title: NMR_lung_animal#514, rep 3

city: Tampa

first: Joseph

last: Kissil

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: H Lee Moffitt Cancer Center and Research Institute

description:
Library name: 514-Count
10X Genomics Chromium 3'

data_processing:
Data processing, including demultiplexing, barcode processing, alignment, and gene counting, was carried out with the 10X Genomics CellRanger v8.0.0 software, and results were visualized using the 10X Genomics Loupe Browser v8.0. Data analysis methods are provided in the Supplementary Information
Assembly: Naked_mole-rat_maternal, INSDC Assembly GCA_944319715.1
Supplementary files format and content: Tab-separted value files and matrix files

organism: Heterocephalus glaber

source_name: Lung

extract_protocol:
Lungs were inflated with 1X PBS and collected from NMR and mice. Tumors were removed from normal tissue manually using forceps and scissors. Tumors were dissociated into single cells as described in the supplementary methods. Cell suspensions were washed twice with 1X PBS containing 0.04% BSA.
Single-cell RNA sequencing was conducted using the 10X Genomics Chromium X/IX (10X Genomics, Pleasanton, CA) at the Molecular Genomics Core of the Moffitt Cancer Center and Research Institute. Following wash steps, cells were resuspended in the same buffer (1X PBS with 0.04% BSA) according to the 10X Genomics cell preparation protocol. Cell viability and counts were assessed using AO/PI dual fluorescent staining and analyzed with the Nexcelom Cellometer K2 (Nexcelom Bioscience LLC, Lawrence, MA). Subsequently, cells were loaded onto the 10X Genomics Chromium Single Cell Controller at a concentration of 1,000 cells/µl, aiming to encapsulate 10,000 cells per sample. Individual cells, reagents, and 10X Genomics gel beads were encapsulated into nanoliter-sized Gel Beads in Emulsion (GEMs). Reverse transcription of poly-adenylated mRNA occurred within each droplet at 53°C. cDNA libraries were prepared in a single bulk reaction following the 10X Genomics Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 guidelines, and 50,000 sequencing reads per cell were generated using the Illumina NovaSeq 6000 instrument

value: Lung

tag: genetic modification

value: Eml4-alk inversion, loss of Rb and p53

tag: timepoint

value: 15 weeks post infection


title: H3K27me3 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep2 (ChIP)

status: Public on Aug 19 2025

type: SRA

city: Vienna

first: Vikas

last: Shukla

state: Vienna

address: Dr.Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description: Library name: TH28

library_source: genomic

data_processing:
Reads were trimmed with Trim Galore with options --stringency 1  --length 5 --paired
Trimmed reads were aligned to reference genome MpTak1v7.1 using bowtie2 with --sensitive option
Aligned SAM files were converted to sorted BAM files using samtools
Aligned sorted BAM files for ChIP and Iput samples were used to create BigWig files using deeptools like this: bamCompare -b1 ${test_bam} -b2 ${control_bam} -o ${out}.bw -p max
Assembly: https://marchantia.info/data/MpTak1_v7.1/
Supplementary files format and content: BigWig file containing ChIP signal normalized to input

molecule: genomic DNA

organism: Marchantia polymorpha

source_name: 14d thalli

growth_protocol: Plants were cultured on half-strength Gamborg’s B5 medium solidified with 1% (w/v) agar under continuous white light at 22°C

extract_protocol:
Two-week-old thalli started from gemmae of M. polymorpha Tak-1 wild type were collected and cross-linked using 1% formaldehyde in 1× PBS under vacuum on ice for 10 min. The cross-linking reaction was quenched by adding 2 M glycine to achieve a final concentration of 0.125 M under vacuum on ice for 10 min. Excess solution was removed from cross-linked tissue by blotting with paper towels. Cross-linked tissue was then snap frozen in liquid nitrogen and ground to a fine powder using mortar and pestle. The powder was transferred into a 50-ml plastic tube and suspended in 40 ml of MP1 buffer (10 mM MES-KOH buffer pH 5.3, 10 mM NaCl, 10 mM KCl, 0.4 M sucrose, 2% (w/v) PVP-10, 10 mM MgCl2, 10 mM 2-mercaptoethanol, 6 mM EGTA, 1× cOmplete protease inhibitor cocktail). Suspended samples were then filtered twice through one layer of Miracloth, once through a 40 μm nylon mesh, and twice through a 10 μm nylon mesh. Filtered samples were centrifuged at 3000 × g at 4°C for 10 min, and the supernatant was discarded. The pellet was washed using 15 ml of MP2 buffer (10 mM MES-KOH buffer pH 5.3, 10 mM NaCl, 10 mM KCl, 0.25 M sucrose, 10 mM MgCl2, 10 mM 2-mercaptoethanol, 0.2% Triton-X 100, 1× cOmplete protease inhibitor cocktail) three times. The final pellet was then resuspended in 5 ml of MP3 buffer (10 mM MES-KOH buffer pH 5.3, 10 mM NaCl, 10 mM KCl, 1.7 M sucrose, 2 mM MgCl2, 10 mM 2-mercaptoethanol, 1× cOmplete protease inhibitor cocktail) and centrifuged at 16 000 × g at 4°C for 1 h. After centrifugation, the supernatant was discarded, and the pellet was resuspended in 900 μl of covaris buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris–HCl pH 8.0, 1× cOmplete protease inhibitor cocktail). The resuspended pellet containing the chromatin fraction was fragmented using a Covaris E220 High-Performance Focused Ultrasonicator for 15 min at 4°C (duty factor, 5.0; peak incident power, 140.0; cycles per burst, 200) in a 1-ml Covaris milliTUBE. Sheared chromatin was centrifuged at 20 000 × g at 4°C for 10 min, and the supernatant was transferred into a new 5-ml tube and diluted by adding 2.7 ml of ChIP dilution buffer (0.01% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7mM Tris-HCl pH 8.0, 167 mM NaCl). Diluted chromatin was cleared by incubating with proteinA/G beads (Thermo Fisher Scientific, Waltham, MA, USA) at 20 rpm spinning at 4°C for 1 h. Beads were removed by magnetic racks and precleared chromatin was separated into five tubes and incubated with 1 μg of specific antibodies for histone H2A variants () at 20 rpm spinning at 4°C overnight. Chromatin bound by antibodies was collected by incubating with protein A/G beads for 3 h. The beads were collected by magnetic racks and washed twice with a low salt wash buffer (20 mM Tris–HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 0.1% SDS), once with a high salt wash buffer (20 mM Tris–HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 0.1% SDS), once with a LiCl wash buffer (10 mM Tris–HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL CA-630 and 0.1% sodium deoxycholate), and twice with a TE buffer (10 mM Tris–HCl pH 8.0 and 1 mM EDTA). Immunoprecipitated DNA was eluted using 500 μl elution buffer (1% SDS and 0.1 M NaHCO3) at 65°C for 15 min. To reverse cross-link, eluted DNA was mixed with 51 μl of reverse cross-link buffer (40 mM Tris–HCl pH 8.0, 0.2 M NaCl, 10 mM EDTA, 0.04 mg ml−1 proteinase K; Thermo Fisher Scientific) and incubated at 45°C for 3 h and then at 65°C for 16 h. After cross-link reversal, DNA was treated with 10 μg of RNase A (Thermo Fisher Scientific), incubated at room temperature for 30 min and purified using the MinElute PCR purification kit (Qiagen).
ChIP-seq library was generated from ChIPed DNAs using Ovation® Ultralow Library Systems V2 (Tecan, Männedorf, Switzerland).

tag: tissue

value: 14d thalli

tag: genotype

value: Mpez1,Mpknox2 double mutant


title: PBS-1

city: Stanford

first: Angela

last: Galdamez

state: California

address: 450 Jane Stanford Way

country: USA

institute: Stanford University

description: Library name: PBS-1

library_source: transcriptomic

data_processing:
Sequencing data was aligned to Mus_musculus_GCF_000001635.27_GRCm39 using the HISAT2 alignment program (v2.0.4)
Gene expression and normalized reads (in FPKM) were quantified using RSEM software (v1.2.18)
Differential expression analysis between control and drug-treated groups, along with the statistical significance, was determined using the DESeq2 package (v1.4.5)
Sequencing saturation-Perl script is used for sequencing saturation analysis.
Assembly: Integrative Genomics Viewer genome (IGV) browser to view the reads align to the genome
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: excel file includes FPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
Cornea and lens were removed and retina was harvested using Rneasy miniplus kit (Quagen)/ >2ug of total RNA eas used for the construction of sequencing libarieis.
DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing preperation - Stranded mRNA library

treatment_protocol: Salubrinal (10 μM), ISRIB (10 μM), Ceapin-A7 (10 μM), AA147 (10 μM) and Tunicamycin (10 μM) were all dissolved in sterile-filtered saline with 0.05-0.1% dimethyl sulfoxide. 1 μL of each drug was administored into both eyes via intravitreal injection using 33-gauge Hamilton syringe needle. For control, 1 μL of saline containing 0.05-0.1% of DMSO was administored into both eyes via intravitreal injection using 33-gauge Hamilton syringe needle.

value: Retina

value: WT

tag: treatment

value: PBS


title: HepG2 siControl replicate 3 QuantSeq Rev V2 3'end seq of whole cell RNA

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Biophysics

institute: University of Pennsylvania

description: Library name: WC_siNTP_3

data_processing:
Cutadapt was used to remove adapter sequences and polyA or polyT sequences.
Trimmed reads were aligned to the genome using STAR (v2.6.1a) with the following parameters --outFilterType BySJout --outFilterMultimapNmax 200 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6   --seedPerWindowNmax 10 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1
Uniquely mapped reads were used to generate bigwig coverage files for each strand. To call clusters, read coverage was for all samples was combined and polyA site (PAS) clusters were defined as continuous regions with more than 10 reads covering every position and more than 20 reads overall in the merged samples. The site of cleavage and polyadenylation was defined as the single nucleotide with highest coverage across merged samples. In the case of a tie, the 3’ most position was used.
Assembly: hg38
Supplementary files format and content: tab seperated file containing the read cluster boundaries, single position of highest coverage, and read counts for each sample.
Supplementary files format and content: bigwig files for forward and reverse strand containing all unique reads for each sample.

organism: Homo sapiens

growth_protocol: Low passage HepG2 cells were grown on 10 cm plates to 75% confluency in 10 mL DMEM+10% FBS

extract_protocol:
Cells were lysed on ice for 5 minutes in 10mM Tris-HCl pH 8.0, 0.32 sucrose, 3mM CaCl2,  2mM MgCl2, 0.1mM EDTA 0.1% NP40 1mM DTT plus 0.04U/ul RNasin. Total RNA was extracted using TRIzol following the manufacturer's protocol. For fractionation samples, low speed centrifugation was used to separate the fractions with the supernatant added to TRIzol for cytoplasmic and pellet lysed in TRIzol for nuclear fractions.
RNA quality for all samples and fractions was verified using a BioAnlyzer. Further QC and library preparation using QuantSeq Rev V2 (Lexogen) was carried out by Lexogen and subjected to single end, stranded sequencing.

