title: Forestomach, Big_lesions, Batch1, Rep1

city: CAMBRIDGE

first: Maria

middle: Pilar

last: Alcolea

state: Cambridgeshire

address: Jeffrey Cheah Biomedical centre, Puddicombe way

department: Cambridge Stem Cell Institute

institute: University of Cambridge

description: 10x Genomics

data_processing:
The raw scRNA-Seq data was processed using CellRanger (version 3.0.2).
Assembly: Ensembl GRCm38/mm10; release 92
Supplementary files format and content: Tab-separated values (tsv) files and matrix (mtx) files

source_name: Forestomach, big lesions

extract_protocol:
For scRNA-Seq, Fucci2a male mice were sacrificed 8 months after DEN treatment (age-matched mice were used as controls). After dissection as described above, tissues were flattened with the epithelial side up and visible tumour lesions were marked by making a half-cut using a 1 mm diameter punch under the dissecting microscope. Then, oesophagi and forestomachs were cut in half and incubated in 50 mM EDTA in PBS containing 1 U/µl RNAse Inhibitor (Life Technologies; AM2696) at 37°C for 30 minutes. Following incubation, the epithelium was carefully peeled away from the stroma using fine forceps. Epithelium and stroma were each flattened individually and tumours labelled with the half incision described above were then fully excised using 0.5-2 mm punch biopsies. Pools of biopsies from two to four animals (details below) were further processed as follows. Stroma was thoroughly minced and incubated in 4 mg/ml collagenase type 4 (Thermo Fisher Scientific; 17104019) in DMEM with 1 U/ml RNAse inhibitor for 1 h at 37°C in a rotator. EDTA was added to the samples at a final concentration of 5 mM and the suspension was diluted 1:5 in collection buffer (2% heat-inactivated fetal bovine serum (Life Technologies, 26140079), 25 mM HEPES (Life Technologies, 15630056) in PBS to reduce the collagenase activity. Cell suspensions were filtered through a 100 µm cell strainer, centrifuged at 300 × g for 5 min at 4°C, and resuspended in collection buffer before an additional filtering step with a 40 µm FlowMi tip filter (Thermo Fisher Scientific, 15342931) was performed to obtain single-cell suspensions. Cells were then centrifuged at 300 × g for 5 min at 4°C and resuspended in collection buffer containing 1 U/µl RNAse. In parallel, the epithelium was thoroughly minced and incubated for 10 min at 37°C in 0.5 mg/ml dispase (Sigma; D4818) in PBS containing 1 U/µl RNAse to create an epithelial cell suspension. EDTA was then added to the samples at a final concentration of 5 mM and the suspension diluted 1:5 in collection buffer to reduce the dispase activity. A single-cell suspension was obtained by filtering the samples through a 30 µm cell strainer. Cells were then centrifuged at 300 × g for 10 min at 4°C and resuspended in collection buffer containing 1 U/µl RNAse. Epithelial and stromal cells were then pooled together by condition (Ctrl, DEN, Tumour) prior to proceeding to library production for scRNA-seq.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit (v3) and sequenced at the Genomics Core Facility of Cancer Research UK (CRUK), Cambridge Institute following the manufacturer’s instructions

treatment_protocol: To generate lesions in the upper gastrointestinal tract, mice were treated with Di-ethyl-nitrosamine (DEN) (Sigma, Cat. Nr. N0756) at 40 mg per litre in Ribena-flavoured water for 24h on three alternate days a week (i.e., Monday, Wednesday and Friday) for eight weeks; all other days, animals received DEN-free Ribena-flavoured water. Control animals received DEN-free Ribena-flavoured water.

value: Forestomach, big lesions

value: epithelial and stromal cells

tag: genotype

value: DEN (diethylnitrosamine)


title: dre.embryo.pool_PFHxA_600_3

status: Public on Dec 23 2025

type: SRA

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

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

library_source: transcriptomic

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

molecule: total RNA

organism: Danio rerio

source_name: pool of 10 whole embryos

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

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

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

tag: tissue

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

tag: cell type

value: 5 days

value: PFHxA

tag: treatment

tag: replicate

tag: row

value: E

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: ottawa

tag: rna yield_ng_u_l

tag: rin

tag: protocol

value: TempO-Seq

tag: sample id


title: WT L. interrogans, EMJH, replicate 3

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description:
Library name: Int3_EMJH_S3
D3-Liver_Int-EMJH_raw_counts.txt

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

organism: Leptospira interrogans

source_name: serovar manilae

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

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

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

value: serovar manilae

value: WT L. interrogans, EMJH


title: dre.embryo.pool_PFHxA_200_3

value: D


title: iPSC-derived neural progenitors, disomic, non_targeting_ASO, Library C9_NC_3

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: C9_NC_3
bulk RNA-seq (BGI)

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

organism: Homo sapiens

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

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

value: iPSC-derived neural progenitors

value: disomic

tag: library id

tag: group

tag: batch

tag: in final_analysis

value: TRUE


title: WT L. interrogans, EMJH, replicate 2

description:
Library name: Int2_EMJH_S2
D3-Liver_Int-EMJH_raw_counts.txt

tag: tissue


title: WT_HC_CnC10_GFPneg_rep3

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

description: Library name: WT_HC_CnC10_GFPneg_rep3

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

organism: Mus musculus

source_name: extracted RNA from sorted 50K neuronal nuclei

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

value: Brain, hippocampus

tag: genotype

value: C57BL/6J, NuTRAP transgenic

tag: cell type

value: neurons

tag: neuronal population

value: bystander neurons

tag: disease stage_(days_post_challenge)

tag: age

value: 6 weeks

tag: biological replicate


title: dre.embryo.pool_PFDS_0.2_4

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: PFDS

tag: treatment

tag: replicate

tag: row

value: F

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

value: mixed


title: WT_HC_CnC10_GFPneg_rep2

description: Library name: WT_HC_CnC10_GFPneg_rep2


title: dre.embryo.pool_PFHxA_60_3

value: 5 days

value: PFHxA

value: C

tag: FISH origin

value: ottawa

tag: rna yield_ng_u_l

tag: rin

tag: protocol

value: TempO-Seq

tag: sample id


title: iPSC-derived neural progenitors, disomic, non_targeting_ASO, Library C9_NC_2

description:
Library name: C9_NC_2
bulk RNA-seq (BGI)

tag: cell type

value: iPSC-derived neural progenitors

tag: genotype

value: disomic

tag: library id

tag: group

tag: batch

tag: in final_analysis


title: iPSC-derived neural progenitors, trisomy 21, untreated, Library C13-1_8522509006577

description:
Library name: C13-1_8522509006577
bulk RNA-seq (BGI)
counts_comb_bulk_in_vitro_ASO_exp_E22.tsv

tag: cell line

value: trisomy 21

tag: treatment

value: untreated

value: DS

value: TRUE


title: dre.embryo.pool_PFHxA_20_3

tag: tissue

tag: replicate

tag: row

value: D

tag: column


title: Oesophagus, DEN, Batch1, Rep1

description: 10x Genomics

library_source: transcriptomic single cell

source_name: Oesophagus, lesion-free DEN-treated

value: Oesophagus, lesion-free DEN-treated

value: epithelial and stromal cells

value: DEN (diethylnitrosamine)


title: dre.embryo.pool_PFHxS_6_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: PFHxS

value: E

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin


title: dre.embryo.pool_PFHxA_6_3

value: 5 days

value: PFHxA

value: B

tag: rna yield_ng_u_l

tag: rin

tag: protocol

tag: sample id


title: iPSC-derived neural progenitors, disomic, non_targeting_ASO, Library C9_NC_1

description:
Library name: C9_NC_1
bulk RNA-seq (BGI)

tag: cell type

value: iPSC-derived neural progenitors

tag: genotype

tag: library id

tag: group


title: Oesophagus, Control, Batch1, Rep1

description: 10x Genomics

source_name: Oesophagus, control

value: Oesophagus, control

tag: treatment

value: Ctrl


title: impdh2-0 knockdown 8 days after germination replicate 3

city: Kaiserslautern

first: Torsten

last: Möhlmann

address: Paul-Ehrlich-Str

department: Biology

country: Germany

institute: University of Kaiserslautern

description:
Library name: impdh2ko8d biol rep 3
IMPDH2ko8d_3

data_processing:
The data processing steps are according to Novogene methods: Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignment: Algorithm for mapping sequences: HISAT2 is selected to map the filtered sequenced reads to the reference genome. In general, HISAT2 supports genomes of any size, including those larger than 4 billion bases and most of the parameters are set to default. Spliced reads of RNA Seq data can be effictively aligned using HISAT2. HISAT2 v2.0.5 was run using the --dta --phred33 parameters.
Assembly: ncbi_arabidopsis_thaliana_gca_000001735_1_tair10
Supplementary files format and content: FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: plants were grown for 4-8 days under short days (10h light/14h dark) at 120 mE, 65% relative humidity, 21°C in standard soil substrate

extract_protocol:
RNA was extracted from leaves  using the NucleoSpin® RNA Plant Kit (Macherey-Nagel) according to the manufacturer's instructions. 50 mg of fresh plant material was used for this purpose. The RNA was eluted from the column with 40 μl of RNase-free ddH2O
Library construction was perfomed by Novogene Sequencing Service. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

