title: Taproot and lateral roots, control condition, degradome, biol rep 1

description: Library name: TR_LR-CT-D_rep1


title: wOB,1-day pupa(p1),rep3

status: Public on Apr 22 2025

type: SRA

city: Ames

first: Ping

last: Kang

state: Iowa

address: 3266 Molecular Biology Building 2437 Pammel Drive

department: GDCB

country: USA

institute: Iowa State University

library_source: transcriptomic

data_processing:
The raw sequencing reads were processed through Novogene's in-house perl script to remove low quality reads
The reference genome and gene model annotation files were downloaded from genome website. Hisat2 (v2.0.5) was used to generate the index of the reference genome and the mapping of pair-end reads
The gene expression level was quantify by FeatureCounts (v1.5.0-p3)
The differential expression analysis is performed by DESeq2R package (1.20.0)
The clusterProfiler R package was used for the Gene Ontology (GO) and KEGG enrichment analysis of differential gene expression. The protein-protein interaction network is constructed
Assembly: Drosophila_melanogaster.BDGP6.46
Supplementary files format and content: "gene_fpkm.xls" is the excel table that includes the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene for each sample.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Whole body

extract_protocol:
The samples were transferred to 1.7 ml centrifuge tube with a stainless-steel ball and 500ml Trizol. A0 was collected on the CO2 and transferred to a 1.7 ml centrifuge tube with a stainless-steel ball and 500ml Trizol. Tissuelyzer was used to smash the flies. About 15 pupa or flies were used in a biological replicate. Three biological replicates for each time points per genotype(wild type and Ptth mutants). RNA was sent to NOVOGENE for library and sequence after the total RNA was treated with DNase by the Turbo DNA-free kit (Invitrogen by Thermo Fisher Scitific, AM1907).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the cDNA was synthesized using random hexamer primers.  The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

tag: tissue

value: Whole body

tag: developmental stage

value: 1-day pupa(p1)

tag: genotype

value: wOB


title: Autism patient (ASD) 14

type: genomic

city: Cairo

first: Amal

last: Mohamed

address: El-Bohooth

department: Human Cytogenetics

country: Egypt

institute: National Research Centre

description: Hybridization to SNP

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: We use Affymetrix fluidic station for wash and stain microchips.We used Affymetrix scanner 3000

data_processing: We use ChAS software to analyse the generated cell files

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nano Quant instrumentation (Applied Biosystems), and agarose gel electrophoresis.

tag: disease state

value: ASD


title: 108AB

city: Zurich

first: Holger

last: Moch

address: Schmelzbergstrasse 12

department: Institute of Pathology and Molecular Pathology

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
EaCon, ASCAT
Merged Merged AT and GC data

label: biotin

source_name: FFPE Tumour

label_protocol: Affymetrix protocol

extract_protocol: Maxwell FFPE Tissue DNA Purification

value: Kidney (ccRCC)


title: YS602_WT_Control_rep1

city: Urbana

first: Hong

last: Jin

state: Illinois

address: 600 S Mathews Ave

department: Biochemistry

institute: University of Illinois at Urbana-Champaign

description: Library name: YS602_WT_Control_rep1

data_processing:
Adapters were trimmed from sequenced reads using cutadapt v1.18 and barcodes were split using fastx barcode splitter in the Fastx-toolkit.
Unique molecular identifiers (UMI) were extracted and deduplicated using UMI tools v1.01.
Reads were aligned to the Saccharomyces cerevisiae.R64-1-1.107 reference genome (Ensemble) by STAR v2.7.3a.
BedGraph profiles and RNA content were separated by bedtools v2.29.2 and SAMtools v1.10.2, respectively.
Read counts were quantified for each gene using htseq-count v 0.11.3 and fivepseq 1.0.064 was employed to analysis 5 ends positions.
Assembly: Saccharomyces cerevisiae.R64-1-1.107 reference genome (Ensemble)
Supplementary files format and content: processed data in csv format, which is the raw count of sequencing reads for each transcripts

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Wildtype and mutant yeast cells were grown in 50 ml YEPD and harvested at an OD600 value of 0.6.

extract_protocol:
Cells were lysed using glass beads and total mRNA was extracted using phenol–chloroform. 50 ug of total mRNA was used as the starting material to perform 5PSeq.
Poly(A)-containing mRNA was enriched using 100 µl oligo(dT) beads (Dynabeads oligo (dT)25, Life Technologies) for 5P samples while randomly generated fragments of total RNA were prepared as controls. Both 5P and control RNAs were fragmented at 80˚C for 5 min. Following reverse transcription and second strand generation, overnight incubation at 4 °C with M-280 streptavidin beads (Life Technologies) was performed instead of 30 min at room temperature, as suggested for maximum capture of the cDNA. The final DNA adapter ligation reaction was carried out for 2hrs at 16˚C. Following PCR, each sample was purified separately with HighPrep beads (Magbio) as suggested and their quality was checked using Agilent 2100 Bioanalyzer. A Qubit 2.0 Fluorometer (Life Technologies) was used to determine the concentration of each library. Libraries were pooled in equal molar ratios and fragments were enriched between 300 and 500 nt for the library. The final libraries were sequenced using Illumina NovaSeq 6000.

treatment_protocol: Harvested cells were resuspended in a lysis buffer containing 50 mM Tris-HCl (pH 8.1), 130 mM NaCl, 5 mM EDTA, and 5% SDS.

tag: cell type

value: yeast cell

tag: strain

value: WT

tag: treatment

value: mRNA degradation intermediate


title: YS602_WT_Control_rep2

description: Library name: YS602_WT_Control_rep2


title: 106AB


title: 318_PB-DLBCL

type: RNA

city: Leiden

first: Ruben

last: de Groen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: See manufacturer's protocol for the nanoString nCounter Assay System

data_processing: Data was log2 transformed and standardized by geometric mean, followed by normalization with the housekeeping genes using R. Further analyses were additionally performed with R.

label: Fluorescent tag barcodes

source_name: PB-DLBCL

extract_protocol: RNA was isolated from fresh frozen with TRIzol (Invitrogen) and Rneasy Mini Kit (Qiagen) and from deparaffinized <10 μm sections of FFPE tissues with the Tissue Preparation System (TPS) robot (Siemens Healthcare Diagnostics). RNA was quantified with the Qubit RNA BR Assay kit with the Qubit Fluorometer (Invitrogen).

tag: gender

value: Female

value: FFPE

tag: status after 5 years

value: Alive

tag: age

tag: ann arbor stage

value: IE


title: wOB,1-day pupa(p1),rep2


title: YS602_WT_5Pseq_rep1

description: Library name: YS602_WT_5Pseq_rep1


title: Autism patient (ASD) 22

description: Hybridization to SNP


title: Autism patient (ASD) 10

description: Hybridization to SNP


title: YS602_WT_5Pseq_rep2

description: Library name: YS602_WT_5Pseq_rep2


title: 317_Nodal-DLBCL-GCB

scan_protocol: See manufacturer's protocol for the nanoString nCounter Assay System

source_name: Nodal-DLBCL-GCB

value: I


title: wOB,1-day pupa(p1),rep1


title: 103AB


title: 105AB


title: wOB,white pupa(p0),rep3

value: white pupa(p0)


title: wOB,3-day pupa(p3),rep2

value: 3-day pupa(p3)


title: MC38, SMARCD1 KO, IFN, rep3

city: Shanghai

first: Gang

last: Fu

address: 197 Ruijin Rd. II, Shanghai

country: China

institute: Shanghai Jiaotong University School of medicine affiliated Ruijin Hospital

data_processing:
trimmomatic 0.36
FastQC 0.11.2
HISAT2 2.1.0
RSeQC 2.6.1
The raw image data files obtained were converted into sequenced reads by  Casava base calling. Data processing with Trimmomatic is carried out in the following steps:1) Remove sequences with N bases; 2) Remove the adapter sequence from the reads. The reference genome was used as the reference sequence. HISAT2 and RSeQC were used to compare them.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes TPM for each sample

organism: Mus musculus

extract_protocol:
total cellular RNA or RNA in polysome fraction was extracted using TRIZOL (Invitrogen #15596026). mRNA was reversely transcribed into cDNA using HiScript III 1st Strand cDNA Synthesis Kit (Vazyme, R312-01).
Sequencing were performed  according to the manufacturer’s instructions. mRNA was purified from total RNAs by using poly-T oligo-attached magnetic beads and fragmented by the fragmentation buffer.First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then using RNase H to degrade the RNAs. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3′ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
The library was initially quantified, then diluted to 1.5 ng/μl, and the insert size of the library is detected. After the library is qualified, the different libraries are pooled according to the effective concentration and the target amount of data off the machine, then being sequenced. The end reading of 150 bp pairing is generated.

tag: cell line

value: murine colorectal carcinoma

value: SMARCD1 knockout

value: IFN stimulation


title: MC38, SMARCD1 KO, IFN, rep2


title: 316_Nodal-DLBCL-GCB

label_protocol: See manufacturer's protocol for the nanoString nCounter Assay System

value: II


title: Autism patient (ASD) 3

description: Hybridization to SNP


title: wOB,white pupa(p0),rep2

value: Whole body

value: wOB


title: 102AB

value: Kidney (ccRCC)


title: 100AB


title: 315_Nodal-DLBCL-GCB

value: Male

value: Dead


title: wOB,white pupa(p0),rep1


title: 99AB


title: MC38, SMARCD1 KO, rep3

value: WT


title: wOB,L3-96h-AEL,rep3


title: Autism patient (ASD) 2

description: Hybridization to SNP Cy

value: ASD


title: 314_Nodal-DLBCL-GCB

value: FFPE


title: Autism patient (ASD) 5

description: Hybridization to SNP


title: 98AB


title: Autism patient (ASD) 7

description: Hybridization to SNP


title: 313_Nodal-DLBCL-GCB

value: Alive


title: 312_Nodal-DLBCL-GCB

value: Female


title: Autism patient (ASD) 15

description: Hybridization to SNP


title: 97AB


title: Autism patient (ASD) 9

description: Hybridization to SNP


title: wOB,L3-96h-AEL,rep2


title: wOB,L3-96h-AEL,rep1


title: MC38, SMARCD1 KO, rep1


title: MC38, SMARCD1 KO, rep2


title: Autism patient (ASD) 4

description: Hybridization to SNP


title: 309_Nodal-DLBCL-GCB


title: 96AB


title: wOB,L3-72h-AEL,rep3


title: MC38, IFN, rep2


title: MC38, SMARCD1 KO, IFN, rep1


title: wOB,L3-72h-AEL,rep2


title: 307_PB-DLBCL

value: IE


title: 308_Polyostotic-DLBCL

source_name: Polyostotic-DLBCL

value: IV


title: MC38, IFN, rep1


title: wOB,L3-72h-AEL,rep1


title: 94AB


title: MC38, IFN, rep3


title: 306_Polyostotic-DLBCL


title: MC38, rep3


title: 93AB


title: MC38, rep2


title: 90AB


title: 305_Polyostotic-DLBCL


title: Autism patient (ASD) 6

description: Hybridization to SNP


title: 95AB


title: MC38, rep1


title: 302_PB-DLBCL


title: ptth,old-female,rep1

data_processing:
The reference genome and gene model annotation files were downloaded from genome website. STAR (2.7.3a) was used to generate the index of the reference genome and the mapping of the raw sequencing reads
The gene expression level was quantify by htseq (0.11.2)
The differential expression analysis is performed by DESeq2(1.20.0)
Assembly: Drosophila_melanogaster.BDGP6.22.98
Supplementary files format and content: "Female_normalized_counts.xlsx" file includes the normalized reads count of each gene for each sample.

