title: YC-5

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description: Library name: YC_5

data_processing:
Initial evaluation of the quality of raw RNA-seq fastq file was conducted utilizing FASTQC (v0.12.1).
The BBduk module within the bbmap toolkit (v39.80) was conducted with specific parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=t, trimq=10, and minlength=20 to eliminate adapter sequences and low-quality reads.
The cleaned reads were mapped to the mouse reference genome (build GRCm39, Ensembl release 115) through the STAR aligner (v2.7.10b)
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) along with the gene structure file (GRCm39.115.gtf).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

source_name: Ovary

growth_protocol: Eight- and 38-week-old BALB/c female mice were purchased from the Central Lab. Animal Inc.(Seoul, Korea). All mice were maintained on an ad libitum diet in a specific pathogen-free room under a 12-hour light-dark cycle. All animal handling and experimental procedures were approved by the Korea Institute of Oriental Medicine Institutional Animal Care and Use Committee (approval number 25-057).

extract_protocol:
After four weeks of compound administration, a post-ovulatory state was induced by intraperitoneal injection of 5 IU PMSG followed 48 h later by 5 IU hCG. Ovaries were collected 16-18h after hCG administration, weighed, and immediately preserved in liquid nitrogen until RNA extraction.  Each ovary sample was immersed in 1 mL  TRIzol reagent (Invitrogen) and homogenized using a disposable grinder (Biomasher II; 890863; LMS Co., Tokyo, Japan).
Total RNA was isolated using Trizol reagent (Invitrogen). The quality of purity and integrity of the extracted RNA samples were analyzed using a NanoDrop ND-2000 Spectrophotometer (Thermo Inc., DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). RNA library was constructed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. The compound administration experiment was conducted in two independent animal experimental batches. Each batch included 14 compound-treated groups and corresponding young control (YC) and old control (OC) groups. Mice in both batches followed the same treatment schedule, post-ovulatory induction procedure, and ovary collection protocol. RNA extraction, library preparation, and sequencing were performed together for all samples. Batch assignment is indicated in the sample metadata.

treatment_protocol: Mice were randomly divided into groups of n=3 each. Aged mice (38 weeks old) were orally administered either distilled water containing 0.5% Dimethyl sulfoxide (DMSO; D2650; Sigma-Aldrich, St. Louis, MO, USA) or each of the 28 single compounds at a dose of 5 mg/kg, five times a week for four weeks.

value: Ovary

value: Wildtype

value: DMSO

tag: batch

value: Batch 2

tag: strain

value: BALB/c


title: YC-6

status: Public on Jul 06 2026

type: SRA

description: Library name: YC_6

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: YC-4

description: Library name: YC_4


title: PA1766-1

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1766.xlsx

data_processing:
RNA-seq reads were mapped to the Pseudomonas aeruginosa (NC_002516.2) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Assembly: Pseudomonas aeruginosa (NC_002516.2)
Supplementary files format and content: xlsx files were generated from RNA-seq, containing the differential expressional genes.

molecule: polyA RNA

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

growth_protocol: RNA-seq(LB)

extract_protocol:
The Pseudomonas aeruginosa PAO1 wild type strain and the HP mutants were inoculated into LB with corresponding antibiotics overnight cultured at 37 °C. Then the strains were one hundred times diluted into fresh LB. Before harvested, the P. aeruginosa strains were cultured for 3 h until OD600 to 0.6, at 37 °C with 220 rpm shaking. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4 °C). RNA extraction was performed by using the TianGen RNA extraction kit with the recommended DNase digestion. After removing rRNA by following the RiboRid protocol, mRNA was used to construct the cDNA library according to the NEBNext Ultra II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina).
NEBNext UltraTM II RNA Library Prep Kit protocol

treatment_protocol: grow until mid-log phase

value: Pseudomonas aeruginosa PAO1

value: PA1766 mutant

value: grow until mid-log phase in LB


title: artificial insemination 32 days, sample 4

type: RNA

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

hyb_protocol: Hybridization to the Affymetrix® miRNA 4.1 Array strips was carried out at 48ºC for 20 hours

scan_protocol: GeneAtlas® System (Affymetrix)

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Transcriptome Analysis Console (TAC) 4.0.1 (Thermo Fisher Scientific Co.) using the Robust Multi-array Average (RMA) algorithm

label: biotin

organism: Bos taurus

source_name: artificial insemination 32 days

label_protocol: Total RNA (500 ng/sample) was labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific Co.), according to the manufacturer’s instructions

growth_protocol: Samples were kept in RNAlater (Thermo Fisher Scientific®) before RNA extraction

extract_protocol: Total RNA was extracted using the miRVana kit from Thermo Fisher Scientific Co.