treatment_protocol: Samples of  Col-0 (wild-type control) plants and impdh2-0  were harvested after 3 hours of light  in three biological replicates. 3 days old Col-0 was compared to 4 days old impdh2-0 at a similar developmental stage and 6 days old Col-0 was compared to 8 days old impdh2-0 at a similar developmental stage

tag: tissue

value: shoot

tag: cell line

tag: age

value: 8 day old

value: knock out


title: IMM_7D Replicate 3 RNA-Seq

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

description:
Library name: IMM_7D_3
Immediate repairing nerve Day 7 Replicate 3 RNA-Seq

data_processing:
RNA-Seq read quality controls and preprocessing was performed by removing reads with sequencing adapter, with more then 10% of uncertain nucleotides, or with more than 50% of low-quality nucleotides.
Processed reads were aligned on Rattus norvegicus gene annotations from Ensembl (ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4) using HISAT2 v2.0.5 in default settings.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene. Then the Fragment Per Kilobase Mapped reads (FPKM) of each gene was calculated based on the length of the gene
Gene level differential expression analysis was conducted using the R package DESeq2 v1.38.3 . Specifically, a time point-adjusted comparison between delayed and immediate groups was performed, while paired differential analysis was performed to evaluate differences among time points. Differentially Expressed Genes (DEGs) were defined when associated with median FPKM >1 in at least one sample group and a Benjamini-Hochberg-adjusted p-value (adj. p) <0.05.
Assembly: rnor6
Supplementary files format and content: Raw_count

organism: Rattus norvegicus

source_name: Median nerve

extract_protocol:
RNA was isolated using TRIzol Reagent (Life Technologies) following the manufacturer’s protocol. Briefly, 500 μl of TRIzol reagent were added directly to frozen nerve samples, which were mechanically dissociated using a pestle. The resulting RNA pellet was resuspended in 12 μl of sterile RNase-free water.
RNA samples were quantified, and their quality and purity were assessed using the Agilent 5400 system, yielding an RNA integrity number (RIN) greater than 6. For non-directional library construction, mRNA was purified from 400 ng of total RNA using poly-T oligo-attached magnetic beads. First-strand cDNA synthesis was performed using random hexamer primers, while the second strand was synthesized using dTTP. Post-reverse transcription steps included end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked using Qubit and Real-Time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms based on effective library concentration and data amount.

value: Median nerve

tag: Sex

value: female

value: WT

value: Immediate repair after cut injury

tag: time

value: Day 7


title: IMM_7D Replicate 4 RNA-Seq

description:
Library name: IMM_7D_4
Immediate repairing nerve Day 7 Replicate 4 RNA-Seq


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D1, Library C13_P1_3

description:
Library name: C13_P1_3
bulk RNA-seq (BGI)

value: trisomy 21

tag: batch

tag: in final_analysis

value: TRUE


title: IMM_7D Replicate 2 RNA-Seq

description:
Library name: IMM_7D_2
Immediate repairing nerve Day 7 Replicate 2 RNA-Seq


title: impdh2-0 knockdown 8 days after germination replicate 2

description:
Library name: impdh2ko8d biol rep 2
IMPDH2ko8d_2


title: Forestomach, Small_lesions, Batch1, Rep1

description: 10x Genomics

source_name: Forestomach, small lesions

value: Forestomach, small lesions

value: epithelial and stromal cells

value: DEN (diethylnitrosamine)


title: dre.embryo.pool_PFOS_12_5

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: 5 days

value: PFOS

tag: replicate

tag: row

value: F

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: mixed

value: TempO-Seq


title: Oesophagus, Small_lesions, Batch1, Rep1

description: 10x Genomics

source_name: Oesophagus, small lesions

value: Oesophagus, small lesions

tag: cell type

tag: genotype


title: iPSC-derived neural progenitors, disomic, untreated, Library C9_NT_1

description:
Library name: C9_NT_1
bulk RNA-seq (BGI)

value: iPSC-derived neural progenitors

value: disomic

tag: treatment

value: untreated

tag: sample id

tag: library id

tag: group

value: CON


title: impdh2-0 knockdown 8 days after germination replicate 1

description:
Library name: impdh2ko8d biol rep 1
IMPDH2ko8d_1

tag: tissue

value: shoot

tag: cell line

tag: age

value: 8 day old

value: knock out


title: IMM_7D Replicate 1 RNA-Seq

description:
Library name: IMM_7D_1
Immediate repairing nerve Day 7 Replicate 1 RNA-Seq

value: Median nerve

tag: Sex

value: female

value: WT

value: Immediate repair after cut injury

tag: time

value: Day 7


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D1, Library C13_P1_2

description:
Library name: C13_P1_2
bulk RNA-seq (BGI)

value: trisomy 21

tag: batch

tag: in final_analysis

value: TRUE


title: WT L. interrogans, EMJH, replicate 1

description:
Library name: Int1_EMJH_S1
D3-Liver_Int-EMJH_raw_counts.txt

value: serovar manilae

value: WT L. interrogans, EMJH


title: dre.embryo.pool_PFOS_4_5

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

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: 5 days

value: PFOS

tag: replicate

tag: row

value: A

tag: column

tag: plate

value: mixed

tag: rna yield_ng_u_l

tag: rin

tag: protocol

value: TempO-Seq


title: IMM_21D Replicate 5 RNA-Seq

description:
Library name: IMM_21D_5
Immediate repairing nerve Day 21 Replicate 5 RNA-Seq

tag: genotype

tag: treatment

value: Day 21


title: wild-type control plants 6 days after germination replicate 3

description:
Library name: WT6d biol rep 3
WT6d_3

value: shoot

value: 6 day old

value: wild type


title: iPSC-derived neural progenitors, trisomy 21, untreated, Library C13_NT_3

description:
Library name: C13_NT_3
bulk RNA-seq (BGI)

tag: cell type

value: iPSC-derived neural progenitors

value: untreated

tag: sample id

tag: library id

tag: group

value: DS


title: IMM_21D Replicate 4 RNA-Seq

description:
Library name: IMM_21D_4
Immediate repairing nerve Day 21 Replicate 4 RNA-Seq

tag: tissue

value: Median nerve

tag: Sex

value: female

value: WT

value: Immediate repair after cut injury


title: dre.embryo.pool_PFBS_8_4

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: PFBS

value: C

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: ottawa


title: wild-type control plants 6 days after germination replicate 1

description:
Library name: WT6d biol rep 1
WT6d_1

tag: age


title: iPSC-derived neural progenitors, trisomy 21, untreated, Library C13_NT_2

description:
Library name: C13_NT_2
bulk RNA-seq (BGI)

value: trisomy 21

tag: batch

tag: in final_analysis

value: TRUE


title: iPSC-derived neural progenitors, trisomy 21, untreated, Library C13_NT_1

description:
Library name: C13_NT_1
bulk RNA-seq (BGI)


title: impdh2-0 knockdown 4 days after germination replicate 3

description:
Library name: impdh2ko4d biol rep 3
IMPDH2ko4d_3

value: shoot

value: 4 day old

value: knock out


title: dre.embryo.pool_PFOS_40_5

value: 5 days

value: PFOS

tag: replicate

tag: row

value: G

tag: column

tag: plate

value: mixed

tag: rna yield_ng_u_l

tag: rin

value: TempO-Seq


title: IMM_21D Replicate 3 RNA-Seq

description:
Library name: IMM_21D_3
Immediate repairing nerve Day 21 Replicate 3 RNA-Seq

value: Median nerve

value: female

tag: genotype

value: WT

tag: treatment

tag: time

value: Day 21


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D1, Library C13_P1_1

description:
Library name: C13_P1_1
bulk RNA-seq (BGI)

tag: cell type

value: iPSC-derived neural progenitors

tag: sample id

tag: library id

tag: group


title: dre.embryo.pool_PFOA_400_5

tag: tissue

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: PFOA

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: protocol


title: iPSC-derived neural progenitors, trisomy 21, non_targeting_ASO, Library C13_NC_3

description:
Library name: C13_NC_3
bulk RNA-seq (BGI)

value: trisomy 21

tag: batch

tag: in final_analysis

value: TRUE


title: dre.embryo.pool_PFOS_0.4_5

tag: replicate

tag: row

value: H

tag: column

tag: plate

tag: rna yield_ng_u_l


title: wild-type control plants 6 days after germination replicate 2

description:
Library name: WT6d biol rep 2
WT6d_2

value: shoot

tag: age

value: 6 day old

tag: genotype

value: wild type


title: iPSC-derived neural progenitors, trisomy 21, PKNOX1_ASO_design_D1, Library C13_P1_4

description:
Library name: C13_P1_4
bulk RNA-seq (BGI)

tag: cell type

tag: treatment

tag: sample id

tag: library id


title: IMM_21D Replicate 2 RNA-Seq

description:
Library name: IMM_21D_2
Immediate repairing nerve Day 21 Replicate 2 RNA-Seq

tag: tissue

tag: Sex

value: Immediate repair after cut injury

tag: time


title: IMM_21D Replicate 1 RNA-Seq

description:
Library name: IMM_21D_1
Immediate repairing nerve Day 21 Replicate 1 RNA-Seq


title: dre.embryo.pool_PFOA_120_5

tag: cell line

value: 5 days

value: D

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: mixed

tag: rin

tag: protocol


title: impdh2-0 knockdown 4 days after germination replicate 2

description:
Library name: impdh2ko4d biol rep 2
IMPDH2ko4d_2

value: 4 day old

value: knock out


title: IMM_14D Replicate 4 RNA-Seq

description:
Library name: IMM_14D_4
Immediate repairing nerve Day 14 Replicate 4 RNA-Seq

