city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

description:
Library name: RasmussenEncephalitisHC_NeuNpos_Patient2
nuclei from neuronal (NeuN positive) sorted population from hippocampal resections

data_processing:
R1 reads were used to identify both cell barcodes and UMI using UMI-tools version 1.0.1 with the following settings: “--bc-pattern='(?P<cell_1>.{16})(?P<umi_1>.{12})' --extract-method=regex --knee-method=distance --method=umis --set-cell-number=15000 –ed-above-threshold=discard”
After read extraction and addition of cell barcodes and UMI to headers of R2 reads, fastq reads were mapped to the ENSEMBL reference genome using STAR version 2.7.1a with standard settings except that any reads mapping to more than one location in the genome (ambiguous reads) were discarded (m = 1)
All reads mapping in the proper orientation within exons and introns were reported using featureCounts version 1.6.4 UMI counts were calculated using UMI-tools with ‘--per gene --gene-tag=XT --assigned-status-tag=XS --per-cell’ arguments.
Assembly: GRCh38.96
Supplementary files format and content: Tab-separated table of gene counts per cell barcode

source_name: Brain

extract_protocol:
To perform single nuclear RNA-seq, we FAN-sorted nuclei from . Each sample represents 10000   sorted nuclei. sorted nuclei were adjusted to 5.5x105 cells/mL of PBS, 0.04% BSA before proceeding with droplet generation.
Library was performed according to the manufacter's instructions Chromium Next GEM Single Cell 3ʹ Kit v3.1 (CG000204)

value: Brain

value: neuronal  population


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous, biol rep 2

status: Public on Dec 23 2025

type: SRA

city: Brussels

first: Yue

last: Tong

state: Brussels

address: Route de Lennik, 808

country: Belgium

institute: Université Libre de Bruxelles

description:
Library name: R6C_IPSBETA_MACS_HOM_2
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads

library_source: transcriptomic

data_processing:
Raw read quality was assessed using FastQC (v0.12.1)
Low-quality reads and adapter sequences were removed using fastp (v0.23.2)
Salmon (v1.10.3) was used to quantify filtered raw reads using pseudo-alignment on the transcriptome reference derived from GRCh38 primary assembly (Genecode version 46).
Assembly: GRCh38
Supplementary files format and content: Salmon quantification file with .sf extention, tab separated. Headers: Name (of transcripts), Length, EffectiveLength, TPM, NumReads. Each row represents one transcript.

molecule: total RNA

organism: Homo sapiens

source_name: pancreatic differentiation

growth_protocol: The iPSC cell lines: ULBi012.31 (this study), ULBi012.8 (this study), ULBi012.31 CR3 (this study), ULBi012.31 CR41 (this study) were cultured in Matrigel-coated plates (Corning, BDAA356231) in E8 medium as described (PMID: 30247717). The 7-stage differentiation into ß-cells was done as described (PMID: 36060810) (PMID: 30247717). Cells were seeded at 2.5 × 106 cells per 3.5 cm diameter well in E8 medium containing 10 μM ROCK inhibitor (StemCell Technologies, 72304, Y-27632). Differentiation was started 24 hours later. After reaching the pancreatic progenitor stage (stage 4), cells were plated in microwell plates at 900 cells per microwell (AggreWell400, StemCell Technologies, 34411) to allow islet-like aggregate formation until 1 week into stage 7.

extract_protocol:
Total RNA from MACS-purified iPSC-ß cells was isolated using the RNeasy Plus Micro kit (Qiagen, 74034). RNA concentration and integrity were measured using the Bioanalyzer RNA 6000 Nano assay (Agilent, 5067-1511) on the Agilent 2100 Bioanalyzer.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7760L) for samples sequenced by Illumina NovaSeq6000 and Novogene NGS Stranded RNA Library Prep Set (Novogene, PT044) for samples sequenced by Illlumina NovaSeq X Plus. Paired-end sequencing (2x151bp) was performed at 200 million reads.

tag: tissue

value: pancreatic differentiation

tag: cell line

tag: cell type

value: human induced pluripotent stem cell derived pancreatic beta-like cell aggregates

tag: genotype

value: homozygous INS c.16C>T

tag: batch


description:
Library name: RasmussenEncephalitisHC_NeuNpos_Patient1
nuclei from neuronal (NeuN positive) sorted population from hippocampal resections

library_source: transcriptomic single cell

molecule: nuclear RNA


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-F17

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain

tag: age

value: 8 weeks

tag: brain region

value: FC

tag: gender

value: M


title: Jurkat EZH2-KO C9 3

city: Dublin

first: Jonathan

last: Bond

address: Belfield

country: Ireland

institute: Systems Biology Ireland, UCD

data_processing:
.fq files were QC assesed using FASTQC
Reads were pseudoaligned using kallisto
TPM values were used for downstream analysis
Assembly: hg38
Supplementary files format and content: .tsv

source_name: Jurkat

extract_protocol:
RNA was extracted from 3-5 million cells using the RNAeasy kit (Qiagen, 74104). Three independent RNA extractions were performed at serial passages for all cell lines to provide biological replicates. Extracted RNA was snap-frozen in liquid nitrogen and stored at -80C. RNA quality was assessed in-house using a Bioanalyzer (Agilent 2100 Bioanalyzer) prior to submission for sequencing.
Performed by Novogene

value: Jurkat

value: EZH2-KO (C9)


title: Jurkat EZH2-KO C9 2


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-E6


title: Jurkat EZH2-KO C9 1


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-E18


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-E5


title: Jurkat EZH2-KO A7 3

value: EZH2-KO (A7)


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13_D31_2

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: C13_D31_2
bulk RNA-seq (Singleron)

data_processing:
Raw sequencing data (fastq files) were demultiplexed, mapped to the human genome (GRCh38) and quantified by Singleron using the AccuraCode (v1.2.0) pipeline.
Assembly: GRCh38
Supplementary files format and content: Gene level count matrix of all samples combined samples

molecule: polyA RNA

growth_protocol: Two protocols were used to generate neural progenitor cells (iNPCs) and neurons (iNEU) from iPSCs as indicated in the sample metadata. A protocol used by the lab of Dean Nizetic (DN), based on the Gibco protocol (Thermo Fisher Scientific, MAN0008031), and protocol based on neurospheres developed by Su-Chun Zhang (SCZ; Wang et al., 2023). For the DN protocol, NPCs  between passages 6 and 10 were expanded in Geltrex-coated 6-well culture plates prepared by diluting a 60 μL Geltrex aliquot in 6 mL cold DMEM/F12, incubated at 37°C for at least 60 minutes. Cells were thawed, centrifuged at 300 × g for 5 minutes, and resuspended in Neural Expansion Medium (NEM) with 5 μM ROCK inhibitor Y27632 (STEMCELL Technologies) at a density of 1-2 million cells per well. Media changes were performed the next day with complete NEM, and then changed every other day thereafter. For neuronal differentiation, NPCs were dissociated with Accutase (Thermo Fisher Scientific) and seeded onto Poly-L-ornithine/Laminin-coated 24-well culture plates at a density of 70,000 cells per well in NEM with 5 μM Y27532. Media change was performed the next day with complete BrainPhys Neuronal Medium (STEMCELL Technologies), and then changed every four days for two weeks. After which, BrainPhys Neuronal Medium is supplemented with 2 μg/mL Laminin for media changes every four days till the desired experimental endpoint. For the SCZ protocol, iPSCs were transitioned to Neural Differentiation Medium (NDM), consisting of a 1:1 mixture of DMEM/F12 (Thermo Fisher Scientific) and Neurobasal medium (Thermo Fisher Scientific) supplemented with 1× GlutaMAX (Thermo Fisher Scientific), 0.5× N2 (STEMCELL Technologies), 0.5× B27 (STEMCELL Technologies), 100 μM ascorbic acid (Sigma-Aldrich). On the next day, dual SMAD inhibition was initiated by supplementing NDM with 10 μM SB431542 (Tocris) and 2 μM DMH1 (Tocris). Cells were cultured for seven days with daily medium changes. Cells were then dissociated with Versene and transferred to low attachment flasks in NDM supplemented with 10 ng/mL basic fibroblast growth factor (bFGF, STEMCELL Technologies) and 0.5 μM Thiazovivin to promote neurosphere formation. Neurospheres were maintained with medium changes every three days until the experimental endpoint. To differentiate neurons, neurospheres were dissociated using TrypLE (Thermo Fisher Scientific) and seeded onto Poly-L-ornithine/Laminin-coated 24-well culture plates at a density of 70,000 cells per well in Neuron Medium, composed of Neurobasal medium supplemented with 1× GlutaMAX, 1× B27 with vitamin A (STEMCELL Technologies), 10 ng/mL brain-derived neurotrophic factor (BDNF, Thermo Fisher Scientific), 10 ng/mL glial cell line-derived neurotrophic factor (GDNF, Thermo Fisher Scientific), 1 µM dibutyryl cyclic AMP (dbcAMP, STEMCELL Technologies), and 200 µM ascorbic acid. 0.1 µM Compound E (Merck Millipore) was added on the first day of plating and withdrawn during subsequent medium changes. Neuronal cultures were maintained with medium changes every four days until the indicated endpoint.