treatment_protocol: Animal handling and sample collection were conducted at the Experimental Station Hildegard Georgina Von Pritzelwiltz in Londrina, PR, Brazil, with approval from the Animal Research Ethics Committee of ESALQ/USP (Protocol #2018.5.1252.11.5, CEUA nº 2018-21). Non-lactating Nelore cows (Bos taurus indicus) with an average body condition score (BCS) of 3.0 ± 0.04 were selected and synchronized using a timed-AI protocol with estradiol benzoate. Artificial insemination (AI) and in vitro embryo production (IVF) were performed using semen from a single Angus bull (Bos taurus taurus). On day 0, cows in the AI group were inseminated, while embryos were transferred to the IVF group on day 6.5. Slaughter took place on days 18 and 32 after AI and on days 12 and 26 post-embryo transfer (IVF group), representing key periods for maternal recognition (18 days) and early placental attachment (32 days). After slaughter, the reproductive tracts were immediately removed and kept on ice. On day 18, uterine horns were flushed with a saline solution to confirm pregnancy by embryo presence; on day 32, pregnancy was diagnosed via ultrasonography one day prior. Uterine fluid from 16 cows was collected and centrifuged to isolate extracellular vesicles, classified by size and concentration for AI and IVF on days 18 and 32. Samples from day 18 of the estrous cycle served as controls. These samples were kept in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. RNA extraction was performed using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific®), according to manufacturer’s instructions.Microarray was conducted with 16 samples (n=4 treatment/grup).

value: extracellular vesicles


title: YC-3

description: Library name: YC_3

value: Batch 1


title: YC-2

description: Library name: YC_2


title: PA1531-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1531.xlsx

value: PA1531 mutant


title: artificial insemination 32 days, sample 3


title: YC-1

description: Library name: YC_1


title: artificial insemination 32 days, sample 2


title: PA1531-1


title: Tribolium_NBs rep 8

city: Göttingen

first: Noel

last: Cabañas

address: (GZMB) Justus-von-Liebig-Weg 11

department: Evolutionary Developmental Genetics

country: Germany

institute: University of Göttingen

description:
Library name: TcastGFP8
10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were analyzed following the standard CellRanger pipelines (7.1.0). First, we used “cellranger mkref” to build a custom reference genome giving as input the Tribolium castaneum genome (Tcas5.2) and the transcriptome (OGS3) that included the tGFP sequence. To perform sequence alignment and produce the count matrices, we used “cellranger count” with the FASTQ files and the custom reference genome. The resulting matrices were aggregated with “cellranger aggr”. Data analyses such as quality control of the counts, integration and diffrential expression analysis were performed using the toolkit Scanpy, scvi-tools, and PyDESeq2 respectively.
Assembly: Tribolium castaneum genome (Tcas5.2) and the transcriptome (OGS3) that included the tGFP sequence
Supplementary files format and content: h5ad binary files containing the raw counts, and tab-separated file containing cell annotation metadata

organism: Tribolium castaneum

source_name: Embryonic neuroblasts

growth_protocol: Adult Tribolium beetles were reared at 32 °C with 40 percent humidity in whole-grain flour type 1050 and transferred to wheat flour type 450 for embryo collections