value: Median nerve

value: female

value: WT

value: Day 14


title: iPSC-derived neural progenitors, trisomy 21, non_targeting_ASO, Library C13_NC_2

description:
Library name: C13_NC_2
bulk RNA-seq (BGI)

value: iPSC-derived neural progenitors

tag: group

tag: batch

tag: in final_analysis


title: dre.embryo.pool_PFOA_40_5

value: pool of 10 whole embryos

value: 120-hours post fertilization

tag: genotype

value: PFOA

tag: replicate

tag: row

value: F

tag: column

tag: plate

tag: rna yield_ng_u_l

value: TempO-Seq


title: IMM_14D Replicate 3 RNA-Seq

description:
Library name: IMM_14D_3
Immediate repairing nerve Day 14 Replicate 3 RNA-Seq

tag: tissue

tag: Sex

tag: treatment


title: impdh2-0 knockdown 4 days after germination replicate 1

description:
Library name: impdh2ko4d biol rep 1
IMPDH2ko4d_1

value: shoot

tag: cell line

tag: age


title: IMM_14D Replicate 2 RNA-Seq

description:
Library name: IMM_14D_2
Immediate repairing nerve Day 14 Replicate 2 RNA-Seq

value: Immediate repair after cut injury

tag: time


title: dre.embryo.pool_PFOA_12_4

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

tag: cell type

value: 5 days

value: C

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: rin

tag: sample id


title: wild-type control plants 3 days after germination replicate 3

description:
Library name: WT3d biol rep 3
WT3d_3

value: 3 day old

tag: genotype

value: wild type


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D3, Library C13_G3_2

description:
Library name: C13_G3_2
bulk RNA-seq (BGI)

value: trisomy 21

tag: library id

tag: group

tag: batch

tag: in final_analysis

value: TRUE


title: iPSC-derived neural progenitors, trisomy 21, non_targeting_ASO, Library C13_NC_1

description:
Library name: C13_NC_1
bulk RNA-seq (BGI)


title: dre.embryo.pool_PFOS_1.2_5

tag: tissue

value: PFOS

tag: replicate

tag: row

value: E

tag: column

tag: plate

value: mixed

tag: rna yield_ng_u_l

tag: protocol


title: wild-type control plants 3 days after germination replicate 2

description:
Library name: WT3d biol rep 2
WT3d_2

tag: cell line

tag: age


title: IMM_14D Replicate 1 RNA-Seq

description:
Library name: IMM_14D_1
Immediate repairing nerve Day 14 Replicate 1 RNA-Seq

value: Median nerve

tag: Sex

value: female

value: WT

tag: treatment

tag: time

value: Day 14


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D3, Library C13_G3_1

description:
Library name: C13_G3_1
bulk RNA-seq (BGI)

tag: cell type

value: iPSC-derived neural progenitors

tag: genotype

tag: sample id


title: dre.embryo.pool_PFOA_4_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: PFOA

value: B

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

tag: rin

value: TempO-Seq


title: dre.embryo.pool_PFHxS_400_3

tag: tissue

value: 5 days

value: PFHxS

tag: replicate

tag: row

value: A

value: ottawa


title: DEL_7D Replicate 5 RNA-Seq

description:
Library name: DEL_7D_5
Delayed repairing nerve Day 7 Replicate 5 RNA-Seq

value: Delayed repair after cut injury

value: Day 7


title: wild-type control plants 3 days after germination replicate 1

description:
Library name: WT3d biol rep 1
WT3d_1

value: shoot

value: 3 day old

value: wild type


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D1, Library C13_G1_2

description:
Library name: C13_G1_2
bulk RNA-seq (BGI)

value: trisomy 21

tag: library id

tag: group

tag: batch

tag: in final_analysis

value: TRUE


title: DEL_7D Replicate 4 RNA-Seq

description:
Library name: DEL_7D_4
Delayed repairing nerve Day 7 Replicate 4 RNA-Seq

value: Median nerve

tag: Sex

value: female

value: WT


title: iPSC-derived neural progenitors, trisomy 21, GABPA_ASO_design_D1, Library C13_G1_1

description:
Library name: C13_G1_1
bulk RNA-seq (BGI)

tag: cell line

value: iPSC-derived neural progenitors

tag: treatment


title: Day 28 post-BPNI_2

city: Wuhan

first: Jiaxin

last: Wang

address: No. 1037, Luoyu Road, Hongshan District, Wuhan City, Hubei Province

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description:
Library name: D28_2
10X Genomics

data_processing:
Raw sequencing data were first processed using CellRanger v7.0.0. The data were demultiplexed to generate FASTQ files. Sequencing reads were then aligned to the Rattus norvegicus reference genome (Rnor_6.0), followed by filtering, UMI counting, and generation of a gene-barcode matrix using cellular barcodes. Subsequently, data normalization was performed using the CellRanger Aggr function, yielding the final gene expression matrix per cell.
Assembly: Ensembl release version 104
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bladder

extract_protocol:
Place a sterile RNase-free culture dish containing an appropriate amount of calciumfree and magnesium-free 1 × PBS on ice, the rat bladder tissue was transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers. Tissue s were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS， V/V）, then pipetting 5-10 times with a Pasteur pipett.The resulting cell suspension was filtered by passing through 70-30um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer(MACS 130-094-183, 10×)and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads(MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C(repeat twice). The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
After adjusting the cell suspension to an optimal density, single-cell libraries were constructed using the Chromium Single Cell 3ʹ Reagent Kits (10x Genomics). Following quality control, the resulting libraries were subjected to high-throughput sequencing in paired-end mode on the NovaSeq 6000 sequencing system.

value: Bladder

tag: cell type

value: BPNI


title: dre.embryo.pool_PFHxS_200_3

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: 5 days

tag: genotype

value: H

tag: column

tag: plate

tag: rna yield_ng_u_l

tag: protocol

value: TempO-Seq


title: dre.embryo.pool_PFHxS_60_3

value: PFHxS

value: G

tag: processing batch

tag: rna extraction_batch

tag: FISH origin

value: ottawa

tag: rin

tag: sample id


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D1, Library C13_B1_4

description:
Library name: C13_B1_4
bulk RNA-seq (BGI)

tag: library id

tag: group


title: Day 3 post-BPNI_3

description:
Library name: D3_3
10X Genomics

tag: tissue

tag: batch


title: Day 28 post-BPNI_1

description:
Library name: D28_1
10X Genomics

tag: cell line


title: dre.embryo.pool_control_ottawa_0_6

tag: treatment

tag: replicate

tag: row

value: B


title: DEL_7D Replicate 3 RNA-Seq

description:
Library name: DEL_7D_3
Delayed repairing nerve Day 7 Replicate 3 RNA-Seq

tag: Sex

tag: genotype

value: Delayed repair after cut injury

tag: time

value: Day 7


title: DEL_7D Replicate 2 RNA-Seq

description:
Library name: DEL_7D_2
Delayed repairing nerve Day 7 Replicate 2 RNA-Seq

value: Median nerve


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D1, Library C13_B1_3

description:
Library name: C13_B1_3
bulk RNA-seq (BGI)

tag: cell type

value: trisomy 21

tag: in final_analysis

value: TRUE


title: DEL_7D Replicate 1 RNA-Seq

description:
Library name: DEL_7D_1
Delayed repairing nerve Day 7 Replicate 1 RNA-Seq

value: female

value: WT


title: Day 3 post-BPNI_1

description:
Library name: D3_1
10X Genomics

value: Bladder

value: BPNI


title: dre.embryo.pool_PFBS_8_3

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: PFBS

value: F

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: rna yield_ng_u_l

tag: protocol


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D1, Library C13_B1_2

description:
Library name: C13_B1_2
bulk RNA-seq (BGI)

value: iPSC-derived neural progenitors

tag: sample id

tag: library id

tag: group


title: Day 3 post-BPNI_2

description:
Library name: D3_2
10X Genomics

tag: tissue

tag: cell line

tag: treatment

tag: batch


title: DEL_21D Replicate 3 RNA-Seq

description:
Library name: DEL_21D_3
Delayed repairing nerve Day 21 Replicate 3 RNA-Seq

tag: Sex

tag: genotype

value: Day 21


title: iPSC-derived neural progenitors, trisomy 21, BACH1_ASO_design_D1, Library C13_B1_1

description:
Library name: C13_B1_1
bulk RNA-seq (BGI)

tag: cell type


title: dre.embryo.pool_PFBA_600_3

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: 5 days

value: PFBA

tag: replicate

tag: row

tag: FISH origin

value: ottawa

tag: rin

value: TempO-Seq


title: Con-3

description:
Library name: Cont_3
10X Genomics

value: Sham-operated


title: DEL_21D Replicate 2 RNA-Seq

description:
Library name: DEL_21D_2
Delayed repairing nerve Day 21 Replicate 2 RNA-Seq

value: Median nerve

value: Delayed repair after cut injury

tag: time


title: C.difficile_sensitive,erythromycin, merged

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: cdiff_S_ery

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 9nt for c.difficile) to observe R/K-x-R/K motif specific ribosome stalling.
Assembly: GCF_018885085.1
Supplementary files format and content: bedgraph file containing perbase genome coverage of the mapped umique reads at 5' end for forward strand.
Supplementary files format and content: bedgraph file containing  perbase genome coverage of the mapped umique reads at 5' end for reverse strand.
Supplementary files format and content: tab delimited txt file contaning read count in the gene body (discarding the start and termination regions) relative to the distance from amino acid
Supplementary files format and content: tab delimited txt file contaning read count in the gene body (discarding the start and termination regions) relative to the distance from tripeptide (last amino acid is at A site)
Supplementary files format and content: tab delimited txt file contaning summary of the processed each sample data

organism: Clostridioides difficile

source_name: erythromycin sensitive isolates

growth_protocol: C.difficile sensitive and resistant strain(4 biological replicates)are cultured in BHI broth at 37°C in anaerobic chamber.