treatment_protocol: Cells were treated with 120 pmol of DDX55 siRNA or non-targeting pool (NTP) siRNA  with 25 uL RNAiMAX with forward transfection protocol using Opti-MEM. Cells were harvested 45-50 hours post transfection and resuspended in 2 mL DPBS for RNA and protein extraction

tag: cell line

tag: cell type

value: hepatocellular carcinoma

value: siRNA non-targeting pool


title: J-Lat 10.6, p400, ChIP, unstimulated, Rep1

city: Jupiter

first: Susana

middle: T

last: Valente

state: FL

address: 130 Scripps Way

department: Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
644-13
P400_NS_n_of_2_NORMsort.bw
P400_NS_n_of_2_MACS2__peaks.broadPeak

data_processing:
FASTQC
Read trimming with trim_galore (--paired --length 24 --stringency 3)
Align with bowtie2 (-p 16 --no-mixed --no-discordant -1)
Removed duplicates with samtools
Peaks were called with macs2 (callpeak  --broad -f BAMPE -g hs -q 0.05 -B)
For visualization, bam files for replicates were merged using samtools, deepTools was used to convert BAM files to bedgraph format (bamCoverage), and and then the bdg files were normalized across samples to library size prior to conversion to bigwig format (bedGraphToBigWig).
Assembly: custom genome GRCh38 with HIV-R7/E-/GFP inserted into chromosome 9 at position 136,468,578, shifting the remaining chromosome 9 by 10,200 bp (the length of the HIV insertion), including a repeat of the “ACAAA” sequence in the SEC16A intron that became duplicated upon HIV integration
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak

source_name: J-Lat 10.6 cells

growth_protocol: J-Lat 10.6 cells were maintained in RPMI 1640 supplemented with 2.0 mM L-glutamine/100 U/ml penicillin/100 µg/ml streptomycin and 10% heat-inactivated FBS (complete RPMI) and cultured at 37°C and 5% CO2.

extract_protocol:
Native ChIP was performed using MNase to fragment chromatin to mono-to pentanucleosomes sizes.
ChIP DNA libraries for next-generation sequencing on the Illumina platform were constructed based on the protocol of NEB Next Ultra II DNA Library Prep Kit (#E7103, NEB) using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, # E6440S)

treatment_protocol: Cells were transduced with the indicated shRNAs in pMKO.1-puro. Two days post transduction cells were selected with 4 µg/ml puromycin for one week, after which cells were collected for Native ChIP-seq

value: J-Lat 10.6 cells

tag: chip antibody

value: Unstimulated


title: HepG2 siControl replicate 2 QuantSeq Rev V2 3'end seq of whole cell RNA

description: Library name: WC_siNTP_2


title: J-Lat 10.6, RNAPII, ChIP, TNFa, Rep1

description:
644-12
PolII_TNF_n_of_2_NORMsort.bw
PolII_TNF_n_of_2_MACS2__peaks.broadPeak

value: RNA polymerase II (Millipore, #05-623)

value: TNFa stimulated


title: H3K27me3 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep1 (ChIP)

description: Library name: TH27


title: HepG2 siControl replicate 1 QuantSeq Rev V2 3'end seq of whole cell RNA

description: Library name: WC_siNTP_1


title: NMR_lung_animal#394, rep 1

description:
Library name: 394-Count
10X Genomics Chromium 3'

library_source: transcriptomic single cell

molecule: polyA RNA


title: 231 -G EV, rep1

city: wuhan

first: Wei

last: Yan

state: Hubei

address: Bayi Street 229 in Wuchang district

department: College of life science

country: China

institute: Wuhan University

description: 231-G EV-1

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller soft-ware, v1.8).
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5’,3‘-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature miRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor miRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2. The abundance of miRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads(CPM).
The miRNAs differentially expressed are screened based on the count value with R package edgeR.
For 231 EV-2 and 231-G EV-2, after cluster generation, the library preparations were sequenced on an Illumina platform and 50 bp single-end reads were generated. The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HIASAT software. The mapped reads of each sample were assembled by StringTie in a reference-based approach. Low-quality bases (Sanger base quality of < 20) of the 3’ end were trimmed using in-house perl scripts, and then the sequencing adapters were removed with the fastx toolkit software.All identical sequences of sizes ranging from 18 to 32nt were counted and eliminated from the initial data set.The assembled unique sequences were used for a BLAST search of the Rfam database, version 10.1, to remove non-miRNA sequences (rRNA, tRNA, snoRNA etc.). Bowtie2 was used to annotate the chromosomal location against the reference genome data. Through a BLAST search of the miRbase, version 21.0, the highly matched sequences were used to count and analyze the known miRNA expression profile. The characteristics of hairpin structure of miRNA precursor could be used to predict novel miRNA. Mireap or miRDeep2 were used to predict novel miRNA, and the Dicer cleavage site and the minimum free energy of the small RNA tags were unannotated in the former steps. Meanwhile, in-house scripts were used to obtain the identified miRNA base bias on the first position with certain length and on each position of all identified miRNA.The expression level of each miRNA was calculated according to the transcripts TPM method.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts and CPM/TPM values for each Sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3‘-aminoacyl (charged)deacylation to 3‘-OH for 3’-adaptor ligation, 3‘-cP (2’,3‘-cyclic phosphate) removal to 3’-OH for 3‘-adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5‘-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. For 231 EV-2 and 231-G EV-2, RNA was prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA) using 1 μg of total RNA.
1) 3’-adapter ligation; 2) 5‘-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 134∼160bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range).For 231 EV-2 and 231-G EV-2, sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: When MDA-MB-231 cells fusion reaches 90%, replace with EV free DMEM or glucose free medium and continue to culture for 12 h. The medium was collected and pre-cleared by centrifugation at 500 × g for 15 min and then at 10,000 × g for 20 min.EVs were pelleted by ultracentrifugation at 110,000 × g for 70 min, and resuspended in PBS.

value: epithelial cell


title: NPR1-GFP hy5-R3

city: Peking

first: Liu

last: Pengtao

state: Peking

address: West Campus of China Agricultural University, Haidian District, Beijing

department: College of Plant Protection

institute: China Agriculture University

description: Library name: NPR1-GFP hy5-R3

data_processing:
The clean data were aligned to the Arabidopsis Col-0 genome (TAIR10) using the HISAT2 program with default parameters.
Assembly: TAIR10.1
Supplementary files format and content: Comma-Separated Values file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Seeds were first surface-sterilized with 70% ethanol containing 0.05% Tween® 20 for 10 minutes, then washed four times with sterilized water, stratified at 4℃ for 3 days, and grown on MS plates containing 1% sucrose at 22°C under white-light conditions (100 μmol m–2 s–1; 16 hours light/8 hours dark) for all experiments. Plants for pathogen inoculation were grown in a Percival chamber with controlled light, temperature (22 ± 0.2°C), and humidity (65%) under an 8-hour light/16-hour dark photoperiod. Light was set at 100 µmol m−2 s−1 during the day and 0 µmol m−2 s−1 at night. To reduce location effects, plant trays were moved to random locations within the growth chambers every two days

extract_protocol:
Leaves collected from 3-week-old plants infiltrated with Pst DC3000 (2 × 105 cfu/mL) or a control were ground to powder in liquid nitrogen, total RNA was extracted using TRIzol® Reagent (Invitrogen, 15596018) according to the manufacturer’s instructions.
The library construction was carried out by BGI (Beijing Genomics Institute)

treatment_protocol: Leaves of 3-week-old Arabidopsis infiltrated with Pst DC3000 at 0 or 24 hours post infiltration

value: leaves

value: NPR1-GFP hy5

value: leaves of 3-week-old Arabidopsis infiltrated with Pst DC3000 at 24 hours post infiltration


title: NMR_lung_animal#510, rep 2

description:
Library name: 510-Count
10X Genomics Chromium 3'

value: Lung

value: Eml4-alk inversion, loss of Rb and p53


title: FCDIIB spatial transcriptomics, sample H

city: Toronto

first: Phedias

last: Diamandis

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

description: Library name: SpRNAseq_FCDIIB_H

data_processing:
SpaceRanger-2.1.1
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz (spatial barcodes); features.tsv.gz (gene IDs); matrix.mtx.gz (gene expression counts); aligned_fiducials.jpg (aligned fiducials of tissue image); detected_tissue_image.jpg (image of tissue and spots); scalefactors_json.json (scalefactors); tissue_hires_image.png (hi res tissue image); tissue_lowres_image.png (low res tissue image); tissue_positions.csv (index of spot barcodes and coordinates)
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Region of interest selection was supported by a deep learning tool and supervised by a pathologist. Formalin-fixed paraffin-embedded (FFPE) tissue sections were prepared following the Visium CytAssist Tissue Preparation Guide (CG000518, 10X Genomics).
Library construction and sequencing were conducted following the Visium CytAssist Spatial Gene Expression Reagent Kits User Guide (CG000495, 10X Genomics).

value: Brain


title: 231 EV, rep1

description: 231 EV-1


title: Input wild-type Tak1, 14d thalli, biol rep1 (Input)

description: Library name: TH25

value: 14d thalli

value: wild-type Tak1


title: NPR1-GFP hy5-R2

description: Library name: NPR1-GFP hy5-R2


title: FCDIIB spatial transcriptomics, sample G

description: Library name: SpRNAseq_FCDIIB_G


title: NPR1-GFP hy5-R1

description: Library name: NPR1-GFP hy5-R1


title: H3 ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH24


title: SW1353 YBX1 irCLIP replicate 3

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

description: Extracted RNA was reverse transcribed using primer irCLIP_ddRT_31 /5Phos/ WWW CGTAT NNNN AGATCGGAAGAGCGTCGTGAT /iSp18/ GGATCC /iSp18/ TACTGAACCGC Reads start with 5'-NNNNATACGNNN, where N are random bases.

data_processing:
basecalling was done with bcl2fastq v2.19.1 and samples were demultiplexed with iCount v2.0.0 (https://github.com/tomazc/iCount)
Peaks were first derived on individual replicates of CLIP using iCount peaks on iMAPS at https://imaps.genialis.com. The crosslink positions were grouped by gene id.
Peaks were called using iCount version 2.0.1.dev with the significance FDR threshold of 0.05
The Cross-link sites (per sample) were all merged and peak calling was done. iCount clusters was used to cluster together the crosslink sites that were separated by 20 base pairs and merge them.
Assembly: GRCh38
Supplementary files format and content: tab deliminated text and peak height

source_name: Bone

growth_protocol: SW1353 cells were grown in DMEM, high glucose, pyruvate supplemented with 10% FBS, and 5% penicillin/streptomycin, and maintained at 37°C with 5% CO2.

