title: Largemouth bass Spleen, 24h post-challenge, Fc, biological replicate 2 [27M2S]

description:
Library name: 27M2S
Flavobacterium columnare single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Sample_Rat_HN_Soma11

status: Public on Jul 31 2026

type: SRA

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 South University Ave

department: Biology

country: USA

institute: University of Pennsylvania

description: Library name: Rat_HN_Soma11

library_source: transcriptomic single cell

data_processing:
We combined the Ensembl genes annotations (downloaded from Ensembl Genome Browser, Dec. 2015) and UCSC genes annotations (downloaded from UCSC, Dec. 2015) to quantify reads with VERSE using options “-s 1 -z 3 --nonemptyModified”
We combined the Ensembl genes annotations (downloaded from Ensembl Genome Browser, Dec. 2015) and UCSC genes annotations (downloaded from UCSC, Dec. 2015) to quantify reads with VERSE using options “-s 1 -z 3 --nonemptyModified” (Zhu et al. 2016, doi:https://doi.org/10.1101/053306)
Assembly: rn6
Supplementary files format and content: *.verse.exon.cnts.txt: tab delimited text files containing raw gene counts.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: hippocampus

growth_protocol: Hippocampal neurons from embryonic day 18 (E18) rat (Sprague Dawley) were cultured as described in (Buchhalter and Dichter 1991) for 15 days.

extract_protocol:
A micropipette was used to aspirate the soma, which was deposited into a tube containing first strand synthesis buffer and RNase inhibitor and placed on ice. A separate micropipette was used to aspirate the dendrites, which were deposited into a separate tube as above. Samples underwent first strand synthesis within 30 minutes of collection. Poly-adenylated RNA was amplified using three rounds of the aRNA in vitro transcription-based amplification method, as described in (Morris, Singh, and Eberwine 2011). The quality and quantity of the amplified RNA was verified using a Bioanalyzer RNA assay.
Sequencing libraries were prepared using a modified Illumina TruSeq Stranded kit protocol, we ommited that the initial poly-A capture step as the aRNA amplification procedure already selects for poly-adenylated RNA. Samples were sequenced on a  NextSeq (75bp paired-end) to an average depth of 30 million reads.

tag: tissue

value: hippocampus

tag: cell type

value: pyramidal neurons

tag: genotype

value: wildtype

tag: strain

value: Sprague Dawley

tag: rounds of_arna_amplification

tag: cell compartment

value: Soma


title: Sample_Rat_HN_Dend11

description: Library name: Rat_HN_Dend11

value: Dendrites


title: Day14-Epigenetic modification with 7gRNAs Replicate 1

city: Tehran

first: Massoud

last: Vosough

address: Bani Hashem Sq.

country: Iran

institute: Royan Institute

description:
Library name: GC131328
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

library_source: transcriptomic

data_processing:
RNA was extracted and quality control was performed as mentioned above. Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system. Single-end reads were generated. To assess the quality control, FastQC v0.11.7 was used. Adapters were filtered with Trimmomatic v0.39 or ea-utils fastq-mcf v1.05 where needed. HISAT2 was used for splice-aware alignment against the reference genome hg38 using the default parameters. Reads mapping to multiple loci in the reference genome were discarded. The resulting BAM alignment files were handled with Samtools v1.5. Quantification of reads per gene was performed with FeatureCounts from Subread package or HT-seq Count v0.10.0, Python v2.7.14.
To integrate the data from untreated HGC-27 cells and Day 3 post trasnfection cells with Day 14 post transfection cells Batch correction was performed using the ComBat-seq from the Bioconductor package sva.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including the raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Stomach

growth_protocol: The HGC-27 cells were grown in  DMEM/F-12 supplemented with 10% fetal bovine serum and 100 µg/mL penicillin, and 100 µg/mL streptomycin. The selection media for culturing cells after the transfection was supplemented with 3 μg/mL doxycycline and 5 μg/mL Blasticidin S for about three days.

extract_protocol:
The RNA extraction wsa performed using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) according to the manufacturer’s instructions with addition of DNAseI from the On-Column DNase I Digestion kit (Sigma-Aldrich).
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: Stomach

tag: cell line

value: Human gastric carcinoma cell line

tag: treatment

value: Tr.HGC-27-KRAB cells transfected with the DNMT3AL domain and 7gRNAs

tag: batch


title: Largemouth bass Gill, 24h post-challenge, Fc, biological replicate 3 [27M3G]

city: Auburn

first: Timothy

middle: James

last: Bruce

state: AL

address: 203 Swingle Hall

department: School of Fisheries, Aquaculture and Aquatic Sciences

institute: Auburn University

description:
Library name: 27M3G
Flavobacterium columnare single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

data_processing:
Raw reads assessed with FastQC/MultiQC; trimmed with fastp (Q20, 50 bp minimum length). Mean retention 97.9% across 7.1 billion reads.
Transcript quantification with Salmon (decoy-aware index GCF_014851395.1, k=31, --libType A, 30 bootstraps, seqBias/gcBias/posBias corrections). Mean mapping rate 82.84%.
Gene-level import with tximeta (lengthScaledTPM), rounded for DESeq2. Pre-filter: rowSums(counts>=10)>=2. Gill: 23,561 genes; Spleen: 22,152 genes.
DESeq2 differential expression: ~group design, reference=t0_Pre, ashr LFC shrinkage. 72 pairwise contrasts (36/tissue). Significance: padj<0.05, |log2FC|>=1 (BH correction).
Annotation: org.Msalmoides.eg.db v1.0.0 (NCBI RefSeq GFF3 + ZFIN GO GAF 2026-04-01 + OrthoDB v12.2 Actinopterygii). 68.9% of genes annotated with at least one GO term.
Please note that the three samples (11B3G, 15J2G, 29R3G) were intentionally excluded from the processed data files due to gDNA contamination, as indicated by mapping rates below 25% (21.4%, 20.9%, and 15.9%, respectively). These samples failed quality control and were not included in the DESeq2 model or any downstream analyses. Their raw FASTQ files are deposited for transparency and completeness, but they do not appear in the processed count matrices (raw_counts_gill.csv, vst_normalized_counts_gill.csv, DESeq2_all_contrasts_gill.csv) for this reason.
Assembly: GCF_014851395.1 (ASM1485139v1, Micropterus salmoides, NCBI RefSeq)
Supplementary files format and content: raw_counts_gill.csv / raw_counts_spleen.csv: CSV, raw gene count matrix (genes x samples); rows=NCBI gene IDs, columns=sample IDs.
Supplementary files format and content: vst_normalized_counts_gill.csv / vst_normalized_counts_spleen.csv: CSV, VST-normalized expression values from DESeq2.
Supplementary files format and content: DESeq2_all_contrasts_gill.csv / DESeq2_all_contrasts_spleen.csv: CSV, annotated DESeq2 results (gene_id, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, gene_symbol, contrast) for all 36 contrasts per tissue.
Supplementary files format and content: Stage5_DEG_summary.tsv: TSV, summary of significant DEGs (up/down/total) per contrast.
Supplementary files format and content: Msalmoides_master_annotation_GO.tsv: TSV, master gene annotation for GCF_014851395.1 (gene_id, gene_symbol, drerio_symbol, GO terms, ortholog information).

organism: Micropterus salmoides

source_name: Gill

growth_protocol: Largemouth bass were maintained in recirculating freshwater systems prior to challenge.

extract_protocol:
Total RNA was extracted from DNA/RNA Shield-preserved tissue at Azenta Inc. RNA quality assessed by TapeStation
Paired-end RNA-Seq libraries prepared from polyA-selected RNA using NEBNext Ultra II. Libraries sequenced on Illumina NovaSeq X (paired-end, 150 bp)

treatment_protocol: Fish were challenged by immersion with Aeromonas veronii, Aeromonas hydrophila, Flavobacterium columnare, or coinfections, or mock-challenged. Gill and spleen were dissected at 0h, 12h, and 24h post-challenge and preserved in DNA/RNA Shield (Zymo Research, Inc.).

value: Gill

tag: sample group


title: Sample_Rat_HN_Dend9

description: Library name: Rat_HN_Dend9


title: Sample_Rat_HN_Dend8

description: Library name: Rat_HN_Dend8


title: Day3-Treated with only 5gRNAs Replicate 2

description:
Library name: GC119571
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: HGC-27 cells transfected with only 5gRNAs


title: BJ fibroblast, Global ATAC-see control, added EDTA, bio rep 6

city: Redwood City

first: Yihao

last: Yang

state: CA

address: 2600 Bridge Parkway

institute: Altos Labs

description:
Library name: BJ_EDTA_0mM_REP6
NextSeq P3

library_source: genomic

data_processing:
For downstream analysis, sequencing data were processed using the nf-core/cutandrun pipeline (v2.1.2) with default parameters, except that MACS2 peak calling was run in narrow peak mode on reads pooled across all six replicates.
The BJ_EDTA_0mM_REP* samples are controls and lack processed data.
Assembly: hg38
Supplementary files format and content: UCSC binary format of genome-wide coverage (.bigWig) and ENCODE BED6+4 tab-delimited peak calls from pooled 6 ATAC-see samples (.narrowPeak)

molecule: genomic DNA

source_name: skin

growth_protocol: Cells were cultured in DMEM + 15% FBS + 1X NEAA (non-essential amino acids; Cat# 11140050) and maintained at 37oC and 5% CO2 in a humidified incubator.

extract_protocol:
Following imaging on a Nikon Eclipse Ti2 inverted microscope as described above, HBSS was aspirated and replaced with a reverse-crosslinking solution adapted from (Chen et al., 2016), consisting of 50 mM Tris-HCl, 1 mM EDTA, 1% SDS, 0.2 M NaCl and 250 ug/ml proteinase K. Cells were physically detached using a cell scraper, transferred to microcentrifuge tubes, and incubated overnight at 65°C with agitation at 1,000 rpm in a thermomixer. DNA was subsequently purified using the MinElute Reaction Cleanup Kit (Qiagen, Cat#: 28204) according to the manufacturer's instructions.
DNA was amplified using 11, 14, and 17 PCR cycles with NEBNext® HiFi 2× PCR Master Mix (NEB, M0541S) and pre-mixed Illumina DNA/RNA UD Indexes (Set A; cat. no. 20091646), following the PCR protocol described in (Buenrostro et al., 2013). Library quality was assessed by Agilent TapeStation, and products from all three cycle numbers were pooled and purified using 1.8× SPRI beads (Beckman Coulter, cat. no. B23318). Sequencing was performed on an Illumina NextSeq 2000 (P3 flow cell) with paired-end 50 + 50 bp reads and 10 bp dual-indexing (50/10/10/50 cycle configuration).

