title: Aged_5w_Sham_Hi_1

description: Library name: Aged_5w_Sham_Hi_1

value: Hippocampus

value: Adult

value: 18 to 25 months


title: iPSC C.1, day14, CD45+

status: Public on Jun 27 2025

type: SRA

city: New York

first: Emily

last: Mace

state: NY

country: USA

institute: Columbia University Irving Medical Center

library_source: transcriptomic

data_processing:
The FASTQ files were generated using FastQC (v0.11.7) and trimmed reads (Trimmomatic 0.38) were mapped to UCSC hg38 with HISAT2 (v2.1.0, Bowtie2 2.3.4.1), splice-aware aligner. The sequencing depth is between 58 and 80 million mappable reads. Transcript is assembled by StringTie (v2.1.3b) and abundance of genes are calculated as read counts and FPKM.
Assembly: USCS_hg38
Supplementary files format and content: txt file with count and RPKM

molecule: total RNA

organism: Homo sapiens

source_name: iPSC

growth_protocol: NK cell differentiation from iPSC was performed as described in Knorr et al. (27). Briefly, 9000 cells per well were plated on 96 well polystyrene round bottomed microwell plates (Fisher Scientific, 262162) for EB formation in APEL-2 media (StemCell Technologies, 5275) containing 10μM ROCK inhibitor, 40ng/ml SCF (Peprotech, 300-07), 20ng/ml BMP (R&D, 314-BP), 20ng/ml VEGF (R&D, 293-VE), and 1μM GSK inhibitor (CHIR99021; StemCell Technologies, 72052). EBs were cultured for six days. For autologous stroma supported differentiation, day 6 EBs were transferred to gelatin (Millipore, ES-006-B) coated 24 well plates (4EB/well; Fisher Scientific, 08-772-1C) with NK cell differentiation basal media supplemented with 5ng/ml IL-3 (1st week only; Peprotech, 200-03), 10ng/ml IL-15 (Peprotech, 200-15), 10ng/ml Flt3L (Peprotech, 300-19), 20ng/ml SCF, and 20ng/ml IL-7 (Peprotech, 200-07). NK cell differentiation basal media is made with 55% DMEM (Fisher Scientific, 11965118), 28% Hems F12 (Fisher Scientific, 10-080-CV), 15% human AB serum (GeminiBio, 100-512), 1% L-Glutamax (Fisher Scientific, 35050079), 1% Penicillin/streptomycin (100U/ml), 25μM BME (Fisher Scientific, 21985023), 50 μM Ethanolamine (Sigma, E0135-100ML), 25 μg/mL Ascorbic acid (Sigma, A5960-25G), and 5 ng/mL sodium selenite (Sigma, S5261-25G). After transfer, the cells from EB propagate and differentiate to NK cells in the 24 well plate for 35 days with weekly half media change.

extract_protocol:
2~10 X 10^4 cells were lysed, and RNA was collected with NucleoSpin RNA XS kit (Takara, 740902) according to the manufacturer’s protocol. RNA quality control was performed using the Agilent 2100 Bioanalyzer System.
Libraries were generated with SMARTer stranded RNA-Seq kit (Takara, 634839).

tag: cell line

value: iPSC

tag: cell type

tag: genotype

value: GINS4 WT/WT

tag: treatment

value: NK differentiation


title: Aged_5w_Sham_Hi_2

city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description: Library name: Aged_5w_Sham_Hi_2

data_processing:
The sequencing company used CASAVA version 1.8.2 (Illumina, San Diego, CA) was for the base calling
We used STAR 2.7.5c (Dobin et al., 2013, PMID: 23104886) with the default parameters for alignment of the short reads to the reference genome.
We used the GENCODE mouse gene annotation, version M33, for alignment and quantification.
We used RSEM version 1.3.3 (PMID: 21816040) for the gene and RNA-isoform level quantifications.
Assembly: Mouse reference genome GRCm39 (Ensembl release 100)
Supplementary files format and content: These are tab-limited, gzipped text files that contain Ensembl gene IDs and gene expression levels in FPKM (fragments per kilobase of transcript per million mapped reads) and TPM (transcripts per million).

molecule: polyA RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Following euthanasia 24 hours and 5 weeks after GA/OP, mice were perfused with 50 mL of ice-cold saline. Total RNA was isolated from the OB and hippocampus (HI) of both sham and GA/OP mice using a miRNeasy isolation kit (Cat# 217084, Qiagen). In brief, approximately 600ul of Buffer RLT were added to each sample and disrupted in a Precellys 24 Touch homogenizer. The aqueous phase containing RNA was collected, mixed with ethanol, and applied to a silica membrane spin column. After a series of washes to remove contaminants, RNA was eluted in RNase-free water. A minimum of 100ng was sent to the University of Maryland Institute for Genome Sciences and Novogene for downstream sequencing assays.
Library preparations were performed by the University of Maryland Institute for Genome Sciences (Baltimore, MD) and Novogene (Sacramento, CA) for sequencing on the Illumina platform (paired-end, 150 bp). mRNA was enriched using poly-A pulldown

tag: tissue

tag: developmental stage

tag: age

tag: Sex

value: male

tag: strain

value: Sham

tag: time point

value: 5 weeks after General Anesthesia and Operation

tag: biological replicate


title: MelST cells, input control 2

city: Barcelona

first: Neus

last: Mestre-Farràs

state: Barcelona

address: C/ Doctor AIguader 88

country: Spain

institute: CRG

data_processing:
RNA-seq data was processed using the nf-core/rnaseq v3.10.1 Nextflow pipeline (Ewels PA et al. 2020, Patel, H. et al. 2020). Reads were mapped with STAR and RSEM was used to quantify read counts
Assembly: hg38
Supplementary files format and content: tab separated values. In "rsem.merged.gene_counts.tsv" all samples are merged: each row contains a different gene and each column a different sample.
Supplementary files format and content: tab separated values. In the genes.results, only data from one sample is included. Raw counts, FPKM and TPM quantification are included.

source_name: MelST

growth_protocol: cells were cultured in DMEM-Glutamax media (Gibco 31966021) supplemented with 7% FBS (Gibco 10270106) and 1% penicillin-streptomycin (Gibco 15070063) at 37°C and 5% CO2 and grown upon 80% confluency

extract_protocol:
Cells were lysed in hypotonic gentle lysisbuffer (10 mM Tris-Hcl, 10 mM NaCL, 2 mM EDTA and 0.5% triton) and centrifuged for 10 min at maximum speed at 4°C. Supernatant was diluted in 1xNet buffer (50 mM Tris-Hcl, 150 mM NaCl, 0.1% NP40, 1 mM EDTA and RNAse inhibitor (Promega, #N2111) and incubated for 2h at 4°C on a wheel with 50 ul Dynabeads A previously coupled to 3 ug eIF2A or IgG antibody, respectively. Afterwards beads were washed 5 times with 500 ul 1xNet buffer. RNA was extracted from the remaining beads using Trizol. For input samples, RNA was directly extracted with Trizol after extract collection.
RNA immunoprecipitations (RIP) were performed under native conditions using an eIF2A antibody (abcam #ab169528), an IgG rabbit control antibody and Dynabeads A (invitrogen, #10002D).. Libraries were prepared with poly-A selection for 50bp Illumina sequencing

value: MelST

value: Immortalized melanocytes


title: MelST cells, input control 1


title: iPSC II.2, day14, CD45-

value: GINS4 V171L/Q191X


title: agm04-dpi00

type: RNA

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

hyb_protocol: Overnight hybridization according to standard NanoString protocol

scan_protocol: Scanned and quantified via nCounter SPRINT profiler according to standard protocol

data_processing:
Raw RCC files were background-thresholded using the NSolver v4.0 default parameters to generate the sample matrix. Downstream normalization and differential expression analyses were performed via limma.
Background-thresholded mRNA counts

organism: Chlorocebus sabaeus

source_name: African green monkey, whole blood, 0 days postinfection

extract_protocol: Total RNA extracted from AVL spiked with carrier RNA via the QIAgen Viral RNA Kit

tag: nhp

tag: dpi

tag: outcome

value: Succumbed

tag: status

value: Baseline

tag: qcfilter

value: FALSE


title: MelSTR cells, IgG control 3

source_name: MelSTR

value: MelSTR

value: Ras transformed melanocytes


title: Aged_5w_IsoOP_OB_5

description: Library name: Aged_5w_IsoOP_OB_5

source_name: Olfactory Bulb

value: Olfactory Bulb

value: 2% isoflurane (2hr) and midline laparotomy


title: agm07-dpi14

source_name: African green monkey, whole blood, 14 days postinfection

value: Late

value: TRUE


title: iPSC II.2, day14, CD45+

value: iPSC


title: Aged_5w_IsoOP_OB_4

description: Library name: Aged_5w_IsoOP_OB_4

value: Adult

value: 18 to 25 months


title: MelSTR cells, IgG control 2


title: iPSC I.1, day14, CD45-

value: GINS4 Q191X/WT

value: NK differentiation


title: agm07-dpi07

source_name: African green monkey, whole blood, 7 days postinfection

value: Middle


title: MelSTR cells, IgG control 1


title: iPSC I.1, day14, CD45+


title: agm07-dpi04

source_name: African green monkey, whole blood, 4 days postinfection

value: Early


title: MelST cells, IgG control 3

value: MelST

value: Immortalized melanocytes


title: Aged_5w_IsoOP_OB_2

description: Library name: Aged_5w_IsoOP_OB_2

value: male

value: 5 weeks after General Anesthesia and Operation


title: iPSC I.2, day14, CD45-

value: GINS4 V171L/WT


title: Aged_5w_IsoOP_OB_1

description: Library name: Aged_5w_IsoOP_OB_1


title: MelST cells, IgG control 2


title: agm07-dpi03

source_name: African green monkey, whole blood, 3 days postinfection

value: Succumbed


title: iPSC I.2, day14, CD45+


title: agm07-dpi00

value: Baseline


title: MelST cells, IgG control 1


title: Aged_5w_IsoOP_Hi_4

description: Library name: Aged_5w_IsoOP_Hi_4

value: Hippocampus

value: 2% isoflurane (2hr) and midline laparotomy


title: iPSC II.1, day14, CD45+

value: GINS4 V171L/Q191X


title: Aged_5w_IsoOP_Hi_3

description: Library name: Aged_5w_IsoOP_Hi_3


title: mcy02-dpi35

organism: Macaca fascicularis

source_name: Cynomolgus macaque, whole blood, 35 days postinfection

value: Survived

value: Recovered

value: TRUE


title: iPSC II.1, day14, CD45-

value: iPSC


title: iPSC II.1-Cor, day6, CD34+

value: GINS4 WT/WT

value: EB formation


title: mcy02-dpi28

source_name: Cynomolgus macaque, whole blood, 28 days postinfection


title: MSC-si-SERPING-rep2_IL6+

city: Seattle

first: Betty Chentzu

last: Yu

state: WA

address: 1100 Fairview Ave N

department: Computational Biology

institute: Fred Hutchinson Cancer Center

description: Library name: IP3_2

data_processing:
STAR 2.7.11b was used to align paired reads to the genome index. Command: STAR --runThreadN 8 --genomeDir {dirname_here} --readFilesIn '{fname_here} {fname_here} --readFilesCommand zcat --outFileNamePrefix --outFileNamePrefix {user_option} --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate Htseq-count was used to calculate read counts. Command: htseq-count -i gene_id {bam_fname_here} {gtf_fname_here} -r pos -s no -f bam > {output_fname_here} Fragments per kilobase transcript per million mapped reads (FPKM) were quantified by the following method: for each sample, for each gene HTseq-count values were divided by gene length in kilobases (quantified by GTFtools; Command: python2.7 GTFtools_0.6.9/gtftools.py -l {output_fname} {gtf_fname}) and divided the total sample count in millions.
Assembly: hg38
Supplementary files format and content: Read counts calculated by Htseq at different conditions (ISS, RSS, with and without IL-6) for two biological replicates.

source_name: adipose tissues

growth_protocol: Primary adipose derived cell (Lifeline) were maintained on gelatin-coated tissue culture plates with medium specific for MSC growing (StemLife MSC Medium Complete Kit, Lifeline) .Cells were maintained at 37℃ in a cell incubator containing 5% CO2.

extract_protocol:
As indicated, cells were harvested and RNA was extracted from all samples
RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer. Only samples with RNA integrity number (RIN) ≥8 were used for downstream processing. For library preparation, 500 ng to 1 µg of high-quality total RNA was used as input. mRNA was enriched using poly(A) selection with oligo-dT magnetic beads to isolate polyadenylated transcripts. Strand-specific RNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s protocol. Libraries were indexed, PCR-amplified, purified, and size-selected (~300 bp inserts), and quality control was performed using Qubit and Bioanalyzer prior to sequencing.