extract_protocol:
Cell pellets were resuspended in lysis buffer and sonicated in the Bioruptor (Diagenode) for 10 cycles with alternating 30 s on/off at low intensity. 1 mg/mL of the protein was treated with Turbo DNase I (Ambion) and high (2.5 U/mL) or low (0.8 U/mL) RNase I (Ambion)
Purified RNA was reverse transcribed into cDNA, using Superscript IV with distinct primers irCLIP_ddRT for each replicate. The PCR was amplified using Platinum™ II Hot-Start PCR Master Mix (Thermo Fisher Scientific). The final PCR libraries were purified by agarose gel electrophoresis on a 6% TBE gel, DNA in the range of 150-400nt was gel extracted using Costar SpinX column (Corning Incorporated, 8161) and submitted for sequencing.
irCLIP-seq

treatment_protocol: SW1353 cells were crosslinked (150mJ/cm2) at 254 nm with a Bio-Rad Laboratories GS Gene Linker chamber

value: Bone

value: fibroblast

tag: antibody

value: Anti-YB1 antibody (ab12148)


title: FCDIIB spatial transcriptomics, sample F

description: Library name: SpRNAseq_FCDIIB_F


title: H3 ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH23


title: SW1353 YBX1 irCLIP replicate 2

description: Extracted RNA was reverse transcribed using primer irCLIP_ddRT_30 /5Phos/ WWW CGATC NNNN AGATCGGAAGAGCGTCGTGAT /iSp18/ GGATCC /iSp18/ TACTGAACCGC Reads start with 5'-NNNNGATCGNNN, where N are random bases.


title: NPR1-GFP-R3

description: Library name: NPR1-GFP-R3


title: NPR1-GFP-R2

description: Library name: NPR1-GFP-R2


title: H2AKUb ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH21


title: SW1353 YBX1 irCLIP replicate 1

description: Extracted RNA was reverse transcribed using primer irCLIP_ddRT_36 /5Phos/ WWW GATGA NNNN AGATCGGAAGAGCGTCGTGAT /iSp18/ GGATCC /iSp18/ TACTGAACCGC Reads start with 5'- NNNNTCATCNNN, where N are random bases.


title: Decidualized Endometrial Stromal Fibroblasts (dESF), Replicate 3

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

description: Library name: D15

data_processing:
Alignment with GRCh38
Gene counting with featureCounts
Transcripts per Million calculations
Assembly: GRCh38
Supplementary files format and content: TPM values in Excel

source_name: Endometrium

extract_protocol:
mRNA Extraction
Standard Illumina mRNA library prep

value: Endometrium

value: Primary

value: Fibroblast


title: Decidualized Endometrial Stromal Fibroblasts (dESF), Replicate 2

description: Library name: D14


title: FCDIIB spatial transcriptomics, sample D

description: Library name: SpRNAseq_FCDIIB_D


title: H2AKUb ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH22


title: Input wild-type Tak1, 14d thalli, biol rep2 (Input)

description: Library name: TH26


title: NPR1-GFP-R1

description: Library name: NPR1-GFP-R1


title: J-Lat 10.6, RNAPII, ChIP, unstimulated, Rep1

description:
644-11
PolII_NS_n_of_2_NORMsort.bw
PolII_NS_n_of_2_MACS2__peaks.broadPeak

value: J-Lat 10.6 cells

value: RNA polymerase II (Millipore, #05-623)

value: Unstimulated


title: H3K4me3 ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH20


title: H3K4me3 ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH19


title: Decidualized Endometrial Stromal Fibroblasts (dESF), Replicate 1

description: Library name: D13


title: hy5-215-R3

description: Library name: hy5-215-R3

value: leaves


title: Extravillious Trophoblasts (EVT), Replicate 3

description: Library name: D12

source_name: Placenta

value: Placenta

value: Trophoblast stem cell-derived EVT

value: Trophoblast


title: hy5-215-R2

description: Library name: hy5-215-R2

value: leaves of 3-week-old Arabidopsis infiltrated with Pst DC3000 at 24 hours post infiltration


title: H3K9me1 ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH18


title: hy5-215-R1

description: Library name: hy5-215-R1


title: Extravillious Trophoblasts (EVT), Replicate 2

description: Library name: D11


title: Col-0-R3

description: Library name: Col-0-R3


title: H3K9me1 ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH17


title: Extravillious Trophoblasts (EVT), Replicate 1

description: Library name: D10


title: H3K27me1 ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH16


title: Col-0-R2

description: Library name: Col-0-R2


title: Extravillious Trophoblasts (EVT) co-cultured with dESF, Replicate 3

description: Library name: D9


title: Col-0-R1

description: Library name: Col-0-R1


title: Extravillious Trophoblasts (EVT) co-cultured with dESF, Replicate 2

description: Library name: D8


title: hy5-215-24hpi-R3

description: Library name: hy5-215-24hpi-R3


title: Extravillious Trophoblasts (EVT) co-cultured with dESF, Replicate 1

description: Library name: D7


title: H3K27me3 ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH14


title: hy5-215-24hpi-R2

description: Library name: hy5-215-24hpi-R2


title: H3K27me3 ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH13


title: J-Lat 10.6, p400, ChIP, unstimulated, Rep2

description:
660-3
P400_NS_n_of_2_NORMsort.bw
P400_NS_n_of_2_MACS2__peaks.broadPeak

value: TNFa stimulated


title: Input in wild-type Tak1, 14d thalli, biol rep3 (Input)

description: Library name: TH12

value: 14d thalli


title: Control # 13

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: Transcriptomic profiling of peripheral blood mononuclear cells from patients with Parkinson’s disease and control subjects.

hyb_protocol: Scanned on an Agilent G2505B scanner and Agilent-014850 whole Human genome microarrays 4x44K (Probe Name version).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Control # 13

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1650 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Blood from control and PD subjects was collected in Vacutainer® CPT Cell Preparation Tubes (Becton Dickinson, Le Pont-de-Claix, France) and PBMC from human samples were isolated on a ficoll gradient. Total RNA from 5 x 106 cells was isolated using RNeasy mini-columns (Qiagen, Courtaboeuf, France). RNA concentration was measured by  absorbance at 260nm using a NanoDrop ND-1000 spectrophotometer. RNA quality and integrity were checked using the RNA 6000 NanoChip kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France). All samples included in the study had a RIN>9.

tag: disease

value: None (control)

value: peripheral blood mononuclear cells (PBMC)


title: Control # 11

source_name: Control # 11


title: Control # 10

source_name: Control # 10


title: Control # 12

source_name: Control # 12


title: Control # 9

source_name: Control # 9


title: Control # 7

source_name: Control # 7


title: Control # 8

source_name: Control # 8


title: Control # 6

source_name: Control # 6


title: Decidualized Endometrial Stromal Fibroblasts (dESF) co-cultured with EVTs, Replicate 2

description: Library name: D5


title: Input in wild-type Tak1, 14d thalli, biol rep2 (Input)

description: Library name: TH11

value: wild-type Tak1


title: H3K27me1 ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH15


title: Decidualized Endometrial Stromal Fibroblasts (dESF) co-cultured with EVTs, Replicate 1

description: Library name: D4


title: Input in wild-type Tak1, 14d thalli, biol rep1 (Input)

description: Library name: TH10


title: Endometrial Stromal Fibroblasts (ESF), Replicate 3

description: Library name: D3


title: Col-0-24hpi-R2

description: Library name: Col-0-24hpi-R2


title: Decidualized Endometrial Stromal Fibroblasts (dESF) co-cultured with EVTs, Replicate 3

description: Library name: D6


title: Col-0-24hpi-R1

description: Library name: Col-0-24hpi-R1


title: Endometrial Stromal Fibroblasts (ESF), Replicate 2

description: Library name: D2


title: Control # 5

source_name: Control # 5


title: hy5-215-0hpi-R3

description: Library name: hy5-215-0hpi-R3

value: leaves of 3-week-old Arabidopsis infiltrated with Pst DC3000 at 0 hours post infiltration


title: H2A.M.2 ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH08

source_name: 14d thalli


title: hy5-215-24hpi-R1

description: Library name: hy5-215-24hpi-R1


title: Control # 3

source_name: Control # 3


title: H2A.M.2 ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH07


title: Endometrial Stromal Fibroblasts (ESF), Replicate 1

description: Library name: D1

value: Endometrium


title: Control # 4

source_name: Control # 4


title: hy5-215-0hpi-R2

description: Library name: hy5-215-0hpi-R2

source_name: leaves


title: hy5-215-0hpi-R1

description: Library name: hy5-215-0hpi-R1


title: Col-0-24hpi-R3

description: Library name: Col-0-24hpi-R3


title: Day3 control 2

city: Cambridge

first: Jingwei

last: Zhang

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: 10x Genomics

data_processing:
The cells from mouse lungs were subjected to sequencing using an Illumina HiSeq2500 platform. The sequencing data was aligned to a reference meta-genome comprising human hg38 (GRCh38), mouse mm10 (GRCm38), and tdTomato sequences with Cell Ranger. We used the Ensemble version 98 gene annotation to assign unique molecular identifiers (UMIs) to genes.
Assembly: hg38, mm10
Supplementary files format and content: tab delimited value and matrix files

organism:
Homo sapiens
Mus musculus

source_name: lung

extract_protocol:
The lungs harvested from control or bleomycin-treated mice were lysed into single-cell suspensions and were subjected to transcriptome profiling using scRNA sequencing
Cells were processed using the 10X Genomics Chromium Controller with the Single Cell 3ʹ v3 Reagent Kit, according to manufacturer’s directions. Briefly, a target number of cells per library was roughly achieved by loading 1.6 times the target number of cells in suspension, along with barcoded beads and partitioning oil, into the Chromium Controller, in order to create GEMs (Gel Beads in Emulsion). The Chromium Controller combines individual cells, first strand master mix, and gel beads containing barcoded oligonucleotides into single-cell droplets for first strand cDNA synthesis, so that each cell is marked with its own unique barcode during reverse transcription. The 3’ beads contain a poly(dT) oligo that enables the production of barcoded, full-length cDNA from poly-adenylated mRNA. After first strand synthesis is complete, the emulsion is dissolved and the cDNA is pooled for bulk processing as a single sample. The sample is fragmented, end-repaired, A-tailed and ligated with universal adapters. A second sample barcode is then added during the PCR step, allowing for unique library identification. The end result is a single library representing one cell suspension, containing data for each individual cell.

treatment_protocol: For the samples of day3 or day7 bleomycin, mice transplanted with Sum159 ITGB4 low clone 1 cells were treated with bleomycin through trachea.