extract_protocol:
For RNA extraction. using Trizol method and following by DNase treatment(Ambion). RNA concentration was quantified by Qubit RNA BR Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA Catalog number: Q10210). RNA-Seq libraries were constructed using 300 ng of total RNA and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA. Catalog number: E7420). RNA concentrations were measured using Qubit RNA BR Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA Catalog number: Q10210). Poly(A) mRNA was isolated using NEBNext Oligo d(T)25 beads and fragmented into 200 nt in size. After first strand and second strand cDNA synthesis, each cDNA library was ligated with a NEBNext adaptor and barcoded with an adaptor-specific index. Twelve libraries were pooled in equal concentrations, and sequenced using Illumina HiSeq 3000 platform (single-end, 50 bp reads format).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the cDNA was synthesized using random hexamer primers.  The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

tag: Sex

value: female

value: old


title: 89AB


title: Autism patient (ASD) 1

description: Hybridization to SNP array


title: 88AB


title: 298_PB-DLBCL


title: 87AB


title: WOB,old-female,rep3


title: IRI_CD45pos1

city: shanghai

first: Junqi

last: Wu

state: shanghai

address: No. 507 Zhengmin Road, Shanghai 200443, China.

institute: Shanghai Pulmonary Hospital

description: Library name: IRI_CD45pos1

library_source: transcriptomic single cell

data_processing:
PISA (v0.12b, https://github.com/shiquan/PISA) was used to process the raw sequencing data of scRNA-seq and generate a cell versus gene UMI count matrix. The reference genome was downloaded from the Ensemble assembly: Sscrofa11.1. Downstream analysis was conducted using Seurat (5.5.3) in R (v4.2.2). Cells were excluded if the number of detected genes were less than 200 and greater than 5000. Cells with more than 10% mitochondrial gene counts (ATP6, ATP8, COX1, COX2, COX3, CYTB, ND2, ND3, ND4, ND4L, ND5, ND6) were also excluded. The Pig ND1 gene was not included in MT-based filtering due to high sequence variant in pigs. DoubletFinder (v2.0.4) was used to eliminate doublets in each library using default parameters. The count matrix was normalized (‘NormalizeData’ function), and variable genes were determined using Seurat’s “FindVariableGenes” function with default parameters (selection.method = “vst”, nfeatures = 2000). Merged data from each library was scaled (‘ScaleData’ function) and principal component analysis was performed (‘RunPCA’ function). Harmony (v1.2.0) was used to remove batch effects in libraries. UMAP (‘RunUMAP’ function) and the shared nearest neighbour (‘FindNeighbors’ function) was followed using harmony embeddings instead of PCA. Clusters were identified via the “FindClusters” function. ‘FindAllMarkers’ and ‘FindMarkers’ function in Seurat were used with default parameters to perform differentially expressed gene (DEG) analysis between clusters and groups. DEGs with adjusted p values < 0.05 were filtered out for downstream analysis.
Assembly: Sscrofa11.1
Supplementary files format and content: barcodes.tsv.gz -single cell barcodes
Supplementary files format and content: features.tsv.gz - gene names
Supplementary files format and content: matrix.mtx.gz - raw counts

organism: Sus scrofa domesticus

source_name: lung

extract_protocol:
After retrograde perfusion, tissue specimen from the donor’s right lung was collected as control group, and the allograft after 8-hour reperfusion was harvested as IRI group. 3 pairs of lung specimen in each group were used for single cell RNA sequencing. Lungs tissues were immediately placed in MACS Tissue Storage Solution (Miltenyi Inc, 130-100-008), and then digested using a lung dissociation kit (Miltenyi Inc, 130-095-927) following the manufacturer’s instructions. Cell solution was filtered with 100 μm and 40 μm cell strainers respectively, and underwent RBC lysis using erythrocytes lysate (Biosharp, BL503B). For donor samples, the whole cells were then processed for single-cell RNA sequencing (scRNA-seq). For recipient samples, we performed fluorescence-activated cell sorting in order to obtain more cell types. Cell suspension from transplanted lungs were stained with FITC CD45 antibody (ThermoFisher, 11-9459-42) and Zombie Aqua™ Fixable Viability Kit (Biolegend, 423101). CD45 positive cells were sorted from 2 samples and CD45 negative cells were sorted from 1 sample using a BD FACSAriaTM II flow cytometer (BD Biosciences, USA).
scRNA-seq was conducted by BGI Genomics (Beijing, China). Briefly, scRNA-seq library was generated using the DNBelab C Series HT Single-Cell RNA Library kit (MGI, 940-000047-00, China) following the manufacturer's protocol, followed by sequencing on the DNBSEQ-T7 platform at the China National Gene Bank (CNGB).

value: lung


title: IRI_CD45pos2

description: Library name: IRI_CD45pos2


title: 297_Nodal-DLBCL-GCB


title: WOB,old-female,rep2


title: 85AB


title: ptth,old-female,rep3


title: IRI_CD45neg

description: Library name: IRI_CD45neg


title: WOB,old-female,rep1


title: Con3

description: Library name: Con3


title: 86AB


title: ptth,old-female,rep2


title: 296_Polyostotic-DLBCL


title: 294_PB-DLBCL


title: 84AB


title: Con2

description: Library name: Con2


title: ptth,young-female,rep3

value: young


title: 83AB


title: CK2

city: Beijing

first: Qiang

last: Cao

address: 12 Zhongguancun South Street, Haidian District, Beijing

institute: Chinese Academy of Agricultural Sciences

data_processing:
The filtered high-quality sequence is compared to the reference genome of the species.
According to the comparison results, the expression amount of each gene was calculated.
The samples were further analyzed for expression difference.
Assembly: IWGSC RefSeq v1.1
Supplementary files format and content: tab-delimited text file include FPKM values for each Sanple

organism: Triticum aestivum

source_name: vegetative tissue

extract_protocol:
RNA was harvested using a Tiangen RNA-prep Pure Plant kit. 0.5 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA 6000 nano kit following manufacture's protocols.

value: vegetative tissue

value: mesophyll cells

value: Pst innoculated


title: 292_PB-DLBCL


title: 299_Nodal-DLBCL-GCB

value: II


title: Con1

description: Library name: Con1


title: CK1


title: 290_PB-DLBCL

value: Male


title: 79AB

value: Kidney (ccRCC)


title: S1

value: WT


title: 81AB


title: E14.40

city: Exeter

first: Nicholas

middle: E

last: Clifton

address: RILD Building

country: United Kingdom

institute: University of Exeter

hyb_protocol: The fragmented, biotin-labelled DNA was denatured and hybridised overnight to the Illumina Mouse Methylation BeadChip arrays.

scan_protocol: Post-hybridisation, arrays underwent single-base extension using hapten-labelled dideoxynucleotides. The incorporated biotin labels were detected using a fluorescently labelled streptavidin conjugate. Arrays were scanned using an Illumina iScan system, and fluorescence intensities were quantified to determine methylation levels at each CpG site.

data_processing: DNA methylation data quality control was performed using a bespoke pre-processing pipeline (https://github.com/ew367/mouseArray). In brief, methylated and unmethylated signal intensities at each position were extracted from raw IDAT files using the ENmix R package and converted to beta values reflecting the proportion of DNA methylation at  each position. All samples achieved a minimum median methylated or unmethylated signal intensity value of 2000 with fewer than 1% of probes failing the detection P-value threshold of 0.05, determined with ENmix. All samples passed a bisulfite conversion efficiency threshold of 90% (mean = 96%). Principal component analyses were used to evaluate sample clustering. Following sample QC, we performed probe filtering. 24,860 probes flagged in the Illumina manifest as exhibiting high technical variability were removed. Additional probes failing the detection threshold of 0.05 in more than one sample were also excluded. The resulting data matrix was quantile normalized using the wateRmelon R package. The final dataset included 50 samples and DNA methylation estimates for 262,086 genomic positions (247,810 autosomal sites and 14,276 sex chromosome sites).

source_name: Frontal cortex

label_protocol: Bisulfite-converted genomic DNA was subjected to whole-genome amplification using random priming and φ29 DNA polymerase. During this amplification, biotin-labelled nucleotides were incorporated into the DNA strands. The amplified DNA was then enzymatically fragmented to achieve optimal fragment sizes for hybridisation.

growth_protocol: The knockout allele was generated through a knockout-first design targeting exon 4, giving premature termination of Setd1a transcripts and effective elimination of functional Setd1a protein from the mutant allele. This closely models the molecular effect of human SETD1A loss-of-function mutations, many of which are protein-truncating variants

extract_protocol: Frontal cortex tissue was dissected from male Setd1a+/− and wild type littermates at embryonic day 14.5 (E14.5), E18.5, postnatal day 7 (P7), P35 and P70. Tissue was snap frozen on dry ice and stored at -80C. Frontal cortices (n = 5 per genotype per timepoint) were homogenized by Dounce grinding and DNA extracted using the AllPrep DNA/RNA micro kit (Qiagen, UK). Approximately 500 ng of DNA from each sample was treated with sodium bisulfite using the EZ-96 DNA methylation kit (Zymo Research, CA, USA).

value: Frontal cortex


title: 288_Nodal-DLBCL-GCB

value: FFPE

value: I


title: S2


title: 287_Nodal-DLBCL-GCB

value: Alive


title: 77AB


title: 76AB


title: P70.163


title: E18.28

value: heterozygous Setd1a mutant


title: 78AB


title: R1


title: 75AB


title: P35.205


title: 284_Nodal-DLBCL-GCB


title: Cow6, 300PA

city: East Lansing

first: G. Andres

last: Contreras

state: MI

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

data_processing:
Data quality control was performed with FastQC v.0.11
After data filtering, clean reads were mapped to the bovine genome
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: bosTau7
Supplementary files format and content: excel xlsx content is fpkm

organism: Bos taurus

source_name: Subcutaneous Adipose Tissue

growth_protocol: Medium containing 10% FBS, 5.85g/500ml Dulbecco’s Modified Eagle’s Medium/F12, 44.05 mM sodium bicarbonate, 100 µM L-Ascorbic acid, 33 µM biotin, 17 µM pantothenate, 2 mM 1% L-glutamine, 1 unit/100 ml antibiotic-antimycotic, 20 mM HEPES, 5 µM troglitazone, 0.5 mmol/L of isobutyl-1-methylaxanthine, 5 μg/mL of insulin, 10 mM acetate, 1 μmol/L of dexamethasone. Isobutyl-1-methylaxanthine and dexamethasone were used only during the first 48 h of adipogenic induction.