treatment_protocol: Human MSCs were first transduced with a lentiviral construct expressing dCas9-KRAB (e.g., pSLQ6604 driven by the SFFV promoter) and cultured for 3 days to allow protein expression. Cells were then sorted based on KRAB expression to enrich for successfully transduced populations. These enriched cells were subsequently transduced with individual lentiviral sgRNAs and cultured for 72 hours, followed by puromycin selection (2 μg/mL) for 48 hours to ensure sgRNA integration. After selection, cells were allowed to recover and expand over several passages. Finally, RNA was harvested for downstream transcriptional profiling. Where indicated, cells were treated with 10 ng/mL recombinant human IL-6 (Abcam, ab259381) to assess inflammatory senescence phenotypes under cytokine-induced stress.

value: adipose tissues

value: human primary mesenchymal stem cells (MSC) derived from adipose tissues


title: MSC-si-SERPING-rep1_IL6+

description: Library name: IP3_1


title: Aged_5w_IsoOP_Hi_2

description: Library name: Aged_5w_IsoOP_Hi_2

value: Adult

value: 18 to 25 months


title: MSC-si-CMKLR1-rep2_IL6+

description: Library name: IP2_2


title: mcy02-dpi21

source_name: Cynomolgus macaque, whole blood, 21 days postinfection

value: FALSE


title: Aged_5w_IsoOP_OB_3

description: Library name: Aged_5w_IsoOP_OB_3

value: Olfactory Bulb

value: male

value: 5 weeks after General Anesthesia and Operation


title: agm07-dpi10

source_name: African green monkey, whole blood, 10 days postinfection

value: Succumbed

value: Late


title: Aged_5w_IsoOP_Hi_1

description: Library name: Aged_5w_IsoOP_Hi_1

value: Hippocampus

value: 2% isoflurane (2hr) and midline laparotomy


title: iPSC C.1, day6, CD34+


title: mcy02-dpi14

source_name: Cynomolgus macaque, whole blood, 14 days postinfection

value: Survived


title: iPSC II.2, day6, CD34+

value: GINS4 V171L/Q191X


title: MSC-si-CMKLR1-rep1_IL6+

description: Library name: IP2_1


title: Aged_2h_Iso_Op_OB_7

description: Library name: Aged_2h_Iso_Op_OB_7

value: 24 hours after General Anesthesia and Operation


title: Aged_5w_IsoOP_Hi_5

description: Library name: Aged_5w_IsoOP_Hi_5


title: MSC-NC-rep2-R1_IL6+

description: Library name: IP1_2


title: mcy02-dpi10

source_name: Cynomolgus macaque, whole blood, 10 days postinfection

value: TRUE


title: MSC-NC-rep1-R1_IL6+

description: Library name: IP1_1


title: Aged_2h_Iso_Op_OB_6

description: Library name: Aged_2h_Iso_Op_OB_6


title: iPSC I.2, day6, CD34+

source_name: iPSC

value: iPSC

value: GINS4 V171L/WT

value: EB formation


title: iPSC I.1, day6, CD34+

value: GINS4 Q191X/WT


title: Aged_2h_Iso_Op_OB_5

description: Library name: Aged_2h_Iso_Op_OB_5

value: Adult

value: 18 to 25 months


title: mcy02-dpi04

source_name: Cynomolgus macaque, whole blood, 4 days postinfection

value: Early


title: mcy02-dpi07

source_name: Cynomolgus macaque, whole blood, 7 days postinfection

value: Middle


title: iPSC II.1, day6, CD34+


title: MSC-si-SERPING-rep2_IL6-

description: Library name: IM3_2

value: adipose tissues

value: human primary mesenchymal stem cells (MSC) derived from adipose tissues


title: Aged_2h_Iso_Op_OB_4

description: Library name: Aged_2h_Iso_Op_OB_4

value: Olfactory Bulb

value: male


title: iPSC II.1-Cor, day0, pluripotent

value: pluripotent

value: GINS4 WT/WT

value: no treatment


title: mcy02-dpi03

source_name: Cynomolgus macaque, whole blood, 3 days postinfection

value: Survived


title: MSC-si-SERPING-rep1_IL6-

description: Library name: IM3_1


title: Aged_2h_Iso_Op_OB_3

description: Library name: Aged_2h_Iso_Op_OB_3

value: 2% isoflurane (2hr) and midline laparotomy

value: 24 hours after General Anesthesia and Operation


title: iPSC C.1, day0, pluripotent

value: iPSC


title: mcy08-dpi14

value: Succumbed

value: Late

value: TRUE


title: Aged_2h_Iso_Op_OB_2

description: Library name: Aged_2h_Iso_Op_OB_2

value: Adult

value: 18 to 25 months


title: mcy02-dpi00

source_name: Cynomolgus macaque, whole blood, 0 days postinfection

value: Baseline


title: iPSC II.2, day0, pluripotent

value: GINS4 V171L/Q191X


title: Aged_2h_Iso_Op_OB_1

description: Library name: Aged_2h_Iso_Op_OB_1

source_name: Olfactory Bulb


title: MSC-si-CMKLR1-rep2_IL6-

description: Library name: IM2_2

value: adipose tissues

value: human primary mesenchymal stem cells (MSC) derived from adipose tissues


title: MSC-NC-rep2_IL6-

description: Library name: IM1_2


title: Aged_Sham_OB_6

description: Library name: Aged_Sham_OB_6

value: Olfactory Bulb

value: male

value: Sham


title: MSC-NC-rep1_IL6-

description: Library name: IM1_1


title: iPSC I.2, day0, pluripotent

value: pluripotent

value: GINS4 V171L/WT

value: no treatment


title: mcy08-dpi07

value: Middle


title: Aged_Sham_OB_5

description: Library name: Aged_Sham_OB_5

value: 24 hours after General Anesthesia and Operation


title: mcy08-dpi04

value: Succumbed

value: Early


title: Aged_Sham_OB_4

description: Library name: Aged_Sham_OB_4


title: MSC-si-SAMM50-rep1

description: Library name: M2_1


title: iPSC I.1, day0, pluripotent

value: iPSC

value: GINS4 Q191X/WT


title: mcy08-dpi03

value: TRUE


title: Aged_Sham_OB_3

description: Library name: Aged_Sham_OB_3

value: Adult

value: 18 to 25 months


title: MSC-NC-rep2

description: Library name: M1_2

value: adipose tissues


title: Aged_Sham_OB_2

description: Library name: Aged_Sham_OB_2


title: MSC-si-CMKLR1-rep1_IL6-

description: Library name: IM2_1

value: human primary mesenchymal stem cells (MSC) derived from adipose tissues


title: iPSC II.1, day0, pluripotent

value: GINS4 V171L/Q191X


title: mcy05-dpi14

value: Late


title: mcy08-dpi10


title: MT_1

city: Los Angeles

first: Shuo

last: Li

state: CA

address: 630 Charles E Young Dr S

institute: UCLA

library_source: genomic

data_processing:
The raw bisulfite sequencing reads were trimmed by cutadapt to remove sequencing adapters.
The trimmed reads were then aligned to hg19 reference genome by Bismark.
Then duplicated reads from PCR amplification were identified and removed by Bismark.
The deduplicated reads were then sorted and indexed using samtools.
The methylation level was calculated at every CpG site by Bismark.
Assembly: hg19
Supplementary files format and content: methylation level (beta value) at CpG sites in the bed format
The columns of the bed.gz files are:
Column 1: chromosome ID
Column 2: start coordinate
Column 3: end coordinate
Column 4: number of unmethylated alleles
Column 5: number of methylated alleles
Column 6: number of total alleles (methylated + unmethylated)
Column 7: methylation level (beta value, i.e. ratio of methylated alleles)

molecule: genomic DNA

source_name: MT

growth_protocol: The therapeutic cells were generated from an Ex Vivo HSC-derived CAR-NKT cell culture

extract_protocol:
Genomic DNA from samples was isolated with QIAGEN DNeasy Blood & Tissue kit following the corresponding manufacturer’s protocols.
The isolated genomic DNA was sonicated by Covaris system. Size selection by Ampure XP beads (Beckman-Coulter) was performed to enrich DNA fragments of around 250 bp in average sizes before library construction. In brief, 0.7 volume beads were added to the fragmented genomic DNA. After incubation, the supernatant was transferred to a new tube and an additional 1.3 volume beads were added (“0.5×–2× bead size selection”). After washing two times with 80% ethanol, genomic DNA was eluted with 40 ul EB buffer. Subsequently,  200ng genomic DNA was used for DNA library preparation with NEBNext Ultra II DNA library prep Kit (Cat#E7645). DNA library preparation has the following steps: DNA fragments end prep, adaptor ligation, size selection or purification of Adaptor-ligated DNA with Ampure XP beads, bisulfite conversion by Epitect Fast DNA Bisulfite Kits (QIAGEN, Cat#59826), PCR enrichment of Adaptor-ligated DNA, and purification of PCR product with 0.9x Ampure XP beads.  The average size of resulting DNA fragments was around 480bp, validated by Tapestation. The libraries were then subjected to sequencing on Illumina NovaSeq sequencer with 2x150bp configuration (Azenta).

treatment_protocol: The therapeutic cells were engineered with mesothelin-targeting CAR

value: MT


title: MNKT_3

source_name: MNKT

value: MNKT


title: Aged_2h_Iso_Op_Hi_7

description: Library name: Aged_2h_Iso_Op_Hi_7

source_name: Hippocampus

value: Hippocampus

value: male

value: 2% isoflurane (2hr) and midline laparotomy


title: mcy05-dpi19

source_name: Cynomolgus macaque, whole blood, 19 days postinfection


title: Saline, Female, rep2

city: La Jolla

first: Ye Ji

last: Shin

address: 9500 Gilman Dr

institute: University of California, San Diego

description: Library name: SF11

data_processing:
The adaptor sequences and low-quality reads were trimmed using Trimmomatic with LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed FASTQ reads were aligned to the rn7 genome using STAR with --outSAMtype BAM Unsorted --outFilterMismatchNmax 5 --outFilterMultimapNmax 1.
Gene-level read counts were generated using HTSeq. htseq-count was used for quantification with --stranded=no --idattr=gene_id --type=exon --mode=union
Normalization and differential expressed genes were performed using DESeq2 in R.
Assembly: rn7
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Central Amygdala

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen™) following manufacturer’s instructions.
NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext UltraExpress® RNA Library Prep Kit (NEB, E3330) were used for RNA-seq library preparation, following manufacturer’s instructions.

value: Central Amygdala

value: Saline


title: Aged_Sham_OB_1

description: Library name: Aged_Sham_OB_1

value: Olfactory Bulb

value: Sham

value: 24 hours after General Anesthesia and Operation


title: MT_3


title: Saline, Female, rep1

description: Library name: SF10


title: MNKT_2


title: Saline, Male, rep6

description: Library name: SM12


title: mcy05-dpi07

value: Succumbed

value: Middle

value: TRUE


title: mcy05-dpi10


title: MSC-si-SAMM50-rep2

description: Library name: M2_2

value: adipose tissues


title: Saline, Male, rep5

description: Library name: SM11


title: LHCN-M2 cells,SMCHD1KO, HiC, clone2

city: Grand Rapids

first: Gerd

last: Pfeifer

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Research Institute

data_processing:
Data are process by Juicer to align to genome and generate KR normalized contact matrix
Contact matrix is visualzied by juicebox
Assembly: hg19
Supplementary files format and content: hic, contacts

growth_protocol: LHCN-M2 cells were cultured on 0.1% gelatin-coated tissue culture plates in DMEM / medium 199 (4:1) supplemented with 15% fetal bovine serum, 0.02 M HEPES, 0.03 μg/ml zinc sulfate, 1.4 μg/ml vitamin B12, 0.055 μg/ml dexamethasone, 2.5 ng/ml hepatocyte growth factor, 10 ng/ml basic FGF, 60 units/ml penicillin and 60 μg/ml streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
The cells were cross-linked with 1% formaldehyde for exactly 10 min at room temperature. Add 1.25 ml of 2.5 M glycine to quench the reaction for 5 min at room temperature. After washing, proceed immediately to DSG cross-linking for 40 min at room temperature. Cross-linked cells were lysed in ice-cold lysis buffer containing 10 μL protease inhibitor cocktail. the nuclei were digested with 400 U DdeI and 400 U DpnII (NEB) at 37 C overnight with interval shaking (900 rpm, 30 s on, 4 min off).
Incubate the Hi-C samples with Biotinylation buffer (7 μL 10× NEBuffer 3.1, 1.5 μL 10 mM dCTP, 1.5 μL 10 mM dGTP, 1.5 μL 10 mM dTTP,  37.5 μL 0.4 mM biotin-14-dATP, 11 μL H2O, 10uL Klenow DNA polymerase) 4 hours at 23°C in a Thermomixer (900 rpm, 30 s on, 4 min off).  Incubate ligation Mix (240 μL 5× ligation buffer, 120 μL 10% Triton X-100, 12 μL 10 mg/ml BSA, 243 μL H2O, 50 μL 1 U/ μL T4 DNA ligase) with biotinylation mix for 4 hr at 16°C in a Thermomixer with interval shaking (900 rpm, 30 s on, 4 min off). Prepare biotin removal reactions in PCR tubes as described below: 15 μg of Hi-C DNA sample, 13 μL 10× NEB buffer 2.1, 3.25 μL 1 mM dATP,  3.25 μL 1 mM dGTP, 13 μL 1 mM 3000 U/ml T4 DNA polymerase, up to 130 μL with water. Transfer two 65-μl aliquots from each 130-μl reaction to a thermocycler with following cycling parameters: 20 °C for 4 hr, 75°C for 20 min, hold at 4°C. Sonicate samples on Covaris E220 Evo sonicator to shear a fragment size distribution 300-500bp. The products were then purified with MyOne Streptavidin C1 beads (65001, Thermo Fisher Scientific), dA-tailed, ligated to 3 mL 15 mM NEBNext Adaptor for Illumina at 37 C for 2h.  Hi-C libraries were then amplified with 4 cycles of PCR. In situ Hi-C on WT and Smchd1-/- LHCN-M2 cells were performed in two biological replicates, which were sequenced on Illumina HiSeq with 150-bp paired-end read runs.