value: lung

value: lung from mice infected with Sam164

tag: time

value: control at day 3


title: Control # 1

source_name: Control # 1


title: Sporadic PD patient # 7

source_name: Sporadic PD patient # 7

value: Sporadic Parkinson’s disease


title: Control # 2

source_name: Control # 2


title: H2A.X.2 ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP )

description: Library name: TH05


title: Day7 Bleomycin

description: 10x Genomics

value: lung from mice infected with Sam162

value: day 7 after bleomycin treatment

value: mice treated with bleomycin


title: H2A.M.2 ChIP-seq in wild-type Tak1, 14d thalli, biol rep3 (ChIP)

description: Library name: TH09


title: Col-0-0hpi-R3

description: Library name: Col-0-0hpi-R3

value: leaves


title: Col-0-0hpi-R2

description: Library name: Col-0-0hpi-R2


title: H2A.X.1 ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH04


title: Sporadic PD patient # 5

source_name: Sporadic PD patient # 5


title: Sporadic PD patient # 6

source_name: Sporadic PD patient # 6


title: H2A.X.1 ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH03


title: Sporadic PD patient # 4

source_name: Sporadic PD patient # 4


title: Day3 Bleomycin 1

description: 10x Genomics

value: lung from mice infected with Sam160

value: day 3 after bleomycin treatment


title: Col-0-0hpi-R1

description: Library name: Col-0-0hpi-R1


title: Day7 control

description: 10x Genomics

value: lung from mice infected with Sam161

value: control at day 7


title: H2A.Z ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH02

value: 14d thalli


title: Day3 Bleomycin 2

description: 10x Genomics

value: lung from mice infected with Sam163


title: H2A.X.2 ChIP-seq in wild-type Tak1, 14d thalli, biol rep2 (ChIP)

description: Library name: TH06

value: wild-type Tak1


title: P3 Pc pool2 6% ficoll layer (primary asci)

city: Newport

first: Aaron

last: Albee

state: KY

address: 17 Youngs Ct

institute: University of Cincinnati

description:
Library name: P3 Pc pool2 6_ ficoll layer (primary asci)
10X Genomics

data_processing:
Raw sequencing reads from scRNA-seq experiments were processed using Cell Ranger v9.0 (10x Genomics). Reads were aligned to the Pneumocystis carinii B80 reference genome with removal of Major surface glycoprotein genes (Accession: GCF_001477545.1). Genes detected in fewer than 10 cells were excluded, and cell-level quality control (QC) filtering was applied using the following thresholds: UMI per cell (<400), genes per cell (<200), and gene expression complexity (log10[genes per UMI] ≤ 0.8) to remove low-quality, doublet, or damaged cells that would result in technical noise  .
Assembly: Pneumocystis carinii B80 reference genome
Supplementary files format and content: TSV and matrix files

organism: Pneumocystis carinii

extract_protocol:
single-cell RNA sequencing (scRNA-seq) was performed using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) from 10x Genomics. To facilitate the lysis of P. carinii asci, which possesses a robust β-1,3-D-glucan cell wall, 1 µL of Zymolyase 100T (10 mg/mL; Asmbio, Cambridge, MA) was added to the gel bead mix before droplet generation. This enzymatic treatment enhances cell wall digestion, thereby improving the efficiency of in-droplet lysis during the scRNA-seq workflow. Briefly, cells were resuspended in the master mix and loaded into the Chromium chip with partitioning oil and gel beads to generate gel bead-in-emulsions (GEMs). Polyadenylated RNA underwent reverse transcription within each GEM, incorporating an Illumina TruSeq Read one primer sequence, a Unique Molecular Identifier (UMI), and a 10x Barcode.
Post GEM-recovery, barcoded cDNA was purified using Silane DynaBeads and amplified via 14 cycles of PCR. The amplified cDNA was then enzymatically fragmented, size-selected, adapter-ligated, and subjected to sample index PCR to construct sequencing libraries. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 platform using an S4 flow cell with the following parameters: Read 1: 28 cycles; i7 Index: 10 cycles; i5 Index: 10 cycles; Read 2: 90 cycles.

value: ficol hypaque gradient seperation in 2,-, 4-, 6-, 8-, 10-, and 12% layers


title: Sporadic PD patient # 2

source_name: Sporadic PD patient # 2

value: peripheral blood mononuclear cells (PBMC)


title: H2A.Z ChIP-seq in wild-type Tak1, 14d thalli, biol rep1 (ChIP)

description: Library name: TH01


title: yeast-TT-50fmol

city: Heidelberg

first: Jiří

last: Koubek

address: INF 345

department: ZMBH

country: Germany

institute: Heidelberg University

description: Library name: yeast-50fmol

data_processing:
demultiplexed libraries were trimmed via cutadapt to remove universal linkers
unique molecular identifiers were extracted
rRNA sequences were removed by alignment against known rRNA
rRNA-depleted reads were aligned to corresponding genome
Assembly: E.coli GCA_000499485.1, yeast GCA_000146045.2, mouse GRCm39, GCA_000001635.9, human GRCh38p10, GCA_000001405.25
Supplementary files format and content: hdf5 files contain p-site assigned reads
Library strategy: Ribo-Seq

organism: Saccharomyces cerevisiae

extract_protocol:
total RNA was extracted via phenol:chlorophorm extraction
libraries were prepared according to Ingolia et al (2009) and by a method described within the accompanying manuscript

tag: strain


title: Sporadic PD patient # 1

source_name: Sporadic PD patient # 1


title: yeast-TT-5pmol

description: Library name: yeast-5pmol


title: Sporadic PD patient # 3

source_name: Sporadic PD patient # 3


title: ΔTreg SSP+ aCD4_2

first: Blanda

last: Di Luccia

state: CALIFORNIA

address: 299 Campus drive

department: Microbiology and Immunology

source_name: Colonic tissue

extract_protocol: Total RNA was extracted from colonic tissues of ΔTreg SSP (n=3) and ΔTreg SSP + anti-CD4 (n=3) mice using the RNAeasy Kit (Qiagen) following the manufacturer’s instructions and quantified by NanodropA total of 25 ng of RNA was used for NanoString nCounter assay and the codeset for Mouse Fibrosis Panel (NanoString) was utilized. The hybridization, processing, and acquisition were performed at the NanoString facility (NanoString Technologies, Seattle, WA). The normalization and differential expression analysis were conducted using NSolver 4.0 software (NanoString).

treatment_protocol: 8-12 weeks old F1 (Foxp3DTRx 129X1/SvJ, n=6) mice were starved overnight and infected with Salmonella Typhimurium SL1344 (STm) by feeding the mice with 20 uL of the bacterial suspension (5x109 CFU/mL) directly into the mouth using a pipette. The SSP state was induced by streptomycin treatment (5 mg) 14 days after STminfection. Then, F1-SSP (n=6) mice were intraperitoneally (i.p.) injected with 50 mg/kg DT on days 21 and 22 after infection and with 10 mg/kg DT on day 25 after infection (DTreg SSP). Additionally, DTreg SSP were i.p. injected with anti-CD4+ antibody (n=3) or isotype control (n=3).

tag: gender

value: Male

value: Injected with Diphteria toxin and ant-CD4+ antibody

value: Foxp3DTR x 129X1/SvJ


title: ΔTreg SSP+ aCD4_3

hyb_protocol: The hybridization, processing, and acquisition were performed at the NanoString facility (NanoString Technologies, Seattle, WA).

data_processing: The normalization and differential expression analysis were conducted using NSolver 4.0 software (NanoString).


title: Embryo, day19.5, replicate 3, scRNAseq

city: Beijing

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

institute: National Institute of Biological Sciences, Beijing

description: 10× Genomics

data_processing:
CellRanger V3.0.3 for  reads alignment, filtering, barcode counting, and UMI counting
Seurat V4.3.0 for downstream analysis
Assembly: mm10
Supplementary files format and content: Table-separated values files and matrix files

source_name: Small intestine

extract_protocol:
For samples from E12.5 to E19.5, isolated intestinal samples were washed in cold Dulbecco’s phosphate-buffered saline (DPBS, Gibco, C14190500CP) to remove intestinal contents. The E19.5d tissues were opened longitudinally and sliced into small fragments for the following digestion. The embryonic (E12.5d, E13.5d, E14.5d, and E15.5d) tissues were directly pooled into the tube with collagenase I (Gibco, 17100-017) and elastase (Sigma, E2058) to perform digestion at room temperature to obtain cell mixture. The cell mixture was then passed through a 40-µm filter to obtain the single-cell suspension. The obtained single-cell suspension was centrifuged at 300g for 10 min, and incubated with ACK lysis buffer (Gibco, A10492-01) for 1 min on the ice. Another centrifugation at 300g for 10 min was performed and the supernatant was removed. The final fraction was mixed in suitable DPBS with 0.05% BSA and Propidium Iodide. For Lmo3_E19.5 samples, small intestines were collected at E19.5, minced into small pieces, and processed in a solution composed of DNaseI (Merk, 10104159001), and Y27632 (R&D Sytems, 1254/50 ,5000X) in TrypLE (Gibco, 12605-010) for about 15min in 37℃ on 150rpm shaker. The remaining tissues were further digested in digestion buffer containing 1.2mg/ml Collagenase (Sigma, C2139-1G), 1mg/ml Dispase II (Gibco, 17105041), 0.1mg/ml DNase I, and Y27632 in Hank’s balanced salt solution (HBSS. Gibco 14170-112) for 20min in 37℃, 150rpm shaker. Tissues were resuspended every 6min through pipetting. The reaction was stopped by adding 3-volume of wash buffer containing 5% FBS (Gibco, 16000-044), Gentamicin / Amphotericin (Gibco, 50-0640, 500X), Penicillin / Streptomycin B (Gibco, 15140-122,100X), HEPES (Sigma, H0887-100ML,100X), Y27632 in F12 culture medium (Gibco, 11765-054). The lysates were passed through 70-μm filters, centrifuged at 300g for 8 min, and resuspended in the wash buffer. 1ml ACK lysis buffer was added to remove the red blood cells on ice for 4min. The remaining cells were washed twice with wash buffer and filtered again with 40-μm Millipore. The final fraction was resuspended into the wash buffer with 1ug/ml DAPI.
Cell suspensions with at least 80% cell viability were diluted to the appropriate concentration and loaded on a 10x Genomics Chromium Single Cell Controller (Pleasanton, CA) with a target of about 5000 cells per sample. Single-cell library preparation was completed using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2 strictly following the manufacturer’s protocol.

value: Small intestine

value: wildtype


title: P3 Pc pool1 10&12% ficoll layer (primary asci)

description:
Library name: P3 Pc pool1 10_12_ ficoll layer (primary asci)
10X Genomics


title: PD patient # 7

source_name: PD patient # 7

value: Parkinson’s disease


title: ΔTreg SSP_3

value: Injected with Diphteria toxin


title: Embryo, day19.5, replicate 2, scRNAseq

description: 10× Genomics


title: Embryo, day19.5, replicate 1, scRNAseq

description: 10× Genomics


title: P3 Pc pool1 8% ficoll layer (primary asci)

description:
Library name: P3 Pc pool1 8_ ficoll layer (primary asci)
10X Genomics


title: ΔTreg SSP+ aCD4_1


title: P3 Pc Pool1 2&4% ficoll layer (primary trophic)

description:
Library name: P3 Pc Pool1 2_4_ ficoll layer (primary trophic)
10X Genomics


title: PD patient # 6

source_name: PD patient # 6


title: Day3 control 1

description: 10x Genomics

value: lung

value: lung from mice infected with Sam159

value: control at day 3


title: P3 Pc pool2 2&4% ficoll layer (primary trophic)

description:
Library name: P3 Pc pool2 2_4_ ficoll layer (primary trophic)
10X Genomics


title: Embryo, day15.5, replicate 1, scRNAseq

description: 10× Genomics


title: PD patient # 3

source_name: PD patient # 3


title: PD patient # 2

source_name: PD patient # 2


title: P3 Pc pool2 10&12% ficoll layer (primary asci)

description:
Library name: P3 Pc pool2 10_12_ ficoll layer (primary asci)
10X Genomics


title: P2 Pc S3 10&12% ficoll layer (primary asci)

description:
Library name: P2 Pc S3 10_12_ ficoll layer (primary asci)
10X Genomics


title: A23051 week 11 post-infection

city: Seattle

first: John

middle: K

last: Bui

state: WA

address: 1100 Fairview Ave. N.

