title: fetal brain, trisomy 21, Library B11D2G_atac, Chromatin Accessibility

description:
Library name: B11D2G_atac
10X Multiome (scRNA/ATAC-seq)

tag: tissue

value: fetal brain

value: trisomy 21

tag: sample id


title: dre.embryo.pool_control_pfna_0_3

status: Public on Dec 23 2025

type: SRA

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

description: Chemical-exposed embryos were compared to one of three control groups, defined with the 'chemical' variable. 'control_mixed' was the contrast group for PFDS, PFDS, PFOA and PFOS. 'control_ottawa' was the contrast group for PFBA, PFBS, PFHxA and PFHxS. 'control_pfna` was the contrast group for PFNA. control_excluded samples were outliers and not used in any contrast

library_source: transcriptomic

data_processing:
Fastq sequence files were trimmed using fastp v0.23.2
Trimmed sequenes were aligned to a reference genome constructed from the 190820 Zebrafish S1500 (v1.0) probe manifest using the STAR aligner (v2.7.10b)
Count matrix generation was through the QuasR package (v1.44.0) run in R (v4.4.1).
Assembly: Biospyder Zebrafish S1500+ Surrogate Gene Set
Supplementary files format and content: single_pfas_processed_counts.txt' is a genes (probes) by samples count matrix of raw counts

molecule: total RNA

organism: Danio rerio

source_name: pool of 10 whole embryos

growth_protocol: Zebrafish embryos were cultured in water from the ZebTEC housing system (Techniplast, Montreal, Canada) maintaining a temperature of 28 Celsius degrees, pH of 7.4, and conductivity of 2-400μS.

extract_protocol:
Total RNAs were extracted using a Qiagen Mini kit (Qiagen, Toronto, Canada), followed by the manufacter's protocol
RNA libraries were prepared in a 96-sample TempO-Seq S1500+ Zebrafish Surrogate Assay panel (BioSpyder Technologies, California, USA). Each sample was diluted with an equal volume of 2X Enhanced Lysis Buffer. All samples were annealed with detector oligo probes and sequentially processed in digestion, ligation, and amplification steps according to the manufacturer’s protocol. Equal amounts of each sample’s libraries were pooled in a 1.5 ml microtube and purified using NucleoSpin® Gel and PCR Cleanup Kits (Macherey-Nagel, Düren, Germany). Purified pooled libraries were sequenced on an Illumina NextSeq 2000 using a P2 Reagent kit and a 100 cycle flow cell (Illumina, USA).
TempO-Seq S1500+ Zebrafish Surrogate Assay

treatment_protocol: Zebrafish embryos were exposed from 4 hours post fertilization (hpf) to 120 hpf in 0.1 % dimethylsulfoxide (DMSO) plus chemical

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

tag: cell type

value: 5 days

tag: genotype

tag: treatment

tag: replicate

tag: row

value: E

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: ottawa

tag: rna yield_ng_u_l

tag: rin

tag: protocol

value: TempO-Seq


title: fetal brain, disomic, Library B12C2G_atac, Chromatin Accessibility

city: London

first: Michael

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: B12C2G_atac
10X Multiome (scRNA/ATAC-seq)

library_source: genomic

data_processing:
Raw demultiplexed sequencing data (fastq files) were mapped to the human genome (GRCh38) and quantified using cellranger-arc (v2.0.2; 10X Genomics)
Cellranger output was loaded, merged and further processed in an R environment (R v4.3.3), using the Seurat single cell analysis package v5.1.052,53 , with the Signac extension (v1.13.0). The detailed analysis pipeline can be found here: https://github.com/lattkem1/Down_Syndrome_Multiome
Assembly: GRCh38
Supplementary files format and content: Compressed cellranger-arc count matrices, features and cell barcodes
Supplementary files format and content: rda files containing the Seurat objects with labelled cell clusters and sample metadata (for complete dataset and filtered excitatory lineage cells)

molecule: genomic DNA

organism: Homo sapiens

source_name: fetal brain

extract_protocol:
Fresh-frozen fetal tissue from surgical terminations of pregancy from UK hospitals was collected by the "Human Developmental Biology Resource" (HDBR, https://www.hdbr.org/). 10-50 mg of fetal tissue were processed using a protocol based on dx.doi.org/10.17504/protocols.io.bvhhn336. After removal from dry ice, tissue was immediately suspended in Homogenisation Buffer (10 mM Tris-HCl pH7.4, 320 mM Sucrose, 3 mM CaCl2, 3 mM MgCl2), supplemented freshly with 0.1% NP-40, 1 mM DTT and 1 U/µl RNAse inhibitor (Protector (Sigma #3335402001), RiboLock (Thermo Fisher, PN-EO0382), or RNaseOUT (Thermo Fisher, 10777019) RNase inhibitor). The tissue was then immediately homogenised using a 1-ml dounce homogeniser and exactly after 5 min diluted with 1 volume of Homogenisation Buffer (without NP-40), filtered (30 µm mesh size) to remove large debris, and centrifuged (500g, 5 min, 4°C) to collect raw nuclei. Raw nuclei were resuspended in Homogenisation Buffer (without NP-40) and mixed with 1 volume 50% iodixanol buffer (10 mM Tris-HCl pH7.4, 3 mM CaCl2, 3 mM MgCl2, 1 mM DTT, 0.5 U/µl RNAse inhibitor). This suspension was carefully overlaid on a 29% iodixanol buffer (as above + 160 mM sucrose), and centrifuged (6000g, 30 min, 4°C). The nuclei pellet was resuspended in a Lysis Buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT, 0.5 U/µl RNAse inhibitor, 0.1% Tween-20, 0.1% NP-40, 0.001% digitonin), and after exactly 2 min nuclei were diluted in 10 volumes wash buffer (lysis buffer without NP-40, digitonin), and centrifuged (500g, 5 min, 4°C) to collect the nuclei, which were then resuspended in 1x Nuclei Buffer (from the “Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle”; 10X Genomics PN-1000283/PN-1000285; supplemented with 1 mM DTT, 0.5 U/µl RNAse inhibitor).
snRNA-seq and snATAC-seq libraries were prepared using a 10X Genomics Chromium X and the “Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle” (10X Genomics PN-1000283/PN-1000285) according to manufacturer’s instructions. Libraries were sequenced using Illumina Nextseq2000 or Novaseq6000 sequencers.

value: disomic

tag: name

tag: library igf_id

tag: group

value: CON

tag: dev stage_pcw

tag: Sex

value: female

tag: library type

value: Chromatin Accessibility

tag: in final_analysis

value: TRUE


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_2, 8-hpf (RBPscan)

city: Québec

first: Dmitry

last: Kretov

state: Québec

department: Oncology Division

institute: CRCHU de Québec - Université Laval

description: Library name: ZF_BoxB_N22-ADARcd_8_rep2

library_source: other

data_processing:
paired-end reads were merged using the BBMap suite.
Counting of A-to-G conversions in Recorder mRNA associated with the presence of BoxB elements was conducted using a custom Python script.
Assembly: N/A.
Supplementary files format and content: A CSV file was generated containing the sequences of motifs identified in Recorder mRNA (BoxB or Empty) along with associated metrics. These metrics include the occurrence of motifs, the number of edited reads, the total number of A-to-G edits, the total number of reads in the library for all motifs, and the percentage of A-to-G editing.

molecule: other

source_name: whole embryo, 8 hpf

extract_protocol:
Total RNA from zebrafish embryos was extracted using TRIzol (ThermoFisher #15596026).
Sequencing was performed on PCR amplicons of the 3' UTR of Recorder mRNA, either containing or lacking BoxB elements. The PCR reaction amplified the 3' UTR region of the Recorder mRNA, which includes the BoxB elements and the Recorder hairpin. Partial Illumina adapters present in the Recorder mRNA are complementary to sections of the i5 and i7 TruSeq Illumina primers, which also contain unique barcodes and sequencing adapters.

tag: tissue

value: whole embryo, 8 hpf

tag: genotype

value: WT


title: ZF_Recorder-Empty_N22-dreADARcd, rep_1, 8-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_8_rep1


title: dre.embryo.pool_control_pfna_0_1

tag: cell line

tag: cell type

tag: treatment

tag: replicate

tag: row

tag: column

tag: sample id


title: fetal brain, trisomy 21, Library B11D1E_gex, Gene Expression

description:
Library name: B11D1E_gex
10X Multiome (scRNA/ATAC-seq)

library_source: transcriptomic single cell

molecule: polyA RNA

value: DS

value: male

value: Gene Expression


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_3, 6-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_6_rep3

source_name: whole embryo, 6 hpf

value: whole embryo, 6 hpf


title: CTL replicate 3

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

country: USA

institute: Johns Hopkins University

description: Library name: CTL3

data_processing:
Read level quality control was performed with fastp v0.20.1 and multiqc v1.17 to confirm appriorate read depth and quality. Subsequently STAR v2.7.10a with GENCODE GRCm38 V29 was used to perform alignment and transcript counting.
Assembly: GENCODE GRCm38 V29
Supplementary files format and content: Counts output from STAR

organism: Mus musculus

source_name: Muscle

extract_protocol:
Harvested tissue were immediately placed into TRIzol (Invitrogen) after mouse euthanasia. All samples were subsequently snap frozen on dry ice and stored at -80°C until use. Prior to starting RNA extraction, samples were thawed on ice and homogenized with approximately six to eight ceramic beads (2.8 mm; OMNI International) using the Bead Ruptor 12 (OMNI International). The Bead Ruptor was programmed to the highest speed for 3 rounds of 15 seconds. Subsequent chloroform extraction was utilized on the homogenized samples. The RNeasy PLUS Mini Kit (Qiagen) was used for RNA isolation and purification according to manufacturer’s instructions.
Extracted RNA was submitted to Psomagen for QC, Library Prep, and bulk RNA-sequencing. Briefly, TruSeq stranded mRNA library kit was used and pair-end sequencing was performed using the Illumina NovaSeq X platform, generating approximately 50 million paired-end reads per sample.

treatment_protocol: C57BL/6 female mice were randomized into two groups: control or antibiotics. For the induction of antibiotic-induced microbiota depletion, mice were treated with broad-spectrum antibiotics in drinking water. Mice were treated with antibiotics for one week. The antibiotics cocktail was comprised of four antibiotics: ampicillin (1g/L; MWI), vancomycin (500 mg/L), metronidazole (1g/L; MWI), and neomycin (1g/L) dissolved in sterile distilled water provided ad libitum via regular drinking bottles. Control animals were given sterile distilled water.  Bilateral muscle defects in the murine quadricep were created. Briefly, mice were anesthetized and maintained using 2-2.5% isoflurane. 5 mg/kg of carprofen (Rimadyl, MWI Animal Health) was injected subcutaneously for pain relief. Hair was removed above the quadricep with an electric razor (Oster) and the area was sterilized with 70% ethanol. After a 1-1.5-cm skin incision was created above the quadricep muscle, approximately 3 mm x 4 mm x 4 mm segment of quadricep was resected using surgical scissors to create a defect space. The bilateral defects were filled with 50 µl/quadricep of 200mg/mL of MicroMatrix Urinary Bladder Matrix (Integra) hydrolyzed in sterile 1X Dulbecco’s phosphate buffered saline (DPBS) (Gibco) acquired from Integra. The skin incision was closed through the use of surgical sutures.  Quadriceps implanted with ECM at day 42-post VML surgery were harvested and RNA extracted as described above (See qRT-PCR: Tissue preparation, RNA extraction).

value: Muscle

value: GENCODE GRCm39 vM27

value: VML with ECM without antibiotics


title: CTL replicate 5

description: Library name: CTL5


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_2, 6-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_6_rep2


title: Native animal C (ST)

