC-seq_HLF_BAF155-R1064K_rep1

description:
Library name: JR801
ATAC-seq


title: RHH8995: ArteryTL:long, BloodTL:long

description: Library name: RHH8995


title: R1 cell, WT, Day 0 repeat 1


title: RHH8994: ArteryTL:short, BloodTL:long

description: Library name: RHH8994


title: ATAC-seq_HLF_BAF155-KO_rep1

description:
Library name: JR800
ATAC-seq


title: IP Sham (Immunoprecipitated RNA fraction from the Sham control group) rep 6

description: Library name: NKHV12


title: overhang_screen_7mer_rep3

city: Cambridge

first: Dario

last: Bressan

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description:
Screen for ligation overhang sequences, 7-mer length
Ligation overhang screen

library_source: other

data_processing:
The fastq files containing raw sequencing reads were first filtered using the cutadapt package (v4.1) using the following options: -a AGATCGGAA -m [lenght of overhang] -M [length of overhang +1]. This extracted the sequence corresponding to each ligated 6-mer or 7-mer overhang in the library. The resulting files were processed through a custom python script counting the number of occurrences of each overhang, producing a final csv file with overhang counts.
Assembly: None
Supplementary files format and content: Csv file including the frequency of each overhang sequence, defined as number of reads including the sequence in the sequenced data the UMI counts for each gene in each spatial area, as well as the normalized counts (normalized by total number of UMI), and the fold and log10 expression ratios between the two spatial areas.
Library strategy: ligation overhang screening, direct library production by ligating elements including Illumina flow-cell adapters

molecule: other

organism: synthetic construct

source_name: artifical DNA

growth_protocol: All animal procedures were performed in accordance with the Animal (Scientific Procedures) Act 1986 under UK Home Office project license PAD85403A. Animals were housed under standard husbandry conditions per UK Home Office and Institute regulations. Individually ventilated cages housed four to five animals under a 12-h light, 12-h dark cycle at the CRUK Cambridge Institute animal facility. Relative humidity was kept between 45 and 65% with a temperature range of 20-24°C. Animals had free access to water and pelleted food. Embryos samples were taken at embryonic day 16.5 from ethically euthanised pregnant dams following timed mating.

extract_protocol:
No extraction protocol, starting DNA oligonucleotides were synthesized with desalting purification and used as received
Eight oligonucleotides (BL358 to BL365) were synthesized with normal desalting purification. The oligos were annealed to produce two double-stranded DNA molecules (A and B) containing a constant region corresponding to the truseq P5 and P7 sequences plus a multiplexing sequencing indes, and a random 6-mer or 7-mer sequence protruding at the 5' end. Oligos were annealed at 30 uM concentration in 2X SSC by running the following program in a thermocycler: 1) 95C for 5 minutes, 2) ramp down to 65 at 0.1C/second, 3) hold at 65C for 5 minutes, 4) ramp down to 12C at 0.1C/second, 5) hold at 12C.
The A and B dsDNA molecules for each overhang length (6-mer or 7-mer) were diluted to 3.334 uM in 2X SSX and used to assemble a ligation reaction as follows: 2 uL 10x T4 ligase buffer, 1 uL of each annealed dsDNA (final 166.7 nM), 1 uL T4 DNA ligase (NEB M0202M), 15 uL nuclease-free water. Ligation was performed for 3 minutes at 22C, following by heat-inactivation at 65C for 10 minutes. The ligated molecules were purified by running the whole reaction volume on a 2% TBE agarose gel. The gel was stained in 1:10000 SYBR-gold (Thermo Scientific) and the bands corresponding to the ligation products were purified using the Qiagen Qiaquick gel extraction kit using the supplier's standard protocol. Library concentration was estimated by tapestation (DNA5000 screentape) and qPCR (KAPA Illumina library quantification kit)

tag: sample type

value: Artificial DNA


title: RHH8993: ArteryTL:long, BloodTL:long

description: Library name: RHH8993


title: IP Sham (Immunoprecipitated RNA fraction from the Sham control group) rep 5

description: Library name: NKHV11


title: Npapy_bulbs

city: Trois-Rivières

first: Karen

middle: Cristine

last: Goncalves dos Santos

address: 3351 boul des Forges

department: Departement de Chimie, Biochimie, Physique et Sciences Forensiques

institute: Université du Québec à Trois-Rivières

description:
Library name: SRR6041662
Hotchandani, T., de Villers, J. & Desgagne-Penix, I. Developmental regulation of the expression of amaryllidaceae alkaloid biosynthetic genes in Narcissus papyraceus. Genes (Basel) 10, doi:10.3390/genes10080594 (2019)

