title: RNA_TTX_AP5_shControl_Replicate1

value: Primary cortical neurons

value: AAV treatment from DIV8 to DIV13. Pre-silencing of neuronal activity using tetrodotoxin (TTX, 1-2 µM, hellobio) at DIV12 for 24 hours, and D-AP5 (100 µM, Tocris) for six hours before collection.


title: E18, mixed brain cell population, w/o treatment, rep 6

status: Public on Jul 31 2026

type: SRA

city: Paris

first: Tabitha

last: Rücker

address: 25, rue du Docteur Roux

country: France

institute: Institut Pasteur

library_source: transcriptomic

data_processing:
Adapter trimming was performed with cutadapt v. 3.1 (parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA x.fastq). Trimmed sequences were aligned using RNA STAR aligner (v. 2.7.8a) against the GRCm38/mm10 reference. For Gap-aware read counting featureCounts (v. 2.0.1) was applied.
Read counts were normalized by rlog transformation with DESeq2 and subjected to downstream analyses.
Assembly: mm10
Supplementary files format and content: comma-separated value file includes raw counts for each sample (countTable_RNAseq.csv).
Supplementary files format and content: comma-separated value file includes normalized counts of each sample (rld_transformed_counts.csv).

molecule: total RNA

organism: Mus musculus

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted from frozen aliquots of 10,000 sorted cells using the RNeasy® Micro Kit (Qiagen, #74004).
From total RNA cDNA was synthesized, PolyA enriched and amplified using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, # 634891). cDNA was then further processed with the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1096).

tag: tissue

value: cerebral cortex

tag: cell type

value: mixed population of brain cells

tag: transgene constructs

value: pCAG-tDimer

tag: age

value: 18 days old embryo (E18)

tag: treatment

value: w/o

tag: harvest mode


title: RNA_Basal_shNup153_2_Replicate3

city: Dresden

first: Abhinav

last: Soni

state: Saxony

address: Tatzberg 41

department: Nuclear architecture in neural plasticity and aging

country: Germany

institute: German Center for Neurodegenerative Diseases, Dresden

description: RNA sample collected from basal state primary cortical neurons treated with AAV-shControl from DIV8 to DIV13. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.

data_processing:
FastQC was used to perform basic quality control of the sequencing data. Fragments were aligned to the mouse reference (mm10) with support of the Ensembl 98 splice sites using the gsnap aligner (v2020-12-16) . Fragments per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1) .
Assembly: mm10
Supplementary files format and content: Processed data file 'CountData_Basalstate_RNASeq.txt' & 'CountData_TTX_AP5_RNASeq.txt'  includes matrix of count per genes for RNA-Sequencing dataset in basal state PCNs and TTX-AP5 treated PCNs respectively.

molecule: polyA RNA

source_name: Primary cortical neurons

growth_protocol: Embryonic cortices (embryonic day 17.5-19.5) (C57/BL6 mice) from one litter were dissected and pooled together to be processed as a single biological replicate. Dissociated primary cortical neurons were plated in Poly-Dl-Ornithine Hydrobromide coated plates. Cells were maintained in incubators at 37°C with a CO2 concentration of 5%. 30% medium was replaced at DIV4 and DIV8 with Brain Phys Neuronal Culture Medium (STEMCELL Tec), supplemented with 2% SM1-NC (STEMCELL Tec).

extract_protocol:
poly-dT enrichment from total RNA, followed by strand specific RNA-seq library preparation (Ultra II Directional RNA Library Prep, NEB). Purified libraries were quantified on a Fragment analyser (Agilent) and sequenced on an IlluminaNovaSeq 6000 in 100bp paired-end mode to a depth of 30-55 million fragments per library.
Samples confirmed to have sufficient Nup153 knockdown were further processed for RNA sequencing. To remove any contaminating DNA, samples were treated with TURBO DNAase (Life Technologies), and RNA integrity was checked by Bioanalyzer (Agilent). Only samples with RIN number greater than 8 were used for further processing. A total of 3-4 biological replicates were used for each condition analyzed in the study, with one biological replicate being primary neurons derived from pooled cortical tissue from embryos of one litter.
mRNA was isolated from an average of 150-300 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). Ligation was performed using the NEBNext Adapter of the NEBNext Multiplex Oligos for Illumina Kit. After ligation, the adapters were depleted by XP bead purification (Beckman Coulter). Unique dual indexing was used during the subsequent PCR enrichment (12 cycles) with amplification primers carrying the same sequence for i7 and i5 indices (primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After purification, libraries were quantified on a Fragment Analyzer (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 in 100 bp paired-end mode to a depth of 30-55 million fragments per library.

value: AAV treatment from DIV8 to DIV13 in basal state primary cortical neurons

tag: owner

value: Abhinav Soni & Tomohisa Toda


title: znf804a-light,hom,rep1

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

country: USA

institute: UMass Chan Medical School

description: Library name: Sample 21

data_processing:
Paired-end and single-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
To analyze splicing and produce the sample_#.isoforms.results.gz files, rsem-calculate-expression from the 1.3.3 version was run with the following commands:   --paired-end \   --bam \   --calc-pme \   --num-threads 4 \
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.
Supplementary files format and content: Isoform quantification from RSEM

organism: Danio rerio

source_name: 6 dpf head with eyes, 4 heads combined

extract_protocol:
RNA was extracted using the MicroElute Total RNA Kit (Omega Bio-Tek R6834-02), with a 15-min incubation with Dnase I.
Libraries were constructed using an in-house protocol based on SMART-Seq2, followed by Nextera XT Library Preparation (FC-131-1096).

value: 6 dpf head with eyes, 4 heads combined

tag: genotype

value: znf804a homozygous mutant

tag: sample group


title: znf804a-dark,hom,rep4

description: Library name: Sample 20


title: 16-097H2_Lung2

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description:
Library name: 16-097H2_Lung2
16-097H2_Lung2

data_processing:
Amplified, target-enriched libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA), employing a 2x 100-cycle paired-end sequencing strategy
FASTQ files were generated using Illumina’s bclconvert v3.10.5 and trimmed with Agilent Locatit v3.0
The RNA sequencing reads were aligned to the Gencode GRCh38.primary_assembly reference genome using STAR29 (v2.7.7a).
Gene-level quantification was conducted with HTSeq30 (v0.11.0) using Gencode V22 primary assembly annotations.
Counts per million ( cpm) reads were calculated using the cpm() function from R package, edgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts per million (cpm) values for each Sample.

organism: Homo sapiens

source_name: Lung

growth_protocol: Total RNA was extracted from flash-frozen tissue samples using the Maxwell RSC RNA FFPE Kit (Promega, Madison, WI, USA) on the automated Maxwell RSC 48 instrument (Promega)

extract_protocol:
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Library size distribution was validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).
RNA-seq libraries were pooled (70-plex) and clustered onto an P2-100 flow cell.

treatment_protocol: untreated

value: Lung

value: Metastatic

value: Flash-frozen


title: 16-097G2_Lung1

description:
Library name: 16-097G2_Lung1
16-097G2_Lung1


title: znf804a-dark,hom,rep3

description: Library name: Sample 19


title: E18, mixed brain cell population, w/o treatment, rep 4


title: RNA_Basal_shNup153_2_Replicate2


title: 16-097J4_Liver1

description:
Library name: 16-097J4_Liver1
16-097J4_Liver1

source_name: Liver

value: Liver


title: RNA_Basal_shNup153_2_Replicate1


title: znf804a-dark,hom,rep2

description: Library name: Sample 18


title: E18, mixed brain cell population, w/o treatment, rep 3


title: 16-097AA_Bone

description:
Library name: 16-097AA_Bone
16-097AA_Bone

source_name: Bone

value: Bone


title: RNA_Basal_shNup153_1_Replicate3


title: znf804a-dark,hom,rep1

description: Library name: Sample 17


title: 16-079N3_LN2

description:
Library name: 16-079N3_LN2
16-079N3_LN2

source_name: LN

value: LN


title: E18, mixed brain cell population, w/o treatment, rep 2


title: znf804a-light,wt,rep4

description: Library name: Sample 16

value: wildtype


title: 16-079M3_LN1

description:
Library name: 16-079M3_LN1
16-079M3_LN1


title: E18, mixed brain cell population, w/o treatment, rep 1


title: RNA_Basal_shNup153_1_Replicate2

value: Primary cortical neurons


title: RNA_Basal_shNup153_1_Replicate1


title: E18, mixed brain cell population, w/o treatment, rep 5

value: cerebral cortex


title: znf804a-light,wt,rep3

description: Library name: Sample 15


title: 16-079H1_Liver2

description:
Library name: 16-079H1_Liver2
16-079H1_Liver2


title: RNA_Basal_shControl_Replicate4


title: E17, pNeuroD cell population, w/o treatment, rep 6

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: 17 days old embryo (E17)


title: znf804a-light,wt,rep2

description: Library name: Sample 14


title: 16-079G2_Liver1

description:
Library name: 16-079G2_Liver1
16-079G2_Liver1


title: E17, pNeuroD cell population, w/o treatment, rep 5

value: w/o


title: RNA_Basal_shControl_Replicate3

value: AAV treatment from DIV8 to DIV13 in basal state primary cortical neurons


title: znf804a-light,wt,rep1

description: Library name: Sample 13


title: 16-079FF_Bone

description:
Library name: 16-079FF_Bone
16-079FF_Bone


title: RNA_Basal_shControl_Replicate2

value: Abhinav Soni & Tomohisa Toda


title: E17, pNeuroD cell population, w/o treatment, rep 4


title: znf804a-dark,wt,rep4

description: Library name: Sample 12

value: 6 dpf head with eyes, 4 heads combined


title: 16-070P2_LN2

description:
Library name: 16-070P2_LN2
16-070P2_LN2


title: RNA_Basal_shControl_Replicate1


title: znf804a-dark,wt,rep3

description: Library name: Sample 11


title: E17, pNeuroD cell population, w/o treatment, rep 3


title: vector control TRIM28-ChIP replicate 3

city: Copenhagen N

first: Daniel

middle: Martin

last: Messerschmidt

state: Zealand

address: 3C Blegdamsvej, Building 18

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description: Library name: vecTR28_3

library_source: genomic

data_processing:
Raw reads were aligned to mm10 genome using Bowtie2 (default parameters), before sorting the bam files with samtools sort.Bigwig files were generated with the bamCoverage fonction of deeptools2.0, using the options --normalizeUsing RPKM --binSize 25 --smoothLength 100. Peaks were called with Macs2 callpeak (default parameters).
Assembly: mm10
Supplementary files format and content: bigwig files showing read coverage

molecule: genomic DNA

source_name: mouse embryonic stem cell

growth_protocol: Embryonic stem cells were cultured under standard LIF/FCS conditions.