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

institute: University College London

data_processing:
For spatial transcriptomics: Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. For single-nucleus transcriptomics: single nucleus suspensions were prepared and processed using the Chromium Single Cell 3’ Reagent Kits v3
Single nucleus Transcriptomics: Files were processed using 10X Genomics CellRanger 7.0.1. Fastq files were generated with `mkfastq`, and processed files with `count`. Multiplexed samples (P1, P2_R, P3) were demultiplexed using vireoSNP v0.5.8.
Assembly: ENSEMBL sus scrofa reference genome v11.1
Supplementary files format and content: Spatial transcriptomics: All files necessary to load data with Seurat's Load10X_Spatial function. Namely, Spaceranger count's spatial output directory (with image data) and filtered_feature_bc_matrix.h5 gene expression matrix. Contents of spatial directory (paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs): aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot.
Supplementary files format and content: Single-nucelus transcriptomics: Raw and filtered count matrices produced by cellranger. Cellbender outputs. For multiplexed samples (P1, P2_R, P3), also includes bam files and inter-sample vcf files.
Library strategy: Spatial transcriptomics

organism: Sus scrofa

source_name: Esophagus

growth_protocol: For single-nucleus data, minipig cells were culture in proliferation medium both in 2D in flasks (pre-bioreactor samples) or in 3D injected (post-bioreactor samples) in a decellularised porcine oesophageal scaffold in a custom bioreactor.

extract_protocol:
For spatial transcriptomics, the grafts were collected at 1, 3 and 6 months post orthotopic transplantation in minipigs.
Cells pre-bioreactor were cultured in proliferation medium in flasks, Cells post-bioreactor were cultured in proliferation medium in bioreactor in dynamic conditions for 7 days.
For single-nucleus data, an aliquot of cells was collected on the day of scaffold injection and stored in freezing medium in LN2 (pre-bioreactor). Nuclei were isolated from 25um sections of recellularised scaffold and snap frozen pelleted cell mix, using Chromium Nuclei Isolation Kit (product code: 1000494, 10X Genomics, Pleasanton, CA), following 10X Genomics user guide CG000505, treating cell pellet in the same manner as the tissue.  For spatial transcriptomics data, slices of tissue were collected from OCT-embedded oesophageal samples collected post-mortem.

value: Esophagus


title: CTL replicate 4

description: Library name: CTL4


title: fetal brain, trisomy 21, Library B11D1E_atac, Chromatin Accessibility

description:
Library name: B11D1E_atac
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

value: trisomy 21


title: CTL replicate 1

description: Library name: CTL1


title: CTL replicate 2

description: Library name: CTL2


title: S.aureus,ctr,rep1

city: Solna

first: Honglian

last: Liu

address: Tomtebodavägen 23

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

description: Library name: sa_ctr1_S13_R1_001

data_processing:
sequencing data are transfered to fastq.gz files and demultiplexed using bcl2fastq/2.20.0
fastq.gz files are quality/adpter trimmed using cutadapt/4.8 with parameter set to "-a AGATCGGAAGAGCAC --minimum-length 28 -e 0.2 -o 9 --nextseq-trim=20"
quality/adapter trimmed fastq files are extracted UMI using umi_tools/1.0.0 with command line set to "umi_tools extract --bc-pattern NNNNNNNN"
mapping is processed with star alignent program/2.7.11a, with parameters set to "star -- readFilesCommand gunzip -c  --outSAMtype BAM SortedByCoordinate --alignEndsType Extend5pOfRead1 --outFilterMatchNminOverLread 0.9 --outFilterMultimapNmax 12 --alignIntronMax 1 --outReadsUnmapped Fastx"
Deduplication is processed for the output bam files using "umi_tools dedup" command
bed graph are generated using bedtools/2.31.0 using "bedtools genomecov -bg -5 -strand - -ibam" and "bedtools genomecov -bg -5 -strand + -ibam" command
RNA types are counted using bedtools/2.31.0 using "bedtools intersect"
Deduplicated bam files are processed to fivepseq package/1.3.5 for context specific ribosome stalling analysis.
Assembly: GCF_000009045.1(B.subtilis), GCF_018885085.1(C.difficile), GCF_000013425.1(S.aureus), GCF_000393015.1(E.faecalis)
Supplementary files format and content: bedgraph file containing perbase genome coverage of the mapped umique reads at 5' end for forward strand.
Supplementary files format and content: bedgraph file containing  perbase genome coverage of the mapped umique reads at 5' end for reverse strand.
Supplementary files format and content: tab delimited txt file contaning number of reads mapped to different group of RNA.
Supplementary files format and content: tab delimited txt file containing reads count at each position by aligning to translational start site, with first nucleotide of last codon at 0 position.
Supplementary files format and content: tab delimited txt file containing reads count at each position by aligning to translational stop site, with first nucleotide of last codon at 0 position.
Supplementary files format and content: tab delimited txt file contaning read count in the gene body (discarding the start and termination regions) relative to the distance from amino acid
Supplementary files format and content: tab delimited txt file contaning summary of the processed each sample data

organism: Staphylococcus aureus

growth_protocol: B.subtilis and S.aureus is cultured in LB media at 37°C in incubator. L.plantarum is cultured in MRS broth at 37°C in incubator. C.difficile is cultured in BHI broth at 37°C in anaerobic chamber. E.faecalis is cultured in NYCIII media at 37°C in anaerobic chamber.

extract_protocol:
Total RNA is extracted using following phenol-chloroform and beads beating protocol.           1.Set up the following tubes: Tube 1 (2ml ): 500μL phenol/chloroform (acidic pH4.5) Tube 2 (2ml): 500μL chloroform Tube 3 (1.5ml): 40μL 3 M NaOAc pH 5.2 2.Add 150μL LET (25 mM Tris, pH 8.0, 100 mM LiCl, 20 mM EDTA) to frozen cell pellet. 3.Add 150μL phenol (water saturated pH 6). 4.Add equal volume (approx. 300μL) of glass beads (Sigma-AldrichG8772-500G) and vortex at RT in MultiMixer for 2 min at top speed. 5.Add 250μL nuclease free MQ H2O and 250μL phenol/chloroform (acidic pH4.5). 6.Vortex in MultiMixer for an additional 2 min followed by centrifugation at RT for 1 min at 14,000 rpm. 7.Remove aqueous phase (approx 450μL - top layer) and add to Tube #1. Vortex 30 sec and spin 1 min at 14,000 rpm. 8.Remove aqueous phase and add to Tube #2. Vortex 30 sec and spin 1 min at 14,000 rpm. 9.Remove aqueous phase and add to Tube #3; mix well. Add 1 mL 100% EtOH, mix, and place at -80 °C O/N or at -20 °C for 30min 10. Collect RNA by centrifugation at 4 °C for 20 min at 14,000 rpm. 11. Discard Sup and wash pellet with 500μL 70% EtOH Spin for 2 min at 14,000 rpm . 12. Discard Sup and centrifuge again for 1 min at 14,000 rpm 13. Discard Sup and centrifuge again for 1 min at 14,000 rpm 14. Remove residual EtOH by pipetting and air dry for 1-2 min 15. Resuspend pellet in 30-50μL autoclaved MQ H2O
200ng total extracted RNA is used for library preparation using s5PSeq library prepartion protocol. Ribosomal RNA Hybridization: rRNA was blocked using 2 μM mixture of 146 universal blocking oligonucleotides and 20 μM of two species-specific oligonucleotides targeting the 5’ ends of 16S and 23S rRNAs (Table S1). Hybridization was performed in the presence of 50 mM NaCl using the following program: 75 °C for 5 minutes, 65 °C for 5 minutes, followed by a stepwise hybridization with a temperature decrease of 3 °C every 2 minutes until 35 °C. RNA Adapter Ligation: Single-stranded RNA adapters containing unique molecular identifiers (UMIs) and barcodes were ligated using T4 RNA ligase 1, 1 mM ATP, and 1X T4 RNA ligation buffer at 25 °C for 1 hour. Ligated RNA was purified using RNA CleanXP beads (1.8X volume). Reverse Transcription and template RNA Depletion: Reverse transcription was performed using random hexamers to generate first-strand cDNA. Template RNA was degraded by incubating with 28.6 mM NaOH at 65 °C for 20 minutes. The reaction was neutralized with an equivalent concentration of Tris-HCl, and cDNA was purified using Ampure XP beads (1.8X volume). PCR Amplification and size selection: Libraries were amplified by PCR using Illumina adapters with dual barcodes (0.25 μM) and Phusion HSII master mix for 15 cycles. Libraries were size-selected using a dual size-selection strategy (0.6X–0.8X Ampure XP beads) to isolate 400–600 bp fragments. Library sequencing: Final library concentrations were quantified using Qubit DNA HS assays, and 650 pM libraries were loaded onto the Illumina NextSeq 2000 platform for sequencing.

treatment_protocol: Exponetially growing bacteria culture(OD600=0.6-0.8) are collected by centrification, the supernatent are removed, an the cell pellets are frozen immediately on dry ice, and stored in -20°C for RNA extraction.

value: wild type

value: untreated


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_1, 8-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_8_rep1


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_1, 6-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_6_rep1


title: CTL replicate 0

description: Library name: CTL


title: fetal brain, disomic, Library B11C1C_gex, Gene Expression

description:
Library name: B11C1C_gex
10X Multiome (scRNA/ATAC-seq)

value: disomic

value: CON


title: S.aureus,s5PSeq,rep2

description: Library name: sa_bo2_S16_R1_001


title: fetal brain, disomic, Library B11C1C_atac, Chromatin Accessibility

description:
Library name: B11C1C_atac
10X Multiome (scRNA/ATAC-seq)

value: Chromatin Accessibility

value: TRUE


title: ZF_Recorder-Empty_N22-dreADARcd, rep_3, 8-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_8_rep3

value: whole embryo, 8 hpf

value: WT


title: ZF_Recorder-Empty_N22-dreADARcd, rep_3, 6-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_6_rep3


title: ZF_Recorder-Empty_N22-dreADARcd, rep_2, 6-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_6_rep2


title: S.aureus,s5PSeq,rep1

description: Library name: sa_bo1_S15_R1_001


title: ABX replicate 5

description: Library name: ABX5

value: VML with ECM with antibiotics


title: Kidney, Uninfected Hamster, Day3, replicate 4

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description:
Library name: D3_UNINF_H4_Kidney_S16
D1-D3_Kidney_raw_counts.txt

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.15.3)
FeatureCounts 2.0.1 with the multimapper option was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Gene ontology (GO) enrichment analyses were performed using the Cytoscape app ClueGO (version 2.5.3)
Assembly: Leptospira interrogans serovar manilae, NZ_CP011931.1 and Golden Syrian hamsters, KB708127.1
Supplementary files format and content: *raw_counts.txt

organism: Mesocricetus auratus

source_name: Kidney

growth_protocol: Leptospira strains were cultivated aerobically in Ellighausen-McCullough-Johnson-Harris liquid medium (EMJH) at 30°C with shaking at 100 rpm.

extract_protocol:
Liver and kidneys tissues of hamsters were resuspended in QIAzol lysis reagent (Qiagen) with a stainless-steel bead of 5 mm (Qiagen) and homogenized with a Qiagen TissueLyser (two cycles of one-minute at 25 Hz, with a one-minute break between cycles in ice). Total RNA was extracted from the homogenized samples using the RNeasy Mini Kit (Qiagen), with a DNAse digestion (Qiagen) incorporated into the protocol. In the case of the in vitro condition of L. interrogans, the harvested exponentially growing bacteria culture were resuspended in QIAzol lysis reagent, and total RNA was extracted using the RNeasy Mini Kit with a DNAse treatment.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus prep kit with the addition of custom primer that target L. interrogans rRNA following manufacturer's protocol.

treatment_protocol: Four-week-old Golden Syrian hamsters (RjHan:AURA, Janvier Labs) were infected (4 per group) via intraperitoneal injection with 108 L. interrogans, with the number of bacteria enumerated using a Petroff-Hausser counting chamber.