extract_protocol:
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.
In vitro differentiated NPC or neuron cultures (neurons matured to day 30) were dissociated with Accutase, pelleted, and flash frozen. Samples were stored in -80C until further processing. Library preparation and bulk-RNA-seq were performed using AccuraCode® RNAseq Kit (Singleron Biotechnologies).

value: iPSC-derived neurons

value: trisomy 21

tag: sample id

tag: group

value: DS

tag: protocol

value: DN

tag: in final_analysis

value: TRUE


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-D6


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-G17


title: Jurkat EZH2-WT 1

value: WT


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-D18


title: Jurkat EZH2-WT 2


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-C5


title: Jurkat EZH2-KO A7 2


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-C18


title: Jurkat EZH2-WT 3


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-C17


title: WT L. interrogans, Hamster, Day3, replicate 2

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_INF_H3_Liver_S2_L0012345
D3-Liver_Int-EMJH_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: Leptospira interrogans

source_name: serovar manilae

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: serovar manilae

tag: treatment

value: WT L. interrogans, Hamster, Day3


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-D17


title: WT L. interrogans, Hamster, Day3, replicate 1

description:
Library name: D3_INF_H2_Liver_S1_L0012345
D3-Liver_Int-EMJH_raw_counts.txt


title: Jurkat EZH2-KO A7 1


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-B6


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-B18


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-E17


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-C6


title: C.difficile_sensitive, erythromycin, bio4, rep7

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: sample_cdif_S4_7_promethion

data_processing:
Reads are real-time basedcalled with Guppy basecaller while sequencing in supper accurate(SUP) basecalling mode, with minimum Q score se to 10.
bastcalled fastq files are merged and demultiplexed using minibar.py (https://github.com/calacademy-research/minibar.git)
Replicates are merged and subsampled using seqtk/1.4-r122
fastq 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"
UMI extracted reads are mapped to C.difficile reference genome using minimap2/.28-r1209 using minimap2 -ax map-ont, and sorted by coordnated by samtools/1.2.
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
Deduplicated bam files are processed to fivepseq package/1.3.5 for context specific ribosome stalling analysis. Parameters are set to "-tripeptide-pos -9" (last amino acid is at A site which is 9nt for c.difficile) to observe R/K-x-R/K motif specific ribosome stalling.
Assembly: GCF_018885085.1
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 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 read count in the gene body (discarding the start and termination regions) relative to the distance from tripeptide (last amino acid is at A site)
Supplementary files format and content: tab delimited txt file contaning summary of the processed each sample data

organism: Clostridioides difficile

source_name: erythromycin sensitive isolates

growth_protocol: C.difficile sensitive and resistant strain(4 biological replicates)are cultured in BHI broth 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. Subsequenctly nanopore libraries are prepared using nanopore ligration kit v14 (SQK-LSK114) and following library preparation instruction. 96 samples (4 biological replicates, 12 technical replicates) are pooled together and loaded onto PromethION flow cell for sequencing 3 days(72 hours).

treatment_protocol: Exponetially growing bacteria culture(OD600=0.6-0.8) is treated with erythromycin for 10min. After 10min, cells are spinned, the supernatent are removed, an the cell pellets are frozen immediately on dry ice, and stored in -20°C for RNA extraction

value: erythromycin sensitive isolates


title: C.difficile_sensitive, erythromycin, bio4, rep9

description: Library name: sample_cdif_S4_9_promethion


title: C.difficile_sensitive, erythromycin, bio4, rep6

description: Library name: sample_cdif_S4_6_promethion


title: C.difficile_sensitive, erythromycin, bio4, rep8

description: Library name: sample_cdif_S4_8_promethion


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-A6


title: C.difficile_sensitive, erythromycin, bio4, rep5

description: Library name: sample_cdif_S4_5_promethion


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-B17


title: WT L. interrogans, Hamster, Day3, replicate 3

description:
Library name: D3_INF_H4_Liver_S3_L0012345
D3-Liver_Int-EMJH_raw_counts.txt


title: C.difficile_sensitive, erythromycin, bio4, rep4

description: Library name: sample_cdif_S4_4_promethion


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-B5


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-A5


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-A18


title: C.difficile_sensitive, erythromycin, bio4, rep3

description: Library name: sample_cdif_S4_3_promethion


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-A17


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-P16


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-O4


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-P4


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-P3


title: C.difficile_sensitive, erythromycin, bio4, rep11

description: Library name: sample_cdif_S4_11_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-O3


title: C.difficile_sensitive, erythromycin, bio3, rep9

description: Library name: sample_cdif_S3_9_promethion


title: C.difficile_sensitive, erythromycin, bio4, rep12

description: Library name: sample_cdif_S4_12_promethion


title: C.difficile_sensitive, erythromycin, bio4, rep10

description: Library name: sample_cdif_S4_10_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-O16


title: C.difficile_sensitive, erythromycin, bio4, rep1

description: Library name: sample_cdif_S4_1_promethion


title: C.difficile_sensitive, erythromycin, bio3, rep8

description: Library name: sample_cdif_S3_8_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-O15


title: C.difficile_sensitive, erythromycin, bio3, rep7

description: Library name: sample_cdif_S3_7_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-N4


title: C.difficile_sensitive, erythromycin, bio3, rep5

description: Library name: sample_cdif_S3_5_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-N3


title: C.difficile_sensitive, erythromycin, bio3, rep4

description: Library name: sample_cdif_S3_4_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-N16


title: C.difficile_sensitive, erythromycin, bio4, rep2

description: Library name: sample_cdif_S4_2_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-N15


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-M4


title: C.difficile_sensitive, erythromycin, bio3, rep12

description: Library name: sample_cdif_S3_12_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-M3


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-P15


title: C.difficile_sensitive, erythromycin, bio3, rep2

description: Library name: sample_cdif_S3_2_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-M16


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-L4


title: C.difficile_sensitive, erythromycin, bio3, rep10

description: Library name: sample_cdif_S3_10_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-L3


title: C.difficile_sensitive, erythromycin, bio3, rep1

description: Library name: sample_cdif_S3_1_promethion


title: C.difficile_sensitive, erythromycin, bio2, rep8

description: Library name: sample_cdif_S2_8_promethion


title: C.difficile_sensitive, erythromycin, bio2, rep9

description: Library name: sample_cdif_S2_9_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-M15


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-L15


title: C.difficile_sensitive, erythromycin, bio3, rep6

description: Library name: sample_cdif_S3_6_promethion


title: C.difficile_sensitive, erythromycin, bio2, rep7

description: Library name: sample_cdif_S2_7_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-L16


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-K4


title: C.difficile_sensitive, erythromycin, bio2, rep5

description: Library name: sample_cdif_S2_5_promethion


title: C.difficile_sensitive, erythromycin, bio2, rep6

description: Library name: sample_cdif_S2_6_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-K3


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-K16


title: C.difficile_sensitive, erythromycin, bio2, rep4

description: Library name: sample_cdif_S2_4_promethion


title: C.difficile_sensitive, erythromycin, bio2, rep3

description: Library name: sample_cdif_S2_3_promethion


title: C.difficile_sensitive, erythromycin, bio2, rep2

description: Library name: sample_cdif_S2_2_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-J4


title: C.difficile_sensitive, erythromycin, bio3, rep11

description: Library name: sample_cdif_S3_11_promethion


title: C.difficile_sensitive, erythromycin, bio2, rep12

description: Library name: sample_cdif_S2_12_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-J16


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-J3


title: C.difficile_sensitive, erythromycin, bio2, rep10

description: Library name: sample_cdif_S2_10_promethion


title: C.difficile_sensitive, erythromycin, bio3, rep3

description: Library name: sample_cdif_S3_3_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-J15


title: C.difficile_sensitive, erythromycin, bio2, rep11

description: Library name: sample_cdif_S2_11_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-I3


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-I16


title: C.difficile_sensitive, erythromycin, bio2, rep1

description: Library name: sample_cdif_S2_1_promethion


title: C.difficile_sensitive, erythromycin, bio1, rep7

description: Library name: sample_cdif_S1_7_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-H4


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-I15


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-H3


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-H16


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-I4


title: C.difficile_sensitive, erythromycin, bio1, rep4

description: Library name: sample_cdif_S1_4_promethion


title: C.difficile_sensitive, erythromycin, bio1, rep3

description: Library name: sample_cdif_S1_3_promethion


title: C.difficile_sensitive, erythromycin, bio1, rep5

description: Library name: sample_cdif_S1_5_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-K15


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-G4


title: C.difficile_sensitive, erythromycin, bio1, rep12

description: Library name: sample_cdif_S1_12_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-G3