data_processing:
Raw data were downloaded from the Sequencing Read Archive (SRA) using sra-toolkit 3.0.9, then quality control was performed using fastp 0.23.4 (mean quality = 20; unqualified percent limit = 30; cut-front window-size = 5; cut-right window size = 4; cut-right mean quality = 15; length required = 50).
Assembly was carried out with Trinity 2.14.0 default parameters, followed by removal of redundant transcripts with CD-HIT-EST 4.8.1 (-c 0.97, -l 200). Removal of contaminants was done through submission to NCBI TSA.
Expression quantification was performed using kallisto 0.46.1 and with Salmon 1.4.0, with the support scripts align_and_estimate_abundance.pl and abundance_estimates_to_matrix.pl from Trinity.
Assembly: DBNKRN000000000
Supplementary files format and content: Narcissus_papyraceus_gene_counts.txt: Read count table, with trinity genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_papyraceus_gene_TPM.txt: Transcripts per million table, with trinity genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_papyraceus_isoform_counts.txt: Read count table, with trinity gene isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_papyraceus_isoform_TPM.txt: Transcripts per million table, with trinity gene isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_papyraceus_gene_counts_salmon.txt: Read count table, with trinity genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_papyraceus_gene_TPM_salmon.txt: Transcripts per million table, with genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_papyraceus_isoform_counts_salmon.txt: Read count table, with isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_papyraceus_isoform_TPM_salmon.txt: Transcripts per million table, with isoforms in the rows and accession numbers of samples in the columns.

organism: Narcissus papyraceus

source_name: bulbs

growth_protocol: Dormant bulbs

extract_protocol:
CTAB method described by (Singh and Desgagne-Penix 2017)
RNAseq

value: bulbs


title: overhang_screen_7mer_rep2


title: Leucojum aestivum bulbs

description: Library name: SRR14196981

data_processing:
Raw data were downloaded from the Sequencing Read Archive (SRA) using sra-toolkit 3.0.9, then quality control was performed using fastp 0.23.4 (mean quality = 20; unqualified percent limit = 30; cut-front window-size = 5; cut-right window size = 4; cut-right mean quality = 15; length required = 50).
Assembly was carried out with Trinity 2.14.0 default parameters, followed by removal of redundant transcripts with CD-HIT-EST 4.8.1 (-c 0.97, -l 200).
Expression quantification was performed using kallisto 0.46.1 and with Salmon 1.4.0, with the support scripts align_and_estimate_abundance.pl and abundance_estimates_to_matrix.pl from Trinity.
Assembly: TSA:  DBNIJJ000000000
Supplementary files format and content: Leucojum_aestivum_gene_counts.txt: Read count table, with trinity genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Leucojum_aestivum_gene_TPM.txt: Transcripts per million table, with trinity genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Leucojum_aestivum_isoform_counts.txt: Read count table, with trinity gene isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Leucojum_aestivum_isoform_TPM.txt: Transcripts per million table, with trinity gene isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Leucojum_aestivum_gene_counts_salmon.txt: Read count table, with genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Leucojum_aestivum_gene_TPM_salmon.txt: Transcripts per million table, with genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Leucojum_aestivum_isoform_counts_salmon.txt: Read count table, with isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Leucojum_aestivum_isoform_TPM_salmon.txt: Transcripts per million table, with isoforms in the rows and accession numbers of samples in the columns.

organism: Leucojum aestivum

source_name: bulb

value: bulb


title: Eimeria acervulina Sporulated 30 months replicate 3

city: Bradenton

first: Matthew

middle: S

last: Tucker

state: Florida

address: 5000 Lakewood Ranch Blvd.

institute: LECOM

description: Library name: Sporulated 30 months-rep3

data_processing:
Geneious Prime 2024.07
Sequence reads (forward, reverse) were imported into Geneious Prime and paired
Reads were paired and trimmed with the plugin BBDUK (v. 38.84) with settings: minimum quality 20, Trim Low quality; minimum overlap 20, Trim adapters based on paired rad overhangs; minimum length 30 bp, discard short reads
Trimmed reads were aligned to the NCBI E. acervulina Houghton reference strain sequence EAH001 using the Geneious RNA mapper. After mapping, expression metrics were calculated per sample, including Transcripts Per Million (TPM). Data were screened for genes meeting specified thresholds throughout the time course.  The DESeq2 package, as implemented in Geneious, calculated pairwise differential expression between 0 and 30 month cohorts in grouped technical replicates.  We used thresholds of log2 fold change (FC) >1.5 or <-1.5 with adjusted p-value <0.05 to determine significantly differentially expressed genes. Significantly differentially regulated  genes meeting specified criteria were identified for further analysis.
Assembly: NCBI assembly EAH001 and ToxoDB v68
Supplementary files format and content: Aged E. acervulina mean TPM.xlsx contains mean TPM per cohort
Supplementary files format and content: Aged E. acervulina Mean log2 mapped reads.xlsx contains mean log2 mapped reads for cohorts

organism: Eimeria acervulina

source_name: oocyst

growth_protocol: Broiler chickens wre infected by oral gavage with xx oocysts of E. acervulina strain APU-1 . This experiment involved multiple propagations of oocysts that were ultimately stored at 4°C for various time periods, up to 30 months.

extract_protocol:
Total RNA was extracted from frozen oocyst Trizol pellets (unsporulated and sporulated cohorts).  Oocysts were thawed and ground with a Teflon pestle. Homogenates werre mixed with chloroform and centrifuged at 12,000 g for 15 minutes at 4°C. The upper aqueous phase was transferred to new tubes and mixed with isopropanol to precipitate total RNA. Total RNA was then washed with 75% ethanol and dried before resuspending in molecular grade DEPC-treated water. Total RNA was quantified using a ThermoFisher Scientific Qubit 3.0 fluorometer and quality was assessed using an Agilent Bioanalyzer 2100 (with RNA 6000 nano kit) and Agilent Tapestation 4150 (with High Sensitivity Screen Tape and reagents). RNA samples were frozen at -80°C. Prior to RNA-Seq, DNA was removed from total RNA with an Invitrogen Turbo DNA-free kit.
Libraries were produced from ~200 ng of total RNA from three techincal replicates per cohort using an Illumina stranded mRNA Prep Kit (ligation). For some libraries, excess Illumina adapter was removed by gel electrophoresis size selection using a Blue Pippin instrument. Bioanalyzer and Tapestation analysis determined the average library size of cohorts ranged 324-379 bp. Libraries were sequenced on a MiSeq using a 600 cycle MiSeq Reagent kit at 15 pM loading concentration.