extract_protocol:
genomic DNA
ChIP was performed as previously described {Guccione:2007dy}. Chromatin was fragmented using a BRANSON Digital Sonifier (#S540D) to 250-1000bp fragments, precleared and incubated with antibodies overnight. Antibody/chromatin complexes were incubated for 50% Protein-G Sepharose slurry and washed before elution/decrosslinking in 1% SDS and 0.1 M NaHCO3. DNA was column purified with QIAquick PCR purification Kit, Qiagen.ChIP DNA concentrations were measured with the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were prepared with the NEBNext Ultra II DNA Library Preparation Kit for Illumina (NEB), following manufacturer’s instructions. PCR conditions were adjusted to starting material concentrations and final elution volumes were reduced. Libraries were quantified by Bioanalyzer (High Sensitivity DNA Kit, Agilent) and PCR (KAPA Library Quantification Kit for Illumina, Roche). ChIP-Seq libraries were pooled and sequenced on the NextSeq500, as a single end (76bp) run

tag: cell line

value: mouse embryonic stem cell

value: antibody:alpha-TRIM28, Abcam ab10484, 5ug


title: 16-070M6_LN1

description:
Library name: 16-070M6_LN1
16-070M6_LN1

value: Metastatic


title: E17, pNeuroD cell population, w/o treatment, rep 2


title: znf804a-dark,wt,rep2

description: Library name: Sample 10


title: CHIP_Input_Basal_shNup153_2_Replicate2

description: CHIP input sample collected from basal state primary cortical neurons treated with AAV-shControl from DIV8 to DIV13. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.

data_processing:
To align ChIP-seq reads, the nf-core/atacseq pipeline was used (v2.0). After alignment and filtering of reads, the nf-core pipeline generated separate bigwig files, which were used for visualization of reads in the IGV browser.
Assembly: mm10
Supplementary files format and content: Processed data files includes bigwig files for each samples.

extract_protocol:
CHIP samples were subjected to Illumina library preparation using the NEBnext Ultra II DNA library preparation chemistry (New England Biolabs, E7645L). The libraries were size-selected with XP beads. The resulting libraries were checked for quality and quantified using a Fragment Analyzer (Agilent) NGS Fragment Kit (1-6000bp). The final libraries were subjected to 100bp paired-end sequencing on the Illumina NovaSeq6000 platform at a depth of 35-55 million fragments per library.
PCNs were collected in the basal state at DIV13. PCNs were fixed by adding 16% formaldehyde (VWR International) directly to the media to a final concentration of 1% for 10 minutes at RT. Residual formaldehyde was quenched by adding 1M glycine (Carl Roth) directly to the media to a final concentration of 0.1M for 15 minutes at RT. After quenching, PCNs were washed twice with cold PBS solution containing protease inhibitor (Sigma Aldrich) (PBS-PI) for five minutes each. Cells were scraped from the plates and collected in a 1.5ml tube, pelleted by centrifugation at 300 G, and washed with PBS-PI. Samples were either stored at -80°C or processed directly for chromatin immunoprecipitation.  For ChIP-Seq of HDAC1 and H3K27ac, 1.5mM EGS (ethylene glycol bis succinimidyl succinate) was applied for 15 minutes at RT prior to formaldehyde fixation, followed by two 5-minute washes with PBS. A total of two biological replicates were used for ChIP-Seq for each condition. Samples were thawed and lysed in 1 ml of ChIP lysis buffer for 10 min at 4°C on a rotator. Samples were washed in ChIP Wash buffer for 10 min at 4°C and resuspended in ChIP buffer for sonication. Samples were sonicated using a focused-ultrasonicator (Covaris).   After confirming the size of the fragments, the samples were pre-cleaned with 10 µl of Dynabeads Protein G (Life Technologies) for 1 hour at 4°C, and then the samples were incubated with 2 ug of primary antibodies at 4°C overnight on a rotator. The next day, Dynabeads were added into the samples for 2 hours, and the tubes were rotated at 4°C. Dynabeads were separated from the samples using a magnetic stand DynaMagTM (Thermo Fisher). The beads were sequentially washed with low-salt buffer, high-salt buffer, lithium chloride buffer and twice with TE 1X buffer (IDTE). The bound chromatin was eluted from the Dynabeads by incubating it in 100 ul of elution buffer. Following RNase A and proteinase K treatments, DNA was purified using a standard phenol chloroform extraction method.
ChIP samples were subjected to Illumina fragment library preparation using the NEBnext Ultra II DNA library preparation chemistry (New England Biolabs, E7645L). Briefly, DNA fragments were end-repaired, A-tailed and ligated to unique-dual indexed Illumina Truseq adapters (IDT, prehybridized UDI-UMI Adapters for Illumina, 0.15 µM adapter per reaction). The resulting libraries were PCR-amplified for 15 cycles using universal primers (primer 1: CAAGCAGAAGACGGCATACGAGAT and Primer 2: AATGATACGGCGACCACCGA*G; *: Phosphothioate bond) and purified using XP beads (Beckman Coulter). The libraries were size-selected with XP beads. The resulting libraries were checked for quality and quantified using a Fragment Analyzer (Agilent) NGS Fragment Kit (1-6000bp). The final libraries were subjected to 100bp paired-end sequencing on the Illumina NovaSeq6000 platform at a depth of 35-55 million fragments per library.


title: 16-070I4_Liver-2

description:
Library name: 16-070I4_Liver-2
16-070I4_Liver-2

value: Flash-frozen


title: E17, pNeuroD cell population, w/o treatment, rep 1


title: znf804a-dark,wt,rep1

description: Library name: Sample 9


title: CHIP_Input_Basal_shNup153_2_Replicate1


title: 16-070H7_Liver1

description:
Library name: 16-070H7_Liver1
16-070H7_Liver1

value: Liver


title: E17, mixed brain cell population, w/o treatment, rep 6

value: mixed population of brain cells

value: pCAG-tDimer


title: CHIP_Input_Basal_shControl_Replicate2


title: 15-109I9_Liver3

description:
Library name: 15-109I9_Liver3
15-109I9_Liver3


title: CHIP_H3K27ac_Basal_shNup153_2_Replicate2

description: CHIP sample collected from basal state primary cortical neurons treated with AAV-shControl from DIV8 to DIV13. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.


title: znf804a-light,het,rep4

description: Library name: Sample 8

value: znf804a heterozygous mutant


title: znf804a-light,het,rep3

description: Library name: Sample 7


title: 15-109H8_Liver2

description:
Library name: 15-109H8_Liver2
15-109H8_Liver2


title: E17, mixed brain cell population, w/o treatment, rep 5


title: E17, mixed brain cell population, w/o treatment, rep 4


title: znf804a-light,het,rep2

description: Library name: Sample 6


title: 15-109G5_Liver1

description:
Library name: 15-109G5_Liver1
15-109G5_Liver1


title: E17, mixed brain cell population, w/o treatment, rep 3


title: CHIP_H3K27ac_Basal_shNup153_2_Replicate1

value: Primary cortical neurons


title: CHIP_H3K27ac_Basal_shControl_Replicate2


title: 15-109DD_Bone

description:
Library name: 15-109DD_Bone
15-109DD_Bone

value: Bone


title: E17, mixed brain cell population, w/o treatment, rep 2

value: cerebral cortex


title: znf804a-dark,het,rep4

description: Library name: Sample 4


title: 15-108L5_Lung2

description:
Library name: 15-108L5_Lung2
15-108L5_Lung2

value: Lung


title: E17, mixed brain cell population, w/o treatment, rep 1

value: 17 days old embryo (E17)


title: CHIP_H3K27ac_Basal_shControl_Replicate1


title: znf804a-light,het,rep1

description: Library name: Sample 5


title: CHIP_Basal_Input_Replicate2

description: CHIP input sample collected from basal state primary cortical neurons treated at DIV13.Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.

value: No treatment


title: znf804a-dark,het,rep3

description: Library name: Sample 3


title: 15-108K6_Lung-1

description:
Library name: 15-108K6_Lung-1
15-108K6_Lung-1


title: E16, pNeuroD cell population, w/o treatment, rep 6

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: 16 days old embryo (E16)

value: w/o


title: CHIP_Basal_Input_Replicate1

value: Abhinav Soni & Tomohisa Toda


title: znf804a-dark,het,rep2

description: Library name: Sample 2

value: 6 dpf head with eyes, 4 heads combined


title: 15-108J1_Liver2

description:
Library name: 15-108J1_Liver2
15-108J1_Liver2

source_name: liver

value: liver

value: Metastatic

value: Flash-frozen


title: CHIP_Basal_HDAC1_Replicate2

description: CHIP sample collected from basal state primary cortical neurons treated at DIV13.Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.


