title: L.plantarum, untreated, merged

description: Library name: lpl_UT

data_processing:
sequencing data are transfered to fastq.gz files and demultiplexed using bcl2fastq/2.20.0
fastq.gz files are quality/adpter trimmed using cutadapt/4.8 with parameter set to "-a AGATCGGAAGAGCAC --minimum-length 28 -e 0.2 -o 9 --nextseq-trim=20"
quality/adapter trimmed fastq files are extracted UMI using umi_tools/1.0.0 with command line set to "umi_tools extract --bc-pattern NNNNNNNN"
mapping is processed with star alignent program/2.7.11a, with parameters set to "star -- readFilesCommand gunzip -c  --outSAMtype BAM SortedByCoordinate --alignEndsType Extend5pOfRead1 --outFilterMatchNminOverLread 0.9 --outFilterMultimapNmax 12 --alignIntronMax 1 --outReadsUnmapped Fastx"
Deduplication is processed for the output bam files using "umi_tools dedup" command
bed graph are generated using bedtools/2.31.0 using "bedtools genomecov -bg -5 -strand - -ibam" and "bedtools genomecov -bg -5 -strand + -ibam" command
RNA types are counted using bedtools/2.31.0 using "bedtools intersect"
Deduplicated bam files are processed to fivepseq package/1.3.5 for context specific ribosome stalling analysis. Parameters are set to "-tripeptide-pos -8" (last amino acid is at A site which is 8nt for b.subtilis and l.plantarum) when processing erythromycin treated samples, to observe R/K-x-R/K motif specific ribosome stalling.amino acid /motif specif peaks are normalized by library size( NumOfReadsDownsampled from data_summary.txt table)
Assembly: GCF_000009045.1(b.subtilis), GCF_009913655.1(l.plantarum)
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: Lactiplantibacillus plantarum

source_name: ATCC 8014

growth_protocol: b.subtilis is cultured in LB media at 37°C in incubator. L.plantarum is cultured in MRS broth at 37°C in incubator.

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
2ug total extracted RNA is used for library preparation using HT-5PSeq library prepartion protocol (Zhang and Pelechano 2021) ,with some modification. In brief, 2µg total RNA was ligated over night at 16˚C to r5P_RNA_MPX oligo (CrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU rXrXrXrXrXrX rNrNrNrNrNrNrNrN) carrying a sample barcode (rX) and unique molecular identifiers (rN). Ligase was deactivated using 10mM EDTA and incubation at 65˚C for 15minutes (up to 8 individual barcoded RNA ligations were pooled). Ligated RNA pools were purified with Phenbol chloroform Isoamylalcohol, and Ethanol NaOAc precipitation of aqueous layer. Total RNA of Ligated pool was quantified to not exceed 5µg and reverse transcribed using random hexamer (5Pseq-RT, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN, 20µM) oligos to prime. Remaining RNA was degraded using NaOH and ribosomal  RNA was removed using previously described rRNA DNA oligo probes (2µM) and duplex-specific nuclease (DSN, Evrogen) digestion . Optimal probe: sample ratio was estimated prior by quantifying RT sample with Qubit to measure ssDNA. rRNA depleted cDNA was amplified by PCR (16 cycles) and purified purified using 1.6x volumes of RNACleanXP beads (Beckman Coulter) and quantified using Qubit HS DNA Kit. 17ng of each final product was pooled (1318 excluded because no yield after PCR) and enriched for fragments with between 300-700nt using Ampure XP (0.75V-0.55V). Size selected HT-5P Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequenced using a NextSeq2000 Illumina sequencer (P3 50cycles kit).

treatment_protocol: Exponetially growing bacteria culture(OD600=0.6-0.8) is treated with different concentrations of chloramphenicol and 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: ATCC 8014

tag: genotype

value: wild type

value: untreated


title: OTHER,metagenome for B017m3 at 3mon

status: Public on Dec 23 2025

type: SRA

city: Nanjing

first: xinyuan

last: ge

state: Jiangsu

address: Longmian Road 818

country: China

institute: Nanjing Medical University School of Public Health

description:
Library name: B017m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B017m3 at 3mon

library_source: genomic

data_processing:
Raw sequencing reads were quality-filtered, trimmed, and decontaminated to remove host sequences. Taxonomic profiling was performed using MetaPhlAn (v4.1.4) to generate species-level relative abundance profiles for downstream analysis.
Supplementary files format and content: Processed data files include species-level relative abundance tables derived from whole-metagenome shotgun sequencing of fecal samples collected before and after the 3-month aerobic exercise intervention. Only species detected in multiple samples were retained for downstream analysis. Taxonomic annotation was performed using MetaPhlAn (v4.1.4). Files are provided in tab-delimited text format, with rows representing species and columns representing samples.

molecule: genomic DNA

organism: feces metagenome

source_name: feces

growth_protocol: Not applicable. Fecal samples were collected directly from human participants without microbial culture.

extract_protocol:
Microbial DNA was extracted from fecal samples using a standardized bead-beating and column-based DNA extraction protocol.
Shotgun metagenomic DNA libraries were prepared from extracted microbial DNA and sequenced on the Illumina platform using paired-end 150 bp reads.

treatment_protocol: Fecal samples were collected from participants in the 3-month aerobic exercise intervention group at baseline and after the intervention. Samples were paired for each participant. Only intervention group samples (n=33) are included in this dataset.

tag: tissue

value: feces

tag: treatment

value: exercise

tag: timepoint


title: Recurrent HGSOC patients 073

city: Incheon

first: Seong-Woo

last: Park

address: 265, Harmony-ro, Yeonsu-gu

country: South Korea

institute: Incheon National University

description: Library name: OBGY0111

library_source: transcriptomic

data_processing:
The quality of raw data was ensured using the FastQC v0.11.9.
Adapter sequences were trimmed using Trimfastq from Fabio v2.1.0, then trimmed FASTQ files were aligned to GRCh37.p13 using STAR v2.7.10.
Assembly: GRCh37.p13
Supplementary files format and content: TXT file containing detected gene fusions.
Supplementary files format and content: TXT file containing detected gene fusions.

molecule: total RNA

organism: Homo sapiens

source_name: Tumor tissue

extract_protocol:
RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue sections of HGSOC patients RNeasy Plus Kits (Qiagen, NY, USA).
Library preparation was performed using the TruSight Oncology 500 (TSO500) panel (Illumina, San Diego, CA, USA).

tag: disease status

value: Recurrent

tag: tumor stage

value: IIB

tag: Sex

value: Female

value: Tumor tissue


title: L.plantarum, untreated, rep2

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: lpl_UT_1_rep1

tag: cell type


title: Primary HGSOC patients 075

description: Library name: OBGY0108

value: Primary

value: IIIC


title: dre.embryo.pool_PFDS_2_1

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

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

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

tag: cell line

value: 120-hours post fertilization

value: 5 days

value: PFDS

tag: replicate

tag: row

value: F

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: mixed

tag: rna yield_ng_u_l

tag: rin

tag: protocol

value: TempO-Seq

tag: sample id


title: Primary HGSOC patients 069

description: Library name: OBGY0121

tag: tissue


title: L.plantarum, untreated, rep1

description: Library name: lpl_UT_02_rep1

value: ATCC 8014

tag: genotype

value: wild type

tag: treatment


title: C.difficile_resistant, untreated, subsample

description: Library name: cdiff_resistant_ctr_merged_30000

data_processing:
.pod5 files are basedcalled in fast basecalling mode using Dorado(MinKnow software), with minimum Q score set to 8.
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 resistant 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. 12 samples (4 biological replicates, 3 technical replicates) are pooled together (50fmol) and loaded onto flongle flow cell for sequencing overnight.