value: human myoblast

value: SMCHD1 knockout


title: LHCN-M2 cells,SMCHD1KO, HiC, clone1


title: mcy08-dpi00

value: Baseline


title: Aged_2h_Iso_Op_Hi_4

description: Library name: Aged_2h_Iso_Op_Hi_4

value: Adult

value: 18 to 25 months


title: mcy05-dpi04

value: Early


title: Aged_2h_Iso_Op_Hi_5

description: Library name: Aged_2h_Iso_Op_Hi_5

value: Hippocampus

value: male


title: MSC-NC-rep1

description: Library name: M1_1

value: human primary mesenchymal stem cells (MSC) derived from adipose tissues


title: Saline, Male, rep4

description: Library name: SM10

value: Central Amygdala

value: Saline


title: MT_2

value: MT


title: LHCN-M2 cells, wildtype, HiC, clone2

value: WT


title: Aged_2h_Iso_Op_Hi_3

description: Library name: Aged_2h_Iso_Op_Hi_3

value: 2% isoflurane (2hr) and midline laparotomy

value: 24 hours after General Anesthesia and Operation


title: mcy05-dpi03

value: Succumbed

value: TRUE


title: Saline, Male, rep3

description: Library name: SM09


title: Aged_2h_Iso_Op_Hi_2

description: Library name: Aged_2h_Iso_Op_Hi_2


title: mcy06-dpi14

value: Late


title: mcy05-dpi00


title: LHCN-M2 cells, wildtype, HiC, clone1

value: human myoblast


title: Aged_2h_Iso_Op_Hi_6

description: Library name: Aged_2h_Iso_Op_Hi_6


title: MNKT_1

value: MNKT


title: AC16 cells, Doxorubicin 112 hrs, Day6, Repeat 3

city: Taipei City

first: An-Chi

last: Wei

address: No. 1, Sec. 4, Roosevelt Rd., Da’an Dist.

department: Graduate Institute of Biomedical Electronics and Bioinformatics

country: Taiwan

institute: National Taiwan University

data_processing:
The quality control of the raw reads generated from the sequencing step was conducted using fastp v0.23.2
Low-quality reads and artificial adapters were trimmed using Trimmomatic v0.38 (parameters: LEADING: 3, TRAILING: 3, SLIDINGWINDOW: 4:20, MINLEN: 36)
Processed reads were mapped to GRCh38.p13 using STAR v2.7.8 (parameters- outSAMattributes: NH HI AS nM XS, twopassMode: Basic, quantMode: GeneCounts)
Raw counts were calculated using htseq-count v0.13.5 (parameters- stranded=no, mode=union)
Assembly: GRCh38.p13
Supplementary files format and content: text file includes raw counts for each sample

growth_protocol: AC16 cells were maintained in DMEM/F12 with 12% fetal bovine serum (FBS) and 1% antibiotic containing Penicillin-Streptomycin(10000 U/ml Penicillin and 10mg/ml Streptomycin), and grown in a CO2 incubator at 37°C and 5% CO2

extract_protocol:
The total RNA of the harvested cells was extracted using EasyPrep total RNA kit (Biotools, Taiwan), and a total amount of 3 μg RNA per sample was used.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations

treatment_protocol: Before havesting, three groups of cells were cultured in a medium containing 0.1uM doxorubicin (Abcam, UK) for two, four, and six days, respectively.

value: cardiomyocytes

value: Doxorubicin 0.1uM 112hrs


title: Saline, Male, rep1

description: Library name: SM01


title: Aged_2h_Iso_Op_Hi_1

description: Library name: Aged_2h_Iso_Op_Hi_1

value: Adult

value: 18 to 25 months


title: mcy06-dpi10


title: Aged_Sham_Hi_6

description: Library name: Aged_Sham_Hi_6

value: Hippocampus

value: male

value: Sham


title: mcy06-dpi07

value: Middle


title: AC16 cells, Doxorubicin 112 hrs, Day6, Repeat 2


title: Fentanyl, Female, rep2

description: Library name: FF02

value: Central Amygdala

value: Fentanyl


title: Aged_Sham_Hi_5

description: Library name: Aged_Sham_Hi_5


title: mcy06-dpi04

value: Early


title: AC16 cells, Doxorubicin 112 hrs, Day6, Repeat 1

value: WT


title: AC16 cells, Doxorubicin 96 hrs, Day6, Repeat 3

value: Doxorubicin 0.1uM 96hrs


title: Aged_Sham_Hi_4

description: Library name: Aged_Sham_Hi_4

value: 24 hours after General Anesthesia and Operation


title: Fentanyl, Female, rep1

description: Library name: FF01


title: Fentanyl, Male, rep5

description: Library name: FM05


title: mcy06-dpi00

value: Succumbed

value: Baseline

value: TRUE


title: Aged_Sham_Hi_2

description: Library name: Aged_Sham_Hi_2


title: Aged_Sham_Hi_3

description: Library name: Aged_Sham_Hi_3


title: mcy06-dpi03


title: Saline, Male, rep2

description: Library name: SM02

value: Saline


title: AC16 cells, Doxorubicin 96 hrs, Day6, Repeat 2

value: cardiomyocytes


title: Fentanyl, Male, rep4

description: Library name: FM04


title: Fentanyl, Male, rep3

description: Library name: FM03


title: AC16 cells, Doxorubicin 48 hrs, Day6, Repeat 3

value: Doxorubicin 0.1uM 48hrs


title: mcy10-dpi10

value: Late


title: Fentanyl, Male, rep2

description: Library name: FM02


title: Young_2h_Iso_Op_OB_12

description: Library name: Young_2h_Iso_Op_OB_12

value: Olfactory Bulb

value: Adult

value: 10 to 12 weeks

value: 2% isoflurane (2hr) and midline laparotomy


title: AC16 cells, Doxorubicin 96 hrs, Day6, Repeat 1


title: AC16 cells, Doxorubicin 48 hrs, Day6, Repeat 2


title: mcy10-dpi07

value: Middle


title: Young_2h_Iso_Op_OB_3

description: Library name: Young_2h_Iso_Op_OB_3

value: male


title: AC16 cells, Doxorubicin 48 hrs, Day6, Repeat 1


title: Fentanyl, Male, rep6

description: Library name: FM06

value: Central Amygdala

value: Fentanyl


title: Biofilm 72 h , biol rep 4

city: Cambridge

first: Rahan

middle: Rudland

last: Nazeer

address: Hopkins Building, Downing Site, Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
Library name: Sample 16
72D

data_processing:
Quality of the raw reads contained in the fastQ files was done with FASTQC (v12.0). The samples were then aligned to the PAO1 genome (NC_002516.2) using the BWA aligner (v1.1.5). The bam files produced as output were then exported from BaseSpace and R (v4.5.0) was used for further analysis. Reads were mapped to transcripts using featureCounts and DESeq2 was then employed to normalise those reads, and to conduct differential expression analysis. Subsequent visualisation was performed with ggplot2, using significance thresholds set to |log2FC| > 1.5 and an adjusted p-value < 0.05.
Assembly: NC_002516.2
Supplementary files format and content: csv file containing normalised read counts

molecule: cytoplasmic RNA

organism: Pseudomonas aeruginosa

source_name: Biofilm

growth_protocol: PAO1 cells were  grown either in a 200 mL Erlenmeyer flask, agitated at 200 rpm, for the planktonic culture, or in 175cm2 tissue culture flasks at 25 rpm, for the biofilm cultures. Both were grown in AGSY medium at 37C.

extract_protocol:
Cell lysis and phase separation was achieved using Max Bacterial Reagent (Ambion), Trizol and chloroform. The aqueous phase was then loaded onto the column of the Monarch Spin RNA Cleanup Kit and the protocol was followed.
RNA integrity was determined using an Agilent 2100 Bioanalyzer electropherogram. Ribosomal RNA depletion was carried out with the Ribo-Zero rRNA Removal Kit (Illumina). The TruSeq Stranded mRNA Library Prep Kit (Illumina) was then used for library preparation of the transcripts.

treatment_protocol: Cells were sedimented by centrifugation ( 3,220 x g, 15 min, 4C). Those cells grown in the biofilm were sedimented twice by centrifugation (3,220 x g, 30 min, 4C), with an intermediate step of vortexing in 7% NaCl between spins to separate cells from matrix material.

value: Biofilm

value: WT


title: mcy10-dpi03

value: Succumbed

value: Early


title: AC16 cells, Control, Day6, Repeat 3

value: DMEM


title: Young_2h_Iso_Op_OB_2

description: Library name: Young_2h_Iso_Op_OB_2

value: 24 hours after General Anesthesia and Operation


title: AC16 cells, Control, Day6, Repeat 2

value: cardiomyocytes


title: mcy10-dpi12

source_name: Cynomolgus macaque, whole blood, 12 days postinfection

value: TRUE


title: Biofilm 72 h , biol rep 3

description:
Library name: Sample 15
72C


title: mcy03-dpi19

value: Late


title: AC16 cells, Control, Day6, Repeat 1


title: Biofilm 72 h , biol rep 2

description:
Library name: Sample 14
72B


title: Young_2h_Iso_Op_OB_1

description: Library name: Young_2h_Iso_Op_OB_1

value: Olfactory Bulb


title: Biofilm 72 h , biol rep 1

description:
Library name: Sample 13
72A


title: Aged_Sham_Hi_1

description: Library name: Aged_Sham_Hi_1

value: Hippocampus

value: Adult

value: 18 to 25 months

value: Sham


title: 50-VLP10 Day3 post infection

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description: Library name: Sample 50

data_processing:
reads trimmed using Trimmomatic 0.39
Aligned to reference genome using STAR 2.7.11a with encode suggested parameter
Assembly: Cavpor3.0 ensembl 112
Supplementary files format and content: count matrix text file

organism: Cavia porcellus

source_name: Whole blood

extract_protocol:
For day 54, RNA was extracted from whole blood using the Qiagen Rneasy Protect Animal Blood Kit. For day 59, RNA was extracted using Zymo Research Direct-zol RNA Micro Prep Kit.
mRNA sequencing librarier were prepared using NEBNext PolyA module and NEBNext ultra ii directional RNA library preparation kit following manufacturer's recommended procedure