extract_protocol:
media was removed, wells were rinsed with 200 µL 1X PBS, then 200 µL of RNA lysis buffer was added. RNA extraction and purification was performed using Maxwell RSC simplyRNA Cells Kit (Promega; AS1390) in the Maxwell Instrument.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

treatment_protocol: Cells were treated during induction and for 4 d or treated for 7 d, 48 h after induction, doing 60% media changes every 48 h. Treatments include basal medium (CON), basal medium supplemented with palmitic acid (PA), oleic acid (OA), or mixture of PA and OA (60-40) at 300µM.

value: Subcutaneous Adipose Tissue

value: Adipocytes

tag: time


title: 291_Nodal-DLBCL-GCB

value: Female


title: Cow6, 60-40


title: P7.19


title: P70.164


title: 289_Nodal-DLBCL-GCB


title: 286_Nodal-DLBCL-GCB


title: 285_Nodal-DLBCL-GCB


title: E18.27


title: Cow6, CON

value: CON


title: 74AB


title: 80AB


title: E14.37


title: R2


title: 283_Nodal-DLBCL-GCB


title: P7.21


title: 281_PB-DLBCL


title: P70.133


title: 71AB


title: Cow5, 60-40


title: P35.213


title: Cow6, 300OA


title: Cow5, 300OA


title: 70AB


title: P35.204


title: 279_PB-DLBCL

value: IE


title: 69AB


title: E18.18


title: Cow5, 300PA


title: Cow4,60-40


title: 280_PB-DLBCL

value: IIE


title: 278_Nodal-DLBCL-GCB


title: Cow5, CON


title: 68AB


title: 277_Nodal-DLBCL-GCB

value: IB


title: Cow4, 300OA


title: 67AB


title: P70.160


title: 73AB


title: Cow4, 300PA


title: 66AB


title: 276_Nodal-DLBCL-GCB

value: IIA


title: P35.196


title: Cow4, CON


title: E18.9


title: 64AB


title: Cow3, 60-40


title: P7.16


title: Cow3, 300OA


title: 63AB


title: 270_PB-DLBCL


title: 272_PB-DLBCL


title: 62AB


title: E18.17


title: E14.36


title: E14.39


title: Cow3, 300PA


title: Cow3, CON


title: 263_Polyostotic-DLBCL

value: IV


title: 61AB


title: 269_PB-DLBCL

value: Male


title: 274_PB-DLBCL


title: P70.159


title: 65AB

value: Kidney (ccRCC)


title: 59AB


title: P35.206

value: WT


title: Cow2, 60-40


title: Cow2, 300OA


title: 254_PB-DLBCL

value: Dead


title: E18.8

value: Frontal cortex


title: 273_PB-DLBCL

value: FFPE


title: 252_Nodal-DLBCL-GCB


title: 250_Nodal-DLBCL-GCB

value: Alive


title: Cow2, 300PA


title: 58AB


title: P7.20


title: Cow2, CON


title: 57AB


title: Cow1, 60-40


title: 55AB


title: 247_Nodal-DLBCL-GCB

value: II


title: P7.4


title: 60AB


title: 54AB


title: E14.21


title: 53AB


title: Cow1, 300OA

value: Subcutaneous Adipose Tissue


title: P7.18


title: 246_Nodal-DLBCL-GCB

value: I


title: 243_PB-DLBCL

value: Female


title: P35.194

value: heterozygous Setd1a mutant


title: 51AB


title: Cow1, CON

value: Adipocytes

value: CON


title: Cow1, 300PA


title: E18.13


title: 50AB


title: A97854

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description:
Moderate-plane of nutrition
A97854_L

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS-UCD1.2) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab delimited txt file of merged gene read counts

source_name: hypothalamic arcuate nucleus

growth_protocol: Holstein-Friesian bull calves were fed differentially either a High plane of nutrition (n=15) or a Moderate plane of nutrition (n=15)  from 2-12 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.0 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
RNA was  precipitated and purified from arcuate nucleus samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates. The Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates.

value: hypothalamic arcuate nucleus

value: Holstein-Friesian

value: Moderate


title: P70.157


title: 49AB


title: A97821

description:
Moderate-plane of nutrition
A97821_L


title: P7.5


title: 48AB


title: 227_Nodal-DLBCL-GCB

value: Male


title: 237_Polyostotic-DLBCL

value: IV


title: 207_Polyostotic-DLBCL


title: 220_Nodal-DLBCL-GCB


title: 214_PB-DLBCL


title: E14.17


title: 47AB

value: Kidney (ccRCC)


title: A73759

description:
Moderate-plane of nutrition
A73759_L


title: P7.10


title: 46AB


title: 206_Nodal-DLBCL-GCB

value: Dead


title: A61973

description:
Moderate-plane of nutrition
A61973_L


title: A61965

description:
Moderate-plane of nutrition
A61965_L


title: 205_Nodal-DLBCL-GCB


title: P35.202

value: Frontal cortex

value: WT


title: E18.12


title: 44AB


title: A57867

description:
Moderate-plane of nutrition
A57867_L


title: 192_Nodal-DLBCL-GCB

value: FFPE

value: Alive


title: 191_Nodal-DLBCL-GCB

value: II


title: 43AB


title: A57826

description:
Moderate-plane of nutrition
A57826_L


title: E14.43


title: A87886

description:
Moderate-plane of nutrition
A87886_L


title: 185_Polyostotic-DLBCL


title: 42AB


title: P7.1


title: E18.11


title: A51980

description:
Moderate-plane of nutrition
A51980_L


title: A47874

description:
Moderate-plane of nutrition
A47874_L


title: A47825

description:
Moderate-plane of nutrition
A47825_L


title: 182_Nodal-DLBCL-GCB


title: 40AB


title: 39AB


title: 45AB


title: 175_Nodal-DLBCL-GCB


title: P35.195


title: 38AB


title: P70.131


title: A41971

description:
Moderate-plane of nutrition
A41971_L


title: P70.158


title: 37AB


title: 171_Nodal-DLBCL-GCB


title: 157_Polyostotic-DLBCL


title: A21978

description:
Moderate-plane of nutrition
A21978_L


title: A37865

description:
Moderate-plane of nutrition
A37865_L


title: 36AB


title: E14.13


title: 35AB


title: 149_Polyostotic-DLBCL


title: 188_PB-DLBCL

value: IXE


title: E14.42


title: 140_PB-DLBCL

value: IE


title: A12937

description:
Moderate-plane of nutrition
A12937_L


title: P7.13


title: 33AB


title: A93760

description:
High-plane of nutrition
A93760_H

value: High


title: E18.10

value: heterozygous Setd1a mutant


title: 32AB


title: 102_PB-DLBCL

value: Female


title: 30AB


title: 94_PB-DLBCL


title: P70.162


title: A92928

description:
High-plane of nutrition
A92928_H

value: hypothalamic arcuate nucleus


title: P35.192


title: A81983

description:
High-plane of nutrition
A81983_H

value: Holstein-Friesian


title: 29AB


title: 93_PB-DLBCL

value: Fresh frozen

value: IIE


title: E14.12


title: 91_PB-DLBCL

value: Male


title: 28AB

value: Kidney (ccRCC)


title: A47858

description:
High-plane of nutrition
A47858_H


title: A77860

description:
High-plane of nutrition
A77860_H


title: Lateral roots, drought stress, miRNA, biol rep 2

city: Poznań

first: Paulina

last: Kościelniak-Wawro

address: Uniwersytetu Poznańskiego 6

department: Faculty of Biology, Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

description:
Library name: LR_DS_S_rep2
Column name in counts_shortstack.csv; LR-DS-2-S

data_processing:
Raw sequencing data underwent rigorous preprocessing, beginning with adapter trimming and quality filtering using Cutadapt, with minimum length thresholds set at 20 nucleotides for mRNA and 15 nucleotides for miRNA. Quality assessment was performed using FastQC, followed by alignment to the Quercus robur PM1N reference genome using HISAT2 for transcriptome data and Bowtie/ShortStack for miRNA analysis.
Assembly: Qrob_PM1N.fa.gz (https://urgi.versailles.inra.fr/download/oak/)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Quercus robur

source_name: root

growth_protocol: The study utilized Quercus robur L. seedlings grown from acorns obtained from the National State Forests' storage facility in Jarocin, Poland. Seedlings were cultivated using two distinct methods: in specialized rhizotron systems consisting of 30 × 50 cm transparent chambers with 2-3 cm spacing between plexiglass plates, and in conventional containers measuring 18 cm deep by 50 mm wide with a volume of 0.275 dm³. Both cultivation systems employed a standardized growth substrate composed of a 5:1 volumetric ratio of peat to perlite, supplemented with dolomite for pH adjustment and a slow-release fertilizer (Osmocote 15-9-12-2 N-P-K-Mg) at a concentration of 2.5 kg/m³. After one year of growth, container-grown seedlings were transplanted into rhizotrons to simulate natural field transplantation conditions. All plants were maintained in a semi-closed foil greenhouse at the Institute of Dendrology, Polish Academy of Sciences in Kórnik, Poland, with an automated irrigation system featuring drainage mechanisms to prevent waterlogging.

extract_protocol:
Meristematic zones from both taproots and lateral roots were collected from all experimental groups (control and drought-stressed plants from both cultivation methods). Total RNA was extracted using Total RNA Purification Kits from Norgen Biotek, followed by additional purification with RNA Clean-Up and Concentration Kits. RNA quality was rigorously assessed through three complementary methods: concentration measurement via Nanodrop spectrophotometry, integrity evaluation by agarose gel electrophoresis, and precise quality scoring using an Agilent 2100 Bioanalyzer, with only samples achieving RNA Integrity Numbers (RIN) greater than 8 proceeding to library construction.
High-quality RNA samples were processed into cDNA libraries using the TruSeq Stranded mRNA LT Sample Prep Kit, followed by sequencing on an Illumina NovaSeq platform configured for 150 bp paired-end reads for transcriptome, 50 bp single-end reads for miRNA and 50 bp single-end reads for degradome. The sequencing strategy encompassed comprehensive profiling of mRNA transcripts, miRNA molecules, and degradome fragments, with a minimum sequencing depth of 20 million reads per sample to ensure robust data acquisition. All library preparations and sequencing runs were performed in triplicate to guarantee experimental reproducibility.

treatment_protocol: Following an 8-week acclimatization period under optimal watering conditions from April to June, transplanted container seedlings were subjected to controlled drought stress for 4 weeks during the peak summer period. The treatment involved reducing soil moisture to 25% of control levels by restricting water availability to the lower quarter of the rhizotron depth, encouraging taproot growth into deeper soil layers. Environmental conditions were meticulously monitored using SM150 soil moisture sensors at 15 cm and 45 cm depths, with surface temperature recorded by HOBO Pro v2 monitoring systems (average temperatures: 23.44°C at soil surface, 20.48°C at 2m height). Plant physiological responses were tracked through daily chlorophyll fluorescence measurements using a Pocket PEA fluorimeter, with particular focus on PSII efficiency parameters (Fo/Fm, Fv/Fm, Fv/Fo) and the comprehensive Performance Index (PI) to determine the onset of severe photosynthetic stress.