treatment_protocol: This experiment involved multiple oocyst propagations that created separate batches of oocysts that were stored at 4°C. Each propgation was essentially the same. On day six post-inoculation, feces from each bird infected with E. acervulina were harvested.  Oocysts were isolated from chicken feces by flotation on saturated salt solution and washed with water.  The final preparation of oocysts was resuspended in 2% v/v potassium dichromate and incubated in a 29°C shaking water bath with aeration. For one propagation, a sample of unsporulated oocysts was collected prior to incubation and saved for RNA extraction. In another propagation, oocysts were allowed  to sporulate for 24 hours and a sample was collected and saved for RNA extraction after 24 hours (0 months, sporulated sample). In all other propagations, sporulated oocysts were stored in bottles at 4C. After certain periods of storage at 4C (4, 8, 13, 18, 25, 29, 30 months), samples were collected from bottles for RNA extraction. Each oocyst sample was washed with deionized water and then incubated with sodium hypochlorite for 15 minutes. Oocysts were washed again repeatedly and Trizol was added to the pellets before freezing at -80°C.

tag: strain

value: oocyst

tag: time

value: 30 months

tag: source

value: oocysts from chicken feces


title: IP Sham (Immunoprecipitated RNA fraction from the Sham control group) rep 3

description: Library name: NKHV9

value: Anterior Cingulate Cortex

value: wildtype, C57BL6/J, injected in the Habenula with an AAVrg-CaMKIIa-m.Cherry-RPL10a-WPRE-SV40


title: RHH8992: ArteryTL:short, BloodTL:short

description: Library name: RHH8992

value: Arterial wall


title: RHH8991: ArteryTL:long, BloodTL:long

description: Library name: RHH8991


title: overhang_screen_6mer_rep3

description:
Screen for ligation overhang sequences, 6-mer length
Ligation overhang screen


title: IP Sham (Immunoprecipitated RNA fraction from the Sham control group) rep 2

description: Library name: NKHV8


title: Eimeria acervulina Sporulated 30 months replicate 2

description: Library name: Sporulated 30 months-rep2

tag: cell type


title: overhang_screen_6mer_rep2


title: IP Sham (Immunoprecipitated RNA fraction from the Sham control group) rep 1

description: Library name: NKHV7

tag: treatment


title: RHH8989: ArteryTL:long, BloodTL:short

description: Library name: RHH8989

tag: tissue


title: Eimeria acervulina Sporulated 30 months replicate 1

description: Library name: Sporulated 30 months-rep1


title: Input (Input RNA fraction), naive mice rep 3

description: Library name: NKHV6

extract_protocol:
P2695
Absolutely Nanoprep kit (Agilent),with DNase treatment
P2695 : Full length cDNA were generated from 1 ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.
P2836 : Full length cDNA were generated from 1ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

tag: genotype

value: NA (naive mice)


title: overhang_screen_6mer_rep1


title: Eimeria acervulina Sporulated 29 months replicate 3

description: Library name: Sporulated 29 months-rep3

value: 29 months


title: RHH8988: ArteryTL:long, BloodTL:short

description: Library name: RHH8988


title: PaTu-8902_xenograft

type: genomic

city: Shinagawa-ku

first: Takahiro

last: Ebata

state: Tokyo

department: Epigenomics

country: Japan

institute: Hoshi University

hyb_protocol: Bisulfite converted DNA was amplified. Fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (Hiscan) and standard recommended Illumina scanner setting

data_processing:
RnBeads package in R environment (v4.1.1)
Average Beta

label: Cy3 and Cy5

source_name: Pancreas

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted using EpiTect bisulfite kit (Qiagen)