value: Kidney

value: Uninfected Hamster, Day3


title: neural graft, trisomy 21, Library G24D4E_atac, Chromatin Accessibility

description:
Library name: G24D4E_atac
10X Multiome (scRNA/ATAC-seq)

library_source: genomic single cell

data_processing:
Raw demultiplexed sequencing data (fastq files) were mapped to the human genome (GRCh38) and quantified using cellranger-arc (v2.0.2; 10X Genomics)
Cellranger output was loaded, merged and further processed in an R environment (R v4.3.3), using the Seurat single cell analysis package v5.1.052,53 , with the Signac extension (v1.13.0). The detailed analysis pipeline can be found here: https://github.com/lattkem1/Down_Syndrome_Multiome
Assembly: GRCh38
Supplementary files format and content: Compressed cellranger-arc count matrices, features and cell barcodes
Supplementary files format and content: rda files containing the Seurat objects with cells mapped to fetal cortex cell clusters, or to subsetted excitatory lineage clusters of the fetal tissue (only RNA; including data from additonal cells analysed with Singleron Celescope technology)

source_name: neural graft

growth_protocol: iPSCs were differentiated to cortical progenitors and injected into the brains of adult immunodeficient mice. Grafts were dissected 12-24 weeks after transplantation.

extract_protocol:
~10-50 mg of graft tissue were processed using a protocol based on dx.doi.org/10.17504/protocols.io.bvhhn336.  In some cases, grafts from multiple mice were pooled to get enough tissue for nuclei isolation. After removal from dry ice, tissue was immediately suspended in Homogenisation Buffer (10 mM Tris-HCl pH7.4, 320 mM Sucrose, 3 mM CaCl2, 3 mM MgCl2), supplemented freshly with 0.1% NP-40, 1 mM DTT and 1 U/µl RNAse inhibitor (Protector (Sigma #3335402001), RiboLock (Thermo Fisher, PN-EO0382), or RNaseOUT (Thermo Fisher, 10777019) RNase inhibitor). The tissue was then immediately homogenised using a 1-ml dounce homogeniser and exactly after 5 min diluted with 1 volume of Homogenisation Buffer (without NP-40), filtered (30 µm mesh size) to remove large debris, and centrifuged (500g, 5 min, 4°C) to collect raw nuclei. Raw nuclei were resuspended in Homogenisation Buffer (without NP-40) and mixed with 1 volume 50% iodixanol buffer (10 mM Tris-HCl pH7.4, 3 mM CaCl2, 3 mM MgCl2, 1 mM DTT, 0.5 U/µl RNAse inhibitor). This suspension was carefully overlaid on a 29% iodixanol buffer (as above + 160 mM sucrose), and centrifuged (6000g, 30 min, 4°C). The nuclei pellet was resuspended in a Lysis Buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT, 0.5 U/µl RNAse inhibitor, 0.1% Tween-20, 0.1% NP-40, 0.001% digitonin), and after exactly 2 min nuclei were diluted in 10 volumes wash buffer (lysis buffer without NP-40, digitonin), and centrifuged (500g, 5 min, 4°C) to collect the nuclei, which were then resuspended in 1x Nuclei Buffer (from the “Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle”; 10X Genomics PN-1000283/PN-1000285; supplemented with 1 mM DTT, 0.5 U/µl RNAse inhibitor).
snRNA-seq and snATAC-seq libraries were prepared using a 10X-Genomics Chromium X and the “Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle” (10X Genomics PN-1000283/PN-1000285) according to manufacturer’s instructions. Libraries were sequenced using Illumina Nextseq2000 or Novaseq6000 sequencers.

value: neural graft

value: neural cells

value: DS

value: male

tag: weeks post_transplantation


title: ABX replicate 3

description: Library name: ABX3

value: Muscle

value: GENCODE GRCm39 vM27


title: ABX replicate 4

description: Library name: ABX4


title: ZF_Recorder-Empty_N22-dreADARcd, rep_1, 6-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_6_rep1

value: whole embryo, 6 hpf


title: S.aureus,ctr,rep2

description: Library name: sa_ctr2_S14_R1_001

value: wild type

value: untreated


title: Kidney, Uninfected Hamster, Day3, replicate 3

description:
Library name: D3_UNINF_H3_Kidney_S15
D1-D3_Kidney_raw_counts.txt


title: neural graft, trisomy 21, Library G24D3D_gex, Gene Expression

description:
Library name: G24D3D_gex
10X Multiome (scRNA/ATAC-seq)

value: trisomy 21

tag: name

value: Gene Expression


title: neural graft, trisomy 21, Library G24D3D_atac, Chromatin Accessibility

description:
Library name: G24D3D_atac
10X Multiome (scRNA/ATAC-seq)

tag: library igf_id

value: Chromatin Accessibility

value: TRUE


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_2, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_4_rep2

source_name: whole embryo, 4 hpf

value: whole embryo, 4 hpf

value: WT


title: ABX replicate 2

description: Library name: ABX2

value: VML with ECM with antibiotics


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_1, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_4_rep1


title: Kidney, Uninfected Hamster, Day3, replicate 2

description:
Library name: D3_UNINF_H2_Kidney_S14
D1-D3_Kidney_raw_counts.txt

value: Kidney

value: Uninfected Hamster, Day3


title: ABX replicate 1

description: Library name: ABX1


title: ZF_Recorder-Empty_N22-dreADARcd, rep_3, 4-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_4_rep3


title: neural graft, disomic, Library G21C1K_gex, Gene Expression

description:
Library name: G21C1K_gex
10X Multiome (scRNA/ATAC-seq)

value: neural graft

value: neural cells

value: disomic

tag: group

value: CON


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_3, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_4_rep3


title: E185No18ff1

city: Otsu

first: Dai

last: Ihara

address: Tsukinowatyo Seta

department: Anatomy

country: Japan

institute: Shiga University of Medical Science

description: Library name: X8No13.dcKO

data_processing:
Trim Galore (adapter trimming and quality filtering)
STAR (alignment to reference genome)
RSEM (transcript quantification)
DESeq2 (differential expression analysis)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: cerebral cortex

extract_protocol:
RNeasy Mini Kit (QIAGEN) was used to corect RNA.
RNA was harvested using RNeasy Mini Kit (QIAGEN) . 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using cDNA Library Preparation Using TruSeq Stranded mRNA Kit (Illumina Inc.) following manufacturer's protocols.

value: cerebral cortex

tag: age


title: Kidney, Infected Hamster, Day3, replicate 3

description:
Library name: D3_INF_H3_Kidney_S11
D1-D3_Kidney_raw_counts.txt

value: Infected Hamster, Day3


title: Kidney, Uninfected Hamster, Day3, replicate 1

description:
Library name: D3_UNINF_H1_Kidney_S13
D1-D3_Kidney_raw_counts.txt


title: neural graft, disomic, Library G21C1K_atac, Chromatin Accessibility

description:
Library name: G21C1K_atac
10X Multiome (scRNA/ATAC-seq)

tag: Sex

value: male


title: ABX replicate 0

description: Library name: ABX

value: Muscle

value: GENCODE GRCm39 vM27


title: Kidney, Infected Hamster, Day3, replicate 4

description:
Library name: D3_INF_H4_Kidney_S12
D1-D3_Kidney_raw_counts.txt


title: neural graft, trisomy 21, Library G24D4E_gex, Gene Expression

description:
Library name: G24D4E_gex
10X Multiome (scRNA/ATAC-seq)

value: trisomy 21

value: DS

tag: library type

value: Gene Expression


title: E185No17ff1

description: Library name: X8No10_dcKO


title: Kidney, Infected Hamster, Day3, replicate 2

description:
Library name: D3_INF_H2_Kidney_S10
D1-D3_Kidney_raw_counts.txt


title: neural graft, disomic, Library G13C1E_gex, Gene Expression

description:
Library name: G13C1E_gex
10X Multiome (scRNA/ATAC-seq)

tag: in final_analysis

value: TRUE


title: Kidney, Infected Hamster, Day3, replicate 1

description:
Library name: D3_INF_H1_Kidney_S9
D1-D3_Kidney_raw_counts.txt

tag: tissue


title: E185No13dcKO1

description: Library name: X7No6_dcKO

tag: genotype


title: ZF_Recorder-Empty_N22-dreADARcd, rep_1, 4-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_4_rep1

value: whole embryo, 4 hpf

value: WT


title: fetal brain, disomic, Library B14C1

description:
Library name: B14C1
bulk RNA-seq (ribodepleted total RNA)

data_processing:
Raw demultiplexed sequencing data (fastq files) were mapped to the human genome (GRCh38) and quantified using the nf-core/rnaseq pipeline (v.3.18.0; doi:10.5281/zenodo.1400710)
Assembly: GRCh38
Supplementary files format and content: Gene level count matrix of all samples combined

extract_protocol:
Fresh-frozen fetal tissue from surgical terminations of pregancy from UK hospitals was collected by the "Human Developmental Biology Resource" (HDBR, https://www.hdbr.org/). Total RNA was extracted from ~2-10 mg of fetal human brain tissue using the RNeasy Plus Micro kit (Qiagen) according to manufacturer’s instructions.
RNA-seq was then performed by the NIHR Imperial BRC Genomics Facility using the NEBNext rRNA Depletion kit v2 (Human/Mouse/Rat) and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. Libraries were sequenced in PE75 mode.

value: fetal brain

tag: dev stage_pcw

value: female


title: neural graft, disomic, Library G13C1E_atac, Chromatin Accessibility

description:
Library name: G13C1E_atac
10X Multiome (scRNA/ATAC-seq)

value: neural graft

tag: cell line

tag: cell type

value: Chromatin Accessibility


title: E185No12dcKO1

description: Library name: X7No12.dcKO


title: Kidney, Uninfected Hamster, Day1, replicate 4

description:
Library name: D1_UNINF_H4_Kidney_S8
D1-D3_Kidney_raw_counts.txt

value: Kidney

tag: treatment

value: Uninfected Hamster, Day1


title: fetal brain, trisomy 21, Library B13D3

description:
Library name: B13D3
bulk RNA-seq (ribodepleted total RNA)


title: ZF_Recorder-BoxB_dreADARcd, rep_3 (RBPscan)

description: Library name: ZF_BoxB_ADARcd_rep3

value: whole embryo, 6 hpf


title: ZF_Recorder-BoxB_dreADARcd, rep_2 (RBPscan)

description: Library name: ZF_BoxB_ADARcd_rep2


title: E185No8ff1

description: Library name: X6No3.dcKO

value: cerebral cortex


title: fetal brain, trisomy 21, Library B13D1

description:
Library name: B13D1
bulk RNA-seq (ribodepleted total RNA)


title: E185No7ff1

description: Library name: X5No2_dcKO


title: Kidney, Uninfected Hamster, Day1, replicate 3

description:
Library name: D1_UNINF_H3_Kidney_S7
D1-D3_Kidney_raw_counts.txt


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_3 (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_rep3