value: root

value: wild-type

value: drought stress


title: A42931

description:
High-plane of nutrition
A42931_H


title: 80_Polyostotic-DLBCL

value: IV


title: 77_Polyostotic-DLBCL

value: FFPE

value: Alive


title: 68_PB-DLBCL


title: 26AB


title: Lateral roots, drought stress, miRNA, biol rep 1

description:
Library name: LR_DS_S_rep1
Column name in counts_shortstack.csv; LR-DS-1-S


title: 24AB


title: A93744

description:
High-plane of nutrition
A93744_H


title: A37840

description:
High-plane of nutrition
A37840_H


title: Taproot, drought stress, miRNA, biol rep 3

description:
Library name: TR_DS_S_rep3
Column name in counts_shortstack.csv; TR-DS-3-S


title: A37824

description:
High-plane of nutrition
A37824_H


title: 65_PB-DLBCL


title: 22AB


title: Taproot, drought stress, miRNA, biol rep 1

description:
Library name: TR_DS_S_rep1
Column name in counts_shortstack.csv; TR-DS-1-S


title: 21AB


title: A31979

description:
High-plane of nutrition
A31979_H


title: 54_PB-DLBCL

value: Dead

value: IXE


title: Lateral roots, drought stress, miRNA, biol rep 3

description:
Library name: LR_DS_S_rep3
Column name in counts_shortstack.csv; LR-DS-2-S


title: A27864

description:
High-plane of nutrition
A27864_H

value: High


title: 27AB


title: 20AB


title: 45_Nodal-DLBCL-GCB

value: II


title: A27848

description:
High-plane of nutrition
A27848_H


title: Lateral roots, control condition, miRNA, biol rep 3

description:
Library name: LR_CT_S_rep3
Column name in counts_shortstack.csv; LR-CT-3-S

value: control condition


title: 19AB


title: 44_PB-DLBCL

value: Female

value: IE


title: 40_PB-DLBCL

value: Fresh frozen


title: Lateral roots, control condition, miRNA, biol rep 2

description:
Library name: LR_CT_S_rep2
Column name in counts_shortstack.csv; LR-CT-2-S


title: 67_Polyostotic-DLBCL


title: 18AB


title: A27823

description:
High-plane of nutrition
A27823_H

value: hypothalamic arcuate nucleus

value: Holstein-Friesian


title: 17AB

value: Kidney (ccRCC)


title: Taproot, control condition, miRNA, biol rep 3

description:
Library name: TR_CT_S_rep3
Column name in counts_shortstack.csv; TR-CT-3-S

value: root


title: 38_PB-DLBCL

value: Male

value: IIE


title: A17855

description:
High-plane of nutrition
A17855_H


title: 23AB


title: A13745

description:
High-plane of nutrition
A13745_H


title: 35_PB-DLBCL


title: Taproot, drought stress, miRNA, biol rep 2

description:
Library name: TR_DS_S_rep2
Column name in counts_shortstack.csv; TR-DS-2-S

value: wild-type

value: drought stress


title: 16AB


title: Taproot, control condition, miRNA, biol rep 2

description:
Library name: TR_CT_S_rep2
Column name in counts_shortstack.csv; TR-CT-2-S


title: 32_PB-DLBCL

value: FFPE

value: Alive


title: 15AB


title: CR9-TEN_022_08

city: Katsushika-ku

first: Yuhei

last: Mizunoe

state: Tokyo

address: 6-3-1 Niijuku

department: Department of Medicinal and Life Sciences

country: Japan

institute: Tokyo University of Science

description: Library name: Sample 8

data_processing:
FASTQ files were assessed for quality using FastQC (v0.12.1).
RNA-seq reads were aligned to the Mus musculus reference genome (Ensembl GRCm39) using STAR (v2.7.10b).
Aligned BAM files were indexed using samtools (v1.17).
Read counts were generated using featureCounts (v2.0.3).
Gene expression levels were normalized to TPM based on gene lengths reported by featureCounts.
Assembly: Differentially expressed genes were identified using edgeR (v3.38.4) with an FDR threshold of < 0.05.
Supplementary files format and content: Processed data file was provided as TPM files.
Supplementary files format and content: tab-delimited excel files include TPM values and false discovery ratio (FDR).

source_name: subcutaneous white adipose tissue

extract_protocol:
RNA was harvested using TRIZOL (ThermoFisher/Invitrogen) according to the manufacturer’s protocol.
Standard: 500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420). Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420).

value: subcutaneous white adipose tissue

value: Wild type

value: calorie restriction


title: CR7-TEN_022_07

description: Library name: Sample 7


title: 14AB


title: 31_PB-DLBCL


title: Lateral roots, drought stress, transcriptome, biol rep 3

description: Library name: LR_DS_T_rep3


title: CR3-TEN_022_06

description: Library name: Sample 6


title: Taproot, control condition, miRNA, biol rep 1

description:
Library name: TR_CT_S_rep1
Column name in counts_shortstack.csv; TR-CT-1-S

value: control condition


title: Lateral roots, control condition, miRNA, biol rep 1

description:
Library name: LR_CT_S_rep1
Column name in counts_shortstack.csv; LR-CT-1-S


title: Lateral roots, drought stress, transcriptome, biol rep 2

description: Library name: LR_DS_T_rep2


title: Lateral roots, drought stress, transcriptome, biol rep 1

description: Library name: LR_DS_T_rep1


title: 12AB


title: CR1-TEN_022_05

description: Library name: Sample 5


title: 13AB


title: 21_PB-DLBCL

value: Dead


title: Taproot, drought stress, transcriptome, biol rep 3

description: Library name: TR_DS_T_rep3


title: AL7-TEN_022_04

description: Library name: Sample 4

value: ad libitum


title: 19_PB-DLBCL

value: Female

value: IXE


title: 11AB


title: 17_Polyostotic-DLBCL

value: IV


title: 10AB

value: Kidney (ccRCC)


title: 14_Polyostotic-DLBCL


title: AL5-TEN_022_03

description: Library name: Sample 3


title: Taproot, drought stress, transcriptome, biol rep 2

description: Library name: TR_DS_T_rep2

value: root


title: 9AB


title: AL1-TEN_022_01

description: Library name: Sample 1


title: Taproot, drought stress, transcriptome, biol rep 1

description: Library name: TR_DS_T_rep1


title: 13_PB-DLBCL

value: Male


title: 27_PB-DLBCL

value: Fresh frozen


title: 8AB


title: 12_PB-DLBCL


title: E11.5, CreNeg, Sample 8

city: Rochester

first: Laurie

last: Steiner

state: NY

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

data_processing:
Read alignment with STAR
Read quantification with featureCounts
Differential Expression Analysis with DESeq2
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Erythroblast

growth_protocol: For timed pregnancies, females were monitored for vaginal plugs. The presence of a vaginal plug marked embryonic day 0.5 (E11.5). Embryos were dissected from pregnant females at E11.5.

extract_protocol:
RNA was harvested using the Qiagen Rneasy Kit
Library preparation and sequencing were performed by the University of Rochester Genomics Research Center

value: Erythroblast

value: NCAPH2 +/+


title: Lateral roots, control condition, transcriptome, biol rep 2

description: Library name: LR_CT_T_rep2

value: wild-type


title: E11.5, CreNeg, Sample 6


title: 6AB


title: Lateral roots, control condition, transcriptome, biol rep 1

description: Library name: LR_CT_T_rep1


title: 10_PB-DLBCL

value: FFPE

value: Alive


title: 9_PB-DLBCL

value: IIE


title: 5AB


title: Taproot, control condition, transcriptome, biol rep 3

description: Library name: TR_CT_T_rep3


title: E11.5, CreHet, Sample 4

value: NCAPH2 FL/+ EpoR Cre


title: 4AB


title: AL3-TEN_022_02

description: Library name: Sample 2

value: subcutaneous white adipose tissue

value: Wild type


title: E11.5, CreHet, Sample 1


title: E11.5, CreKO, Sample 5

value: NCAPH2 FL/FL EpoR Cre


title: 8_PB-DLBCL


title: Taproot, control condition, transcriptome, biol rep 2

description: Library name: TR_CT_T_rep2

value: control condition


title: Taproot, control condition, transcriptome, biol rep 1

description: Library name: TR_CT_T_rep1


title: 3AB


title: E11.5, CreKO, Sample 3


title: 2AB


title: Lateral roots, control condition, transcriptome, biol rep 3

description: Library name: LR_CT_T_rep3


title: 7_Polyostotic-DLBCL


title: 6_PB-DLBCL

value: IIXE


title: D120

status: Public on Apr 21 2025

city: Nanjing

first: Zhibo

last: Wang

state: --- Select One ---

address: Tongwei Road, Nanjing City, Jiangsu Province, China

institute: Nanjing agricuture University

description: Library name: sample3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Assembly: Ovis aries Ensembl_release110
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Ovis aries

source_name: Sheep placenta

extract_protocol:
This protocol describes the isolation of frozen tissue nuclei, beginning with pre-cooled reagent preparation including lysis buffer (0.25M sucrose, 5 mM MgAc2, 10 mM Tris-HCl pH 8.0, 1 mM DTT, 0.1 mM EDTA, 1x protease inhibitor, 1U/μl RiboLock RNase Inhibitor), iodixanol solution (0.16M sucrose, 10 mM NaCl₂, 3 mM MgCl₂, 10 mM Tris-HCl pH 7.4, 1U/μl RiboLock RNase Inhibitor, 1mM DTT, 0.1mM PMSF protease inhibitor with adjustable iodixanol concentrations at 30%, 33%, or 50%), and nuclear wash buffer (0.04% BSA, 0.2U/μl RiboLock RNase Inhibitor, 500mM mannitol, 0.1mM PMSF protease inhibitor in PBS). Tissue samples require soybean-sized animal tissues (>0.2g) or plant tissues (>1g) that are blotted dry, minced into 1-2mm³ pieces on ice, flash-frozen in liquid nitrogen for 5 minutes, and stored in ultra-low temperature conditions, with an intact quality control sample separately preserved for RNA integrity verification prior to experiments. The nuclear isolation process involves thawing tissue in lysis buffer within a Dounce homogenizer, sequential grinding with loose and tight pestles (15-20 and 5-10 strokes respectively), filtering through a 70μm strainer, mixing filtrate with 50% iodixanol, followed by layered centrifugation using 33% and 30% iodixanol solutions in 15mL tubes to isolate nuclei through density gradient separation.
ibrary was performed accordina to the manufacter's instructions (sinale cell 3' y2orotocol10xGenomics).Brieflyresuspended in the master mix andI beads into the chip to generate the geoaceo touetnerwitn nanttionInoead_in-emulsion (GEM) The Dolv-A RNAfrom the cell lysate contained in eveny;inale GEM wasretrotranscripted to cDNAan llwmina Ri orme!WMcncontalneseauence, Uniaue Molecular ldentifer (UMl) and the 10x Barcode. The pooledarcoded cDNA was then cleaned uo with Silane DynaBeads, amplified by PCRand the apropiated sized fragments were selected with SPRlselect reagent forsubseauent library construction. During the library construction llumina R2 prime!seauence, paired-end constructs with P5 and P7 seauences and a sample indexwere added

value: Sheep placenta

tag: gestational stage


title: D50

description: Library name: sample1


title: D80

description: Library name: sample2


title: CF d147 Sheep distal lung rep 1

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description:
RNA seq of d147 (birth) CF sheep lung rep1
RNA-seq

data_processing:
Bulk RNA-seq mapped to the sheep (texel, Oar_v4.0) genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Assembly: Texel (ovis aries) sheep genome Oar_v4.0
Supplementary files format and content: Feature assignment of aligned reads to annotated sheep genes in TSV format.