value: Pancreas

tag: cell line

value: cancer


title: Input (Input RNA fraction), naive mice rep 2

description: Library name: NKHV5


title: Eimeria acervulina Sporulated 29 months replicate 2

description: Library name: Sporulated 29 months-rep2


title: PaTu-8902


title: RHH8987: ArteryTL:short, BloodTL:short

description: Library name: RHH8987


title: Input (Input RNA fraction), naive mice rep 1

description: Library name: NKHV4


title: Eimeria acervulina Sporulated 29 months replicate 1

description: Library name: Sporulated 29 months-rep1


title: RHB10331: ArteryTL:long, BloodTL:long

description: Library name: RHB10331


title: RKO_xenograft

source_name: Colon

value: Colon

value: RKO


title: IP (Immunoprecipitated RNA fraction), naive mice rep 3

description: Library name: NKHV3


title: Eimeria acervulina Sporulated 25 months replicate 3

description: Library name: Sporulated 25 months-rep3

value: 25 months


title: RHB10330: ArteryTL:long, BloodTL:short

description: Library name: RHB10330


title: RKO


title: IP (Immunoprecipitated RNA fraction), naive mice rep 2

description: Library name: NKHV2


title: Eimeria acervulina Sporulated 25 months replicate 2

description: Library name: Sporulated 25 months-rep2


title: RHB10329: ArteryTL:long, BloodTL:short

description: Library name: RHB10329


title: Mouse_methylated DNA②

value: brain

value: normal


title: IP (Immunoprecipitated RNA fraction), naive mice rep 1

description: Library name: NKHV1


title: Eimeria acervulina Sporulated 25 months replicate 1

description: Library name: Sporulated 25 months-rep1


title: RHB10328: ArteryTL:long, BloodTL:short

description: Library name: RHB10328


title: Arhgef11Sglt2_DOCA,rep2

description: Library name: A2263_Arhgef11Sglt2_DOCA_S14

value: Kidney


title: Mouse_methylated DNA①


title: Cal_3, Visium

city: Lebanon

first: Edward

last: Usherwood

state: NH

address: Rubin Building, Level 7, 710-53

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

description:
Library name: 137658_6
Fresh froxen spatial transcriptome sequencing

data_processing:
The 'spaceranger count' pipeline (10X Genomics) was used to process raw image and FASTQ files to generate matricies of raw counts using reference mm10-2020-A, Visium Mouse Transcriptome Probe_Set v1, and arguments --cytassist and --image set to the Cytassist image and brightfield microscope image, respectively
Spatial Transcriptomics (ST) data preprocessing and analysis was performed using the Seurat R framework v5.1.0 on the merged ST data across the three CAL-101 and control replicates.
ST analysis pipeline included normalization, variable feature identification, data scaling, linear dimensionality reduction, clustering and non-linear dimensionality reduction. Gene set testing analysis for ST data was performed using the VAM R package v1.1.0.
Assembly: mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.tsv.gz : gene expression counts in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg : aligned fiducials of the itssue image
Supplementary files format and content: detected_tissue_image.jpg : image of tissue and spots
Supplementary files format and content: scalefactors_json.json : scale factors in json format
Supplementary files format and content: tissue_hires_image.png : hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png : low-res image of tissue
Supplementary files format and content: spot_annotations.csv: provides spot level annotation data from downstream analysis
Supplementary files format and content: spot_annotation_dictionary.xlsx provides description for variables in spot_annotations.csv
Library strategy: Spatial Transcriptomics

source_name: resected tumor from skin

growth_protocol: B16-F10 melanoma cells were intradermally injected into B6.129S7-Rag1tm1Mom/J mice

extract_protocol:
Half tumors were resected from the skin and embedded into FFPE blocks.
Visium CytAssist spatial gene expression (10x Genomics)

treatment_protocol: 1 million Pmel Thy1.1 CD8+ T cells were retro-orbitally injected into tumor bearing mice.

value: resected tumor from skin

value: Idelalisib (CAL-101)


title: Human_DNA40%  mixed with mouse_DNA60%②


title: RHB10327: ArteryTL:short, BloodTL:long

description: Library name: RHB10327


title: Eimeria acervulina Sporulated 18 months replicate 3

description: Library name: Sporulated 18 months-rep3

value: oocyst

value: 18 months


title: Cal_2, Visium

description:
Library name: 137658_4
Fresh froxen spatial transcriptome sequencing


title: Eimeria acervulina Sporulated 18 months replicate 2

description: Library name: Sporulated 18 months-rep2

value: oocysts from chicken feces


title: Human_DNA40%  mixed with mouse_DNA60%①


title: RHB10325: ArteryTL:long, BloodTL:long

description: Library name: RHB10325


title: IP Sham (Immunoprecipitated RNA fraction from the Sham control group) rep 4

description: Library name: NKHV10

value: Anterior Cingulate Cortex

value: wildtype, C57BL6/J, injected in the Habenula with an AAVrg-CaMKIIa-m.Cherry-RPL10a-WPRE-SV40

value: Sham


title: Cal_1, Visium

description:
Library name: 137658_2
Fresh froxen spatial transcriptome sequencing


title: Eimeria acervulina Sporulated 18 months replicate 1

description: Library name: Sporulated 18 months-rep1


title: overhang_screen_7mer_rep1

value: Artificial DNA


title: Human_DNA70% mixed with mouse_DNA30%②


title: RHB10324: ArteryTL:short, BloodTL:long

description: Library name: RHB10324

value: Arterial wall


title: Eimeria acervulina Sporulated 13 months replicate 3

description: Library name: Sporulated 13 months-rep3

value: 13 months


title: Ctrl_3, Visium

description:
Library name: 137658_5
Fresh froxen spatial transcriptome sequencing

value: vehicle


title: retina_ 7 day

first: Qingjian

last: Ou

address: NO.500, Zhennan Rd

department: Medical

institute: Tongji University

description:
Library name: Day7
10X Genomics

data_processing:
Raw sequencing data were processed with the Cell Ranger software (10X Genomics) for demultiplexing and alignment to a reference genome (GRCH38).
Assembly: hg38
Supplementary files format and content: Raw counts

source_name: Retina

extract_protocol:
Samples were taken by the suction blister method.Subsequently tissues were enzymatically digested, using trypsin for 45 minutes at 37°C. The resulting single cell suspension was then passed through 100µm and 40µm nylon meshes and through a dead cell removal column before further processing.
Single-cell RNA-seq was performed using the 10X Genomics Chromium Single Cell Controller with the Chromium Single Cell 3′ V3 Kit following the manufacturer's instructions.