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_2 (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_rep2


title: fetal brain, trisomy 21, Library B12D3

description:
Library name: B12D3
bulk RNA-seq (ribodepleted total RNA)

value: male


title: ZF_Recorder-Empty_N22-dreADARcd, rep_2, 4-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_4_rep2


title: Kidney, Uninfected Hamster, Day1, replicate 1

description:
Library name: D1_UNINF_H1_Kidney_S5
D1-D3_Kidney_raw_counts.txt


title: E185No2dcKO1

description: Library name: X4No18.dfl


title: Kidney, Infected Hamster, Day1, replicate 4

description:
Library name: D1_INF_H4_Kidney_S4
D1-D3_Kidney_raw_counts.txt

value: Infected Hamster, Day1


title: Kidney, Uninfected Hamster, Day1, replicate 2

description:
Library name: D1_UNINF_H2_Kidney_S6
D1-D3_Kidney_raw_counts.txt


title: E125No10dcKO1

description: Library name: X3No7_dfl

source_name: elencephalon

value: elencephalon


title: E185No3dcKO1

description: Library name: X5No2.dcKO


title: fetal brain, trisomy 21, Library B12D1

description:
Library name: B12D1
bulk RNA-seq (ribodepleted total RNA)

value: trisomy 21


title: E125No7ff1

description: Library name: X2No8.dfl


title: E125No9ff1

description: Library name: X3No17.dfl


title: Kidney, Infected Hamster, Day1, replicate 2

description:
Library name: D1_INF_H2_Kidney_S2
D1-D3_Kidney_raw_counts.txt


title: Kidney, Infected Hamster, Day1, replicate 3

description:
Library name: D1_INF_H3_Kidney_S3
D1-D3_Kidney_raw_counts.txt


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_1 (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_rep1


title: fetal brain, disomic, Library B12C4

description:
Library name: B12C4
bulk RNA-seq (ribodepleted total RNA)

value: disomic

value: CON


title: ZF_Recorder-Empty_N22-dreADARcd, rep_3 (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_rep3


title: Kidney, Infected Hamster, Day1, replicate 1

description:
Library name: D1_INF_H1_Kidney_S1
D1-D3_Kidney_raw_counts.txt


title: ZF_Recorder-Empty_N22-dreADARcd, rep_1 (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_rep1


title: ZF_Recorder-Empty_N22-dreADARcd, rep_2 (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_rep2


title: Liver, Uninfected Hamster, Day3, replicate 4

description:
Library name: D3_UNINF_H4_Liver_S24
D1-D3_Liver_raw_counts.txt

source_name: Liver

value: Liver

value: Uninfected Hamster, Day3


title: fetal brain, disomic, Library B12C2

description:
Library name: B12C2
bulk RNA-seq (ribodepleted total RNA)

value: TRUE


title: E125No6dcKO1

description: Library name: X2No4_dfl


title: fetal brain, trisomy 21, Library B12D2, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B12D2
bulk RNA-seq (ribodepleted total RNA)

value: fetal brain

value: DS

value: FALSE


title: E125No4ff1

description: Library name: X1No9_dfl


title: ZF_Recorder-BoxB_rep_3 (RBPscan)

description: Library name: ZF_BoxB_rep3

value: WT


title: ZF_Recorder-BoxB_dreADARcd, rep_1 (RBPscan)

description: Library name: ZF_BoxB_ADARcd_rep1


title: fetal brain, disomic, Library B13C2

description:
Library name: B13C2
bulk RNA-seq (ribodepleted total RNA)


title: fetal brain, trisomy 21, Library B11D2

description:
Library name: B11D2
bulk RNA-seq (ribodepleted total RNA)

value: female


title: E125No2dcKO1

description: Library name: X1No7.dfl


title: Liver, Uninfected Hamster, Day3, replicate 3

description:
Library name: D3_UNINF_H3_Liver_S23
D1-D3_Liver_raw_counts.txt


title: ZF_Recorder-BoxB_rep_2 (RBPscan)

description: Library name: ZF_BoxB_rep2


title: Liver, Uninfected Hamster, Day3, replicate 2

description:
Library name: D3_UNINF_H2_Liver_S22
D1-D3_Liver_raw_counts.txt


title: ZF_Recorder-BoxB_rep_1 (RBPscan)

description: Library name: ZF_BoxB_rep1


title: C57BL/6J BMDMs, Untreated

city: Cleveland

first: Rachel

middle: G

last: Scheraga

state: Ohio

address: 2111 E. 96th Street NE4-254a

department: Inflammation and immunity

institute: Cleveland Clinic Foundation

description:
Library name: WT_Untreated
WT_UnT

data_processing:
CellRanger (v3.1.0) was used for alignment of raw FASTQs to mm10 reference genome.
Downstream analyses were performed using the Seurat package (v4) in R (v4.2).
Cells were filtered for >250 nonzero gene counts, >1,000 unique transcripts, <40,000 unique transcripts, and <10% mitochondrial transcripts.
Integration and clustering were performed on a per sample basis. 3,000 features were used for integration. Following principal component analysis UMAPs were visualized with 40 dimensions.
Marker genes were found using “FindAllMarkers” which uses a Wilcoxon Rank Sum test.
Assembly: mm10
Supplementary files format and content: CSV file which contains descriptions of each cell for each sample..
Supplementary files format and content: CSV file which contains a raw count matrix of read counts for each gene for each cell.

source_name: BMDMS

growth_protocol: Primary murine BMDMs were harvested from 8- to 12-wk-old C57BL/6 wild-type or TRPV4-null (Trpv4 KO) mice. BMDMs were differentiated in recombinant M-CSF (50 ng/ml, R&D Systems).

extract_protocol:
Single cell suspensions were mixed with barcoded beads and dispersed into water-in-oil droplets with the 10x Genomics Chromium platform using Microfluidics technology to form GEMS.
Libraries were constructed within the GEMs where poly-A capture occurs and the beads transcribe mRNA into cDNA using reverse transcriptase. A cDNA library was generated using PCR amplification.

treatment_protocol: Cells were treated with LPS at a concentration of 100ng/mL for 24 hours prior to harvest.

value: BMDMS

value: Untreated


title: Liver, Infected Hamster, Day3, replicate 4

description:
Library name: D3_INF_H4_Liver_S20
D1-D3_Liver_raw_counts.txt

value: Infected Hamster, Day3


title: C57BL/6J BMDMs, LPS-Treated

description:
Library name: WT_LPS
WT_LPS

value: 100ng/mL Lipopolysaccharide


title: E.faecalis,ctr,rep1

description: Library name: ef_ctr1_S9_R1_001

organism: Enterococcus faecalis

value: wild type

value: untreated


title: E.faecalis,ctr,rep2

description: Library name: ef_ctr2_S10_R1_001


title: ZF_1000PREs_Control_rep_3 (RBPscan)

description: Library name: ZF_PRE_Control_rep3

data_processing:
paired-end reads were merged using the BBMap suite.
Counting of A-to-G conversions in Recorder mRNA associated with specific PREs was conducted using a custom Python script.
Assembly: N/A.
Supplementary files format and content: A CSV file containing sequences of PREs and associated metrics was generated, including occurrence, number of edited reads, total number of A-to-G edits, total number of reads in the library for all motifs, and the percentage of A-to-G editing.

extract_protocol:
Total RNA from zebrafish embryos was extracted using TRIzol (ThermoFisher #15596026).
Sequencing was performed on PCR amplicons of the 3' UTR of Recorder mRNA containing 1,000 PRE sequences. The PCR reaction was carried out to amplify the 3' UTR region of the Recorder mRNA, which includes PRE motifs and the Recorder hairpin. Partial Illumina adapters present in the Recorder mRNA are complementary to sections of the i5 and i7 TruSeq Illumina primers, which also contain unique barcodes and sequencing adapters.

value: whole embryo, 6 hpf


title: E.faecalis,s5PSeq,rep2

description: Library name: ef_bo2_S12_R1_001


title: ZF_1000PREs_drePum1_ADARcd-0.9pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_Pum1-0.9_rep3


title: fetal brain, disomic, Library B12C1

description:
Library name: B12C1
bulk RNA-seq (ribodepleted total RNA)

value: disomic

value: male


title: ZF_1000PREs_drePum1_ADARcd-1.8pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_Pum1-1.8_rep3


title: Liver, Infected Hamster, Day3, replicate 2

description:
Library name: D3_INF_H2_Liver_S18
D1-D3_Liver_raw_counts.txt

value: Liver


title: Trpv4 KO BMDMs, LPS-Treated

description:
Library name: Trpv4KO_LPS
KO_LPS


title: ZF_1000PREs_drePum1_ADARcd-3.7pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_Pum1-3.7_rep3


title: E.faecalis,s5PSeq,rep1

description: Library name: ef_bo1_S11_R1_001


title: Liver, Infected Hamster, Day3, replicate 1

description:
Library name: D3_INF_H1_Liver_S17
D1-D3_Liver_raw_counts.txt


title: LD611, HDAC1KD3

city: Los Angeles

first: Yonghwan

last: Shin

state: CA

address: 1450 Biggy St

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow
Trimmed sequence reads were mapped to hg38 - GENCODE Genes - release 40 using Partek Flow
Read count extraction and normalization were performed using Partek Flow
Assembly: hg38
Supplementary files format and content: txt file type

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

value: Bladder cancer

value: HDAC1 Knockdown


title: ZF_1000PREs_drePum1_ADARcd-7.5pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_Pum1-7.5_rep3


title: Liver, Uninfected Hamster, Day1, replicate 4

description:
Library name: D1_UNINF_H4_Liver_S16
D1-D3_Liver_raw_counts.txt

value: Uninfected Hamster, Day1


title: fetal brain, disomic, Library B11C2

description:
Library name: B11C2
bulk RNA-seq (ribodepleted total RNA)

value: fetal brain

value: CON

value: TRUE


title: ZF_1000PREs_drePum1_ADARcd-15pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_Pum1-15_rep3

value: WT


title: LD611, HDAC1KD2


title: Liver, Uninfected Hamster, Day1, replicate 3

description:
Library name: D1_UNINF_H3_Liver_S15
D1-D3_Liver_raw_counts.txt


title: LD611, HDAC1KD1


title: Liver, Uninfected Hamster, Day3, replicate 1

description:
Library name: D3_UNINF_H1_Liver_S21
D1-D3_Liver_raw_counts.txt

value: Uninfected Hamster, Day3


title: Liver, Infected Hamster, Day3, replicate 3

description:
Library name: D3_INF_H3_Liver_S19
D1-D3_Liver_raw_counts.txt


title: Trpv4 KO BMDMs, Untreated

description:
Library name: Trpv4KO_Untreated
KO_UnT

source_name: BMDMs

value: BMDMs

value: Untreated


title: Liver, Uninfected Hamster, Day1, replicate 2

description:
Library name: D1_UNINF_H2_Liver_S14
D1-D3_Liver_raw_counts.txt


title: SW13/N, mock2

type: RNA

city: Wakayama

first: Keisuke

last: Ohta

address: 811-1 Kimiidera

department: Microbiology

institute: Wakayama Medical University

description: Gene expression data from mock SW13/N

hyb_protocol: Labeled RNA was hybridized to a ClariomTM S Assay, Human (Thermo Fisher Scientific).

scan_protocol: The array strips were analyzed using GeneChipTM Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: Data were validated using Transcriptome Analysis ConsoleTM v4.0.3 (Thermo Fisher Scientific), and subjected to normalization using the Signal Space Transformation-Robust Multi-array Analysis

label: biotin

source_name: mock SW13/N

label_protocol: Purified RNA was labeled using the GeneChipTM WT Plus Reagent Kit (Thermo Fisher Scientific).

growth_protocol: SW13 cells were cultured in Dulbecco’s modified Eagle’s minimal essential medium containing 5% fetal calf serum. The cells were maintained in a humidified incubator at 37˚C with 5% CO2

extract_protocol: Total RNA of the cells was extracted using ISOGENII according to the manufacturer's instruction.

treatment_protocol: SW13 cells and SW13/N were infected with or without HAZV at an multiplicity of infection of 0.1 for 48 hours.

value: adrenal cortex


title: ZF_1000PREs_drePum1_ADARcd-60pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_Pum1-60_rep3


title: LD611, Control3


title: Liver, Uninfected Hamster, Day1, replicate 1

description:
Library name: D1_UNINF_H1_Liver_S13
D1-D3_Liver_raw_counts.txt


title: LD611, Control2


title: SW13/N, mock3

description: Gene expression data from mock SW13/N


title: ZF_1000PREs_drePum1_ADARcd-120pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_Pum1-120_rep3


title: ZF_1000PREs_Control_rep_2 (RBPscan)

description: Library name: ZF_PRE_Control_rep2


title: Liver, Infected Hamster, Day1, replicate 3

description:
Library name: D1_INF_H3_Liver_S11
D1-D3_Liver_raw_counts.txt

value: Infected Hamster, Day1


title: ZF_1000PREs_drePum1_ADARcd-0.9pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_Pum1-0.9_rep2


title: LD611, Control1


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_59

city: Heidelberg

first: Tang

last: Yiheng

address: Im Neuenheimer Feld 224

department: Department of Neuropathology

country: Germany

institute: Heidelberg University Hospital

data_processing:
Space Ranger v4.0.1
Assembly: GRCh38
Supplementary files format and content: H5/HDF5 archives
Supplementary files format and content: Tar archives of processed Visium data files
Library strategy: Spatial Transcriptomics

source_name: Meningioma

extract_protocol:
Preparation of FFPE and fresh frozen samples for spatial transcriptomics followed protocols from 10X Genomics.
Samples were sequenced on an Illumina NovaSeq 6000 (FFPE) or NextSeq 500 (fresh frozen).