title: E16, pNeuroD cell population, w/o treatment, rep 5


title: znf804a-dark,het,rep1

description: Library name: Sample 1


title: 15-108H1_Liver1

description:
Library name: 15-108H1_Liver1
15-108H1_Liver1

value: Liver


title: CHIP_Basal_HDAC1_Replicate1


title: *AB lta4h mutant zebrafish-M.marinum granuloma cells

city: Durham

first: David

last: Tobin

state: NC

address: 207 Research Drive

institute: Duke University

description:
Library name: lta4hGran
10X Genomics

library_source: transcriptomic single cell

data_processing:
The Molecular Genomics Core’s standard analytical pipeline was used for single cell RNAseq analysis. Briefly, raw base call (BCL) files generated by an Illumina sequencer were demultiplexed into FASTQ, then aligned to the Ensembl zebrafish genome assembly GRCz11.96. Filtering, barcode and UMI counting were performed using the most current version of 10X’s Cell Ranger software. The R package Seurat was used to perform quality control and linear dimensional reduction. Datasets were integrated using FindIntegrationAnchors() and JoinLayers(). Cells were clustered de novo for unbiased cell type discovery using Seurat’s FindNeighbors() and FindClusters() functions, graph-based clustering approach with visualization of cells being achieved through the use of UMAP plots. Cluster specific markers were generated by FindConservedMarkers() and differentially expressed genes between datasets were generated by FindMarkers(). Expression of canonical gene markers were used to annotate clusters with specific cell types
Assembly: Zebrafish GRCz11.96
Supplementary files format and content: Tab-separated values and matrix files

source_name: Granulomas

extract_protocol:
Granulomas were transferred to a 1.5 mL tube and cells were dissociated using 1 mL of 0.05% trypsin/EDTA (ThermoFisher Scientific, 25300054) at 30_x000E_C for 35 minutes with rocking. Cells were collected by centrifugation for 5 min at 300 xg, resuspended in 1x DPBS with 10% FBS on ice, and passed through a 40 mm strainer.
Single cell samples were submitted to the Molecular Genomics Core at Duke Molecular Physiology Institute for library preparation, using Chromium Single Cell 3’ GEM, Library and Gel Bead Kit v3, and gem generation using the 10x Genomics platform. Libraries were sequenced was at Duke Center for Genomic and Computational Biology

treatment_protocol: M. marinum infection

value: Granulomas

value: Granuloma cells

value: immune and stromal


title: E16, pNeuroD cell population, w/o treatment, rep 4

value: cerebral cortex


title: E16, pNeuroD cell population, w/o treatment, rep 3


title: ATAC_TTX_AP5_shNup153_2_Replicate2

description:
ATAC sample collected from pre-silenced primary cortical neurons treated with AAV-shControl from DIV8 to DIV13.Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.
TTX_AP5_shNup153_2_ATAC.bigwig

data_processing:
To align ATAC-seq reads, the nf-core/atacseq pipeline written in the Nextflow domain-specific language was used . Briefly, the nf-core pipeline for ATAC-seq (v2.0) was used to perform a quality check on fasta files generated after sequencing, followed by alignment of reads to the mm10 genome using the bwa aligner and filtering aligned reads. After the quality check, separate bam files for each replicate, and bam files where filtered reads for replicates are merged. The bam files for merged replicates were used to create bigwig files. To create bigwig files for visualization in IGV (v2.11.7), genomcov with -bg option and scaling in bedtools(v2.31.0) was used to create a bedgraph file . Following this, the bedgraph file was converted to a bigwig file using the UCSC tool bedGraphToBigWig .
Assembly: mm10
Supplementary files format and content: Processed data files includes bigwig files for the merged library from the two replicates for each condition i.e. Basal_shControl, Basal_shNup153_2, TTX_AP5_shControl and TTX_AP5_shNup153_2

extract_protocol:
Purified tagmented DNA was PCR amplified and indexed with P5 and P7 primers compatible with Illumina Nextera DNA barcoding. Amplified and indexed DNA was purified and double sided size selection was performed with AMpure XP beads. Libraries were checked for quality and quantity with fragment analyzer. Libraries were then sequenced on the Illumina NovaSeq 6000 in 100 bp paired-end model at a depth of 70-110 million read pairs.
Cells were treated with DNase (Worthington) for 30 min at 37°C to digest any free-floating DNA and DNA from dead cells. Subsequently, PCNs were directly lysed in 1 ml cold ATAC-Seq resuspension buffer (RSB: 10 mM Tris-HCl pH 7.4, 10mM NaCl, and 3 mM MgCl2 in water, containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin). After cell lysis, approximately 50,000 nuclei were centrifuged and washed with 1ml of RSB without detergent. The nuclei were then centrifuged again, the supernatant was removed, and the nuclei were resuspended in 50 µl transposition mix (25 µl 2X Tagmentation DNA buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethylformamide), 2.5 µl transposase (100 nM final), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, and 5 µl water). Transposition reactions were incubated for 30 minutes at 37°C with shaking at 1000 rpm. Samples were then purified using the MinElute PCR clean up kit (Qiagen). Two biological replicates per condition were processed.
A total of 10 µl of purified tagmented DNA was indexed and pre-amplified for the initial 5 PCR cycles with 1x KAPA HiFi HotStart Readymix and 100 nM unique dual-index P5 and P7 primers compatible with Illumina Nextera DNA barcoding, using the following PCR conditions: 72°C for 5 min, 98°C for 30 s, thermocycling for 5 cycles at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Subsequently, qPCR was performed on the LightCycler 480 (Roche) with 1 µl of the pre-amplified material to determine the remaining PCR cycle numbers to avoid saturation and potential bias in library amplification. Purification and double-sided size selection of amplified libraries was performed using AMPure XP beads (Beckmann Coulter), and libraries were checked for their quality and quantity on a Fragment Analyzer (Agilent). Libraries were sequenced on the Illumina NovaSeq 6000 in 100 bp paired-end mode to a depth of 70-110 million read pairs.

value: Primary cortical neurons

value: AAV treatment from DIV8 to DIV13. Pre-silencing of neuronal activity using tetrodotoxin (TTX, 1-2 µM, hellobio) at DIV12 for 24 hours, and D-AP5(100 µM, Tocris) for six hours before collection.


title: Metastatic 18-101

description:
Library name: 18-101M3_Kidney
Primary 18-101

source_name: Renal pelvis

growth_protocol: Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue samples using the Maxwell RSC RNA FFPE Kit (Promega, Madison, WI, USA) on the automated Maxwell RSC 48 instrument (Promega)

value: Renal pelvis


title: HPC_0079664_3

type: RNA

city: San Francisco

first: Jerry

last: Wang

state: CA

address: 513 Parnassus Ave. HSE-860

department: Neurosurgery

institute: University of California, San Francisco

hyb_protocol: Custom 300 gene panel was deployed. Hybridization were prepared in strict accordance to manufacturer specifications.

scan_protocol: Image acquisition and processing was performed in strict accordance to manufacturer specifications using the Xenium In Situ Analyzer (onboard instrument software v2.0.1.0).

data_processing: Xeniumranger v2.0.1.2, R v4.4.1. Data processing details are provided in methods of manuscript.

label: Xenium probe set

source_name: Hippocampus

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Tissue sections were prepared in strict accordance to manufacturer specifications.

value: Hippocampus

tag: tissue preservation method

value: Fresh Frozen

value: Control


title: Day 14 Treated with only 7gRNAs _ Rep 2

city: Tehran

first: Massoud

last: Vosough

address: Bani Hashem Sq.

country: Iran

institute: Royan Institute

description: Library name: GC146807

data_processing:
Trim Galore! (v0.6.7) was employed to trim reads based on quality (PHRED score < 20) and to remove adaptor sequences. Additionally, reads shorter than 20 base pairs were excluded from further analysis. The alignment of the trimmed reads to hg38 (gencode.36.GRCh38.p13) was performed using Bismark (v0.23.1) with a maximum insert size of 500 base pairs. This process was subsequently followed by methylation extraction. Only CpG sites with a minimum coverage of 1000× were retained
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including the raw counts for each sample

source_name: Stomach

growth_protocol: The HGC-27 cells were grown in  DMEM/F-12 supplemented with 10% fetal bovine serum and 100 µg/mL penicillin, and 100 µg/mL streptomycin. The selection media for culturing cells after the transfection was supplemented with 3 μg/mL doxycycline and 5 μg/mL Blasticidin S for about three days.

extract_protocol:
Genomic DNA was extracted from HGC-27 cells following epigenetic silencing, as well as from control cells (those transfected with only gRNAs and untreated cells), using the Puregene Core Kit A (Qiagen) according to the manufacturer's protocol and the quality was assessed using Nanodrop.
The amplified fragments with added tails were then gel-purified and their concentration was measured using Qubit™ dsDNA HS Assay kit (Invitrogen). Each amplicon was first diluted to a concentration of 15 nM, pooled in equimolar amounts per sample, and used for generating libraries with custom primers harboring unique dual indexes. The sequencing was conducted using NovaSeq PE150 for a minimum of 100,000 reads per amplicon.

value: Stomach

value: Human gastric carcinoma cell line

value: HGC-27 cells transfected with only 7gRNAs

tag: batch


title: E16, pNeuroD cell population, w/o treatment, rep 2

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: 16 days old embryo (E16)

value: w/o


title: E16, pNeuroD cell population, w/o treatment, rep 1


title: HPC_0079664_2


title: ATAC_TTX_AP5_shNup153_2_Replicate1

value: Abhinav Soni & Tomohisa Toda


title: ATAC_TTX_AP5_shControl_Replicate2

description:
ATAC sample collected from pre-silenced primary cortical neurons treated with AAV-shControl from DIV8 to DIV13.Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.
TTX_AP5_shControl_ATAC.bigwig


title: Day 7 Treated with only 7gRNAs _ Rep 2

description: Library name: GC146806


title: HPC_0079653_2


title: HPC_0079664_1


title: ATAC_TTX_AP5_shControl_Replicate1


title: Day 14 Epigenetic modification with 7gRNAs _ Rep 2

description: Library name: GC146804

value: Tr.HGC-27-KRAB cells transfected with the DNMT3AL domain and 7gRNAs


title: E16, mixed brain cell population, w/o treatment, rep 6

value: mixed population of brain cells

value: pCAG-tDimer


title: Day 3 Treated with only 7gRNAs _ Rep 2

description: Library name: GC146805


title: E16, mixed brain cell population, w/o treatment, rep 5

value: cerebral cortex


title: ATAC_Basal_shNup153_2_Replicate2

description:
ATAC sample collected from basal state primary cortical neurons treated with AAV-shControl from DIV8 to DIV13. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.
Basal_shNup153_2_ATAC.bigwig

value: Primary cortical neurons

value: AAV treatment from DIV8 to DIV13 in basal state primary cortical neurons


title: HPC_0079653_1

value: Hippocampus


title: Day 7 Epigenetic modification with 7gRNAs _ Rep 2

description: Library name: GC146803


title: E16, mixed brain cell population, w/o treatment, rep 4


title: E16, mixed brain cell population, w/o treatment, rep 3


title: Day 3 Epigenetic modification with 7gRNAs _ Rep 2

description: Library name: GC146802


title: ATAC_Basal_shControl_Replicate2

description:
ATAC sample collected from basal state primary cortical neurons treated with AAV-shControl from DIV8 to DIV13. Sample was sequenced on Illumina NovaSeq 6000 in 100 bp paired-end mode.
Basal_shControl_ATAC.bigwig


title: ATAC_Basal_shNup153_2_Replicate1


title: HPC_0079641_3

value: FFPE


title: HPC_0079641_2

value: Control


title: Control HGC-27 Rep 2

description: Library name: GC146801

value: Stomach

value: No Treatment


title: E16, mixed brain cell population, w/o treatment, rep 2


title: ATAC_Basal_shControl_Replicate1


title: HPC_0079641_1


title: E16, mixed brain cell population, w/o treatment, rep 1


title: Day 14 Treated with only 7gRNAs _ Rep 1

description: Library name: GC146800

value: Human gastric carcinoma cell line

value: HGC-27 cells transfected with only 7gRNAs


title: Raptor WT C6

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023).
An alignment reference was generated from the mm39 mouse genome and GENCODE comprehensive gene annotations (vM31), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter.
About 30-50 million uniquely mapped reads were acquired per sample. DESeq2 package v1.36.0 (Love et al. 2014) was used to perform sample-level quality control, low count filtering, normalization and downstream differential gene expression analysis.
Assembly: mm39
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

source_name: brown adipocyte

growth_protocol: HIB-1B cells were grown in DMEM medium with 10% FBS.