value: Whole blood

tag: day

value: Day 59 post-vaccination/ Day 3 post-infection

value: VLP mRNA vaccine 10 μg


title: mcy03-dpi10


title: Fentanyl, Male, rep1

description: Library name: FM01

value: Central Amygdala

value: Fentanyl


title: Young_Sham_OB_13

description: Library name: Young_Sham_OB_13

value: 10 to 12 weeks

value: male


title: Biofilm 48 h , biol rep 4

description:
Library name: Sample 12
48D

value: Biofilm

value: WT


title: 49-VLP10 Day3 post infection

description: Library name: Sample 49


title: Young_2h_Iso_Op_OB_5

description: Library name: Young_2h_Iso_Op_OB_5

value: 2% isoflurane (2hr) and midline laparotomy

value: 24 hours after General Anesthesia and Operation


title: mcy03-dpi14

value: Succumbed

value: Late

value: TRUE


title: Young_Sham_OB_11

description: Library name: Young_Sham_OB_11

value: Olfactory Bulb

value: Adult


title: mcy10-dpi04

value: Early


title: Young_Sham_OB_10

description: Library name: Young_Sham_OB_10

value: Sham


title: Biofilm 48 h , biol rep 3

description:
Library name: Sample 11
48C


title: mcy03-dpi07

value: Middle


title: Young_Sham_OB_8

description: Library name: Young_Sham_OB_8


title: 47-VLP10 Day3 post infection

description: Library name: Sample 47

value: Whole blood

value: Day 59 post-vaccination/ Day 3 post-infection

value: VLP mRNA vaccine 10 μg


title: Biofilm 48 h , biol rep 2

description:
Library name: Sample 10
48B


title: mcy10-dpi00

value: Baseline


title: Young_Sham_OB_4

description: Library name: Young_Sham_OB_4

value: 10 to 12 weeks

value: male


title: 46-VLP10 Day3 post infection

description: Library name: Sample 46


title: mcy03-dpi03


title: Biofilm 48 h , biol rep 1

description:
Library name: Sample 9
48A

value: Biofilm

value: WT


title: Young_2h_Iso_Op_Hi_12

description: Library name: Young_2h_Iso_Op_Hi_12

value: Hippocampus

value: 2% isoflurane (2hr) and midline laparotomy

value: 24 hours after General Anesthesia and Operation


title: Biofilm 24 h , biol rep 4

description:
Library name: Sample 8
24D


title: mcy03-dpi00

value: Succumbed

value: TRUE


title: 45-GP7.5 Day3 post infection

description: Library name: Sample 45

value: GP mRNA vaccine 7.5 μg


title: 44-GP7.5 Day3 post infection

description: Library name: Sample 44


title: mcy07-dpi10

value: Late


title: Biofilm 24 h , biol rep 2

description:
Library name: Sample 6
24B


title: Biofilm 24 h , biol rep 3

description:
Library name: Sample 7
24C


title: 48-VLP10 Day3 post infection

description: Library name: Sample 48


title: Young_2h_Iso_Op_Hi_5

description: Library name: Young_2h_Iso_Op_Hi_5

value: Adult


title: Young_2h_Iso_Op_Hi_3

description: Library name: Young_2h_Iso_Op_Hi_3


title: 43-GP7.5 Day3 post infection

description: Library name: Sample 43


title: Biofilm 24 h , biol rep 1

description:
Library name: Sample 5
24A


title: mcy07-dpi07

value: Middle


title: 41-GP7.5 Day3 post infection

description: Library name: Sample 41

value: Whole blood


title: Planktonic 5 h , biol rep 4

description:
Library name: Sample 4
5D

source_name: Planktonic

value: Planktonic


title: mcy03-dpi04

value: Early


title: mcy07-dpi04


title: Young_2h_Iso_Op_Hi_1

description: Library name: Young_2h_Iso_Op_Hi_1


title: Young_Sham_Hi_13

description: Library name: Young_Sham_Hi_13

value: Sham


title: 40-VLP4 Day3 post infection

description: Library name: Sample 40

value: Day 59 post-vaccination/ Day 3 post-infection

value: VLP mRNA vaccine 4 μg


title: mcy07-dpi03

value: FALSE


title: 39-VLP4 Day3 post infection

description: Library name: Sample 39


title: Planktonic 5 h , biol rep 3

description:
Library name: Sample 3
5C

value: WT


title: Young_Sham_Hi_11

description: Library name: Young_Sham_Hi_11

value: Hippocampus

value: 10 to 12 weeks

value: male


title: mcy07-dpi00

value: Succumbed

value: Baseline


title: 38-VLP4 Day3 post infection

description: Library name: Sample 38


title: mcy07-dpi11

source_name: Cynomolgus macaque, whole blood, 11 days postinfection

value: TRUE


title: Young_Sham_Hi_10

description: Library name: Young_Sham_Hi_10

value: 24 hours after General Anesthesia and Operation


title: mcy09-dpi35

source_name: Cynomolgus macaque, whole blood, 35 days postinfection

value: Survived

value: Recovered


title: 37-VLP4 Day3 post infection

description: Library name: Sample 37

value: Whole blood


title: Young_2h_Iso_Op_Hi_2

description: Library name: Young_2h_Iso_Op_Hi_2

value: Adult

value: 2% isoflurane (2hr) and midline laparotomy


title: mcy09-dpi28

source_name: Cynomolgus macaque, whole blood, 28 days postinfection


title: Planktonic 5 h , biol rep 1

description:
Library name: Sample 1
5A

value: Planktonic


title: Planktonic 5 h , biol rep 2

description:
Library name: Sample 2
5B


title: Young_Sham_Hi_8

description: Library name: Young_Sham_Hi_8

value: Sham


title: Young_Sham_Hi_4

description: Library name: Young_Sham_Hi_4


title: Endosperm replicate 3

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Read alignment + counting; Cell Ranger count; version 6.0.0
Assembly: Zea mays B73 V4
Supplementary files format and content: h5 file containing raw and filtered count matrix (output Cell Ranger count)
Supplementary files format and content: Merged Seurat file in .rds format

molecule: nuclear RNA

organism: Zea mays

source_name: Endosperm

growth_protocol: Kernels were put in pre-wetted Jiffy-7® pellet and kept in controlled greenhouse conditions (300 μE.m−2.s−1 light intensity, 16 h light, 26°C and 8 h dark, 22°C). Seedlings were then transferred to 10 L pots containing controlled release fertilizer (2.0 kg/m3, Osmocote® Professional potting mixture, Scotts International B.V.) and moved to a larger greenhouse until grown to maturity.

extract_protocol:
10 endosperms from 3 independent ears of the B73 inbred line were manually dissected, transferred into 2mL of LB01 buffer (15mM Tris, 2nM Na2EDTA, 0.5mM spermine, 80mM KCL, 20mM NaCl, 0.1% (v/v) Triton X-100, pH = 8.0, 60U/mL RNasin Plus RNAse Inhibitor (Promega)), on a glass container put on ice. Endosperms were finely chopped with a razor blade during around 30s and the solution was aspired through a 100µm nylon mesh with a needle-less syringa. The filtered solution was stained with 20µg/mL of propidium iodide (PI) during 5min before nuclei were purified by Fluorescence Activated Cell Sorting (FACS) on a BD FACSAria II device. Around 100.000 nuclei were sorted in a 1.5mL Eppendorf and were subsequently centrifuged 5 min at 500g to concentrate them at the bottom of the tube.
Nuclear suspensions were loaded into a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit (V3 chemistry for repeat 1, V3.1 chemistry for repeat 2+3, 10X Genomics) according to the manufacturer’s instructions.

value: Endosperm

tag: ecotype


title: 36-VLP4 Day3 post infection

description: Library name: Sample 36

value: Day 59 post-vaccination/ Day 3 post-infection

value: VLP mRNA vaccine 4 μg


title: mcy09-dpi21

source_name: Cynomolgus macaque, whole blood, 21 days postinfection


title: 35-GP3 Day3 post infection

description: Library name: Sample 35

value: GP mRNA vaccine 3 μg


title: Endosperm replicate 2

description: 10X Genomics


title: Endosperm replicate 1

description: 10X Genomics


title: mcy09-dpi10

source_name: Cynomolgus macaque, whole blood, 10 days postinfection

value: Late


title: 34-GP3 Day3 post infection

description: Library name: Sample 34


title: 33-GP3 Day3 post infection

description: Library name: Sample 33


title: WT, BMDM, Saa3 treated, scRNAseq (EFGH)

city: Taipei

first: Jian-Da

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd., Da'an Dist.

department: Department of Biochemical Science & Technology

description:
Library name: Sample2_EFGH
ParseBiosciences

data_processing:
The sequencing data was demultiplexed and mapped to database(mm10, GRCm38) with the commercial pipeline(ParseBiosciences-Pipeline.v1.2.1). The sequence reads from different samples was then distributed based on different Round 1 barcode with R(v4.4.2). To exclude low-quality cells, we filtered cells with nFeature_RNA > 200, nFeature_RNA < 2000, and percent.mt < 45, adjusting the filter parameters for each sample based on violin plots of RNA feature counts and mitochondrial percentages per cell.
Assembly: mm10, GRCm38
Supplementary files format and content: rds file

source_name: BMDM ( Bone marrow-derived macrophage)

extract_protocol:
After sacrificing the mouse and disinfecting it with 70% ethanol, expose the hind limb muscles by pulling down the skin. Remove the main muscles near the lower limb and carefully isolate the femur and tibia. Place the bones into a petri dish containing ice-cold HBSS with 1% P/S/A and remove any excess muscle. Cut off the bone ends and transfer the bones into a 0.2ml PCR tube with a small hole at its base, placed inside a 1.5 ml tube. Centrifuge at 4000g in 4 °C for 30 secs to collect the bone marrow cells, then resuspend them in culture medium. Filter the cell suspension through a 70 μm strainer to remove clumps, centrifuge again to discard the supernatant, and finally resuspend the cell pellet in bone marrow culture medium.
The split-pool barcoding process, following the Evercode™ WT v2 protocol, consisted of three rounds. In Round 1, cells were distributed into wells, and sample-specific barcodes were applied to the fixed cells using an in-cell reverse transcription (RT) reaction. Cells from all wells were then pooled together. In Round 2, cells were redistributed across a plate, and an in-cell ligation was performed to append the second barcode. The cells from each well were again pooled together. In Round 3, cells were split across a plate, and a third barcode was appended with another in-cell ligation. After pooling cells from each well, the pooled cells were divided across multiple sublibraries. The cells were then lysed, and the library was fragmented, end-repaired, and went through A-tailing followed by the ligation of the sequencing adaptor. The library was then labeled with a fourth sublibrary-specific barcode. The quality of dsDNA libraries was analyzed using the High Sensitivity D5000 ScreenTape Kit (Agilent) and concentrations were assessed with the Qubit dsDNA HS Kit (Thermo Fisher Scientific). Libraries were sequenced on a NovaSeq X Plus (Illumina) with 10% PhiX.

treatment_protocol: Bone marrow cells harvested from Wild-type C57BL/6J (WT) mice were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin/streptomycin/amphotericin B (P/S/A), and 20 ng/mL macrophage colony-stimulating factor (M-CSF). On day 3, the medium was replaced with 10 mL fresh medium. On day 5, an additional 2 mL of medium was added. After seven days of culture, adherent macrophages were detached using Accutase and treated with 100 ng/mL SAA3 protein. The cell suspension was adjusted to a density of 5 × 10⁶ cells/mL, seeded into a 48-well plate, and cultured for 24 hours. Then BMDMs were fixed and permeabilized according to the Evercode™ Fixation v2 protocol.

tag: cell type

value: BMDM ( Bone marrow-derived macrophage)

value: 7 weeks

value: Male

value: Cell cultured 7days, SAA3 treated, fixed and permeabilized

tag: batch

value: Batch 2:E, F, G, and H


title: WT, BMDM, Saa3 treated, scRNAseq (ABCD)

description:
Library name: Sample2_ABCD
ParseBiosciences

tag: genotype

tag: treatment

value: Batch 1:A, B, C, and D


title: mcy09-dpi14

source_name: Cynomolgus macaque, whole blood, 14 days postinfection

value: Survived

value: TRUE


title: WT, BMDM, Ctrl, scRNAseq (EFGH)

description:
Library name: Sample1_EFGH
ParseBiosciences

value: Cell cultured 7 days, fixed and permeabilized


title: OE_NC3

city: Yinchuan

first: Lan

last: Feng

address: West Helan Mountain Road.XixiaDistrict,Yinchuan,China

department: College of Animal Science and Techology

country: China

institute: Ningxia university

description: Library name: sample12

data_processing:
Raw data of fastq format were firstly processed by fastp software (version 0.23.0), low-quality reads, reads containing poly-N and reads with insert size less than 18bp were removed and adaptor sequences from the reads were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Deduplicated Reads were mapped to the reference genome of Bos Taurus from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/263/795/GCF_002263795.2_ARS-UCD1.3/ using STRA software (version 2.7.6a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: GCF_002263795.2_ARS-UCD1.3
Supplementary files format and content: raw_counts_All_Samples.txt
Supplementary files format and content: All_samples_rpkm.csv

organism: Bos taurus

source_name: Transfection of pcDNA3.1-NC cells

extract_protocol:
The total RNA of each of above listed samples was extracted using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
A amount of 2 μg total RNA per sample was used for stranded RNA sequencing library preparation using polyA selection method and KC-DigitalTM Stranded mRNA Library Prep Kit(Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer's instruction.