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

value: erythromycin sensitive isolates


title: DEL_21D Replicate 1 RNA-Seq

description:
Library name: DEL_21D_1
Delayed repairing nerve Day 21 Replicate 1 RNA-Seq

value: female

value: WT


title: C.difficile_sensitive,untreated, merged

description: Library name: cdiff_S_Ctr

value: untreated


title: Con-1

description:
Library name: Cont_1
10X Genomics

value: Bladder


title: dre.embryo.pool_PFBA_80_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: E

tag: column

tag: plate

tag: processing batch

tag: rna extraction_batch

tag: rna yield_ng_u_l


title: DEL_14D Replicate 4 RNA-Seq

description:
Library name: DEL_14D_4
Delayed repairing nerve Day 14 Replicate 4 RNA-Seq

tag: tissue

value: Day 14


title: C.difficile_sensitive,untreated, bio3

description: Library name: cdiff_S_Ctr_rep3_S45_R1_001


title: dre.embryo.pool_PFBS_25_3

tag: cell line

value: PFBS

value: G

tag: protocol

tag: sample id


title: DEL_14D Replicate 3 RNA-Seq

description:
Library name: DEL_14D_3
Delayed repairing nerve Day 14 Replicate 3 RNA-Seq

tag: Sex

tag: treatment


title: DEL_14D Replicate 2 RNA-Seq

description:
Library name: DEL_14D_2
Delayed repairing nerve Day 14 Replicate 2 RNA-Seq

tag: genotype


title: C.difficile_sensitive,untreated, bio1

description: Library name: cdiff_S_Ctr_rep1_S21_R1_001

tag: cell type


title: dre.embryo.pool_PFOA_400_4

value: 5 days

value: PFOA

tag: replicate

tag: row

value: H

value: mixed


title: dre.embryo.pool_PFDS_0.06_4

value: PFDS

tag: FISH origin

tag: rin

value: TempO-Seq


title: dre.embryo.pool_PFBA_25_3

value: PFBA

value: D

tag: column

value: ottawa


title: C.difficile_sensitive,untreated, bio2

description: Library name: cdiff_S_Ctr_rep2_S33_R1_001

value: erythromycin sensitive isolates

value: untreated


title: DEL_14D Replicate 1 RNA-Seq

description:
Library name: DEL_14D_1
Delayed repairing nerve Day 14 Replicate 1 RNA-Seq

value: Median nerve

value: female

value: WT

value: Delayed repair after cut injury

tag: time


title: dre.embryo.pool_PFBA_8_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: C

tag: plate

tag: processing batch


title: Shweta Kapila, High yielding, Rep3

city: Old Goa

first: Amiya

middle: Ranjan

last: Sahu

state: Goa

address: ICAR-Central Coastal Agricultural Research Institute

department: Animal Genetics and Breeding

country: India

description:
Library name: Sample 9
SK3

data_processing:
Paired-end sequencing (2 × 150 bp) was performed using the Illumina NovaSeqXplus to generate 60 million reads per sample. Demultiplexed FASTQ files were imported into Strand NGS v4.0 for alignment and analysis. Adapter trimming and quality filtering were performed using Trimmomatic, ensuring clean reads for downstream analyses. Raw sequencing data underwent pre-alignment QC and post-alignment QC assessment using FastQC.  Clean reads were aligned to the genome and transcriptome of Bos indicus using Strand NGS v4.0.  Gene annotations and locations were derived from NCBI Entrez Gene files. Transcript annotations (RefSeq) were obtained from the gff3 files available on NCBI.
Assembly: GCF_000247795.1_Bos_indicus_1.0 assembly
Supplementary files format and content: Raw_Counts

organism: Bos indicus

source_name: Blood

extract_protocol:
The PaXgene Blood RNA kit was used to extract Total RNA from high yielding Gir (n=3), low yielding Gir (n=3), high yielding Shweta Kapila (n=3) and low yielding Shweta Kapila (n=3) cows
Libraries were constructed using a modified NEBNext RNA Ultra II directional protocol. Ribosomal RNA (rRNA) was removed using biotinylated oligos and rRNA removal beads and RNA was subsequently fragmented using divalent cations at elevated temperatures. The first strand of cDNA was synthesized using random hexamers and reverse transcriptase, followed by double-stranded cDNA synthesis. Strand specificity was maintained by replacing thymine with uracil and selectively digesting the second strand using the USER enzyme. Enriched cDNA was indexed through limited-cycle PCR, followed by AMPure bead purification.

value: Blood

value: PBMC

value: Female

value: High yeild


title: Shweta Kapila, Low yielding, Rep2

institute: ICAR-Central Coastal Agricultural Research Institute

description:
Library name: Sample 11
SK5

value: Low Yeild


title: Shweta Kapila, Low yielding, Rep1

description:
Library name: Sample 10
SK4


title: C.difficile_resistant,untreated, merged

description: Library name: cdiff_R_Ctr

source_name: erythromycin resistant isolates

value: erythromycin resistant isolates


title: C.difficile_resistant,erythromycin, merged

description: Library name: cdiff_R_ery


title: dre.embryo.pool_PFDS_6_3

value: 5 days

value: PFDS

value: F

tag: rna extraction_batch

value: mixed

tag: rna yield_ng_u_l

value: TempO-Seq


title: CTR_NERVE Replicate 5 RNA-Seq

description:
Library name: CTR_NERVE_5
Control nerve Replicate 5 RNA-Seq

tag: tissue

value: Median nerve

value: female

value: No treatment, healthy nerve

value: Day 0


title: Shweta Kapila, High yielding, Rep2

description:
Library name: Sample 8
SK2

tag: cell line


title: dre.embryo.pool_PFBA_250_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: PFBA

value: E

value: ottawa

tag: protocol

tag: sample id


title: Con-2

description:
Library name: Cont_2
10X Genomics

value: Bladder

tag: treatment

value: Sham-operated

tag: batch


title: C.difficile_resistant,untreated, bio3

description: Library name: cdiff_R_Ctr_rep3_S47_R1_001

tag: cell type

value: erythromycin resistant isolates

value: untreated


title: Shweta Kapila, Low yielding, Rep3

description:
Library name: Sample 12
SK7

value: Blood

value: PBMC

tag: genotype

value: Female

value: Low Yeild


title: Shweta Kapila, High yielding, Rep1

description:
Library name: Sample 7
SK1

value: High yeild


title: CTR_NERVE Replicate 3 RNA-Seq

description:
Library name: CTR_NERVE_3
Control nerve Replicate 3 RNA-Seq

value: Median nerve

tag: Sex

value: female

value: WT


title: dre.embryo.pool_PFDS_2_3

value: pool of 10 whole embryos

value: 5 days

value: PFDS

tag: replicate

tag: row

tag: FISH origin

value: mixed

value: TempO-Seq


title: C.difficile_resistant,untreated, bio2

description: Library name: cdiff_R_Ctr_rep2_S35_R1_001


title: Gir, Low yielding, Rep3

description:
Library name: Sample 6
G6


title: Gir, Low yielding, Rep2

description:
Library name: Sample 5
G5


title: CTR_NERVE Replicate 2 RNA-Seq

description:
Library name: CTR_NERVE_2
Control nerve Replicate 2 RNA-Seq

value: No treatment, healthy nerve

tag: time

value: Day 0


title: dre.embryo.pool_PFDA_12_3

value: 120-hours post fertilization

value: PFDA

value: A

tag: column

tag: plate

tag: rin


title: dre.embryo.pool_PFDS_0.6_3

value: D

tag: processing batch

tag: rna extraction_batch

tag: rna yield_ng_u_l


title: C.difficile_resistant,untreated, bio1

description: Library name: cdiff_R_Ctr_rep1_S23_R1_001

value: erythromycin resistant isolates

value: untreated


title: dre.embryo.pool_PFDA_4_3

tag: tissue

tag: cell line

value: H

tag: protocol


title: C.difficile_sensitive, erythromycin, bio4, rep5

description: Library name: cdif_S4_6_S55_R1_001

value: erythromycin sensitive isolates

tag: treatment


title: Gir, Low yielding, Rep1

description:
Library name: Sample 4
G4

value: Blood

value: PBMC

tag: cell type

value: Female

value: Low Yeild


title: CTR_NERVE Replicate 1 RNA-Seq

description:
Library name: CTR_NERVE_1
Control nerve Replicate 1 RNA-Seq

value: Median nerve

value: female

tag: genotype

value: WT


title: Recurrent HGSOC patients 001

city: Incheon

first: Seong-Woo

last: Park

address: 265, Harmony-ro, Yeonsu-gu

country: South Korea

institute: Incheon National University

description: Library name: SS2215507

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.