extract_protocol:
HIB-1B cells were lysated by Trizol reagent (Invitrogen). RNA was extracted using the Zymo Quick-RNA Miniprep kit.
The total RNA samples were QC'd.  mRNA enrichment and cDNA library preparation were performed utilizing stranded mRNA (polyA-selected) sample prep kit. Sequencing was performed at Paired-End 150 bp on the Illumina NovaSeq 6000.  The file deliverable was a demultiplexed FASTQ containing the PF reads, targeting a mean of ~30M reads/sample.

treatment_protocol: HIB-1B cells were differentiated in DMEM medium with 10% FBS and 1 μM rosiglitazone for three days and maintained in DMEM medium with 10% FBS for 1 day.

value: brown adipocyte

value: WT


title: Day 7 Treated with only 7gRNAs _ Rep 1

description: Library name: GC146799


title: HPC_0079638_3


title: Raptor WT C5


title: E14, pGlast cell population, w/o treatment, rep 6

value: neuronal progenitor cells

value: pGlast-dsRed/pCAG-Venus

value: 14 days old embryo (E14)

value: w/o


title: Day 3 Treated with only 7gRNAs _ Rep 1

description: Library name: GC146798


title: E14, pGlast cell population, w/o treatment, rep 5


title: HPC_0079638_2


title: Raptor WT C4


title: HPC_0079638_1


title: Day 14 Epigenetic modification with 7gRNAs _ Rep 1

description: Library name: GC146797

value: Tr.HGC-27-KRAB cells transfected with the DNMT3AL domain and 7gRNAs


title: Raptor WT C2


title: CTX_0034154_1

source_name: Middle Temporal Gyrus

value: Middle Temporal Gyrus

value: Fresh Frozen


title: E14, pGlast cell population, w/o treatment, rep 4

value: cerebral cortex


title: Raptor S791D C6


title: Day 7 Epigenetic modification with 7gRNAs _ Rep 1

description: Library name: GC146796


title: CTX_0033771_1


title: E14, pGlast cell population, w/o treatment, rep 3


title: Day 3 Epigenetic modification with 7gRNAs _ Rep 1

description: Library name: GC146795


title: E14, pGlast cell population, w/o treatment, rep 2


title: Raptor S791D C5


title: CTX_0034026_1


title: Control HGC-27 Rep 1

description: Library name: GC146794


title: E14, pGlast cell population, w/o treatment, rep 1


title: CTX_0034024_1


title: E14, mixed brain cell population, w/o treatment, rep 6

value: mixed population of brain cells

value: pCAG-Venus


title: Raptor S791D C4


title: H1-HSC_shDDX21_RNAseq_Rep3

city: Shatin

first: Hoi-Hung

middle: Hoi Hung

last: Cheung

state: NT

address: Rm.707, School of Biomedical Sciences, Area 39, The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: H1-HSC_shDDX21_RNAseq_Rep3

data_processing:
Reads were aligned to UCSC mm10 or hg38 using STAR aligner:  --outFilterMultimapNmax 20 \         --alignSJoverhangMin 8 \         --alignSJDBoverhangMin 1 \         --outFilterMismatchNmax 999 \         --outFilterMismatchNoverReadLmax 0.04 \         --alignIntronMin 20 \         --alignIntronMax 1000000 \         --alignMatesGapMax 1000000 \         --sjdbScore 1 \
Raw count matrix produced by counting exons with featureCounts
Only genes where 2 or more samples have CPM >1 where retained
RLE normalization was performed using DEseq2
Assembly: mm10 and hg38
Supplementary files format and content: Raw count matrix
Supplementary files format and content: DEseq2-RLE normalized count matrix with Log2 fold change of inidvidual samples after normalization

source_name: H1 hESC

growth_protocol: HSC differentiation from H1 hESC with performed with STEMdiff™ Hematopoietic Kit (Stemcell Tech)

extract_protocol:
Dissected fetal livers were washed twice with PBS and kept in fetal liver juice (2%FBS/1mM EDTA/10mMGlucose/PBS) on ice. Cell suspension was obtained by trituration and strained with a sterile 70um cell strainer. Cells were first stained with lineage-biotin antibodies (Gr1, Cd11b, CD3, B220, Ter119) and fixable viability stain 450, washed and subsequently stained with (cKit-APC and streptavidin-APC/Cy7). Live lineage- cKit+ cells were sorted with BD FACSDiscover™ S8 Cell Sorter. Cells were kept on ice or 4oC throughout harvest and sorting. For H1 differntiated HSC (CD34+, CD45+, CD43+, shRNA+) cells, live cells were sorted by BD FACSDiscover™ S8 Cell Sorter 2 days post transduction after staining with surface antibodies and fixable viability stain 450.
Total RNA was extracted with microprep RNA kit (Zymo). mRNA-enriched cDNA library was prepared using mRNA-seq Lib Prep Module for Illumina (abclonal).

treatment_protocol: HSC derived from H1 hESC was transduced with shRNA-mCherry lentivirus

value: H1 hESC

value: H1 differentiated hematopoietic stem cell (CD34+ CD45+ CD43+ shRNA+)

value: lentivirus shDDX21-mCherry


title: H1-HSC_shDDX21_RNAseq_Rep2

description: Library name: H1-HSC_shDDX21_RNAseq_Rep2


title: Raptor S791D C3


title: Varuna-WRR, 96 Hrs, Infected

city: New Delhi

first: Prajjwal

last: Rai

state: New Delhi

address: IARI, Pusa campus

department: Division of Plant Pathology

country: India

institute: Indian Agricultural Research Institute

description:
Library name: VarunaWRRI96
RNA-seq of Brassica juncea leaf using Qiagen plant rna extraction kit

data_processing:
Trim_galore for adapter and quality trimming
Trinity for denovo transcript assembly
Kallisto for transcript expression quantification
Assembly: Denovo
Supplementary files format and content: tab delimited text files includes gene expression for all samples

organism: Brassica juncea

source_name: leaf

extract_protocol:
RNA extraction using Qiagen plant rna extraction kit
RNA QC is checked using Qubit, GEL and Bioanalyser,Qiagen mrna library kit is used for the preparation of libraries according to the manufacturer's protocols

value: leaf

tag: phenotype

value: Varuna-WRR

value: 96 Hrs, Infected


title: Lung, KO, 24wk

city: Daejeon

first: Woogil

last: Song

address: KAIST, Daejeon 34141, Korea

department: Graduate School of Medical science and engineering

country: South Korea

institute: KAIST

description: 10x Genomics

data_processing:
All data were processed by cellranger v3.0.2 and manipulated and visualized by R v4.1.1 and Seurat v4.0.2.
Assembly: mm9
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, h5

molecule: nuclear RNA

extract_protocol:
Single nucleus RNA was extracted from the lungs of βPIX deficient or wild-type mice.
cDNA libraries were constructed using a single-nucleus RNA-seq kit, following standard protocols.

value: Lung

value: alveolar type 2 (AT2) cells


title: Varuna, 96 Hrs, Mock

description:
Library name: VarunaM96
RNA-seq of Brassica juncea leaf using Qiagen plant rna extraction kit

value: Varuna

value: 96 Hrs, Mock


title: E14, mixed brain cell population, w/o treatment, rep 5

source_name: cerebral cortex

value: 14 days old embryo (E14)

value: w/o


title: H1-HSC_shDDX21_RNAseq_Rep1

description: Library name: H1-HSC_shDDX21_RNAseq_Rep1


title: E14, mixed brain cell population, w/o treatment, rep 4


title: Lung, Vehicle, 24wk

description: 10x Genomics


title: Varuna, 96 Hrs, Infected

description:
Library name: VarunaI96
RNA-seq of Brassica juncea leaf using Qiagen plant rna extraction kit


title: E14, mixed brain cell population, w/o treatment, rep 3


title: Lung, KO, 4wk

description: 10x Genomics


title: H1-HSC_shNC_RNAseq_Rep2

description: Library name: H1-HSC_shNC_RNAseq_Rep2

value: lentivirus shNC-mCherry


title: H1-HSC_shNC_RNAseq_Rep3

description: Library name: H1-HSC_shNC_RNAseq_Rep3


title: Varuna, 48 Hrs, Infected

description:
Library name: VarunaI48
RNA-seq of Brassica juncea leaf using Qiagen plant rna extraction kit

value: 48 Hrs, Infected


title: Lung, Vehicle, 4wk

description: 10x Genomics


title: Varuna-WRR, 96 Hrs, Mock

description:
Library name: VarunaWRRM96
RNA-seq of Brassica juncea leaf using Qiagen plant rna extraction kit


title: H1-HSC_shNC_RNAseq_Rep1

description: Library name: H1-HSC_shNC_RNAseq_Rep1


title: E14, mixed brain cell population, w/o treatment, rep 1

value: cerebral cortex


title: E14, mixed brain cell population, w/o treatment, rep 2

value: mixed population of brain cells


title: 3_td.neg, YS-derived microglia

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
See detailed in method part
Assembly: mm10
Supplementary files format and content: raw count, CPM files were included

source_name: brain

extract_protocol:
Brain homogenization followed by FACS
Double standard complementary DNA (cDNA) was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol

value: brain

value: YS-derived microglia


title: Varuna, 48 Hrs, Mock

description:
Library name: VarunaM48
RNA-seq of Brassica juncea leaf using Qiagen plant rna extraction kit

value: 48 Hrs, Mock


title: 2_td.neg, YS-derived microglia


title: Obesity_3

city: Nanjing

first: Huichen

state: Jiangsu

address: Qixia District, Xianlin Road No.163

country: China

institute: Nanjing university

description: Library name: SAMPLES6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
E exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPM values for each Sample ...