treatment_protocol: Performed ATAC-see: Cells cultured in 12-well glass-bottom plates (Cell Vis) were washed once with HBSS containing calcium and magnesium (HBSS + Ions; Thermo Fisher, Cat# 14025134) at room temperature. Cells were subsequently fixed using freshly diluted 1% (w/v) paraformaldehyde (PFA; Cat# 50-980-494) in HBSS + ions for 10 min at room temperature. Any alternative fixation conditions are explicitly detailed in the respective figure legends. Fixation was quenched via three sequential washes with HBSS + ions. Following fixation, plates were immediately processed for ATAC-see, subjected to immunofluorescent staining, or stored at 4°C for up to one week. Transposomes (3.4 µM stock) were diluted 20-fold to a final working concentration of 170 nM in 1× Tagment DNA (TD) buffer (10 mM TAPS, pH 8.0, 5 mM MgCl₂, 10% N,N-dimethylformamide; prepared from a 2× stock) supplemented with 0.1% IGEPAL CA-630, and mixed thoroughly by pipetting. The working transposome solution was sonicated in a bath sonicator at 37 kHz for 60 seconds at 80% amplitude. To remove residual aggregates, the solution was passed through a 0.22 µm syringe filter (Cat# SLGVR33RS). A combined single-step cell permeabilization and tagmentation (PermNTag) was initiated by adding 100 µL of the filtered working transposome solution to each well of the fixed cells. Plates were incubated at 37°C for the designated duration (typically 1 hour). To control for background fluorescence and determine specificity, 20mM EDTA was added to the tagmentation solution for control samples. Tagmentation was quenched by washing the cells twice with calcium/magnesium-free HBSS (HBSS w/o Ions; Cat# 14065056) supplemented with 40 mM EDTA and 0.01% SDS. Cells were then washed three times with standard HBSS at room temperature, counterstained with Hoechst 33342 (1:1000 dilution, Invitrogen) for 15–25 min, washed three additional times with HBSS, and stored at 4°C until microscopic imaging.

value: skin

value: BJ

value: fibroblast

value: WT

value: tagmentation solution + 20mM EDTA


title: Sample_Rat_HN_Soma8

description: Library name: Rat_HN_Soma8


title: Day3-Treated with only 5gRNAs Replicate 1

description:
Library name: GC119570
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.


title: Largemouth bass Gill, 24h post-challenge, Fc, biological replicate 2 [27M2G]

description:
Library name: 27M2G
Flavobacterium columnare single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: BJ fibroblast, Global ATAC-see control, added EDTA, bio rep 5

description:
Library name: BJ_EDTA_0mM_REP5
NextSeq P3


title: Largemouth bass Gill, 24h post-challenge, Fc, biological replicate 1 [27M1G]

description:
Library name: 27M1G
Flavobacterium columnare single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Day3-Treated with only 7gRNAs Replicate 2

description:
Library name: GC119569
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: HGC-27 cells transfected with only 7gRNAs


title: BJ fibroblast, Global ATAC-see control, added EDTA, bio rep 4

description:
Library name: BJ_EDTA_0mM_REP4
NextSeq P3


title: Largemouth bass Spleen, 24h post-challenge, Ah, biological replicate 3 [25J3S]

description:
Library name: 25J3S
Aeromonas hydrophila single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

source_name: Spleen

value: Spleen

value: Aeromonas hydrophila single infection


title: Day3-Treated with only 7gRNAs Replicate 1

description:
Library name: GC119568
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.


title: Sample_Rat_HN_Soma7

description: Library name: Rat_HN_Soma7

value: hippocampus

value: pyramidal neurons

value: wildtype


title: Largemouth bass Spleen, 24h post-challenge, Ah, biological replicate 2 [25J2S]

description:
Library name: 25J2S
Aeromonas hydrophila single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: BJ fibroblast, Global ATAC-see control, added EDTA, bio rep 3

description:
Library name: BJ_EDTA_0mM_REP3
NextSeq P3


title: TPR1-GFP_eds1-2_Input

city: Cologne

first: Thomas

last: Griebel

address: Carl-von-Linne-Weg 10

department: Department of Plant Microbe Interactions

country: Germany

institute: Max-Planck Institute for Plant Breeding Research

description:
negative control for peak calling
log2ratio_H3K9aceds1_bs1.bw

data_processing:
Sequencing (1 x 75 bp, Illumina NextSeq 500) was performed by Institute of Integrative Biology of the Cell (Saclay, France).
Short reads were trimmed to delete the adaptors sequence (Cutadapt-1.9.1) and mapped onto the TAIR10 Arabidopsis thaliana genome using bowtie2 v2.3.3 with “--very-sensitive “ preset parameters. Duplicated mapped reads were removed using picard v1.119 with the command "MarkDuplicates VALIDATION_STRINGENCY = SILENT REMOVE_DUPLICATES = true  ASSUME_SORTED = true" and reads with MAPQ <10 were filtered with samtools v1.6
Read density was scored over non-overlapping 20-bp bins using the utiliy deepTools bamCoverage v3.0.0 (Ramírez et al, 2016) with the command “bamCoverage -p 16 -bs 20 --smoothLength 200 -of bigwig --normalizeUsing RPGC
Genome_build: A. thaliana reference genome TAIR10
Supplementary_files_format_and_content: The bigwig file provided for visualization in IGV (Thorvaldsdóttir et al., 2013) was prepared with bamCompare (--operation subtract --binSize 1) using merged BAM files for input and TPR1-GFP or TPR1 GFP eds1-2 samples.

organism: Arabidopsis thaliana

source_name: 6-week old leaves

growth_protocol: Plants were grown on soil with a daily 10 h light period (150-200 μE/m2s) at 22 °C and 60 % relative humidity. Plant leaf material was harvested after 6 weeks of growth.

extract_protocol:
ChIP and library preparation was done using 2 g leaf material of TPR1-GFP and TPR1-GFP eds1-2 as described (Latrasse et al., 2017) by using Anti-acetyl-Histone H3 Lys 9 antibody (07-352, Millipore).
Library was created by using the NEB Next Ultra II DNA Library Prep Kit

treatment_protocol: untreated

value: pTPR1:TPR1-GFP eds1-2

tag: chip/antibody

value: Input


title: Untreated HGC-27 gastric cancer cells Replicate 3

description:
Library name: GC119567
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: Stomach

value: Human gastric carcinoma cell line

value: No Treatment


title: BJ fibroblast, Global ATAC-see control, added EDTA, bio rep 2

description:
Library name: BJ_EDTA_0mM_REP2
NextSeq P3


title: Largemouth bass Spleen, 24h post-challenge, Ah, biological replicate 1 [25J1S]

description:
Library name: 25J1S
Aeromonas hydrophila single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Untreated HGC-27 gastric cancer cells Replicate 2

description:
Library name: GC119566
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.


title: TPR1-GFP_eds1-2_H3K9Ac_r2

description:
TPR1-GFP eds1-2 H3K9Ac ChIP
log2ratio_H3K9aceds1_bs1.bw


title: BJ fibroblast, Global ATAC-see control, added EDTA, bio rep 1

description:
Library name: BJ_EDTA_0mM_REP1
NextSeq P3


title: Largemouth bass Gill, 24h post-challenge, Ah, biological replicate 3 [25J3G]

description:
Library name: 25J3G
Aeromonas hydrophila single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: TPR1-GFP_Col-0_H3K9Ac_r2

description:
TPR1-GFP Col-0 H3K9Ac ChIP
log2ratio_H3K9acWT_bs1.bw

value: pTPR1:TPR1-GFP Col-0


title: Untreated HGC-27 gastric cancer cells Replicate 1

description:
Library name: GC119565
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.


title: Largemouth bass Gill, 24h post-challenge, Ah, biological replicate 2 [25J2G]

description:
Library name: 25J2G
Aeromonas hydrophila single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: TPR1-GFP_Col-0_Input

description:
negative control for peak calling
log2ratio_H3K9acWT_bs1.bw


title: BJ fibroblast, Global ATAC-see, bio rep 5

description:
Library name: BJ_Glbl_0mM_REP5
NextSeq P3

value: skin

value: BJ

value: tagmentation solution


title: Largemouth bass Gill, 24h post-challenge, Ah, biological replicate 1 [25J1G]

description:
Library name: 25J1G
Aeromonas hydrophila single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Day3-Epigenetic modification with 5gRNAs Replicate 2

description:
Library name: GC119563
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: Tr.HGC-27-KRAB cells transfected with the DNMT3AL domain and 5gRNAs


title: TPR1-GFP_eds1-2_H3K9Ac_r1


title: BJ fibroblast, Global ATAC-see, bio rep 4

description:
Library name: BJ_Glbl_0mM_REP4
NextSeq P3

value: fibroblast

value: WT


title: Largemouth bass Spleen, 24h post-challenge, Av, biological replicate 3 [23F3S]

description:
Library name: 23F3S
Aeromonas veronii single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen

value: Aeromonas veronii single infection


title: Day3-Epigenetic modification with 5gRNAs Replicate 1

description:
Library name: GC119562
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.


title: TPR1-GFP_Col-0_H3K9Ac_r1


title: BJ fibroblast, Global ATAC-see, bio rep 3

description:
Library name: BJ_Glbl_0mM_REP3
NextSeq P3


title: Day3-Epigenetic modification with 7gRNAs Replicate 3

description:
Library name: GC119561
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: Tr.HGC-27-KRAB cells transfected with the DNMT3AL domain and 7gRNAs


title: Largemouth bass Spleen, 24h post-challenge, Av, biological replicate 2 [23F2S]

description:
Library name: 23F2S
Aeromonas veronii single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909030010_R06C01]

type: genomic

city: London

first: Sasha

last: Howard

address: JVSC Charterhouse Square

department: Endocrinology

country: United Kingdom

institute: Queen Mary University London

hyb_protocol: Sequencing using the Illumina Infinium Methylation EPIC array BeadChip (850K) was carried out by the Epigenomic Services from Diagenode (Cat nr. G02090000).

scan_protocol: Standard Ilumina protocol

data_processing:
A pipeline following that of Barrett et al (Barrett et al. 2022) was used for a second round of quality control and normalisation of the samples. Quality control, annotation of CpG sites and differential methylation analysis was undertaken in R Studio using the dmpFinder function from the minfi package along with bumphunter.
*processed value definition: Average Beta

label: Cy3 and Cy5

source_name: Peripheral blood

label_protocol: Standard Ilumina protocol

extract_protocol: Genomic DNA was isolated from peripheral blood leukocytes from all patients and family members using standard procedures

value: Peripheral blood

value: patient with delayed puberty


title: Day14-Epigenetic modification with 7gRNAs Replicate 2

description:
Library name: GC131329
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.


title: BJ fibroblast, Global ATAC-see, bio rep 2

description:
Library name: BJ_Glbl_0mM_REP2
NextSeq P3


title: Sample_Rat_HN_Soma9

description: Library name: Rat_HN_Soma9

value: hippocampus

value: pyramidal neurons

value: wildtype

value: Sprague Dawley

value: Soma


title: Largemouth bass Spleen, 24h post-challenge, Fc, biological replicate 1 [27M1S]

description:
Library name: 27M1S
Flavobacterium columnare single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Largemouth bass Spleen, 24h post-challenge, Av, biological replicate 1 [23F1S]

description:
Library name: 23F1S
Aeromonas veronii single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Day3-Epigenetic modification with 7gRNAs Replicate 2

description:
Library name: GC119560
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: Stomach

value: Human gastric carcinoma cell line


title: Peripheral blood from patient with delayed puberty [206909030010_R08C01]


title: BJ fibroblast, Global ATAC-see, bio rep 1

description:
Library name: BJ_Glbl_0mM_REP1
NextSeq P3

value: skin

value: BJ


title: Largemouth bass Gill, 24h post-challenge, Av, biological replicate 3 [23F3G]

description:
Library name: 23F3G
Aeromonas veronii single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: Day3-Epigenetic modification with 7gRNAs Replicate 1

description:
Library name: GC119559
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.