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 resistant isolates

value: untreatd


title: OTHER,metagenome for B009m3 at 3mon

description:
Library name: B009m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B009m3 at 3mon

value: feces

value: exercise

tag: timepoint


title: dre.embryo.pool_PFHxA_200_1

tag: cell type

value: PFHxA

value: G

value: ottawa


title: Primary HGSOC patients 078

description: Library name: OBGY0103

tag: disease status

value: Primary

tag: tumor stage

value: IIIC

tag: Sex

value: Female

value: Tumor tissue


title: OTHER,metagenome for B008m3 at 3mon

description:
Library name: B008m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B008m3 at 3mon


title: Primary HGSOC patients 076

description: Library name: OBGY0106

value: IIB


title: OTHER,metagenome for B273 at baseline

description:
Library name: B273
Whole-metagenome shotgun sequencing
OTHER,metagenome for B273 at baseline

value: baseline


title: dre.embryo.pool_PFHxA_600_1

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: 5 days

tag: replicate

tag: row

value: H

tag: column


title: dre.embryo.pool_control_mixed_0_3

value: C

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: mixed

value: TempO-Seq


title: dre.embryo.pool_PFHxS_6_1

value: PFHxS

tag: rna yield_ng_u_l

tag: rin

tag: protocol

tag: sample id


title: L.plantarum,erythromycin_2.5ug/ml, merged

description: Library name: lpl_ERY_5x

value: ATCC 8014

tag: genotype

value: wild type

tag: treatment


title: L.plantarum,erythromycin_2.5ug/ml, rep2

description: Library name: lpl_ERY_5_rep2

tag: cell type


title: dre.embryo.pool_PFOS_40_2

tag: tissue

value: PFOS

value: B


title: Primary HGSOC patients 080

description: Library name: OBGY0099

tag: disease status

value: Primary

tag: tumor stage

value: IVB

tag: Sex


title: L.plantarum, erythromycin_0.5ug/ml, merged

description: Library name: lpl_ERY_1x


title: Primary HGSOC patients 077

description: Library name: OBGY0105

value: IIIC

value: Female

value: Tumor tissue


title: Primary HGSOC patients 081

description: Library name: OBGY0096

value: IVA


title: OTHER,metagenome for B003m3 at 3mon

description:
Library name: B003m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B003m3 at 3mon

value: feces

value: exercise

tag: timepoint


title: L.plantarum,erythromycin_2.5ug/ml, rep3

description: Library name: lpl_ERY_5_rep3


title: OTHER,metagenome for B277 at baseline

description:
Library name: B277
Whole-metagenome shotgun sequencing
OTHER,metagenome for B277 at baseline

value: baseline


title: Recurrent HGSOC patients 079

description: Library name: OBGY0101

value: Recurrent


title: Primary HGSOC patients 082

description: Library name: OBGY0089


title: Primary HGSOC patients 074

description: Library name: OBGY0110


title: L.plantarum, untreated, rep3

description: Library name: lpl_UT_5_rep3

value: untreated


title: dre.embryo.pool_PFDS_0.6_1

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: 5 days

value: PFDS

tag: replicate

tag: row

value: F

tag: column

value: mixed

value: TempO-Seq


title: dre.embryo.pool_PFOS_1.2_2

value: PFOS

value: A

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin


title: Primary HGSOC patients 083

description: Library name: OBGY0084

value: Primary

value: IIIC

value: Female


title: OTHER,metagenome for B264 at baseline

description:
Library name: B264
Whole-metagenome shotgun sequencing
OTHER,metagenome for B264 at baseline

value: feces


title: OTHER,metagenome for B250 at baseline

description:
Library name: B250
Whole-metagenome shotgun sequencing
OTHER,metagenome for B250 at baseline

value: exercise


title: dre.embryo.pool_PFDS_0.2_2

value: B

tag: rna yield_ng_u_l

tag: rin

tag: protocol

tag: sample id


title: OTHER,metagenome for B263 at baseline

description:
Library name: B263
Whole-metagenome shotgun sequencing
OTHER,metagenome for B263 at baseline

tag: tissue

tag: treatment

value: baseline


title: dre.embryo.pool_PFOS_12_2

tag: cell type

tag: genotype


title: L.plantarum,erythromycin_2.5ug/ml, rep1

description: Library name: lpl_ERY_5_rep1

value: ATCC 8014

value: wild type


title: L.plantarum, erythromycin_0.1ug/ml, rep3

description: Library name: lpl_ERY_02_rep3


title: L.plantarum, erythromycin_0.5ug/ml, rep2

description: Library name: lpl_ERY_1_rep2


title: OTHER,metagenome for B258 at baseline

description:
Library name: B258
Whole-metagenome shotgun sequencing
OTHER,metagenome for B258 at baseline

tag: timepoint


title: L.plantarum, erythromycin_0.1ug/ml, rep2

description: Library name: lpl_ERY_02_rep2


title: dre.embryo.pool_PFOS_4_2

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: E


title: OTHER,metagenome for B253 at baseline

description:
Library name: B253
Whole-metagenome shotgun sequencing
OTHER,metagenome for B253 at baseline


title: OTHER,metagenome for B237 at baseline

description:
Library name: B237
Whole-metagenome shotgun sequencing
OTHER,metagenome for B237 at baseline


title: dre.embryo.pool_PFOS_0.4_2

value: 5 days

tag: replicate


title: Primary HGSOC patients 085

description: Library name: OBGY0081

tag: disease status

tag: tumor stage

value: IVA

tag: Sex

value: Tumor tissue


title: L.plantarum, erythromycin_0.5ug/ml, rep1

description: Library name: lpl_ERY_1_rep1


title: L.plantarum, erythromycin_0.1ug/ml, merged

description: Library name: lpl_ERY_02x


title: dre.embryo.pool_PFOA_120_2

value: PFOA

tag: row

tag: column

tag: plate

tag: processing batch

value: mixed

value: TempO-Seq


title: dre.embryo.pool_PFOA_40_2

value: A

tag: rna extraction_batch

tag: FISH origin

tag: rna yield_ng_u_l

tag: rin


title: Primary HGSOC patients 087

description: Library name: OBGY0076

value: Primary

value: Female

tag: tissue


title: L.plantarum, chloramphenicol_40ug/ml, rep3

description: Library name: lpl_CAM_5_rep3

tag: cell type

tag: treatment


title: OTHER,metagenome for B235 at baseline

description:
Library name: B235
Whole-metagenome shotgun sequencing
OTHER,metagenome for B235 at baseline

value: feces

value: exercise

tag: timepoint


title: L.plantarum, chloramphenicol_40ug/ml, merged

description: Library name: lpl_CAM_5x

tag: genotype


title: OTHER,metagenome for B205 at baseline

description:
Library name: B205
Whole-metagenome shotgun sequencing
OTHER,metagenome for B205 at baseline

value: baseline


title: Primary HGSOC patients 086

description: Library name: OBGY0077

value: IVB


title: Primary HGSOC patients 084

description: Library name: OBGY0083

value: IC


title: dre.embryo.pool_PFOA_400_2

value: pool of 10 whole embryos

tag: cell line

tag: replicate

value: B

tag: protocol

tag: sample id


title: Primary HGSOC patients 090

description: Library name: OBGY0051

tag: disease status

tag: tumor stage

tag: Sex


title: OTHER,metagenome for B211 at baseline

description:
Library name: B211
Whole-metagenome shotgun sequencing
OTHER,metagenome for B211 at baseline


title: L.plantarum, erythromycin_0.1ug/ml, rep1

description: Library name: lpl_ERY_02_rep1

value: ATCC 8014

value: wild type


title: OTHER,metagenome for B209 at baseline

description:
Library name: B209
Whole-metagenome shotgun sequencing
OTHER,metagenome for B209 at baseline


title: dre.embryo.pool_PFOA_12_1

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: 120-hours post fertilization

value: 5 days

tag: row

value: H

tag: column

tag: plate

tag: processing batch


title: Primary HGSOC patients 089

description: Library name: OBGY0053

value: Tumor tissue


title: L.plantarum, chloramphenicol_8ug/ml, merged

description: Library name: lpl_CAM_1x


title: L.plantarum, chloramphenicol_40ug/ml, rep2

description: Library name: lpl_CAM_5_rep2


title: OTHER,metagenome for B197 at baseline

description:
Library name: B197
Whole-metagenome shotgun sequencing
OTHER,metagenome for B197 at baseline


title: dre.embryo.pool_PFOA_4_1

value: PFOA

value: G

tag: rna extraction_batch

tag: FISH origin

value: mixed

tag: rna yield_ng_u_l

tag: rin

value: TempO-Seq


title: OTHER,metagenome for B161 at baseline

description:
Library name: B161
Whole-metagenome shotgun sequencing
OTHER,metagenome for B161 at baseline

tag: tissue

value: feces

tag: treatment

tag: timepoint


title: dre.embryo.pool_PFHxS_20_1

tag: cell line

tag: cell type

tag: genotype

value: PFHxS

tag: replicate

value: D

value: ottawa


title: Primary HGSOC patients 093

description: Library name: OBGY0041

tag: disease status

value: Primary

tag: tumor stage

value: III

value: Female


title: L.plantarum, chloramphenicol_8ug/ml, rep3

description: Library name: lpl_CAM_1_rep3

value: ATCC 8014


title: L.plantarum, chloramphenicol_40ug/ml, rep1

description: Library name: lpl_CAM_5_rep1

value: wild type


title: Recurrent HGSOC patients 092

description: Library name: OBGY0043

value: Recurrent

value: IVB

tag: Sex


title: dre.embryo.pool_PFHxS_200_1

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: 5 days

tag: row

value: F

tag: column

tag: protocol

tag: sample id


title: Primary HGSOC patients 091

description: Library name: OBGY0049

value: IA

value: Tumor tissue


title: dre.embryo.pool_PFHxS_60_1

value: E

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: TempO-Seq


title: dre.embryo.pool_control_mixed_0_2

tag: tissue

tag: treatment

value: A

value: mixed

tag: rna yield_ng_u_l

tag: rin


title: Primary HGSOC patients 088

description: Library name: OBGY0070

value: Primary


title: Primary HGSOC patients 094

description: Library name: OBGY0039

value: IIIA


title: OTHER,metagenome for B158 at baseline

description:
Library name: B158
Whole-metagenome shotgun sequencing
OTHER,metagenome for B158 at baseline