value: Retina


title: RHH8990: ArteryTL:short, BloodTL:short

description: Library name: RHH8990


title: Eimeria acervulina Sporulated 13 months replicate 2

description: Library name: Sporulated 13 months-rep2


title: Human_DNA70% mixed with mouse_DNA30%①

value: Colon

value: cancer


title: Ctrl_2, Visium

description:
Library name: 137658_3
Fresh froxen spatial transcriptome sequencing


title: retina_ 3 day

description:
Library name: Day3
10X Genomics


title: Human_DNA②


title: Ctrl_1, Visium

description:
Library name: 137658_1
Fresh froxen spatial transcriptome sequencing


title: retina_ 0 day

description:
Library name: Day0
10X Genomics


title: Eimeria acervulina Sporulated 13 months replicate 1

description: Library name: Sporulated 13 months-rep1


title: Human_DNA①


title: siEgr2_6

city: Nanjing

first: Ming

last: Xiao

address: 101 Longmian Avenue

institute: NMU

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: medial prefrontal cortex

extract_protocol:
The differentiated OLs were treated with siEgr2 for 48 hours to knock out Egr2.RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA library was constructed using the Illumina platform according to the manufacturer’s instruction

value: medial prefrontal cortex

value: primery oligodendrocytes


title: Cal101-3, CSP

description:
Library name: 175396_0006, CSP
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Cal101-3_barcodes.tsv.gz
Cal101-3_features.tsv.gz
Cal101-3_matrix.mtx.gz

data_processing:
The 'cellranger multi' pipeline (10X Genomics) was used to process raw FASTQ files to generate matricies of read counts using genome reference mm10-2020-A and a custom feature barcoding reference detailing individually purchased TotalSeq-B antibodies (BioLegend)
Single-cell RNA-sequencing (scRNA-seq) preprocessing and analysis was performed using the Seurat R framework v5.1.0 on the merged scRNA-seq data across the three CAL-101 and control replicates. scRNA-seq analysis pipeline included normalization, variable feature identification, data scaling, linear dimensionality reduction, clustering, non-linear dimensionality reduction and differential expression analysis.
Cell-typing analysis for scRNA-seq data was performed using the SingleR R package v2.0.0. Additionally, gene set testing analysis and cytokine activity estimation was performed for scRNA-seq data using the VAM R package v1.1.0 and the scaper package v0.1.0, respectively.
mm10-2020-A
Assembly: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.tsv.gz : gene expression counts in Matrix Market Exchange format
Supplementary files format and content: cell_annotations.csv: provides spot level annotation data from downstream analysis
Supplementary files format and content: cell_annotation_dictionary.xlsx provides description for variables in spot_annotations.csv
Supplementary files format and content: feature_reference.csv: cellranger reference file for feature barcoding sequences

molecule: protein

extract_protocol:
Half tumors were resected from the skin, manually dissociated, processed with collagenase IV solution, then sorted for Live CD45.2+ cells on a BD FacsAria Fusion cell sorter. Cells were then incubated with the Total-Seq-B Mouse Universal Cocktail (BioLegend)
Chromium Single Cell NextGEM 3’ v3.1 kit with Feature Barcoding technology for Cell Surface Protein (10x Genomics, CG000390)

value: resected tumor from skin


title: Eimeria acervulina Sporulated 8 months replicate 3

description: Library name: Sporulated 8 months-rep3

value: 8 months


title: Eimeria acervulina Sporulated 8 months replicate 2

description: Library name: Sporulated 8 months-rep2

value: oocyst


title: Cal101-2, CSP

description:
Library name: 175396_0005, CSP
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Cal101-2_barcodes.tsv.gz
Cal101-2_features.tsv.gz
Cal101-2_matrix.mtx.gz

value: Idelalisib (CAL-101)


title: siEgr2_5


title: Cal101-1, CSP

description:
Library name: 175396_0004, CSP
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Cal101-1_barcodes.tsv.gz
Cal101-1_features.tsv.gz
Cal101-1_matrix.mtx.gz


title: siEgr2_4


title: Eimeria acervulina Sporulated 8 months replicate 1

description: Library name: Sporulated 8 months-rep1

value: oocysts from chicken feces


title: Control_3, CSP

description:
Library name: 175396_0003, CSP
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Control-3_barcodes.tsv.gz
Control-3_features.tsv.gz
Control-3_matrix.mtx.gz


title: siEgr2_3


title: Eimeria acervulina Sporulated 4 months replicate 3

description: Library name: Sporulated 4 months-rep3

value: 4 months


title: siEgr2_2


title: Eimeria acervulina Sporulated 4 months replicate 2

description: Library name: Sporulated 4 months-rep2


title: Control_2, CSP

description:
Library name: 175396_0002, CSP
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Control-2_barcodes.tsv.gz
Control-2_features.tsv.gz
Control-2_matrix.mtx.gz


title: Control_1, CSP

description:
Library name: 175396_0001, CSP
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Control-1_barcodes.tsv.gz
Control-1_features.tsv.gz
Control-1_matrix.mtx.gz


title: Eimeria acervulina Sporulated 4 months replicate 1

description: Library name: Sporulated 4 months-rep1


title: siEgr2_1


title: Cal101-3, scRNA-seq

description:
Library name: 175396_0006, scRNA-seq
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Cal101-3_barcodes.tsv.gz
Cal101-3_features.tsv.gz
Cal101-3_matrix.mtx.gz


title: FS1024_8

city: Moscow

first: Ivan

last: Kiselev

address: Ostrovitianov st. 1

country: Russia

institute: Pirogov Russian National Research Medical Universitty

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Illumina iScan array scanner and standard software with recommended Illumina scanner setting.