title: Peripheral blood from patient with delayed puberty [206909030010_R07C01]


title: Largemouth bass Gill, 24h post-challenge, Av, biological replicate 2 [23F2G]

description:
Library name: 23F2G
Aeromonas veronii single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: BJ fibroblast, Targeted ATAC-see, LaminB1, high-salt (300mM NaCl)

description:
Library name: BJ_LamB1_300mM
NextSeq P3

data_processing:
Reads were processed with nf-core/atacseq (Ewels et al., 2020) (v2.1.2), aligned to GRCh38 and peaks called with MACS2 (Zhang et al., 2008), yielding narrowPeak files. Peaks were annotated with ChIPseeker (Yu et al., 2015) against the UCSC hg38 known-gene model (TxDb.Hsapiens.UCSC.hg38.knownGene; gene symbols from org.Hs.eg.db); feature proportions are shown as pie charts. Lamin A/C and Lamin B1 targeted ATAC-see coverage at 300 mM and 0 mM was expressed as a log2 ratio over the BJ IgG 0 mM control with deepTools (Ramírez et al., 2016) bamCompare (10-kb bins, 30-kb smoothing, read-count scaling, reads extended to fragment length, duplicates ignored, GRCh38 effective genome size 2.91 × 10⁹ bp). For each mark, peaks from the 0 mM, 300 mM and Global 0 mM sets were merged per chromosome into non-overlapping consensus regions (overlapping or directly abutting intervals joined), and each region was assigned to the combination of sets contributing at least one peak, giving the seven membership classes of the UpSet (Lex et al., 2014) plot (drawn in Python). Distances were computed between peak summits (narrowPeak point-source offset, or interval midpoint where absent) within chromosomes. Gained peaks were defined as 0 mM peaks overlapping no same-mark 300 mM peak (21,524 for H3K4me3, 60.2%; 40,268 for H3K27ac, 39.4%). For each gained peak, the distance to the nearest 300 mM summit was compared with that of a non-anchor accessibility background (Global 0 mM peaks not overlapping a 300 mM peak; n = 127,659 for H3K4me3, 79,672 for H3K27ac) and a uniform null (gained summits randomized within each chromosome’s peak span). Distance distributions were compared by one-sided Mann–Whitney U test with Cliff’s δ as the effect size (H3K4me3 δ = +0.21; H3K27ac δ = +0.16; both P ≈ 0). Given the large sample sizes (10⁴–10⁵), effect sizes and the distance-resolved enrichment are emphasized over nominal P values. A fixed random seed was used for all randomizations and bootstrapping. Overlap, distance and locality analyses and all custom figures were implemented in Python 3.12 with NumPy (Harris et al., 2020), pandas (Virtanen et al., 2020), SciPy (McKinney, 2010) (statistical tests) and Matplotlib (Hunter, 2007); coverage, log2-ratio and metagene analyses used deepTools (Lex et al., 2014); peaks were called with MACS2 (Zhang et al., 2008) within nf-core/atacseq (Ewels et al., 2020) ; annotation used ChIPseeker (Yu et al., 2015); tracks were viewed in IGV (Robinson et al., 2011).
Assembly: GRCh38
Supplementary files format and content: UCSC binary format of genome-wide coverage (.bigWig) and ENCODE BED6+4 tab-delimited peak calls from pooled 6 ATAC-see samples (.narrowPeak)

extract_protocol:
Following imaging on a Nikon Eclipse Ti2 inverted microscope as described above, reverse cross-linking was performed as in and performed as in (Kirkland et al., In press). Briefly, HBSS was aspirated and replaced with a reverse-crosslinking solution adapted from (Chen et al., 2016a) consisting of 50 mM Tris-HCl, 1 mM EDTA, 1% SDS, 0.2 M NaCl and 250 ug/ml proteinase K. Cells were physically detached using a cell scraper, transferred to microcentrifuge tubes, and incubated overnight at 65°C with agitation at 1,000 rpm in a thermomixer. DNA was subsequently purified using the MinElute Reaction Cleanup Kit (Qiagen, Cat#: 28204) according to the manufacturer's instructions.
Eluted DNA was amplified using 11, 14, and 17 PCR cycles with NEBNext® HiFi 2× PCR Master Mix (NEB, M0541S) and pre-mixed Illumina DNA/RNA UD Indexes (Set A; cat. no. 20091646), following the PCR protocol described in (Buenrostro et al., 2013). Library quality was assessed by Agilent TapeStation, and products from all three cycle numbers were pooled and purified using 1.8X SPRI beads (Beckman Coulter, cat. no. B23318). Sequencing was performed on an Illumina NextSeq 2000 (P3 flow cell) with paired-end 50 + 50 bp reads and 10 bp dual-indexing (50/10/10/50 cycle configuration).

treatment_protocol: 100,000 cells were seeded per well of 12-well glass-bottom plates, and cultured for 24 hours at 37°C and 5% CO₂ under standard growth conditions to allow for firm cellular attachment and morphological recovery. To begin the assay, cells were rinsed with Hank's Balanced Salt Solution (HBSS) containing calcium and magnesium (Fisher Scientific, Cat. No. 14065056) and lightly fixed using 1% paraformaldehyde (PFA) (Electron Microscopy Sciences, Cat. No. 15714) in HBSS containing calcium and magnesium for 10 minutes at room temperature. Following fixation, cells were washed three times with HBSS containing calcium and magnesium. Plates were now stored at 4C, or used immediately for tATAC-see. HBSS without calcium and magnesium (Fisher Scientific, Gibco, Cat. No. 4185052) was now used from this point. First, cells were permeabilized using 0.5% Igepal (Abcam, Cat. No. ab285400) in HBSS for 15 minutes at room temperature. To minimize non-specific binding, cells were blocked for 60 minutes at room temperature in a blocking buffer consisting of 2% BSA (Sigma-Alrich, Cat. No. A7906) and 0.1% Igepal in HBSS. Cells were subsequently incubated with primary antibody at appropriate concentrations prepared in blocking buffer for 1-2 hours at room temperature or overnight at 4C. Cells were washed with HBSS containing 0.1% Igepal, three times for 10 minutes. Next, cells were incubated with appropriate secondary antibodies, diluted in blocking buffer for 60 minutes at room temperature. Prior to enzyme tethering, cells were again washed three times for 10 minutes, each in 0.1% Igepal in HBSS. For spatial targeting, cells were incubated with Cy5-loaded pAG-Tn5 (1:100 dilution, 34nM) in a tethering buffer containing 1% BSA, 0.1% Igepal, 300 mM NaCl (total with HBSS, thus 163 mM added) (Teknova, Cat. No. S0250), 2.5 mM EDTA (Invitrogen, via Fisher Scientific, Cat. No. AM9262), and HBSS for 1 hour at room temperature. Unbound enzyme was strictly removed via three 10-minute high-salt washes consisting of 300 mM NaCl,  2.5 mM EDTA and 0.1% Igepal in HBSS. Note: When establishing new targets and cell lines, perform a visual check to ensure removal of non-specific DNA bound Tn5 for IgG controls, and specific signal for targets. Increased salt concentration or longer washes may be necessary. A quick rinse was performed using 0.1% Igepal in HBSS with 300 mM NaCl to dilute residual EDTA before adding TD buffer prepared from a 2X stock with final TD concentrations: 10 mM TAPS, pH 8.0, 5 mM MgCl₂, 10% N,N-dimethylformamide, 1% BSA. EDTA was added at 20 mM for background control samples, and appropriate volumes of NaCl for salt titration and DNA footprint experiments. Plates were then incubated at 37°C for 1 hour with optional gentle agitation. All tagmentation reactions were immediately quenched for 5 minutes using a stop buffer containing 300 mM NaCl, 0.01% SDS (Invitrogen, via Fisher Scientific, Cat. No. 15-553-027), and 40 mM EDTA. Cells were subsequently rinsed with HBSS three times before nuclei were counterstained with 1:1000 Hoechst 33342 (Invitrogen, via Fisher Scientific, Cat. No. H3570) for 25-minutes to enable nuclear segmentation, and rinsed again three times with HBSS. The primary antibodies and dilutions utilized were: rabbit anti-Lamin A/C (Proteintech, Cat. No. 10298, 1:400), rabbit anti-Lamin B1 (Proteintech, Cat. No. 12987, 1:500), rabbit anti-H3K27ac (Abcam, Cat. No. ab4729, 1:1000), mouse anti-H3K4me3 (Active Motif, Cat. No. 61379, 1:500), and an IgG control (Invitrogen via Fisher Scientific, Cat. No. PI31235, 1:500).

value: fibroblast

tag: tatac-see antibody

value: high-salt


title: Peripheral blood from patient with delayed puberty [206909030010_R05C01]


title: THP1-Macrophage, 48hr, Knockdown, Infected (R12186)

city: New Delhi

first: Dhiraj

last: Kumar

address: Aruna Asaf Ali Marg,

country: India

institute: International Centre for Genetic Engineering and Biotechnology

data_processing:
Reads mapped using Salmon against Gencode 40 human genome GRCh38
Used tximeta, fishpond and SummarizedExperiment to obtain genes expression based on GENCODE v40 annotation
Normalisation done using approach as described in fishpond library for swish methodology
Assembly: Human genome GRCh38
Supplementary files format and content: comma-separated text file includes expression values for each Sample

source_name: THP-1 Macrophages

extract_protocol:
Total RNA was extracted from THP-1 macrophages, following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol) followed by a Qiagen RNeasy Micro clean-up procedure. RNA was analyzed on Agilent Bioanalyser for quality assessment with RNA Integrity Number (RIN) range from 7.5 to 10 and median of RIN 9.8.
cDNA libraries were prepared using 2 ng of total RNA using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1. Addition of 20 μM TSO; 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (28 samples/lane).
2 X 151bp.

tag: subject

value: THP-1 Macrophages

tag: time

value: 48 Hr

value: p62 knockdown

tag: infection

value: Mtb


title: BJ fibroblast, Targeted ATAC-see, LaminB1, low-salt (0mM NaCl)

description:
Library name: BJ_LamB1_0mM
NextSeq P3

value: WT

value: Lamin B1 (Proteintech, Cat. No. 12987, 1:500)

value: low-salt


title: Sample_Rat_HN_Dend7

description: Library name: Rat_HN_Dend7

value: hippocampus

value: pyramidal neurons

value: wildtype

value: Dendrites


title: Largemouth bass Gill, 24h post-challenge, Av, biological replicate 1 [23F1G]

description:
Library name: 23F1G
Aeromonas veronii single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Aeromonas veronii single infection


title: THP1-Macrophage, 48hr, Knockdown, Infected (R12185)


title: Peripheral blood from patient with delayed puberty [206909030010_R04C01]

value: Peripheral blood

value: patient with delayed puberty


title: Largemouth bass Spleen, 24h post-challenge, Av, biological replicate 3 [23E3S]

description:
Library name: 23E3S
Aeromonas veronii single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen


title: BJ fibroblast, Targeted ATAC-see, LaminAC, high-salt (300mM NaCl)

description:
Library name: BJ_LamAC_300mM
NextSeq P3

value: skin

value: BJ

value: fibroblast

value: Lamin A/C (Proteintech, Cat. No. 10298, 1:400)


title: THP1-Macrophage, 48hr, Knockdown, Infected (R12184)

value: THP-1 Macrophages

value: 48 Hr

value: p62 knockdown


title: BJ fibroblast, Targeted ATAC-see, LaminAC, low-salt (0mM NaCl)