value: feces

value: exercise

tag: timepoint

value: baseline


title: L.plantarum, chloramphenicol_8ug/ml, rep1

description: Library name: lpl_CAM_1_rep1

tag: cell type

value: ATCC 8014

tag: genotype

value: wild type


title: dre.embryo.pool_PFBS_8_1

value: pool of 10 whole embryos

tag: cell line

value: PFBS

tag: replicate

value: D

value: ottawa


title: Primary HGSOC patients 095

description: Library name: OBGY0038

tag: disease status

tag: tumor stage

value: IIIC

tag: Sex

value: Female


title: OTHER,metagenome for B155 at baseline

description:
Library name: B155
Whole-metagenome shotgun sequencing
OTHER,metagenome for B155 at baseline


title: L.plantarum, chloramphenicol_1.6ug/ml, rep3

description: Library name: lpl_CAM_02_rep3


title: OTHER,metagenome for B154 at baseline

description:
Library name: B154
Whole-metagenome shotgun sequencing
OTHER,metagenome for B154 at baseline


title: dre.embryo.pool_PFBS_25_1

value: 120-hours post fertilization

value: 5 days

tag: row

value: E

tag: column

tag: protocol

tag: sample id


title: Recurrent HGSOC patients 096

description: Library name: OBGY0033

value: Recurrent

value: R

value: Tumor tissue


title: OTHER,metagenome for B085 at baseline

description:
Library name: B085
Whole-metagenome shotgun sequencing
OTHER,metagenome for B085 at baseline

value: feces


title: OTHER,metagenome for B164 at baseline

description:
Library name: B164
Whole-metagenome shotgun sequencing
OTHER,metagenome for B164 at baseline

value: exercise


title: OTHER,metagenome for B084 at baseline

description:
Library name: B084
Whole-metagenome shotgun sequencing
OTHER,metagenome for B084 at baseline

value: baseline


title: L.plantarum, chloramphenicol_1.6ug/ml, merged

description: Library name: lpl_CAM_02x

value: ATCC 8014


title: dre.embryo.pool_PFBS_80_2

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: TempO-Seq


title: OTHER,metagenome for B131 at baseline

description:
Library name: B131
Whole-metagenome shotgun sequencing
OTHER,metagenome for B131 at baseline

tag: tissue

tag: treatment


title: L.plantarum, chloramphenicol_1.6ug/ml, rep2

description: Library name: lpl_CAM_02_rep2

tag: cell type

value: wild type


title: Primary HGSOC patients 099

description: Library name: OBGY0027

value: Primary

value: IIA


title: Primary HGSOC patients 100

description: Library name: OBGY0026


title: L.plantarum, chloramphenicol_1.6ug/ml, rep1

description: Library name: lpl_CAM_02_rep1

tag: genotype


title: dre.embryo.pool_PFBA_80_2

value: pool of 10 whole embryos

tag: cell line

value: PFBA

value: C

value: ottawa

tag: rna yield_ng_u_l

tag: rin


title: CM_nodule_rna_rep3

city: Kunming

first: Dingjie

last: Wang

state: Yunnan

address: NO. 132 Lanhei Road

institute: Kunming Institute of Botany, Chinese Academy of Sciences

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

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

organism: Chamaecrista pumila

source_name: nodule

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

value: nodule


title: Primary HGSOC patients 098

description: Library name: OBGY0030

tag: disease status

tag: tumor stage

value: IIIC

value: Female


title: Primary HGSOC patients 097

description: Library name: OBGY0031

tag: Sex


title: dre.embryo.pool_PFBA_600_2

value: 120-hours post fertilization

value: 5 days

tag: replicate

tag: row

tag: column


title: OTHER,metagenome for B068 at baseline

description:
Library name: B068
Whole-metagenome shotgun sequencing
OTHER,metagenome for B068 at baseline

value: feces

tag: timepoint


title: dre.embryo.pool_PFBA_25_1

value: B

tag: plate

tag: processing batch

tag: protocol

tag: sample id


title: CM_nodule_rna_rep2

tag: tissue


title: dre.embryo.pool_PFBA_8_1

tag: cell type

tag: treatment

tag: rna extraction_batch

tag: FISH origin


title: Primary HGSOC patients 101

description: Library name: OBGY0025

value: IC

value: Tumor tissue


title: dre.embryo.pool_PFOS_40_1

tag: cell line

tag: genotype

value: PFOS

value: mixed

tag: rna yield_ng_u_l

tag: rin

value: TempO-Seq


title: CM_nodule_rna_rep1


title: dre.embryo.pool_control_ottawa_0_3

tag: replicate

value: A


title: CM_root_rna_rep2

source_name: root

value: root


title: CM_root_rna_rep1


title: dre.embryo.pool_PFOS_12_1

value: pool of 10 whole embryos

tag: row


title: Recurrent HGSOC patients 102

description: Library name: OBGY0023

tag: disease status

value: Recurrent

tag: tumor stage

tag: Sex


title: OTHER,metagenome for B040 at baseline

description:
Library name: B040
Whole-metagenome shotgun sequencing
OTHER,metagenome for B040 at baseline

value: exercise

tag: timepoint

value: baseline


title: OTHER,metagenome for B052 at baseline

description:
Library name: B052
Whole-metagenome shotgun sequencing
OTHER,metagenome for B052 at baseline


title: OTHER,metagenome for B062 at baseline

description:
Library name: B062
Whole-metagenome shotgun sequencing
OTHER,metagenome for B062 at baseline


title: Primary HGSOC patients 104

description: Library name: OBGY0020

value: Primary

value: IIIC


title: B.subtilis,HT-5PSeq

description: Library name: bsub_ht5pseq

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

organism: Bacillus subtilis

source_name: 168 trpC2

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

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

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

value: 168 trpC2

value: trpC knockdown

value: untreated


title: Recurrent HGSOC patients 103

description: Library name: OBGY0021

value: IVB

value: Female


title: dre.embryo.pool_PFOS_4_1

value: 120-hours post fertilization

value: 5 days

value: H

tag: column

tag: plate

tag: processing batch

tag: protocol


title: OTHER,metagenome for B031 at baseline

description:
Library name: B031
Whole-metagenome shotgun sequencing
OTHER,metagenome for B031 at baseline

tag: tissue

value: feces

tag: treatment


title: Primary HGSOC patients 106

description: Library name: OBGY0011

value: Tumor tissue


title: B.subtilis,ctr,rep2

description: Library name: bs_ctr2_S2_R1_001

tag: cell type


title: Primary HGSOC patients 105

description: Library name: OBGY0018


title: dre.embryo.pool_PFOS_1.2_1

tag: cell line

value: PFOS

value: B

tag: rna extraction_batch

tag: FISH origin

value: mixed

value: TempO-Seq

tag: sample id


title: OTHER,metagenome for B166 at baseline

description:
Library name: B166
Whole-metagenome shotgun sequencing
OTHER,metagenome for B166 at baseline

value: exercise

value: baseline


title: B.subtilis,ctr,rep1

description: Library name: bs_ctr1_S1_R1_001

tag: genotype


title: Primary HGSOC patients 107

description: Library name: OBGY0008

value: Primary

value: IIIC


title: dre.embryo.pool_PFOS_0.4_1

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

tag: replicate

tag: row

value: G

tag: rna yield_ng_u_l

tag: rin


title: OTHER,metagenome for B032 at baseline

description:
Library name: B032
Whole-metagenome shotgun sequencing
OTHER,metagenome for B032 at baseline

tag: timepoint


title: B.subtilis,s5PSeq,rep2

description: Library name: bs_bo2_S4_R1_001

value: 168 trpC2

value: trpC knockdown

value: untreated


title: Primary HGSOC patients 108

description: Library name: OBGY0007

tag: disease status

tag: tumor stage

tag: Sex

value: Female


title: OTHER,metagenome for B009 at baseline

description:
Library name: B009
Whole-metagenome shotgun sequencing
OTHER,metagenome for B009 at baseline


title: OTHER,metagenome for B017 at baseline

description:
Library name: B017
Whole-metagenome shotgun sequencing
OTHER,metagenome for B017 at baseline