source_name: plasma extracellular vesicles

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plasma extracellular vesicles


title: Varuna-WRR, 48 Hrs, Mock

description:
Library name: VarunaWRRM48
RNA-seq of Brassica juncea leaf using Qiagen plant rna extraction kit

value: leaf


title: 1_td.neg, YS-derived microglia


title: Obesity_2

description: Library name: SAMPLES5


title: Varuna-WRR, 48 Hrs, Infected

description:
Library name: VarunaWRRI48
RNA-seq of Brassica juncea leaf using Qiagen plant rna extraction kit

value: Varuna-WRR


title: Obesity_1

description: Library name: SAMPLES4


title: No antibody, wild-type

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

description:
Library name: Input2
Input2

data_processing:
The ChIP-Seq data were mainly processed using the nf-core/chipseq pipeline v2.1.0 with custom adjustments.
Raw reads were trimmed with Trim Galore (https://github.com/FelixKrueger/TrimGalore) and aligned to the reference genome using BWA (Li & Durbin, 2009). Following alignment, duplicates were marked with Picard (http://broadinstitute.github.io/picard/), and data quality was assessed with phantompeakqualtools (Landt et al., 2012) and deepTools (Ramírez et al., 2016).
Peaks were called by MACS3 (Zhang et al., 2008) using input samples as controls, with regions corresponding to the non-nuclear genome blacklisted. Consensus peaks were then generated using BEDTools (Quinlan & Hall, 2010). For normalization, read coverage was scaled using four gene-desert regions (chr1:1444000-1488000, chr9:1200000-1290000, chr18:0-120000, chr30:0-96000) as internal controls, yielding sample-specific scaling factors.
Differential binding analysis was conducted with DiffBind v3.16.0 (Ross-Innes et al., 2012), utilizing edgeR (Robinson et al., 2010) for statistical testing and applying the previously derived scaling factors for normalization.
Assembly: NoIMET1v2
Supplementary files format and content: bigWig (except for input sample)

organism: Nannochloropsis oceanica

source_name: Colonial

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, a trace metal mixture (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and a vitamin mixture (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl) (Kang et al., 2015). The cells were first cultured in f/2 medium at 25 °C with 50±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5 cm). The seed cultures were bubbled with air. At the logarithmic growth phase (OD750=2), the cells were harvested via centrifugation and then washed with fresh medium, before being used for the following experiments.

extract_protocol:
N. oceanica cells (1-2 * 108 cells/mL) from 40 mL cultures were fixed for 30 min with 1% formaldehyde (Sigma, USA) at room temperature. After fixation, the cells were incubated at room temperature for 10 min with 0.15 M glycine. Nuclei were isolated as described previously (Wei & Xu, 2018). The isolated nuclei were resuspended in sonication buffer, and the chromatin was sheared by sonication with Covaris S220 to achieve an average fragment size of around 200-1000 bp. Set aside 20 µl to be used as an input sample and keep at 4°C. The rest of the sheared chromatin were incubated with Histone H3K36me3 antibody (pAb) (Cat. No. 61902, Active Motif) and processed using the True MicroChIP-seq Kit (Cat. No. C01010132, Diagenode). Immunocomplexes were captured, washed thoroughly, and then reversed cross-linked to release bound DNA. Finally, purified ChIP-DNA and input DNA were qualified.
DNA libraries were constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Cat. No. ND607, Vazyme). The final library was sequenced on an Illumina instrument with 2×150-bp reads.

treatment_protocol: For both mutant and wild-type (WT) strains, cells were cultured in liquid f/2 medium and maintained at 25 °C under a light intensity of 50 μmol photons m-2 s-1 with aeration until they reached the logarithmic growth phase (OD750 = 2). Subsequently, the cells were harvested and resuspended to an OD750 of 0.5, with three biological replicates. The cultures were then incubated for eight days in flasks at 25 °C, under a fixed light intensity, with shaking at 200 rpm. Two light treatments were set up: high light (about 300 μmol photons·m-2·s-1) and normal light (about 50 μmol photons·m-2·s-1).

value: Colonial

tag: strain

value: WT

value: Normal light

tag: antibody

value: No antibody


title: Early parasitemia - replicate 2

city: Antwerp

first: Pieter

last: Monsieurs

address: Nationalestraat 155

country: Belgium

institute: Institute of Tropical Medicine

description: Library name: SC2_B_L_2026

data_processing:
Analysis of the scRNA-seq data was performed as described in Briggs et al 66 with minor modifications. Akin to Briggs et al 66, the reference genomes for T. congolense IL3000, T. brucei EATRO1125, and L. major Friedlin were modified so that to the end of each annotated coding region in the .gtf file, 2,500 bp were added; if the annotation overlapped with neighbouring genomic features, these extra regions were only extended to the base before the next annotated feature. As both Trypanosoma genome assemblies used in scRNA-seq analysis are haplotype-resolved and therefore contain duplicate sequences, to avoid issues with multimapping, annotations only for a single set of chromosomes (‘haplotype’) for each genome was used as a core set of annotations (haplotype A for T. congolense, and haplotype1 for T. brucei). Next, any putative VSG genes on the other haplotype contigs that were not present in the core set (based on all-vs-all blastp search of translated gene and pseudogene annotations, using the following criteria for ‘identical genes’: ≥95% identity, allowing for up to 1% difference in length), were added to the annotation list, as these are likely distinct VSG sequences and should be considered for mapping. This collapsed set of annotations was used for all scRNAseq analysis. Two genome files were then compiled using 10x Genomics Cell Ranger (version cellranger-9.0.1) mkref function (default settings): one containing the T. congolense and L. major genomes, and another containing the T. brucei and L. major genomes. Reads were then mapped to the corresponding genomes using Cell Ranger count function (default settings), generating a counts matrix for each (available in Zenodo). In the case of the in vivo samples, where L. major cells were not added, these were still aligned to the Trypanosome/Leishmania genome to allow for comparison with the in vitro data. The resulting Cell Ranger matrixes were imported into R (v4.4.1) using Seurat (v5.3.1), where all the analysis was then performed (the detailed script is available in Zenodo). As in Briggs et al 66, for each matrix a Seurat object was created using the min.cells = 5 and min.features = 3 settings, meaning genes were kept if detected in at least 5 cells, and only cells where 3 genes were detected we kept; although stringent (eg this would exclude genes present in one cell in the sample), these filters did not affect the downstream analysis, and gave more confidence to the genes being detected. In each sample, cells were then categorised as one of the three species or multiplets, based both on the classification given by Cell Ranger and the percentage of transcripts from each species (> 95% as T. congolense, > 95% as T. brucei, and > 90% L. major but < 5% T. congolense/T. brucei transcripts as L. major cell; the remaining cells were considered multiplets). L. major-labelled cells and multiplets were then excluded from the Seurat objects, leaving 19,889 T. congolense cells and 17,684 T. brucei cells from the in vitro samples, and 29,280 T. congolense IL3000 cells and 52,365 T. brucei cells from the in vivo samples for the downstream analysis. The cells were further filtered based on the following quality control (QC) parameters: number of transcripts per cell (> -1.5x Median Absolute deviation (MAD) and < 3.5x MAD), number of genes per cell (> -1.5x MAD and < 3.5x MAD), percentage of kDNA RNA (> -1.5x MAD and < 3.5x MAD) and percentage of rRNA RNA (> -1.5x MAD and < 3.5x MAD). In the case of the in vitro samples, a cutoff based on the percentage of VSG RNA was also used (> -1x MAD and < 3x MAD for T. congolense and > -1.5x MAD and < 3x MAD for T. brucei). Post-QC, 15,127 T. congolense cells and 13,160 T. brucei cells from the in vitro samples, and 26,887 T. congolense IL3000 cells and 45,412 T. brucei cells from the in vivo samples remained. The samples were then normalised and log2-transformed using Scran (v1.32.0)58. With VSGs being excluded, a list of highly variable genes for each sample (950 genes for T. congolense and 1,387 T. brucei genes for the in vitro samples, 1,438 for T. congolense IL3000 and 1,062 for T. brucei in vivo samples) was obtained by intersecting the top 3000 variable genes resulting from two independent methods: Scran and Scater (uses log2-transformed counts) and Seurat (uses the raw counts). These were added to the Seurat objects and used for scaling (linear transformation) the data and running linear dimension reduction (PCA) using Seurat. The dimensionality of the Seurat objects was then assessed based on the obtained PCA scores, and the number of top principal components (PCs, dimensions) containing most of the data was inferred by analysis of the output from the ElbowPlot function (Seurat). Next, Seurat's FindNeighbors and FindClusters were used, together with the visualisation package clustree (v0.5.1), to infer which resolution to use, in combination with the dimensions (PCs) defined above, for the non-linear dimensional reduction (UMAP) using Seurat. For the in vitro samples, cluster quality was checked by extracting the unique top 5 genes per cluster and plotting their average expression across clusters using the DotPlot and HeatMap functions from Seurat.
Assembly: Trypanosoma congolense IL3000 (from Krasilnikova et al, BioRXiv10.64898/2026.02.19.706783)
Supplementary files format and content: Filtered outputs from CellRanger software (features, barcodes, matrix)

organism: Trypanosoma congolense

source_name: whole organism

growth_protocol: For T. congolense KTT/MSOROM7C1, bloodstream forms were collected from infected murine hosts 12 days after tsetse bite, corresponding to an estimated parasitaemia of approximately 107.2 trypanosomes/mL

extract_protocol:
Cells were DEAE-cellulose purified from infected blood and processed independently for single-cell RNA sequencing.
For Chromium (10x Genomics) library preparation, approximately 10,000 cells from each replicate or sample were loaded onto a Chromium Controller, and libraries were prepared using the Chromium Single Cell 3′ Gene Expression v4 kit according to the manufacturer's instructions.

treatment_protocol: For strain KTT/MSOROM7C1, two independent biological replicates were generated from separate infected mice.

value: whole organism


title: Early parasitemia - replicate 1

description: Library name: SC1_B_1211_L


title: 3_td.pos, MDM

value: MDM


title: 0.5%glucoseSD7mM KCl BIO REP3

city: Shanghai

first: Jintao

last: Huang

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: 0.5SD7KR3

data_processing:
Genes and transcripts were then quantified from the STAR-aligned reads (Aligned.sortedByCoord.out.bam) using RSEM (version 1.3.3).
Assembly: S. cerevisiae R64-1-1 reference genome using STAR (version 2.7.1a) with a 2-pass procedure.
Supplementary files format and content: Raw sequencing data are available in SRA. Data processing and analysis details are described in the Methods section.