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-G16


title: C.difficile_sensitive, erythromycin, bio1, rep11

description: Library name: sample_cdif_S1_11_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-G15


title: C.difficile_sensitive, erythromycin, bio1, rep10

description: Library name: sample_cdif_S1_10_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-F4


title: C.difficile_sensitive, erythromycin, bio1, rep8

description: Library name: sample_cdif_S1_8_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-F16


title: C.difficile_resistant, erythromycin, bio4, rep9

description: Library name: sample_cdif_R4_9_promethion

source_name: erythromycin resistant isolates

value: erythromycin resistant isolates


title: C.difficile_sensitive, erythromycin, bio1, rep6

description: Library name: sample_cdif_S1_6_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-F3


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-F15


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-H15


title: C.difficile_sensitive, erythromycin, bio1, rep9

description: Library name: sample_cdif_S1_9_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-E4


title: C.difficile_resistant, erythromycin, bio4, rep6

description: Library name: sample_cdif_R4_6_promethion


title: C.difficile_resistant, erythromycin, bio4, rep7

description: Library name: sample_cdif_R4_7_promethion


title: C.difficile_resistant, erythromycin, bio4, rep5

description: Library name: sample_cdif_R4_5_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-E16


title: C.difficile_resistant, erythromycin, bio4, rep3

description: Library name: sample_cdif_R4_3_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-E3


title: C.difficile_resistant, erythromycin, bio4, rep4

description: Library name: sample_cdif_R4_4_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-D4


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-E15


title: C.difficile_resistant, erythromycin, bio4, rep2

description: Library name: sample_cdif_R4_2_promethion


title: C.difficile_resistant, erythromycin, bio4, rep12

description: Library name: sample_cdif_R4_12_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-D3


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-D16


title: C.difficile_resistant, erythromycin, bio4, rep11

description: Library name: sample_cdif_R4_11_promethion


title: C.difficile_sensitive, erythromycin, bio1, rep1

description: Library name: sample_cdif_S1_1_promethion


title: C.difficile_resistant, erythromycin, bio4, rep10

description: Library name: sample_cdif_R4_10_promethion


title: C.difficile_resistant, erythromycin, bio4, rep1

description: Library name: sample_cdif_R4_1_promethion


title: C.difficile_resistant, erythromycin, bio3, rep9

description: Library name: sample_cdif_R3_9_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-D15


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-C4


title: C.difficile_resistant, erythromycin, bio4, rep8

description: Library name: sample_cdif_R4_8_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-C3


title: C.difficile_resistant, erythromycin, bio3, rep8

description: Library name: sample_cdif_R3_8_promethion


title: C.difficile_resistant, erythromycin, bio3, rep7

description: Library name: sample_cdif_R3_7_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-C16


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-B4


title: C.difficile_resistant, erythromycin, bio3, rep6

description: Library name: sample_cdif_R3_6_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-B3


title: C.difficile_resistant, erythromycin, bio3, rep4

description: Library name: sample_cdif_R3_4_promethion


title: C.difficile_resistant, erythromycin, bio3, rep5

description: Library name: sample_cdif_R3_5_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-B16


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-B15


title: C.difficile_resistant, erythromycin, bio3, rep2

description: Library name: sample_cdif_R3_2_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-A3


title: C.difficile_resistant, erythromycin, bio3, rep12

description: Library name: sample_cdif_R3_12_promethion


title: C.difficile_resistant, erythromycin, bio3, rep11

description: Library name: sample_cdif_R3_11_promethion


title: C.difficile_resistant, erythromycin, bio3, rep1

description: Library name: sample_cdif_R3_1_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-C15


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-P13


title: C.difficile_resistant, erythromycin, bio2, rep9

description: Library name: sample_cdif_R2_9_promethion


title: C.difficile_resistant, erythromycin, bio2, rep7

description: Library name: sample_cdif_R2_7_promethion


title: C.difficile_resistant, erythromycin, bio3, rep10

description: Library name: sample_cdif_R3_10_promethion


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-P1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-P2


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-A15


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-O13


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-O2


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-O14


title: C.difficile_resistant, erythromycin, bio2, rep8

description: Library name: sample_cdif_R2_8_promethion


title: C.difficile_resistant, erythromycin, bio2, rep4

description: Library name: sample_cdif_R2_4_promethion


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-P14


title: C.difficile_resistant, erythromycin, bio3, rep3

description: Library name: sample_cdif_R3_3_promethion


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-A4


title: AMB_201013_8wk_2A_3A_2_P10-2-P7-A16


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-O1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-N13


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-N14


title: C.difficile_resistant, erythromycin, bio2, rep3

description: Library name: sample_cdif_R2_3_promethion


title: C.difficile_resistant, erythromycin, bio2, rep10

description: Library name: sample_cdif_R2_10_promethion


title: C.difficile_resistant, erythromycin, bio2, rep5

description: Library name: sample_cdif_R2_5_promethion


title: C.difficile_resistant, erythromycin, bio2, rep6

description: Library name: sample_cdif_R2_6_promethion


title: C.difficile_resistant, erythromycin, bio2, rep1

description: Library name: sample_cdif_R2_1_promethion


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-N1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-M2


title: Pig Frontal Cortex, Animal ID 43-14, WT, female

city: College Station

first: Sarah

last: Christian

state: TX

address: 4467 TAMU

institute: Texas A&M University

description:
Library name: sample43-14
10x Genomics Gene Expression 3' v3

data_processing:
Cellranger (7.2.0) mkref was used to create a custom pig (Sus scrofa) reference, then count was used to align reads and generate count matrices for each sample. Default parameters were used, with the exception of --include introns = false.
Analysis was performed in Seurat after SoupX ambient RNA contamination.  Barcodes were excluded that had feature counts >5 or <3 median absolute deviations and ≥5% mitochondrial genes
After initial Seurat CCA integration (dims = 30, resolution = 0.5), clusters with an average of <900 features per cell were filtered out as they represented barcodes with neuronal debris.  Final figures and analysis were then generated with Seurat CCA integration (dims = 20, resolution = 0.5).
scType was used to generate initial cell type labels
Assembly: A custom version of NCBI Sus scrofa 11.1 was created, provided as reference_fasta.fa
Supplementary files format and content: A single RDS file with all sample information and processing, including normalization, integration, and filtering.

organism: Sus scrofa

source_name: Frontal Cortex

extract_protocol:
Tissues were flash frozen on liquid nitrogen and stored at -80*C until use in 10X Nuclei Isolation Kit (PN-1000493). Approximately 25 mg of tissue was used and the  kit protocol and provided reagents were used to isolate and suspend nuclei.
Libraries were constructed according to the 10x Genomics Single Cell Gene Expression 3' v3 library preparation protocol, and followed by sequencong on the Illumina NovaSeq 6000.

value: Frontal Cortex

value: 10 days

tag: Sex

value: female

value: wildtype


title: Pig Frontal Cortex, Animal ID 43-10, UBE3A mat. del., female

description:
Library name: sample43-10
10x Genomics Gene Expression 3' v3

value: UBE3A maternal deletion


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-M14

value: 8 weeks

value: FC

value: M


title: C.difficile_resistant, erythromycin, bio2, rep2

description: Library name: sample_cdif_R2_2_promethion


title: C.difficile_resistant, erythromycin, bio1, rep8

description: Library name: sample_cdif_R1_8_promethion


title: C.difficile_resistant, erythromycin, bio2, rep11

description: Library name: sample_cdif_R2_11_promethion


title: Pig Frontal Cortex, Animal ID 43-7, UBE3A mat. del., female

description:
Library name: sample43-7
10x Genomics Gene Expression 3' v3


title: C.difficile_resistant, erythromycin, bio1, rep9

description: Library name: sample_cdif_R1_9_promethion


title: Pig Frontal Cortex, Animal ID 43-11, UBE3A mat. del., male

description:
Library name: sample43-11
10x Genomics Gene Expression 3' v3

value: male


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-N2


title: Bradyzoites, Day0Repeat

city: Riverside

first: Emma

middle: H.

last: Wilson

state: California

address: 169 Aberdeen Dr, Multidisciplinary Research Building

department: Division of Biomedical Sciences

institute: University of California, Riverside School of Medicine

description:
Library name: Sample 2_Day0Repeat
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) Assembly: ME49 Toxoplasma Reference Genome.
Assembly: ME49 Toxoplasma Reference Genome
Supplementary files format and content: Tab separated values files and matrix files.

organism: Toxoplasma gondii

source_name: Purified from infected mouse brains

growth_protocol: Toxoplasma gondii parasites were maintained in CBA mice.

extract_protocol:
Toxoplasma tissue cysts were purified from brain homogenate using a percoll density gradient. Tissue cysts were treated with pepsin-HCl mixture to excyst bradyzoites. All parasites were used for scRNA seq. Library preparation was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, parasites were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
Library construction was performed according to 10X Genomics manusfacturer's instructions (10X Genomics Chromium Next GEM Single Cell 3' v3.1).