title: B.subtilis,s5PSeq,rep1

description: Library name: bs_bo1_S3_R1_001


title: dre.embryo.pool_PFOA_120_1

value: 120-hours post fertilization

value: 5 days

value: PFOA

value: H

tag: column

tag: plate

tag: processing batch

tag: protocol


title: L.plantarum, chloramphenicol_8ug/ml, rep2

description: Library name: lpl_CAM_1_rep2

tag: cell type

value: ATCC 8014

value: wild type

tag: treatment


title: dre.embryo.pool_PFOA_40_1

tag: tissue

tag: cell line

tag: rna extraction_batch

tag: FISH origin

value: mixed

value: TempO-Seq


title: OTHER,metagenome for B003 at baseline

description:
Library name: B003
Whole-metagenome shotgun sequencing
OTHER,metagenome for B003 at baseline

value: feces

value: exercise

value: baseline


title: OTHER,metagenome for B008 at baseline

description:
Library name: B008
Whole-metagenome shotgun sequencing
OTHER,metagenome for B008 at baseline


title: dre.embryo.pool_PFHxS_400_1

value: pool of 10 whole embryos

tag: genotype

value: PFHxS

tag: replicate

tag: row

value: F

value: ottawa

tag: sample id


title: OTHER,metagenome for B063 at baseline

description:
Library name: B063
Whole-metagenome shotgun sequencing
OTHER,metagenome for B063 at baseline

tag: timepoint


title: B.subtilis, untreated, rep3

description: Library name: bsub_UT_5x_rep2

value: 168 trpC2

value: trpC knockdown

value: untreated


title: dre.embryo.pool_PFBS_600_1

value: 120-hours post fertilization

value: 5 days

value: PFBS

value: E

tag: rna yield_ng_u_l

tag: rin


title: dre.embryo.pool_PFOA_400_1

value: PFOA

value: A

tag: column


title: dre.embryo.pool_PFBS_250_2

tag: plate

value: TempO-Seq


title: B.subtilis, untreated, rep1

description: Library name: bsub_UT_02x_rep2


title: HXC1

first: Yaxu

last: Liang

state: 江苏省

address: 江苏省南京市玄武区南京农业大学

institute: Nanjing agricultural university

description:
Library name: sample4
H114_HC1

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
we used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: GCF_000003025.6_Sscrofa11.1_genomic.fna
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: polyA RNA

organism: Sus scrofa

source_name: ileum

extract_protocol:
Total RNA was extracted from ileum and colon samples using the Trizol method. Poly(A) + mRNA was isolated from total RNA using Dynabeads Oligo(dT)25
RNA was reverse transcribed into cDNA using random oligonucleotides, Super Script II, DNA Polymerase I, and RNase H. Adapters were ligated to both ends of cDNA fragments. Double-stranded cDNA of approximately 450 bp were selected using the AMPure XP bead-based purification system (Beckman Coulter, Beverly, CA, USA). Adapter-ligated libraries were enriched through polymerase chain reaction (PCR) amplification using the Illumina PCR Primer Cocktail for 15 cycles. The amplified libraries were purified using the AMPure XP system and quantified using the Agilent High Sensitivity DNA Assay on a Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Paired-end sequencing was performed on the NovaSeq X platform (Illumina, San Diego, CA, USA).

value: ileum

tag: Sex

value: female

value: HXC


title: SANT1 treatment, hTEM.v3, day6

city: Hong Kong

first: Tianming

last: Wu

state: Hong Kong

address: LKS Int Biomed Sci Bldg

department: School of Biomedical Sciences

institute: Chinese University of Hong Kong

description:
Library name: scRNA_Sample12
scRNA-seq

library_source: transcriptomic single cell

data_processing:
For scRNA-seq data, fastq reads were generated using 10x Genomics cellranger (v9.0.1) pipeline. For Visium HD data, sastq reads were generated using 10x Genomics cellranger (v3.1.3) pipeline. Both processings are with default settings.
Assembly: GRCh38
Supplementary files format and content: For scRNA-seq processed data, RDS objects for each hTEM.v1/2/3
Supplementary files format and content: Spatial processed data includes: barcodes.tsv.gz, features.tsv.gz,  Matrix.mtx.gz, aligned_fiducials.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png

extract_protocol:
For scRNA-seq, hTEM embryoids were washed twice with DPBS to remove excessive Matrigel. Then embryoids were dissociated by using Accutase : TrypLE 1:1 at 37 °C for 10-15 min. Single cells were counted and adjusted to 106/ml in 1 ml N2B27 basal medium, filtered through a 40 μm cell strainer. For Visium HD, embryoids were snap frozen and OCT embedded followed by frozen sectioning using a cryostat microtome at 10 µm. All buffers in contact with the sectioning slides wer epre-treated with RNaseOUT (Thermo, 10777019) to preserve RNA integrity.
For scRNA-seq, single cells were loaded onto Chromium Single Cell 3' Library and Gel Bead Kit v3.1 or v4 (10x Genomics). Follow the cDNA-amplification reaction, quality control and quantification was performed on the Agilent 4200 Tapestation using the High Sensitivity D5000 kit (Agilent Technologies). Illumina sequencing libraries were constructed by fragmentation, end repair, A-tailing and double-sided size selection, adaptor ligation and sample-index PCR. Quality control and quatification of final libraries were performed on the Agilent 4200 Tapestation using the D1000 kit and Qubit 4. Libraries were then sequenced on NextSeq 2000 with a customized sequencing run formation until sufficient saturation was reached. For Visium HD, PFA fixed and OCT frozen sectioning (hTEM.v2 and hTEM.v3) slides were subject to the Visium HD Fixed Frozen Tissue Preparation Handbook (10x Genomics, CG000764) for the workflows. Sequencing was conducted by the Single Cell & Spatial Omics Core, School of Biomedical Sciences at The Chinese University of Hong Kong (https://www3.sbs.cuhk.edu.hk/en/core_laboratories/single-cell-omics-core/.).


title: VANGL2-LOF, hTEM.v3, day6

description:
Library name: scRNA_Sample13
scRNA-seq


title: VisiumHD, hTEM.v3, day4, longitudinal

description:
Library name: Spatial_Sample3
Visium HD

data_processing:
For scRNA-seq data, fastq reads were generated using 10x Genomics cellranger (v9.0.1) pipeline. For Visium HD data, sastq reads were generated using 10x Genomics cellranger (v3.1.3) pipeline. Both processings are with default settings.
Assembly: GRCh38
Supplementary files format and content: For scRNA-seq processed data, RDS objects for each hTEM.v1/2/3
Supplementary files format and content: Spatial processed data includes: barcodes.tsv.gz, features.tsv.gz,  Matrix.mtx.gz, aligned_fiducials.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png
Library strategy: Spatial Transcriptomics