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: For each RNA-sequencing (RNA-Seq) condition, three independent biological replicates were included for each of the four conditions (2% glucose/1 mM K⁺, 2% glucose/7 mM K⁺, 0.5% glucose/1 mM K⁺, and 0.5% glucose/7 mM K⁺).

extract_protocol:
RNA was extracted using M5 HiPer Universal Plus RNA Mini Kit (Mei5 Biotech, Beijing, China) according to manufacturer instructions. All RNA samples used had an RNA Integrity Number (RIN) > 8. All qualified RNA samples were shipped to Novogene Co., Ltd. (Beijing, China) for library preparation and sequencing.
Sequencing was performed on an Illumina NovaSeq 6000 platform with a paired-end 150 bp (PE150) strategy (Zhao et al., 2023). Each sample yielded approximately 6 Gb of clean data after adapter trimming and quality filtering, with Q30 ≥ 93% and >75% of reads uniquely mapped to the S. cerevisiae R64-1-1 reference genome using STAR (version 2.7.1a) with a 2-pass procedure.

value: yeast cell


title: nonObesity_3

description: Library name: SAMPLES3


title: No antibody, NO07G02030 knockout

description:
Library name: Input1
Input1


title: 0.5%glucoseSD7mM KCl BIO REP2

description: Library name: 0.5SD7KR2

treatment_protocol: For each RNA-sequencing (RNA-Seq) condition, three independent biological replicates were included for each of the four conditions (2% glucose/1 mM K⁺, 2% glucose/7 mM K⁺, 0.5% glucose/1 mM K⁺, and 0.5% glucose/7 mM K⁺).


title: nonObesity_2

description: Library name: SAMPLES2


title: 2_td.pos, MDM


title: 1_td.pos, MDM


title: 0.5%glucoseSD7mM KCl BIO REP1

description: Library name: 0.5SD7KR1


title: Wild-type control, high light, rep 2

description:
Library name: HL_WT2
HL_WT2

value: High light


title: PNI_Cut_3

city: Xi’an

first: Weikun

last: Qian

address: 277 West Yanta Road

institute: The First Affiliated Hospital of Xi’an Jiaotong University

data_processing:
hisat2 v2.0.5 and featureCounts v1.5.0-p3
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Paired-end clean reads were aligned to the Mus Musculus (GRCm38/mm10) using hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
genome build/assembly: mm10
processed data files format and content: tab-delimited text file include raw counts for each Sample
processed data files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Pancreatic cancer orthotropic transplanted tumor tissues

growth_protocol: General condition: All the mice were reared in a specific pathogen-free (SPF) professional chamber, with the temperature controlled at 24 °C and a 12 h/12 h light/dark cycle. The food, water, and bedding used by the KPC mice were sterilized. Stress induction: Mice were growing in 50 ml centrifuge tube (contains air holes) for ventilation for 6 h/day (last at least 6 weeks) to mimic the chronic stress environment of human. Orthotopic transplant tumor model establishment: Firstly, 7-week-old littermates of WT C57 mice were divided into control and neurotomy group randomly; Then, after 1-week adaptation period, the prepared primary pancreatic cancer cell from LSL-KrasG12D/+;Trp53fl/+;Pdx1-Cre mice named KPC cells mixed with moderate medium and Matrix-gel (1×105 cells/ml) was injected into the tail of pancreas in each anesthetized mice.

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following Mnanufacturers protocol.

treatment_protocol: Before the stress and transplant, different with the sham-operated group, in sympathetic neurotomy group, we carefully explored the mouse abdominal cavity with the aid of a microscope and identified the coeliac artery (CA) and superior mesenteric artery (SMA), and we then precisely excised the mesangial tissue and the recognizable nerve-like structures (mainly composed by the efferent fiber of the celiac ganglion in the retroperitoneal plexus, which belongs to the sympathetic nerve components that innervates the pancreas, grows around and along with the arteries) around the CA and SMA.

tag: Sex

value: Male

value: Primary pancreatic cancer cell from LSL-KrasG12D/+;Trp53fl/+;Pdx1-Cre mice

value: WT C57 mice

value: Sympathetic neurotomy


title: Wild-type control, high light, rep 1

description:
Library name: HL_WT1
HL_WT1


title: 0.5%glucoseSD1mM KCl BIO REP3

description: Library name: 0.5SD1KR3


title: nonObesity_1

description: Library name: SAMPLES1


title: 12Z_IL1+ 1µM CDD3013_Rep2

city: Houston

first: FEI

last: YUAN

state: TX

address: 1 Baylor Plaza

department: Pathology & Immunology

institute: Baylor College of Medicine

description: Library name: A10

data_processing:
First, fastp is used for quality control and preprocessing, which includes adapter trimming, quality filtering, and removal of low-complexity reads to enhance downstream analysis.
Next, the cleaned reads are aligned to the human hg38 reference genome using STAR (Spliced Transcripts Alignment to a Reference), a highly efficient and accurate splice-aware aligner optimized for RNA-seq data.
Once aligned, gene expression levels are quantified using featureCounts, which assigns mapped reads to genomic features such as exons or genes based on an annotation file.
Assembly: hg38
Supplementary files format and content: Feature count matrix in Tab Separated Values (TSV) format

growth_protocol: 12Z cells were grown in DMEM supplemented with 10% FBS and antibiotics.

extract_protocol:
Cells were collected in RLT lysis buffer and RNA was isolated using the RNEasy Mini kit with the on-column DNAse I digest from Qiagen.
mRNA library preparation (poly A enrichment)

treatment_protocol: Cells were starved overnight in DMEM without phenol red and 2% charcoal stripped FBS. Then pre-treated with vehicle (DMSO) or inhibitors for 30 minutes prior to treatment with 10ng/ml IL1beta for 6 hours.

value: epithelial cells from peritoneal endometriosis

value: 10ng/ml IL1beta+1µM CDD_3013

tag: time


title: PNI_Cut_2

source_name: Pancreatic cance rorthotropic transplanted tumor tissues

tag: tissue


title: NO07G02030 overexpression, high light, rep 2

description:
Library name: HL_OE2
HL_OE2

tag: cell type


title: 0.5%glucoseSD1mM KCl BIO REP2

description: Library name: 0.5SD1KR2


title: NO07G02030 overexpression, high light, rep 1

description:
Library name: HL_OE1
HL_OE1


title: 12Z_IL1+ 1µM CDD3013_Rep1

description: Library name: A9


title: 0.5%glucoseSD1mM KCl BIO REP1

description: Library name: 0.5SD1KR1


title: 12Z_IL1+ 10µM CDD2728_Rep2

description: Library name: A8

value: 10ng/ml IL1beta+10µM CDD_2728


title: PNI_Cut_1

value: Pancreatic cancer orthotropic transplanted tumor tissues


title: NO07G02030 knockout, high light, rep 2

description:
Library name: HL_KO2
HL_KO2


title: PNI_Control_3

value: Shamoperation


title: 2%glucoseSD7mM KCl BIO REP3

description: Library name: 2SD7KR3


title: 12Z_IL1+ 10µM CDD2728_Rep1

description: Library name: A7


title: NO07G02030 knockout, high light, rep 1

description:
Library name: HL_KO1
HL_KO1

value: Colonial


title: PNI_Control_2


title: 2%glucoseSD7mM KCl BIO REP2

description: Library name: 2SD7KR2

value: WT


title: 12Z_IL1+ 1µM CDD2728_Rep2

description: Library name: A6

value: 10ng/ml IL1beta+1µM CDD_2728


title: PNI_Control_1


title: Wild-type control, normal light, rep 2

description:
Library name: NL_WT2
NL_WT2

value: Normal light


title: 2%glucoseSD7mM KCl BIO REP1

description: Library name: 2SD7KR1


title: 12Z_IL1+ 1µM CDD2728_Rep1

description: Library name: A5


title: Wild-type control, normal light, rep 1

description:
Library name: NL_WT1
NL_WT1


title: 2%glucoseSD1mM KCl BIO REP3

description: Library name: 2SD1KR3


title: 12Z_IL1B_Rep2

description: Library name: A4

value: 10ng/ml IL1beta


title: sHA-X-4

first: Zhenzhen

address: 163 Xianlin Avenue, Qixia District

department: School of Life Sciences

institute: Nanjing University

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. And raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses. The clean reads were mapped using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.  Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The data were normalized and averaged. Then the genes related to hepatic function were analyzed by HemI (Heatmap Illustrator, version 1.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts of each sample

source_name: spleen

extract_protocol:
Total RNA was extracted from the spleen in the sHA-X-remodelled group (sHA-X group, n=4) and the speen in the PBS-treated group (PBS group, n=3 ) samples using TRIzol (Invitrogen, CA, USA)  at 30 days after hepatocytes were transplanted according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: spleen

value: sHA-X


title: NO07G02030 overexpression, normal light, rep 2

description:
Library name: NL_OE2
NL_OE2


title: 2%glucoseSD1mM KCl BIO REP2

description: Library name: 2SD1KR2

value: yeast cell


title: 12Z_IL1B_Rep1

description: Library name: A3


title: NO07G02030 overexpression, normal light, rep 1

description:
Library name: NL_OE1
NL_OE1


title: sHA-X-3


title: sHA-X-2


title: 2%glucoseSD1mM KCl BIO REP1

description: Library name: 2SD1KR1


title: 12Z_Veh_Rep2

description: Library name: A2

value: Vehicle


title: NO07G02030 knockout, normal light, rep 2

description:
Library name: NL_KO2
NL_KO2


title: sHA-X-1


title: 12Z_Veh_Rep1

description: Library name: A1


title: PBS-3

value: PBS


title: SPExp CD8 Depleted Brain 2

city: Iowa City

first: Cori

middle: E.