data_processing: Raw methylation data processing was performed using minfi R package v. 1.40.0. Quality control was assessed with the qcReport and plotQC functions. Functional normalization was performed using the SWAN (Subset-quantile Within Array Normalization) method via the preprocessSWAN function. Probes with a detection p-value above 0.01, multi-hit probes, probes containing single nucleotide polymorphisms (SNPs) and probes located on sex chromosomes (X and Y) were excluded from the subsequent analysis to avoid potential confounding effects. Cell type composition for each sample was estimated from the raw data using the estimateCellCounts function with an appropriate reference dataset. Statistical differences in cell proportions between sample groups were evaluated using Tukey's HSD test. Beta values were converted to M-values for statistical modeling.

source_name: PBMCs

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from PBMCs using Qiagen DNA Mini Kit according to standard instructions.

value: PBMCs

value: Glatiramer acetate

tag: timepoint

tag: patientid

value: female


title: siNC_6

value: NC


title: Eimeria acervulina Sporulated 0 months replicate 3

description: Library name: Sporulated 0 months-rep3

value: 0 months


title: FS1022_8

tag: Sex


title: Cal101-2, scRNA-seq

description:
Library name: 175396_0005, scRNA-seq
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Cal101-2_barcodes.tsv.gz
Cal101-2_features.tsv.gz
Cal101-2_matrix.mtx.gz


title: Eimeria acervulina Sporulated 0 months replicate 2

description: Library name: Sporulated 0 months-rep2


title: siNC_5


title: Cal101-1, scRNA-seq

description:
Library name: 175396_0004, scRNA-seq
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Cal101-1_barcodes.tsv.gz
Cal101-1_features.tsv.gz
Cal101-1_matrix.mtx.gz


title: Eimeria acervulina Sporulated 0 months replicate 1

description: Library name: Sporulated 0 months-rep1


title: siNC_4


title: FS1018_8


title: FS1020_8


title: Eimeria acervulina Unsporulated replicate 3

description: Library name: Unsporulated-rep3

value: Unsporulated


title: Control_3, scRNA-seq

description:
Library name: 175396_0003, scRNA-seq
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Control-3_barcodes.tsv.gz
Control-3_features.tsv.gz
Control-3_matrix.mtx.gz

value: vehicle


title: FS1024_4


title: siNC_3


title: FS1022_4


title: Control_2, scRNA-seq

description:
Library name: 175396_0002, scRNA-seq
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Control-2_barcodes.tsv.gz
Control-2_features.tsv.gz
Control-2_matrix.mtx.gz


title: Eimeria acervulina Unsporulated replicate 2

description: Library name: Unsporulated-rep2


title: siNC_2


title: FS1020_4


title: FS1018_4


title: Control_1, scRNA-seq

description:
Library name: 175396_0001, scRNA-seq
single cell 3' sequencing with Feature Barcoding technology for Cell Surface Protein
Control-1_barcodes.tsv.gz
Control-1_features.tsv.gz
Control-1_matrix.mtx.gz


title: Eimeria acervulina Unsporulated replicate 1

description: Library name: Unsporulated-rep1


title: siNC_1


title: E13.5 Notch-induced ovaries from Nr5a1-cre dams-rep6

status: Public on Jun 02 2026

city: Research Triangle Park

first: Yu-Ying

last: Chen

address: 111 TW Alexander Dr

institute: National Institute of Environmental Health Sciences

description:
Library name: Sample13
36Sf1notch

data_processing:
For single-cell analysis, FASTQ files were processed using CellRanger (v. 7.0.0) with default setting using a custom mm10 reference genome that incorporated the sfGFP-Myc reporter allele, which contains two copies of superfolder GFP (sfGFP) followed by six Myc epitope sequences.  For RNA-seq analysis, raw paired-end FASTQ files were trimmed using Trim Galore (v. 0.6.10), with the following parameters: --quality 20, --illumina, --stringency 5, --length 20, and --paired. The mm10 reference genome and NCBI RefSeq GTF annotation were downloaded from the UCSC Genome Browser on January 9, 2025 and used to generate a STAR (v. 2.6.0c) genome index. Trimmed reads were aligned to the mm10 reference using STAR, producing coordinate-sorted BAM files, which were indexed with samtools (v. 1.18). Gene-level quantification was performed with featureCounts (Subread, v. 2.0.6) using the RefSeq annotation, specifying paired-end mode (-p) and reverse-stranded orientation (-s 2).
Assembly: mm10
Supplementary files format and content: CellRanger filtered_feature_bc_matrix output files for single-cell analysis and count matrix for RNA-seq analysis