treatment_protocol: Toxoplasma gondii infection

value: Purified from infected mouse brains

value: Bradyzoites

value: Infected CBA mice


title: C.difficile_resistant, erythromycin, bio2, rep12

description: Library name: sample_cdif_R2_12_promethion


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-L14


title: C.difficile_resistant, erythromycin, bio1, rep7

description: Library name: sample_cdif_R1_7_promethion


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-M13


title: Bradyzoites, Day0

description:
Library name: Sample 1_Day0
10X Genomics


title: Pig Frontal Cortex, Animal ID 43-12, WT, male

description:
Library name: sample43-12
10x Genomics Gene Expression 3' v3


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-M1


title: C.difficile_resistant, erythromycin, bio1, rep6

description: Library name: sample_cdif_R1_6_promethion


title: Pig Frontal Cortex, Animal ID 39-7, WT, male

description:
Library name: sample39-7
10x Genomics Gene Expression 3' v3


title: C.difficile_resistant, erythromycin, bio1, rep5

description: Library name: sample_cdif_R1_5_promethion


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-L2


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-L13


title: Graft animal E 3-months (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

description: PVD

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

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: C.difficile_resistant, erythromycin, bio1, rep4

description: Library name: sample_cdif_R1_4_promethion


title: Graft animal D 1-month (ST)

description: PVC


title: C.difficile_resistant, erythromycin, bio1, rep3

description: Library name: sample_cdif_R1_3_promethion


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-L1


title: Pig Frontal Cortex, Animal ID 39-8, UBE3A mat. del., male

description:
Library name: sample39-8
10x Genomics Gene Expression 3' v3


title: Pig Frontal Cortex, Animal ID 43-5, WT, female

description:
Library name: sample43-5
10x Genomics Gene Expression 3' v3


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-K2


title: Graft animal A 6-months (ST)

description: PVA


title: Native domestic pig 2 (ST)


title: C.difficile_resistant, erythromycin, bio1, rep12

description: Library name: sample_cdif_R1_12_promethion


title: Graft animal B 6-months (ST)

description: PVB


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-K14


title: C.difficile_resistant, erythromycin, bio1, rep2

description: Library name: sample_cdif_R1_2_promethion


title: C.difficile_resistant, erythromycin, bio1, rep10

description: Library name: sample_cdif_R1_10_promethion


title: Graft animal C Pre-implant (ST)


title: Native domestic pig 1 (ST)


title: ATAC-Seq 229E 10 March 2022

city: Richland

first: Lindsey

middle: N

last: Anderson

state: WA

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

description:
pnnl-ATAC-30
infected_6

data_processing:
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/)
Reads were aligned to the human genome using Bowtie2 (https://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Duplicate alignments were removed using GATK (https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard).
Alignments mapping to mitochondria were removed using ATACseqQC (https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html).
Peaks were called using MACS3 (https://macs3-project.github.io/MACS/index.html)
Blacklist regions were filtered using ChIPQC (https://bioconductor.org/packages/release/bioc/html/ChIPQC.html)
Peaks were counted and annotated using ChIPQC.
Assembly: human genome GRCh38
Supplementary files format and content: narrowPeak (individual files for each sample) and peak counts (single matrix)

source_name: liver

growth_protocol: Huh7 cells were grown in low glucose DMEM media with 10% fetal bovine serum and Gibco antibiotic/amtimycotic.

extract_protocol:
Samples were processed using Active Motif's Bulk ATAC-Seq kit (according to manufacturer's instructions).
ATAC-Seq libraries were processed using Active Motif's Bulk ATAC-Seq kit (according to manufacturer's instructions) to generate bar coded library samples for RNA Seq analysis.

treatment_protocol: Cells were mock-infected (phosphate buffered saline) or infected with human coronavirus 229E (MOI 3, replication competent), or UV treated/inactivated human coronavirus 229E for 24 hours prior to sample collection.

value: liver

value: immortalized human liver epithelial cells

value: infected


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-K13


title: C.difficile_resistant, erythromycin, bio1, rep11

description: Library name: sample_cdif_R1_11_promethion

value: erythromycin resistant isolates


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-K1


title: ATAC-Seq 229E 9 March 2022

description:
pnnl-ATAC-29
infected_5


title: animal C Post-bioreactor (SN)

description: Cher-ReCell-nuclei

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.

source_name: Primary mesenchymal cells derived from minipig abdominal muscle

value: combination of mesoangioblasts and fibroblast in a ratio 7:3


title: C.difficile_resistant, erythromycin, bio1, rep1

description: Library name: sample_cdif_R1_1_promethion


title: Graft animal F 3-months (ST)


title: ATAC-Seq 229E 8 March 2022

description:
pnnl-ATAC-28
infected_4


title: ATAC-Seq 229E 7 March 2022

description:
pnnl-ATAC-27
infected_3


title: ATAC-Seq 229E 6 March 2022

description:
pnnl-ATAC-26
infected_2


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-J2


title: ATAC-Seq 229E 5 March 2022

description:
pnnl-ATAC-25
infected_1


title: C.difficle_sensitive, erythromycin, merged

description: Library name: merged_sensitive_promethion

value: erythromycin sensitive isolates


title: animal C Pre-bioreactor (SN)

description: Cher-Injected-nuclei

value: Primary mesenchymal cells derived from minipig abdominal muscle


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-J13


title: C.difficle_sensitive, erythromycin, subsample

description: Library name: merged_sensitive_promethion_30000


title: ATAC-Seq UV treated 229E 10 March 2022

description:
pnnl-ATAC-20
uv_9

value: infected inactivated virus


title: ATAC-Seq UV treated 229E 8 March 2022

description:
pnnl-ATAC-18
uv_7


title: ATAC-Seq UV treated 229E 9 March 2022

description:
pnnl-ATAC-19
uv_8


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-J1


title: ATAC-Seq UV treated 229E 7 March 2022

description:
pnnl-ATAC-17
uv_6


title: C.difficile_resistant, erythromycin, merged

description: Library name: merged_resistant_promethion


title: ATAC-Seq UV treated 229E 5 March 2022

description:
pnnl-ATAC-15
uv_4


title: ATAC-Seq UV treated 229E 6 March 2022

description:
pnnl-ATAC-16
uv_5


title: ATAC-Seq UV treated 229E 4 March 2022

description:
pnnl-ATAC-14
uv_3


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-I13


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-I2


title: C.difficile_resistant, erythromycin,subsample

description: Library name: merged_resistant_promethion_30000


title: C.difficile_sensitive, erythromycin, bio1, rep2

description: Library name: sample_cdif_S1_2_promethion


title: ATAC-Seq UV treated 229E 2 March 2022

description:
pnnl-ATAC-12
uv_2


title: ATAC-Seq Mock 9 March 2022

description:
pnnl-ATAC-09
mock_8

value: mock


title: ATAC-Seq UV treated 229E 1 March 2022

description:
pnnl-ATAC-11
uv_1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-I14

value: 8 weeks


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-J14

value: FC


title: ATAC-Seq Mock 7 March 2022

description:
pnnl-ATAC-07
mock_7


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-I1

value: M


title: skin

city: Chengdu

first: Yeyu

last: Chen

state: --- Select One ---

address: The Fishery Institute of The Sichuan Academy of Agricultural Sciences, No.1611 Xiyuan Street

country: China

institute: Fisheries Research Institute, Sichuan Academy of Agricultural Sciences

description: Library name: skin

data_processing:
The data were processed using software cell ranger.
Assembly: PRJNA1121939 and PRJNA658459
Supplementary files format and content: RDA

organism: Acipenser dabryanus

source_name: skin

extract_protocol:
The tissues were washed in precooled DPBS and cut into pieces. Briefly, enzyme solution was added to digest the tissue. The digestion was terminated with DMEM, and the cells were washed. The single-cell suspensions were mixed with 0.4% Trypan blue dye at a 9:1 ratio, and the number and survival rate of the cells were deter_x0002_mined using a Countess® II Automated Cell Counter.
The cell suspensions were loaded on a 10×Genomics GemCode single-cell instrument that generated single-cell gel bead-in-emulsion (GEM) plates. Libraries were generated and sequenced from the cDNA with Chromium Next GEM Single Cell 3′ Reagent Kits v3.1.