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: IVB

tag: Sex

value: Tumor tissue


title: CTR_NERVE Replicate 4 RNA-Seq

description:
Library name: CTR_NERVE_4
Control nerve Replicate 4 RNA-Seq

value: No treatment, healthy nerve

value: Day 0


title: Primary HGSOC patients 002

description: Library name: SS2214517

value: Primary

value: IIIC


title: C.difficile_sensitive, erythromycin, bio4, rep3

description: Library name: cdif_S4_4_S39_R1_001


title: dre.embryo.pool_PFDA_0.4_3

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

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: 5 days

value: PFDA

tag: replicate

tag: row

value: B

tag: FISH origin

value: mixed

value: TempO-Seq

tag: sample id


title: Gir, High yielding, Rep3

description:
Library name: Sample 3
G3

value: Blood

value: PBMC

value: Female

value: High yeild


title: dre.embryo.pool_PFDA_1.2_3

value: C

tag: column

tag: plate

tag: rin


title: Gir, High yielding, Rep2

description:
Library name: Sample 2
G2


title: Primary HGSOC patients 003

description: Library name: SS2213255

value: Tumor tissue


title: Gir, High yielding, Rep1

description:
Library name: Sample 1
G1


title: dre.embryo.pool_PFDA_0.12_3

value: A

tag: processing batch

tag: rna extraction_batch

tag: rna yield_ng_u_l


title: Primary HGSOC patients 004

description: Library name: SS2209402

value: IVB

tag: tissue


title: C.difficile_sensitive, erythromycin, bio4, rep2

description: Library name: cdif_S4_3_S31_R1_001

value: erythromycin sensitive isolates

tag: treatment


title: dre.embryo.pool_PFBS_600_4

tag: cell line

tag: cell type

value: PFBS

value: H

value: ottawa

tag: protocol


title: Primary HGSOC patients 005

description: Library name: SS2180551

tag: disease status

value: Primary

tag: tumor stage

value: IIIC


title: FcM_1962

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Sciences

country: USA

institute: Cornell University

description: Library name: Sample6_FcM_1962

data_processing:
Adaptor sequences were trimmed
Trimmed sequence reads were mapped to ARS-UCD1.2 using STAR
Gene-level counts were obtained with EdgeR
Normalized gene-level counts using TMM in EdgeR and paire-wise comparisions performed
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited files

organism: Bos taurus

source_name: Fibrocytes

growth_protocol: The pellet of nucleated blood cells was resuspended in either a simple medium routinely used for culturing bovine fibroblasts [16]: Fibroblast medium [Fb; composition: Dulbecco’s High Glucose DMEM, 20% fetal bovine serum, penicillin-streptomycin, and non-essential amino acids (Gibco)], or in a modified mesenchymal stem cell medium: Fibrocyte medium [FbC; composition: Dulbecco’s High Glucose DMEM, 20% fetal bovine serum, penicillin-streptomycin, non-essential amino acids, 10nM dexamethasone, 0.1mM L-ascorbic acid-2-phosphate, 10ng/mL PDGF- bb(GoldBio), 10ng/ml EGF (GoldBio), 0.5μM A83-01(Cayman Chemical Company), and 1.5μM CHIR99021(Cayman Chemical Company)]. Resuspended cells were plated on 0.1% gelatin- coated cell culture dishes and incubated at 37 ̊C in an atmosphere of 5% CO2

extract_protocol:
RNA was extracted using RNAqueous Micro Total RNA Isolation Kit (Thermo Fisher Scientific)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Fibrocytes


title: C.difficile_sensitive, erythromycin, bio3, rep5

description: Library name: cdif_S3_6_S54_R1_001


title: FcM_1951

description: Library name: Sample4_FcM_1951


title: Primary HGSOC patients 006

description: Library name: SS2171265

value: IIIB

tag: Sex


title: FcM_1944

description: Library name: Sample5_FcM_1944


title: dre.embryo.pool_PFBS_250_4

value: pool of 10 whole embryos

value: 120-hours post fertilization

value: 5 days

tag: genotype

tag: replicate

tag: row

value: G

value: TempO-Seq


title: dre.embryo.pool_control_excluded_0_2

value: D

tag: column

tag: FISH origin

tag: sample id


title: C.difficile_sensitive, erythromycin, bio3, rep4

description: Library name: cdif_S3_5_S46_R1_001


title: Primary HGSOC patients 007

description: Library name: SS2166736

value: Female

value: Tumor tissue


title: Primary HGSOC patients 008

description: Library name: SS2166116

value: IVB


title: FbM_1951

description: Library name: Sample3_FbM_1951


title: dre.embryo.pool_PFBA_250_3

value: PFBA

value: E

tag: plate

tag: processing batch

tag: rin


title: C.difficile_sensitive, erythromycin, bio3, rep2

description: Library name: cdif_S3_3_S30_R1_001

value: erythromycin sensitive isolates


title: C.difficile_sensitive, erythromycin, bio3, rep3

description: Library name: cdif_S3_4_S38_R1_001


title: dre.embryo.pool_PFOS_40_4

tag: tissue

value: PFOS

value: C

tag: rna extraction_batch

value: mixed

tag: rna yield_ng_u_l


title: FbM_1944

description: Library name: Sample2_FbM_1944

tag: cell type

value: Fibrocytes


title: C.difficile_sensitive, erythromycin, bio4, rep1

description: Library name: cdif_S4_2_S23_R1_001

tag: treatment


title: FbM_1962

description: Library name: Sample1_FbM_1962


title: Primary HGSOC patients 009

description: Library name: SS2165809

tag: disease status

value: Primary

value: IIIC


title: Primary HGSOC patients 011

description: Library name: SS2159212

tag: tumor stage


title: dre.embryo.pool_PFOS_12_4

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: B

tag: protocol


title: Primary HGSOC patients 010

description: Library name: SS2164961

tag: Sex


title: C.difficile_sensitive, erythromycin, bio3, rep1

description: Library name: cdif_S3_2_S22_R1_001


title: dre.embryo.pool_PFOS_4_4

value: 5 days

tag: genotype

tag: replicate

tag: row

value: A

value: TempO-Seq


title: C.difficile_sensitive,untreated, bio3

description: Library name: sensitive_Ctr_rep3

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

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.