value: Transfection of pcDNA3.1-NC cells

value: Overexpression vector construction:The construction of HGFAC-NC gene overexpression vector was carried out by Shanghai Biotechnology, the simple process was to connect the CDS region of HGFAC gene NC to the pcDNA3.1 vector, and the double enzyme digestion was carried out for verification, and the gel electrophoresis test showed that the pcDNA3.1-NC overexpression vector was successfully constructed.


title: mcy09-dpi07

source_name: Cynomolgus macaque, whole blood, 7 days postinfection

value: Middle


title: 32-GP3 Day3 post infection

description: Library name: Sample 32

tag: tissue

value: Whole blood


title: WT, BMDM, Ctrl, scRNAseq (ABCD)

description:
Library name: Sample1_ABCD
ParseBiosciences

tag: age


title: OE_NC2

description: Library name: sample11


title: OE_NC1

description: Library name: sample10


title: 31-GP3 Day3 post infection

description: Library name: Sample 31

value: Day 59 post-vaccination/ Day 3 post-infection


title: mcy09-dpi00

source_name: Cynomolgus macaque, whole blood, 0 days postinfection

value: Baseline


title: mcy09-dpi03

source_name: Cynomolgus macaque, whole blood, 3 days postinfection

value: Early


title: 30-PBS Day3 post infection

description: Library name: Sample 30

value: PBS


title: si_NC3

description: Library name: sample9

source_name: Transfection of NC cells

value: Transfection of NC cells

value: Cell transfection:After the adipocytes were cultured to the best state and digested, each group of cells was counted and prepared into 1.0×10^5 cells-mL-1, 2 mL of non-antimicrobial medium was added to each well of a six-well plate, and 130 µL of cells were spread into each well, and cultured overnight at 37°C in a 5% CO2 incubator; after 12-20 h, observe that the cell fusion rate reaches 70%~90%, and then transfect; prepare NC plasmid and transfection reagent diluents. After 12-20 h, observe that the cell fusion rate reaches 70%~90% for transfection; prepare plasmid and transfection reagent dilutions. Mix the transfection reagents well and incubate at room temperature for 5 minutes; transfer liquid A to liquid B and mix well, let it stand at room temperature for 15 minutes; transfer the cells into 6-well plates with 1000 µL of opti/MEMI pre-filled, and change the medium to complete medium after 6 hours; after 48 hours of transfection, harvest the cells with TRIZOL and use them for the next step directly, or store them in the refrigerator at -80℃ for spare parts. After 48 h of transfection, cells were harvested by TRIZOL and then used directly in the next experiment or stored in -80℃ refrigerator.


title: mcy04-dpi15

source_name: Cynomolgus macaque, whole blood, 15 days postinfection

value: Succumbed

value: Late


title: mcy09-dpi04

source_name: Cynomolgus macaque, whole blood, 4 days postinfection


title: Cell culture, methanol, lanthanum, rep1

city: Berkeley

first: Charlotte

middle: Charlie

last: Mineo

address: 421 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

description:
Library name: 004_Methanol_La_3456
column name in both processed files: 004_Methanol_La_3456

data_processing:
Read demultiplexing, read trimming, and run analytics were performed using DRAGEN v3.10.12, an on-board analysis software on the NextSeq2000 by SeqCoast Genomics.
KBase was used to align 12 million 2 x 150 bp paired-end reads per sample via HISAT2 v2.1.0 to the Bradyrhizobium sp.  USDA 3456 genome.
Transcripts were assembled via StringTie v2.1.5 to generate FPKM values
DESeq2 v1.20.0 was used to generate gene counts and call differentially expressed genes
Assembly: NCBI Reference Sequence: NZ_VIDU00000000.1. Accessed via MAGE WGS VIDU01.1 (https://mage.genoscope.cns.fr/microscope/mage/viewer.php?O_id=13238)
Supplementary files format and content: gene_count_matrix_succ_MeOH_all.csv : Contains gene count information for all samples
Supplementary files format and content: FPKM_matrix_Succ_MeOH_All.tsv : Contains FPKM values for all samples

organism: Bradyrhizobium sp. USDA 3456

source_name: cell culture

growth_protocol: 5 mL preculures of Bradyrhizobium sp. USDA 3456 were grown in Methylobacterium PIPES (MP) minimal media supplemented with 15 mM succinate (Millipore Sigma). Precultures were grown overnight in 14-mL polystyrene round-bottom plastic culture tubes (Falcon) at 30°C and 200 rpm in an Innova S44i incubator shaker (Eppendorf). Pre-cultures were washed in MP by centrifugation at 2000 x g for 10 minutes and diluted into 50 mL of fresh MP with indicated substrate for a starting OD600 of 0.1.

extract_protocol:
40 mL of culture were harvested at mid-exponential phase (OD600 of 0.5-1 for all conditions) by centrifugation at 4°C at 2000 x g for 10 minutes. Total RNA was extracted using the Qiagen RNeasy Kit and quantified. rRNA depletion using the Ribo-Zero RNA Plus rRNA Depletion Kit (Illumina) was performed by SeqCoast Genomics.
Samples were prepared for whole genome sequencing using an Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Microbiome and unique dual indexes by SeqCoast Genomics. Sequencing was performed by SeqCoast Genomics on the Illumina NextSeq2000 platform using a 300 cycle flow cell kit to produce 2x150bp paired reads.

treatment_protocol: Pre-cultures of 5 mL preculures of Bradyrhizobium sp. USDA 3456 were grown and prepared as described above and used to inoculate triplicate 250-mL glass culture flasks containing 50 mL of MP with 10 µM lanthanum chloride supplemented and either 50 mM methanol or 15 mM succinate as a carbon source. The starting OD600 was 0.1.

value: cell culture

value: Wildtype USDA 3456

value: methanol and lanthanum


title: Cell culture,succinate, lanthanum, rep3

description:
Library name: 003_Succinate_La_3456
column name in both processed files: 003_Succinate_La_3456

value: succinate and lanthanum


title: 27-PBS Day3 post infection

description: Library name: Sample 27

source_name: Whole blood


title: si_NC1

description: Library name: sample7


title: Cell culture, methanol, lanthanum, rep3

description:
Library name: 006_Methanol_La_3456
column name in both processed files: 006_Methanol_La_3456


title: Cell culture, methanol, lanthanum, rep2

description:
Library name: 005_Methanol_La_3456
column name in both processed files: 005_Methanol_La_3456


title: Cell culture,succinate, lanthanum, rep2

description:
Library name: 002_Succinate_La_3456
column name in both processed files: 002_Succinate_La_3456


title: OE_2

description: Library name: sample5

source_name: Transfection of pcDNA3.1-HGFAC cells

value: Transfection of pcDNA3.1-HGFAC cells

value: Overexpression vector construction:The construction of HGFAC gene overexpression vector was carried out by Shanghai Biotechnology, the simple process was to connect the CDS region of HGFAC gene to the pcDNA3.1 vector, and then carry out double enzyme digestion for verification, and gel electrophoresis showed that the construction of pcDNA3.1-HGFAC overexpression vector was successful.


title: 28-PBS Day3 post infection

description: Library name: Sample 28


title: mcy04-dpi10

value: TRUE


title: 26-PBS Day3 post infection

description: Library name: Sample 26


title: OE_3

description: Library name: sample6


title: mcy04-dpi07

value: Middle


title: OE_1

description: Library name: sample4


title: lsr-complemented strain stationary phase biol rep 3

city: Muenster

first: Ulrich

last: Dobrindt

state: NRW

address: Mendelstrasse 7

department: Institute of Hygiene

country: Germany

institute: University of Münster

description: Library name: Sample 18

data_processing:
Raw sequence reads were quality checked using quality control tools FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC ( DOI: 10.1093/bioinformatics/btw354).
Adaptor trimming by Cutadapt (doi.org/10.14806/ej.17.1.200) with subsequent quality control, alignment of reads using burrows-wheeler alignment (doi.org/10.1093/bioinformatics/btp324) to the genome of E. coli 83972 with a subsequent strandedness check using RSeQC (DOI: 10.1093/bioinformatics/bts356 ) and quality control, count reading using featureCounts (doi.org/10.1093/bioinformatics/btt656) and a subsequent differentially expressed gene analysis using DESeq2 (www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: The reads were mapped to the genome sequence of E. coli 83972 (accession numbers CP058220 and CP058221).
Supplementary files format and content: xlsx file including raw counts for all samples

organism: Escherichia coli

source_name: strain 83972 attB::lsr

growth_protocol: Overnight cultures of E. coli strains 83972 and 83972 attB::lsr were diluted to a final optical density OD600 = 0.02 in 200 mL LB and incubated at 37 degrees Celsius and 180 rpm (three biological replicates per strain). At indicated time points, 70 mL of culture (lag phase), 5 mL of culture (exponential phase), or 2 mL of culture (stationary phase) were harvested.

extract_protocol:
The bacterial pellet was resuspended in 70 µL lysis buffer (lysozyme in TE buffer, 85 mg/mL, pH 8). After 10 min incubation at RT and gentle vortexing every 10 s, 1 mL TRizol ® (Thermo Fisher Scientific) was added and the isolation process was continued according to the manufacturer's protocol. 10 µg of isolated total RNA were used for DNA digestion, using the Turbo DNase (Turbo-DNA-free™ Kit, Thermo Fisher Scientific) in the presence of 1 U/µl RiboLock RNAse Inhibitor (Fermentas) for 1 h.
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3' adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified (11 PCR cycles) to about 10-20 ng/µl using a high fidelity DNA polymerase. The TruSeq barcode sequences, which are part of the 5' TruSeq sequencing adapters were used. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: At the indicated time points, the indicated volume of the bacterial culture was added to the 0.2x volume of pre-chilled stop solution (95 % ethanol, 5 % phenol), vortexed and incubated for 5 min on ice. Cells were pelleted for 5 min at 5,000 g, flash frozen in a dry ice-ethanol bath and stored at −80° C.

tag: cell line

value: strain 83972 attB::lsr


title: Cell culture,succinate, lanthanum, rep1

description:
Library name: 001_Succinate_La_3456
column name in both processed files: 001_Succinate_La_3456


title: 25-VLP10-Day54

description: Library name: Sample 25

value: Whole blood

value: Day 54 post-vaccination

value: VLP mRNA vaccine 10 μg


title: 24-VLP10-Day54

description: Library name: Sample 24


title: 29-PBS Day3 post infection

description: Library name: Sample 29

value: Day 59 post-vaccination/ Day 3 post-infection

value: PBS


title: s_NC2

description: Library name: sample8

value: Transfection of NC cells

value: Cell transfection:After the adipocytes were cultured to the best state and digested, each group of cells was counted and prepared into 1.0×10^5 cells-mL-1, 2 mL of non-antimicrobial medium was added to each well of a six-well plate, and 130 µL of cells were spread into each well, and cultured overnight at 37°C in a 5% CO2 incubator; after 12-20 h, observe that the cell fusion rate reaches 70%~90%, and then transfect; prepare NC plasmid and transfection reagent diluents. After 12-20 h, observe that the cell fusion rate reaches 70%~90% for transfection; prepare plasmid and transfection reagent dilutions. Mix the transfection reagents well and incubate at room temperature for 5 minutes; transfer liquid A to liquid B and mix well, let it stand at room temperature for 15 minutes; transfer the cells into 6-well plates with 1000 µL of opti/MEMI pre-filled, and change the medium to complete medium after 6 hours; after 48 hours of transfection, harvest the cells with TRIZOL and use them for the next step directly, or store them in the refrigerator at -80℃ for spare parts. After 48 h of transfection, cells were harvested by TRIZOL and then used directly in the next experiment or stored in -80℃ refrigerator.