extract_protocol:
We collected 35-50 hours old embryos of Tribolium and transferred them into a washing basket. We washed the embryos several times in Milli-Q water, and subsequently dechorionated the embryos with 5% bleach for 3 minutes under constant shaking. We washed the embryos extensively with Milli-Q water. Henceforth, we kept all solutions, tubes, and embryos on ice. Using a paintbrush, we transferred the embryos into a 2 mL dounce homogenizer prefilled with 1 mL of Schneider’s medium mixed with 1% BSA. We then mechanically dissociated the embryos by using approximately 15 strokes of the pestle A. We decanted the homogenate into a 1.5 mL vial and centrifuged it at 50g for 3 minutes at 4 °C to remove chunks of tissue. We decanted the supernatant into a new 1.5 mL vial and centrifuged it at 300g for three minutes at 4 °C. We discarded the supernatant and resuspended the pellet in one milliliter of Schneider’s medium mixed with 1% BSA. We filtered the suspension with a 20 μm cell strainer coated with a thin layer of 1% BSA and centrifuged again for three minutes at 4°C. Finally, the cell pellet was resuspended in 50 μL of cold Schneider’s medium mixed with 1% BSA supplemented with 0.8% protector RNase-inhibitor and 1x Protease Inhibitor Cocktail. Using a cell sorter SH800S cells were sorted for one hour. To set the gating parameters for FACS, we used unstained cell suspensions from wild-type Tribolium embryos as a negative control and DAPI stained wild-type embryos to set the gating for live versus dead cells. Once the gating parameters were set, we started by analyzing all events in our samples stained with DAPI using the forward scatter (FSC-A) and the side scatter (BSC-A) without gating. We then gated using forward scatter (FSC-A) and side scatter (FSC-W) to discard doublets. We then created a third plot using forward scatter (FSC-A) and fluorescent (DAPI), selecting DAPI-negative cells. Finally, these selected events were plotted again using phycoerythrin (PE) versus fluorescent (GFP) to exclude auto-fluorescent cells and to identify a small cell population of highly GFP-fluorescent cells. We sorted the highly GFP-fluorescent cells into a centrifuge tube coated and prefilled with 50 μL of ice-cold Schneider’s medium mixed with 1% BSA.
We generated single-cell RNA libraries using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 and a 10x Chromium controller (10x Genomics) following the manufacturer’s protocol instructions. The resulting cDNA libraries were quantified using a bioanalyzer and sequenced in an Illumina NextSeq 2000 Sequencing Systems (Illumina, Inc.) to an average depth of 50,000 reads per cell.

treatment_protocol: No treatment

value: Embryonic neuroblasts

tag: cell type

value: Neuroblasts

value: turbo GFP

tag: developmental stage

value: Embryo

tag: age

value: 35-50 hours


title: OC-6

description: Library name: OC_6


title: Tribolium_NBs rep 7

description:
Library name: TcastGFP7
10x Genomics


title: OC-5

description: Library name: OC_5


title: PA1527-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1527.xlsx

value: PA1527 mutant


title: artificial insemination 32 days, sample 1


title: Tribolium_NBs rep 6

description:
Library name: TcastGFP6
10x Genomics


title: artificial insemination 18 days, sample 4

source_name: artificial insemination 18 days


title: PA1527-1


title: OC-4

description: Library name: OC_4

value: Ovary


title: Tribolium_NBs rep 5

description:
Library name: TcastGFP5
10x Genomics


title: artificial insemination 18 days, sample 3


title: PA1518-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1518.xlsx

value: PA1518 mutant


title: OC-3

description: Library name: OC_3

value: Wildtype

value: DMSO


title: Tribolium_NBs rep 4

description:
Library name: TcastGFP4
10x Genomics


title: artificial insemination 18 days, sample 2


title: PA1518-1


title: OC-2

description: Library name: OC_2

value: BALB/c


title: Tribolium_NBs rep 3

description:
Library name: TcastGFP3
10x Genomics


title: artificial insemination 18 days, sample 1


title: PA1427-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1427.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA1427 mutant


title: OC-1

description: Library name: OC_1


title: liver, DIO Rosuva+GGOH 5

city: NEW YORK

first: Lale

last: Ozcan

state: NY

address: 630 West 168th Street, Black Building: 9-905, Molecular Medicine

country: USA

institute: COLUMBIA UNIVERSITY

description: Library name: LY20

data_processing:
Base calling was performed using Illumina RTA, and BCL files were converted to FASTQ format using bcl2fastq2 (v2.19) with adapter trimming. Reads were pseudoaligned to the mouse reference transcriptome (GRCm38) using kallisto (v0.44.0). Gene-level estimated counts and TPM values were generated using the tximport R package. Differential gene expression analysis was performed using DESeq2
Assembly: GRCm38/mm10
Supplementary files format and content: Processed data consist of tab-delimited text files containing gene-level estimated counts (est_counts_genes_kallisto.txt) and gene-level TPM values (tpm_values_genes_kallisto.txt) generated from kallisto pseudoalignment and summarized using tximport. Rows correspond to genes and columns correspond to individual biological samples.