institute: University of Washington

description:
Library name: Sample 6
Specific instrument uncertain as this is proprietary information by Quintarabio, which performed the sequencing

library_source: other

data_processing:
Sequence data files were processed using an in-house deep sequencing analysis pipeline that has been uploaded to Github (https://github.com/jbui2-ui/SIV-Env-Sequence-Analysis). Translations were generated and aligned to SIVmac239 (genbank M33262), with substitution frequencies enumerated in the processed data file.
Assembly: SIVmac239 (genbank M33262)
Supplementary files format and content: Tab-delimited .csv file contains the frequencies of each amino acid substitution

molecule: other

organism: Macaca mulatta

source_name: Serum

extract_protocol:
Viral RNA was isolated from serum samples using the QIAamp MinElute Virus Spin Kit or QIAamp Viral RNA mini (Qiagen), following the manufacturer’s protocol.
Reverse transcription of purified RNA was performed using the SuperScript IV First-Strand Synthesis System (Thermo Fisher Scientific) and the reverse primer 5’-CTC TCT CTT CAG CTG GGT-3’ with additional adaptor sequence and a 4-nucleotide index sequence for multiplexing. Residual primers and dNTPs were removed using ExoSAP-IT PCR Product Cleanup Reagent (Applied Biosystems). The resulting complementary DNA (cDNA) was amplified by PCR using the KAPA HiFi HotStart ReadyMix PCR Kit (Roche), forward primer 5’-GTA GAT GTC TAG GGG AAG GAC-3’ and reverse primer targeting the adaptor sequence. PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter), and excess primers and dNTPs were again removed with ExoSAP-IT. DNA quality and fragment size distribution were evaluated using the Agilent Genomic DNA ScreenTape System, and concentrations were determined via Qubit fluorometric quantification (Thermo Fisher). Purified amplicons were submitted to Quintara for long-read sequencing.

value: Serum

value: HDAd-control


title: PD patient # 4

source_name: PD patient # 4


title: PD patient # 5

source_name: PD patient # 5


title: ΔTreg SSP_1


title: P2 Pc S2 6&8% ficoll layer (primary asci)

description:
Library name: P2 Pc S2 6_8_ ficoll layer (primary asci)
10X Genomics


title: Embryo, day14.5, replicate 1, scRNAseq

description: 10× Genomics


title: A22065 week 11 post-infection

description:
Library name: Sample 5
Specific instrument uncertain as this is proprietary information by Quintarabio, which performed the sequencing


title: P3 Pc pool1 6% ficoll layer (primary asci)

description:
Library name: P3 Pc pool1 6_ ficoll layer (primary asci)
10X Genomics


title: Embryo, day13.5, replicate 3, scRNAseq

description: 10× Genomics


title: PD patient # 1

source_name: PD patient # 1


title: ΔTreg SSP_2


title: P2 Pc S1 2&4% ficoll layer (primary trophic)

description:
Library name: P2 Pc S1 2_4_ ficoll layer (primary trophic)
10X Genomics


title: A22054 week 11 post-infection

description:
Library name: Sample 4
Specific instrument uncertain as this is proprietary information by Quintarabio, which performed the sequencing


title: P1 Pc S4 10% ficoll layer (primary asci)

description:
Library name: P1 Pc S4 10_ ficoll layer (primary asci)
10X Genomics


title: ATXN2 patient # 6

source_name: ATXN2 patient # 6

value: Spinocerebellar ataxia type 2


title: A21140 week 11 post-infection

description:
Library name: Sample 3
Specific instrument uncertain as this is proprietary information by Quintarabio, which performed the sequencing


title: P1 Pc S3 8% ficoll layer (primary asci)

description:
Library name: P1 Pc S3 8_ ficoll layer (primary asci)
10X Genomics


title: Embryo, day13.5, replicate 1, scRNAseq

description: 10× Genomics


title: ATXN2 patient # 5

description: Transcriptomic profiling of peripheral blood mononuclear cells from patients with Parkinson’s disease and control subjects.

source_name: ATXN2 patient # 5


title: A21138 week 7 post-infection

description:
Library name: Sample 2
Specific instrument uncertain as this is proprietary information by Quintarabio, which performed the sequencing


title: P1 Pc S2 6% ficoll layer (primary asci)

description:
Library name: P1 Pc S2 6_ ficoll layer (primary asci)
10X Genomics


title: A21137 week 11 post-infection

description:
Library name: Sample 1
Specific instrument uncertain as this is proprietary information by Quintarabio, which performed the sequencing


title: Embryo, day12.5, replicate 2, scRNAseq

description: 10× Genomics


title: Embryo, day12.5, replicate 1, scRNAseq

description: 10× Genomics


title: P1 Pc S1 2% ficoll layer (primary trophic)

description:
Library name: P1 Pc S1 2_ ficoll layer (primary trophic)
10X Genomics


title: ATXN2 patient # 2

source_name: ATXN2 patient # 2


title: Embryo, day13.5, replicate 2, scRNAseq

description: 10× Genomics


title: flower buds, abh1-8, rep 1, mRNA

status: Public on Aug 18 2025

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

description: Library name: S4_80

data_processing:
Raw read quality was diagnosed using FastQC.
Trim Galore (Babraham Bioinformatics) was used for adapter and low-quality read trimming with PHRED score < 20.
Reads were aligned to the TAIR10 genome assembly using STAR (Dobin et al 2014).
FeatureCounts (Liao et al 2014) was used for determine transcript abundance on gene-level features extracted from the TAIR10 annotation (GTF) retrived from EnsemblPlants (Kersey et al 2016) for either sense (-s 2, reverse-stranded) or antisense (-s 1, forward-stranded) transcripts.
Bedtools (genomecov -bga -split -scale) was used to generate a bedGraph file from the BAM files. A per-million scaling factor was provided to the -scale flag, determined by 1,000,000/total fragments (total fragments = [samtools view -F 260 -c]/2).
bedGraphToBigWig (kentUtils) was used to convert bedGraph files to bigWig files for visualizing read depth across TAIR10 features.
Assembly: TAIR10
Supplementary files format and content: .bigWig: files for visualizing scaled read coverage (RPM) in a genome browser (e.g. IGV) for each sample for the plus or minus strand.
Supplementary files format and content: .counts: raw counts computed by FeatureCounts for sense (featureCounts -s 2) or antisense (featureCounts -s 1) transcripts mapping to gene-level features.

source_name: Early-stage flower bud

growth_protocol: Seeds were sown onto moist soil (treated overnight with diatomaceous earth), supplemented with 10 g/L Jack’s Professional 15-16-17 Peat-Lite water-soluble fertilizer (JR Peters, Allentown, PA, USA) and NemAttack (Arbico Organics, Tucson, AZ, USA), and stratified in the dark for 48 h at 4 °C. Plants were grown at 22 °C under a 16-h-light (100-150 µmol m-2 s-1)/8-h-dark photoperiod. Approximately 20-30 mg of early-stage flower buds (stages 1-12) were harvested from 10-week old plants. Excised buds were immediately frozen in liquid nitrogen and stored at -80 °C. Biological replicates represent pooled flower buds collected from independently grown plants.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrgen). Details available at Protocols.io: dx.doi.org/10.17504/protocols.io.36wgq4enyvk5/v2.
mRNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

value: Early-stage flower bud

tag: ecotype


title: flower buds, abh1-8, rep 2, mRNA

description: Library name: S5_82


title: flower buds, WT, rep 3, mRNA

description: Library name: S3_49

value: WT


title: flower buds, WT, rep 2, mRNA

description: Library name: S2_41


title: HER2-zero patient 24

type: genomic

city: Durham

first: Maggie

middle: L

last: DiNome

state: NC

address: 308 Research Dr, RM 215B

department: Department of Surgery

institute: Duke University

description: DNA from breast cancer FFPE tissue

hyb_protocol: 200 ng of bisulfite-converted DNA was whole-genome amplified, enzymatically fragmented, and hybridized on the Infinium MethylationEPIC v2.0 BeadChip (900K, Illumina) by the Epigenomic Services from Diagenode (Cat nr. G02090000).

scan_protocol: The array was scanned with the iScan system from Illumina according to the manufacturer's guidelines.

data_processing:
Data normalization and quality control were performed using the R package ChAMP (v.2.36.0). Batch effects were tested and corrected using the ComBat function in ChAMP, and probes with a detection p-value above 0.01 were excluded. Probes targeting non-CG dinucleotides, single nucleotide polymorphisms, and chromosome Y were removed from downstream analyses.
Processed data: Beta-values, corrected for batch effect from the different sample origin and other potential batches in the arrays.

label: Cy3 and Cy5

source_name: Breast Cancer

label_protocol: The DNA was deaminated with the EZ-96 DNA Methylation Kit (Zymo Research).

extract_protocol: DNA was extracted from 8-10 um thick tissue sections by microdissection with a needle. 4 um thick H&E slides were used as a template. DNA was purified using the Quick-DNA FFPE Miniprep kit (#D3067, Zymo Research). DNA was quantified using a Qubit with the Qubit 1X dsDNA High Sensitivity kit (Q33230, Invitrogen).

tag: age

value: Breast Cancer

tag: breast cancer subtype

value: Triple-Negative Breast Cancer

tag: her2 score

tag: her2 status

tag: Sex

value: Female


title: ATXN2 patient # 3

source_name: ATXN2 patient # 3

tag: tissue

value: peripheral blood mononuclear cells (PBMC)


title: flower buds, WT, rep 1, mRNA

description: Library name: S1_40

tag: genotype


title: HER2-low patient 34

description: DNA from breast cancer FFPE tissue


title: ATXN2 patient # 1

source_name: ATXN2 patient # 1


title: HER2-zero patient 23

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 33

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 22

description: DNA from breast cancer FFPE tissue


title: C56BL/6J_12weeksold_rep2

city: Houston

first: Gerarda

last: Cappuccio

address: 1250 Morsund street

institute: Baylor College of Medicine

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix GeneChip® Mouse Gene 1.0 ST Array using Affymetrix Hybridization Oven 640, GeneChip® Fluidics Station 450, and GeneChip® Scanner 3000

data_processing:
Digital Sorting algorithm
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.na36.mm10.probeset.csv

label: biotin

source_name: C56BL/6J, mouse, 12 weeks old

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Dentate gyri dissected from mice aged between 4 and 12 weeks

extract_protocol: To micro-dissect both dentate gyri, a hypodermic needle tip was used to cut along both edges of the dentate gyrus which ensured clean dissection with exclusion of all other hippocampal regions . Tissue was mechanically dissociated using fine tweezers. DNase was added, followed by tissue tituration using a 1000 µL pipette (up and down 10 times).