source_name: sheep distal lung epithelial tissue

extract_protocol:
50-100mg of sample was excised from frozen tissue and mixed with 1mL TRIzol Reagent and ceramic beads over ice. Tissue was homogenized and incubated at RT to dissociate the nucleoprotein complex. Solution was then mixed with 200uL chloroform, centrifuged, and the aqueous phase removed. RNA was precipitated with 100% isopropanol, washed with 75% ethanol, and solubilized in water.
RNA concentration and purity were measured by nanodrop and 1ug was used for library preperation.

tag: subject

value: CF donor

value: Day 147 (birth)

tag: sample


title: CF d147 Sheep distal lung rep 2

description:
RNA seq of d147 (birth) CF sheep lung rep2
RNA-seq


title: CF d147 Sheep proximal lung rep 2

source_name: sheep proximal lung epithelial tissue


title: CF d147 Sheep proximal lung rep 1


title: CF d120 Sheep distal lung rep 1

description:
RNA seq of d120 CF sheep lung rep1
RNA-seq

value: Day 120


title: CF d100 Sheep distal lung rep 2

description:
RNA seq of d100 CF sheep lung rep2
RNA-seq

value: Day 100


title: CF d120 Sheep distal lung rep 2

description:
RNA seq of d120 CF sheep lung rep2
RNA-seq


title: CF d80 Sheep distal lung rep 2

description:
RNA seq of d80 CF sheep lung rep2
RNA-seq

value: Day 80


title: CF d65 Sheep distal lung rep 2

description:
RNA seq of d65 CF sheep lung rep2
RNA-seq

value: Day 65


title: CF d80 Sheep distal lung rep 1

description:
RNA seq of d80 CF sheep lung rep1
RNA-seq


title: CF d65 Sheep distal lung rep 1

description:
RNA seq of d65 CF sheep lung rep1
RNA-seq


title: CF d100 Sheep proximal lung rep 2


title: CF d120 Sheep proximal lung rep 2


title: CF d120 Sheep proximal lung rep 1


title: CF d80 Sheep proximal lung rep 2


title: CF d65 Sheep proximal lung rep 2


title: WT d120 Sheep distal lung rep 1

description:
RNA seq of d120 WT sheep lung rep1
RNA-seq

value: healthy donor


title: CF d65 Sheep proximal lung rep 1


title: 5_Polyostotic-DLBCL

value: Male

tag: tissue

value: FFPE

value: IV


title: WT d100 Sheep distal lung rep 1

description:
RNA seq of d100 WT sheep lung rep1
RNA-seq


title: WT d120 Sheep distal lung rep 2

description:
RNA seq of d120 WT sheep lung rep2
RNA-seq


title: WT d100 Sheep distal lung rep 2

description:
RNA seq of d100 WT sheep lung rep2
RNA-seq


title: WT d80 Sheep distal lung rep 1

description:
RNA seq of d80 WT sheep lung rep1
RNA-seq


title: WT d147 Sheep distal lung rep 2

description:
RNA seq of d147 (birth) WT sheep lung rep2
RNA-seq


title: WT d65 Sheep distal lung rep 1

description:
RNA seq of d65 WT sheep lung rep1
RNA-seq


title: CF d100 Sheep distal lung rep 1

description:
RNA seq of d100 CF sheep lung rep1
RNA-seq


title: WT d147 Sheep proximal lung rep 1

description:
RNA seq of d147 (birth) WT sheep lung rep1
RNA-seq


title: WT d120 Sheep proximal lung rep 1


title: WT d80 Sheep distal lung rep 2

description:
RNA seq of d80 WT sheep lung rep2
RNA-seq


title: WT d100 Sheep proximal lung rep 2


title: WT d100 Sheep proximal lung rep 1


title: WT d65 Sheep proximal lung rep 2

description:
RNA seq of d65 WT sheep lung rep2
RNA-seq


title: CF d100 Sheep proximal lung rep 1


title: WT d147 Sheep proximal lung rep 2


title: WT d65 Sheep proximal lung rep 1


title: Rat si080-DV25PG5 10 nM REP1

first: Gengshen

last: Song

state: Beijing

address: No. 6, Hongda ZhongLu, Beijing Economic-Technological Development Area

institute: Beijing Youcare Kechuang Pharmaceutical Technology Co., Ltd.

description: Library name: R42-1

data_processing:
Raw RNAseq reads were trimmed and filtered using Trimmomatic software. Filtered reads were aligned to human or rat genomes using HISAT2 and expression was quantified using StringTie. Differentially expressed genes were analyzed using DESeq.
Assembly: hg38/rn6
Supplementary files format and content: .xls file containing ENSEMBL gene id, Mean TPM, log2FoldChange, p value and q value

organism: Rattus norvegicus

source_name: primary hepatocyte

extract_protocol:
Hepatocytes were cultured for 48 h before being harvested with TRIzol (Invitrogen, 15596018CN) according to manufacturer's instructions.
RNA extracted from TRIzol was used for cDNA library preparation using the Hieff mRNA Library Prep Kit (Yeasen, 12309ES08) and sequenced on a HiSeq sequencer (Illumina), according to the manufacturer’s instructions.

value: primary hepatocyte


title: Rat si080-DV25PG5 10 nM REP2

description: Library name: R42-2


title: WT d80 Sheep proximal lung rep 2


title: Rat si080-DV25PG5 10 nM REP3

description: Library name: R42-3


title: Rat si080-DV25PG5 100 nM REP2

description: Library name: R41-2


title: Rat si080-DV25PG5 100 nM REP3

description: Library name: R41-3


title: Rat si080-DV25PG5 100 nM REP1

description: Library name: R41-1


title: WT d65 Sheep distal lung rep 2


title: Rat si097-DV29PG5 10 nM REP3

description: Library name: R32-3


title: Rat si097-DV29PG5 1 nM REP2

description: Library name: R33-2


title: WT d120 Sheep proximal lung rep 2


title: Rat si097-DV29PG5 10 nM REP2

description: Library name: R32-2


title: Rat si097-DV29PG5 1 nM REP3

description: Library name: R33-3


title: Rat si097-DV29PG5 10 nM REP1

description: Library name: R32-1


title: Rat si097-DV29PG5 100 nM REP3

description: Library name: R31-3


title: Rat si060-DV25Pd7BG5 1 nM REP3

description: Library name: R23-3


title: Rat si097-DV29PG5 100 nM REP1

description: Library name: R31-1


title: Rat si060-DV25Pd7BG5 1 nM REP2

description: Library name: R23-2


title: WT d80 Sheep proximal lung rep 1


title: Rat si097-DV29PG5 100 nM REP2

description: Library name: R31-2


title: Rat si060-DV25Pd7BG5 10 nM REP2

description: Library name: R22-2


title: Rat si060-DV25Pd7BG5 10 nM REP1

description: Library name: R22-1


title: Rat si060-DV25Pd7BG5 100 nM REP3

description: Library name: R21-3


title: Rat si060-DV25Pd7BG5 100 nM REP2

description: Library name: R21-2


title: Rat Zilebesiran 1 nM REP2

description: Library name: R13-2


title: Rat Zilebesiran 1 nM REP1

description: Library name: R13-1


title: Rat Zilebesiran 1 nM REP3

description: Library name: R13-3


title: Rat Zilebesiran 10 nM REP3

description: Library name: R12-3


title: Rat Zilebesiran 10 nM REP1

description: Library name: R12-1


title: Rat Zilebesiran 10 nM REP2

description: Library name: R12-2


title: Rat si097-DV29PG5 1 nM REP1

description: Library name: R33-1


title: Rat Zilebesiran 100 nM REP3

description: Library name: R11-3


title: Rat Zilebesiran 100 nM REP2

description: Library name: R11-2


title: Rat si060-DV25Pd7BG5 1 nM REP1

description: Library name: R23-1


title: Rat Zilebesiran 100 nM REP1

description: Library name: R11-1


title: Rat si060-DV25PG5 1 nM REP2

description: Library name: R73-2


title: Rat Control REP2

description: Library name: RNC-2


title: Rat Control REP1

description: Library name: RNC-1


title: Rat si060-DV25PG5 1 nM REP3

description: Library name: R73-3


title: Rat Control REP3

description: Library name: RNC-3


title: Rat si060-DV25PG5 1 nM REP1

description: Library name: R73-1


title: Rat si060-DV25PG5 10 nM REP1

description: Library name: R72-1


title: Rat si060-DV25PG5 10 nM REP3

description: Library name: R72-3


title: Rat si060-DV25PG5 100 nM REP3

description: Library name: R71-3


title: Rat si060-DV25Pd7BG5 10 nM REP3

description: Library name: R22-3


title: Rat si060-DV25PG5 100 nM REP2

description: Library name: R71-2


title: Rat si060-DV25Pd7BG5 100 nM REP1

description: Library name: R21-1


title: Rat si060-DV25PG5 100 nM REP1

description: Library name: R71-1


title: Rat si060-DV25PG5 10 nM REP2

description: Library name: R72-2


title: Rat si061-DV27PG5 1 nM REP3

description: Library name: R63-3


title: Rat si061-DV27PG5 1 nM REP1

description: Library name: R63-1


title: Rat si061-DV27PG5 1 nM REP2

description: Library name: R63-2


title: Rat si061-DV27PG5 10 nM REP3

description: Library name: R62-3


title: Rat si061-DV27PG5 10 nM REP2

description: Library name: R62-2


title: WT d147 Sheep distal lung rep 1


title: Rat si061-DV27PG5 100 nM REP3

description: Library name: R61-3


title: Rat si061-DV27PG5 100 nM REP2

description: Library name: R61-2


title: Rat si098-DV29Pd7BG5 1 nM REP3

description: Library name: R53-3


title: Rat si098-DV29Pd7BG5 1 nM REP2

description: Library name: R53-2


title: Rat si098-DV29Pd7BG5 1 nM REP1

description: Library name: R53-1


title: Rat si098-DV29Pd7BG5 10 nM REP3

description: Library name: R52-3


title: Rat si098-DV29Pd7BG5 100 nM REP2

description: Library name: R51-2


title: Rat si098-DV29Pd7BG5 100 nM REP3

description: Library name: R51-3


title: Rat si098-DV29Pd7BG5 10 nM REP1

description: Library name: R52-1


title: Rat si098-DV29Pd7BG5 100 nM REP1

description: Library name: R51-1


title: Rat si080-DV25PG5 1 nM REP3

description: Library name: R43-3


title: Rat si080-DV25PG5 1 nM REP2

description: Library name: R43-2


title: ZMC-Vab3A-5-3

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v1.8.4
FastQ files were mapped using Tophat v.2.1.0 (parameters: -x 1 --no-coverage-search --no-convert-bam --no-novel-juncs --no-novel-indels -T –transcriptome-index=$TRANSCRIPTOME_INDEX $REFERENCE_DNA_TOPLEVEL)
Counting of reads per gene was done using featureCounts: v1.5.0 (parameters:  -s 0 -a $ANNOTATION)
RPKMs were calculated based on the gene length given by featureCounts.
Assembly: Ensembl (WBcel235.85)
Supplementary files format and content: Excel sheet (xlsx) containing counts, RPMs and RPKMs