source_name: Ovary

extract_protocol:
For single cell collection, ovary pairs from E16.5 Hes1+/CreERT2; ROSA+/Sun1-sfGFP animals that were lineage-labeled at E10.5 (1 injection of 1mg/10g body weight tamoxifen (Sigma-Aldrich, T5648) in corn oil ( Sigma-Aldrich, C8267)) were collected in ice-cold 1X PBS containing 0.04% bovine serum albumin (BSA; Sigma, A9576), cut into smaller pieces, and transferred into dissociation buffer: 0.04% BSA, 1.2 U/mL Dispase II (Millipore Sigma, 4942078001), 1 mg/mL collagenase B (Millipore Sigma, 11088807001), and 5 U/mL DNase I (Millipore Sigma; 101041590001) in 1X PBS. Tissue pieces were incubated at 37 °C and gently pipetted every 5 min for 20 – 30 min. To stop the enzymatic reaction, tissues were diluted with an equal volume of cold 0.04% BSA/ PBS, passed through a 40 µm FLOWMI cell strainer (SP Bel-Art, 136800040), and washed by pelleting at 350 rcf for 5 min at 4 °C, before resuspending in 110 µL cold DMEM/F12 (Thermo Fisher, 11330032). Cells were cryopreserved by adding 1:1 filtered cryoprotectant (20% DMSO in heat-inactivated FBS, HI-FBS; Thermo Fisher, 16140071) and frozen at −80°C, with each pair of the ovary in a cryovial, before long-term storage in liquid nitrogen. Once genotypes were further confirmed through PCR (Transnetyx, Inc), two cryovials containing sfGfp+ cells were rapidly thawed at 37°C for 1 min and pooled into one new 1.5 mL tube. This pooled sample contained cells from four ovaries from two animals carrying the sfGfp allele. The cryovial was rinsed three times with 300 µL of 10% HI-FBS/ DMEM/F12 pre-warmed at 37 °C using wide-bore tips, adding each rinse dropwise with gentle agitation. Cells were pelleted at 350 rcf for 5 min at 4 °C, resuspended in 50 µL 0.04% BSA/ PBS.  For bulk RNA-seq, E13.5 Notch-induced (Tg(Nr5a1-cre)+; ROSA+/Notch) and control (Tg(Nr5a1-cre)+; ROSA+/+) ovary pairs were collected. As matings were performed by crossing either male or female Tg(Nr5a1-cre) with ROSA+/Notch, we collected two pairs of Notch-induced ovaries from ROSA+/Notch dams, four pairs of Notch-induced ovaries from Tg(Nr5a1-cre) dams, three pairs of control ovaries from ROSA+/Notch dams, and three pairs of control ovaries from Tg(Nr5a1-cre) dams, yielding six biological replicates for each genotype. Each ovary pair was dissected and snap-frozen in 50 µL of extraction buffer from the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, 12204-01) and stored at −80°C. For RNA isolation, samples were thawed on ice, vortexed, mixed with an equal volume of 70% ethanol, and applied to pre-conditioned columns. On-column DNA digestion was performed using the RNase-Free DNase Set (Qiagen, 79254), at a final concentration of around 0.34 U/µL for 15 min at RT. After two washes, RNA was eluted in 11 µL of elution buffer. RNA quantity and quality were measured using the Qubit RNA High Sensitivity kit (Invitrogen, Q32852) and the High Sensitivity RNA Screen Tape Analysis (Agilent, 5067-5579) on the Agilent TapeStation 4200.
Library preparation and sequencing were performed at the NIEHS Epigenomics and DNA Sequencing Core Facility. For single-cell RNA-seq, cells were counted and examined for viability with AO/PI staining using a Luna FX7cell counter (Logos Biosystems). Up to 16,000 live cells were loaded into the Single Cell Chip to generate single cell emulsion in Chromium Controller with Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics, 1000268). Reverse transcription of mRNA and cDNA amplification were carried out following the manufacture’s instruction (10x Genomics, 1000268). The amplified cDNA was further fragmented to construct NGS libraries. Sequencing was performed on an Illumina NovaSeq 6000 using a S1 flow cell with i7 index 10bp, i5 index 10bp, achieving a depth of ~20,000 read pairs per cell.  For bulk RNA-seq, Libraries were made using the TruSeq Stranded mRNA (Illumina, 20020594) according to the manufacturer’s protocol. Approximately 250 ng of total RNA from each sample was used for poly(A) mRNA enrichment followed by cDNA synthesis and library construction. Sequencing was performed on an Illumina NextSeq 500 sequencer using a SP flow cell to generate paired-end 150-bp reads. Sequencing yielded ~80 million reads per sample. FASTQ files were generated using bcl2fastq/DRAGEN with default parameters.