treatment_protocol: Not applicable

value: female

tag: organ

value: brain

tag: region

value: hippocampus

value: dentate gyrus


title: flower buds, abh1-8, rep 3, mRNA

description: Library name: S6_83


title: HER2-low patient 32

description: DNA from breast cancer FFPE tissue


title: C56BL/6J_12weeksold_rep1


title: ATXN2 patient # 4

source_name: ATXN2 patient # 4


title: C56BL/6J_8weeksold_rep1

source_name: C56BL/6J, mouse, 8 weeks old


title: C56BL/6J_8weeksold_rep2


title: C56BL/6J_4weeksold_rep2

source_name: C56BL/6J, mouse, 4 weeks old


title: C56BL/6J_6weeksold_rep1

source_name: C56BL/6J, mouse, 6 weeks old


title: HER2-zero patient 21

description: DNA from breast cancer FFPE tissue


title: C56BL/6J_10weeksold_rep2

source_name: C56BL/6J, mouse, 10 weeks old


title: C56BL/6J_4weeksold_rep1


title: HER2-zero patient 20

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 30

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 31

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 29

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 19

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 18

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 28

description: DNA from breast cancer FFPE tissue


title: C56BL/6J_6weeksold_rep2


title: HER2-zero patient 17

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 16

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 15

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 14

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 13

description: DNA from breast cancer FFPE tissue


title: C56BL/6J_10weeksold_rep1


title: Limousine - muscle tissue_rep 1

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 1 of 8. Limousine muscle tissue

hyb_protocol: For hybridization, Microarray Hybridization Chamber (Agilent, USA) and Hyb-Buffer (Agilent, USA) were used according to manufacturer protocol.

scan_protocol: Microarray Scanner (model G2565CA) with SureScan High-Resolution Technology (Agilent, USA).

data_processing:
Microarray data were extracted, the background subtracted and LOWESS normalisation performed using the standard procedures contained in the Agilent Feature Extraction (FE) Software Version 10.7.3.1.
The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

organism: Bos taurus

source_name: Limousine (LIM)_musculus semitendinosus

label_protocol: MiRNA Complete Labeling and Hyb Kit (Version 2.3, December 2010) (Agilent) was used for labeling, according to manufacturer protocol.

extract_protocol: Total RNA including miRNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 8 were included into the analysis.

tag: cattle breed

value: Limousine (LIM)

value: bull

value: 15 months

value: muscle- m. semitendinosus

tag: molecule subtype

value: miRNA


title: Limousine - muscle tissue_rep 5

description: Biological replicate 5 of 8. Limousine muscle tissue


title: Limousine - muscle tissue_rep 8

description: Biological replicate 8 of 8. Limousine muscle tissue


title: Limousine - muscle tissue_rep 7

description: Biological replicate 7 of 8. Limousine muscle tissue


title: HER2-zero patient 11

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 10

description: DNA from breast cancer FFPE tissue


title: Limousine - muscle tissue_rep 4

description: Biological replicate 4 of 8. Limousine muscle tissue


title: Limousine - muscle tissue_rep 6

description: Biological replicate 6 of 8. Limousine muscle tissue


title: Holstein-Friesian - muscle tissue_rep 8

description: Biological replicate 8 of 8. Holstein-Friesian muscle tissue

value: Holstein-Friesian (HF)


title: HER2-low patient 27

description: DNA from breast cancer FFPE tissue


title: Holstein-Friesian - muscle tissue_rep 2

description: Biological replicate 2 of 8. Holstein-Friesian muscle tissue


title: Holstein-Friesian - muscle tissue_rep 6

description: Biological replicate 6 of 8. Holstein-Friesian muscle tissue


title: Holstein-Friesian - muscle tissue_rep 3

description: Biological replicate 3 of 8. Holstein-Friesian muscle tissue


title: Limousine - muscle tissue_rep 2

description: Biological replicate 2 of 8. Limousine muscle tissue


title: Holstein-Friesian - muscle tissue_rep 7

description: Biological replicate 7 of 8. Holstein-Friesian muscle tissue


title: Hereford - muscle tissue_rep 7

description: Biological replicate 7 of 8. Hereford muscle tissue

source_name: Hereford (HER)_musculus semitendinosus

value: Hereford (HER)


title: HER2-zero patient 12

description: DNA from breast cancer FFPE tissue


title: Limousine - muscle tissue_rep 3

description: Biological replicate 3 of 8. Limousine muscle tissue


title: Hereford - muscle tissue_rep 5

description: Biological replicate 5 of 8. Hereford muscle tissue


title: Hereford - muscle tissue_rep 6

description: Biological replicate 6 of 8. Hereford muscle tissue


title: Holstein-Friesian - muscle tissue_rep 4

description: Biological replicate 4 of 8. Holstein-Friesian muscle tissue


title: HER2-zero patient 9

description: DNA from breast cancer FFPE tissue


title: Holstein-Friesian - muscle tissue_rep 1

description: Biological replicate 1 of 8. Holstein-Friesian muscle tissue


title: Holstein-Friesian - muscle tissue_rep 5

description: Biological replicate 5 of 8. Holstein-Friesian muscle tissue


title: HER2-low patient 26

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 24

description: DNA from breast cancer FFPE tissue


title: Healthy-PBMCs

city: Ho Chi Minh

first: HongThai

last: LeNguyen

address: 764, Vo Van Kiet

department: Tuberculosis Group

country: Viet Nam

institute: Oxford University Clinical Research Unit

description:
Library name: healthy
10x Genomics

data_processing:
Sequencing data was processed using Cell Ranger v7.1.0 (10x Genomics). Namely, reads were aligned to a GRCh38 reference genome (v3.0.0) and gene expression matrices generated using cellranger count. SoupX (v1.6.2) was used to remove ambient RNA contamination [38]. Doublets were removed using Scrublet (v0.0.4) with default parameters [39]. The data from all samples were combined using the merge function in Seurat v4.3.1 [40]. Low quality cells with < 500 genes detected or > 10% of reads aligned to the mitochondrial genome were removed. Genes expressed in fewer than five cells were removed. After quality control, data was analyzed using Seurat v4.3.1 [40]. Raw count data was normalized using sctransform [41] with percent mitochondrial reads and the number of unique molecular identifier (UMI) counts regressed out. Variance stabilizing transformation was performed to identify the 3,000 most variable genes, which were used for principal component analysis (PCA). Batch effects from different donors were removed using Harmony [42]. A shared nearest neighbor graph was constructed using the top 30 Harmony components, and clustering was performed with the Louvain algorithm (resolution 1.9). Data was visualized using UMAP of the top 30 Harmony PCs.
Assembly: 10x human reference (GRCh38)
Supplementary files format and content: h5: Matrix files

source_name: blood

extract_protocol:
As part of routine hospital procedure, 5-10 ml of CSF and 1 ml heparinized blood were collected. 2-3 ml of CSF were sent to the hospital laboratory for routine tests for viral, bacterial, or fungal infection. The remaining CSF was concentrated by centrifugation at 300 × g for 10 min and re-suspended in 700 µl of CSF supernatant. This CSF deposit was used for TB diagnostic tests, including 100 μl for Ziehl-Neelsen smear, 200 μl for Xpert MTB/RIF, and 200 μl was stored at -80°C for future use. The remaining 200 μl of CSF was used for scRNA-seq if processed within four hours of collection, with ≥ 75 cells/µl deposit, and no artificial blood contamination (evidenced by > 200 RBCs/μl CSF total) [15]. After re-centrifugation (300 × g, 5 min), CSF pellets were resuspended in 50 μl PBS containing 0.04% bovine serum albumin (BSA, Sigma) and counted. Blood was processed alongside CSF, with PBMCs isolated using density gradient centrifugation with Histopaque 1077 (Sigma) following the manufacturer’s instructions.
Single-cell suspensions were loaded onto a 10x Genomics Chromium Controller. One patient sample was loaded per channel with a target capture rate of 4,000 cells, while the healthy control PBMCs had a target capture rate of 1,000 cells. Libraries were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s instructions. The library from the healthy control PBMCs was sequenced internally on an Illumina MiSeq to a mean depth of 20,922 reads per cell, with a sequencing saturation of 66.1%. Patient libraries were sequenced on an Illumina NovaSeq 6000 (BGI, Hong Kong) to a mean depth of 33,072-163,448 reads per cell, with a sequencing saturation of 54.0-91.6%.

value: blood

tag: cell type

value: PBMCs

value: healthy

tag: batch


title: Hereford - muscle tissue_rep 4

description: Biological replicate 4 of 8. Hereford muscle tissue


title: HER2-low patient 23

description: DNA from breast cancer FFPE tissue

value: Breast Cancer

value: Triple-Negative Breast Cancer


title: HER2-low patient 22

description: DNA from breast cancer FFPE tissue

value: Female


title: Hereford - muscle tissue_rep 8

description: Biological replicate 8 of 8. Hereford muscle tissue


title: Hereford - muscle tissue_rep 3

description: Biological replicate 3 of 8. Hereford muscle tissue


title: HER2-zero patient 8

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 25

description: DNA from breast cancer FFPE tissue


title: Hereford - muscle tissue_rep 1

description: Biological replicate 1 of 8. Hereford muscle tissue


title: HER2-low patient 21

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 19

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 20

description: DNA from breast cancer FFPE tissue


title: HDF, rep1

city: Guangzhou

first: Yueming

last: Sun

state: Guangdong

address: 74th Zhong Shan two street

department: basic medicine

institute: Sun Yat-sen University

description: Library name: B1

data_processing:
Sequencing reads were trimmed for adaptor sequence/low quality sequence using trim_galore version 0.6.2(parameter -q 20 --length 25 -e 0.1)
Trimmed sequence reads were mapped to GRCh38/hg38 using hisat2 version 2.1.0
Read count extraction were performed using HTSeq version 0.11.2 (parameter -a 10 -t exon)
Assembly: hg38
Supplementary files format and content: raw counts for each sample, The sample names MSC1/2/3 were replaced with "A1/2/3", and similarly, HDF1/2/3 were renamed as "B1/2/3".

source_name: Skin

extract_protocol:
Total RNA was extracted using a Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.  RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
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 doublestranded cDNA fragments were end repaired, A base added, and ligated to lllumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X). Polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co.(Guangzhou,China).

value: Skin

tag: cell line

value: cultured Dermal fibroblasts

value: Dermal fibroblasts


city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

description:
Library name: Bcells
BD Rhapsody

data_processing:
Standard integration, clustering and comparison procedures were performed with the R package Seurat (V.4.0.4)[PMID: 29608179]. Gene set enrichment analysis (GSEA) was performed using the fgsea method (https://github.com/ctlab/fgsea). The volcano plot was generated using the EnhancedVolcano R package (https://github.com/kevinblighe/EnhancedVolcano). Activation signature were evaluated using UCell.
Assembly: GRCh38
Supplementary files format and content: Zipped file, processed expression data.