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol–chloroform (isoamyl pH4) extraction method (Phenol:Chloroform:Iso-amyl alcohol (125:24:1), Sigma).
Libraries were prepared using the TruSeq RNA library preparation kit v2 (Illumina) following the manufacturer's instructions.

treatment_protocol: Synchronized young adult worms were treated with empty vector (L4440), vab-3a and vab-3c RNAis and collected at 5 days of adulthood

value: whole worm

value: hermaphrodite

value: 5 days

value: RNAi Vab3 isof A/N2


title: ZMC-Vab3A-5-2


title: ZMC-Vab3C-5-3

value: RNAi Vab3 isof C/N2


title: ZMC-Vab3C-5-2


title: ZMC-Vab3A-5-1


title: ZMC-Vab3C-5-1


title: Rat si061-DV27PG5 10 nM REP1

description: Library name: R62-1


title: ZMC-Control-5-3

value: RNAi L4440/N2


title: prp21-ABA_PolII_rep2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

description: Library name: Sample 8

library_source: genomic

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C for 14 d.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

treatment_protocol: The Arabidopsis seedlings were grown on MS with 0.1 mM ABA for 14d.

value: Arabidopsis seedlings

tag: condition

value: abscisic acid

tag: chip antibody

value: Millipore, 05-623


title: ZMC-Control-5-1


title: prp21_PolII_rep2

description: Library name: Sample 6

tag: genotype


title: prp21-ABA_PolII_rep1

description: Library name: Sample 7

tag: cell type


title: WT-ABA_PolII_rep2

description: Library name: Sample 4

value: wild type


title: Rat si061-DV27PG5 100 nM REP1

description: Library name: R61-1


title: WT_PolII_rep2

description: Library name: Sample 2


title: prp21_14day_RNAseq_rep2

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

source_name: Arabidopsis thaliana

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 2, 7, or 14 days old, under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 2, 7, or 14 days old Arabidopsis plants with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).

value: Arabidopsis thaliana


title: WT-ABA_PolII_rep1

description: Library name: Sample 3


title: WT_PolII_rep1

description: Library name: Sample 1


title: Rat si098-DV29Pd7BG5 10 nM REP2

description: Library name: R52-2


title: WT_14day_RNAseq_rep2


title: prp21_14day_RNAseq_rep1


title: Rat si080-DV25PG5 1 nM REP1

description: Library name: R43-1


title: prp21_7day_RNAseq_rep2


title: WT_14day_RNAseq_rep1


title: sam-UTD-DN0106-DRGL-S5-1

city: Richardson

first: Theodore

last: Price

state: Texas

address: 800 W. Campbell Road

department: Neuroscience

institute: The University of Texas at Dallas

description:
Library name: sam-UTD-DN0106-DRGL-S5-1
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.

data_processing:
Raw data were processed with the 10X SpaceRanger pipeline
Assembly: GRCh38.p10 and GRCh38.p13
Supplementary files format and content: raw and filtered gene counts matrices, cloupe files for !0x loupe browser, barcode positions/coordinates, csv file of annotated barcodes
Library strategy: Spatial Transcriptomics

source_name: dorsal root ganglia

extract_protocol:
Human DRGs were collected from neurologically dead organ donors through a collaboration with the Southwest Transplant Alliance or from AnaBios
Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain.

value: dorsal root ganglia

tag: batch


title: sam-UTD-DN0106-DRGL-S5-2

description:
Library name: sam-UTD-DN0106-DRGL-S5-2
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: prp21_7day_RNAseq_rep1


title: sam-UTD-DN0095-DRGL3-S2-1

description:
Library name: sam-UTD-DN0095-DRGL3-S2-1
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: sam-UTD-DN0095-DRGL3-S2-3

description:
Library name: sam-UTD-DN0095-DRGL3-S2-3
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: sam-UTD-DN0095-DRGL3-S2-2

description:
Library name: sam-UTD-DN0095-DRGL3-S2-2
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: WT_7day_RNAseq_rep2


title: sam-UTD-DN0134-DRGL3-S1-3

description:
Library name: sam-UTD-DN0134-DRGL3-S1-3
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: WT_7day_RNAseq_rep1


title: prp21_2day_RNAseq_rep2


title: sam-UTD-DN0134-DRGL3-S1-2

description:
Library name: sam-UTD-DN0134-DRGL3-S1-2
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: WT_2day_RNAseq_rep2


title: prp21_PolII_rep1

description: Library name: Sample 5


title: sam-UTD-DN0134-DRGL3-S1-1

description:
Library name: sam-UTD-DN0134-DRGL3-S1-1
Human DRGs were collected within 4 hrs of cross-clamp from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: prp21-ABA_RNAseq_rep2


title: prp21_2day_RNAseq_rep1


title: WT_2day_RNAseq_rep1


title: CF d80 Sheep proximal lung rep 1

description:
RNA seq of d80 CF sheep lung rep1
RNA-seq

value: CF donor

value: Day 80


title: W3, DGA treated, biol rep1

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Library name: W3_DGA_01

data_processing:
Concatenated base call files (.cbcl) generated from the sequencing run were converted to a FASTQ file for each sample by the DRAGEN BCL Convert pipeline. The .cbcl files were further analyzed by the DRAGEN RNA pipeline to generate transcript quantification results at the gene level (.quant.genes.sf).
Assembly: Human reference genome hg38-alt-aware
Supplementary files format and content: Files in .sf format containing transcript quantification results at the gene level.

growth_protocol: Human iPSCs were maintained as single-cell cultures (no colony formation) on COAT-1 pre-coated 6-well tissue culture plates in the Cellartis DEF-CS Culture System (Takara Bio USA, San Jose, CA) at 37˚C in a humidified incubator supplied with 5% CO2. Hepatocyte differentiation from the iPSC lines were conducted using the Cellartis iPS Cell to Hepatocyte Differentiation System (Takara Bio USA), and instructions from the manufacturer were followed.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.
Sequencing libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit (San Diego, CA) following protocols provided by the manufacturer.

treatment_protocol: Hepatocytes differentiated from iPSCs on day 23 were exposed to 3.0 mM DGA or 10.0 μM UA in duplicate (n = 2) for 24 h.

tag: ethnicity

value: NHW

value: iPSC-derived hepatocytes

tag: treatment

value: DGA


title: W3, DGA treated, biol rep2

description: Library name: W3_DGA_02


title: prp21-ABA_RNAseq_rep1


title: W3, control, biol rep2

description: Library name: W3_CTL_02

value: control


title: W3, UA treated, biol rep1

description: Library name: W3_UA_01

value: UA


title: prp21_RNAseq_rep2


title: prp21_RNAseq_rep1


title: W3, UA treated, biol rep2

description: Library name: W3_UA_02


title: WT-ABA_RNAseq_rep2


title: W3, control, biol rep1

description: Library name: W3_CTL_01


title: W2, UA treated, biol rep1

description: Library name: W2_UA_01


title: WT_RNAseq_rep2


title: WT-ABA_RNAseq_rep1


title: prp21-ABA_PATseq_rep1

data_processing:
Basecalling performed using bcl2fastq.
Poly(A) strings were removed and aligned to TAIR10 using STAR.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 14 days old, under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 14-day-old Arabidopsis plants with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing).


title: prp21-ABA_PATseq_rep2


title: W2, control, biol rep2

description: Library name: W2_CTL_02


title: W2, DGA treated, biol rep1

description: Library name: W2_DGA_01


title: W2, DGA treated, biol rep2

description: Library name: W2_DGA_02


title: prp21_PATseq_rep2


title: W2, control, biol rep1

description: Library name: W2_CTL_01


title: W1, UA treated, biol rep2

description: Library name: W1_UA_02


title: W1, UA treated, biol rep1

description: Library name: W1_UA_01


title: WT-ABA_PATseq_rep2


title: W1, DGA treated, biol rep1

description: Library name: W1_DGA_01


title: WT-ABA_PATseq_rep1


title: W1, DGA treated, biol rep2

description: Library name: W1_DGA_02


title: prp21_PATseq_rep1


title: WT_PATseq_rep1


title: Urticaral rash of SCAN02_4

city: Kyoto

first: Naotomo

last: Kambe

state: Kyoto

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Dermatology

institute: Kyoto University

description: Spatial Transcriptomics

data_processing:
Spatial transcriptome analysis was outsourced, using the Xenium Human Skin Gene Expression Panel and a custom probe (J6KP72) created based on scRNA-seq analysis of peripheral blood neutrophils, selecting the top 60 genes specifically expressed in IL1B-positive and IL1B-negative cells, respectively
The analysis was performed following the manufacturer's protocol.

source_name: FFPE

extract_protocol: In two cases, SCAN01 and SCAN02, skin biopsies were performed at two distinct sites using 6 mm punch biopsies prior to canakinumab administration. The samples were formalin-fixed, paraffin-embedded, and sectioned onto Xenium-compatible slides.