last: Fain

state: Iowa

address: 25 S. Grand Ave, Carver College of Medicine

department: Pathology

institute: University of Iowa

description:
Library name: Sample 8
Sample preparation: Chromium Nuclei Isolation Kit with RNase Inhibitor, 10X Chromium Single Cell 3' Expression (GEM-X) v4 kit for chemistry.Library preparation: Dual Index Kit TT Set A, 96 rxn

data_processing:
Raw base call files were demultiplexed to FASTQ format.
FASTQ files were processed using Cell Ranger v9.0.
Sequencing reads were aligned to the Mus musculus reference genome (mm39), and gene expression count matrices were generated using the Cell Ranger count pipeline.
Filtered feature-barcode matrices containing high-quality nuclei were generated for downstream analyses.
Assembly: mm39
Supplementary files format and content: HDF5 (.h5) filtered feature-barcode matrices generated by Cell Ranger v9.0 containing gene-by-nucleus UMI count matrices for each sample.

source_name: whole brain

growth_protocol: C57BL/6 mice were maintained under specific pathogen-free (SPF) conditions with food and water provided ad libitum according to institutional animal care guidelines.

extract_protocol:
Whole brains were dissociated, nuclei were isolated using the 10x Genomics Nuclei Isolation Kit with RNase Inhibitor according to the manufacturer's protocol, and nuclei were counted and quality assessed prior to library preparation.
Single-nucleus RNA-seq libraries were prepared using the 10x Genomics Chromium GEM-X Single Cell 3′ Gene Expression v4 platform according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq X instrument.

treatment_protocol: Mice received sequential peripheral infections (SPExp) or remained uninfected as controls. One treatment group additionally received CD8 T cell depletion prior to tissue collection. Whole brains were harvested at the experimental endpoint 30 dpi of last infection.

value: whole brain

value: 30 days past non-CNS pathogen infection, 2 doses anti-CD8 antibody

value: All samples processed same day by same person. All run together on same Novaseq chip


title: E13.5 LK Ddx21-cKO_RNAseq_Rep3

description: Library name: E13.5 LK Ddx21-cKO_RNAseq_Rep3

source_name: Fetal liver

value: Fetal liver

value: LK (Lineage- Kit+) Hematopoietic progenitor cell

value: Vav-Cre; Ddx21f/f


title: NO07G02030 knockout, normal light, rep 1

description:
Library name: NL_KO1
NL_KO1


title: SPExp CD8 Depleted Brain 1

description:
Library name: Sample 7
Sample preparation: Chromium Nuclei Isolation Kit with RNase Inhibitor, 10X Chromium Single Cell 3' Expression (GEM-X) v4 kit for chemistry.Library preparation: Dual Index Kit TT Set A, 96 rxn


title: endometriotic stromal cells, IL1beta + 1µM CDD2728, rep 3

description: Library name: O143_2728_3

data_processing:
First, fastp is used for quality control and preprocessing, which includes adapter trimming, quality filtering, and removal of low-complexity reads to enhance downstream analysis.
Next, the cleaned reads are aligned to the human hg38 reference genome using HISAT2, a fast and memory-efficient splice-aware aligner that accurately maps RNA-seq reads, accounting for splicing events and transcript variations.
Once aligned, gene expression levels are quantified using featureCounts, which assigns mapped reads to genomic features such as exons or genes based on an annotation file.
Assembly: hg38
Supplementary files format and content: Feature count matrix in Tab Separated Values (TSV) format

source_name: endometriotic stromal cells

growth_protocol: Patient cells were grown in DMEM/F12 supplemented with 10% FBS and antibiotics.

extract_protocol:
Cells were collected in RLT lysis buffer and RNA was isolated using the RNEasy Micro kit with the on-column DNAse I digest from Qiagen.
mRNA library preparation (poly A enrichment)

treatment_protocol: Cells were starved overnight in DMEM/F12 without phenol red and 2% charcoal stripped FBS. Then pre-treated with vehicle (DMSO) or inhibitors for 30 minutes prior to treatment with 10ng/ml IL1beta +/- inhibitors for 6 hours.

value: endometriotic stromal cells

value: stromal cells from endometrioma


title: Wild-type control, high light, rep 3

description:
Library name: HL_WT3
HL_WT3

data_processing:
RNA-seq data were mainly analyzed with the nf-core/rnaseq pipeline (v3.14.0).
Raw reads underwent quality control and adapter trimming using Trim Galore (https://github.com/FelixKrueger/TrimGalore). Ribosomal RNA reads were subsequently removed with SortMeRNA (Kopylova et al., 2012).
The resulting high-quality reads were aligned to the N. oceanica IMET1 reference genome (Gong et al., 2020) using STAR (Dobin et al., 2013), with intron length parameters set to “--alignIntronMin 20 --alignIntronMax 3000”. Duplicate reads were marked using Picard (http://broadinstitute.github.io/picard/).
Transcript abundance was then quantified with Salmon (Patro et al., 2017). Differential gene expression analysis was performed based on the Salmon output using the nf-core/differentialabundance pipeline (v1.5.0).
Assembly: NoIMET1v2
Supplementary files format and content: gene_counts_matrix.txt : tab-delimited text file includes raw counts for genes in each sample
Supplementary files format and content: gene_tpm_matrix.txt : tab-delimited text file includes TPM values for genes in each sample

extract_protocol:
Total RNA was isolated from wild-type (WT) and mutant cells using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer’s standard protocol. RNA purity and concentration were determined with a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), while RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
For library preparation, 2 μg of qualified total RNA per sample was used as the starting material. RNA-seq libraries were subsequently constructed with the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) in accordance with the manufacturer’s guidelines. The final library was sequenced on an Illumina instrument with 2×150-bp reads.

value: Colonial

value: WT

value: High light


title: PBS-2


title: endometriotic stromal cells, IL1beta + 1µM CDD2728, rep 2

description: Library name: O143_2728_2

value: 10ng/ml IL1beta+1µM CDD_2728


title: SPExp Brain 3

description:
Library name: Sample 6
Sample preparation: Chromium Nuclei Isolation Kit with RNase Inhibitor, 10X Chromium Single Cell 3' Expression (GEM-X) v4 kit for chemistry.Library preparation: Dual Index Kit TT Set A, 96 rxn

value: 30 days past non-CNS pathogen infection


title: Wild-type control, high light, rep 2

description:
Library name: HL_WT2
HL_WT2


title: PBS-1

value: spleen


title: SPExp Brain 2

description:
Library name: Sample 5
Sample preparation: Chromium Nuclei Isolation Kit with RNase Inhibitor, 10X Chromium Single Cell 3' Expression (GEM-X) v4 kit for chemistry.Library preparation: Dual Index Kit TT Set A, 96 rxn


title: endometriotic stromal cells, IL1beta + 1µM CDD2728, rep 1

description: Library name: O143_2728_1


title: Wild-type control, high light, rep 1

description:
Library name: HL_WT1
HL_WT1


title: endometriotic stromal cells, IL1beta, rep 3

description: Library name: O143_IL1_3

value: 10ng/ml IL1beta


title: SPExp Brain 1

description:
Library name: Sample 4
Sample preparation: Chromium Nuclei Isolation Kit with RNase Inhibitor, 10X Chromium Single Cell 3' Expression (GEM-X) v4 kit for chemistry.Library preparation: Dual Index Kit TT Set A, 96 rxn


title: MPC5  Setdb2KO  high-glucose, anti-SETDB2

city: Beijing

first: Lanfang

last: Li

state: State...

address: China-japan Friendship Hospital

institute: China-japan Friendship Hospital

description: Library name: Sample 4

data_processing:
The raw sequence data were firstly quality trimmed by fatsp software to obtain the clean reads. Then the clean reads were aligned to theGRCm39 using Bowtie2  and subsequently analyzed by the SEACR software based the‘stringent’parameter to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that we considered to be putative binding sites.  Visualization of peak distribution along genomic regions of interested genes was performed with IGV.Peaks were then annotated using chipseeker software to obtain the genes and gene annotations about peaks. Significant Motif of peaks were analyzed by MEME and DREME software[6] and aligned to the motif database.
Assembly: GRCm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using ultrasonication system.
The libraries were constructed using  HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina according to the manufacturer’s instructions

value: Mouse podocyte

value: KO

value: high-glucose


title: NO07G02030 overexpression, high light, rep 3

description:
Library name: HL_OE3
HL_OE3


title: MPC5  Setdb2KO  high-glucose, anti-H3K9me3

description: Library name: Sample 3


title: Uninfected Brain 3

description:
Library name: Sample 3
Sample preparation: Chromium Nuclei Isolation Kit with RNase Inhibitor, 10X Chromium Single Cell 3' Expression (GEM-X) v4 kit for chemistry.Library preparation: Dual Index Kit TT Set A, 96 rxn

value: whole brain

value: vehicle injected controls-mock infection


title: endometriotic stromal cells, IL1beta, rep 2

description: Library name: O143_IL1_2


description:
Library name: HL_OE2
HL_OE2


title: MPC5  Setdb2WT  high-glucose, anti-SETDB2

description: Library name: Sample 2


title: endometriotic stromal cells, IL1beta, rep 1

description: Library name: O143_IL1_1


title: Uninfected Brain 2

description:
Library name: Sample 2
Sample preparation: Chromium Nuclei Isolation Kit with RNase Inhibitor, 10X Chromium Single Cell 3' Expression (GEM-X) v4 kit for chemistry.Library preparation: Dual Index Kit TT Set A, 96 rxn

value: All samples processed same day by same person. All run together on same Novaseq chip


description:
Library name: HL_OE1
HL_OE1


title: MPC5  Setdb2WT  high-glucose, anti-H3K9me3

description: Library name: Sample 1


title: Uninfected Brain 1

description:
Library name: Sample 1
Sample preparation: Chromium Nuclei Isolation Kit with RNase Inhibitor, 10X Chromium Single Cell 3' Expression (GEM-X) v4 kit for chemistry.Library preparation: Dual Index Kit TT Set A, 96 rxn


title: NO07G02030 knockout, high light, rep 3

description:
Library name: HL_KO3
HL_KO3


title: endometriotic stromal cells, vehicle, rep 3

description: Library name: O143_Veh_3

value: Vehicle


title: Cre+/Setdb2fl/fl DKD Glomeruli, rep 3

description: Library name: Sample 6

data_processing:
The fastp software  were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
The HISAT2 were used to map reads to the reference genome.
The mapped reads of each sample were assembled using StringTie with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare .
StringTie was used to perform expression level for mRNAs by calculating FPKM(FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR .
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Glomeruli