title: lsr-complemented strain stationary phase biol rep 2

description: Library name: Sample 17


title: mcy04-dpi03

value: Succumbed

value: Early


title: mcy04-dpi14

value: Late


title: 23-VLP10-Day54

description: Library name: Sample 23


title: si_2

description: Library name: sample2

source_name: Transfection of si cells

value: Transfection of si cells

value: Cell transfection:After the adipocytes were cultured to the best state and digested, each group of cells was counted and prepared into 1.0×10^5 cells-mL-1, 2 mL of non-antimicrobial medium was added to each well of a six-well plate, and 130 µL of cells were spread into each well, and cultured overnight at 37°C in a 5% CO2 incubator; after 12-20 h, observe that the cell fusion rate reaches 70%~90%, and then transfect; prepare the plasmid and transfection reagent diluent. After 12-20 h, observe that the cell fusion rate reaches 70%~90% for transfection; prepare the plasmid and transfection reagent dilution solution. Mix the transfection reagents well and incubate at room temperature for 5 minutes; transfer liquid A to liquid B and mix well, let it stand at room temperature for 15 minutes; transfer the cells into 6-well plates with 1000 µL of opti/MEMI pre-filled, and change the medium to complete medium after 6 hours; after 48 hours of transfection, harvest the cells with TRIZOL and use them for the next step directly, or store them in the refrigerator at -80℃ for spare parts. After 48 h of transfection, cells were harvested by TRIZOL and then used directly in the next experiment or stored in -80℃ refrigerator.


title: mcy04-dpi00

value: Baseline


title: si_1

description: Library name: sample1


title: lsr-complemented strain stationary phase biol rep 1

description: Library name: Sample 16


title: 22-VLP10-Day54

description: Library name: Sample 22


title: lsr-complemented strain logarithmic phase biol rep 2

description: Library name: Sample 14


title: P13_PE_HiC

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

description: HiSeq X PE 150bp

data_processing:
Hi-C reads were  mapped with Open2C distiller-nextflow pipeline v0.3.3 (Abdennur et al., Bioinformatics 2009). Reads were mapped with bwa mem v0.7.17-r1188 (Li et al., Bioinformatics 2009) to the GRCh38/hg38 human reference genome.
Mapped reads were parsed and filtered with pairtools v0.3.064. Only reads with MAPQ>30 were considered for the Hi-C matrix generation.
Cool files were created by cooler v0.8.1165 and balanced via “balance” function with default parameters.
Assembly: hg38/GRCh38
Supplementary files format and content: .mcool, 1-2-5-10-20-50-100-200-500-1000-2000-5000kb resolution

source_name: Pleural Effusion

growth_protocol: Flash-frozen tissue

extract_protocol:
For each sample, a minimum of 10×50µM sections (tissue samples) or ~10×10e6 of cryopreserved cells (pleural effusions) were cross-linked, digested using using MboI (New England Biolabs), and Hi-C library preparation was performed as previously described (Rao et al., Cell 2014; Donaldson Collier, Nat Genet 2019).
Quality and quantification of the Hi-C libraries was assessed using the 2100 Bioanalyzer (Agilent, DNA 7500 kit). Biological replicates were pooled and subjected to sequencing using with paired-end setup using the sequencer indicated in the description field of each sample.

value: Pleural Effusion

tag: genome build

value: Tumor (Metastasis)

tag: restriction enzyme

value: MboI


title: mcy01-dpi14

value: TRUE


title: 21-VLP10-Day54

description: Library name: Sample 21

value: Whole blood


title: mcy01-dpi10


title: lsr-complemented strain logarithmic phase biol rep 1

description: Library name: Sample 13

value: strain 83972 attB::lsr


title: mcy04-dpi04


title: 20-GP7.5-Day54

description: Library name: Sample 20

value: Day 54 post-vaccination

value: GP mRNA vaccine 7.5 μg


title: si_3

description: Library name: sample3


title: lsr-complemented strain lag phase biol rep 3

description: Library name: Sample 12


title: P08_PE_HiC

description: HiSeq X PE 150bp + NovaSeq6000 PE 61bp


title: 18-GP7.5-Day54

description: Library name: Sample 18


title: 19-GP7.5-Day54

description: Library name: Sample 19


title: P14_PE_HiC

description: HiSeq X PE 150bp


title: mcy01-dpi07

value: Middle


title: mcy01-dpi19

source_name: Cynomolgus macaque, whole blood, 19 days postinfection


title: lsr-complemented strain logarithmic phase biol rep 3

description: Library name: Sample 15


title: lsr-complemented strain lag phase biol rep 2

description: Library name: Sample 11


title: P07_PE_HiC

description: HiSeq X PE 150bp


title: mcy01-dpi04


title: P06_PE_HiC

description: HiSeq X PE 150bp


title: lsr-complemented strain lag phase biol rep 1

description: Library name: Sample 10


title: 17-GP7.5-Day54

description: Library name: Sample 17


title: P15_PE_HiC

description: HiSeq X PE 150bp


title: 16-GP7.5-Day54

description: Library name: Sample 16


title: mcy01-dpi03


title: Wild type stationary phase biol rep 3

description: Library name: Sample 9

source_name: strain 83972

value: strain 83972


title: mcy01-dpi00


title: 15-VLP4-Day54

description: Library name: Sample 15

value: VLP mRNA vaccine 4 μg


title: Wild type stationary phase biol rep 2

description: Library name: Sample 8


title: 14-VLP4-Day54

description: Library name: Sample 14


title: Wild type stationary phase biol rep 1

description: Library name: Sample 7


title: 13-VLP4-Day54

description: Library name: Sample 13


title: 12-VLP4-Day54

description: Library name: Sample 12


title: NIH3T3 pLXSH replicate 3

city: Edmonton

first: Serhiy

last: Havrylov

state: Alberta

address: 8-29 Medical Sciences Building

department: Medical Genetics

country: Canada

institute: University of Alberta

description: Library name: Sample 6

data_processing:
Obtained data were de-multiplexed using Illumina's bcl2fastq2. De-multiplexed read sequences were aligned to the Mus musculus (mm10) reference sequence.
Assembly: mm10
Supplementary files format and content: FPKM values for each sample

growth_protocol: NIH3T3 cells expressing Foxc1 ORF or pLXSH vector were cultured in DMEM media supplemented with 10% FBS, 100 U/ml pennicillin and 100 ug/ml streptomycin.

extract_protocol:
RNA was isolated using RNeasy Plus Mini Kit (Qiagen).
Samples were prepped following the standard protocol for the NEBnext Ultra II Stranded mRNA (New England Biolabs).

value: fibroblast

value: pLXSH


title: NIH3T3 pLXSH replicate 1

description: Library name: Sample 4


title: NIH3T3 Foxc1 replicate 2

description: Library name: Sample 2

value: Foxc1 OE


title: 22 month old females

city: Stony Brook

first: Leonard

middle: YM

last: Cheung

state: New York

address: 101 Nicolls Road

institute: Stony Brook University

description: Library name: 6890-LC-4

data_processing:
Demultiplexed fastqs were processed using Cellranger Single Cell Suite v3.1.0
Assembly: mm10
Supplementary files format and content: zipped versions of the matrix tables, with list of barcodes (column names for matrix) and features (i.e. genes, row names for matrix)

source_name: pituitary gland

extract_protocol:
Pooled single-nuclei RNAseq samples of 3 individual pituitary glands per pool, male and female 5 and 22 month old UM-HET3 wild-type mice. Tissue was snap frozen in dry ice and nuclei prepped with the 10X Genomics Nuclei Prep Kit.
Libraries were made on the 10X Genomics 3' gene expression NextGem platform by the University of Michigan Advanced Genomics Core targeting 10,000 cells per sample.

value: pituitary gland


title: Wild type logarithmic phase biol rep 1

description: Library name: Sample 4


title: 22 month old males

description: Library name: 6890-LC-3


title: NIH3T3 pLXSH replicate 2

description: Library name: Sample 5


title: NIH3T3 Foxc1 replicate 3

description: Library name: Sample 3


title: Wild type logarithmic phase biol rep 2

description: Library name: Sample 5


title: 11-VLP4-Day54

description: Library name: Sample 11


title: Wild type logarithmic phase biol rep 3

description: Library name: Sample 6


title: 10-GP3-Day54

description: Library name: Sample 10

value: GP mRNA vaccine 3 μg


title: Wild type lag phase biol rep  3

description: Library name: Sample 3


title: NIH3T3 Foxc1 replicate 1

description: Library name: Sample 1


title: Wild type lag phase biol rep 1

description: Library name: Sample 1


title: 5 month old males

description: Library name: 6890-LC-1


title: 9-GP3-Day54

description: Library name: Sample 9


title: Wild type lag phase biol rep 2

description: Library name: Sample 2


title: 7-GP3-Day54

description: Library name: Sample 7


title: KPC subcutaneous tumor, treated with EIPA, rep5

first: Cosimo

last: Commisso

address: 10901 N. Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

hyb_protocol: 50 ng RNA of each sample was hybridized using the NanoString PanCancer Immune CodeSet (Cat# XT-CSO-MIP1-12) according to the manufacturer's instructions.

scan_protocol: Absolute read counts were quantified by the nCounter digital analyzer (nanoString).

data_processing: Data normalization was performed in nSolver analysis software version 3.0 using default settings. Normalized counts for sample EIPA_Rep5 are average values from normalized counts of two tumor samples from the same mouse.

source_name: KPC subcutaneous tumor

extract_protocol: Frozen tumor portions were lysed on ice in the lysis buffer provided in the PureLink RNA Mini Kit (Thermo Fisher Scientific) using a Kimble pellet pestle motor, and total RNA was isolated using the kit.

treatment_protocol: Portions of heterotopic KPC.4662 tumors treated with vehicle or EIPA-filled osmotic pumps over 6 days were snap frozen in liquid nitrogen immediately after harvest.

value: EIPA


title: 5 month old females

description: Library name: 6890-LC-2


title: Foxc1 ab1

description: Library name: Sample 1

data_processing:
Peak calling was done with MACS2 software on Galaxy platform (usegalaxy.org) using stringent (q-value <= 0.05) and relaxed (p-value <= 0.05) significance cut-offs.
Assembly: mm10
Supplementary files format and content: bigWig CPM values, narrow peaks for each sample

source_name: Gli2-mGFP NIH3T3 Foxc1 OE

growth_protocol: Gli2-mGFP NIH3T3 reporter cells expressing Foxc1 ORF were cultured in DMEM media supplemented with 10% FBS, 100 U/ml pennicillin and 100 ug/ml streptomycin.

extract_protocol:
Prior to cross-linking media were replaced with fresh DMEM supplemented with 10% FBS. To crosslink proteins to DNA, paraformaldehyde (PFA) solution was added to cell media to a final concentration of 6%. After 10 min incubation at room temperature remaining PFA was quenched by addition of 10X glycine solution. Glycine solution was added to each plate and incubated for additional 5 min at room temperature to quench the remaining PFA. Cross-linked chromatin was prepared and immunoprecipitated using Simple ChIP plus Enzymatic Chromatin IP Kit (New England Biolabs). Chromatin was reverse-crosslinked using Proteinase K digestion and purified according to kit manufacturers instructions.
ChIP-seq libraries were prepared using the NEBNext Ultra II Library Prep Kit (New England Bioloabs). Library preparation and sequencing was performed at the BRC Sequencing Core (University of British Columbia, Vancouver, BC).

value: Gli2-mGFP NIH3T3 Foxc1 OE


title: Foxc1 ab2

description: Library name: Sample 2


title: 8-GP3-Day54

description: Library name: Sample 8


title: 5-PBS-Day54

description: Library name: Sample 5

value: PBS


title: LHCN-M2 cells, wildtype, RNA, clone5

data_processing:
Sequencing was performed with an Illumina NextSeq 500 machine and 75 bp paired-end runs were performed.
paired-end RNAseq reads were trimmed using TrimGalore with defaut parameters.
Trimmed reads were aligned to the mouse genome mm9 with STAR (v2.5.1) , and gene count were performed using a STAR (v2.5.1)
The limma (v3.38.2) statistical package19 was used to call the differential expressed gene.
Assembly: hg19
Supplementary files format and content: bigWig,  counts coverage

extract_protocol:
Total RNA was isolated with PureLink RNA Mini Kit (Invitrogen).
Total RNA integrity was verified by Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified with NanoDrop 8000 instrument (Thermo Fisher). RNA-seq libraries were prepared from total RNA with the KAPA RNA HyperPrep kit with RiboErase (KAPA Biosystems , according to the manufacturer’s protocols.