title: VisiumHD, hTEM.v2, day7, longitudinal

description:
Library name: Spatial_Sample1
Visium HD


title: VisiumHD, hTEM.v3, day6.5, longitudinal

description:
Library name: Spatial_Sample4
Visium HD


title: B.subtilis,erythromycin_2.5ug/ml, rep3

description: Library name: bsub_ERY_5x_rep3


title: dre.embryo.pool_PFBA_600_1

value: pool of 10 whole embryos

value: PFBA

value: D

tag: processing batch

tag: protocol


title: NOTO-LOF, hTEM.v3, day6

description:
Library name: scRNA_Sample11
scRNA-seq

tag: cell type


title: LDC3

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample24
L114_JC3

source_name: colon

tag: tissue

value: colon

tag: treatment

value: LDC


title: VisiumHD, hTEM.v2, day7, transverse

description:
Library name: Spatial_Sample2
Visium HD

tag: cell line


title: B.subtilis,erythromycin_2.5ug/ml, rep2

description: Library name: bsub_ERY_5x_rep2

value: 168 trpC2

value: trpC knockdown


title: B.subtilis, untreated, merged

description: Library name: bsub_UT

value: untreated


title: HNXC1

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample1
H_N114_HC1

value: HNXC


title: dre.embryo.pool_PFBA_250_1

value: 120-hours post fertilization

value: 5 days

value: C

tag: rna extraction_batch

tag: FISH origin

value: ottawa


title: hTEM.v3, day7

description:
Library name: scRNA_Sample10
scRNA-seq


title: dre.embryo.pool_PFBA_80_1

tag: genotype

tag: replicate

value: TempO-Seq


title: LDC2

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample23
L114_JC2


title: HNXC3

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample3
H_N114_HC3

value: ileum


title: B.subtilis,erythromycin_2.5ug/ml, rep1

description: Library name: bsub_ERY_5x_rep1


title: HNXC2

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample2
H_N114_HC2

value: female


title: dre.embryo.pool_control_mixed_0_1

tag: row

value: H

value: mixed

tag: sample id


title: B.subtilis,erythromycin_2.5ug/ml, merged

description: Library name: bsub_ERY_5x


title: dre.embryo.pool_PFDS_0.06_1

value: pool of 10 whole embryos

value: PFDS

tag: rna yield_ng_u_l


title: B.subtilis, erythromycin_0.5ug/ml, merged

description: Library name: bsub_ERY_1x


title: hTEM.v3, day5

description:
Library name: scRNA_Sample8
scRNA-seq


title: B.subtilis, erythromycin_0.5ug/ml, rep3

description: Library name: bsub_ERY_1x_rep3


title: LNDC3

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample21
L_N114_JC3

value: colon

value: LNDC


title: dre.embryo.pool_control_ottawa_0_2

value: B

tag: rin


title: hTEM.v3, day4

description:
Library name: scRNA_Sample7
scRNA-seq


title: dre.embryo.pool_PFDS_0.2_1

tag: column


title: LNDC2

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample20
L_N114_JC2


title: B.subtilis, erythromycin_0.5ug/ml, rep2

description: Library name: bsub_ERY_1x_rep2

value: 168 trpC2

value: trpC knockdown


title: hTEM.v3, day3

description:
Library name: scRNA_Sample6
scRNA-seq


title: B.subtilis, erythromycin_0.1ug/ml, merged

description: Library name: bsub_ERY_02x


title: hTEM.v2, day7

description:
Library name: scRNA_Sample5
scRNA-seq


title: dre.embryo.pool_PFDA_0.4_1

value: PFDA

value: G

tag: plate


title: LNDC1

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample19
L_N114_JC1

tag: Sex


title: B.subtilis, untreated, rep2

description: Library name: bsub_UT_1x_rep2

value: untreated


title: hTEM.v3, day6

description:
Library name: scRNA_Sample9
scRNA-seq


title: HDC3

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample18
H114_JC3

value: HDC


title: LDC1

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample22
L114_JC1

value: LDC


title: dre.embryo.pool_PFBS_250_1

value: 120-hours post fertilization

value: 5 days

value: PFBS

value: F

tag: processing batch

value: ottawa

value: TempO-Seq


title: B.subtilis, erythromycin_0.1ug/ml, rep3

description: Library name: bsub_ERY_02x_rep3


title: HDC2

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample17
H114_JC2

value: female


title: hTEM.v2, day5

description:
Library name: scRNA_Sample4
scRNA-seq


title: HDC1

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample16
H114_JC1

value: colon


title: B.subtilis, erythromycin_0.1ug/ml, rep2

description: Library name: bsub_ERY_02x_rep2


title: hTEM.v1, day7

description:
Library name: scRNA_Sample3
scRNA-seq


title: B.subtilis, erythromycin_0.1ug/ml, rep1

description: Library name: bsub_ERY_02x_rep1


title: dre.embryo.pool_PFBS_80_1

value: pool of 10 whole embryos

value: E

tag: protocol


title: HNDC3

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample15
H_N114_JC3

value: HNDC


title: hTEM.v1, day5

description:
Library name: scRNA_Sample2
scRNA-seq

tag: cell type


title: dre.embryo.pool_reference_rna_2_NA_4

description: Sequencing control. Not used in any contrast.

tag: tissue

value: H

tag: sequencing control


title: hTEM.v1, day4

description:
Library name: scRNA_Sample1
scRNA-seq

tag: cell line


title: HNDC2

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample14
H_N114_JC2

tag: treatment


title: dre.embryo.pool_control_ottawa_0_1

value: A

tag: rna extraction_batch

tag: FISH origin


title: dre.embryo.pool_reference_rna_2_NA_3

tag: genotype

tag: replicate

value: G


title: B.subtilis, chloramphenicol_40ug/ml, merged

description: Library name: bsub_CAM_5x

value: 168 trpC2

value: trpC knockdown


title: HNDC1

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample13
H_N114_JC1


title: dre.embryo.pool_reference_rna_2_NA_2

tag: row

tag: sample id


title: B.subtilis, chloramphenicol_40ug/ml, rep2

description: Library name: bsub_CAM_5x_rep2


title: LXC3

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample12
L114_HC3

value: ileum

value: LXC


title: dre.embryo.pool_reference_rna_2_NA_1

value: 120-hours post fertilization

value: 5 days

tag: rna yield_ng_u_l

tag: rin


title: B.subtilis, chloramphenicol_40ug/ml, rep1

description: Library name: bsub_CAM_5x_rep1


title: dre.embryo.pool_reference_rna_1_NA_4

value: F

tag: column

tag: plate


title: LXC2

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample11
L114_HC2

tag: Sex


title: fetal brain, trisomy 21, Library B18D1R_atac, Chromatin Accessibility

city: London

first: Michael

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: B18D1R_atac
10X Multiome (scRNA/ATAC-seq)

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

source_name: fetal brain

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

value: fetal brain

value: trisomy 21

tag: name

tag: library igf_id

tag: group

value: DS

tag: dev stage_pcw

tag: library type

value: Chromatin Accessibility

tag: in final_analysis

value: TRUE


title: LXC1

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample10
L114_HC1

tag: tissue

value: female

tag: treatment


title: B.subtilis, chloramphenicol_8ug/ml, merged

description: Library name: bsub_CAM_1x

tag: cell type

tag: genotype


title: dre.embryo.pool_reference_rna_1_NA_3

value: pool of 10 whole embryos

tag: cell line

tag: replicate

tag: row

value: E

tag: processing batch

tag: rna extraction_batch

tag: sequencing control

tag: FISH origin

value: ottawa

tag: protocol

value: TempO-Seq


title: B.subtilis, chloramphenicol_8ug/ml, rep3

description: Library name: bsub_CAM_1x_rep3

value: 168 trpC2


title: fetal brain, disomic, Library B18C2M_gex, Gene Expression

description:
Library name: B18C2M_gex
10X Multiome (scRNA/ATAC-seq)

value: disomic

tag: sample id

tag: name

tag: library igf_id

value: CON

tag: Sex

value: Gene Expression


title: B.subtilis, chloramphenicol_8ug/ml, rep2

description: Library name: bsub_CAM_1x_rep2

value: trpC knockdown


title: dre.embryo.pool_reference_rna_1_NA_2

value: 120-hours post fertilization

value: 5 days

tag: column

tag: plate

tag: rna yield_ng_u_l

tag: rin


title: LNXC3

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample9
L_N114_HC3

tag: tissue

value: ileum

tag: treatment

value: LNXC


title: LNXC2

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample8
L_N114_HC2


title: dre.embryo.pool_reference_rna_1_NA_1

tag: cell line

tag: cell type

tag: genotype

tag: replicate


title: fetal brain, disomic, Library B20C1M_gex, Gene Expression

description:
Library name: B20C1M_gex
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

tag: group

tag: dev stage_pcw

value: male

tag: library type

tag: in final_analysis


title: B.subtilis, chloramphenicol_40ug/ml, rep3

description: Library name: bsub_CAM_5x_rep3


title: B.subtilis, chloramphenicol_1.6ug/ml, merged

description: Library name: bsub_CAM_02x


title: dre.embryo.pool_control_pfna_0_16

tag: row

value: G

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: protocol

tag: sample id


title: LNXC1

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample7
L_N114_HC1

tag: Sex

value: female


title: B.subtilis, chloramphenicol_1.6ug/ml, rep3

description: Library name: bsub_CAM_02x_rep3


title: fetal brain, disomic, Library B20C1M_atac, Chromatin Accessibility

description:
Library name: B20C1M_atac
10X Multiome (scRNA/ATAC-seq)

tag: tissue

tag: name

tag: library igf_id

value: Chromatin Accessibility

value: TRUE


title: fetal brain, disomic, Library B18C1S_atac, Chromatin Accessibility

description:
Library name: B18C1S_atac
10X Multiome (scRNA/ATAC-seq)


title: HXC3

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample6
H114_HC3

tag: treatment

value: HXC


title: fetal brain, trisomy 21, Library B18D1R_gex, Gene Expression

description:
Library name: B18D1R_gex
10X Multiome (scRNA/ATAC-seq)

tag: genotype

value: trisomy 21

value: DS


title: B.subtilis, chloramphenicol_1.6ug/ml, rep2

description: Library name: bsub_CAM_02x_rep2

tag: cell type

value: 168 trpC2


title: fetal brain, trisomy 21, Library B17D1K_gex, Gene Expression

description:
Library name: B17D1K_gex
10X Multiome (scRNA/ATAC-seq)

tag: group


title: HXC2

address: 江苏省南京市玄武区南京农业大学

description:
Library name: sample5
H114_HC2


title: dre.embryo.pool_control_pfna_0_14

value: pool of 10 whole embryos

tag: cell line

tag: replicate

value: D

tag: column

tag: plate

value: ottawa

tag: rna yield_ng_u_l

tag: rin

value: TempO-Seq


title: ZF_1000PREs_drePum1-ADARcd-100pg_rep_3 (RBPscan)