value: Meningioma


title: Liver, Infected Hamster, Day1, replicate 1

description:
Library name: D1_INF_H1_Liver_S9
D1-D3_Liver_raw_counts.txt


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_54


title: ZF_1000PREs_drePum1_ADARcd-30pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_Pum1-30_rep3

value: whole embryo, 6 hpf


title: Liver, Infected Hamster, Day1, replicate 2

description:
Library name: D1_INF_H2_Liver_S10
D1-D3_Liver_raw_counts.txt


title: ZF_1000PREs_drePum1_ADARcd-1.8pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_Pum1-1.8_rep2


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_53


title: ZF_1000PREs_drePum1_ADARcd-3.7pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_Pum1-3.7_rep2


title: SW13/N, HAZV-infected2

description: Gene expression data from HAZV-infected SW13/N

source_name: HAZV-infected SW13/N


title: SW13/N, HAZV-infected1


title: SW13/N, mock1

description: Gene expression data from mock SW13/N


title: Liver, Infected Hamster, Day1, replicate 4

description:
Library name: D1_INF_H4_Liver_S12
D1-D3_Liver_raw_counts.txt


title: ZF_1000PREs_drePum1_ADARcd-7.5pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_Pum1-7.5_rep2


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_41


title: ZF_1000PREs_drePum1_ADARcd-15pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_Pum1-15_rep2


title: ZF_1000PREs_drePum1_ADARcd-30pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_Pum1-30_rep2


title: SW13, HAZV-infected3

description: Gene expression data from HAZV-infected SW13

source_name: HAZV-infected SW13


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_35


title: SW13, HAZV-infected2


title: SW13/N, HAZV-infected3


title: hIL6_2h_rep3

city: Amsterdam

first: Josje

last: Huisman

state: Noord-Holland

address: Meibergdreef 9

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

description: Library name: IL6_2h_rep3

data_processing:
Sequence reads were trimmed with trimmomatic v2.1.1
Reads were aligned to the mm10 genome using HISAT2 v2.1.0
Counts were produced using featureCounts V2.1.1
Assembly: mm10
Supplementary files format and content: Gene counts in a csv file

extract_protocol:
Qiagen Mini RNA isolation kit
Roche KAPA hyper mRNA

tag: strain

tag: time


title: SW13, HAZV-infected1


title: IFNy_2h_rep3

description: Library name: IFNy_2h_rep3

value: IFNy


title: hIL6_2h_rep4

description: Library name: hIL6_2h_rep4


title: IFNy_2h_rep4

description: Library name: IFNy_2h_rep4


title: SW13, mock1

description: Gene expression data from mock SW13

source_name: mock SW13


title: IL6_IFNy_2h_rep2

description: Library name: IL6_IFNy_2h_rep2


title: ZF_1000PREs_drePum1_ADARcd-60pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_Pum1-60_rep2


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_32


title: ZF_1000PREs_drePum1_ADARcd-120pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_Pum1-120_rep2


title: SW13, mock3

description: Gene expression data from mock SW13


title: ZF_1000PREs_Control_rep_1 (RBPscan)

description: Library name: ZF_PRE_Control_rep1


title: IL6_IFNy_2h_rep1

description: Library name: IL6_IFNy_2h_rep1


title: 10

city: Boston

first: Toby

middle: Black

last: Lanser

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: 10_S86_

data_processing:
Preprocessing was done using Trimmomatic and ambient ribosomal RNA was filtered using sortMERNA. Transcriptome alignments were conducted using the Salmon  tool with its standard parameters. The R software (version 4.2.1) and DESeq2 package.
Assembly: hg38
Supplementary files format and content: salmon quant files

source_name: Blood

extract_protocol:
BM neutrophils were isolated using MACS neutrophil selection (Miltenyi Biotec Inc., MA, USA).
Cells lysed with RLT Plus buffer and submitted to next generation sequencing by Ilumina 2x150, 6Gb (40M pair end reads per sample).

value: Blood

value: neutrophils

value: Veh


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_52


title: Ctrl_2h_rep2

description: Library name: Ctrl_2h_rep2

value: Ctrl


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_39


title: ET062595

type: genomic

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented  and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard   recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018.   PMID: 30085201

label: Cy3 and Cy5

organism: Peromyscus maniculatus bairdii

label_protocol: Standard Illumina Protocol

extract_protocol: Quick-DNA Miniprep Plus Kit (Zymo Research, Cat#D4069) following manufacturers instructions

tag: x

tag: sid

tag: externalsampleid

tag: externalsamplename

tag: sampletype

value: DNA

value: M

value: Tail

tag: species

value: BW

tag: relatedness

tag: idatsfound

value: FALSE

tag: extbasename

tag: row

tag: col

tag: project

value: male

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Ear

tag: specieslatinname


title: SW13, mock2

description: Gene expression data from mock SW13

tag: tissue


title: ZF_1000PREs_drePum1_ADARcd-1.8pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_Pum1-1.8_rep1

source_name: whole embryo, 6 hpf

tag: genotype

value: WT


title: ET062596

tag: x

tag: sid

tag: age

tag: Sex

value: F

value: female


title: Ctrl_2h_rep1

description: Library name: Ctrl_2h_rep1

tag: cell type

value: BMDMs

tag: strain

tag: treatment

tag: time


title: ZF_1000PREs_drePum1_ADARcd-3.7pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_Pum1-3.7_rep1

value: whole embryo, 6 hpf


title: 7

description: Library name: 07_S83_


title: 8

description: Library name: 08_S84_


title: pSTAT3_2hIFNyIL6_rep2

description: Library name: pSTAT3_2hIFNyIL6_rep2

data_processing:
Sequence reads were trimmed with trimmomatic v2.1.1
Reads were aligned to the mm10 genome using HISAT2 v2.1.0
Peaks were identified by using HOMER to call unfiltered 200-bp peaks (parameters -L 0 -C 0 -fdr 0.9 -size 200) and running mergePeaks on replicates of the same sample with the default parameters to find reproducible peaks.
BigWigs were produced from HOMER tag directories
Assembly: mm10
Supplementary files format and content: BigWigs

molecule: protein

source_name: BMDM

extract_protocol:
Hoeksema, et al, Sci Adv, 2021
Roche KAPA Hyper DNA kit

value: BMDM

tag: chip antibody

value: pSTAT3 (Cell Signaling Technologies, Cat# 9131)


title: 9

description: Library name: 09_S85_

value: Blood

value: neutrophils


title: 6

description: Library name: 06_S82_

value: Veh


title: ZF_1000PREs_drePum1_ADARcd-7.5pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_Pum1-7.5_rep1


title: ZF_1000PREs_drePum1_ADARcd-15pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_Pum1-15_rep1


title: pSTAT1_2hIFNyIL6_rep1

description: Library name: pSTAT1_2hIFNyIL6_rep1

value: pSTAT1 (Invitrogen, Cat# 33-3400)


title: ZF_1000PREs_drePum1_ADARcd-0.9pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_Pum1-0.9_rep1


title: ET062592

tag: externalsampleid

tag: externalsamplename

tag: sampletype

value: DNA

value: M

tag: species

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

tag: col


title: ET062591

tag: x

tag: sid

tag: tissue

value: Tail

value: BW

tag: project

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Muscle

tag: specieslatinname


title: ET06259

tag: externalsampleid

tag: age

tag: Sex

value: FALSE

value: male

value: Ear


title: ET062590

tag: externalsamplename

tag: sampletype

tag: species

value: Lung


title: 3

description: Library name: 03_S79_

tag: cell type

tag: treatment

value: T+G


title: pSTAT3_2hIFNyIL6_rep1

description: Library name: pSTAT3_2hIFNyIL6_rep1

tag: strain

tag: chip antibody

tag: genotype

value: WT

tag: time


title: ZF_1000PREs_drePum1_ADARcd-60pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_Pum1-60_rep1

tag: tissue

value: whole embryo, 6 hpf


title: Pol2_2hIFNy_rep1

description: Library name: Pol2_2hIFNy_rep1

value: BMDM

value: RNApol2 (Diagenode, Cat # C15200253)

value: IFNg


title: ET062588

tag: x

tag: sid

value: F

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

tag: col

tag: project

value: female

tag: maxagecaesar

value: Bladder


title: 5

description: Library name: 05_S81_

value: Blood

value: neutrophils


title: ET062589

tag: externalsampleid

tag: externalsamplename

tag: sampletype

value: DNA

tag: age

tag: Sex

value: Tail

tag: species

value: BW

tag: gestationtimeinyears

tag: highmaxagecaesar

tag: specieslatinname


title: ET062593

tag: x

tag: sid

value: M

tag: tissue

value: FALSE

value: male


title: ZF_7N_hsaPum2-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_hsaPum2_rep3

data_processing:
paired-end reads were merged using the BBMap suite.
Counting of A-to-G conversions in Recorder mRNA associated with specific 7-mer motifs was conducted using a custom Python script.
Assembly: N/A.
Supplementary files format and content: A CSV file containing sequences of 7-mer motifs and associated metrics was generated, including occurrence, number of edited reads, total number of A-to-G edits, total number of reads in the library for all motifs, and the percentage of A-to-G editing.

extract_protocol:
Total RNA from zebrafish embryos was extracted using TRIzol (ThermoFisher #15596026).
Sequencing was performed on PCR amplicons of the 3'UTR of Recorder mRNA containing randomized 7-mer motifs. The PCR reaction was carried out to amplify the 3'UTR region of the Recorder mRNA, which includes 7-mer motifs and the Recorder hairpin. Partial Illumina adapters present in the Recorder mRNA are complementary to sections of the i5 and i7 TruSeq Illumina primers, which also contain unique barcodes and sequencing adapters.

tag: genotype


title: Pol2_2hIFNy_rep2

description: Library name: Pol2_2hIFNy_rep2

tag: cell type

tag: strain

tag: chip antibody

tag: treatment

tag: time


title: pSTAT1_2hIFNyIL6_rep2

description: Library name: pSTAT1_2hIFNyIL6_rep2

value: pSTAT1 (Invitrogen, Cat# 33-3400)


title: Pol2_ctrl_rep2

description: Library name: Pol2_ctrl_rep2

value: WT

value: Ctrl


title: 2

description: Library name: 02_S78_

value: T+G


title: 4

description: Library name: 04_S80_


title: ZF_7N_hsaPum2-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_hsaPum2_rep2

value: whole embryo, 6 hpf


title: Pol2_ctrl_rep1

description: Library name: Pol2_ctrl_rep1

value: BMDM

value: RNApol2 (Diagenode, Cat # C15200253)


title: pSTAT3_2hIFNy_rep2

description: Library name: pSTAT3_2hIFNy_rep2

value: pSTAT3 (Cell Signaling Technologies, Cat# 9131)

value: IFNg


title: ET062594

tag: externalsampleid

tag: externalsamplename

value: F

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

tag: col

tag: project

value: female

tag: maxagecaesar

value: Brain


title: IFNγ+Tamoxifen, replicate 3

city: Fort Lauderdale

first: Vladimir

last: Beljanski

state: FL

address: 3300 S. University Drive

department: NSU MD

institute: Nova Southeastern Uni

description: Sample 6c

data_processing:
After the completion of sequencing, raw sequencing data were transformed to FASTQ format using the bcl2fastq2 v2.20 software (Illumina)
FASTQ files were processed through an analysis pipeline using the Partek Flow software (Build version 10.0.22.0424; Partek)
Low-quality reads for either end with Phred quality score below 20 and sequences shorter than 15nt were removed
The trimmed high-quality clean reads were aligned to human genome (Ensembl GRCh38) using Bowtie-1.0.0 allowing one mismatch and up to 3 genomic locations
MicroRNA expression was quantified by counting the number of reads aligning to the miRBase database, release 22.1 (miRBase v22.1)
Normalization and evaluation of miRNAs differential expression was done using R package DESeq2
Assembly: GRCh38
Supplementary files format and content: comma-delimited file includes raw counts for each Sample

source_name: Bone marrow MSC

growth_protocol: MSCs isolated commercially from bone marrow (American Type Culture Collection) were grown using T-182 Flasks until 80-90 % confluence in Mesenchymal Stem Cell Basal Medium supplemented with the growth kit for Adipose, Umbilical and Bone Marrow-derived MSCs (American Type Culture Collection). Serum full media was subsequently replaced with StemXVivo Serum-Free Human MSC Expansion Media (R&D Systems)

extract_protocol:
Exosomes were isolated from serum-free media using Total Exosome Isolation Reagent kit (Invitrogen) based on the manufacturer’s protocol with an increase in centrifuge time from 1 hour to 1.5 hours. Isolated exosomes were subsequently resuspended in 1 mL Takara Lysis Buffer and small RNAs were isolated using NucleoSpin miRNA kit (Takara Bio USA, Inc). The samples were further purified with RNeasy MinElute kit (Qiagen), with an increase in 100% ethanol volume from 250uL to 900uL.
Sequencing libraries were prepared using the Illumina TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol. A total of 6 sequencing libraries per run were pooled and normalized to 2 nM and denatured according to Illumina’s NextSeq System Denature and Dilute Libraries Guide.