value: human myoblast

value: SMCHD1 knockout


title: KPC subcutaneous tumor, treated with EIPA, rep3


title: Input

description: Library name: Sample 3


title: KPC subcutaneous tumor, treated with EIPA, rep2


title: KPC subcutaneous tumor, treated with EIPA, rep4


title: LHCN-M2 cells, wildtype, RNA, clone6


title: 6-GP3-Day54

description: Library name: Sample 6

value: Whole blood


title: LHCN-M2 cells, wildtype, RNA, clone3

value: WT


title: KPC subcutaneous tumor, treated with EIPA, rep1


title: KPC subcutaneous tumor, treated with DMSO, rep5

value: DMSO


title: 3-PBS-Day54

description: Library name: Sample 3

value: Day 54 post-vaccination


title: LHCN-M2 cells, wildtype, RNA, clone2


title: 2-PBS-Day54

description: Library name: Sample 2


title: SL_Al-treatment-rep2

city: Kurashiki

first: Yoshiyuki

last: Tsuchiya

state: Okayama

department: Institute of Plant Science and Resources

country: Japan

institute: Okayama University

description: Gene expression after 18hr in 100µM Al-treated tobacco cell culture

hyb_protocol: Cy3-labelled cRNA samples (1.65 µg) were fragmented at 60°C for 30 minutes and hybridized on to Agilent Tobacco Oligo DNA Microarray (4 × 44k, AMADID: 021113). Hybridization was carried out in a incubation chamber at 65°C for 17 hours.

scan_protocol: The slide was scanned at a resolution of 5 µm using an Agilent Microarray Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: The scanned images were analyzed using Feature Extraction Software (Agilent Technologies). To analyze image and signal intensity, raw data of the scanning were processed with the software GeneSpring GX 10 (Agilent Technologies), and normalized to shift to the 75 percentile.

organism: Nicotiana tabacum

source_name: cell, wild-type SL, Aluminum treatment, replication2

label_protocol: The cDNA was synthesized from 200 ng each of total RNA samples; the cRNA was subsequently labelled with Cy3 fluorescent dye using the Low Input Quick Amp Labeling Kit, One-color (Agilent Technologies), following the manufacturer’s instructions. The cRNA target solution was prepared after labelled cRNA was purified using RNeasy mini spin columns (Qiagen).

growth_protocol: The suspension-cultured tobacco cell lines were grown in an Erlenmeyer flask on a rotary shaker operated at 100 rpm at 25°C in the dark.

extract_protocol: The total RNA from cells was extracted using RNeasy Plant Mini Kit (Qiagen) with DNase treatment following the manufacturer's instructions.

treatment_protocol: Tobacco cells at the log phase under normal growth condition were withdrawn, washed and then cultured without (control) or with 100 µM AlCl3 at a cell density of 10 mg FW per mL in treatment medium (Ca-sucrose solution containing 3 mM CaCl2, 3% sucrose and 20 mM MES (pH 5.0) for 18 h on a rotary shaker operating at 100 rpm at 25 °C.

value: cultured cell

tag: treatment condition

value: Al-treatment


title: SL_control-rep3

description: Gene expression after 18hr in 0µM Al-treated tobacco cell culture

source_name: cell, wild-type SL, control condition, replication13

value: Control (without Al-treatment)


title: 1-PBS-Day54

description: Library name: Sample 1


title: variovorax, mM9 sucrose, rep6

status: Public on Jun 26 2025

city: Houston

first: Jonathan

middle: J.

last: Silberg

address: 6100 Main St

institute: Rice University

description: Library name: mM9sucrose_6

data_processing:
Raw paired-end FASTQ files were processed using a custom Python (v3.9.21) pipeline (https://github.com/bbshockey/SeqSorcerer_May27_2025). The pipeline was modified to include parameters specific to this study. Quality trimming and FastQC analysis were performed using Trim Galore v0.6.10 (https://github.com/FelixKrueger/TrimGalore) with the settings "--fastqc", "--paired", "--length", "20","--clip_R2", "15", "--three_prime_clip_R1", and "15". The reference genome was indexed and aligned with HISAT2 (10.1038/s41587-019-0201-4) (v2.2.1). The BAM files were processed with SAMtools (10.1093/bioinformatics/btp352) (v1.9). Transcript counts were quantified via featureCounts from the Subread package (10.1093/nar/gkt214) (v2.0.1) with the parameters, '-a', gtf_file, '-o', output_file, '-T', '2', '-s', '2', '-Q', '0', '-t', 'CDS', '-g', 'transcript_id', '--minOverlap', '1', '--fracOverlap', '0', '--fracOverlapFeature', '0', and '-p'.
Assembly: The assembled reference genome and annotations were previously described (10.1128/msystems.00372-22).
Supplementary files format and content: Transcript counts in .txt format

organism: Variovorax beijingensis

source_name: bacteria

extract_protocol:
ZymoBIOMICS RNA Miniprep Kit
Zymo-Seq RiboFree Total RNA Library Kit

value: bacteria


title: variovorax, mM9 sucrose, rep4

description: Library name: mM9sucrose_4


title: LHCN-M2 cells, wildtype, RNA, clone1


title: variovorax, mM9 sucrose, rep1

description: Library name: mM9sucrose_1


title: KPC subcutaneous tumor, treated with DMSO, rep3


title: variovorax, mM9 sucrose, rep5

description: Library name: mM9sucrose_5


title: variovorax, mM9 sucrose, rep2

description: Library name: mM9sucrose_2


title: variovorax, mM9 sucrose, rep3

description: Library name: mM9sucrose_3


title: variovorax, mM9, rep5

description: Library name: mM9_5


title: SL_control-rep2

source_name: cell, wild-type SL, control condition, replication2


title: KPC subcutaneous tumor, treated with DMSO, rep4


title: KPC subcutaneous tumor, treated with DMSO, rep1


title: KPC subcutaneous tumor, treated with DMSO, rep2


title: 4-PBS-Day54

city: Galveston

description: Library name: Sample 4


title: variovorax, mM9, rep4

description: Library name: mM9_4


title: variovorax, mM9, rep6

description: Library name: mM9_6


title: LHCN-M2 cells, wildtype, RNA, clone4


title: SL_control-rep1

source_name: cell, wild-type SL, control condition, replication1


title: variovorax, mM9, rep1

description: Library name: mM9_1


title: SL_Al-treatment-rep3

source_name: cell, wild-type SL, Aluminum treatment, replication3


title: SL_Al-treatment-rep1

source_name: cell, wild-type SL, Aluminum treatment, replication1


title: variovorax, M2, rep6

description: Library name: M2_6


title: variovorax, M2, rep5

description: Library name: M2_5


title: variovorax, M2, rep4

description: Library name: M2_4


title: variovorax, M2, rep3

description: Library name: M2_3


title: variovorax, Q1, rep6

description: Library name: Q1_6


title: variovorax, M2, rep1

description: Library name: M2_1


title: variovorax, Q1, rep5

description: Library name: Q1_5


title: variovorax, M2, rep2

description: Library name: M2_2


title: variovorax, mM9, rep3

description: Library name: mM9_3


title: variovorax, Q1, rep4

description: Library name: Q1_4


title: Female Uterus, 167 mg/kg/day 73FTOH, Animal r91

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description: Library name: p23_10109_r91_u

data_processing:
Raw sequencing reads (FASTQ files) were aligned to known probe sequences listed in the TempO-Seq probe manifest using HISAT2 to compute a matrix of read counts for each probe in each sample.
Assembly: TempO-seq Rat S1500+ v1.2
Supplementary files format and content: Count table CSV files contain a row for each known probe and a column for each sample. Each cell contains the number of reads from a single cell uniquely aligned to a single probe sequence
Supplementary files format and content: Probe manifest CSV file contains a row for each known probe with the probe name, sequence, and target gene

source_name: Uterus

growth_protocol: Male and female Sprague Dawley (Crl:CD(SD), Charles River Laboratory) rats are purchased at 6 – 8 weeks of age. Upon receipt, the animals are placed on a standard, purified laboratory diet and reverse osmosis treated drinking water ad libitum. The specific brand and type of food and source of the water should be noted in Appendix II (Detailed Animal Study Report) of the individual assessment. After a 7- to 14-day quarantine and acclimation period, the animals are weighed and randomly assigned by weight to chemical exposure and control groups. Only clinically healthy animals are used in the study. The target age for initiating exposure is 8 - 10 weeks.

extract_protocol:
Treated and control animals are necropsied approximately 24 hours after the last exposure. Carbon dioxide asphyxiation is used as the method of euthanasia, with death confirmed by a secondary method such as exsanguination or cervical dislocation. The following tissues were dissected from each animal: kidney, liver, adrenal gland, brain, heart, lung, ovary (females), spleen, testis (males), thyroid, thymus, and uterus (females). Tissue samples were collected within ten minutes of termination. The left liver lobe, right kidney, left lung, both testis, uterus, heart, spleen, thymus and whole brain were sectioned into 5mm^3 pieces. Samples from these larger tissues were then individually divided into at least 3 cryovials. At least two of the samples from each tissue in each animal were preserved in RNAlater™ (Thermo Fisher Scientific) at 4°C overnight and then frozen at approximately -20°C for up to 3 weeks before transferring to approximately -80°C. At least one sample from each larger tissue is frozen immediately in liquid nitrogen and stored at approximately -80°C.   The smaller bilateral tissues: adrenal glands, thyroid gland, and ovaries (female) are placed into two cryovials and preserved in RNALater with the left side of the tissue or gland going into the first cryovial and the right side going into the second cryovial. The first tube of RNALater preserved tissue is submitted for sequencing. For each tissue undergoing transcriptomic analysis, total RNA is extracted from one of the aliquots stored in RNAlater™.
The isolated total RNA is used to perform targeted RNA sequencing (RNA-seq) using the BioSpyder TempO-Seq rat S1500+ assay (v1.2) according to manufacturer’s instructions. No specific RNA purity or integrity criteria are applied to the RNA samples as the TempO-Seq assay has been designed to provide high quality gene expression measurements on whole cell lysates, purified RNA, and formalin-fixed paraffin embedded tissue.

treatment_protocol: For oral gavage studies, at least four male and four female rats per dose group receive the vehicle alone or test article in vehicle via gavage (5 or 10 ml/kg) for five days. Animals are weighed daily prior to administration and are observed twice daily, once during administration and once in the late afternoon, at least six hours apart, for assessment of moribundity and mortality. Formal clinical observations are performed on the first day post-dosing and prior to necropsy. Moribund animals or animals exhibiting overt clinical toxicity are removed from the study. The temperature in the experimental animal room is maintained at a target of 22°C (± 3°C) with a relative humidity that is ideally between 50-60% but is at least 30% and preferably not to exceed 70% other than during room cleaning. Lighting is artificial with a sequence of 12 hours light, 12 hours dark. Animals are housed individually or caged in small groups of no more than three animals of the same sex in accordance with local institutional animal care and use requirements.

tag: Sex

value: Female

value: Uterus

tag: strain

value: Sprague Dawley

value: 8-10 weeks

value: 167 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:167 mg/kg/day

value: dose group:7

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)

value: route of_exposure:Oral gavage

tag: sample qc_issue

value: No Issue


title: Female Uterus, 500 mg/kg/day 73FTOH, Animal r92

description: Library name: p23_10109_r92_u

value: 500 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:500 mg/kg/day

value: dose group:8


title: Female Uterus, 500 mg/kg/day 73FTOH, Animal r94

description: Library name: p23_10109_r94_u


title: Female Uterus, 167 mg/kg/day 73FTOH, Animal r89

description: Library name: p23_10109_r89_u


title: variovorax, Q1, rep2

description: Library name: Q1_2


title: Female Uterus, 500 mg/kg/day 73FTOH, Animal r96

description: Library name: p23_10109_r96_u


title: variovorax, Q1, rep3

description: Library name: Q1_3


title: Female Uterus, 500 mg/kg/day 73FTOH, Animal r95

description: Library name: p23_10109_r95_u


title: Female Uterus, 167 mg/kg/day 73FTOH, Animal r87

description: Library name: p23_10109_r87_u


title: Female Uterus, 50 mg/kg/day 73FTOH, Animal r86

description: Library name: p23_10109_r86_u

value: 50 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:50 mg/kg/day

value: dose group:6


title: Female Uterus, 167 mg/kg/day 73FTOH, Animal r88

description: Library name: p23_10109_r88_u


title: Female Uterus, 50 mg/kg/day 73FTOH, Animal r84

description: Library name: p23_10109_r84_u


title: Female Uterus, 500 mg/kg/day 73FTOH, Animal r93

description: Library name: p23_10109_r93_u


title: Female Uterus, 167 mg/kg/day 73FTOH, Animal r90

description: Library name: p23_10109_r90_u


title: Female Uterus, 16.7 mg/kg/day 73FTOH, Animal r81

description: Library name: p23_10109_r81_u

value: 16.7 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:16.7 mg/kg/day

value: dose group:5


title: Female Uterus, 16.7 mg/kg/day 73FTOH, Animal r80

description: Library name: p23_10109_r80_u

value: Female

value: Uterus

value: Sprague Dawley


title: Female Uterus, 16.7 mg/kg/day 73FTOH, Animal r79

description: Library name: p23_10109_r79_u

value: 8-10 weeks


title: Female Uterus, 16.7 mg/kg/day 73FTOH, Animal r78

description: Library name: p23_10109_r78_u


title: Female Uterus, 50 mg/kg/day 73FTOH, Animal r83

description: Library name: p23_10109_r83_u


title: Female Uterus, 50 mg/kg/day 73FTOH, Animal r82

description: Library name: p23_10109_r82_u


title: Female Uterus, 5 mg/kg/day 73FTOH, Animal r75

description: Library name: p23_10109_r75_u

value: 5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:5 mg/kg/day

value: dose group:4


title: Female Uterus, 16.7 mg/kg/day 73FTOH, Animal r77

description: Library name: p23_10109_r77_u

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)