source_name: PBMCs

extract_protocol:
Sorted Δ42PD-1+, PD-1+ and double negative B cells at 48 hours after the treatment with α-IgM/G F(ab’)2 and CH34 or isotype control IgG2b.
Isolated Δ42PD-1+, PD-1+ T and Δ42PD-1-PD-1- T cells were labeled with sample tag and Ab tag before loaded into BD Phapsody for RNA exraction, RNA was extracted according to BD Rhapsody protocol library was prepared according to BD Rhapsody protocol single-cell RNA-seq

value: B cells


title: HER2-low patient 18

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 7

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 6

description: DNA from breast cancer FFPE tissue


title: Hereford - muscle tissue_rep 2

description: Biological replicate 2 of 8. Hereford muscle tissue


title: HDF, rep2

description: Library name: B2


title: MSC, rep3

description: Library name: A3

source_name: Bone marrow

value: Bone marrow

value: cultured mesenchymal stromal cells

value: mesenchymal stromal cells


title: CRg1-F_DMSO_rep1

city: Research Triangle Park

first: Brian

last: Chorley

address: US EPA, 109 TW Alexander Dr

institute: US EPA

description:
Library name: CRg1-F
10X Genomics

data_processing:
Raw data generated using the 10X Chromium were processed following a standardized pipeline. Libraries were sequenced on an Illumina platform, producing paired-end reads with 28 bp for Read 1 (containing cell and molecular barcode information), 91 bp for Read 2 (cDNA sequences), and an 8 bp index read for sample identification.
The resulting BCL files were converted to FASTQ format using the Cell Ranger mkfastq tool, which also demultiplexed libraries based on sample index barcodes. Reads were then aligned to the human reference genome (GRCh38) using the STAR aligner embedded within the Cell Ranger software suite.
Transcript quantification was performed by extracting unique molecular identifiers (UMIs), filtering out low-quality reads, and collapsing UMIs to account for amplification artifacts, yielding a digital gene expression (DGE) matrix for each cell.
Assembly: GRCh38
Supplementary files format and content: matrix and tab-separated files

source_name: liver

growth_protocol: Terminally differentiated human hepatic cells (NoSpin HepaRG™) provided directly from the distributer (Lonza, Morrisville, NC) were seeded at 3X10^3 cells/cm2 in 24-well plates coated with rat tail collagen (Sigma-Aldrich, Saint Louis, MO) at a density of approximately 5 µg/cm2. After dispersion and seeding, cells were allowed to settle in the plate at room temperature for ~2 hrs in a biosafety cabinet before being transferred to an incubator set at 37°C, 5% CO2. Cells were incubated for 7 days in HepaRG Base Medium with Supplement (MH100; Lonza) plus Thawing and Plating additive (MHTAP; Lonza) before treatments, changing the media every 48-72 hrs. During cellular treatment, 0.1% DMSO was used as a vehicle control, corresponding to the final vehicle percentage for all solubilized chemicals. Treatments were carried out for 24 hrs before termination.

extract_protocol:
Following treatment, cells were dissociated into a single cell suspension, cell counts and viability were determined with a fluorometric Nexcelom Cellometer automated cell counter (Nexcelom Biosciences, Lawrence, MA) using Acridine Orange (AO)/Propidium Iodide (PI) stain (Perkin Elmer, Inc., Waltham, MA), following manufacturer’s instructions, and then the cells were fixed and processed for single-cell library construction. Cells were initially incubated for 11 min at 37°C in 0.25% Trypsin-EDTA (Thermo Fisher Scientific) with 40 mM DTT, 0.1 mg/ml actinomycin D, 1 mg/ml anisomycin, and 6 mM RNaseOUT recombinant ribonuclease inhibitor (Thermo Fisher Scientific, Waltham, MA) in 250 µl volume, followed by an additional 15 min 37°C incubation after adding 250 µl 0.5% Collagenase Type 1 (Worthington, Lakewood, NJ) in EBSS (Earle's Balanced Salt Solution) and DTT (Dithiothreitol) 40mM  DTT (Dithiothreitol) and 6mM RNaseOUT. Using a wide-bore pipette tip, cells were then dissociated by gentle pipetting for 10 min, 2 ml of 37°C HepaRG Base Medium was added to stop enzymatic activity, and cells were pelleted at 200 xg for 3 min at 4°C. After media removal, cells were resuspended in 1 ml cell suspension media (1X PBS, 0.5% Opti-Prep Density Gradient Medium (Sigma-Aldrich), 0.1% Bovine Serum Albumin Fraction V (Thermo Fisher Scientific, Waltham, MA), 6 mM RNaseOUT) pre-chilled to 4°C. The cells were pelleted twice more at 200 xg for 3 min at 4°C, washing each time with fresh Cell Suspension Media. After the final wash, cells were filtered through a 40 µm nylon cell strainer, transferred, and stored in a Lo-Bind tube.
Single-cell HepaRG suspensions were barcoded and prepped for sequencing using the Chromium Next GEM Single Cell 3’ Reagent Kit A (v3.1; 10X Genomics), following the manufacturer’s instructions, with an input of 10,000 cells per sample. Then nanoliter scaled Gel Beads-in-emulsion (GEMs) were partitioned to capture single cells as well as a master mix of Illumina TruSeq Read 1 primers, 10X barcodes, unique molecule identifiers (UMI), poly(dT) primers, and reverse transcription enzymes, followed by cells lysing and a cDNA synthesis reaction. After contents were released from the GEMs, pooled barcoded cDNA was purified by silane magnetic beads and amplified by PCR. After fragmentation, Illumina Read 2, P5, P7, and a sample index were added to the pooled amplified cDNA before paired-end sequencing on an Illumina NovaSeq 6000, using a S2 flow cell. Sample library prep traces were verified and quantified on a Bioanalyzer High Sensitivity DNA chip (Agilent).

treatment_protocol: 0.1% dimethyl sulfoxide (DMSO) was used as the vehicle control.

value: liver

value: HepaRG

value: hepatocyte

tag: biological rep

tag: treatment

value: vehicle (DMSO)

tag: timepoint


title: CRg2-F_DMSO_rep2

description:
Library name: CRg2-F
10X Genomics


title: HER2-low patient 17

description: DNA from breast cancer FFPE tissue

tag: age


title: HER2-low patient 15

description: DNA from breast cancer FFPE tissue

tag: breast cancer subtype


title: HER2-low patient 16

description: DNA from breast cancer FFPE tissue

tag: her2 score


title: MSC, rep1

description: Library name: A1


title: IP-group4

first: Penghan

last: Huang

address: 107 Yan Jinag West Road

institute: Sun Yat-Sen University

description: Library name: B20201T

data_processing:
Data analysis was performed by R (v.4.2.1) software and limma (v.3.54.2) software packages.
Assembly: GRCh38
Supplementary files format and content: including raw counts for each sample

source_name: Breast cancer

extract_protocol:
Total RNA was extracted using Trizol rent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
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 reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA).

value: Breast cancer

value: immune-promotion

value: bulk


title: HER2-low patient 14

description: DNA from breast cancer FFPE tissue

source_name: Breast Cancer

value: Breast Cancer

tag: her2 status


title: IP-group3

description: Library name: B1941T


title: HER2-zero patient 5

description: DNA from breast cancer FFPE tissue

value: Triple-Negative Breast Cancer

tag: Sex


title: HER2-low patient 13

description: DNA from breast cancer FFPE tissue

tag: tissue

value: Female


title: HDF, rep3

description: Library name: B3

value: Skin


title: IP-group1

description: Library name: B1862T


title: IP-group5

description: Library name: B2T


title: IM-group10

description: Library name: B19152T

value: immune-median (intermediate levels of immune activation)


title: HER2-low patient 12

description: DNA from breast cancer FFPE tissue


title: IM-group9

description: Library name: B19224T


title: HER2-low patient 11

description: DNA from breast cancer FFPE tissue


title: MSC, rep2

description: Library name: A2


title: IM-group8

description: Library name: B20137T


title: HER2-zero patient 4

description: DNA from breast cancer FFPE tissue


title: HER2-zero patient 3

description: DNA from breast cancer FFPE tissue


title: IM-group7

description: Library name: B20198T


title: HER2-low patient 10

description: DNA from breast cancer FFPE tissue


title: IM-group6

description: Library name: B20177T


title: IM-group5

description: Library name: B2000T


title: HER2-low patient 9

description: DNA from breast cancer FFPE tissue


title: IM-group4

description: Library name: B1819T


title: IM-group3

description: Library name: B1816T


title: HER2-low patient 8

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 6

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 7

description: DNA from breast cancer FFPE tissue


title: IP-group2

description: Library name: B1874T


title: IM-group2

description: Library name: B20140T


title: IS-group5

description: Library name: B20175T

value: immune-suppression


title: HER2-zero patient 2

description: DNA from breast cancer FFPE tissue


title: HER2-low patient 5

description: DNA from breast cancer FFPE tissue


title: IM-group1

description: Library name: B1830T


title: HER2-low patient 3

description: DNA from breast cancer FFPE tissue


title: IS-group3

description: Library name: B1969T


title: HER2-low patient 4

description: DNA from breast cancer FFPE tissue


title: IS-group4

description: Library name: B20155T


title: HER2-low patient 1

description: DNA from breast cancer FFPE tissue


title: IS-group2

description: Library name: B1964T


title: HER2-low patient 2

description: DNA from breast cancer FFPE tissue


title: IS-group1

description: Library name: B19135T


title: wildtype cells, 9 weeks and 2 days of differentiation

city: Bruxelles

first: Miriam

last: Cnop

address: Route de Lennik 808 CP618

department: Faculté de Medecine

country: Belgium

institute: Université Libre de Bruxelles

description:
Library name: 1A2446LC5w2d
10x Genomics

data_processing:
For the analyses, we used 10x Genomics Cell Ranger v9.0.1 and Seurat v5.2.1, to identify and annotate the clusters. scDblFinder v1.12.0 was employed for doublet/multiplet handling, and SoupX v1.6.2 for removing cell free RNA.
Assembly: GRCh38.p13
Supplementary files format and content: csv files summarizing quality metrics and sequencing statistics generated by Cell Ranger for each individual sample.

extract_protocol:
Extended culture (S7 plus 5 weeks) iPSC-β cell aggregates were washed twice with EDTA and dissociated with Accumax (Sigma Aldrich) for 16 min at 37°C. Cells were washed twice in 1% BSA PBS, centrifuged at 300 g for 5 min, filtered using a cell strainer capped tube with 35 µM nylon mesh (Corning, US), counted and adjusted to a 1000 cell/µL concentration. Cell number and viability were evaluated by two researchers using a haemocytometer, after staining with 0.4% Trypan blue (Sigma Aldrich).
Between 4910 to 9721 cells were loaded per experiment into the 10× Chromium Single Cell Platform (10X Genomics) using the Next GEM Single Cell 3′ library and Gel Bead Kit (v3.1 chemistry). Cells were processed according to manufacturer's instructions

tag: genotype

value: wildtype


title: br_5548_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

city: Loma Linda

first: Erik

middle: J

last: Behringer

state: CA

address: 11041 Campus St.