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Glomeruli

value: Cre+/Setdb2fl/fl DKD


title: endometriotic stromal cells, vehicle, rep 2

description: Library name: O143_Veh_2

value: endometriotic stromal cells

value: stromal cells from endometrioma


title: ESCC cell line-2

city: SHANTOU

first: Dajia

address: No. 22 Xinling Road

institute: Shantou University Medical College

description: Library name: KYSE510

data_processing:
The default parameters of Trimmomatic were applied for the removal of adapter from Illumina platform FASTQ sequences and the trimming of sequence files according to the base quality values. This process generated clean raw data, which was then suitable for further analysis.
For each sample, quality assessment was performed using the FastQC and MultiQC procedures.
Bowtie2 was employed to align the reads derived from ATAC-seq sequencing data to the corresponding human reference genome, with the default parameters utilized in the analysis.
To ensure unbiased signal detection, repetitive sequences generated by PCR amplification were removed using the Picard. MACS2 callpeak was used for the purpose of identifying and confirming open regions of chromatin.
The mainstream tool HOMER performs motif analysis of accessible chromatin regions of interest, facilitating the identification of potential regulatory factor binding sites within these regions.
Assembly: hg38
Supplementary files format and content: BigWig

extract_protocol:
For fibroblasts and ESCC cell lines,cells were digested and counted, and 5 × 10^5  cells were used directly for ATAC-seq experiment. For ESCC tissues, nuclei were isolated by cryogenic grinding (LUKYM, 80 Hz, 20 seconds). Following isolation and counting, 5 × 10^5 nuclei were used for subsequent experiments. The ATAC-seq assay followed the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).
The DNA was purified with VAHTS DNA Clean Beads (Vazyme, N411-01) and amplified with barcode primers using the TruePrep DNA Library Prep Kit (Vazyme, TD501-01). Finally, all ATAC-seq libraries were sequenced using the Illumina NovaSeq 6000 platform (Novogene).

value: ESCC cell line

tag: disease state

value: esophageal squamous cell carcinoma


title: Cre+/Setdb2fl/fl DKD Glomeruli, rep 2

description: Library name: Sample 5


title: NO07G02030 knockout, high light, rep 2

description:
Library name: HL_KO2
HL_KO2

value: Colonial

value: High light


title: RNA-seq in DKO littermate bud ectoderm E9.75, rep3

city: Santander

first: Marian

last: Ros

address: 22nd Albert Einstein St.

country: Spain

institute: IBBTEC-CSIC-SODERCAN

description: Library name: RNASEQ_ect_dko_DKO_rep3

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and reads filtered and adaptor-trimmed with fastp (Chen et al 2018).
Reads were mapped to the mouse reference assembly (GRCm38), using HiSat2 (Kim et al 2019) with the option --dta-cufflinks, which enabled direct transcript assembly with StringTie (Pertea et al 2015)..
Read count means, fold-change (FC) and values were calculated with DEseq2 (Anders & Huber, 2010).
Assembly: mm10
Supplementary files format and content: Big Wig of RNAseq reads for single KOs and raw count table for double KOs

source_name: limb bud ectoderm

extract_protocol:
Ectoderms were isolated with fine forceps from E10.5 forelimb buds of Sp8KO, SP6KO and WT, and from E9.75 forelimb buds of DKO and WT embryos, after digestion with 0.25% trypsin for 20 min. on ice. The ectoderms of ~2 forelimb buds were used for each replicate.
SMART-Seq v4 Ultra Low Input RNA for Sequencing, Nextera XT DNA Library Preparation Kit

value: limb bud ectoderm

value: ectoderm


title: Primary PCa, patient with bone-metastatic disease, donor RC_03

city: Melbourne

first: xin

last: liu

address: 305 Graattan St

country: Australia

institute: Peter mac

description: Library name: RC_03_RARP

data_processing:
RNA-seq analysis was performed in R (v4.1.0). Clean reads (no adapter contamination, < 20% undecided bases, > 50% high quality bases) were aligned using the RSubread package (v2.8.1). An index was built using the Ensembl Homo sapiens GRCh38 primary assembly genome file and alignment was performed using subjunc with default settings.
Gene counts were obtained using featureCounts using the Ensembl Homo sapiens GRCm38 version 105 GTF annotation file, with isPairedEnd = TRUE, useMetaFeatures = TRUE and strandSpecific = 0.
Ensembl gene IDs were annotated using the biomaRt package (v2.50.1) and a DGEList object was created with the counts and gene annotation using the edgeR package (v3.36.0). A design matrix was constructed incorporating the sample group (NBmRC, BmRC, LN or Bone met).
Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method. Counts were transformed using the voom method and a linear model was fit using the edgeR voomLmFit function, incorporating sample weights and using donor as a blocking factor.
Differential gene expression analyses were performed using the limma (v3.50.0) package. Groups were compared using the contrasts.fit function and moderated t-statistics were calculated using the treat function with a 1.2-fold cut-off. Differentially expressed genes were determined using a false discovery rate-adjusted (FDR) p-value < 0.05.
Assembly: hg38
Supplementary files format and content: PCa_Met_processed.xlsx contains processed counts (tab 1) and voom-transformed expression values (tab 2).

source_name: Primary adenocarcinoma

extract_protocol:
Total RNA was extracted from fresh frozen tissue (n = 50) using the AllPrep DNA/RNA Mini kit (Qiagen, Maryland U.S.A) according to manufacturer’s instructions. RNA yield was quantified using the Qubit RNA High Sensitivity Assay (Invitrogen) with the Qubit 2.0 Fluorometer. RNA quality was assessed using the RNA 6000 Pico Kit on the Agilent 2100 Bioanalyzer.
One microgram of total RNA (RIN > 6.5) was used as input into the TruSeq RNA Sample Preparation Kit v2 (Illumina). cDNA fragments were end repaired, adenylated, adaptors-ligated, purified and PCR enriched. Two samples did not pass pre-sequencing QC (RC_02_RARP, RC_17_RARP). Sequencing (n = 48) was performed on the Illumina HiSeq3000 (PE-150, 20 million paired reads per sample) by Novogene Bioinformatics (Hong Kong).

value: Primary adenocarcinoma

tag: donor

tag: cancer type

value: Prostate cancer

tag: group

value: BmRC

tag: group description

value: BmRC denotes primary tumor tissue from patient with bone-metastatic PCa

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: endometriotic stromal cells, vehicle, rep 1

description: Library name: O143_Veh_1

tag: cell line

tag: treatment


title: RNA-seq in DKO littermate bud ectoderm E9.75, rep2

description: Library name: RNASEQ_ect_dko_DKO_rep2

tag: genotype


title: NO07G02030 knockout, high light, rep 1

description:
Library name: HL_KO1
HL_KO1

tag: strain


title: RNA-seq in DKO littermate bud ectoderm E9.75, rep1

description: Library name: RNASEQ_ect_dko_DKO_rep1


title: Cre+/Setdb2fl/fl DKD Glomeruli, rep 1

description: Library name: Sample 4


title: SW620cell,SOWAHA,siRNA ,siSOWAHA-3

city: Chengdu

first: Xiaohong

middle: Huang

last: Yi

state: Sichuan

address: 1166 Liutai Avenue, Wenjiang District, Chengdu City

department: School of Basic Medical Science

institute: CDUTCM

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < researchspecies > was sequenced run with Illumina NovaseqTM 6000 sequence platform.
Using the Illumina paired-end RNA-seq,approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.
get high quality clean reads, reads were further filtered by Cutadapt,(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9).including the Q20, Q30 and GC-content of the clean data.
The raw sequence data have been extractd and normolizated.
Assembly: GRCh38
Supplementary files format and content: text file including raw read counts for each sample
Supplementary files format and content: text file including raw fpkm values for each sample

source_name: colorectum cancer

growth_protocol: Colorectal cells SW620 were obtained from ATCC (Manassas, USA). Cell lines were maintained in DMEM medium (Gibco, ThermoFisher, China) supplemented with 100U/ml penicillin-streptomycin (HyCloneTM, Utah, USA) and 10% fetal bovine serum (FBS, ExCell, China), at 37 ℃ in a 5% CO2 incubator.

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

treatment_protocol: SOWAHA-siRNA (siSOWAHA)/NC-siRNA (siNC) and transfection reagent (Dharma FECT1, Dharmacon Reagents, USA)  were mixed and left to stand for 30 minutes. The resulting mixture was then evenly added to the bottom of a 10cm plate, with 7× 105 cells seeded in each plate. After 72 hours of transfection, the total mRNA was extracted and the transfection efficiency of siRNA was measured.

value: colorectum cancer

value: SOWAHA knockdown

value: knock-down


title: Wild-type control, normal light, rep 3

description:
Library name: NL_WT3
NL_WT3

value: WT

value: Normal light


title: Cre-/Setdb2fl/fl DKD Glomeruli, rep 3

description: Library name: Sample 3

value: Glomeruli

value: Cre-/Setdb2fl/fl DKD


title: RNA-seq in WT (DKO littermate) bud ectoderm E9.75, rep3

description: Library name: RNASEQ_ect_dko_WT_rep3


title: SW620cell,SOWAHA,siRNA ,siSOWAHA-2


title: Wild-type control, normal light, rep 2

description:
Library name: NL_WT2
NL_WT2


title: Cre-/Setdb2fl/fl DKD Glomeruli, rep 2

description: Library name: Sample 2

value: Cre-/Setdb2fl/fl  DKD


title: RNA-seq in WT (DKO littermate) bud ectoderm E9.75, rep2

description: Library name: RNASEQ_ect_dko_WT_rep2


title: Wild-type control, normal light, rep 1

description:
Library name: NL_WT1
NL_WT1


title: SW620cell,SOWAHA,siRNA ,siSOWAHA-1


title: RNA-seq in WT (DKO littermate) bud ectoderm E9.75, rep1

description: Library name: RNASEQ_ect_dko_WT_rep1


title: SW620cell,SOWAHA,siRNA ,NC3


title: Cre-/Setdb2fl/fl DKD Glomeruli, rep 1

description: Library name: Sample 1


title: DKD Glomeruli, rep 3

description: Library name: Sample 6

value: DKD


title: NO07G02030 overexpression, normal light, rep 3

description:
Library name: NL_OE3
NL_OE3

value: Colonial


title: SW620cell,SOWAHA,siRNA ,NC2


title: DKD Glomeruli, rep 2

description: Library name: Sample 5


title: NO07G02030 overexpression, normal light, rep 2

description:
Library name: NL_OE2
NL_OE2