value: skin


title: stomach

description: Library name: stomach

source_name: stomach

value: stomach


title: spiral intestine

description: Library name: spiral intestine

source_name: spiral intestine

value: spiral intestine


title: spleen

description: Library name: spleen

source_name: spleen

value: spleen


title: ATAC-Seq Mock 6 March 2022

description:
pnnl-ATAC-06
mock_6


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-H2


title: ATAC-Seq Mock 5 March 2022

description:
pnnl-ATAC-05
mock_5


title: rectum

description: Library name: rectum

source_name: rectum

value: rectum


title: ATAC-Seq Mock 4 March 2022

description:
pnnl-ATAC-04
mock_4

value: liver


title: ATAC-Seq Mock 3 March 2022

description:
pnnl-ATAC-03
mock_3

value: immortalized human liver epithelial cells


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-H14


title: ATAC-Seq Mock 2 March 2022

description:
pnnl-ATAC-02
mock_2


title: ATAC-Seq Mock 10 March 2022

description:
pnnl-ATAC-10
mock_9


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-H13


title: pyloric caecum

description: Library name: pyloric caecum

source_name: pyloric caecum

value: pyloric caecum


title: muscle

description: Library name: muscle

source_name: muscle

value: muscle


title: BA4 KO P20 infected mouse 4

city: Columbus

first: Jacob

last: Yount

state: OH

address: 460 W 12th Ave, BRT 790

department: Microbial Infection and Immunity

institute: The Ohio State University

description: Library name: BA4_KO_4

data_processing:
The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer's instructions. The samples were sequenced using a 2 × 150 bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de‐multiplexed using Illumina bcl2fastq 2.17 software. One mis‐match was allowed for index sequence identification.
Assembly: GRCm38
Supplementary files format and content: csv file containing raw counts for all samples

source_name: Lung

extract_protocol:
RNA was extracted from lung tissue homogenates from day 2 post infection using TRIzol (Invitrogen). Following separation with 1-bromo-3-chloropropane, aqueous phase was collected, and RNA was precipitated with ethanol. Precipitated RNA was isolated and sent to GENEWIZ, LLC/Azenta US, Inc (South Plainfield, NJ, USA).
RNA library preparation and sequencing was performed with the following methods as provided by GENEWIZ: “The RNA samples received were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (New England Biolabs, Ipswich, MA, USA).

value: Lung

value: Infected with BA.4 KO Passage 20 virus


title: BA4 KO P20 infected mouse 3

description: Library name: BA4_KO_3


title: BA4 KO P20 infected mouse 2

description: Library name: BA4_KO_2


title: midkidney

description: Library name: midkidney

source_name: midkidney

value: midkidney


title: heart

description: Library name: heart

source_name: heart

value: heart


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-G2


title: Beta KO P20 infected mouse 4

description: Library name: Beta_KO_4

value: Infected with Beta KO Passage 20 virus


title: headkidney

description: Library name: headkidney

source_name: headkidney

value: headkidney


title: liver

description: Library name: liver


title: BA4 WT P20 infected mouse 3

description: Library name: BA4_WT_3

value: Infected with BA.4 WT Passage 20 virus


title: BA4 WT P20 infected mouse 2

description: Library name: BA4_WT_2


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-G14

value: 8 weeks

value: FC

value: M


title: BA4 KO P20 infected mouse 1

description: Library name: BA4_KO_1


title: Beta KO P20 infected mouse 2

description: Library name: Beta_KO_2


title: BA4 WT P20 infected mouse 4

description: Library name: BA4_WT_4


title: gonad

description: Library name: gonad

source_name: gonad

value: gonad


title: Beta KO P20 infected mouse 3

description: Library name: Beta_KO_3


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-F2


title: BA4 WT P20 infected mouse 1

description: Library name: BA4_WT_1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-G13


title: Beta KO P20 infected mouse 1

description: Library name: Beta_KO_1


title: gill

description: Library name: gill

source_name: gill

value: gill


title: Beta WT P20 infected mouse 3

description: Library name: Beta_WT_3

value: Infected with Beta WT Passage 20 virus


title: Beta WT P20 infected mouse 4

description: Library name: Beta_WT_4


title: Beta WT P20 infected mouse 2

description: Library name: Beta_WT_2


title: ATAC-Seq Mock 1 March 2022

description:
pnnl-ATAC-01
mock_1

value: liver

value: mock


title: duodenum

description: Library name: duodenum

source_name: duodenum (smallintestine)

value: duodenum (smallintestine)


title: eye

description: Library name: eye

source_name: eye

value: eye


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-F14


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-H1


title: Beta WT P20 infected mouse 1

description: Library name: Beta_WT_1

value: Lung


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-F13


title: MA10 infected mouse 4

description: Library name: MA10_WT_4

value: Infected with MA10 virus


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-G1


title: MA10 infected mouse 2

description: Library name: MA10_WT_2


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-E2


title: Mock infected mouse 4

description: Library name: PBS_WT_4

value: Saline mock control


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-F1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-E14


title: MA10 infected mouse 1

description: Library name: MA10_WT_1


title: Mock infected mouse 3

description: Library name: PBS_WT_3


title: brain

description: Library name: brain

source_name: brain

value: brain


title: MA10 infected mouse 3

description: Library name: MA10_WT_3


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-E13


title: IFNGR_HC_CC30_GFPpos_rep2

description: Library name: IFNGR_HC_CC30_GFPpos_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.7.1 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Assembly: GRCm38.96
Supplementary files format and content: Tab-separated table of gene counts per sample

source_name: extracted RNA from sorted 50K neuronal nuclei

extract_protocol:
To perform RNA-seq, we FAN-sorted neurons from hippocapi and brainstems at different time points after intravenous wtLCMV challenge. Each biological replicate represents 50000  neuronal nuclei sorted in buffer RLT with 1% ß-mercaptoethanol and processed with RNeasy plus Micro Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain, hippocampus

value: C57BL/6J, NuTRAP transgenic IFNGR floxed

value: neurons

tag: neuronal population

value: virus-exposed neurons

tag: disease stage_(days_post_challenge)

value: 8.4 weeks

tag: biological replicate


title: iPSC-derived neural progenitors, disomic, untreated, Library C9-2_NPC

description:
Library name: C9-2_NPC
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

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 samples

growth_protocol: A protocol used by the lab of Dean Nizetic (DN), based on the Gibco protocol (Thermo Fisher Scientific, MAN0008031), was used to generate neural progenitor cells (iNPCs) from iPSCs.  NPCs  between passages 6 and 10 were expanded in Geltrex-coated 6-well culture plates prepared by diluting a 60 μL Geltrex aliquot in 6 mL cold DMEM/F12, incubated at 37°C for at least 60 minutes. Cells were thawed, centrifuged at 300 × g for 5 minutes, and resuspended in Neural Expansion Medium (NEM) with 5 μM ROCK inhibitor Y27632 (STEMCELL Technologies) at a density of 1-2 million cells per well. Media changes were performed the next day with complete NEM, and then changed every other day thereafter. For neuronal differentiation, NPCs were dissociated with Accutase (Thermo Fisher Scientific) and seeded onto Poly-L-ornithine/Laminin-coated 24-well culture plates at a density of 70,000 cells per well in NEM with 5 μM Y27532. Media change was performed the next day with complete BrainPhys Neuronal Medium (STEMCELL Technologies), and then changed every four days for two weeks. After which, BrainPhys Neuronal Medium is supplemented with 2 μg/mL Laminin for media changes every four days till the desired experimental endpoint.

extract_protocol:
Total RNA was extracted from NPCs using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme) according to manufacturer’s protocol.
RNA samples were stored in -80oC before processing by DNBSEQ eukaryotic strand-specific transcriptome resequencing (BGI Genomics).

tag: cell line

value: iPSC-derived neural progenitors

value: disomic

value: untreated

tag: library id

value: CON

value: TRUE


title: Mock infected mouse 2

description: Library name: PBS_WT_2

tag: tissue


title: WT_BS_CC70_GFPpos_rep2

description: Library name: WT_BS_CC70_GFPpos_rep2

value: Brain, brainstem

tag: genotype

value: C57BL/6J, NuTRAP transgenic

tag: cell type

value: 15 weeks


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-E1

tag: strain

tag: age

value: 8 weeks

value: FC

value: M


title: IFNGR_HC_CC30_GFPpos_rep1

description: Library name: IFNGR_HC_CC30_GFPpos_rep1


title: WT_BS_CC70_GFPpos_rep3

description: Library name: WT_BS_CC70_GFPpos_rep3


title: iPSC-derived neural progenitors, disomic, untreated, Library C9-2

description:
Library name: C9-2
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: batch


title: iPSC-derived neural progenitors, disomic, untreated, Library C9-1_NPC

description:
Library name: C9-1_NPC
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: sample id


title: iPSC-derived neural progenitors, disomic, untreated, Library C9-1

description:
Library name: C9-1
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: group