treatment_protocol: Serum full media was subsequently replaced with StemXVivo Serum-Free Human MSC Expansion Media (R&D Systems) containing one of the following: CQ (10 mM), TX (5 mM), IFN (500 units), IFN+CQ or IFN+TX. Conditioned media was collected and replaced after 24 h and collected again at 48 h from two separate flasks and combined.

tag: cell line

value: Bone marrow MSC

value: mesenchymal stem cells

value: IFNγ+Tamoxifen


title: IFNγ+Tamoxifen, replicate 2

description: Sample 6b


title: pSTAT3_2hIFNy_rep1

description: Library name: pSTAT3_2hIFNy_rep1


title: ET062587

tag: x

tag: sid

tag: sampletype

value: DNA

tag: age

tag: Sex

tag: tissue

value: Tail

tag: species

value: BW

value: FALSE

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Ear

tag: specieslatinname


title: ZF_1000PREs_drePum1_ADARcd-120pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_Pum1-120_rep1

tag: genotype

value: WT


title: IFNγ+Tamoxifen, replicate 1

description: Sample 6a

tag: cell type

tag: treatment


title: 1

description: Library name: 01_S77_

value: Blood

value: neutrophils

value: T+G


title: ZF_7N_dreG3bp1-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_dreG3bp1_rep3

value: whole embryo, 6 hpf


title: ET062584

tag: externalsampleid

tag: externalsamplename

value: M

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

tag: col

value: male

value: Muscle


title: IFNγ+ Chloroquine, replicate 3

description: Sample 5c

tag: cell line

value: IFNγ+ Chloroquine


title: ZF_7N_dreG3bp1-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_dreG3bp!_rep2


title: ZF_7N_dreG3bp1-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_dreG3bp1_rep1


title: IFNγ+ Chloroquine, replicate 2

description: Sample 5b

value: Bone marrow MSC


title: pSTAT3_ctrl_rep1

description: Library name: pSTAT3_ctrl_rep1

value: BMDM

tag: strain

tag: chip antibody

value: pSTAT3 (Cell Signaling Technologies, Cat# 9131)

value: Ctrl

tag: time


title: ET062583

tag: x

tag: sid

tag: sampletype

value: DNA

tag: age

tag: Sex

tag: tissue

value: Tail

tag: species

tag: project

tag: maxagecaesar

tag: gestationtimeinyears

value: Brain


title: ET062586

tag: externalsampleid

tag: externalsamplename

value: F

value: BW

tag: relatedness

tag: idatsfound

value: FALSE

tag: extbasename

value: female

tag: highmaxagecaesar

value: Bladder

tag: specieslatinname


title: IFNγ+ Chloroquine, replicate 1

description: Sample 5a

tag: cell line

tag: cell type

value: mesenchymal stem cells

tag: genotype

value: WT

tag: treatment


title: pSTAT1_2hIFNy_rep1

description: Library name: pSTAT1_2hIFNy_rep1

tag: strain

tag: chip antibody

value: pSTAT1 (Invitrogen, Cat# 33-3400)

value: IFNg

tag: time


title: ET062585

tag: x

tag: sid

tag: sampletype

tag: age

tag: Sex

value: M

tag: tissue

tag: species

tag: row

tag: col

tag: project

value: male

value: Ear


title: ET062582

tag: externalsampleid

tag: externalsamplename

tag: relatedness

tag: idatsfound

tag: extbasename

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Skin

tag: specieslatinname


title: ZF_7N_hsaPum2-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_hsaPum2_rep1

value: whole embryo, 6 hpf

tag: genotype


title: ZF_7N_dreHnrpnD-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_dreHnrnpD_rep2


title: IFNγ, replicate 2

description: Sample 4b

tag: cell line

value: Bone marrow MSC

tag: cell type

tag: treatment

value: IFNγ


title: ZF_1000PREs_drePum1_ADARcd-30pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_Pum1-30_rep1

tag: tissue


title: pSTAT1_ctrl_rep2

description: Library name: pSTAT1_ctrl_rep2

value: BMDM

tag: strain

tag: chip antibody

value: Ctrl

tag: time


title: IFNγ, replicate 3

description: Sample 4c


title: ET062580

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

value: DNA

tag: age

tag: Sex

value: Tail

tag: species

value: BW

tag: row

tag: col

tag: project

value: Muscle


title: IFNγ, replicate 1

description: Sample 4a

tag: cell line

value: mesenchymal stem cells

tag: genotype


title: pSTAT3_ctrl_rep2

description: Library name: pSTAT3_ctrl_rep2

tag: cell type

value: pSTAT3 (Cell Signaling Technologies, Cat# 9131)

value: WT

tag: treatment


title: ZF_7N_dreHnrpnD-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_dreHnrnpD_rep3

tag: tissue


title: ET06258

tag: externalsamplename

tag: relatedness

tag: idatsfound

value: FALSE

tag: extbasename

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

tag: specieslatinname


title: ZF_7N_dreHnrnpD-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_dreHnrnpD_rep1


title: pSTAT1_2hIFNy_rep2

description: Library name: pSTAT1_2hIFNy_rep2

tag: strain

tag: chip antibody

value: pSTAT1 (Invitrogen, Cat# 33-3400)

value: IFNg

tag: time


title: ZF_7N_drePurb-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_drePurb_rep3


title: pSTAT1_ctrl_rep1

description: Library name: pSTAT1_ctrl_rep1


title: WT_IL6_2h_rep2

description: Library name: WT_IL6_2h_rep2

value: BMDMs


title: ET062581

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

tag: age

tag: Sex

value: F

tag: species

tag: row

tag: col

tag: project

value: female


title: ZF_7N_drePurb-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_drePurb_rep2

tag: tissue

value: whole embryo, 6 hpf

tag: genotype


title: WT_IL6_2h_rep1

description: Library name: WT_IL6_2h_rep1

tag: cell type

tag: treatment


title: Tamoxifen, replicate 3

description: Sample 3c

tag: cell line

value: Bone marrow MSC

value: Tamoxifen


title: Tamoxifen, replicate 2

description: Sample 3b


title: ET062579

tag: externalsamplename

tag: relatedness

tag: idatsfound

tag: extbasename

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Brain

tag: specieslatinname


title: ZF_7N_drePurb-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_drePurb_rep1


title: ZF_7N_dreHuR-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_dreHuR_rep3


title: WT_IFNg_2h_rep2

description: Library name: WT_IFNg_2h_rep2

tag: strain

tag: time


title: ET062577

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

value: DNA

tag: age

tag: Sex

tag: species

tag: row

tag: col

value: Ear


title: ET062576

tag: externalsamplename

value: M

tag: tissue

value: Tail

value: BW

tag: relatedness

tag: idatsfound

tag: project

value: male

value: Bladder


title: ZF_7N_dreHuR-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_dreHuR_rep2

tag: genotype

value: WT


title: WT_Ctrl_2h_rep2

description: Library name: WT_Ctrl_2h_rep2

tag: cell type

tag: strain

tag: treatment

value: Ctrl


title: WT_IFNg_2h_rep1

description: Library name: WT_IFNg_2h_rep1

value: IFNg

tag: time


title: ZF_7N_dreHuR-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_dreHuR_rep1


title: Chloroquine, replicate 2

description: Sample 2b

tag: cell line

value: mesenchymal stem cells

value: Chloroquine


title: WT_Ctrl_2h_rep1

description: Library name: WT_Ctrl_2h_rep1

value: BMDMs


title: ET062575

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

value: F

value: FALSE

tag: extbasename

value: female

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Fibroblast

tag: specieslatinname


title: Chloroquine, replicate 1

description: Sample 2a

value: Bone marrow MSC


title: ET062574

tag: externalsamplename

value: DNA

tag: age

tag: Sex

tag: tissue

tag: species

tag: relatedness

tag: idatsfound

tag: row

tag: col

value: Adipose


title: ZF_7N_hsaHuR-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_hsaHuR_rep2

value: whole embryo, 6 hpf

tag: genotype


title: STAT3KO_IFNg_2h_rep2

description: Library name: STAT3KO_IFNg_2h_rep2

tag: cell type

tag: strain

tag: treatment

tag: time


title: STAT3KO_IFNg_2h_rep1

description: Library name: STAT3KO_IFNg_2h_rep1


title: ZF_7N_hsaHuR-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_hsaHuR_rep3


title: No treatment, replicate 3

description: Sample 1c

tag: cell line


title: No treatment, replicate 2

description: Sample 1b


title: STAT3KO_Ctrl_2h_rep2

description: Library name: STAT3KO_Ctrl_2h_rep2


title: No treatment, replicate 1

description: Sample 1a


title: ZF_7N_hsaHuR-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_hsaHuR_rep1


title: Chloroquine, replicate 3

description: Sample 2c


title: ET062573

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

value: Tail

value: BW

tag: extbasename

tag: project

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Brain


title: ET062578

tag: externalsamplename

tag: age

tag: Sex

value: M

tag: tissue

tag: species

tag: relatedness

tag: idatsfound

tag: row

value: male

value: Ear

tag: specieslatinname


title: ZF_7N_dreCth1-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_dreCth1_rep3

tag: genotype

value: WT


title: Tamoxifen, replicate 1

description: Sample 3a

tag: cell line

tag: cell type

value: mesenchymal stem cells

tag: treatment

value: Tamoxifen


title: ET062572

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

value: F

tag: extbasename

tag: col

tag: project

value: Muscle


title: STAT3KO_Ctrl_2h_rep1

description: Library name: STAT3KO_Ctrl_2h_rep1

value: BMDMs

tag: strain

value: Ctrl

tag: time


title: ET062571

tag: externalsamplename

tag: age

tag: Sex

tag: tissue

tag: species

tag: relatedness

value: FALSE

value: female

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar


title: ET062570

tag: x

tag: sid

value: DNA

tag: idatsfound

tag: row

tag: specieslatinname


title: ZF_7N_dreCth1-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_dreCth1_rep2

value: whole embryo, 6 hpf

tag: genotype


title: ET06257

tag: externalsampleid

tag: sampletype

value: Tail

tag: extbasename

tag: col

tag: project


title: STAT3WT_IFNg_2h_rep2

description: Library name: STAT3WT_IFNg_2h_rep2

tag: cell type

tag: strain

tag: treatment

value: IFNg

tag: time


title: ZF_7N_dreCth1-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_dreCth1_rep1

tag: tissue


title: ET062569

tag: externalsamplename

tag: age

tag: Sex

tag: species

value: BW

tag: relatedness

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar

value: Brain


title: STAT3WT_IFNg_2h_rep1

description: Library name: STAT3WT_IFNg_2h_rep1

tag: genotype


title: STAT3WT_Ctrl_2h_rep2

description: Library name: STAT3WT_Ctrl_2h_rep2


title: STAT3WT_Ctrl_2h_rep1

description: Library name: STAT3WT_Ctrl_2h_rep1


title: E. crypticus_WELGRO 1000 21days_ replicate3

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 1000 mg WELGRO/kg soil for 21 days