city: Québec

first: Dmitry

last: Kretov

state: Québec

department: Oncology Division

institute: CRCHU de Québec - Université Laval

description: Library name: ZF_PRE_drePum1-100_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

source_name: whole embryo, 6 hpf

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

value: whole embryo, 6 hpf

value: WT


title: fetal brain, trisomy 21, Library B17D1K_atac, Chromatin Accessibility

description:
Library name: B17D1K_atac
10X Multiome (scRNA/ATAC-seq)

tag: dev stage_pcw

tag: library type

tag: in final_analysis


title: fetal brain, disomic, Library B17C2M_gex, Gene Expression

description:
Library name: B17C2M_gex
10X Multiome (scRNA/ATAC-seq)

value: disomic

tag: sample id

value: CON

tag: Sex

value: Gene Expression


title: dre.embryo.pool_control_pfna_0_13

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: tissue

value: 120-hours post fertilization

value: 5 days

tag: row

value: H

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: protocol


title: fetal brain, disomic, Library B18C2M_atac, Chromatin Accessibility

description:
Library name: B18C2M_atac
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

tag: genotype

tag: name

tag: library igf_id

tag: group

value: female

value: Chromatin Accessibility

value: TRUE


title: fetal brain, disomic, Library B18C1S_gex, Gene Expression

description:
Library name: B18C1S_gex
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B17C2M_atac, Chromatin Accessibility

description:
Library name: B17C2M_atac
10X Multiome (scRNA/ATAC-seq)


title: dre.embryo.pool_pfna_450_4

tag: cell line

tag: cell type

value: pfna

tag: treatment

tag: replicate

value: A

tag: column

tag: plate

tag: rna yield_ng_u_l


title: fetal brain, disomic, Library B17C2L_gex, Gene Expression

description:
Library name: B17C2L_gex
10X Multiome (scRNA/ATAC-seq)

tag: tissue

tag: sample id

tag: dev stage_pcw

tag: Sex

tag: library type

tag: in final_analysis


title: dre.embryo.pool_pfna_450_3

value: pool of 10 whole embryos

tag: genotype

tag: row

value: D

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: rin

tag: protocol


title: ZF_1000PREs_drePum1-ADARcd-10pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_drePum1-10_rep3


title: ZF_1000PREs_drePum1-ADARcd-10pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_drePum1-10_rep2


title: dre.embryo.pool_pfna_450_2

tag: cell line

tag: cell type

tag: treatment

tag: replicate

value: B

value: ottawa

value: TempO-Seq


title: fetal brain, disomic, Library B17C2L_atac, Chromatin Accessibility

description:
Library name: B17C2L_atac
10X Multiome (scRNA/ATAC-seq)

tag: tissue

value: disomic

tag: name

tag: library igf_id

tag: group


title: dre.embryo.pool_pfna_450_1

tag: column

tag: plate

tag: rna yield_ng_u_l

tag: sample id


title: fetal brain, trisomy 21, Library B15D1M_gex, Gene Expression

description:
Library name: B15D1M_gex
10X Multiome (scRNA/ATAC-seq)

tag: genotype

value: trisomy 21

value: DS

tag: dev stage_pcw

tag: Sex

tag: library type

tag: in final_analysis


title: B.subtilis, chloramphenicol_1.6ug/ml, rep1

description: Library name: bsub_CAM_02x_rep1

value: 168 trpC2

value: trpC knockdown


title: dre.embryo.pool_control_pfna_0_15

tag: cell line

value: 120-hours post fertilization

value: 5 days

tag: row

value: F

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: rin

tag: protocol


title: ZF_1000PREs_drePum1-ADARcd-10pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_drePum1-10_rep1

tag: tissue

value: whole embryo, 6 hpf

value: WT


title: Donor 28 black Female

type: RNA

city: College Park

first: Erika

middle: Taylor

last: Moore

state: Maryland

address: 3102 A. James Clark Hall

department: Bioengineering

country: USA

institute: University of Maryland

hyb_protocol: RNA samples were hybridized with the nCounter® Inflammation V2 Panel probe set (NanoString Technologies) according to the manufacturer’s instructions. Hybridization reactions were incubated to allow binding of target RNA molecules to color-coded reporter probes and capture probes.

scan_protocol: Hybridized samples were processed and scanned using the NanoString nCounter® Digital Analyzer according to the manufacturer’s protocol. Digital counts for each target gene were collected and exported as RCC files for downstream analysis.

data_processing: The raw data was background-corrected using NanoString control probes and normalized to housekeeping genes. Normalized values were exported for analysis.

source_name: PBMC

label_protocol: No enzymatic amplification or labeling was performed; target RNA molecules were directly hybridized to reporter and capture probes.

extract_protocol: Total RNA was extracted from purified monocytes using the RNeasy Minikit (Qiagen) following the manufacturer’s protocol

value: PBMC

tag: age

value: Female

tag: education

value: Some College


title: Donor 27 black Female

value: College Degree or Higher


title: Donor 29 white Female


title: Donor 30 black Male

value: Male


title: Donor 32 black Female


title: ZF_1000PREs_rep_3 (RBPscan)

description: Library name: ZF_PRE_Control_rep3


title: Donor 31 white Male


title: ZF_1000PREs_drePum1-ADARcd-100pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_drePum1-100_rep2


title: fetal brain, disomic, Library B15C1L_gex, Gene Expression, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B15C1L_gex
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

tag: name

tag: library igf_id

tag: group

value: CON

value: female

value: Gene Expression

value: FALSE


title: Donor 26 black Male


title: ZF_1000PREs_rep_2 (RBPscan)

description: Library name: ZF_PRE_Control_rep2

tag: genotype


title: ZF_1000PREs_drePum1-ADARcd-100pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_drePum1-100_rep1


title: dre.embryo.pool_pfna_40_3

value: pool of 10 whole embryos

tag: cell type

value: pfna

tag: treatment

tag: replicate

tag: column

tag: plate

value: ottawa

tag: rna yield_ng_u_l

value: TempO-Seq

tag: sample id


title: dre.embryo.pool_pfna_40_2

tag: cell line

value: 120-hours post fertilization

value: 5 days

tag: row

value: G

tag: processing batch

tag: rna extraction_batch

tag: FISH origin


title: ZF_1000PREs_rep_1 (RBPscan)

description: Library name: ZF_PRE_Control_rep1

tag: tissue

value: whole embryo, 6 hpf

value: WT


title: dre.embryo.pool_pfna_40_1

value: B

tag: rin

tag: protocol


title: fetal brain, disomic, Library B15C1L_atac, Chromatin Accessibility, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B15C1L_atac
10X Multiome (scRNA/ATAC-seq)

value: disomic

tag: name

tag: library igf_id

tag: group

tag: dev stage_pcw

tag: Sex

tag: library type

value: Chromatin Accessibility

tag: in final_analysis


title: Donor 25 black Female

value: PBMC

tag: age

value: Female

tag: education

value: College Degree or Higher


title: fetal brain, trisomy 21, Library B13D4F_gex, Gene Expression

description:
Library name: B13D4F_gex
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

tag: genotype

value: trisomy 21

tag: sample id

value: DS

value: female

value: Gene Expression

value: TRUE


title: dre.embryo.pool_pfna_40_4

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

tag: cell type

value: pfna

tag: treatment

tag: replicate

tag: row

value: A

tag: column

tag: plate

tag: processing batch

value: ottawa

tag: rna yield_ng_u_l

value: TempO-Seq


title: ZF_1000PREs_ADARcd-100pg_rep_3 (RBPscan)

description: Library name: ZF_PRE_ADARcd_rep3

tag: tissue

value: whole embryo, 6 hpf

value: WT


title: fetal brain, trisomy 21, Library B13D4F_atac, Chromatin Accessibility

description:
Library name: B13D4F_atac
10X Multiome (scRNA/ATAC-seq)

tag: name

tag: library igf_id

tag: group

tag: dev stage_pcw

tag: Sex

value: Chromatin Accessibility


title: fetal brain, trisomy 21, Library B15D1M_atac, Chromatin Accessibility

description:
Library name: B15D1M_atac
10X Multiome (scRNA/ATAC-seq)

tag: genotype

tag: library type

tag: in final_analysis


title: dre.embryo.pool_pfna_4_3

tag: cell line

tag: cell type

value: 5 days

value: C

tag: rna extraction_batch

tag: FISH origin

tag: rin

tag: protocol

tag: sample id


title: Donor 24 black Female

value: PBMC

tag: age

value: Female

tag: education

value: College Degree or Higher


title: dre.embryo.pool_pfna_4_4

tag: tissue

tag: treatment

tag: replicate

tag: row

value: B

tag: column

tag: plate

tag: processing batch

tag: rna yield_ng_u_l


title: ZF_1000PREs_ADARcd-100pg_rep_2 (RBPscan)