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-D2

tag: brain region

tag: gender


title: WT_BS_CC70_GFPpos_rep1

description: Library name: WT_BS_CC70_GFPpos_rep1


title: WT_BS_CC70_GFPneg_rep3

description: Library name: WT_BS_CC70_GFPneg_rep3

value: bystander neurons


title: WT_BS_CC70_GFPneg_rep2

description: Library name: WT_BS_CC70_GFPneg_rep2


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-D13


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D3, Library C13-3_PKNOX-3_8522509006616

description:
Library name: C13-3_PKNOX-3_8522509006616
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: trisomy 21

tag: treatment

tag: in final_analysis


title: blood

description: Library name: blood

source_name: blood

value: blood


title: WT_BS_CC70_GFPneg_rep1

description: Library name: WT_BS_CC70_GFPneg_rep1

value: neurons

tag: neuronal population


title: Mock infected mouse 1

description: Library name: PBS_WT_1

value: Lung

value: Saline mock control


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-D14


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D3, Library C13-3_PKNOX-3_8522509006605

description:
Library name: C13-3_PKNOX-3_8522509006605
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: iPSC-derived neural progenitors


title: WT_BS_CC30_GFPpos_rep2

description: Library name: WT_BS_CC30_GFPpos_rep2

value: virus-exposed neurons

tag: disease stage_(days_post_challenge)

value: 8.4 weeks


title: WT_BS_CC30_GFPpos_rep1

description: Library name: WT_BS_CC30_GFPpos_rep1

tag: biological replicate


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-D1


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D2, Library C13-3_PKNOX-2_8522509006615

description:
Library name: C13-3_PKNOX-2_8522509006615
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell line


title: WT_BS_CC30_GFPneg_rep2

description: Library name: WT_BS_CC30_GFPneg_rep2


title: WT_BS_CC30_GFPneg_rep1

description: Library name: WT_BS_CC30_GFPneg_rep1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-C2


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D2, Library C13-3_PKNOX-2_8522509006604

description:
Library name: C13-3_PKNOX-2_8522509006604
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: library id


title: WT_BS_CC10_GFPneg_rep2

description: Library name: WT_BS_CC10_GFPneg_rep2

tag: tissue

value: 6.4 weeks


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D1, Library C13-3_PKNOX-1_8522509006614

description:
Library name: C13-3_PKNOX-1_8522509006614
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: genotype

value: TRUE


title: WT_BS_CC10_GFPpos_rep1

description: Library name: WT_BS_CC10_GFPpos_rep1

value: Brain, brainstem

tag: cell type


title: WT_BS_CC10_GFPpos_rep2

description: Library name: WT_BS_CC10_GFPpos_rep2

value: C57BL/6J, NuTRAP transgenic


title: WT_BS_CC10_GFPneg_rep1

description: Library name: WT_BS_CC10_GFPneg_rep1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-C13

tag: strain


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-C14

tag: age


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous, biol rep 5

description:
Library name: R6C_IPSBETA_MACS_HOM_5
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads

source_name: pancreatic differentiation

value: pancreatic differentiation

value: human induced pluripotent stem cell derived pancreatic beta-like cell aggregates

value: homozygous INS c.16C>T

tag: batch


title: WT_BS_CnC10_GFPpos_rep1

description: Library name: WT_BS_CnC10_GFPpos_rep1

value: 6 weeks


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-B2

value: 8 weeks

value: FC

value: M


title: WT_BS_CnC10_GFPpos_rep2

description: Library name: WT_BS_CnC10_GFPpos_rep2

value: neurons


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-C1


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous, biol rep 4

description:
Library name: R6C_IPSBETA_MACS_HOM_4
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D3, Library C13-3_Gabpa-3_8522509006619

description:
Library name: C13-3_Gabpa-3_8522509006619
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: trisomy 21

tag: sample id


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D3, Library C13-3_Gabpa-3_8522509006608

description:
Library name: C13-3_Gabpa-3_8522509006608
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: group


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-B14

tag: brain region


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous, biol rep 3

description:
Library name: R6C_IPSBETA_MACS_HOM_3
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: WT_BS_CnC10_GFPneg_rep1

description: Library name: WT_BS_CnC10_GFPneg_rep1

value: bystander neurons


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D2, Library C13-3_Gabpa-2_8522509006618

description:
Library name: C13-3_Gabpa-2_8522509006618
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: iPSC-derived neural progenitors


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-B13

tag: gender


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D1, Library C13-3_Gabpa-1_8522509006617

description:
Library name: C13-3_Gabpa-1_8522509006617
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: treatment


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D2, Library C13-3_Gabpa-2_8522509006607

description:
Library name: C13-3_Gabpa-2_8522509006607
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: in final_analysis


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous, biol rep 1

description:
Library name: R6C_IPSBETA_MACS_HOM_1
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: WT_HC_CC70_GFPpos_rep3

description: Library name: WT_HC_CC70_GFPpos_rep3

value: Brain, hippocampus

tag: neuronal population

value: virus-exposed neurons

value: 15 weeks


title: WT_HC_CC70_GFPpos_rep2

description: Library name: WT_HC_CC70_GFPpos_rep2

tag: disease stage_(days_post_challenge)


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-B1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-A2


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous isogenic corrected, biol rep 2

description:
Library name: R6C_IPSBETA_MACS_HOMCORR_2
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads

value: homozygous INS c.16C>T isogenic corrected


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous isogenic corrected, biol rep 4

description:
Library name: R6C_IPSBETA_MACS_HOMCORR_4
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D1, Library C13-3_PKNOX-1_8522509006603

description:
Library name: C13-3_PKNOX-1_8522509006603
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: TRUE


title: WT_HC_CC70_GFPneg_rep3

description: Library name: WT_HC_CC70_GFPneg_rep3

value: C57BL/6J, NuTRAP transgenic

tag: biological replicate


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D1, Library C13-3_Gabpa-1_8522509006606

description:
Library name: C13-3_Gabpa-1_8522509006606
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell line


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous isogenic corrected, biol rep 3

description:
Library name: R6C_IPSBETA_MACS_HOMCORR_3
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads

value: pancreatic differentiation


title: WT_HC_CC70_GFPpos_rep1

description: Library name: WT_HC_CC70_GFPpos_rep1


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-A13


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-A14


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D3, Library C13-3_Bach1-3_8522509006613

description:
Library name: C13-3_Bach1-3_8522509006613
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: library id


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, homozygous isogenic corrected, biol rep 1

description:
Library name: R6C_IPSBETA_MACS_HOMCORR_1
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads

tag: tissue

value: human induced pluripotent stem cell derived pancreatic beta-like cell aggregates


title: WT_HC_CC70_GFPneg_rep2

description: Library name: WT_HC_CC70_GFPneg_rep2

tag: genotype


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D3, Library C13-3_Bach1-3_8522509006602

description:
Library name: C13-3_Bach1-3_8522509006602
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell type


title: WT_BS_CnC10_GFPneg_rep2

description: Library name: WT_BS_CnC10_GFPneg_rep2

value: Brain, brainstem


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D2, Library C13-3_Bach1-2_8522509006612

description:
Library name: C13-3_Bach1-2_8522509006612
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv


title: WT_HC_CC70_GFPneg_rep1

description: Library name: WT_HC_CC70_GFPneg_rep1


title: HEK_1000PREs_hsPum2-hsADAR2cdWT_rep_3 (RBPscan)

city: Québec

first: Dmitry

last: Kretov

state: Québec

department: Oncology Division

country: Canada

institute: CRCHU de Québec - Université Laval

description: Library name: HEK_PRE_hsPUM2-ADARcd_rep3

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 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.

molecule: other

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: human embryonic kidney

value: WT


title: HEK_1000PREs_hsPum2-hsADAR2cdWT_rep_2 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcd_rep2


title: WT_HC_CC30_GFPpos_rep4

description: Library name: WT_HC_CC30_GFPpos_rep4

value: 8.4 weeks


title: dre.embryo.pool_water_NA_4

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

institute: Carleton University

description: Sequencing control. Not used in any contrast.

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

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

value: 120-hours post fertilization

value: 5 days

value: water

tag: replicate

tag: row

value: D

tag: column

tag: plate

tag: processing batch

tag: sequencing control

tag: protocol

value: TempO-Seq


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D2, Library C13-3_Bach1-2_8522509006601

description:
Library name: C13-3_Bach1-2_8522509006601
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: iPSC-derived neural progenitors

value: trisomy 21

tag: treatment

tag: sample id

tag: group

tag: batch


title: dre.embryo.pool_water_NA_3

value: C


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D1, Library C13-3_Bach1-1_8522509006611

description:
Library name: C13-3_Bach1-1_8522509006611
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: in final_analysis

value: TRUE


title: dre.embryo.pool_water_NA_2

tag: cell line


title: HEK_1000PREs_N22-hsADAR2cdWT_rep_3 (RBPscan)

description: Library name: HEK_PRE_ADARcd_rep3


title: HEK_1000PREs_hsPum2-hsADAR2cdWT_rep_1 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcd_rep1