description:
Library name: BJ_LamAC_0mM
NextSeq P3

value: WT


title: Peripheral blood from patient with delayed puberty [206909030010_R03C01]


title: THP1-Macrophage, 48hr, Knockdown, Uninfected (R12182)

value: Uninfected


title: BJ fibroblast, Targeted ATAC-see, H3K4me3, high-salt (300mM NaCl)

description:
Library name: BJ_K4me3_300mM
NextSeq P3

value: H3K4me3 (Active Motif, Cat. No. 61379, 1:500)

value: high-salt


title: Peripheral blood from patient with normal pubertal age [206909030010_R02C01]

value: patient with normal pubertal age


title: Largemouth bass Spleen, 24h post-challenge, Av, biological replicate 1 [23E1S]

description:
Library name: 23E1S
Aeromonas veronii single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Largemouth bass Spleen, 24h post-challenge, Av, biological replicate 2 [23E2S]

description:
Library name: 23E2S
Aeromonas veronii single infection; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: THP1-Macrophage, 48hr, Knockdown, Uninfected (R12181)


title: Peripheral blood from patient with delayed puberty [206909030010_R01C01]


title: BJ fibroblast, Targeted ATAC-see, H3K4me3, low-salt (0mM NaCl)

description:
Library name: BJ_K4me3_0mM
NextSeq P3

value: low-salt


title: Largemouth bass Gill, 24h post-challenge, Av, biological replicate 3 [23E3G]

description:
Library name: 23E3G
Aeromonas veronii single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill

value: Aeromonas veronii single infection


title: BJ fibroblast, Global ATAC-see, bio rep 6

description:
Library name: BJ_Glbl_0mM_REP6
NextSeq P3

value: tagmentation solution


title: THP1-Macrophage, 48hr, Knockdown, Uninfected (R12180)


title: Day3-Epigenetic modification with 5gRNAs Replicate 3

description:
Library name: GC119564
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: Stomach

value: Human gastric carcinoma cell line

value: Tr.HGC-27-KRAB cells transfected with the DNMT3AL domain and 5gRNAs


title: BJ fibroblast, Targeted ATAC-see, H3K27ac, high-salt (300mM NaCl)

description:
Library name: BJ_K27ac_300mM
NextSeq P3

value: skin

value: BJ

value: fibroblast


title: Peripheral blood from patient with delayed puberty [206909030094_R08C01]

value: Peripheral blood

value: patient with delayed puberty


title: Largemouth bass Gill, 24h post-challenge, Av, biological replicate 2 [23E2G]

description:
Library name: 23E2G
Aeromonas veronii single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: BJ fibroblast, Targeted ATAC-see, H3K27ac, low-salt (0mM NaCl)

description:
Library name: BJ_K27ac_0mM
NextSeq P3

value: WT


title: Peripheral blood from patient with delayed puberty [206909030094_R07C01]


title: THP1-Macrophage, 48hr, Wildtype, Infected (R12178)

value: THP-1 Macrophages

value: 48 Hr

value: Wildtype

value: Mtb


title: Largemouth bass Gill, 24h post-challenge, Av, biological replicate 1 [23E1G]

description:
Library name: 23E1G
Aeromonas veronii single infection; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909030094_R06C01]


title: THP1-Macrophage, 48hr, Wildtype, Infected (R12176)


title: BJ fibroblast, Targeted ATAC-see, IgG, high-salt (300mM NaCl)

description:
Library name: BJ_IgG_300mM
NextSeq P3

value: IgG (Invitrogen via Fisher Scientific, Cat. No. PI31235, 1:500)

value: high-salt


title: Largemouth bass Spleen, 24h post-challenge, Mock, biological replicate 3 [21B3S]

description:
Library name: 21B3S
Sham-injected control; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen

value: Sham-injected control


title: THP1-Macrophage, 48hr, Wildtype, Infected (R12175)


title: Peripheral blood from patient with delayed puberty [206909030094_R05C01]


title: THP1-Macrophage, 48hr, Wildtype, Uninfected (R12174)

value: Uninfected


title: BJ fibroblast, Targeted ATAC-see, IgG, low-salt (0mM NaCl)

description:
Library name: BJ_IgG_0mM
NextSeq P3

value: low-salt


title: Largemouth bass Spleen, 24h post-challenge, Mock, biological replicate 2 [21B2S]

description:
Library name: 21B2S
Sham-injected control; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909030094_R04C01]


title: Human dermal  fibroblast, Targeted ATAC-see, H3K4me3, high-salt (300mM NaCl)

description:
Library name: HDF22M_K4me3_300mM
NextSeq P3

value: Human dermal fibroblast

value: H3K4me3 (Active Motif, Cat. No. 61379, 1:500)


title: THP1-Macrophage, 48hr, Wildtype, Uninfected (R12172)


title: Largemouth bass Spleen, 24h post-challenge, Mock, biological replicate 1 [21B1S]

description:
Library name: 21B1S
Sham-injected control; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Human dermal  fibroblast, Targeted ATAC-see, H3K4me3, low-salt (0mM NaCl)

description:
Library name: HDF22M_K4me3_0mM
NextSeq P3

value: skin


title: Peripheral blood from patient with delayed puberty [206909030094_R03C01]


title: Largemouth bass Gill, 24h post-challenge, Mock, biological replicate 3 [21B3G]

description:
Library name: 21B3G
Sham-injected control; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: THP1-Macrophage, 48hr, Wildtype, Uninfected (R12171)


title: Peripheral blood from patient with delayed puberty [206909030094_R02C01]

value: Peripheral blood


title: Human dermal  fibroblast, Targeted ATAC-see, H3K27ac, high-salt (300mM NaCl)

description:
Library name: HDF22M_K27ac_300mM
NextSeq P3

value: fibroblast


title: Largemouth bass Gill, 24h post-challenge, Mock, biological replicate 2 [21B2G]

description:
Library name: 21B2G
Sham-injected control; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: THP1-Macrophage, 24hr, Knockdown, Infected (R12170)

value: 24 Hr

value: p62 knockdown


title: Peripheral blood from patient with delayed puberty [206909030094_R01C01]

value: patient with delayed puberty


title: Human dermal  fibroblast, Targeted ATAC-see, H3K27ac, low-salt (0mM NaCl)

description:
Library name: HDF22M_K27ac_0mM
NextSeq P3

value: WT


title: Largemouth bass Gill, 24h post-challenge, Mock, biological replicate 1 [21B1G]

description:
Library name: 21B1G
Sham-injected control; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909160065_R08C01]


title: THP1-Macrophage, 24hr, Knockdown, Infected (R12169)

value: THP-1 Macrophages

value: Mtb


title: Human dermal fibroblast, Targeted ATAC-see, IgG, high-salt (300mM NaCl)

description:
Library name: HDF22M_IgG_300mM
NextSeq P3

value: IgG (Invitrogen via Fisher Scientific, Cat. No. PI31235, 1:500)

value: high-salt


title: Largemouth bass Spleen, 24h post-challenge, Mock, biological replicate 3 [21A3S]

description:
Library name: 21A3S
Sham-injected control; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen

value: Sham-injected control


title: Peripheral blood from patient with delayed puberty [206909160065_R07C01]


title: THP1-Macrophage, 24hr, Knockdown, Infected (R12168)


title: VS1049_SCC151_SUV420H1_inhibitor_rep3_rnaseq

city: ROCKVILLE

first: Vassiliki

last: Saloura

state: MARYLAND

address: 11705 STONEWOOD LN

department: TGMB

institute: NCI

description:
Library name: VS1049
bams/VS1049.sorted.markdup.bam

data_processing:
VS912-VS1049: Base calling was performed with RTA (v3.10.30), and reads were demultiplexed with Bcl2fastq (v2.20). Raw reads were adaptor-trimmed using Cutadapt (v1.18) and aligned to the human genome (hg38; GENCODE 30) using STAR (v2.7.0f). Raw read counts for exon regions were quantified at the gene level using the featureCount function in Subread (v2.0.3) with -s 2 option.
VS1752-VS1761: Reads were demultiplexed by Illumina Dynamic Read Analysis for GENomics (Dragen; v4.2.0_b.29). Raw reads were adaptor-trimmed using Cutadapt (v4.0) and aligned to the mouse genome (GRCm39; GENCODE M39) using STAR (v2.7.11b). Raw read counts for exon regions were quantified at the gene level using the featureCount function in Subread (v2.0.3) with -s 2 option.
Assembly: hg38, GRCm39
Supplementary files format and content: tab-delimited text files contain abundance of gene-level raw read counts.

extract_protocol:
RNA was extracted from HN-SCC-151 cells using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA). For the mouse tumors, 30mg of tissue were sub-sampled from frozen parent samples into pre-chilled Lysing Matrix A 2.0 ml tubes (MP Biomedical).  RNA lysates were generated by adding 700uL of Buffer RLT (Qiagen) containing 1% 2-mercaptoethanol to each tube containing tissue and homogenizing 2 x 30 sec. at high speed in a Bead Ruptor 12 (Omni, Inc.).  12.5 ug of linear polyacrylamide (LPA) (bioWorld cat#10510000) was added to each sample and total RNA was purified with a QIAcube Connect MDx using the RNeasy Mini reagent and protocol (Qiagen) with DNase I treatment.  RNA was eluted in 50uL of RNase-free water.
VS912-VS1049: Libraries for HN-SCC-151 cells were prepared using the Illumina® Stranded mRNA Prep and sequenced on NextSeq 2000 P2 with 2x51 bp paired-end reads. VS1752-VS1761: Libraries for MOC1 cells were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760) as described in the manufacturer’s manual and sequenced on NextSeq 2000 with 2x101 bp paired-end reads.

value: human HPV-negative head and neck squamous cell carcinoma cell line

value: Wild type

value: pharmacologic inhibition of SUV420H1 with A-198


title: Largemouth bass Spleen, 24h post-challenge, Mock, biological replicate 2 [21A2S]

description:
Library name: 21A2S
Sham-injected control; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909160065_R06C01]


title: THP1-Macrophage, 24hr, Knockdown, Uninfected (R12166)

value: Uninfected


title: VS1048_SCC151_SUV420H1_inhibitor_rep2_rnaseq

description:
Library name: VS1048
bams/VS1048.sorted.markdup.bam

value: pharmacologic inhibition of SUV420H1 with A-197


title: THP1-Macrophage, 24hr, Knockdown, Uninfected (R12165)


title: Largemouth bass Spleen, 24h post-challenge, Mock, biological replicate 1 [21A1S]

description:
Library name: 21A1S
Sham-injected control; 24h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: VS1047_SCC151_SUV420H1_inhibitor_rep1_rnaseq

description:
Library name: VS1047
bams/VS1047.sorted.markdup.bam

value: pharmacologic inhibition of SUV420H1 with A-196


title: Largemouth bass Gill, 24h post-challenge, Mock, biological replicate 3 [21A3G]

description:
Library name: 21A3G
Sham-injected control; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: Peripheral blood from patient with delayed puberty [206909160065_R05C01]

value: Peripheral blood


title: Peripheral blood from patient with delayed puberty [206909160065_R04C01]


title: THP1-Macrophage, 24hr, Knockdown, Uninfected (R12164)

value: 24 Hr

value: p62 knockdown


title: VS1046_SCC151_DMSO_rep3_rnaseq

description:
Library name: VS1046
bams/VS1046.sorted.markdup.bam

value: unmodified parental cell line


title: Largemouth bass Gill, 24h post-challenge, Mock, biological replicate 2 [21A2G]