value: untreatd


title: C.difficile_sensitive, erythromycin, bio2, rep4

description: Library name: cdif_S2_5_S45_R1_001


title: C.difficile_sensitive, erythromycin, bio2, rep5

description: Library name: cdif_S2_6_S53_R1_001


title: Primary HGSOC patients 012

description: Library name: SS2153839

value: IVB

value: Female

value: Tumor tissue


title: C.difficile_sensitive,untreated, bio2

description: Library name: sensitive_Ctr_rep2

value: erythromycin sensitive isolates


title: C.difficile_sensitive, erythromycin, bio2, rep3

description: Library name: cdif_S2_4_S37_R1_001


title: Recurrent HGSOC patients 013

description: Library name: SS2146489

value: Recurrent

value: IIIB


title: C.difficile_sensitive,untreated, bio1

description: Library name: sensitive_Ctr_rep1


title: dre.embryo.pool_PFOS_1.2_4

value: PFOS

tag: column

tag: FISH origin

value: mixed

tag: sample id


title: C.difficile_sensitive, erythromycin, bio2, rep2

description: Library name: cdif_S2_3_S29_R1_001


title: C.difficile_sensitive, erythromycin, bio4, rep6

description: Library name: sample_cdif_S4_6


title: Primary HGSOC patients 014

description: Library name: SS2142849

value: Primary


title: C.difficile_sensitive, erythromycin, bio2, rep1

description: Library name: cdif_S2_2_S21_R1_001


description: Library name: sample_cdif_S4_5


title: Recurrent HGSOC patients 015

description: Library name: SS2131323

value: III


title: dre.embryo.pool_PFOA_40_4

value: pool of 10 whole embryos

value: PFOA

value: H

tag: plate

tag: processing batch

tag: rin


title: C.difficile_sensitive, erythromycin, bio1, rep5

description: Library name: cdif_S1_6_S52_R1_001


title: dre.embryo.pool_PFOA_120_4

tag: tissue

value: 120-hours post fertilization

value: 5 days

tag: rna extraction_batch

tag: rna yield_ng_u_l


title: C.difficile_sensitive, erythromycin, bio4, rep4

description: Library name: sample_cdif_S4_4

tag: cell type

tag: treatment


title: Primary HGSOC patients 016

description: Library name: SS2123225

tag: disease status

tag: tumor stage


title: dre.embryo.pool_PFBA_8_3

tag: cell line

value: PFBA

value: D

value: ottawa

tag: protocol

value: TempO-Seq


title: C.difficile_sensitive, erythromycin, bio1, rep4

description: Library name: cdif_S1_5_S44_R1_001


title: dre.embryo.pool_PFOA_12_3

tag: genotype

tag: replicate

value: G


title: C.difficile_sensitive, erythromycin, bio1, rep3

description: Library name: cdif_S1_4_S36_R1_001

value: erythromycin sensitive isolates


title: dre.embryo.pool_PFOA_4_3

tag: row

tag: column


title: Primary HGSOC patients 018

description: Library name: SS2115211

value: IVB

tag: Sex

value: Female

value: Tumor tissue


title: Primary HGSOC patients 019

description: Library name: SS2112337

value: IIIB


title: C.difficile_sensitive, erythromycin, bio4, rep3

description: Library name: sample_cdif_S4_3


title: Primary HGSOC patients 017

description: Library name: SS2118814

value: Primary


title: C.difficile_sensitive, erythromycin, bio4, rep2

description: Library name: sample_cdif_S4_2


description: Library name: sample_cdif_S4_1


title: dre.embryo.pool_PFOS_0.4_4

value: PFOS

tag: plate

tag: FISH origin

value: mixed

tag: sample id


title: dre.embryo.pool_PFDS_0.06_3

tag: tissue

value: pool of 10 whole embryos

value: PFDS

value: F

tag: processing batch

tag: rin


title: C.difficile_sensitive, erythromycin, bio1, rep2

description: Library name: cdif_S1_3_S28_R1_001

tag: cell type


title: dre.embryo.pool_control_ottawa_0_5

value: 120-hours post fertilization

value: 5 days

tag: treatment

tag: rna extraction_batch

tag: rna yield_ng_u_l


title: C.difficile_sensitive, erythromycin, bio1, rep1

description: Library name: cdif_S1_2_S20_R1_001


title: Primary HGSOC patients 020

description: Library name: SS2112292

tag: disease status

tag: tumor stage

value: IIIC


title: C.difficile_sensitive, erythromycin, bio3, rep6

description: Library name: sample_cdif_S3_6


title: C.difficile_sensitive, erythromycin, bio3, rep5

description: Library name: sample_cdif_S3_5


description: Library name: cdif_S4_5_S47_R1_001


title: C.difficile_resistant, erythromycin, bio4, rep5

description: Library name: cdif_R4_6_S59_R1_001

value: erythromycin resistant isolates


title: Primary HGSOC patients 021

description: Library name: SS2106755


title: dre.embryo.pool_PFDA_12_2

tag: cell line

tag: genotype

value: PFDA

tag: protocol

value: TempO-Seq


title: C.difficile_sensitive, erythromycin, bio3, rep4

description: Library name: sample_cdif_S3_4

value: erythromycin sensitive isolates


title: dre.embryo.pool_PFDA_4_2

tag: replicate

tag: row

value: E

tag: column


title: C.difficile_resistant, erythromycin, bio4, rep4

description: Library name: cdif_R4_5_S51_R1_001


title: Primary HGSOC patients 022

description: Library name: SS2104482

value: IVB

tag: Sex

value: Female


title: dre.embryo.pool_PFDA_1.2_2

tag: plate

tag: FISH origin

tag: sample id


title: Primary HGSOC patients 023

description: Library name: SS2071919

tag: tissue

value: Tumor tissue


title: C.difficile_resistant, erythromycin, bio4, rep2

description: Library name: cdif_R4_3_S35_R1_001

tag: cell type


title: Primary HGSOC patients 024

description: Library name: SS2070425

value: Primary


title: C.difficile_resistant, erythromycin, bio4, rep3

description: Library name: cdif_R4_4_S43_R1_001

tag: treatment


title: dre.embryo.pool_PFDA_0.12_2

tag: processing batch

tag: rna extraction_batch

tag: rin


title: C.difficile_sensitive, erythromycin, bio3, rep2

description: Library name: sample_cdif_S3_2


title: C.difficile_resistant, erythromycin, bio4, rep1

description: Library name: cdif_R4_2_S27_R1_001


title: dre.embryo.pool_PFBS_600_3

value: PFBS

value: D

value: ottawa

tag: rna yield_ng_u_l


title: C.difficile_resistant, erythromycin, bio3, rep5

description: Library name: cdif_R3_6_S58_R1_001


title: C.difficile_sensitive, erythromycin, bio3, rep1

description: Library name: sample_cdif_S3_1


title: dre.embryo.pool_PFHxS_400_2

value: pool of 10 whole embryos

tag: cell line

value: PFHxS


title: C.difficile_sensitive, erythromycin, bio2, rep6

description: Library name: sample_cdif_S2_6


title: C.difficile_resistant, erythromycin, bio3, rep4

description: Library name: cdif_R3_5_S50_R1_001


title: Recurrent HGSOC patients 026

description: Library name: SS2057730

tag: disease status

value: Recurrent

tag: tumor stage


title: Primary HGSOC patients 027

description: Library name: SS2056361

value: IIIB


title: C.difficile_sensitive, erythromycin, bio2, rep5

description: Library name: sample_cdif_S2_5


title: C.difficile_resistant, erythromycin, bio3, rep3

description: Library name: cdif_R3_4_S42_R1_001


title: dre.embryo.pool_PFHxS_200_2

value: 120-hours post fertilization

value: 5 days

tag: genotype

tag: replicate

tag: protocol


title: dre.embryo.pool_PFHxS_60_2

tag: row

value: C

tag: column


title: Recurrent HGSOC patients 028

description: Library name: SS2056315

value: R

tag: Sex


title: C.difficile_sensitive, erythromycin, bio2, rep3

description: Library name: sample_cdif_S2_3

value: erythromycin sensitive isolates


title: C.difficile_resistant, erythromycin, bio3, rep2

description: Library name: cdif_R3_3_S34_R1_001

value: erythromycin resistant isolates


title: Primary HGSOC patients 029

description: Library name: SS2053409


title: dre.embryo.pool_PFHxS_6_3

tag: plate

tag: FISH origin

value: TempO-Seq

tag: sample id


title: C.difficile_sensitive, erythromycin, bio2, rep2

description: Library name: sample_cdif_S2_2

tag: cell type

tag: treatment


title: C.difficile_sensitive, erythromycin, bio3, rep3

description: Library name: sample_cdif_S3_3


title: C.difficile_resistant, erythromycin, bio3, rep1

description: Library name: cdif_R3_2_S26_R1_001


title: Primary HGSOC patients 030

description: Library name: SS2053339

value: IVA

value: Female

tag: tissue


title: C.difficile_resistant, erythromycin, bio2, rep5

description: Library name: cdif_R2_6_S57_R1_001


title: C.difficile_sensitive, erythromycin, bio2, rep1

description: Library name: sample_cdif_S2_1


title: Primary HGSOC patients 031

description: Library name: SS2053053

value: Primary

value: Tumor tissue


title: dre.embryo.pool_PFHxA_60_2

value: PFHxA

value: B

tag: processing batch

tag: rna extraction_batch

tag: rin


title: C.difficile_sensitive, erythromycin, bio1, rep6

description: Library name: sample_cdif_S1_6


title: dre.embryo.pool_PFHxA_20_2

value: pool of 10 whole embryos

tag: cell line

value: A

value: ottawa

tag: rna yield_ng_u_l


title: Recurrent HGSOC patients 025

description: Library name: SS2066520

tag: disease status

value: Recurrent

tag: tumor stage

value: IIIC


title: C.difficile_resistant, erythromycin, bio2, rep2

description: Library name: cdif_R2_3_S33_R1_001


title: C.difficile_sensitive, erythromycin, bio1, rep5

description: Library name: sample_cdif_S1_5


title: C.difficile_resistant, erythromycin, bio2, rep4

description: Library name: cdif_R2_5_S49_R1_001


title: C.difficile_resistant, erythromycin, bio2, rep3

description: Library name: cdif_R2_4_S41_R1_001


title: dre.embryo.pool_PFHxA_6_2

value: 120-hours post fertilization

value: 5 days

tag: genotype

tag: replicate

value: H

tag: protocol


title: dre.embryo.pool_PFDS_0.06_2

value: PFDS

tag: row

tag: column

value: mixed


title: Recurrent HGSOC patients 033

description: Library name: SS2051456

value: IIIA

tag: Sex


title: C.difficile_sensitive, erythromycin, bio2, rep4

description: Library name: sample_cdif_S2_4

value: erythromycin sensitive isolates


title: C.difficile_sensitive, erythromycin, bio1, rep3

description: Library name: sample_cdif_S1_3


title: C.difficile_sensitive, erythromycin, bio1, rep4

description: Library name: sample_cdif_S1_4


title: Primary HGSOC patients 034

description: Library name: SS2051316

value: IVB

value: Female


title: Primary HGSOC patients 035

description: Library name: SS2042190

value: Primary

value: Tumor tissue


title: dre.embryo.pool_PFHxS_20_3

value: PFHxS

value: B

tag: plate

tag: FISH origin