description: Library name: ZF_PRE_ADARcd_rep2

tag: genotype


title: fetal brain, trisomy 21, Library B13D3H_gex, Gene Expression

description:
Library name: B13D3H_gex
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

value: trisomy 21

tag: name

tag: library igf_id

tag: group

value: DS

tag: dev stage_pcw

tag: Sex

value: male

tag: library type

value: Gene Expression

tag: in final_analysis


title: Donor 22 black Male

tag: age

value: Male

tag: education


title: ZF_1000PREs_ADARcd-100pg_rep_1 (RBPscan)

description: Library name: ZF_PRE_ADARcd_rep1

tag: tissue


title: fetal brain, trisomy 21, Library B13D2D_gex, Gene Expression

description:
Library name: B13D2D_gex
10X Multiome (scRNA/ATAC-seq)

tag: sample id

value: TRUE


title: dre.embryo.pool_pfna_4_1

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

tag: cell type

value: pfna

tag: treatment

tag: replicate

tag: row

value: H

tag: rna extraction_batch

tag: FISH origin

value: ottawa

tag: rin

tag: protocol

value: TempO-Seq


title: fetal brain, trisomy 21, Library B13D3H_atac, Chromatin Accessibility

description:
Library name: B13D3H_atac
10X Multiome (scRNA/ATAC-seq)

tag: genotype

tag: name

tag: library igf_id

tag: group

tag: dev stage_pcw

value: Chromatin Accessibility


title: ZF_Recorder-Empty_N22-dreADARcd-1pg, rep_3, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-1_rep3

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

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

value: whole embryo, 6 hpf

value: WT


title: dre.embryo.pool_pfna_4_2

value: 5 days

value: B

tag: column

tag: plate

tag: processing batch

tag: rna yield_ng_u_l


title: Donor 21 black Male

tag: tissue

value: PBMC

tag: age

tag: Sex

tag: education

value: College Degree or Higher


title: ZF_Recorder-Empty_N22-dreADARcd-1pg, rep_2, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-1_rep2


title: Donor 20 black Male

value: Some College


title: fetal brain, trisomy 21, Library B13D2D_atac, Chromatin Accessibility

description:
Library name: B13D2D_atac
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

value: trisomy 21

tag: sample id

value: DS

value: male

tag: library type

tag: in final_analysis


title: dre.embryo.pool_pfna_200_3

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

tag: cell type

tag: treatment

tag: replicate

tag: row

value: E

tag: rna extraction_batch

tag: FISH origin

tag: rin

tag: protocol


title: ZF_Recorder-Empty_N22-dreADARcd-1pg, rep_1, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-1_rep1

tag: genotype


title: fetal brain, trisomy 21, Library B13D1_gex, Gene Expression

description:
Library name: B13D1_gex
10X Multiome (scRNA/ATAC-seq)

tag: tissue

tag: name

tag: library igf_id

tag: group

tag: dev stage_pcw

value: female

value: Gene Expression

value: TRUE


title: Donor 19 white Male

tag: age

tag: Sex

value: Male

tag: education


title: ZF_Recorder-Empty_N22-dreADARcd-10pg, rep_3, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-10_rep3

value: whole embryo, 6 hpf

value: WT


title: dre.embryo.pool_pfna_200_2

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: cell line

tag: cell type

value: 5 days

value: pfna

tag: column

tag: plate

tag: processing batch

value: ottawa

tag: rna yield_ng_u_l

value: TempO-Seq

tag: sample id


title: Donor 17 white Female

value: PBMC

value: Female

value: Some College


title: fetal brain, trisomy 21, Library B13D1_atac, Chromatin Accessibility

description:
Library name: B13D1_atac
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

value: trisomy 21

value: DS

tag: library type

value: Chromatin Accessibility

tag: in final_analysis


title: Donor 23 black Male

tag: tissue

value: College Degree or Higher


title: dre.embryo.pool_pfna_200_1

value: pool of 10 whole embryos

value: 120-hours post fertilization

tag: genotype

tag: treatment

tag: replicate

tag: row

value: E

tag: rna extraction_batch

tag: FISH origin

tag: rin

tag: protocol


title: ZF_Recorder-Empty_N22-dreADARcd-10pg, rep_1, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-10_rep1

value: whole embryo, 6 hpf


title: fetal brain, disomic, Library B13C2C_gex, Gene Expression

description:
Library name: B13C2C_gex
10X Multiome (scRNA/ATAC-seq)

value: disomic

tag: name

tag: library igf_id

tag: group

value: CON

tag: dev stage_pcw

tag: Sex

value: male

value: Gene Expression

value: TRUE


title: Donor 16 white Female

value: PBMC

tag: age

tag: education


title: dre.embryo.pool_pfna_20_4

tag: cell line

tag: cell type

value: 5 days

value: pfna

value: D

tag: column

tag: plate

tag: processing batch

value: ottawa

tag: rna yield_ng_u_l

value: TempO-Seq

tag: sample id


title: ZF_Recorder-Empty_N22-dreADARcd-10pg, rep_2, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-10_rep2

tag: tissue

tag: genotype

value: WT


title: ZF_Recorder-Empty_N22-dreADARcd-100pg, rep_3, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-100_rep3


title: fetal brain, disomic, Library B13C1_gex, Gene Expression

description:
Library name: B13C1_gex
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

value: female

tag: library type

tag: in final_analysis


title: dre.embryo.pool_pfna_20_3

value: pool of 10 whole embryos

value: 120-hours post fertilization

tag: treatment

tag: replicate

tag: row

value: H

tag: rna extraction_batch

tag: FISH origin

tag: rin

tag: protocol


title: ZF_Recorder-Empty_N22-dreADARcd-100pg, rep_2, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-100_rep2

value: whole embryo, 6 hpf


title: dre.embryo.pool_pfna_200_4

tag: cell line

tag: cell type

value: F


title: dre.embryo.pool_pfna_20_2

tag: column

tag: plate


title: dre.embryo.pool_pfna_20_1

tag: processing batch

tag: rna yield_ng_u_l


title: fetal brain, trisomy 21, Library B12D2D_gex, Gene Expression

description:
Library name: B12D2D_gex
10X Multiome (scRNA/ATAC-seq)

tag: tissue

value: trisomy 21

tag: sample id

tag: name

tag: library igf_id

tag: group

value: DS

tag: dev stage_pcw

tag: Sex

value: male


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_3, 24-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_24_rep3

source_name: whole embryo, 24 hpf

value: whole embryo, 24 hpf

tag: genotype


title: ZF_Recorder-Empty_N22-dreADARcd-100pg, rep_1, 4-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd-100_rep1


title: Donor 11 white Female

value: PBMC

tag: age

value: Female

tag: education

value: Some College


title: Donor 10 white Male

value: Male


title: Donor 9 white Female

value: College Degree or Higher


title: fetal brain, trisomy 21, Library B12D2D_atac, Chromatin Accessibility

description:
Library name: B12D2D_atac
10X Multiome (scRNA/ATAC-seq)

tag: library type

value: Chromatin Accessibility

tag: in final_analysis

value: TRUE


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_2, 24-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_24_rep2

value: WT


title: dre.embryo.pool_control_pfna_0_12

value: pool of 10 whole embryos

tag: cell line

tag: cell type

value: 5 days

tag: treatment

tag: replicate

tag: row

tag: rna extraction_batch

tag: FISH origin

value: ottawa

tag: rin

tag: protocol

value: TempO-Seq


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_1, 24-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_24_rep1

tag: tissue


title: fetal brain, trisomy 21, Library B12D1F_gex, Gene Expression

description:
Library name: B12D1F_gex
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

tag: sample id

tag: name

tag: library igf_id

tag: group

tag: dev stage_pcw

value: Gene Expression


title: dre.embryo.pool_control_pfna_0_11

value: 120-hours post fertilization

tag: genotype

value: D

tag: column

tag: plate

tag: processing batch

tag: rna yield_ng_u_l


title: Donor 14 white Male

tag: age

tag: Sex

tag: education


title: dre.embryo.pool_control_pfna_0_10

tag: cell line

tag: cell type

tag: treatment

tag: replicate

tag: row

tag: rna extraction_batch

tag: FISH origin


title: INPUT100_DAP

description: The DAP-seq was performed following a reported protocol, with some modifications (Bartlett et al., 2017; O'Malley et al., 2016). Briefly, genomic DNA was extracted from wild-type roots 14 days post-inoculation with S. meliloti strain 1021 and sonicated into ~250-bp fragments by Bioruptor Plus at 4°C. The DNA library was constructed using the NEXTflex-Rapid DNA-seq Kit (Beckman Coulter). The coding sequence of MtNIN was cloned into pFN19K HaloTag® T7 SP6 Flexi® vector with HaloTag fused in the N-terminus. The Halo-tagged MtNIN protein was expressed in an invitro TNT SP6 Wheat Germ Master Mix system (Promega) at 25°C for 2h and purified using the magnetic HaloTag beads (Promega). Subsequently, the purified protein was incubated with the prepared DNA library at 25°C for 1h, followed by washing away the unbound DNA fragments with PBS. Thirty microliters of 10 mM Tris–HCl (pH 8.5) buffer was added to the beads and incubated for 10 min at 98°C to elute the bound DNA fragments from the protein. The recovered DNA was PCR-amplified and indexed using the KAPA HiFi HotStart ReadyMix Kit (KAPA).For INPUT100, input DNA libraries were diluted 100 times to prepare as described above to control for background noise.