description:
Library name: 21A2G
Sham-injected control; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909160065_R03C01]

value: patient with delayed puberty


title: Largemouth bass Gill, 24h post-challenge, Mock, biological replicate 1 [21A1G]

description:
Library name: 21A1G
Sham-injected control; 24h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: VS1045_SCC151_DMSO_rep2_rnaseq

description:
Library name: VS1045
bams/VS1045.sorted.markdup.bam


title: THP1-Macrophage, 24hr, Wildtype, Infected (R12160)

value: THP-1 Macrophages

value: Wildtype

value: Mtb


title: Peripheral blood from patient with delayed puberty [206909160065_R02C01]


title: VS1044_SCC151_DMSO_rep1_rnaseq

description:
Library name: VS1044
bams/VS1044.sorted.markdup.bam


title: Largemouth bass Spleen, 12h post-challenge, Ah, biological replicate 3 [15T3S]

description:
Library name: 15T3S
Aeromonas hydrophila single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen

value: Aeromonas hydrophila single infection


title: THP1-Macrophage, 24hr, Wildtype, Infected (R12159)


title: Peripheral blood from patient with delayed puberty [206909160065_R01C01]


title: Largemouth bass Spleen, 12h post-challenge, Ah, biological replicate 2 [15T2S]

description:
Library name: 15T2S
Aeromonas hydrophila single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: VS917_SCC151_si1SUV420H1_rep3_rnaseq

description:
Library name: VS917
bams/VS917.sorted.markdup.bam

value: human HPV-negative head and neck squamous cell carcinoma cell line

value: SUV420H1 knockdown by siRNA


title: THP1-Macrophage, 24hr, Wildtype, Uninfected (R12158)


title: Peripheral blood from patient with delayed puberty [206909030026_R08C01]


title: VS916_SCC151_si1SUV420H1_rep2_rnaseq

description:
Library name: VS916
bams/VS916.sorted.markdup.bam

value: Wild type


title: Largemouth bass Spleen, 12h post-challenge, Ah, biological replicate 1 [15T1S]

description:
Library name: 15T1S
Aeromonas hydrophila single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: THP1-Macrophage, 24hr, Wildtype, Uninfected (R12156)

value: Uninfected


title: Peripheral blood from patient with delayed puberty [206909030026_R07C01]


title: Largemouth bass Gill, 12h post-challenge, Ah, biological replicate 3 [15T3G]

description:
Library name: 15T3G
Aeromonas hydrophila single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: THP1-Macrophage, 24hr, Wildtype, Infected (R12162)


title: VS914_SCC151_siNC_rep3_rnaseq

description:
Library name: VS914
bams/VS914.sorted.markdup.bam

value: non-targeting control siRNA


title: Largemouth bass Spleen, 24h post-challenge, Fc, biological replicate 2 [27N2S]

description:
Library name: 27N2S
Flavobacterium columnare single infection; 24h post-challenge; Spleen; FLAGGED — below-average mapping rate; retained in model (not PCA outlier)
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: VS915_SCC151_si1SUV420H1_rep1_rnaseq

description:
Library name: VS915
bams/VS915.sorted.markdup.bam


title: Largemouth bass Gill, 12h post-challenge, Ah, biological replicate 2 [15T2G]

description:
Library name: 15T2G
Aeromonas hydrophila single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909030026_R06C01]


title: Peripheral blood from patient with delayed puberty [206909030026_R05C01]


title: THP1-Macrophage, 24hr, Wildtype, Uninfected (R12155)


title: VS913_SCC151_siNC_rep2_rnaseq

description:
Library name: VS913
bams/VS913.sorted.markdup.bam


title: Peripheral blood from patient with normal pubertal age [206909030026_R04C01]

value: patient with normal pubertal age


title: Largemouth bass Gill, 12h post-challenge, Ah, biological replicate 1 [15T1G]

description:
Library name: 15T1G
Aeromonas hydrophila single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: THP1-Macrophage, 0hr, Knockdown, Infected (R12154)

value: 0 Hr


title: THP1-Macrophage, 0hr, Knockdown, Infected (R12153)


title: VS912_SCC151_siNC_rep1_rnaseq

description:
Library name: VS912
bams/VS912.sorted.markdup.bam


title: Largemouth bass Spleen, 12h post-challenge, AhFc, biological replicate 3 [19R3S]

description:
Library name: 19R3S
A. hydrophila + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with normal pubertal age [206909030026_R03C01]

value: Peripheral blood


title: VS1043_SCC151_siSUV420H1_H4K20me3_rep4

description: Library name: VS1043

data_processing:
Raw fastq files were trimmed with Cutadapt (v 4.4) and aligned using bowtie (v 2-2.5.1) against hg38. For spike-in controls, the trimmed FASTQ files were aligned against the Escherichia coli MG1655 genome. Duplicated reads were removed using Picard tools (v 2.27.3), and normalization factors were derived based on the uniquely mapped fragments in the corresponding spike-in control data. The enriched regions with H4K20me3 signals were identified using GoPeaks with –broad option and FDR=0.05 options. Raw tag counts were obtained using bedtools (v 2.30.0) and the bedmap function in BEDOPS toolkit (v 2.4.41) for merged peak sites.
Assembly: hg38
Supplementary files format and content: tab delimited BED files contain genomic coordinates of called peaks. BigWig files are provided for IgG and positive control samples (H3K4me3 and H3K27me3).
Library strategy: CUT&Run

extract_protocol:
Cells were obtained freshly from the cell culture dishes with trypsinization, and were counted to have 500,000 cells per reaction.
Libraries were constructed according to SWIFT Accel-NGS 2S Plus DNA lib prep kit


title: Largemouth bass Spleen, 12h post-challenge, AhFc, biological replicate 2 [19R2S]

description:
Library name: 19R2S
A. hydrophila + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: THP1-Macrophage, 0hr, Knockdown, Infected (R12152)

value: p62 knockdown


title: Peripheral blood from patient with normal pubertal age [206909030026_R02C01]


title: THP1-Macrophage, 0hr, Knockdown, Uninfected (R12150)


title: VS1042_SCC151_siSUV420H1_H4K20me3_rep3

description: Library name: VS1042


title: Largemouth bass Spleen, 12h post-challenge, AhFc, biological replicate 1 [19R1S]

description:
Library name: 19R1S
A. hydrophila + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: THP1-Macrophage, 0hr, Knockdown, Uninfected (R12149)


title: THP1-Macrophage, 0hr, Knockdown, Uninfected (R12148)


title: VS1041_SCC151_siSUV420H1_H4K20me3_rep2

description: Library name: VS1041


title: Peripheral blood from patient with normal pubertal age [206909030026_R01C01]


title: Largemouth bass Gill, 12h post-challenge, AhFc, biological replicate 3 [19R3G]

description:
Library name: 19R3G
A. hydrophila + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with normal pubertal age [206909160068_R08C01]


title: VS1040_SCC151_siSUV420H1_H4K20me3_rep1

description: Library name: VS1040


title: THP1-Macrophage, 0hr, Wildtype, Infected (R12146)


title: VS1039_SCC151_siNC_H4K20me3_rep4

description: Library name: VS1039


title: Largemouth bass Gill, 12h post-challenge, AhFc, biological replicate 1 [19R1G]

description:
Library name: 19R1G
A. hydrophila + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: THP1-Macrophage, 0hr, Wildtype, Infected (R12144)


title: Largemouth bass Gill, 12h post-challenge, AhFc, biological replicate 2 [19R2G]

description:
Library name: 19R2G
A. hydrophila + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with normal pubertal age [206909160068_R06C01]


title: Peripheral blood from patient with delayed puberty [206909160068_R07C01]


title: Largemouth bass Spleen, 12h post-challenge, AhFc, biological replicate 3 [19Q3S]

description:
Library name: 19Q3S
A. hydrophila + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with normal pubertal age [206909160068_R05C01]


title: Largemouth bass Spleen, 12h post-challenge, AhFc, biological replicate 2 [19Q2S]

description:
Library name: 19Q2S
A. hydrophila + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: THP1-Macrophage, 0hr, Wildtype, Uninfected (R12142)


title: THP1-Macrophage, 0hr, Wildtype, Infected (R12143)


title: VS1038_SCC151_siNC_H4K20me3_rep3

description: Library name: VS1038


title: Peripheral blood from patient with delayed puberty [206909160068_R04C01]


title: VS1036_SCC151_siNC_H4K20me3_rep1

description: Library name: VS1036


title: Largemouth bass Spleen, 12h post-challenge, AhFc, biological replicate 1 [19Q1S]

description:
Library name: 19Q1S
A. hydrophila + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: THP1-Macrophage, 0hr, Wildtype, Uninfected (R12140)


title: Peripheral blood from patient with delayed puberty [206909160068_R03C01]


title: VS1035_SCC151_H3K27me3_rep2

description: Library name: VS1035


title: Largemouth bass Gill, 12h post-challenge, AhFc, biological replicate 3 [19Q3G]

description:
Library name: 19Q3G
A. hydrophila + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: THP1-Macrophage, 0hr, Wildtype, Uninfected (R12139)


title: Peripheral blood from patient with delayed puberty [206909160068_R02C01]


title: VS1037_SCC151_siNC_H4K20me3_rep2

description: Library name: VS1037


title: VS1034_SCC151_H3K27me3_rep1

description: Library name: VS1034


title: Largemouth bass Gill, 12h post-challenge, AhFc, biological replicate 2 [19Q2G]

description:
Library name: 19Q2G
A. hydrophila + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: VS1033_SCC151_H3K4me3_rep2

description: Library name: VS1033


title: Peripheral blood from patient with delayed puberty [206909160068_R01C01]


title: NZB-D3-lung-M3-R1

city: New York

first: Edmund

middle: C

last: Jenkins

state: NY

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

description: Library name: NZB-D3-lung-M3

data_processing:
Raw FASTQ files (paired-end) were aligned/quantified using the BioJupies web platform (Ma'ayan Lab). Alignment was performed with the platform's default cloud alignment service (Elysium) against the mouse reference transcriptome/genome
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: .csv, normalized counts

organism: Mus musculus

source_name: Lung

extract_protocol:
Mouse tissue samples were collected, homogenize, and preserved in TRIzol reagent (Invitrogen/Thermo Fisher) by the submitter. Preserved samples were shipped to Azenta Life Sciences (GENEWIZ) on dry ice. Total RNA was then extracted by Azenta using a column-based purification method (Qiagen RNeasy or equivalent best-in-class silica-membrane kit with on-column DNase I treatment) according to the manufacturer’s instructions and Azenta’s optimized protocols for TRIzol-preserved samples.
Library preparation was performed by Azenta Life Sciences using a stranded polyA-enriched bulk RNA-seq protocol, based on Illumina or 10x Genomics-compatible reagents (confirm with Azenta report).