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D1, Library C13-3_Bach1-1_8522509006600

description:
Library name: C13-3_Bach1-1_8522509006600
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: library id


title: iPSC-derived neural progenitors, trisomy 21, untreated, Library C13-3_8522509006610

description:
Library name: C13-3_8522509006610
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: untreated

value: DS


title: WT_HC_CC30_GFPpos_rep1

description: Library name: WT_HC_CC30_GFPpos_rep1

tag: tissue

value: Brain, hippocampus

value: C57BL/6J, NuTRAP transgenic

value: neurons

tag: neuronal population

value: virus-exposed neurons

tag: disease stage_(days_post_challenge)

tag: age

tag: biological replicate


title: HEK_1000PREs_N22-hsADAR2cdWT_rep_1 (RBPscan)

description: Library name: HEK_PRE_ADARcd_rep1

tag: cell type

value: human embryonic kidney

tag: genotype

value: WT


title: iPSC-derived neural progenitors, trisomy 21, untreated, Library C13-3_8522509006599

description:
Library name: C13-3_8522509006599
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv


title: dre.embryo.pool_PFDA_1.2_4

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

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: PFDA

tag: replicate

tag: row

value: E

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: mixed

tag: rna yield_ng_u_l

tag: rin


title: AMB_201013_8wk_2A_3A_2_P10-1-G20-A1

tag: strain

value: 8 weeks

tag: brain region

value: FC

tag: gender

value: M


title: dre.embryo.pool_PFDA_12_4

tag: tissue

tag: cell line

value: 5 days

tag: treatment

tag: protocol

value: TempO-Seq

tag: sample id


title: dre.embryo.pool_water_NA_1

tag: cell type

tag: genotype

value: water

tag: replicate

value: C

tag: sequencing control


title: WT_HC_CC30_GFPneg_rep4

description: Library name: WT_HC_CC30_GFPneg_rep4

value: Brain, hippocampus

value: C57BL/6J, NuTRAP transgenic

tag: neuronal population

value: bystander neurons

tag: disease stage_(days_post_challenge)

tag: age

value: 8.4 weeks

tag: biological replicate


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D3, Library C13-1_PKNOX-3_8522509006594

description:
Library name: C13-1_PKNOX-3_8522509006594
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: iPSC-derived neural progenitors

value: trisomy 21

tag: library id

tag: group

tag: batch

tag: in final_analysis

value: TRUE


title: WT_HC_CC30_GFPneg_rep2

description: Library name: WT_HC_CC30_GFPneg_rep2

tag: tissue

value: neurons


title: HEK_1000PREs_N22-hsADAR2cdWT_rep_2 (RBPscan)

description: Library name: HEK_PRE_ADARcd_rep2

tag: cell line

value: human embryonic kidney

value: WT


title: HEK_1000PREs_Control-2_rep_2 (RBPscan)

description: Library name: HEK_PRE_Control-2_rep2


title: HEK_1000PREs_Control-2_rep_1 (RBPscan)

description: Library name: HEK_PRE_Control-2_rep1


title: HEK_1000PREs_Control-2_rep_3 (RBPscan)

description: Library name: HEK_PRE_Control-2_rep3


title: dre.embryo.pool_PFDA_0.4_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: PFDA

tag: treatment

tag: row

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: mixed

tag: rna yield_ng_u_l

tag: rin


title: WT_HC_CC30_GFPneg_rep3

description: Library name: WT_HC_CC30_GFPneg_rep3

tag: genotype

tag: cell type

tag: neuronal population

tag: disease stage_(days_post_challenge)

tag: age


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D2, Library C13-1_PKNOX-2_8522509006593

description:
Library name: C13-1_PKNOX-2_8522509006593
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: sample id

tag: library id

tag: group

tag: batch

tag: in final_analysis


title: dre.embryo.pool_PFDA_0.12_4

tag: tissue

tag: cell line

value: 5 days

tag: treatment

tag: replicate

tag: row

value: D

tag: column

tag: protocol

value: TempO-Seq


title: WT_HC_CC30_GFPneg_rep1

description: Library name: WT_HC_CC30_GFPneg_rep1

value: Brain, hippocampus

tag: genotype

tag: biological replicate


title: WT_HC_CC30_GFPpos_rep3

description: Library name: WT_HC_CC30_GFPpos_rep3

value: C57BL/6J, NuTRAP transgenic

tag: cell type

tag: neuronal population

value: virus-exposed neurons


title: WT_HC_CC30_GFPpos_rep2

description: Library name: WT_HC_CC30_GFPpos_rep2

tag: disease stage_(days_post_challenge)

tag: age

value: 8.4 weeks


title: dre.embryo.pool_PFDA_4_4

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: rna yield_ng_u_l

tag: rin

tag: sample id


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D2, Library C13-1_PKNOX-2_8522509006582

description:
Library name: C13-1_PKNOX-2_8522509006582
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell line

value: iPSC-derived neural progenitors

tag: treatment

tag: library id

tag: group

tag: batch

tag: in final_analysis


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D3, Library C13-1_PKNOX-3_8522509006583

description:
Library name: C13-1_PKNOX-3_8522509006583
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell type

tag: genotype

value: trisomy 21


title: WT_HC_CC10_GFPpos_rep4

description: Library name: WT_HC_CC10_GFPpos_rep4

tag: tissue

tag: neuronal population

tag: disease stage_(days_post_challenge)

value: 6.4 weeks

tag: biological replicate


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D1, Library C13-1_PKNOX-1_8522509006592

description:
Library name: C13-1_PKNOX-1_8522509006592
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: TRUE


title: dre.embryo.pool_PFBS_25_4

value: PFBS

tag: replicate

tag: row

value: B

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

value: ottawa

tag: protocol


title: dre.embryo.pool_PFBA_600_4

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: PFBA

tag: treatment

value: A

tag: FISH origin

tag: rna yield_ng_u_l

tag: rin

tag: sample id


title: HEK_1000PREs_hsPum2-hsADAR2cdMUT_rep_1 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT_rep1

tag: cell type

value: human embryonic kidney

tag: genotype

value: WT


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D3, Library C13-1_Gabpa-3_8522509006597

description:
Library name: C13-1_Gabpa-3_8522509006597
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: library id

tag: group

tag: batch

tag: in final_analysis


title: HEK_1000PREs_N22-hsADAR2cdMUT_rep_3 (RBPscan)

description: Library name: HEK_PRE_ADARcdMUT_rep3


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D1, Library C13-1_PKNOX-1_8522509006581

description:
Library name: C13-1_PKNOX-1_8522509006581
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv


title: WT_HC_CC10_GFPpos_rep3

description: Library name: WT_HC_CC10_GFPpos_rep3

tag: tissue

value: Brain, hippocampus

value: neurons

tag: neuronal population

tag: disease stage_(days_post_challenge)

tag: age

tag: biological replicate


title: WT_HC_CC10_GFPpos_rep2

description: Library name: WT_HC_CC10_GFPpos_rep2

value: C57BL/6J, NuTRAP transgenic

value: virus-exposed neurons


title: dre.embryo.pool_PFHxS_400_4

tag: cell line

value: 5 days

value: PFHxS

tag: replicate

tag: row

value: G

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: protocol

value: TempO-Seq


title: dre.embryo.pool_PFHxS_200_4

tag: cell type

tag: genotype

tag: treatment

value: F

tag: FISH origin

tag: rna yield_ng_u_l

tag: rin

tag: sample id


title: WT_HC_CC10_GFPpos_rep1

description: Library name: WT_HC_CC10_GFPpos_rep1

tag: tissue

tag: neuronal population

tag: disease stage_(days_post_challenge)

tag: age

value: 6.4 weeks


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D3, Library C13-1_Gabpa-3_8522509006586

description:
Library name: C13-1_Gabpa-3_8522509006586
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell line

value: iPSC-derived neural progenitors

value: trisomy 21

tag: library id

tag: group

tag: batch

tag: in final_analysis

value: TRUE


title: dre.embryo.pool_PFBA_25_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: PFBA

tag: replicate

tag: row

value: C

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

value: ottawa

tag: protocol


title: dre.embryo.pool_PFHxS_60_4

tag: cell type

tag: genotype

tag: treatment

value: E

tag: FISH origin

tag: rna yield_ng_u_l

tag: rin

tag: sample id


title: WT_HC_CC10_GFPpos_rep5

description: Library name: WT_HC_CC10_GFPpos_rep5

tag: tissue

value: Brain, hippocampus

value: C57BL/6J, NuTRAP transgenic

value: neurons

tag: neuronal population

tag: disease stage_(days_post_challenge)

tag: age

tag: biological replicate


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D2, Library C13-1_Gabpa-2_8522509006596

description:
Library name: C13-1_Gabpa-2_8522509006596
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell line

tag: library id

tag: group

tag: batch

tag: in final_analysis


title: dre.embryo.pool_PFHxA_600_4

tag: cell type

value: 5 days

value: PFHxA

tag: replicate

tag: row

value: D

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: protocol


title: HEK_1000PREs_hsPum2-hsADAR2cdMUT_rep_3 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT_rep3

value: human embryonic kidney

tag: genotype

value: WT


title: WT_HC_CC10_GFPneg_rep5

description: Library name: WT_HC_CC10_GFPneg_rep5

tag: tissue

tag: neuronal population

value: bystander neurons

tag: disease stage_(days_post_challenge)

value: 6.4 weeks


title: HEK_1000PREs_Control-1_rep_3 (RBPscan)

description: Library name: HEK_PRE_Control-1_rep3

tag: cell line


title: HEK_1000PREs_Control-1_rep_2 (RBPscan)

description: Library name: HEK_PRE_Control-1_rep2


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D2, Library C13-1_Gabpa-2_8522509006585