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts

tag: developmental stage


title: ZF_7N_N22-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_N22_rep3


title: ZF_7N_N22-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_N22_rep2


title: ZF_7N_N22-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_N22_rep1


title: STAT1KO_IFNg_2h_rep2

description: Library name: STAT1KO_IFNg_2h_rep2


title: STAT1KO_IFNg_2h_rep1

description: Library name: STAT1KO_IFNg_2h_rep1


title: ET062567

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

tag: idatsfound

tag: extbasename

tag: row

tag: col

value: Adipose

tag: specieslatinname


title: ZF_7N_dreYbx1-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_dreYbx1_rep2

tag: tissue

value: WT


title: E. crypticus_WELGRO 1000 21days_ replicate2

value: Adult organisms with well developed clitellum


title: STAT1KO_Ctrl_2h_rep2

description: Library name: STAT1KO_Ctrl_2h_rep2

tag: cell type

tag: strain

tag: treatment

tag: time


title: ZF_7N_dreYbx1-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_dreYbx1_rep1


title: ET062565

tag: externalsamplename

tag: age

tag: Sex

value: M

tag: species

tag: relatedness

tag: project

value: male

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar


title: ET062568

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

value: F

tag: idatsfound

tag: extbasename

tag: row


title: ET062566

tag: tissue

tag: col

value: Cerebellum

tag: specieslatinname


title: ZF_7N_dreYbx1-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_dreYbx1_rep3

tag: genotype


title: STAT1KO_Ctrl_2h_rep1

description: Library name: STAT1KO_Ctrl_2h_rep1

tag: cell type

value: BMDMs

tag: strain

tag: treatment

value: Ctrl

tag: time


title: STAT1WT_IFNg_2h_rep2

description: Library name: STAT1WT_IFNg_2h_rep2


title: ZF_7N_drePCBP2-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_drePCBP2_rep2


title: STAT1WT_IFNg_2h_rep1

description: Library name: STAT1WT_IFNg_2h_rep1


title: E. crypticus_WELGRO 500 21days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 500 mg WELGRO/kg soil for 21 days

tag: developmental stage


title: E. crypticus_WELGRO 100 21days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 100 mg WELGRO/kg soil for 21 days


title: E. crypticus_WELGRO 500 21days_ replicate1


title: ET062562

tag: externalsamplename

tag: age

tag: Sex

tag: species

tag: relatedness

value: FALSE

tag: project

tag: maxagecaesar

tag: gestationtimeinyears

tag: highmaxagecaesar


title: ET062564

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

value: DNA

tag: tissue

tag: idatsfound

tag: extbasename

tag: row

tag: col

value: Bladder


title: ZF_7N_drePCBP2-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_drePCBP2_rep1

value: whole embryo, 6 hpf

tag: genotype


title: STAT1WT_Ctrl_2h_rep2

description: Library name: STAT1WT_Ctrl_2h_rep2

tag: cell type

tag: strain

tag: treatment

tag: time


title: E. crypticus_WELGRO 500 21days_ replicate2

tag: developmental stage


title: E. crypticus_WELGRO 100 21days_ replicate2


title: ZF_7N_dreHnrpa0a-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_dreHnrpA0a_rep3


title: STAT1WT_Ctrl_2h_rep1

description: Library name: STAT1WT_Ctrl_2h_rep1


title: ZF_7N_drePCBP2-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_drePCBP2_rep3


title: ZF_7N_dreHnrpa0a-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_dreHnrpA0a_rep2


title: ZF_7N_dreHnrpa0a-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_dreHnrpA0a_rep1


title: ET06256

tag: externalsamplename

tag: age

tag: Sex

value: Tail

tag: species

tag: relatedness

tag: project

value: female

tag: maxagecaesar

tag: gestationtimeinyears

value: Muscle

tag: specieslatinname


title: PTR_root_rna_rep3

city: Kunming

first: Dingjie

last: Wang

state: Yunnan

address: NO. 132 Lanhei Road

country: China

institute: Kunming Institute of Botany, Chinese Academy of Sciences

description: Unstranded library was prepared using VAHTS Universal V6 RNA-seq Library Prep Kit and sequenced using Illumina NovaSeq 6000

data_processing:
For transcriptomes data used in this study, reads were first cleaned using fastp v0.12.4.
Cleaned reads were then aligned to respective genomes with the same version used in SP57 using HISAT2 v2.2.1 with parameters " --mp 3,1" for normal libraries, and "--mp 3,1 --rna-strandness RF" for stranded libraries.
Abundance were esitmated using StringTie2 v2.1.4. Differential expressed genes were identified using DESeq2 v1.34.0 with at least two-fold expression change and Benjamini-Hochberg adjusted p value < 0.05 (Wald test).
Upregulated genes in treatments were retained and used in further analysis.
Assembly: Coriaria nepalensis (GWHESFM00000000); Elaeagnus umbellata (GWHESFO00000000); Alnus trabeculosa (GWHESFN00000000); Chamaecrista pumila (GWHESFQ00000000); Mimosa pudica (ASM325494v1); Populus trichocarpa (P.trichocarpa_v4.1, Populus deltoides x Populus euramericana use this)
Assembly: We have uploaded the newly assembled genomes to NGDC (https://ngdc.cncb.ac.cn/gwh/) and they will be released before March 2, 2025.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Populus deltoides x Populus x canadensis

source_name: root

extract_protocol:
Fresh roots, and nodules if available were gathered from Coriaria nepalensis, Elaeagnus umbellata, Alnus trabeculosa,  Chamaecrista pumila, and Mimosa pudica subsequently froeezed in liquid nitrogen. RNA was extracted using the Trizol (Invitrogen, USA).  For mycorrhizal inoculation of Populus deltoides × P. euramericana cv. ‘‘Nanlin895’’, three cm terminal cuttings were taken from 4-week-old Populus plants and rooted for two weeks in Lloyd & McCown's woody plant medium supplemented with 20 g L-1 sucrose and 5 µM indole-3-butyric acid (Sigma Aldrich). Rooted plants were transplanted to a mixture of vermiculite, sand, and perlite (3 : 1 : 1) containing Rhizophagus irregularis spores and cultured in phytotron with 12 h photoperiod at 25 °C constant temperature. The spores were produced by co-culturing R. irregularis with leeks and diluted to a final concentration of 400 spores per plant 11. The roots of AM-colonized and non-colonized Populus plants were harvested after 8 week post-inoculation and subsequently powdered in liquid nitrogen. Total RNA was extracted using the TRIzol reagent (Invitrogen, USA), three biological replicates were used for each sample.
For roots and nodules samples, rRNAs were first depleted from total RNA using Ribo-off rRNA Depletion Kit (Vazyme, Cat. No.: N409-02). Stranded library was then prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Cat. No.: NR604-01) and sequenced using Illumina NovaSeq 6000 by Frasergen Bioinformatics Co., Ltd. (Wuhan, China).  For mycorrhizal inoculation of Populus deltoides × P. euramericana cv. ‘‘Nanlin895’’, unstranded libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions and sequenced with Illumina NovaSeq 6000 by OE Biotech Co., Ltd. (Shanghai, China).

tag: tissue

value: root


title: E. crypticus_WELGRO 100 21days_ replicate1

value: Whole body extracts


title: ET062560

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

value: BW

tag: idatsfound

tag: extbasename

tag: row

tag: col

tag: highmaxagecaesar


title: ZF_7N_dreAgo2-ADARcd-amanitin_rep_3 (RBPscan)

description: Library name: ZF_7N_dreAgo2ama_rep3

tag: genotype

value: WT


title: PTR_root_rna_rep4


title: E. crypticus_Control 21days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: un-spiked soil for 21 days

tag: developmental stage


title: ET062559

tag: externalsamplename

tag: age

tag: Sex

value: M

tag: species

tag: relatedness


title: ET062561

tag: tissue

tag: project

tag: maxagecaesar

tag: gestationtimeinyears

value: Brain

tag: specieslatinname


title: ZF_7N_dreAgo2-ADARcd-amanitin_rep_2 (RBPscan)

description: Library name: ZF_7N_dreAgo2ama_rep2


title: E. crypticus_Control 21days_ replicate2

value: Adult organisms with well developed clitellum


title: PTR_root_rna_rep2


title: E. crypticus_WELGRO 1000 2days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 1000 mg WELGRO/kg soil for 2 days


title: ET062558

tag: x

tag: sid

tag: externalsampleid

tag: sampletype

tag: idatsfound

value: male

value: Fibroblast


title: E. crypticus_WELGRO 1000 21days_ replicate1


title: ZF_7N_dreAgo2-ADARcd-amanitin_rep_1 (RBPscan)

description: Library name: ZF_7N_dreAgo2ama_rep1

tag: genotype


title: E. crypticus_Control 21days_ replicate1

tag: developmental stage


title: ET062556

tag: externalsamplename

tag: extbasename

tag: row

tag: col

tag: highmaxagecaesar

value: Adipose


title: ET062557

tag: age

tag: Sex

value: F

tag: tissue

tag: species

tag: relatedness

value: FALSE

value: Ear


title: PTR_AM_root_rna_rep4

source_name: arbuscular mycorrhizal root

value: arbuscular mycorrhizal root


title: ZF_7N_dreAgo2-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_dreAgo2_rep3

value: whole embryo, 6 hpf


title: E. crypticus_WELGRO 500 2days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 500 mg WELGRO/kg soil for 2 days


title: E. crypticus_WELGRO 1000 2days_ replicate1


title: E. crypticus_WELGRO 1000 2days_ replicate2


title: ET062555

tag: x

value: DNA

value: Tail

tag: project

value: female

tag: maxagecaesar

tag: gestationtimeinyears

tag: specieslatinname


title: PTR_AM_root_rna_rep3


title: E. crypticus_WELGRO 500 2days_ replicate2

value: Whole body extracts


title: ET062554

tag: sid

tag: externalsampleid

tag: sampletype

value: BW

tag: idatsfound


title: ET062563

tag: externalsamplename

tag: extbasename

tag: row


title: PTR_root_rna_rep1

value: root


title: PTR_AM_root_rna_rep2


title: ZF_7N_dreAgo2-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_dreAgo2_rep1

tag: genotype

value: WT


title: ZF_7N_drePum1-ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_drePum1_rep3


title: E. crypticus_WELGRO 500 2days_ replicate1

tag: developmental stage


title: ET062552

tag: age

tag: Sex

value: M

tag: tissue

tag: col

tag: highmaxagecaesar

value: Brain


title: PTR_AM_root_rna_rep1


title: MP_nodule_rna_rep3

description: rRNA was first depleted from total RNA using Ribo-off rRNA Depletion Kit (Vazyme, Cat. No.: N409-02). Stranded library was then prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Cat. No.:NR604-01 ) and sequenced using Illumina NovaSeq 6000

organism: Mimosa pudica

source_name: nodule

value: nodule


title: ZF_7N_drePum1-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_drePum1_rep2


title: ZF_7N_drePum1-ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_drePum1_rep1


title: E. crypticus_WELGRO 100 2days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: 100 mg WELGRO/kg soil for 2 days


title: E. crypticus_WELGRO 100 2days_ replicate2

value: Adult organisms with well developed clitellum


title: ZF_7N_dreAgo2-ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_dreAgo2_rep2


title: ET062550

tag: x

tag: species

tag: relatedness

tag: project

value: male

tag: maxagecaesar


title: ZF_7N_ADARcd_rep_3 (RBPscan)