value: Lung


title: Largemouth bass Gill, 12h post-challenge, AhFc, biological replicate 1 [19Q1G]

description:
Library name: 19Q1G
A. hydrophila + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: NZB-D3-lung-M2-R1

description: Library name: NZB-D3-lung-M2


title: Largemouth bass Spleen, 12h post-challenge, AvFc, biological replicate 3 [18P3S]

description:
Library name: 18P3S
A. veronii + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: A. veronii + F. columnare coinfection


title: Peripheral blood from patient with delayed puberty [206909160097_R08C01]

value: patient with delayed puberty


title: VS1032_SCC151_H3K4me3_rep1

description: Library name: VS1032


title: Peripheral blood from patient with normal pubertal age [206909160097_R07C01]


title: NZB-D3-lung-M1-R1

description: Library name: NZB-D3-lung-M1


title: Largemouth bass Spleen, 12h post-challenge, AvFc, biological replicate 2 [18P2S]

description:
Library name: 18P2S
A. veronii + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909160097_R06C01]


title: VS1030_SCC151_IgG_rep1

description: Library name: VS1030


title: NZB-D20-M3-lung-R1

description: Library name: NZB-D20-M3-lung


title: VS1012_SCC151_A-196_H4K20me3_rep3

description: Library name: VS1012


title: Largemouth bass Spleen, 12h post-challenge, AvFc, biological replicate 1 [18P1S]

description:
Library name: 18P1S
A. veronii + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: NZB-D20-M2-lung-R1

description: Library name: NZB-D20-M2-lung


title: Peripheral blood from patient with delayed puberty [206909160097_R05C01]


title: VS1011_SCC151_A-196_H4K20me3_rep2

description: Library name: VS1011


title: Largemouth bass Gill, 12h post-challenge, AvFc, biological replicate 3 [18P3G]

description:
Library name: 18P3G
A. veronii + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: NZB-D20-M1-lung-R1

description: Library name: NZB-D20-M1-lung


title: NZB-D10-lung-M3-R1

description: Library name: NZB-D10-lung-M3


title: Largemouth bass Gill, 12h post-challenge, AvFc, biological replicate 2 [18P2G]

description:
Library name: 18P2G
A. veronii + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Sample_Rat_HN_Dend27

description: Library name: Rat_HN_Dend27

value: hippocampus

value: pyramidal neurons

value: wildtype

value: Sprague Dawley

value: Dendrites


title: Peripheral blood from patient with normal pubertal age [206909160097_R04C01]


title: Peripheral blood from patient with delayed puberty [206909160097_R03C01]


title: VS1010_SCC151_A-196_H4K20me3_rep1

description: Library name: VS1010

value: human HPV-negative head and neck squamous cell carcinoma cell line


title: VS1006_SCC151_DMSO_H4K20me3_rep3

description: Library name: VS1006

value: Wild type


title: Largemouth bass Gill, 12h post-challenge, AvFc, biological replicate 1 [18P1G]

description:
Library name: 18P1G
A. veronii + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909160097_R02C01]


title: NZB-D10-lung-M2-R1

description: Library name: NZB-D10-lung-M2


title: VS1005_SCC151_DMSO_H4K20me3_rep2

description: Library name: VS1005


title: Largemouth bass Spleen, 12h post-challenge, AvFc, biological replicate 3 [18O3S]

description:
Library name: 18O3S
A. veronii + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen


title: NZB-D10-lung-M1-R1

description: Library name: NZB-D10-lung-M1


title: VS1004_SCC151_DMSO_H4K20me3_rep1

description: Library name: VS1004


title: Peripheral blood from patient with normal pubertal age [206909160097_R01C01]


title: Largemouth bass Spleen, 12h post-challenge, AvFc, biological replicate 2 [18O2S]

description:
Library name: 18O2S
A. veronii + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909160067_R08C01]


title: ISRIB-9-R1

description: Library name: ISRIB-9


title: VS1003_SCC151_DMSO_H3K27me3_rep2

description: Library name: VS1003


title: Peripheral blood from patient with delayed puberty [206909160067_R07C01]


title: ISRIB-8-R1

description: Library name: ISRIB-8


title: Largemouth bass Gill, 12h post-challenge, AvFc, biological replicate 3 [18O3G]

description:
Library name: 18O3G
A. veronii + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: VS1002_SCC151_DMSO_H3K27me3_rep1

description: Library name: VS1002


title: Largemouth bass Spleen, 12h post-challenge, AvFc, biological replicate 1 [18O1S]

description:
Library name: 18O1S
A. veronii + F. columnare coinfection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909160067_R06C01]


title: ISRIB-7-R1

description: Library name: ISRIB-7


title: VS1001_SCC151_DMSO_H3K4me3_rep2

description: Library name: VS1001


title: Largemouth bass Gill, 12h post-challenge, AvFc, biological replicate 2 [18O2G]

description:
Library name: 18O2G
A. veronii + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: ISRIB-6-R1

description: Library name: ISRIB-6


title: Peripheral blood from patient with delayed puberty [206909160067_R05C01]


title: VS1000_SCC151_DMSO_H3K4me3_rep1

description: Library name: VS1000


title: Largemouth bass Gill, 12h post-challenge, AvFc, biological replicate 1 [18O1G]

description:
Library name: 18O1G
A. veronii + F. columnare coinfection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: ISRIB-5-R1

description: Library name: ISRIB-5


title: Peripheral blood from patient with delayed puberty [206909160067_R04C01]


title: Peripheral blood from patient with delayed puberty [206909160067_R03C01]


title: Largemouth bass Spleen, 12h post-challenge, Fc, biological replicate 3 [17N3S]

description:
Library name: 17N3S
Flavobacterium columnare single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: ISRIB-4-R1

description: Library name: ISRIB-4


title: Bone marrow stem cell, female, 29

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

country: Canada

institute: University of Alberta

description: Library name: AED-4-2-HM-082322_S23

data_processing:
A noise-reduction filter was applied to remove features with a maximum count < 50. Gene counts were normalized using Add: 1.0, TMM, and log2 transformation. Differentially expressed gene (DEG) analysis was performed using limma-trend for cell source, with donor included as a random factor.
Assembly: hg38
Supplementary files format and content: ScAED_ProcessedData_NormalizedCount.txt

source_name: Bone Marrow

growth_protocol: Nasal septal cartilage from three female donors was digested for 22 h in 0.15% (w/v) collagenase type II at 300 U/mg (Worthington, #LS004176). Released cells were plated in T-75 tissue culture flasks (Sarstedt, Germany) for 48 h to recover, then detached and reseeded at 1 × 10⁴ cells/cm². Cells were expanded for 1 week under normoxia (21% O₂, 5% CO₂, ~95% humidity) in high-glucose DMEM supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 10 mM HEPES, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine (PSG; Life Technologies, ON, Canada), 5 ng/mL FGF-2 (Neuromics, USA; cat. PR80001), and 1 ng/mL TGF-β1 (ProSpec, cat. CYT-716), yielding passage 1 (P1) cells. NCs were cryopreserved at P1 and, for experiments, thawed and expanded to P2 under the same conditions.After expansion to P2, cell-laden scaffold constructs were generated in either monoculture or co-culture conditions. For monoculture, NCs (three donors) and BMSCs (one donor) were seeded separately onto cylindrical type I collagen sponge scaffolds (10 mm diameter, 3.5 mm height; Integra LifeSciences) at a density of 5 × 10⁷ cells/cm³. For co-culture, NCs from each donor were mixed with BMSCs at a 1:3 NC:BMSC ratio and seeded onto the same scaffolds at the same total cell density. All constructs were cultured for 6 weeks under hypoxia (3% O₂, 5% CO₂, ~95% humidity) in a defined serum-free chondrogenic medium supplemented with 10 ng/mL TGF-β3, with medium changes twice weekly. Prior to mechanical loading, two constructs per group were harvested for baseline histological analysis. Bone marrow mononuclear cells (MNCs) from one female donor were isolated using Histopaque-1077 (Sigma) according to the manufacturer’s instructions. MNCs were plated in T-75 flasks to allow the adherent BMSC population to establish and expand for 1 week to P1 under hypoxia (3% O₂, 5% CO₂, ~95% humidity) in α-MEM supplemented with 10% (v/v) FBS, 100 mM HEPES, 1 mM sodium pyruvate (Sigma-Aldrich, MO), PSG, and 5 ng/mL FGF-2. For experiments, BMSCs were thawed and expanded to P2 under the same hypoxic conditions.

extract_protocol:
Constructs for RNA seq were harvested (n = 3 per group) and immediately frozen at −80°C in TRIzol reagent (Thermo Fisher Scientific, United States, #15596018). Total RNA was isolated using PureSPIN mini spin columns (Luna Nanotech, Canada, #NK051-250) according to the manufacturer’s instructions.
The remaining isolated RNA was sequenced at the University of British Columbia Biomedical Research Centre using an Illumina NextSeq 2000 platform with paired-end 59 bp × 59 bp reads. FASTQ files were analyzed using Partek Flow (version 12.9.0). Reads were aligned to the human genome using STAR (v2.7.8a), and transcript quantification was performed using the Partek E/M algorithm with the hg38 Ensembl transcript annotation model (release 113_v2).

treatment_protocol: After 6 weeks of pre-culture, constructs were subjected to dynamic compression using a Biodynamic 5210 system (TA Instruments, USA) under hypoxia (3% O₂, 5% CO₂). Scaffolds were placed on custom platforms within chambers containing 110 mL of the same defined, serum-free chondrogenic medium, supplemented with 10 ng/mL TGF-β3, as used during pre-culture. A single loading event consisted of: (i) 10% compressive strain for 5 s; (ii) oscillatory compression between 30% and 40% strain for 10 min; and (iii) a 6 h rest period. The constructs were loaded 4 times per day for 7 days. After completion of loading, constructs were randomly assigned to downstream analyses

value: Bone Marrow

value: Bone marrow Stem cells

value: Hypoxia+DC


title: Peripheral blood from patient with delayed puberty [206909160067_R02C01]


title: Largemouth bass Spleen, 12h post-challenge, Fc, biological replicate 2 [17N2S]

description:
Library name: 17N2S
Flavobacterium columnare single infection; 12h post-challenge; Spleen; FLAGGED — below-average mapping rate; retained in model (not PCA outlier)
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: VS999_SCC151_DMSO_IgG_rep1

description: Library name: VS999


title: Nasal Chondrocytes, Female, 22

description: Library name: AED-3-2-HM-082322_S21

source_name: Nasal Septum Cartilage

value: Nasal Septum Cartilage

value: Nasal Chondrocyte


title: Largemouth bass Spleen, 12h post-challenge, Fc, biological replicate 1 [17N1S]

description:
Library name: 17N1S
Flavobacterium columnare single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909160067_R01C01]

value: Peripheral blood


title: ISRIB-11-R1

description: Library name: ISRIB-11

value: Lung


title: Tab_T1, rep3

city: NANTES

first: Emmanuel

last: SCOTET

state: Loire Atlantique

address: IRS UN, 8 quai Moncousu

country: France

institute: Emmanuel SCOTET

description:
Library name: 79_Tab_T1_3
Tab_T1_3

data_processing:
Base calling was performed directly by sequencing facility using phred-33 standard quality scores
Adapter sequences and low-quality reads were removed using SOAPnuke directly after FASTQ generation by the sequencing facility
Transcript count table from FASTQ files was generated  using subread (2.0.1) by alignment to the human genome (GRCh38) using STAR (2.7.10b) with Ensembl GTF (release 111)
Gene expression changes and statistics were realized using DESeq2 (1.34.0)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes counts after normalization, average expressions by conditions, and results of statistical analysis by DESeq2 (logFC, pval, padj)

source_name: ab T Cells

extract_protocol:
RNA was extracted by RNeasy Plus Micro Kits (Qiagen)
Messenger RNA-Seq libraries were prepared using a SMART-SeqII combined with transposase-based library construction, libraries were circularized, and sequencing was executed by DNA Nanoballs (DNBTM™) technology