description:
Library name: C13-1_Gabpa-2_8522509006585
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: iPSC-derived neural progenitors

value: trisomy 21

tag: treatment

tag: sample id

tag: library id

value: TRUE


title: HEK_1000PREs_Control-1_rep_1 (RBPscan)

description: Library name: HEK_PRE_Control-1_rep1


title: WT_HC_CC10_GFPneg_rep4

description: Library name: WT_HC_CC10_GFPneg_rep4

tag: age

tag: biological replicate


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D3, Library C13-1_Bach1-3_8522509006591

description:
Library name: C13-1_Bach1-3_8522509006591
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell type

tag: group

tag: batch

tag: in final_analysis


title: dre.embryo.pool_PFHxA_60_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

tag: replicate

tag: row

value: G

tag: column

tag: plate

tag: processing batch

tag: FISH origin

tag: rna yield_ng_u_l

tag: rin

value: TempO-Seq


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D1, Library C13-1_Gabpa-1_8522509006595

description:
Library name: C13-1_Gabpa-1_8522509006595
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell line

tag: genotype

tag: treatment


title: HEK_1000PREs_hsPum2-hsADAR2cdMUT_rep_2 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT_rep2


title: WT_HC_CC10_GFPneg_rep3

description: Library name: WT_HC_CC10_GFPneg_rep3

tag: tissue

value: Brain, hippocampus

tag: neuronal population

tag: disease stage_(days_post_challenge)

tag: age


title: WT_HC_CC10_GFPneg_rep1

description: Library name: WT_HC_CC10_GFPneg_rep1

value: C57BL/6J, NuTRAP transgenic

tag: cell type

tag: biological replicate


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D1, Library C13-1_Gabpa-1_8522509006584

description:
Library name: C13-1_Gabpa-1_8522509006584
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: sample id

tag: library id

tag: group

tag: batch

tag: in final_analysis


title: dre.embryo.pool_PFHxA_20_4

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

tag: replicate

tag: row

value: F

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: ottawa

tag: protocol


title: WT_HC_CC10_GFPneg_rep2

description: Library name: WT_HC_CC10_GFPneg_rep2

tag: tissue

tag: genotype

value: neurons

tag: neuronal population

tag: disease stage_(days_post_challenge)


title: HEK293_hsPUM2_hsADAR2cd-T375G/E488Q_NORAD_rep_2 (RBPscan)

description: Library name: HEK_NORAD_hsaPUM2_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.

tag: cell line

tag: cell type


title: dre.embryo.pool_PFHxA_200_4

value: 5 days

value: PFHxA

tag: treatment

value: C

tag: rna yield_ng_u_l

tag: rin

tag: sample id


title: HEK_1000PREs_N22-hsADAR2cdMUT_rep_2 (RBPscan)

description: Library name: HEK_PRE_ADARcdMUT_rep2

value: human embryonic kidney

value: WT


title: HEK293_hsPUM2_hsADAR2cd-T375G/E488Q_NORAD_rep_3 (RBPscan)

description: Library name: HEK_NORAD_hsaPUM2_rep3


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D3, Library C13-1_Bach1-3_8522509006580

description:
Library name: C13-1_Bach1-3_8522509006580
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: iPSC-derived neural progenitors

tag: library id

tag: group

tag: batch

tag: in final_analysis


title: WT_HC_CnC10_GFPpos_rep4

description: Library name: WT_HC_CnC10_GFPpos_rep4

value: virus-exposed neurons

tag: age

value: 6 weeks

tag: biological replicate


title: HEK_1000PREs_N22-hsADAR2cdMUT_rep_1 (RBPscan)

description: Library name: HEK_PRE_ADARcdMUT_rep1


title: dre.embryo.pool_PFHxA_6_4

value: pool of 10 whole embryos

tag: replicate

tag: row

value: B

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: protocol


title: dre.embryo.pool_PFDS_6_4

tag: tissue

tag: cell line

value: 120-hours post fertilization

tag: cell type

tag: genotype

value: PFDS

tag: treatment

value: A

value: mixed

tag: rna yield_ng_u_l


title: WT_HC_CnC10_GFPpos_rep3

description: Library name: WT_HC_CnC10_GFPpos_rep3

value: Brain, hippocampus

value: C57BL/6J, NuTRAP transgenic

tag: neuronal population

tag: disease stage_(days_post_challenge)


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D2, Library C13-1_Bach1-2_8522509006590

description:
Library name: C13-1_Bach1-2_8522509006590
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: trisomy 21

tag: sample id

tag: library id

tag: group

tag: batch

tag: in final_analysis

value: TRUE


title: HEK293_Control_NORAD_rep_3 (RBPscan)

description: Library name: HEK_NORAD_rep3


title: dre.embryo.pool_PFDS_2_4

value: 5 days

tag: replicate

tag: row

value: H

tag: column

tag: plate

tag: processing batch

tag: rin

value: TempO-Seq


title: HEK293_hsPUM2_hsADAR2cd-T375G/E488Q_NORAD_rep_1 (RBPscan)

description: Library name: HEK_NORAD_hsaPUM2_rep1

tag: cell line

tag: cell type

value: human embryonic kidney

value: WT


title: WT_HC_CnC10_GFPpos_rep2

description: Library name: WT_HC_CnC10_GFPpos_rep2

tag: tissue

tag: genotype

value: neurons

value: virus-exposed neurons

tag: age

tag: biological replicate


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D2, Library C13-1_Bach1-2_8522509006579

description:
Library name: C13-1_Bach1-2_8522509006579
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: iPSC-derived neural progenitors

tag: treatment

tag: sample id


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D1, Library C13-1_Bach1-1_8522509006589

description:
Library name: C13-1_Bach1-1_8522509006589
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: library id

tag: group


title: HEK293_Control_NORAD_rep_2 (RBPscan)

description: Library name: HEK_NORAD_rep2


title: dre.embryo.pool_PFDS_0.6_4

value: pool of 10 whole embryos

value: G

tag: rna extraction_batch

tag: FISH origin

tag: rna yield_ng_u_l

tag: protocol


title: WT_HC_CnC10_GFPpos_rep1

description: Library name: WT_HC_CnC10_GFPpos_rep1

tag: neuronal population

tag: disease stage_(days_post_challenge)

value: 6 weeks


title: WT_HC_CnC10_GFPneg_rep4

description: Library name: WT_HC_CnC10_GFPneg_rep4

value: bystander neurons


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D1, Library C13-1_Bach1-1_8522509006578

description:
Library name: C13-1_Bach1-1_8522509006578
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: batch

tag: in final_analysis


title: HEK293_Control_NORAD_rep_1 (RBPscan)

description: Library name: HEK_NORAD_rep1

tag: cell line

tag: cell type


title: HEK293_hsADAR2cd-T375G/E488Q_NORAD_rep_3 (RBPscan)

description: Library name: HEK_NORAD_ADARcd_rep3

tag: genotype


title: iPSC-derived neural progenitors, trisomy 21, untreated, Library C13-1_8522509006588

description:
Library name: C13-1_8522509006588
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

value: untreated

value: DS


title: HEK293_hsADAR2cd-T375G/E488Q_NORAD_rep_2 (RBPscan)

description: Library name: HEK_NORAD_ADARcd_rep2


title: dre.embryo.pool_PFHxS_20_4

tag: tissue

value: 120-hours post fertilization

value: PFHxS

tag: replicate

tag: row

value: F

tag: column

tag: plate

tag: processing batch

value: ottawa

tag: rin


title: dre.embryo.pool_control_mixed_0_4

value: 5 days

tag: treatment

value: H

tag: rna extraction_batch

tag: FISH origin

value: mixed

tag: sample id


title: HEK293_hsADAR2cd-T375G/E488Q_NORAD_rep_1 (RBPscan)

description: Library name: HEK_NORAD_ADARcd_rep1

value: human embryonic kidney

value: WT


title: iPSC-derived neural progenitors, disomic, untreated, Library C9_NT_3

description:
Library name: C9_NT_3
bulk RNA-seq (BGI)

value: disomic

tag: library id

tag: group

value: CON

value: TRUE


title: iPSC-derived neural progenitors, disomic, untreated, Library C9_NT_2

description:
Library name: C9_NT_2
bulk RNA-seq (BGI)

value: iPSC-derived neural progenitors

tag: batch

tag: in final_analysis


title: WT_HC_CnC10_GFPneg_rep1

description: Library name: WT_HC_CnC10_GFPneg_rep1

value: Brain, hippocampus

value: C57BL/6J, NuTRAP transgenic

tag: cell type

value: neurons

tag: neuronal population

tag: disease stage_(days_post_challenge)

tag: age

value: 6 weeks

tag: biological replicate


title: WT L. interrogans, EMJH, replicate 4

description:
Library name: Int4_EMJH_S4
D3-Liver_Int-EMJH_raw_counts.txt

source_name: serovar manilae

tag: tissue

value: serovar manilae

value: WT L. interrogans, EMJH