value: urticarial rash

tag: disease state

value: Schnitzler syndrome


title: L3, UA treated, biol rep2

description: Library name: L3_UA_02

value: LOH


title: Urticaral rash of SCAN02_3

description: Spatial Transcriptomics


title: W1, control, biol rep2

description: Library name: W1_CTL_02


title: W2, UA treated, biol rep2

description: Library name: W2_UA_02


title: W1, control, biol rep1

description: Library name: W1_CTL_01


title: L3, UA treated, biol rep1

description: Library name: L3_UA_01


title: L3, DGA treated, biol rep2

description: Library name: L3_DGA_02


title: Urticaral rash of SCAN02_2

description: Spatial Transcriptomics


title: Urticaral rash of SCAN02_1

description: Spatial Transcriptomics


title: WT_RNAseq_rep1


title: L3, DGA treated, biol rep1

description: Library name: L3_DGA_01


title: L3, control, biol rep2

description: Library name: L3_CTL_02


title: Urticaral rash of SCAN01_5

description: Spatial Transcriptomics


title: Urticaral rash of SCAN01_4

description: Spatial Transcriptomics


title: L3, control, biol rep1

description: Library name: L3_CTL_01


title: L2, UA treated, biol rep2

description: Library name: L2_UA_02


title: L2, UA treated, biol rep1

description: Library name: L2_UA_01


title: Urticaral rash of SCAN01_3

description: Spatial Transcriptomics


title: Urticaral rash of SCAN01_2

description: Spatial Transcriptomics


title: Urticaral rash of SCAN01_1

description: Spatial Transcriptomics


title: L2, DGA treated, biol rep2

description: Library name: L2_DGA_02


title: WT_PATseq_rep2


title: L2, DGA treated, biol rep1

description: Library name: L2_DGA_01


title: L2, control, biol rep1

description: Library name: L2_CTL_01


title: L2, control, biol rep2

description: Library name: L2_CTL_02


title: 4T1 TILs, PEG+PBS, TCR

city: New York

first: Eric Minwei

last: Liu

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: C4T1T_S1
10X Genomics

data_processing:
Single-cell RNA-seq data were aligned to the mouse genome (mm10) and subjected to initial filtering using Cell Ranger v 6.0.1 with default parameters. The feature matrix generated by Cell Ranger was used to perform downstream analysis using R toolkit Seurat (v.4.3.0.1). Cells containing fewer than 500 or more than 40,000 unique molecular identifiers, or more than 25% of reads mapping to mitochondrial genes were removed from consideration. Cell doublets were removed by Scrublet (v.0.2.3). The filtered cell-gene matrix was log-normalized and scaled with default Seurat parameters. 2,000 most variable features (genes) were found using FindVariableFeatures with ‘vst’ option for selection.method. Then, dimensionality reduction using principal component analysis (PCA) was performed for these genes. Clustering was performed on the chosen principal components using the shared nearest neighbor algorithm as implemented in Seurat, with top 10 (30 for T cell sub-clustering) dimensions and resolution of 0.2. The clusters were visualized using the Uniform Manifold Approximation and Projection (UMAP) algorithm. Marker genes for each cluster were identified with Seurat’s function FindAllMarkers (with default parameters and expression fold-change threshold of log2(1.2)(log2(0.5) for T cell sub-clustering).TCR chain assembly was performed using the Cell Ranger pipeline, with default parameters. Cells with low confidence or nonproductive TCR clonotypes were filtered out, specifically only the clonotypes exhibiting both a single alpha chain and a single beta chain were retained for cell assignment.
Assembly: mouse genome (mm10)
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

source_name: Breast tumor

growth_protocol: 4T1 cells were cultured in RPMI-1640 (Thermo Fisher Scientific, Cat.# 11875–119) with 10% FBS (Gemini Bio-products, Cat.# 100–106) and 1X penicillin-streptomycin (Thermo Fisher Scientific, Cat.# 15140122).

extract_protocol:
Fresh 4T1 tumors treated with PEG+PBS or PEG+ADU-S100 were pooled (n=4 per group) and mechanically and enzymatically disaggregated in dissociation buffer consisting of DMEM full media + 100 U/mL collagenase type IV and 50 μg/mL DNase I. Suspension cells were incubated at 37°C for 45 minutes and then further mechanically dissociated. Red blood cells were removed before Live/Dead staining (Biolegend, Cat.# 423111) and Fc blocking. Cells were then stained with antibodies specific for mouse CD45 (Biolegend, Cat.# 103106) and mouse CD3 (Biolegend, Cat.# 100219). Samples were washed and sorted using a BD FACS Melody instrument to isolate viable CD45+ and CD3+ cells. Cells were then washed and assessed for viability. 16,500 cells per condition were loaded onto a 10X Chromium instrument (10X Genomics) per the manufacturer’s instructions.
Single-cell RNA and TCR libraries were generated using the Chromium Single Cell 5′ Library Construction (10X Genomics, Cat.# PN-1000190) and Chromium Single Cell Mouse TCR Amplification kits (10X Genomics, Cat.# PN-1000254) per user guide. Quality control of the completed libraries was performed using the Bioanalyzer High Sensitivity DNA Kit (Agilent, Cat.# 5067–4626) and then sequenced using the Illumina NovaSeq platform.

treatment_protocol: Balb/c mice were inoculated with 100K 4T1 cells followed by PEG with PBS or 100 µg ADU-S100 implantation on Day 6 when tumor volumes reached 75 mm3. On Day 14 after PEG implantation, tumors were harvested and pooled (n=4 per group). We then sorted CD45+ cells by Fluorescence-activated cell sorting (FACS) and performed scRNAseq/TCRseq.

value: Breast tumor

value: CD45+ TILs

value: PEG+PBS


title: 4T1 TILs, PEG+ADU, TCR

description:
Library name: X4T1T_S1
10X Genomics


title: 4T1 TILs, PEG+ADU, Whole Transcriptome

description:
Library name: X4T1G_S1
10X Genomics

data_processing:
Single-cell RNA-seq data were aligned to the mouse genome (mm10) and subjected to initial filtering using Cell Ranger v 6.0.1 with default parameters. The feature matrix generated by Cell Ranger was used to perform downstream analysis using R toolkit Seurat (v.4.3.0.1). Cells containing fewer than 500 or more than 40,000 unique molecular identifiers, or more than 25% of reads mapping to mitochondrial genes were removed from consideration. Cell doublets were removed by Scrublet (v.0.2.3). The filtered cell-gene matrix was log-normalized and scaled with default Seurat parameters. 2,000 most variable features (genes) were found using FindVariableFeatures with ‘vst’ option for selection.method. Then, dimensionality reduction using principal component analysis (PCA) was performed for these genes. Clustering was performed on the chosen principal components using the shared nearest neighbor algorithm as implemented in Seurat, with top 10 (30 for T cell sub-clustering) dimensions and resolution of 0.2. The clusters were visualized using the Uniform Manifold Approximation and Projection (UMAP) algorithm. Marker genes for each cluster were identified with Seurat’s function FindAllMarkers (with default parameters and expression fold-change threshold of log2(1.2)(log2(0.5) for T cell sub-clustering).TCR chain assembly was performed using the Cell Ranger pipeline, with default parameters. Cells with low confidence or nonproductive TCR clonotypes were filtered out, specifically only the clonotypes exhibiting both a single alpha chain and a single beta chain were retained for cell assignment.
Assembly: mouse genome (mm10)
Supplementary files format and content: Tab-separated values files and matrix files


title: L1, UA treated, biol rep1

description: Library name: L1_UA_01


title: 4T1 TILs, PEG+PBS, Whole Transcriptome

description:
Library name: C4T1G_S1
10X Genomics


title: L1, UA treated, biol rep2

description: Library name: L1_UA_02


title: Urticaral rash of SCAN01_6

description: Spatial Transcriptomics


title: L1, DGA treated, biol rep1

description: Library name: L1_DGA_01


title: L1, control, biol rep2

description: Library name: L1_CTL_02


title: L1, control, biol rep1

description: Library name: L1_CTL_01


title: L1, DGA treated, biol rep2

description: Library name: L1_DGA_02


title: C01428

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

description: Library name: Sample 192

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software and sample-specific barcodes to give a FASTQ file for each sample
bcl2fastq2 v2.20 for demultiplexing
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
fastq files were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: templated oligo sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

source_name: liver

extract_protocol:
Mounted, unstained FFPE liver samples were scraped from the slides and processed according to the TempO-Seq® protocol by BioSpyder Technologies
TempO-Seq® protocol by BioSpyder Technologies

treatment_protocol: This study consisted of four arms based on chemical treatment: HFPO-DA (chemical of interest), GW7647 (prototypical PPARa agonist), rosiglitazone (prototypical PPARg agonist), and APAP (prototypical cytotoxic agent). Male mice from each of the three strains (i.e., J:ARC(S), B6129SF2/J, PPARa KO) were randomly allocated based on body weight to each dose group (vehicle control, low, medium, or high) within each study arm (n = 4/dose/strain/arm). Dosing solutions of HFPO-DA, GW7647, and rosiglitazone were administered via oral gavage at a dose volume of 10 mL/kg body weight once per day for five days. The doses were as follows: 0, 3, 15, or 30 mg/kg-d HFPO-DA; 0, 5, 10, or 20 mg/kg-d GW7647; and 0, 5, 10, or 20 mg/kg-d rosiglitazone. APAP was administered to 12-hour fasted mice as a single intraperitoneal (IP) injection at 0, 150, 300, or 600 mg/kg. Feed was restored immediately after APAP dosing and mice were sacrificed 6 hours post-dose. Following the last treatment, mice were euthanized by CO2 anesthesia and exsanguination. Livers were fixed in 10% neutral-buffered formalin, embedded in paraffin (FFPE), and sections approximately 4 – 6 µm in thickness were mounted to glass slides.

value: liver

tag: strain

value: male

value: WT

tag: exposure route

value: oral

tag: exposure duration

value: 5 days

value: 600 mg/kg APAP


title: B3, UA treated, biol rep2

description: Library name: B3_UA_02

value: BAA

tag: cell line


title: B3, UA treated, biol rep1

description: Library name: B3_UA_01

value: iPSC-derived hepatocytes


title: B3, DGA treated, biol rep2

description: Library name: B3_DGA_02

value: DGA


title: C01425

description: Library name: Sample 189

tag: Sex


title: Mouse 161 PBMCs, PEG+PBS, TCR (M6TCR)

description:
Library name: M6TCR_CKDL220025331-1A_HMLG2DSX5_S10
10X Genomics

data_processing:
Single-cell RNA-seq data were aligned to the mouse genome (mm10). After initial filtering with default parameters, the feature matrix generated by Cell Ranger v 6.0.1. was used to perform downstream analysis using R toolkit Seurat (v.4.3.0.1). Cells containing fewer than 1000 unique molecular identifiers with more than 15% of mitochondrial gene content were removed from consideration. Cell doublets were removed by Scrublet (v.0.2.3). The filtered cell-gene matrix was log-normalized and scaled with default Seurat parameters. 3,000 variable features (genes) were found using FindVariableFeatures with ‘vst’ option for selection.method. Then, dimensionality reduction using principal component analysis (PCA) was performed on the 3,000 variable genes. Clustering was performed on the chosen principal components using the shared nearest neighbor algorithm as implemented in Seurat, with top 10 dimensions and resolution of 0.2. The clusters were visualized using the Uniform Manifold Approximation and Projection (UMAP) algorithm. Marker genes for each cluster were identified with Seurat’s function FindAllMarkers (with default parameters and expression fold-change threshold of log2(1.2)). TCR chain assembly was performed using the Cell Ranger pipeline, with default parameters. Cells with low confidence or nonproductive TCR clonotypes were filtered out, specifically only the clonotypes exhibiting both a single alpha chain and a single beta chain were retained for cell assignment.
Assembly: mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

source_name: Peripheral blood

extract_protocol:
Whole blood was spun at 1000 g for 10 min to collect the buffy coat followed by red blood cell lysis. Cells were then washed and assessed for viability. 16,500 cells per condition were loaded onto a 10X Chromium instrument (10X Genomics) per the manufacturer’s instructions.
Single-cell RNA and TCR libraries were generated using the Chromium Single Cell 5′ Library Construction (10X Genomics, Cat.# PN-1000190) and Chromium Single Cell Mouse TCR Amplification kits (10X Genomics, Cat.# PN-1000254) per user guide. Quality control of the completed libraries was performed using the Bioanalyzer High Sensitivity DNA Kit (Agilent, Cat.# 5067–4626) and then sequenced using the Illumina NovaSeq platform.