data_processing:
DAP-Seq reads were first cleaned with fastp v0.12.4 and mapped to the genome of M. truncatula (MtrunA17r5.0) for libraries of MtNIN and INPUT100, and genome of A. thaliana (TAIR11) for library of AtNLP7 using bowtie2 v2.3.4.1 with mode --very-sensitive and maximum fragment length set to 2000.
To remove potential duplicates of reads during PCR in library preparation step, we sorted the resulting alignment with samtools sort v1.17, identified duplicate reads with Picard MarkDuplicates v2.25.4, and removed duplicate reads with tag of 1024 and low-quality alignments with quality score lower than 30 with samtools view v1.17.
Peak positions of candidate binding sites were then predicted using MACS2 v2.2.7.1 with options "--cutoff-analysis" and "--keep-dup all." Statistics of DAP-Seq region were performed using ChIPseeker v1.36.0 by searching the peak position in annotation of M. truncatula, in Watson strand and Crick strand respectively.
Assembly: Medicago truncatula (MtrunA17r5.0-ANR-EGN-r1.9)
Supplementary files format and content: bigWig, narrowPeak (for each sample)
Library strategy: DAP-seq

organism: Medicago truncatula

extract_protocol:
Genomic DNA was extracted from wild-type roots 14 days post-inoculation with S. meliloti strain 1021 and sonicated into ~250-bp fragments by Bioruptor Plus at 4°C.
The DNA library was constructed using the NEXTflex-Rapid DNA-seq Kit (Beckman Coulter). The coding sequence of MtNIN was cloned into pFN19K HaloTag® T7 SP6 Flexi® vector with HaloTag fused in the N-terminus. The Halo-tagged MtNIN protein was expressed in an invitro TNT SP6 Wheat Germ Master Mix system (Promega) at 25°C for 2h and purified using the magnetic HaloTag beads (Promega). Subsequently, the purified protein was incubated with the prepared DNA library at 25°C for 1h, followed by washing away the unbound DNA fragments with PBS. Thirty microliters of 10 mM Tris–HCl (pH 8.5) buffer was added to the beads and incubated for 10 min at 98°C to elute the bound DNA fragments from the protein. The recovered DNA was PCR-amplified and indexed using the KAPA HiFi HotStart ReadyMix Kit (KAPA). Input DNA libraries were diluted 100 times to prepare as described above to control for background noise. The concentration of the indexed DNA was detected by qPCR and normalized. The normalized DNA library was then sequenced using the Illumina NovaSeq 6000 sequencing platform in Shanghai Hanyu Bio-Tech (Shanghai, China).

tag: tissue

value: root


title: ZF_Recorder-Empty_N22-dreADARcd, rep_3, 24-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_24_rep3

value: whole embryo, 24 hpf


title: Donor 3 white Male

value: PBMC


title: Donor 2 black Female

value: Female

value: Some College


title: dre.embryo.pool_control_pfna_0_9

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: A

tag: rin

tag: protocol

tag: sample id


title: MtNIN_DAP


title: fetal brain, disomic, Library B13C1_atac, Chromatin Accessibility

description:
Library name: B13C1_atac
10X Multiome (scRNA/ATAC-seq)

tag: genotype

value: disomic

tag: name

tag: library igf_id

tag: group

value: CON

tag: dev stage_pcw

value: female

tag: library type

value: Chromatin Accessibility

tag: in final_analysis


title: ZF_Recorder-Empty_N22-dreADARcd, rep_2, 24-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_24_rep2

value: WT


title: dre.embryo.pool_control_pfna_0_8

value: pool of 10 whole embryos

tag: cell line

tag: cell type

value: 5 days

value: C

tag: column

tag: plate

tag: processing batch

value: ottawa

tag: rna yield_ng_u_l


title: animal F Pre-bioreactor (SN) & animal A Post-bioreactor (SN)

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

institute: University College London

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

source_name: Primary mesenchymal cells derived from minipig abdominal muscle

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


title: animal D Pre-bioreactor (SN) & animal F Post-bioreactor (SN)

value: Primary mesenchymal cells derived from minipig abdominal muscle


title: ZF_Recorder-Empty_N22-dreADARcd, rep_1, 24-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_24_rep1

tag: tissue


title: Donor 12 white Female

tag: age

tag: Sex

tag: education


title: fetal brain, trisomy 21, Library B12D1F_atac, Chromatin Accessibility

description:
Library name: B12D1F_atac
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

tag: genotype

value: trisomy 21

tag: sample id

value: DS

value: male

value: TRUE


title: fetal brain, disomic, Library B12C2G_gex, Gene Expression

description:
Library name: B12C2G_gex
10X Multiome (scRNA/ATAC-seq)

tag: name

tag: library igf_id

value: Gene Expression


title: dre.embryo.pool_control_pfna_0_7

value: 120-hours post fertilization

tag: treatment

tag: replicate

tag: row

value: A

tag: rna extraction_batch

tag: FISH origin

tag: rin

tag: protocol

value: TempO-Seq


title: fetal brain, disomic, Library B13C2C_atac, Chromatin Accessibility

description:
Library name: B13C2C_atac
10X Multiome (scRNA/ATAC-seq)

value: disomic

tag: group

value: CON

tag: dev stage_pcw

tag: library type

value: Chromatin Accessibility

tag: in final_analysis


title: ZF_Recorder-BoxB_N22-dreADARcd, rep_3, 8-hpf (RBPscan)

description: Library name: ZF_BoxB_N22-ADARcd_8_rep3

source_name: whole embryo, 8 hpf

tag: tissue

value: whole embryo, 8 hpf

value: WT


title: Native domestic pig 3 (ST)

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

value: Esophagus


title: dre.embryo.pool_control_pfna_0_6

value: pool of 10 whole embryos

tag: cell line

tag: cell type

value: 5 days

value: F

tag: column

tag: plate

tag: processing batch

value: ottawa

tag: rna yield_ng_u_l


title: Donor 8 white Male

value: PBMC

tag: age

tag: Sex

value: Male

tag: education

value: Some College


title: animal A Pre-bioreactor (SN) & animal D Post-bioreactor (SN)

value: Primary mesenchymal cells derived from minipig abdominal muscle

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


title: dre.embryo.pool_control_pfna_0_4

value: 120-hours post fertilization

tag: genotype

tag: treatment

tag: replicate

tag: row

value: D

tag: rna extraction_batch

tag: FISH origin

tag: sample id


title: dre.embryo.pool_control_pfna_0_5

tag: tissue

value: E

tag: rin

tag: protocol

value: TempO-Seq


title: fetal brain, trisomy 21, Library B11D2G_gex, Gene Expression

description:
Library name: B11D2G_gex
10X Multiome (scRNA/ATAC-seq)

value: fetal brain

value: trisomy 21

tag: name

tag: library igf_id

tag: group

value: DS

tag: dev stage_pcw

value: female

tag: library type

value: Gene Expression

tag: in final_analysis

value: TRUE


title: fetal brain, disomic, Library B12C1A_atac, Chromatin Accessibility

description:
Library name: B12C1A_atac
10X Multiome (scRNA/ATAC-seq)

value: disomic

value: CON

tag: Sex

value: male

value: Chromatin Accessibility


title: Graft animal C 6-months (ST)

value: Esophagus


title: fetal brain, disomic, Library B12C1A_gex, Gene Expression

description:
Library name: B12C1A_gex
10X Multiome (scRNA/ATAC-seq)

tag: genotype


title: ZF_Recorder-Empty_N22-dreADARcd, rep_2, 8-hpf (RBPscan)

description: Library name: ZF_Empty_N22-ADARcd_8_rep2

value: whole embryo, 8 hpf

value: WT


title: dre.embryo.pool_control_pfna_0_2

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

tag: cell type

value: 5 days

tag: treatment

value: B

tag: column

tag: plate

tag: processing batch

value: ottawa

tag: rna yield_ng_u_l