value: route of_exposure:Oral gavage

value: No Issue


title: Female Uterus, 5 mg/kg/day 73FTOH, Animal r76

description: Library name: p23_10109_r76_u


title: Female Uterus, 50 mg/kg/day 73FTOH, Animal r85

description: Library name: p23_10109_r85_u


title: Female Uterus, 0.05 mg/kg/day 73FTOH, Animal r59

description: Library name: p23_10109_r59_u

value: 0.05 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:0.05 mg/kg/day

value: dose group:1


title: Female Uterus, 5 mg/kg/day 73FTOH, Animal r72

description: Library name: p23_10109_r72_u


title: Female Uterus, 1.7 mg/kg/day 73FTOH, Animal r70

description: Library name: p23_10109_r70_u

value: 1.7 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:1.7 mg/kg/day

value: dose group:3


title: Female Uterus, 0.5 mg/kg/day 73FTOH, Animal r62

description: Library name: p23_10109_r62_u

value: 0.5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:0.5 mg/kg/day

value: dose group:2


title: Female Uterus, 1.7 mg/kg/day 73FTOH, Animal r68

description: Library name: p23_10109_r68_u

value: Female

value: Uterus

value: Sprague Dawley


title: Female Uterus, 5 mg/kg/day 73FTOH, Animal r73

description: Library name: p23_10109_r73_u

value: 8-10 weeks

value: 5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:5 mg/kg/day


title: Female Uterus, 1.7 mg/kg/day 73FTOH, Animal r67

description: Library name: p23_10109_r67_u

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)

value: route of_exposure:Oral gavage


title: variovorax, Q1, rep1

description: Library name: Q1_1

value: bacteria


title: Female Uterus, 1.7 mg/kg/day 73FTOH, Animal r71

description: Library name: p23_10109_r71_u

value: No Issue


title: Female Uterus, Vehicle Control, Animal r54

description: Library name: p23_10109_r54_u

value: 1,2-Propylene glycol control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: dose group:0


title: Female Uterus, Vehicle Control, Animal r55

description: Library name: p23_10109_r55_u


title: Female Uterus, 0.5 mg/kg/day 73FTOH, Animal r64

description: Library name: p23_10109_r64_u


title: Female Uterus, 0.05 mg/kg/day 73FTOH, Animal r61

description: Library name: p23_10109_r61_u

value: 0.05 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:0.05 mg/kg/day

value: dose group:1


title: Female Uterus, 0.5 mg/kg/day 73FTOH, Animal r65

description: Library name: p23_10109_r65_u

value: 0.5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:0.5 mg/kg/day

value: dose group:2


title: Female Uterus, 0.05 mg/kg/day 73FTOH, Animal r60

description: Library name: p23_10109_r60_u

value: Female

value: Uterus

value: Sprague Dawley


title: Female Uterus, 0.05 mg/kg/day 73FTOH, Animal r58

description: Library name: p23_10109_r58_u

value: 8-10 weeks


title: Female Uterus, Vehicle Control, Animal r56

description: Library name: p23_10109_r56_u

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)


title: Female Uterus, Vehicle Control, Animal r50

description: Library name: p23_10109_r50_u

value: route of_exposure:Oral gavage


title: Female Uterus, Vehicle Control, Animal r53

description: Library name: p23_10109_r53_u


title: Female Uterus, Vehicle Control, Animal r52

description: Library name: p23_10109_r52_u


title: Female Uterus, Vehicle Control, Animal r51

description: Library name: p23_10109_r51_u


title: Female Uterus, 0.05 mg/kg/day 73FTOH, Animal r57

description: Library name: p23_10109_r57_u


title: Female Uterus, 5 mg/kg/day 73FTOH, Animal r74

description: Library name: p23_10109_r74_u

value: 5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:5 mg/kg/day

value: dose group:4


title: Female Uterus, 1.7 mg/kg/day 73FTOH, Animal r69

description: Library name: p23_10109_r69_u

value: 1.7 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:1.7 mg/kg/day

value: dose group:3

value: No Issue


title: Female Uterus, Vehicle Control, Animal r49

description: Library name: p23_10109_r49_u

value: 1,2-Propylene glycol control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: dose group:0


title: Female Ovary, 500 mg/kg/day 73FTOH, Animal r96

description: Library name: p22_10109_r96_o

source_name: Ovary

value: Ovary

value: 500 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:500 mg/kg/day

value: dose group:8


title: Female Ovary, 167 mg/kg/day 73FTOH, Animal r91

description: Library name: p22_10109_r91_o

value: Female

value: Sprague Dawley

value: 8-10 weeks

value: 167 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:167 mg/kg/day

value: dose group:7


title: Female Ovary, 167 mg/kg/day 73FTOH, Animal r88

description: Library name: p22_10109_r88_o

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)

value: route of_exposure:Oral gavage


title: Female Ovary, 50 mg/kg/day 73FTOH, Animal r86

description: Library name: p22_10109_r86_o

value: 50 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:50 mg/kg/day

value: dose group:6


title: Female Ovary, 167 mg/kg/day 73FTOH, Animal r89

description: Library name: p22_10109_r89_o

value: No Issue


title: Female Uterus, 0.5 mg/kg/day 73FTOH, Animal r66

description: Library name: p23_10109_r66_u

value: Uterus

value: 0.5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:0.5 mg/kg/day

value: dose group:2


title: Female Uterus, 0.5 mg/kg/day 73FTOH, Animal r63

description: Library name: p23_10109_r63_u


title: Female Ovary, 16.7 mg/kg/day 73FTOH, Animal r81

description: Library name: p22_10109_r81_o

value: Ovary

value: 16.7 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:16.7 mg/kg/day

value: dose group:5


title: Female Ovary, 50 mg/kg/day 73FTOH, Animal r83

description: Library name: p22_10109_r83_o

value: Female

value: Sprague Dawley

value: 8-10 weeks


title: Female Ovary, 167 mg/kg/day 73FTOH, Animal r90

description: Library name: p22_10109_r90_o

value: 167 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:167 mg/kg/day

value: dose group:7

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)


title: Female Ovary, 500 mg/kg/day 73FTOH, Animal r93

description: Library name: p22_10109_r93_o

value: 500 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:500 mg/kg/day

value: dose group:8

value: route of_exposure:Oral gavage


title: Female Ovary, 500 mg/kg/day 73FTOH, Animal r92

description: Library name: p22_10109_r92_o

value: No Issue


title: Female Ovary, 167 mg/kg/day 73FTOH, Animal r87

description: Library name: p22_10109_r87_o


title: Female Ovary, 50 mg/kg/day 73FTOH, Animal r82

description: Library name: p22_10109_r82_o

value: 50 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:50 mg/kg/day

value: dose group:6


title: Female Ovary, 50 mg/kg/day 73FTOH, Animal r85

description: Library name: p22_10109_r85_o

value: Ovary


title: Female Ovary, 500 mg/kg/day 73FTOH, Animal r94

description: Library name: p22_10109_r94_o


title: Female Ovary, 50 mg/kg/day 73FTOH, Animal r84

description: Library name: p22_10109_r84_o


title: Female Ovary, 500 mg/kg/day 73FTOH, Animal r95

description: Library name: p22_10109_r95_o


title: Female Ovary, 16.7 mg/kg/day 73FTOH, Animal r77

description: Library name: p22_10109_r77_o

value: 16.7 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:16.7 mg/kg/day

value: dose group:5


title: Female Ovary, 16.7 mg/kg/day 73FTOH, Animal r80

description: Library name: p22_10109_r80_o

value: Female

value: Sprague Dawley

value: 8-10 weeks


title: Female Ovary, 16.7 mg/kg/day 73FTOH, Animal r78

description: Library name: p22_10109_r78_o


title: Female Ovary, 5 mg/kg/day 73FTOH, Animal r75

description: Library name: p22_10109_r75_o

value: 5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:5 mg/kg/day

value: dose group:4


title: Female Ovary, 5 mg/kg/day 73FTOH, Animal r76

description: Library name: p22_10109_r76_o

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)


title: Female Ovary, 5 mg/kg/day 73FTOH, Animal r74

description: Library name: p22_10109_r74_o


title: Female Ovary, 5 mg/kg/day 73FTOH, Animal r73

description: Library name: p22_10109_r73_o


title: Female Ovary, 5 mg/kg/day 73FTOH, Animal r72

description: Library name: p22_10109_r72_o


title: Female Ovary, 1.7 mg/kg/day 73FTOH, Animal r71

description: Library name: p22_10109_r71_o

value: 1.7 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:1.7 mg/kg/day

value: dose group:3


title: Female Ovary, 1.7 mg/kg/day 73FTOH, Animal r69

description: Library name: p22_10109_r69_o

value: route of_exposure:Oral gavage

value: No Issue


title: Female Ovary, 16.7 mg/kg/day 73FTOH, Animal r79

description: Library name: p22_10109_r79_o


title: Female Ovary, 0.5 mg/kg/day 73FTOH, Animal r63

description: Library name: p22_10109_r63_o

value: 0.5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:0.5 mg/kg/day

value: dose group:2


title: Female Ovary, 0.05 mg/kg/day 73FTOH, Animal r61

description: Library name: p22_10109_r61_o

value: Ovary

value: 0.05 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:0.05 mg/kg/day

value: dose group:1


title: Female Ovary, 0.05 mg/kg/day 73FTOH, Animal r60

description: Library name: p22_10109_r60_o

value: Female

value: Sprague Dawley

value: 8-10 weeks


title: Female Ovary, 0.05 mg/kg/day 73FTOH, Animal r59

description: Library name: p22_10109_r59_o


title: Female Ovary, 0.05 mg/kg/day 73FTOH, Animal r57

description: Library name: p22_10109_r57_o


title: Female Ovary, Vehicle Control, Animal r55

description: Library name: p22_10109_r55_o

value: 1,2-Propylene glycol control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: dose group:0


title: Female Ovary, Vehicle Control, Animal r52

description: Library name: p22_10109_r52_o

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)


title: Female Ovary, 1.7 mg/kg/day 73FTOH, Animal r70

description: Library name: p22_10109_r70_o

value: 1.7 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:1.7 mg/kg/day

value: dose group:3


title: Female Ovary, Vehicle Control, Animal r50

description: Library name: p22_10109_r50_o

value: route of_exposure:Oral gavage

value: No Issue


title: Female Ovary, 0.5 mg/kg/day 73FTOH, Animal r66

description: Library name: p22_10109_r66_o

value: 0.5 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:0.5 mg/kg/day

value: dose group:2


title: Female Ovary, 1.7 mg/kg/day 73FTOH, Animal r68

description: Library name: p22_10109_r68_o

value: Ovary

value: Outlier sample removed


title: Female Ovary, 0.5 mg/kg/day 73FTOH, Animal r65

description: Library name: p22_10109_r65_o

value: Female


title: Female Ovary, 0.5 mg/kg/day 73FTOH, Animal r64

description: Library name: p22_10109_r64_o

value: Sprague Dawley


title: Female Ovary, 1.7 mg/kg/day 73FTOH, Animal r67

description: Library name: p22_10109_r67_o

value: 8-10 weeks


title: Male Testis, 167 mg/kg/day 73FTOH, Animal r42

description: Library name: p21_10109_r42_t

source_name: Testis

value: Male

value: Testis

value: 167 mg/kg/day 73FTOH, 5-day repeat exposure, oral gavage

value: dose:167 mg/kg/day

value: dose group:7


title: Male Testis, 167 mg/kg/day 73FTOH, Animal r41

description: Library name: p21_10109_r41_t

value: chemical name:7:3 Fluorotelomer alcohol (7:3 FTOH)


title: Female Ovary, 0.5 mg/kg/day 73FTOH, Animal r62

description: Library name: p22_10109_r62_o