description: Library name: ZF_7N_dreADARcd_rep3


title: MP_nodule_rna_rep1


title: MP_root_rna_rep2


title: ET062551

tag: sid

tag: externalsampleid

tag: sampletype

value: F

tag: gestationtimeinyears

value: Lung

tag: specieslatinname


title: 9

description: Library name: 24058XR-02-09

data_processing:
Preprocessing was done using Trimmomatic and ambient ribosomal RNA was filtered using sortMERNA. Transcriptome alignments were conducted using the Salmon  tool with its standard parameters. The R software (version 4.2.1) and DESeq2 package.
Assembly: mm10
Supplementary files format and content: salmon quant files

source_name: Lung

tag: cell type

value: neutrophils

tag: treatment

value: Veh


title: 10

description: Library name: 24058XR-02-10


title: MP_nodule_rna_rep2


title: ZF_7N_ADARcd_rep_2 (RBPscan)

description: Library name: ZF_7N_dreADARcd_rep2

value: whole embryo, 6 hpf

tag: genotype


title: MP_root_rna_rep3


title: E. crypticus_Control 2days_ replicate3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: un-spiked soil for 2 days

tag: developmental stage


title: MP_root_rna_rep1

tag: tissue


title: 8

description: Library name: 24058XR-02-08


title: ZF_7N_ADARcd_rep_1 (RBPscan)

description: Library name: ZF_7N_dreADARcd_rep1


title: Eu_nodule_rna_rep3

organism: Elaeagnus umbellata


title: ZF_Control_NORAD_rep_2 (RBPscan)

description: Library name: ZF_NORAD_rep2

data_processing:
paired-end reads were merged using the BBMap suite.
Counting of A-to-G conversions in Recorder mRNA associated with specific NORAD fragments was conducted using a custom Python script.
Assembly: N/A.
Supplementary files format and content: A CSV file containing sequences of NORAD fragments (Motifs) and associated metrics was generated, including occurrence, number of edited reads, total number of A-to-G edits, total number of reads in the library for all motifs, and the percentage of A-to-G editing.

extract_protocol:
Total RNA from zebrafish embryos or HEK293T cells was extracted using TRIzol (ThermoFisher #15596026).
Sequencing was performed on PCR amplicons of the 3'UTR of Recorder mRNA containing NORAD RNA tiling fragments. The PCR reaction was carried out to amplify the 3'UTR region of the Recorder mRNA, which includes NORAD fragments and the Recorder hairpin. Partial Illumina adapters present in the Recorder mRNA are complementary to sections of the i5 and i7 TruSeq Illumina primers, which also contain unique barcodes and sequencing adapters.


title: 7

description: Library name: 24058XR-02-07


title: E. crypticus_WELGRO 100 2days_ replicate1


title: ET062553

tag: externalsamplename

value: DNA

tag: age

tag: Sex

tag: idatsfound

value: FALSE

tag: extbasename

tag: row

tag: col

value: Fibroblast


title: 6

description: Library name: 24058XR-02-06


title: Eu_nodule_rna_rep1


title: 5

description: Library name: 24058XR-02-05

value: T+G


title: E. crypticus_Control 2days_ replicate2

value: Whole body extracts


title: ZF_ADARcd_NORAD_rep_3 (RBPscan)

description: Library name: ZF_NORAD_ADARcd_rep3


title: ET06255

tag: x

tag: sid

value: Tail

tag: species

value: BW

tag: relatedness

tag: project

value: female

tag: maxagecaesar

tag: highmaxagecaesar

value: Cerebellum


title: Eu_root_rna_rep3

value: root


title: 4

description: Library name: 24058XR-02-04

tag: cell type

tag: treatment


title: ZF_Control_NORAD_rep_3 (RBPscan)

description: Library name: ZF_NORAD_rep3

tag: tissue

tag: genotype

value: WT


title: ZF_ADARcd_NORAD_rep_2 (RBPscan)

description: Library name: ZF_NORAD_ADARcd_rep2


title: ZF_Control_NORAD_rep_1 (RBPscan)

description: Library name: ZF_NORAD_rep1


title: ET062549

tag: externalsampleid

tag: externalsamplename

tag: sampletype

tag: age

tag: gestationtimeinyears

value: Adipose

tag: specieslatinname


title: E. crypticus_Control 2days_ replicate1

tag: developmental stage

value: Adult organisms with well developed clitellum


title: Eu_root_rna_rep2


title: 3

description: Library name: 24058XR-02-03

value: Lung


title: Eu_nodule_rna_rep2

value: nodule


title: Eu_root_rna_rep1


title: ET062548

tag: x

tag: sid

tag: Sex

value: F

tag: idatsfound

tag: extbasename

tag: row

tag: col

value: Ear


title: ET062547

value: DNA

value: M

tag: species

tag: relatedness

tag: project

value: male

tag: maxagecaesar

tag: highmaxagecaesar

value: Muscle


title: ZF_hsaPum2-ADARcd_NORAD_rep_3 (RBPscan)

description: Library name: ZF_NORAD_hsaPum2_rep3

tag: tissue

value: whole embryo, 6 hpf

tag: genotype


title: 2

description: Library name: 24058XR-02-02

tag: cell type

value: neutrophils

tag: treatment

value: T+G


title: 1

description: Library name: 24058XR-02-01


title: ET062546

tag: externalsampleid

tag: externalsamplename

tag: sampletype

tag: age

value: Tail

value: BW

value: FALSE

tag: gestationtimeinyears

tag: specieslatinname


title: ET062545

tag: x

tag: sid

tag: Sex

tag: idatsfound

tag: extbasename

tag: row

value: female


title: ET062544

tag: species

tag: relatedness

tag: col

tag: project

tag: maxagecaesar

tag: highmaxagecaesar


title: ET062543

tag: externalsampleid

tag: externalsamplename

tag: tissue


title: ZF_hsaPum2-ADARcd_NORAD_rep_2 (RBPscan)

description: Library name: ZF_NORAD_hsaPum2_rep2

tag: genotype

value: WT


title: ET062542

tag: sampletype

tag: age

tag: gestationtimeinyears

tag: specieslatinname


title: ET062540

tag: x

tag: sid

tag: Sex

tag: idatsfound


title: ZF_ADARcd_NORAD_rep_1 (RBPscan)

description: Library name: ZF_NORAD_ADARcd_rep1


title: ZF_drePum1-ADARcd_NORAD_rep_3 (RBPscan)

description: Library name: ZF_NORAD_drePum1_rep3


title: ET062541

tag: species

tag: relatedness

tag: extbasename

tag: row

value: Adipose


title: ET062539

tag: col

tag: project

tag: maxagecaesar

tag: highmaxagecaesar


title: scRNA-seq of Schisotosoma joponicum:22dpi Female

city: Shanghai

first: SHAOYUN

last: CHENG

address: Songhu Road 2005

department: Department of Microbiology and Microbial Engineering, School of Life Science

institute: Fudan University

description: Library name: Sj_22dpi_female

data_processing:
Raw data was processed and mapped to the Schistosoma japonicum genome (v3) using the Cell Ranger 3.0.0 (10× Genomics) pipeline.
Assembly: SjV3
Supplementary files format and content: h5 files for counts

organism: Schistosoma japonicum

source_name: whole organism

growth_protocol: Twenty female C57 mice were infected percutaneously through the abdomen with 80–200 cercariae. At each time point (14, 18, 22, and 26 dpi), four mice were sacrificed for the recovery of schistosomes

extract_protocol:
Worms were collected from mice by perfusing the hepatic portal vein with 4℃ PBS (Sangon Biotech) and then rinsed in twice in DMEM (5% FBS) (Cheng et al., 2024; Luo et al., 2022; Wang et al., 2017; You et al., 2024). Freshly perfused male and female worms, except 14 dpi worms, which are difficult to distinguish gender under a light microscope, were separated by incubation in a 0.25% solution of tricaine for approximately 5 min. FACS sorting was performed as previously described with minor modifications. Worms were washed twice in 8 mL PBS, then triturated for approximately 15 min in 4 mL 0.125% Trypsin-EDTA (in PBS) until the solution became turbid and no large pieces of worms were left. The trypsin was inactivated by adding an 8 mL 10% FBS DMEM. The dissociated worms were then centrifuged at 500 g for 10 min at 4°C. Next, the worm cells were resuspended in 1 mL of PBS with 10 μL of RQ1 DNAse (Promega M6101) and incubated for 10 min at RT. The worm cells were centrifuged again at 500 g for 10 minutes at 4°C. Then the worm cells were resuspended in 1mL of PBS containing Fixable Viability Dye eFluorTM 506 (1μL/mL) (eBioscience) and incubated for 30 min at 4℃ in the dark. The worm cell suspension was centrifuged at 500 g for 10 minutes at 4°C, then washed twice in PBS, then filtered through a 40 μm cell strainer into a 12×75 mm FACS tube. Filtered cells were then sorted on a MoFlo XDP High-Speed Cell Sorter (BECKMAN COULTER) with 405/460/488/532/561/640nm lasers. Sorts were performed with a 100 μm nozzle, and cells were sorted into sorting media (0.04% BSA in PBS, pH = 7.40).
FACS-sorted cells were centrifuged at 500 g for 10 minutes at 4°C and then resuspended in 0.04% BSA in PBS. Libraries were created using a Chromium Controller (10× Genomics) according to manufacturer guidelines and sequenced using a NovaSeq6000 (Illumina) to generate 150-bp paired-end reads.

tag: tissue

value: whole organism


title: scRNA-seq of Schisotosoma joponicum:26dpi Male

description: Library name: Sj_26dpi_male


title: scRNA-seq of Schisotosoma joponicum:26dpi Female

description: Library name: Sj_26dpi_female


title: ET06254

tag: externalsampleid

tag: externalsamplename

tag: sampletype


title: ZF_hsaPum2-ADARcd_NORAD_rep_1 (RBPscan)

first: Dmitry

last: Kretov

institute: CRCHU de Québec - Université Laval

description: Library name: ZF_NORAD_hsaPum2_rep1

tag: genotype


title: HA and LPS+IFNg treated, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: lps.if.HA.3

data_processing:
RNA-seq data were aligned using bowtie2 algorithm against mm10 mouse genome version and RSEM v1.2.12 software was used to estimate read counts using Ensemble transcriptome version GRCm38.89
Assembly: mm10
Supplementary files format and content: text file of counts

extract_protocol:
Total RNA was extracted from BMDMs using RNeasy Plus Mini Kit (Qiagen, 74136)
Libraries were prepared using Illumina Stranded mRNA Prep kit (500 ng DNase1 treated total RNA was used)

tag: cell type

value: BMDM

tag: ha

value: yes


title: scRNA-seq of Schisotosoma joponicum:22dpi Male

description: Library name: Sj_22dpi_male


title: HA and LPS+IFNg treated, replicate 2

description: Library name: lps.if.HA.2


title: COR_nodule_rna_rep2

organism: Coriaria nepalensis

value: nodule


title: LPS+IFNg treated, replicate 2

description: Library name: lps.if.2

value: no


title: LPS+IFNg treated, replicate 1

description: Library name: lps.if.1


title: HA treated, replicate 3

description: Library name: HA.3


title: COR_nodule_rna_rep1


title: HA and LPS+IFNg treated, replicate 1

description: Library name: lps.if.HA.1


title: ET062538

tag: x

tag: sid

value: DNA

tag: age

tag: Sex

value: M

tag: gestationtimeinyears

tag: specieslatinname


title: ZF_drePum1-ADARcd_NORAD_rep_2 (RBPscan)

description: Library name: ZF_NORAD_drePum1_rep2


title: LPS+IFNg treated, replicate 3

description: Library name: lps.if.3


title: ZF_drePum1-ADARcd_NORAD_rep_1 (RBPscan)

description: Library name: ZF_NORAD_drePum1_rep1


title: scRNA-seq of Schisotosoma joponicum:18dpi Male

description: Library name: Sj_18dpi_male


title: ET062535

value: F

tag: species

tag: relatedness

tag: idatsfound

tag: extbasename

tag: row

tag: col

value: Brain