value: TempO-Seq

tag: sample id


title: C.difficile_resistant, erythromycin, bio1, rep5

description: Library name: cdif_R1_6_S56_R1_001

tag: cell type

value: erythromycin resistant isolates

tag: treatment


title: dre.embryo.pool_PFHxA_600_2

tag: tissue

value: pool of 10 whole embryos

value: PFHxA

value: A

tag: processing batch

tag: rna extraction_batch

value: ottawa


title: C.difficile_sensitive, erythromycin, bio1, rep2

description: Library name: sample_cdif_S1_2


title: dre.embryo.pool_PFDS_2_2

tag: cell line

value: 120-hours post fertilization

value: 5 days

value: G

tag: rna yield_ng_u_l

tag: rin


title: Primary HGSOC patients 036

description: Library name: SS2039846

tag: disease status

tag: tumor stage


title: C.difficile_resistant, erythromycin, bio1, rep4

description: Library name: cdif_R1_5_S48_R1_001


title: dre.embryo.pool_PFDS_0.6_2

tag: genotype

value: PFDS

tag: replicate

value: mixed

tag: protocol


title: Primary HGSOC patients 032

description: Library name: SS2052569

value: IIIC

tag: Sex


title: C.difficile_resistant, erythromycin, bio1, rep3

description: Library name: cdif_R1_4_S40_R1_001


title: Primary HGSOC patients 038

description: Library name: SS2038942

value: Female


title: C.difficile_resistant, erythromycin, bio1, rep2

description: Library name: cdif_R1_3_S32_R1_001


title: Recurrent HGSOC patients 037

description: Library name: SS2039208

value: Recurrent


title: dre.embryo.pool_PFBS_80_4

value: PFBS

tag: row

value: E

tag: column

tag: plate


title: C.difficile_resistant, erythromycin, bio4, rep4

description: Library name: sample_cdif_R4_4

tag: cell type


title: C.difficile_resistant, erythromycin, bio4, rep6

description: Library name: sample_cdif_R4_6

tag: treatment


title: dre.embryo.pool_PFBS_25_2

tag: tissue

value: F

tag: FISH origin

tag: sample id


title: Primary HGSOC patients 039

description: Library name: SS2029051

value: Primary

value: IVB

value: Tumor tissue


title: C.difficile_resistant, erythromycin, bio4, rep5

description: Library name: sample_cdif_R4_5

value: erythromycin resistant isolates


title: C.difficile,HT-5PSeq

description: Library name: cdiff_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

source_name: ATCC 9689

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.

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: ATCC 9689

value: wild type

value: untreated


title: C.difficile_resistant, erythromycin, bio2, rep1

description: Library name: cdif_R2_2_S25_R1_001


title: Recurrent HGSOC patients 040

description: Library name: SS2028780


title: C.difficile_resistant, erythromycin, bio1, rep1

description: Library name: cdif_R1_2_S24_R1_001


title: dre.embryo.pool_PFBS_8_2

value: pool of 10 whole embryos

tag: cell line

value: 120-hours post fertilization

value: 5 days

tag: processing batch

tag: rna extraction_batch

value: ottawa

value: TempO-Seq


title: dre.embryo.pool_PFBA_250_2

value: PFBA

value: D

tag: rna yield_ng_u_l

tag: rin


title: Primary HGSOC patients 042

description: Library name: SS2026934

tag: disease status

tag: tumor stage

value: Female


title: Primary HGSOC patients 041

description: Library name: SS2027136


title: C.difficile_resistant, erythromycin, bio4, rep2

description: Library name: sample_cdif_R4_2


title: C.difficile_resistant, erythromycin, bio4, rep3

description: Library name: sample_cdif_R4_3


title: Primary HGSOC patients 043

description: Library name: SS2026250


title: C.difficile,ctr,rep1

description: Library name: cd_ctr1_S5_R1_001

tag: genotype


title: C.difficile,ctr,rep2

description: Library name: cd_ctr2_S6_R1_001


title: dre.embryo.pool_PFBA_25_2

tag: replicate

tag: protocol


title: dre.embryo.pool_PFBA_80_3

tag: row

value: C

tag: column


title: C.difficile_sensitive, erythromycin, bio1, rep1

description: Library name: sample_cdif_S1_1

tag: cell type

value: erythromycin sensitive isolates


title: C.difficile,s5PSeq,rep2

description: Library name: cd_bo2_S8_R1_001

tag: treatment


title: C.difficile_resistant, erythromycin, bio3, rep6

description: Library name: sample_cdif_R3_6


title: C.difficile_resistant, erythromycin, bio4, rep1

description: Library name: sample_cdif_R4_1


title: dre.embryo.pool_control_excluded_0_1

tag: tissue

tag: plate


title: Primary HGSOC patients 044

description: Library name: SS2023142

value: Primary

value: IIIC

tag: Sex


title: C.difficile_resistant, erythromycin, bio3, rep5

description: Library name: sample_cdif_R3_5


title: dre.embryo.pool_PFOS_40_3

tag: cell line

value: PFOS

value: A

tag: FISH origin

value: mixed

tag: sample id


title: C.difficile_resistant, erythromycin, bio3, rep4

description: Library name: sample_cdif_R3_4

value: erythromycin resistant isolates


title: Primary HGSOC patients 045

description: Library name: SS2017747

value: IVB

value: Tumor tissue


title: Primary HGSOC patients 046

description: Library name: SS2016863


title: dre.embryo.pool_PFOS_4_3

value: pool of 10 whole embryos

value: 120-hours post fertilization

tag: processing batch

tag: rna extraction_batch

tag: rna yield_ng_u_l


title: Primary HGSOC patients 047

description: Library name: SS2015449

tag: disease status

tag: tumor stage


title: C.difficile_resistant, erythromycin, bio3, rep3

description: Library name: sample_cdif_R3_3


title: dre.embryo.pool_PFOS_1.2_3

value: 5 days

tag: genotype

tag: replicate

value: H

tag: rin


title: OTHER,metagenome for B264m3 at 3mon

city: Nanjing

first: xinyuan

last: ge

state: Jiangsu

address: Longmian Road 818

institute: Nanjing Medical University School of Public Health

description:
Library name: B264m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B264m3 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.

value: feces

value: exercise

tag: timepoint


title: OTHER,metagenome for B273m3 at 3mon

description:
Library name: B273m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B273m3 at 3mon


title: C.difficile_resistant, erythromycin, bio3, rep2

description: Library name: sample_cdif_R3_2

tag: cell type


title: Primary HGSOC patients 048

description: Library name: SS2014931

value: Female


title: OTHER,metagenome for B258m3 at 3mon

description:
Library name: B258m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B258m3 at 3mon

tag: treatment


title: dre.embryo.pool_PFOS_0.4_3

source_name: pool of 10 whole embryos

tag: tissue

tag: row

value: B

tag: column

tag: protocol

value: TempO-Seq


title: C.difficile_resistant, erythromycin, bio3, rep1

description: Library name: sample_cdif_R3_1


title: OTHER,metagenome for B253m3 at 3mon

description:
Library name: B253m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B253m3 at 3mon


title: dre.embryo.pool_PFOA_400_3

tag: cell line

value: PFOA

tag: plate

tag: FISH origin


title: dre.embryo.pool_PFOA_120_3

tag: processing batch

tag: rna extraction_batch

tag: sample id


title: Primary HGSOC patients 050

description: Library name: SS2010279

tag: disease status

value: Primary

tag: tumor stage

tag: Sex


title: OTHER,metagenome for B250m3 at 3mon

description:
Library name: B250m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B250m3 at 3mon


title: Recurrent HGSOC patients 051

description: Library name: SR2203699

value: Recurrent

value: IIIB


title: C.difficile_resistant, erythromycin, bio2, rep5

description: Library name: sample_cdif_R2_5


title: C.difficile,s5PSeq,rep1

description: Library name: cd_bo1_S7_R1_001

value: ATCC 9689

tag: genotype

value: wild type

value: untreated


title: OTHER,metagenome for B277m3 at 3mon

description:
Library name: B277m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B277m3 at 3mon

tag: timepoint


title: C.difficile_resistant, erythromycin, bio2, rep4

description: Library name: sample_cdif_R2_4

tag: cell type

value: erythromycin resistant isolates


title: dre.embryo.pool_PFOA_40_3

value: pool of 10 whole embryos

tag: treatment

tag: replicate

value: mixed

tag: rna yield_ng_u_l

tag: rin


title: dre.embryo.pool_PFOS_12_3

tag: tissue

value: 120-hours post fertilization

value: 5 days

value: PFOS

tag: row

value: C

tag: column

tag: protocol


title: C.difficile_resistant, erythromycin, bio2, rep3

description: Library name: sample_cdif_R2_3


title: dre.embryo.pool_PFOA_12_2

tag: cell line

value: A

tag: plate

tag: processing batch

tag: FISH origin


title: OTHER,metagenome for B263m3 at 3mon

description:
Library name: B263m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B263m3 at 3mon

value: feces

value: exercise


title: Recurrent HGSOC patients 053

description: Library name: SR2201037

tag: disease status

tag: tumor stage

value: IVA

value: Female

value: Tumor tissue


title: OTHER,metagenome for B211m3 at 3mon

description:
Library name: B211m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B211m3 at 3mon


title: Primary HGSOC patients 049

description: Library name: SS2014056

value: Primary

value: IIIB

tag: Sex


title: Recurrent HGSOC patients 054

description: Library name: SR2110185

value: Recurrent

value: IIIC


description: Library name: sample_cdif_R2_1

value: erythromycin resistant isolates


title: C.difficile_resistant, erythromycin, bio2, rep6

description: Library name: sample_cdif_R2_6


title: Recurrent HGSOC patients 055

description: Library name: SR2105700


title: dre.embryo.pool_PFBS_600_2

value: pool of 10 whole embryos

tag: genotype

value: PFBS

value: F

tag: rna extraction_batch

value: ottawa

value: TempO-Seq

tag: sample id


title: Recurrent HGSOC patients 056

description: Library name: SR2105061

value: R


title: C.difficile_resistant, erythromycin, bio1, rep5

description: Library name: sample_cdif_R1_5

tag: cell type

tag: treatment


title: dre.embryo.pool_PFBS_250_3

value: 120-hours post fertilization

value: 5 days

tag: replicate

value: G

tag: rna yield_ng_u_l

tag: rin


title: C.difficile_resistant, erythromycin, bio1, rep6

description: Library name: sample_cdif_R1_6


title: OTHER,metagenome for B209m3 at 3mon

description:
Library name: B209m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B209m3 at 3mon