value: ab T Cells

value: SKOV3 + 4 days culture


title: ISRIB-10-R1

description: Library name: ISRIB-10


title: Largemouth bass Gill, 12h post-challenge, Fc, biological replicate 3 [17N3G]

description:
Library name: 17N3G
Flavobacterium columnare single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: ST11_T, Transcriptome library

city: San Francisco

first: Guohua

last: Yuan

address: 1651 4th St Fl 5 521A, Weill Neurosciences Building

institute: UCSF

description: Library name: ST11_T

data_processing:
scRNA-seq analysis 10X transcriptomic libraries were processed using CellRanger (version 7.2.0) and were aligned to the mouse transcriptome mm10-2020-A. Cellranger outputs were processed using Seurat (version 5.2.0). Datasets were processed to remove cells with fewer than 1,000 or greater than 100,000 reads, fewer than 500 or greater than 10,000 genes, or more than 20% of reads corresponding to mitochondrial genes. Doublets were identified and removed by using DoubletFinder (version 2.0.4). Libraries were integrated using Seurat’s “SCTransform” and Harmony (version 0.1.162). Libraries of the seurat project including all regions were integrated by Seurat’s “SCTransform”. Seurat projects of each brain region were integrated by Seurat’s “SCTransform” function and Harmony. To identify clusters, we constructed a shared nearest neighbor (SNN) graph using the 'FindNeighbors' function, and applied clustering through the 'FindClusters' function in Seurat. Iterative clustering to identify subtypes of cells was performed by subsetting into different major cell types (glutamatergic neurons, GABAergic neurons, glia) and using the “FindSubCluster” function in Seurat. Cell identities determined through analysis of iterative clusters were re-assigned to cells in the full Seurat object. Differential expression analysis was conducted using Seurat's “FindMarkers” and “FindAllMarkers” function, and gene expression in clusters was manually analyzed for known markers of given cell types.
STICR barcodes analysis STICR barcode analysis was performed using custom scripts, as previously described in Delgado et al57. First, BBMap (BBMap; sourceforge.net/projects/bbmap/) was used to remove low-quality reads and then extract reads containing STICR barcode sequences. Then, BBMap was used to extract individual STICR barcode fragments that were then aligned to our predefined fragment reference sets using Bowtie59 (version 5.2.1), allowing for up to two mismatches per fragment. Aligned STICR barcodes were compiled into a file containing their corresponding 10X cell barcode and 10X UMI sequences using awk. UMI of STICR barcodes with less than 10 reads were filtered by using awk to remove the noise UMI counts from the sequencing error. Finally, UMI-tools60 (version 0.5.1) was used to remove duplicate STICR barcode/cell barcode (CBC) reads by UMI, allowing for 1-bp mismatches in the UMI. STICR barcodes/CBC) pairings with at least three distinct UMIs were retained. For cells with multiple barcodes detected, only cells with all the same set of barcodes detected are considered as a shared clone, with Jaccard similarity of 1. Barcodes and their corresponding UMI counts were mapped to cells in the Seurat object of transcriptome data by aligning cell barcodes.
Assembly: mm10
Supplementary files format and content: rds
Supplementary files format and content: rds

source_name: Brain

extract_protocol:
Virally injected brains were collected from mouse pups at postnatal day 4. Brains were dissected in ice-cold pre-bubbled artificial cerebrospinal fluid (aCSF), and sectioned into coronal sections. Each brain region was manually dissected out from sliced brains based on the guidance of anatomy atlas from Allen institute. Collected tissue was then dissociated in the solution of papain (Worthington, LK003178) supplemented with 0.5 mg/ml DNase (Sigma Aldrich, DN25-1G) diluted with HBSS (Gibco,14025134) at 37℃. The tissues were incubated at 37℃ for 30-60 min, with gentle trituration every 15 min until samples had no visible chunks.  Papain was quenched by adding 1% BSA (Militeny) to the solution. Samples were spun down and resuspended in HBSS + 0.1% BSA and passed through the 35 um filter into a FACS tube (Falcon, 52235). To isolate and collect virally infected cells, flow cytometry was done using a BD FACSAria III Cell Sorter (BD FACSDiva Software, version 8.0.2) with a 100-µm nozzle. The cell suspensions were first gated on forward scatter, then within this population based on eGFP expression. eGFP-expressing cells were sorted into HBSS + 0.1% BSA for downstream processing on the 10x Genomics Chromium platform. Samples were kept on ice before and after FACS, and the chamber and collection tubes were maintained at 4℃ during sorting.
scRNA-seq library preparation Preparation of scRNA-seq libraries was carried out using a Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #PN-1000075). We input between 10 and 20k cells per lane on a Chromium Chip G and followed the manufacturer protocol for transcriptomic library preparation.  STICR barcode library preparation STICR barcodes were subamplified from each 10X cDNA library using the Q5 Hot Start High Fidelity 2× master mix (NEB, M0494). In brief, 10 μl of cDNA was used as template in a 50 μl PCR reaction containing STICR barcode read 1 and 2 primers (0.5 μM, each) targeting the region immediately upstream of the STICR viral index/barcode as well as the partial Illumina Read1 sequence added during cDNA library preparation (Extended Data Table 3), using the following program: 1, 98 °C, 30 s; 2, 98 °C, 10 s; 3, 62 °C, 20 s; 4, 72 °C, 10 s; 5, repeat steps 2–4 12 times; 6, 72 °C, 2 min; 7, 4 °C, hold. Following PCR amplification, a 0.8–0.6 dual-sided size selection was performed using Ampure XP beads (Beckman Coulter, A63881). The libraries were quantified by Tapestation (Agilent) and pooled for sequencing.

value: Brain


title: DMSO-8-R1

description: Library name: DMSO-8


title: Peripheral blood from patient with delayed puberty [206909170038_R08C01]

value: patient with delayed puberty


title: Co-culture, Female, 29

description: Library name: AED-3-1-HM-082322_S20

source_name: Nasal Septum Cartilage + Bone marrow

value: Nasal Septum Cartilage + Bone marrow

value: Bone marrow Stem cells + Nasal Chondrocyte


title: Largemouth bass Gill, 12h post-challenge, Fc, biological replicate 2 [17N2G]

description:
Library name: 17N2G
Flavobacterium columnare single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: DMSO-7-R1

description: Library name: DMSO-7


title: Peripheral blood from patient with delayed puberty [206909170038_R07C01]


title: Nasal Chondrocytes, Female, 28

description: Library name: AED-2-2-HM-082322_S22


title: Largemouth bass Gill, 12h post-challenge, Fc, biological replicate 1 [17N1G]

description:
Library name: 17N1G
Flavobacterium columnare single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Co-culture, Female, 28

description: Library name: AED-2-1-HM-082322_S19


title: DMSO-6-R1

description: Library name: DMSO-6


title: Peripheral blood from patient with normal pubertal age [206909170038_R06C01]

value: patient with normal pubertal age


title: Nasal Chondrocytes, Female, 26

description: Library name: AED-1-2-HM-082322_S18


title: DMSO-5-R1

description: Library name: DMSO-5


title: Largemouth bass Spleen, 12h post-challenge, Fc, biological replicate 3 [17M3S]

description:
Library name: 17M3S
Flavobacterium columnare single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909170038_R05C01]


title: Largemouth bass Spleen, 12h post-challenge, Fc, biological replicate 2 [17M2S]

description:
Library name: 17M2S
Flavobacterium columnare single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: DMSO-4-R1

description: Library name: DMSO-4


title: Peripheral blood from patient with delayed puberty [206909170038_R04C01]


title: Largemouth bass Spleen, 12h post-challenge, Fc, biological replicate 1 [17M1S]

description:
Library name: 17M1S
Flavobacterium columnare single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: DMSO-3-R1

description: Library name: DMSO-3


title: Largemouth bass Gill, 12h post-challenge, Fc, biological replicate 3 [17M3G]

description:
Library name: 17M3G
Flavobacterium columnare single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: DMSO-2-R1

description: Library name: DMSO-2


title: Donor 1,Female, 34yr, T1F2

description: Library name: AFI6c_MLC-MK-122923_S25

data_processing:
Features with a maximum expression value ≤10 were filtered out before normalization. Expression values were offset by 1, normalized using the trimmed mean of M-values (TMM) method, and log2-transformed for downstream analysis. Differential expression analysis was performed in Partek Flow using the Limma-trend method. Genes were considered differentially expressed at an absolute fold change >2 and a false discovery rate (FDR) <0.05. Functional enrichment analyses, including KEGG and Gene Ontology (GO) analyses, were also performed in Partek Flow.
Assembly: hg38
Supplementary files format and content: .txt

source_name: Nasal speteum

growth_protocol: Freshly isolated nasal chondrocytes (NCs) were seeded into T75 or T175 flasks and cultured under normoxic conditions (21% O2, 5% CO2, 37 °C). No medium change was performed during the first 48 h to support cell attachment. After this initial recovery period, flasks were gently rinsed with DPBS to remove non-adherent cells and debris. Adherent cells were detached with 0.05% w/v trypsin-EDTA (25051CI, Corning) for approximately 5 min at 37 °C and reseeded at 10,000 cells/cm² in complete DMEM. Cultures were monitored for morphological changes and passaged again when 80-90% confluence was reached. At the end of P2, cells from each growth factor condition were collected, and microtissue pellets were formed at 0.5 × 10⁶ cells per pellet by centrifugation at 1500 rpm for 10 min. Pellets were cultured in serum-free chondrogenic medium composed of high-glucose DMEM, 1× ITS+ (354352, Corning, Canada), 1 ng/mL TGF-β3 (ProSpec, Israel), 100 nM dexamethasone, 50 μg/mL ascorbic acid 2-phosphate, 125 μg/mL human serum albumin, 40 μg/mL L-proline, 1% PSG, and 1% HEPES. Three-dimensional cultures were maintained under normoxic conditions (21% O2, 5% CO2, 37 °C) for 3 weeks, with medium changes twice weekly. After 3 weeks of differentiation, cartilage constructs were harvested for morphological, mechanical, histological, immunofluorescence, and biochemical analyses.

extract_protocol:
Total RNA was extracted and purified using the PuroSPIN Total RNA Purification Kit (Luna Nanotech, Canada) according to the manufacturer’s instructions. RNA concentration and purity were measured using a NanoDrop One C spectrophotometer (Thermo Fisher Scientific, Canada).
Raw FASTQ files were analyzed in Partek Flow software (version 10.0.21.0302; Partek Inc., St. Louis, MO, USA) using an established pipeline. Bases with Phred quality scores <20 were trimmed from read ends, and the remaining high-quality reads were aligned to the human reference genome (hg38) using STAR (v2.7.8a). Reads were quantified against the Ensembl_release111_v2 annotation.