value: Ovary

value: Tg(Nr5a1-cre)+; ROSA+/Notch


title: E13.5 Notch-induced ovaries from Nr5a1-cre dams-rep5

description:
Library name: Sample12
30Sf1notch


title: E13.5 Notch-induced ovaries from Nr5a1-cre dams-rep3

description:
Library name: Sample10
25Sf1notch


title: E13.5 Notch-induced ovaries from Nr5a1-cre dams-rep4

description:
Library name: Sample11
20Sf1notch


title: FS1024_0

value: No


title: E13.5 Notch-induced ovaries from ROSA+/Notch dams-rep2

description:
Library name: Sample9
9NICDnotch


title: E13.5 Notch-induced ovaries from ROSA+/Notch dams-rep1

description:
Library name: Sample8
18NICDnotch


title: FS1022_0


title: E13.5 control ovaries from Nr5a1-cre dams-rep6

description:
Library name: Sample7
29Sf1ctrl

value: Tg(Nr5a1-cre)+; ROSA+/+


title: E13.5 control ovaries from Nr5a1-cre dams-rep5

description:
Library name: Sample6
24Sf1ctrl


title: E13.5 control ovaries from Nr5a1-cre dams-rep4

description:
Library name: Sample5
23Sf1ctrl


title: FS1020_0


title: E13.5 control ovaries from ROSA+/Notch dams-rep2

description:
Library name: Sample3
17NICDctrl


title: E13.5 control ovaries from ROSA+/Notch dams-rep3

description:
Library name: Sample4
7NICDctrl


title: E13.5 control ovaries from ROSA+/Notch dams-rep1

description:
Library name: Sample2
14NICDctrl


title: Refed, KO, rep6

city: Edmonton

first: Richard

last: Lehner

state: Alberta

address: 315 Heritage Medical Research Centre, 11207 - 87 Ave

department: Pediatrics

institute: University of Alberta

hyb_protocol: Biotin-labeled sense-strand cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST arrays for 16 hours at 45 °C. Arrays were washed using Affymetrix Fluidics Station 450 protocol (FS450_0002) .

scan_protocol: Affymetrix GeneChip Scanner 3000.

data_processing: Raw CEL files were extracted with R. The intensity values were processed using the rma() function from the oligo package, which performs background correction, quantile normalization, and probe summarization to generate gene-level expression values.

label: biotin

source_name: Refed, KO

label_protocol: Sense-strand cDNA was prepared from total RNA using the Affymetrix WT PLUS Kit and labeled with biotin using biotin allonamide triphosphate.

growth_protocol: AADAC KO and WT mice were fed with western-type diet for one week. Intestinal mucosa was collected in the 12-hour fasted or 2-hour refed states.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and RNA integrity was confirmed using Agilent 2100 Bioanalyzer RNA Nanochips (Agilent Technologies).

treatment_protocol: Intestinal mucosa was collected and snap frozen in liquid N2

value: Small intestine

value: AADAC KO

value: Male

value: 2-hour refeeding, 1 week of western-type diet feeding


title: FS1018_0


title: Refed, KO, rep5


title: Refed, KO, rep4


title: Refed, KO, rep3


title: Refed, WT, rep3

source_name: Refed, WT

value: AADAC WT


title: Refed, WT, rep5


title: Refed, KO, rep2


title: Refed, WT, rep2


title: Refed, WT, rep6


title: Refed, KO, rep1


title: Refed, WT, rep1


title: Refed, WT, rep4


title: Fasted, KO, rep5

source_name: Fasted, KO

value: 12-hour fasting, 1 week of western-type diet feeding


title: Fasted, KO, rep4


title: Fasted, KO, rep2


title: Fasted, KO, rep3


title: Treated to CBRV1-10493 200nM replicate 3

city: Incheon

first: Jeong-In

last: Park

address: 119, Academy-ro

institute: Incheon National University

description: Library name: Ub3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: brain

value: glioblastoma; astrocytoma


title: Treated to CBRV1-10493 200nM replicate 2

description: Library name: Ub2


title: Fasted, WT, rep6

source_name: Fasted, WT


title: Fasted, WT, rep5


title: Fasted, WT, rep4


title: Fasted, WT, rep3


title: Fasted, WT, rep1


title: Fasted, WT, rep2


title: Fasted, KO, rep1


title: Treated to NnK-1 200nM replicate 3

description: Library name: Ug3


title: Treated to CBRV1-10493 200nM replicate 1

description: Library name: Ub1


title: Treated to NnK-1 200nM replicate 2

description: Library name: Ug2


title: Treated to NnK-1 200nM replicate 1

description: Library name: Ug1


title: Control replicate 3

description: Library name: UC3


title: Control replicate 1

description: Library name: UC1


title: VMCUB1, ctrl, rep1 (RNA)

city: Gif-sur-Yvette

first: Lilia

last: Estrada Virrueta

address: 1, Avenue de la Terrasse

description:
Library name: VMCUB1_ctrl_1
3'RNA-seq

data_processing:
Reads were mapped to the UCSC hg19 genome and then counted using star (v2.7.6a).
Statistically significant differences in gene expression were determined by performing a differential analysis using DESeq2 (v1.30.1)
Assembly: hg19
Supplementary files format and content: csv file includes TPM values for each sample

growth_protocol: Cells were cultured in DMEM (MGHU3, VMCUB1) supplemented with 10% fetal bovine serum at 37°C under a 5% CO2 atmosphere.

extract_protocol:
RNA isolates from siTP63-transfected and control cells were prepared using the Qiagen RNA easy minikit supplemented with DNase treatment.
Library were prepared using the QuantSeq 3’mRNA library prep kit.

treatment_protocol: Cells were transfected for 48h with 5 nM siRNA and Lipofectamine RNAi Max reagent (Invitrogen).

value: WT


title: Control replicate 2

description: Library name: UC2


title: VMCUB1, siTP63_83, rep2 (RNA)

description:
Library name: VMCUB1_siTP63_83_2
3'RNA-seq

value: TP63 knockdown