tag: tissue

value: feces

value: exercise

tag: timepoint


title: C.difficile_resistant, erythromycin, bio1, rep4

description: Library name: sample_cdif_R1_4


title: OTHER,metagenome for B197m3 at 3mon

description:
Library name: B197m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B197m3 at 3mon


title: dre.embryo.pool_PFOA_4_2

tag: cell line

value: PFOA

tag: row

tag: column

value: mixed

tag: protocol


title: dre.embryo.pool_control_ottawa_0_4

value: C

tag: plate

tag: processing batch

tag: FISH origin


title: Primary HGSOC patients 052

description: Library name: SR2201768

tag: disease status

value: Primary

tag: tumor stage

value: IVB

tag: Sex

value: Female

value: Tumor tissue


title: Recurrent HGSOC patients 058

description: Library name: SR2102216

value: Recurrent


title: OTHER,metagenome for B237m3 at 3mon

description:
Library name: B237m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B237m3 at 3mon


title: OTHER,metagenome for B205m3 at 3mon

description:
Library name: B205m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B205m3 at 3mon


title: OTHER,metagenome for B235m3 at 3mon

description:
Library name: B235m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B235m3 at 3mon


title: OTHER,metagenome for B164m3 at 3mon

description:
Library name: B164m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B164m3 at 3mon


title: Recurrent HGSOC patients 057

description: Library name: SR2103368

value: IIIC


title: dre.embryo.pool_PFDS_0.2_3

value: pool of 10 whole embryos

tag: cell type

tag: genotype

value: PFDS

tag: rna extraction_batch

tag: sample id


title: Primary HGSOC patients 059

description: Library name: SR2012308

value: IVA


title: C.difficile_resistant, erythromycin, bio2, rep2

description: Library name: sample_cdif_R2_2

value: erythromycin resistant isolates

tag: treatment


title: C.difficile_resistant, erythromycin, bio1, rep3

description: Library name: sample_cdif_R1_3


title: C.difficile_resistant, erythromycin, bio1, rep2

description: Library name: sample_cdif_R1_2


title: dre.embryo.pool_PFDS_6_2

tag: tissue

value: 120-hours post fertilization

value: 5 days

tag: replicate

value: H

tag: rna yield_ng_u_l

tag: rin

value: TempO-Seq


title: OTHER,metagenome for B161m3 at 3mon

description:
Library name: B161m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B161m3 at 3mon

value: feces

value: exercise

tag: timepoint


title: dre.embryo.pool_PFDA_12_1

tag: cell line

value: PFDA

tag: row

value: E

tag: column

value: mixed

tag: protocol


title: Recurrent HGSOC patients 060

description: Library name: SR2006079

tag: disease status

value: IVB

value: Female


title: dre.embryo.pool_PFDA_4_1

value: D

tag: plate

tag: processing batch

tag: FISH origin


title: Recurrent HGSOC patients 061

description: Library name: SR2004995

value: Recurrent

tag: tumor stage

tag: Sex

value: Tumor tissue


title: C.difficile_resistant, erythromycin, bio1, rep1

description: Library name: sample_cdif_R1_1

tag: cell type


title: OTHER,metagenome for B158m3 at 3mon

description:
Library name: B158m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B158m3 at 3mon

tag: treatment


title: OTHER,metagenome for B166m3 at 3mon

description:
Library name: B166m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B166m3 at 3mon

tag: tissue


title: OTHER,metagenome for B155m3 at 3mon

description:
Library name: B155m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B155m3 at 3mon


title: Recurrent HGSOC patients 062

description: Library name: SR2002963

value: IIIC


title: C.difficle_resistant, untreated, rep3

description: Library name: resistant_Ctr_rep3

value: untreatd


title: dre.embryo.pool_PFDA_1.2_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: genotype

tag: replicate

value: F

tag: rna extraction_batch

tag: sample id


title: dre.embryo.pool_PFDA_0.12_1

tag: cell line

value: 120-hours post fertilization

value: 5 days

tag: rna yield_ng_u_l

tag: rin


title: C.difficle_resistant, untreated, rep2

description: Library name: resistant_Ctr_rep2

value: erythromycin resistant isolates


title: OTHER,metagenome for B154m3 at 3mon

description:
Library name: B154m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B154m3 at 3mon

value: feces

tag: timepoint


title: Primary HGSOC patients 063

description: Library name: SF2003515

tag: disease status

value: Primary


title: dre.embryo.pool_PFDA_0.4_2

value: PFDA

tag: row

tag: column

tag: plate

tag: protocol

value: TempO-Seq


title: C.difficle_resistant, untreated, rep1

description: Library name: resistant_Ctr_rep1


title: Recurrent HGSOC patients 064

description: Library name: OBGY0129

tag: tumor stage

tag: Sex


title: OTHER,metagenome for B131m3 at 3mon

description:
Library name: B131m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B131m3 at 3mon

tag: treatment

value: exercise


title: C.difficle_sensitive, erythromycin, merged

description: Library name: cdiff_sensitive_ery_merged

tag: cell type

value: erythromycin sensitive isolates


title: dre.embryo.pool_PFBS_80_3

tag: tissue

tag: genotype

value: PFBS

value: C

tag: processing batch

tag: FISH origin

value: ottawa


title: Primary HGSOC patients 065

description: Library name: OBGY0128

value: Female

value: Tumor tissue


title: OTHER,metagenome for B085m3 at 3mon

description:
Library name: B085m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B085m3 at 3mon


title: OTHER,metagenome for B084m3 at 3mon

description:
Library name: B084m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B084m3 at 3mon


title: dre.embryo.pool_PFBA_8_2

tag: cell line

value: PFBA

tag: replicate

value: B

tag: rna extraction_batch

tag: sample id


title: C.difficle_sensitive, erythromycin, subsample

description: Library name: cdiff_sensitive_ery_merged_30000


title: dre.embryo.pool_PFHxS_20_2

value: pool of 10 whole embryos

value: PFHxS

tag: rna yield_ng_u_l

tag: rin


title: Primary HGSOC patients 067

description: Library name: OBGY0123

tag: disease status

value: IIIC


title: C.difficile_sensitive, untreated, merged

description: Library name: cdiff_sensitive_ctr_merged

value: untreatd


title: OTHER,metagenome for B068m3 at 3mon

description:
Library name: B068m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B068m3 at 3mon

value: feces

tag: timepoint


title: Primary HGSOC patients 066

description: Library name: OBGY0125

value: Primary

value: IB


title: OTHER,metagenome for B063m3 at 3mon

description:
Library name: B063m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B063m3 at 3mon


title: dre.embryo.pool_PFHxS_6_2

value: 120-hours post fertilization

value: 5 days

tag: row

tag: column

tag: plate

tag: protocol

value: TempO-Seq


title: C.difficile_sensitive, untreated, subsample

description: Library name: cdiff_sensitive_ctr_merged_30000

tag: cell type

value: erythromycin sensitive isolates

tag: treatment


title: dre.embryo.pool_PFHxA_200_2

tag: tissue

tag: genotype

value: PFHxA

value: A


title: Recurrent HGSOC patients 068

description: Library name: OBGY0122

value: Recurrent

tag: tumor stage

value: IVB

tag: Sex

value: Female


title: C.difficile_resistant, erythromycin, merged

description: Library name: cdiff_resistant_ery_merged

value: erythromycin resistant isolates


title: OTHER,metagenome for B062m3 at 3mon

description:
Library name: B062m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B062m3 at 3mon

value: exercise


title: OTHER,metagenome for B052m3 at 3mon

description:
Library name: B052m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B052m3 at 3mon


title: Primary HGSOC patients 070

description: Library name: OBGY0116

value: Tumor tissue


title: dre.embryo.pool_PFHxA_20_1

value: pool of 10 whole embryos

tag: cell line

tag: replicate

value: H

tag: processing batch

tag: FISH origin

value: ottawa


title: Primary HGSOC patients 071

description: Library name: OBGY0114

value: Primary


title: dre.embryo.pool_PFHxA_60_1

tag: rna extraction_batch

tag: rna yield_ng_u_l

tag: rin

tag: sample id


title: OTHER,metagenome for B040m3 at 3mon

description:
Library name: B040m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B040m3 at 3mon

value: feces

tag: timepoint


title: C.difficile_resistant, erythromycin,subsample

description: Library name: cdiff_resistant_ery_merged_30000


title: C.difficile_resistant, untreated,merged

description: Library name: cdiff_resistant_ctr_merged

value: untreatd


title: dre.embryo.pool_PFDS_6_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

value: PFDS

tag: row

tag: column

tag: plate

value: mixed


title: Primary HGSOC patients 072

description: Library name: OBGY0113

tag: disease status

value: IIIC


title: dre.embryo.pool_PFHxA_6_1

tag: tissue

tag: cell type

value: PFHxA

tag: treatment

value: G

tag: protocol

value: TempO-Seq


title: OTHER,metagenome for B032m3 at 3mon

description:
Library name: B032m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B032m3 at 3mon


title: OTHER,metagenome for B031m3 at 3mon

description:
Library name: B031m3
Whole-metagenome shotgun sequencing
OTHER,metagenome for B031m3 at 3mon