treatment_protocol: Three growth factor groups were evaluated: DMEM supplemented with 1 ng/mL TGF-β1 (T1), 5 ng/mL FGF-2 (F2), or 1 ng/mL TGF-β1 plus 5 ng/mL FGF-2 (T1F2). Passage 2 (P2) cells were reseeded under their respective growth factor conditions and harvested at confluence for chondrogenic differentiation or molecular analyses

value: Nasal speteum

value: Primary nasal chondrocyte


title: Peripheral blood from patient with delayed puberty [206909170038_R03C01]


title: Largemouth bass Gill, 12h post-challenge, Fc, biological replicate 2 [17M2G]

description:
Library name: 17M2G
Flavobacterium columnare single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Donor 1,Female, 34yr, F2

description: Library name: AFI6b_MLC-MK-122923_S24


title: Co-culture, Female, 26

description: Library name: AED-1-1-HM-082322_S17


title: Peripheral blood from patient with delayed puberty [206909170038_R02C01]


title: DMSO-1-R1

description: Library name: DMSO-1


title: Donor 2,Male, 42yr, T1F2

description: Library name: AFI4c_MLC-MK-122923_S20


title: Donor 1,Female, 34yr, T1

description: Library name: AFI6a_MLC-MK-122923_S23


title: Peripheral blood from patient with delayed puberty [206909170038_R01C01]


title: Largemouth bass Gill, 12h post-challenge, Fc, biological replicate 1 [17M1G]

description:
Library name: 17M1G
Flavobacterium columnare single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Con-NZB-M3-lung-R1

description: Library name: Con-NZB-M3-lung


title: Peripheral blood from patient with delayed puberty [206909170024_R08C01]


title: Donor 2,Male, 42yr, F2

description: Library name: AFI4b_MLC-MK-122923_S19


title: ST8_T, Transcriptome library

description: Library name: ST8_T

value: Wild type


title: Largemouth bass Spleen, 12h post-challenge, Ah, biological replicate 3 [15J3S]

description:
Library name: 15J3S
Aeromonas hydrophila single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Spleen

value: Aeromonas hydrophila single infection


title: Peripheral blood from patient with normal pubertal age [206909170024_R07C01]


title: Sham 1

city: Suzhou

first: Xiaoyu

last: Lin

address: No. 100, Chongwen Road, Suzhou Industrial Park

country: China

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample7

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: Rattus Norvegicus mRatBN7.2 release-110
Supplementary files format and content: .xlsx

organism: Rattus

source_name: Rat pelvic ganglion

extract_protocol:
2.1.1 extraction of Total RNA Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, the integrity of RNA was detected by agarose gel electrophoresis, and the RIN value was determined by Agilent2100. Single library construction requires total RNA ≥1ug, concentration ≥35 ng/ΜL, OD260/280≥1.8, OD260/230≥1.0. 2.1.2oligo DT enrichment for mRNA Eukaryotic mrnas have a structure with a ployA tail at the 3′ end, and using magnetic beads with Oligo (DT) for A-T base pairing with Ploya, mrnas can be isolated from total RNA for analysis of transcriptome information. 2.1.3 fragmentation of mRNA The Illumina Novaseq 6000 platform is used to sequence short sequence fragments, and the enriched mrnas are complete RNA sequences with an average length of several KB, requiring random breaks. By adding fragmentation buffer, the mRNA was randomly cleaved, and small fragments of about 300 bp were isolated by magnetic bead screening. 2.1.4 cDNA synthesis by inversion Under the action of reverse transcriptase, random hexamers were added to synthesize one-stranded cDNA with mRNA as template, and then double-stranded cDNA was synthesized to form a stable double-stranded structure. 2.1.5 ligation of Adaptor The double-stranded cDNA has a sticky End, which is complemented by an End Repair Mix with a flat End, followed by the addition of an“A” base at the 3' End to connect the y-shaped linker. 2.1.6 in silico sequencing on the Illumina platform 1) library enrichment, PCR amplification for 15 cycles; 2) the target band was recovered by 2% agarose gel; 3) TBS380(Picogreen) quantification, mixed to data ratio on machine; 4) Bridge PCR amplification on cBot to generate clusters; 5) Illumina platform sequencing (PE library, read length 2 × 150 BP) .
1) the target RNA was interrupted by adding ion-interrupting reagent and random primer, and the random primer was combined with the target RNA; 2) the target RNA was reversely transcribed into cDNA by adding 1-strand reverse transcription reagent, and the hybrid chain of RNA and cDNA was formed; 3) the RNA in cDNA and RNA hybrid chain was cleaved by adding 2-strand synthetic reagent, and the double-stranded cDNA was synthesized by using the remaining RNA as the primer; 4) the double-stranded cDNA synthesis product was subjected to end-padding and a-addition; the“Y”-shaped linker was ligated; 5) the linker self-connecting fragment was removed by magnetic bead screening; 6) the library template was enriched by PCR amplification; 7) the library was recovered by magnetic beads. Reagent: VAHTS Universal V 8rna-seq Prep Library Kit for Illumina

value: Rat pelvic ganglion


title: Con-NZB-M1-lung-R1

description: Library name: Con-NZB-M1-lung


title: Con-NZB-M2-lung-R1

description: Library name: Con-NZB-M2-lung


title: Peripheral blood from patient with delayed puberty [206909170024_R06C01]


title: Donor 2,Male, 42yr, T1

description: Library name: AFI4a_MLC-MK-122923_S18


title: Largemouth bass Spleen, 12h post-challenge, Ah, biological replicate 2 [15J2S]

description:
Library name: 15J2S
Aeromonas hydrophila single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Donor 1,Female, 19yr, T1F2

description: Library name: AFI1c_MLC-MK-122923_S13


title: Donor 1,Female, 19yr, F2

description: Library name: AFI1b_MLC-MK-122923_S12


title: Largemouth bass Gill, 12h post-challenge, Ah, biological replicate 3 [15J3G]

description:
Library name: 15J3G
Aeromonas hydrophila single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with normal pubertal age [206909170024_R05C01]


title: Con-C57-M2-lung-R1

description: Library name: Con-C57-M2-lung


title: Con-C57-M3-lung-R1

description: Library name: Con-C57-M3-lung


title: Peripheral blood from patient with delayed puberty [206909170024_R04C01]


title: Largemouth bass Spleen, 12h post-challenge, Ah, biological replicate 1 [15J1S]

description:
Library name: 15J1S
Aeromonas hydrophila single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Donor 1,Female, 19yr, T1

description: Library name: AFI1a_MLC-MK-122923_S11


title: Largemouth bass Gill, 12h post-challenge, Ah, biological replicate 2 [15J2G]

description:
Library name: 15J2G
Aeromonas hydrophila single infection; 12h post-challenge; Gill; EXCLUDED from DESeq2 model — gDNA contamination (mapping rate <25%)
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Con-C57-M1-lung-R1

description: Library name: Con-C57-M1-lung


title: Peripheral blood from patient with delayed puberty [206909170024_R03C01]


title: siSOX4 treated HUVEC rep-3

city: Charlottesville

first: Pankaj

state: VA

address: 1340 Jefferson Park Ave

institute: UVA

description: Library name: mRNAS-9-C01_S9

data_processing:
BulkRNASeq: On average we received 55 million paired ends for each of the replicates and they were processed and mapped to from HUVEC and were checked for their quality using the fastqc program http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The results from fastqc were aggregated using multiqc software1. Reads were mapped with the “splice aware” aligner ‘STAR’,2 to the transcriptome and genome of mm10 genome build. The HTseq3 software will be used to count aligned reads that map onto each gene. The count table was imported to R to perform differential gene expression analysis using the DESeq2 package4. Low expressed genes (genes expressed only in a few replicates and had low counts) was excluded from the analysis before identifying differentially expressed genes. Data normalization, dispersion estimates, and model fitting (negative binomial) was carried out with the DESeq function. The log-transformed, normalized gene expression of 500 most variable genes will be used to perform an unsupervised principal component analysis. The differentially expressed genes was ranked based on the log2fold change and FDR corrected p-values. The ranked file was used to perform pathway analysis using GSEA software5.  The enriched pathways were selected based on enrichment scores as well as normalized enrichment scores. The heatmaps were generated using pheatmap function in R, and APA analysis using QAPA  following standard parameter and workflow at UVA Bioinformatics core.
Assembly: hg39
Supplementary files format and content: txt

source_name: HUVEC

growth_protocol: HUVEC cells were seeded into 100mm dish at a density of 1.5 X 106 cells and maintained the cells in Endothelial Cell complete Growth Medium-2

extract_protocol:
RNA was extracted 48 hours post siRNA treatment using TRIzol as per manufacturer’s procedure
RNA was quantified using Qubit 4 and quality was assessed by Agilent Tape station at UVA GATC core. NGS library was prepared and 50-base paired-end bulk sequencing was performed using Illumina NextSeq 2000 sequencing system using UVA GATC core that generated between 100-140 million read per sample

treatment_protocol: HUVEC Cells were transfected with scrambled siRNA and SOX4 siRNA  using Lipofectamine RNAiMAX (for 48 hours followed by cell harvest and RNA extraction.

value: HUVEC

value: Primary

value: pooled

value: siRNA


title: C57-D3-lung-M3-R1

description: Library name: C57-D3-lung-M3

value: Lung


title: Largemouth bass Gill, 12h post-challenge, Ah, biological replicate 1 [15J1G]

description:
Library name: 15J1G
Aeromonas hydrophila single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv

value: Gill


title: Peripheral blood from patient with delayed puberty [206909170024_R02C01]

value: Peripheral blood


title: siSOX4 treated HUVEC rep-2

description: Library name: mRNAS-8-B01_S8


title: C57-D3-lung-M2-R1

description: Library name: C57-D3-lung-M2


title: Peripheral blood from patient with delayed puberty [206909170024_R01C01]

value: patient with delayed puberty


title: Largemouth bass Spleen, 12h post-challenge, Av, biological replicate 3 [13F3S]

description:
Library name: 13F3S
Aeromonas veronii single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv

value: Aeromonas veronii single infection


title: siSOX4 treated HUVEC rep-1

description: Library name: mRNAS-7-A01_S7


title: siControl treated HUVEC rep-3

description: Library name: mRNAS-3-C02_S3


title: C57-D3-lung-M1-R1

description: Library name: C57-D3-lung-M1


title: C57-D20-M3-lung-R1

description: Library name: C57-D20-M3-lung


title: Largemouth bass Spleen, 12h post-challenge, Av, biological replicate 2 [13F2S]

description:
Library name: 13F2S
Aeromonas veronii single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Peripheral blood from patient with delayed puberty [206909030058_R07C01]


title: Peripheral blood from patient with delayed puberty [206909030058_R08C01]


title: siControl treated HUVEC rep-2

description: Library name: mRNAS-2-B02_S2


title: Largemouth bass Spleen, 12h post-challenge, Av, biological replicate 1 [13F1S]

description:
Library name: 13F1S
Aeromonas veronii single infection; 12h post-challenge; Spleen
raw_counts_spleen.csv
DESeq2_all_contrasts_spleen.csv


title: Largemouth bass Gill, 12h post-challenge, Av, biological replicate 3 [13F3G]

description:
Library name: 13F3G
Aeromonas veronii single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909030058_R06C01]


title: C57-D20-M2-lung-R1

description: Library name: C57-D20-M2-lung


title: siControl treated HUVEC rep-1

description: Library name: mRNAS-1-A02_S1


title: Largemouth bass Gill, 12h post-challenge, Av, biological replicate 2 [13F2G]

description:
Library name: 13F2G
Aeromonas veronii single infection; 12h post-challenge; Gill
raw_counts_gill.csv
DESeq2_all_contrasts_gill.csv


title: Peripheral blood from patient with delayed puberty [206909030058_R05C01]


title: C57-D20-M1-lung-R1

description: Library name: C57-D20-M1-lung


title: Peripheral blood from patient with delayed puberty [206909030058_R04C01]


title: c57-D10-lung-M3-R1

description: Library name: c57-D10-lung-M3