department: Basic Sciences

institute: Loma Linda University

description:
Library name: Sample 60
merged_gene_counts.txt: br_5548

data_processing:
RNAseq pipeline v2.1.0
Nextflow v21.10.6
DESeq2 v1.28.0; FDR cutoff, 0.05 & Log2FC cutoff, 0.585
gProfiler v1.0.0; FDR cutoff, 0.05
Assembly: GRCm39
Supplementary files format and content: Text file includes raw counts among all samples
Supplementary files format and content: The XLSX file contains normalized counts among all samples

source_name: brain

extract_protocol:
RNA was harvested and processed using Zymo's Total RNAseq Full Service Package
Zymo-Seq RiboFree Total RNA Library Kit following manufacturer's protocols

treatment_protocol: Dietary CBD was administered daily (80-100 mg/kg/day) in male 3xTg-AD mice and wild-type B6129SF2/J animals from 4.5 to 6.5 mo of age with inclusion of vehicle controls.

value: brain

value: male

value: Vehicle, week 8


title: br_5552_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 57
merged_gene_counts.txt: br_5552


title: br_5546_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 59
merged_gene_counts.txt: br_5546


title: LENG8-depletion, nucleus mRNA-seq, replicate3

city: Irvine

first: Yongsheng

last: Shi

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

description:
Library name: P12
mRNA-seq

data_processing:
For PAS-seq data processing, raw reads were trimmed using Cutadapt (v2.10) to remove (1) a 6-nucleotide linker sequence, (2) poly(A) tails, and (3) any reads that failed trimming. Cleaned reads were then aligned to a concatenated human (hg19) reference genome using STAR (v2.7.3a). For RNA-seq data processing,raw reads were trimmed using Cutadapt (v2.10). Cleaned reads were then aligned to a concatenated human (hg19) reference genome using STAR (v2.7.3a).
Assembly: hg19
Supplementary files format and content: BigWig files

molecule: nuclear RNA

source_name: Kidney

growth_protocol: HEK293T cell lines containing dTAG-Flag in LENG8 N-terninus were cultured in DMEM supplemented with 10% FBS

extract_protocol:
For fragnation analysis, 150 ŒºL of pre-chilled 0.7% NP-40 lysis buffer (10 mM Tris-HCl, 75 mM NaCl, 0.7% NP-40, pH 7.5, supplemented with fresh protease inhibitors) was added. The suspension was pipetted using a 200 ŒºL tip until homogeneous and incubated on ice for 30 seconds. Samples were then centrifuged at 13,300 rpm for 15 seconds to separate the cytoplasmic (supernatant) and nuclear (pellet) fractions. A total of 150 ŒºL of the cytoplasmic supernatant was collected into new tubes for cytoplasmic RNA extraction by TRIzol reagent. The nuclear pellet was washed three times with 1√ó PBS. 1 mL of TRIzol reagent was added to extract nuclear RNAs. For total RNA, total RNA was extracted from cells using TRIzol reagent
Polyadenylated RNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and then purified mRNA was fragmented at 94¬∞C for 3 minutes using the NEBNext Magnesium RNA Fragmentation Module. For PAS-seq analysis, only the 3'end of mRNA was used for library constrcution.All of library construction was followed illumina's protocol

treatment_protocol: The cells were treated with DMSO and dTAG-V1 for 24h seperately

value: Kidney

value: Human embryonic kidney 293 cell line

tag: group

value: Fraction mRNA-seq


title: LENG8-depletion, cytoplasm mRNA-seq, replicate3

description:
Library name: P11
mRNA-seq

molecule: cytoplasmic RNA


title: br_5554_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 58
merged_gene_counts.txt: br_5554


title: mutant cells, clone 37, 9 weeks and 4 days of differentiation

description:
Library name: 59372410LTC5wk4d
10x Genomics

value: clone 37 mutation V59E in TMEM167A


title: br_5549_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 55
merged_gene_counts.txt: br_5549

value: CBD, week 8


title: control, cytoplasm mRNA-seq, replicate3

description:
Library name: P09
mRNA-seq

value: WT

value: DMSO


title: br_5550_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 56
merged_gene_counts.txt: br_5550


title: control, nucleus mRNA-seq, replicate3

description:
Library name: P10
mRNA-seq


title: LENG8-depletion, nucleus mRNA-seq, replicate2

description:
Library name: P08
mRNA-seq


title: br_5547_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 54
merged_gene_counts.txt: br_5547


title: LENG8-depletion, cytoplasm mRNA-seq, replicate2

description:
Library name: P07
mRNA-seq


title: control, nucleus mRNA-seq, replicate2

description:
Library name: P06
mRNA-seq


title: br_5553_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 52
merged_gene_counts.txt: br_5553


title: control, cytoplasm mRNA-seq, replicate2

description:
Library name: P05
mRNA-seq


title: br_5551_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 51
merged_gene_counts.txt: br_5551


title: LENG8-depletion, cytoplasm mRNA-seq, replicate1

description:
Library name: P03
mRNA-seq


title: br_5450_B6129SF2/J, untreated, week 8, age 6.5 mo, male

description:
Library name: Sample 50
merged_gene_counts.txt: br_5450

value: Untreated, week 8


title: br_5446_B6129SF2/J, untreated, week 8, age 6.5 mo, male

description:
Library name: Sample 49
merged_gene_counts.txt: br_5446


title: LENG8-depletion, nucleus mRNA-seq, replicate1

description:
Library name: P04
mRNA-seq


title: br_5447_B6129SF2/J, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 48
merged_gene_counts.txt: br_5447


title: control, nucleus mRNA-seq, replicate1

description:
Library name: P02
mRNA-seq


title: control, cytoplasm mRNA-seq, replicate1

description:
Library name: P01
mRNA-seq


title: mutant cells, clone 48, 9 weeks and 3 days of differentiation

description:
Library name: 59482410LTC5w3d
10x Genomics

value: clone 48 mutation V59E in TMEM167A


title: br_5443_B6129SF2/J, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 47
merged_gene_counts.txt: br_5443


title: HER2-zero patient 1

description: DNA from breast cancer FFPE tissue

value: Breast Cancer

value: Triple-Negative Breast Cancer

value: Female


title: br_5449_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 45
merged_gene_counts.txt: br_5449


title: br_5441_B6129SF2/J, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 46
merged_gene_counts.txt: br_5441


title: Healthy-PBMCs_02

description:
Library name: M_Sc054
10x Genomics

data_processing:
Sequencing data was processed using Cell Ranger v7.1.0 (10x Genomics). Namely, reads were aligned to a GRCh38 reference genome (v3.0.0) and gene expression matrices generated using cellranger count. SoupX (v1.6.2) was used to remove ambient RNA contamination [38]. Doublets were removed using Scrublet (v0.0.4) with default parameters [39]. The data from all samples were combined using the merge function in Seurat v4.3.1 [40]. Low quality cells with < 500 genes detected or > 10% of reads aligned to the mitochondrial genome were removed. Genes expressed in fewer than five cells were removed.After quality control, data was analyzed using Seurat v4.3.1 [40]. Raw count data was normalized using sctransform [41] with percent mitochondrial reads and the number of unique molecular identifier (UMI) counts regressed out. Variance stabilizing transformation was performed to identify the 3,000 most variable genes, which were used for principal component analysis (PCA). Batch effects from different donors were removed using Harmony [42]. A shared nearest neighbor graph was constructed using the top 30 Harmony components, and clustering was performed with the Louvain algorithm (resolution 1.9). Data was visualized using UMAP of the top 30 Harmony PCs.
Assembly: 10x human reference
Supplementary files format and content: Matrix files

extract_protocol:
As part of routine hospital procedure, 5-10 ml of CSF and 1 ml heparinized blood were collected. 2-3 ml of CSF were sent to the hospital laboratory for routine tests for viral, bacterial, or fungal infection. The remaining CSF was concentrated by centrifugation at 300 × g for 10 min and re-suspended in 700 µl of CSF supernatant. This CSF deposit was used for TB diagnostic tests, including 100 μl for Ziehl-Neelsen smear, 200 μl for Xpert MTB/RIF, and 200 μl was stored at -80°C for future use. The remaining 200 μl of CSF was used for scRNA-seq if processed within four hours of collection, with ≥ 75 cells/µl deposit, and no artificial blood contamination (evidenced by > 200 RBCs/μl CSF total) [15]. After re-centrifugation (300 × g, 5 min), CSF pellets were resuspended in 50 μl PBS containing 0.04% bovine serum albumin (BSA, Sigma) and counted. Blood was processed alongside CSF, with PBMCs isolated using density gradient centrifugation with Histopaque 1077 (Sigma) following the manufacturer’s instructions
Single-cell suspensions were loaded onto a 10x Genomics Chromium Controller. One patient sample was loaded per channel with a target capture rate of 4,000 cells, while the healthy control PBMCs had a target capture rate of 1,000 cells. Libraries were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s instructions. One library from the healthy control PBMCs was sequenced internally on an Illumina MiSeq to a mean depth of 20,922 reads per cell, with a sequencing saturation of 66.1%. Other libraries were sequenced on an Illumina NovaSeq 6000 (BGI, Hong Kong) to a mean depth of 33,072-163,448 reads per cell, with a sequencing saturation of 54.0-91.6%.

value: blood

value: tissue

value: PBMCs

value: healthy


title: input DNA, control

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description: Library name: Sample3

data_processing:
Strand NGS software (Strand Life Sciences)
Peak detection was performed using the MACS algorithm.  The significant enrichment of each signal over input-DNA peaks was determined at a P cut-off value of 10-5.
Assembly: hg19
Supplementary files format and content: The processed data files are provided as BED format files (.bed). Each file represents peak summits identified using the MACS2 peak-calling algorithm applied to ChIP-seq data.

growth_protocol: HA-PSF-TFE3-inducible HK-2 cell lines which express HA-PSF-TFE3 in a doxycycline-dependent manner were cultured with advanced DMEM/F-12 supplemented with 1.5% FCS, 100 U/ml penicillin, 100 microg/ml streptomycin.

extract_protocol:
SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (#9005, Cell Signaling) was utilized for ChIP. Cell cross-linking, chromatin preparation and chromatin immunoprecipitation by anti HA Affinity Matrix (#11815016001, Roche) was performed according to the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: HA-PSF-TFE3-inducible HK-2 cells were cultured with 0.2 microg/ml of doxycycline for 24hr.

value: HA-PSF-TFE3-inducible cell

value: Doxycycline +


title: HA-PSF-TFE3_8_ChIP-seq

description: Library name: Sample1

value: Kidney


title: Healthy-PBMCs_03

description:
Library name: M_Sc060
10x Genomics


title: br_5445_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 43
merged_gene_counts.txt: br_5445

value: brain

value: male