treatment_protocol: Balb/c mice were inoculated with 10K 4T1 cells followed by PEG with PBS or 100 µg ADU-S100 implantation on Day 4. On Day 30, another PEG marker with PBS or 100 µg ADU-S100 was implanted. We then collected peripheral blood from one mouse in each group on Day 50 and performed scRNAseq/TCRseq.

value: Peripheral blood

value: PBMCs

value: wild type


title: Mouse 161 PBMCs, PEG+PBS, Whole Transcriptome (M6GEX)

description:
Library name: M6GEX_CKDL220025327-1A_HMLG2DSX5_S4
10X Genomics

data_processing:
Single-cell RNA-seq data were aligned to the mouse genome (mm10). After initial filtering with default parameters, the feature matrix generated by Cell Ranger v 6.0.1. was used to perform downstream analysis using R toolkit Seurat (v.4.3.0.1). Cells containing fewer than 1000 unique molecular identifiers with more than 15% of mitochondrial gene content were removed from consideration. Cell doublets were removed by Scrublet (v.0.2.3). The filtered cell-gene matrix was log-normalized and scaled with default Seurat parameters. 3,000 variable features (genes) were found using FindVariableFeatures with ‘vst’ option for selection.method. Then, dimensionality reduction using principal component analysis (PCA) was performed on the 3,000 variable genes. Clustering was performed on the chosen principal components using the shared nearest neighbor algorithm as implemented in Seurat, with top 10 dimensions and resolution of 0.2. The clusters were visualized using the Uniform Manifold Approximation and Projection (UMAP) algorithm. Marker genes for each cluster were identified with Seurat’s function FindAllMarkers (with default parameters and expression fold-change threshold of log2(1.2)). TCR chain assembly was performed using the Cell Ranger pipeline, with default parameters. Cells with low confidence or nonproductive TCR clonotypes were filtered out, specifically only the clonotypes exhibiting both a single alpha chain and a single beta chain were retained for cell assignment.
Assembly: mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: C01424

description: Library name: Sample 188

value: 300 mg/kg APAP


title: Mouse 173 PBMCs, PEG+ADU, TCR (M7TCR)

description:
Library name: M7TCR_CKDL220025332-1A_HMLG2DSX5_S13
10X Genomics


title: Mouse 173 PBMCs, PEG+ADU, Whole Transcriptome (M7GEX)

description:
Library name: M7GEX_CKDL220025328-1A_HMLG2DSX5_S18
10X Genomics


title: B3, control, biol rep2

description: Library name: B3_CTL_02

value: control


title: C01423

description: Library name: Sample 187


title: C01422

description: Library name: Sample 186


title: B3, control, biol rep1

description: Library name: B3_CTL_01


title: B2, UA treated, biol rep2

description: Library name: B2_UA_02

value: UA


title: C01421

description: Library name: Sample 185


title: S. aureus, FPSS, B

city: bangkok

first: Sirirak

last: Supa-amornkul

address: 272 Payatai

department: Microbiology

country: Thailand

institute: Mahidol University

description: Raw_count_sample2, column D

data_processing:
.sff file from Ion torrent machine was convert to fastq file by sff2fastq code
FastQC program was obtain for determine quality of output sequence
GetSpecificLengthRead.cpp was use for trimmed the sequence before process
EDGE-pro was obtained to detemine transcriptome between two stain forL. monocytogenes
RPKM data from EDGE-pro was compare the expression level by Microsoft Excel progem
Assembly: NC_017544.1
Supplementary files format and content: (.xlsx) excel file include RPKM values for each Sample

organism: Staphylococcus aureus RF122

growth_protocol: S. aureus strain RF122 was used as a wild type strain (WT) in this study. In routine growth condition, both of WT and DsigB were cultured in tryptic soy medium at 37°C with 200 rpm.

extract_protocol:
RNAprotect (Qiagen) was then added to bacterial cultures to stop cellular activity and to stabilize RNA.  RNA was extracted using TRIzol (Invitrogen) followed by RNeasy Mini kit (Qiagen).
RNA libraries for RNAseq were prepared using Ovation® Complete Prokaryotic RNA-Seq Library System

treatment_protocol: 32 µM of FPSS was used to determine the effect on sigmaB regulon of S. aureus


title: B2, UA treated, biol rep1

description: Library name: B2_UA_01


title: S. aureus, FPSS, A

description: Raw_count_sample1, column C


title: S. aureus, FPSS, C

description: Raw_count_sample3 column E


title: C01419

description: Library name: Sample 183

value: 150 mg/kg APAP


title: B2, DGA treated, biol rep2

description: Library name: B2_DGA_02


title: C01426

description: Library name: Sample 190


title: C01427

description: Library name: Sample 191


title: B2, control, biol rep2

description: Library name: B2_CTL_02


title: B3, DGA treated, biol rep1

description: Library name: B3_DGA_01


title: C01418

description: Library name: Sample 182


title: C01417

description: Library name: Sample 181


title: 2032, A.japonica infected, 12hr, biological replicate 3

city: Saint Louis

first: Jennette

last: Codjoe

state: Missouri

address: 1005 N Warson Rd, Suite 305

institute: CoverCress Inc.

description:
Library name: Library 45
Column title in read_counts_raw_all_samples.csv: Aj_C12_2032_3

data_processing:
Reads cleaned with fastp software. Removed adapters and reads with N > 10% or reads containing >50% low quality bases (Qphred ≤ 5).
Cleaned reads aligned to Tarvense_v2 genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 used to count reads mapped to each gene.
Assembly: GenBank assembly GCA_911865555.2
Supplementary files format and content: csv file contains raw read counts for each sample

organism: Thlaspi arvense

source_name: rosette leaf

extract_protocol:
Sclerotinia sclerotiorum samples: Total RNA isolated by NucleoSpin Plant RNA Kit (Machery-Nagel). Alternaria japonica samples: Total RNA isolated by E.Z.N.A. Plant RNA Kit (Omega Bio-tek). 1ug total RNA used for library preparation.
Libraries prepared by NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer's instructions for polyA mRNA enrichment.

value: rosette leaf

tag: time

value: 12 hours

value: mock


title: 2032, Sclerotinia infected, 12hr, biological replicate 2

description:
Library name: Library 41
Column title in read_counts_raw_all_samples.csv: Aj_I12_2032_2

value: Alternaria japonica


title: 2032, mock (for A.japonica infection), 6hr, biological replicate 2

description:
Library name: Library 38
Column title in read_counts_raw_all_samples.csv: Aj_C6_2032_2

value: 6 hours


title: 2032, Sclerotinia infected, 12hr, biological replicate 1

description:
Library name: Library 40
Column title in read_counts_raw_all_samples.csv: Aj_I12_2032_1


title: 2032, mock (for A.japonica infection), 6hr, biological replicate 3

description:
Library name: Library 39
Column title in read_counts_raw_all_samples.csv: Aj_C6_2032_3


title: C01416

description: Library name: Sample 180

value: liver

value: male

value: WT

value: oral

value: 5 days

value: 0 mg/kg APAP


title: 2032, Sclerotinia infected, 12hr, biological replicate 3

description:
Library name: Library 42
Column title in read_counts_raw_all_samples.csv: Aj_I12_2032_3


title: 2032, A.japonica infected, 12hr, biological replicate 2

description:
Library name: Library 44
Column title in read_counts_raw_all_samples.csv: Aj_C12_2032_2


title: C01415

description: Library name: Sample 179


title: 2032, mock (for A.japonica infection), 6hr, biological replicate 1

description:
Library name: Library 37
Column title in read_counts_raw_all_samples.csv: Aj_C6_2032_1


title: B2, control, biol rep1

description: Library name: B2_CTL_01

value: BAA

value: iPSC-derived hepatocytes


title: B1, UA treated, biol rep1

description: Library name: B1_UA_01


title: B1, UA treated, biol rep2

description: Library name: B1_UA_02


title: C01420

description: Library name: Sample 184


title: C01414

description: Library name: Sample 178


title: B2, DGA treated, biol rep1

description: Library name: B2_DGA_01

value: DGA


title: 2032, A.japonica infected, 6hr, biological replicate 1

description:
Library name: Library 34
Column title in read_counts_raw_all_samples.csv: Aj_I6_2032_1


title: B1, DGA treated, biol rep2

description: Library name: B1_DGA_02


title: 2032, A.japonica infected, 6hr, biological replicate 2

description:
Library name: Library 35
Column title in read_counts_raw_all_samples.csv: Aj_I6_2032_2


title: 2032, A.japonica infected, 12hr, biological replicate 1

description:
Library name: Library 43
Column title in read_counts_raw_all_samples.csv: Aj_C12_2032_1


title: C01413

description: Library name: Sample 177


title: MN106, A.japonica infected, 12hr, biological replicate 2

description:
Library name: Library 32
Column title in read_counts_raw_all_samples.csv: Aj_C12_MN106_2


title: MN106, A.japonica infected, 12hr, biological replicate 3

description:
Library name: Library 33
Column title in read_counts_raw_all_samples.csv: Aj_C12_MN106_3


title: C01412

description: Library name: Sample 176

value: 600 mg/kg APAP


title: B1, control, biol rep2

description: Library name: B1_CTL_02

value: control


title: MN106, Sclerotinia infected, 12hr, biological replicate 3

description:
Library name: Library 30
Column title in read_counts_raw_all_samples.csv: Aj_I12_MN106_3


title: MN106, A.japonica infected, 12hr, biological replicate 1

description:
Library name: Library 31
Column title in read_counts_raw_all_samples.csv: Aj_C12_MN106_1


title: C01411

description: Library name: Sample 175


title: MN106, Sclerotinia infected, 12hr, biological replicate 2

description:
Library name: Library 29
Column title in read_counts_raw_all_samples.csv: Aj_I12_MN106_2


title: B1, control, biol rep1

description: Library name: B1_CTL_01


title: MN106, Sclerotinia infected, 12hr, biological replicate 1

description:
Library name: Library 28
Column title in read_counts_raw_all_samples.csv: Aj_I12_MN106_1


title: MN106, mock (for A.japonica infection), 6hr, biological replicate 2

description:
Library name: Library 26
Column title in read_counts_raw_all_samples.csv: Aj_C6_MN106_2


title: C01410

description: Library name: Sample 174