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was isolated from mouse liver. Poly(A)+ RNA was enriched from total RNA by poly(A) selection, followed by library preparation using the Illumina TruSeq RNA library preparation protocol. Libraries were multiplexed and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 100-bp reads.

value: Liver

value: WT

value: Rosuvastatin+GGOH


title: Tribolium_NBs rep 2

description:
Library name: TcastGFP2
10x Genomics


title: PA1427-1

value: grow until mid-log phase in LB


title: OC + Benzoic acid-3

description: Library name: C74_3

value: Benzoic acid

value: Batch 2


title: liver, DIO Rosuva+GGOH 4

description: Library name: LY19


title: Tribolium_NBs rep 1

description:
Library name: TcastGFP1
10x Genomics

value: Embryonic neuroblasts

value: Neuroblasts

value: turbo GFP


title: PA1412-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1412.xlsx

value: PA1412 mutant


title: OC + Benzoic acid-2

description: Library name: C74_2

value: Ovary


title: liver, DIO Rosuva+GGOH 3

description: Library name: LY18


title: PA1412-1


title: ypk2D cells, fluconazole, rep3

city: Iowa City

first: Scott

last: Moye-Rowley

state: Iowa

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

department: Molecular Physiology & Biophysics

institute: University of Iowa

description:
Library name: ypk2_fluconazole_3
7C2KRB_24

data_processing:
FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1.
Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Alignment to the appropriate reference genome using STAR aligner v2.7.* with non-canonical splice junction removal and output of unmapped reads.
Coordinate sorting of BAM files using samtools v1.21.
UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0.
Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RustQC v0.2.1.
Generation of comprehensive QC report using MultiQC v1.33.
Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation.
Assembly: GCA000002545v2_62
Supplementary files format and content: Excel spreadsheet cpm values for each sample
Supplementary files format and content: Normalized counts per million for each condition

organism: Nakaseomyces glabratus

growth_protocol: Isogenic wild-type and ypk2 null cells were grown in YPD medium (yeast extract 1%, peptone 2%, glucose 2%) )

extract_protocol:
Six OD600 units of cells were pelleted from each pre- and post-treatment culture, fixed in Trizol (Invitrogen), and total RNA was purified using a RNeasy Mini Kit (Qiagen).
Library construction and sequencing carried out by Plasmidsaurus as per their standard protocols.

treatment_protocol: Drug treatments were carried out as: (1) 16 µg/ml fluconazole for three hours, (2) 0.25 µg/ml amphotericin B for one hour, and (3) 50 ng/ml caspofungin for one hour.

tag: cell line

value: "KKY2001 ypk2D::HIS3MX6"


title: liver, DIO Rosuva+GGOH 2

description: Library name: LY17


title: OC + Benzoic acid-1

description: Library name: C74_1

value: Wildtype


title: ypk2D cells, fluconazole, rep2

description:
Library name: ypk2_fluconazole_2
7C2KRB_23


title: PA1392-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1392.xlsx

value: PA1392 mutant


title: OC + 4-hydroxybenzoic acid-3

description: Library name: C73_3

value: p-hydroxy benzoic acid (4-hydroxybenzoic acid)

value: BALB/c


title: liver, DIO Rosuva+GGOH 1

description: Library name: LY16


title: ypk2D cells, fluconazole, rep1

description:
Library name: ypk2_fluconazole_1
7C2KRB_22


title: PA1392-1

value: Pseudomonas aeruginosa PAO1


title: OC + 4-hydroxybenzoic acid-2

description: Library name: C73_2


title: ypk2D cells, amphotericin B, rep3

description:
Library name: ypk2_AmB_3
7C2KRB_21


title: liver, DIO GGOH 5

description: Library name: LY15

value: Liver

value: GGOH


title: OC + 4-hydroxybenzoic acid-1

description: Library name: C73_1


title: PA1367-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1367.xlsx

value: PA1367 mutant


title: liver, DIO GGOH 4

description: Library name: LY14

value: WT


title: ypk2D cells, amphotericin B, rep2

description:
Library name: ypk2_AmB_2
7C2KRB_20


title: PA1367-1

value: grow until mid-log phase in LB


title: OC + Protocatechuic acid-3

description: Library name: C72_3

value: Protocatechuic acid

value: Batch 2


title: ypk2D cells, amphotericin B, rep1

description:
Library name: ypk2_AmB_1
7C2KRB_19


title: liver, DIO GGOH 2

description: Library name: LY12


title: OC + Protocatechuic acid-2

description: Library name: C72_2


title: liver, DIO GGOH 3

description: Library name: LY13


title: PA1332-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1332.xlsx

value: PA1332 mutant


title: ypk2D cells, caspofungin, rep3

description:
Library name: ypk2_caspofungin_3
7C2KRB_18


title: PA1332-1


title: liver, DIO GGOH 1

description: Library name: LY11


title: OC + Protocatechuic acid-1

description: Library name: C72_1


title: ypk2D cells, caspofungin, rep2

description:
Library name: ypk2_caspofungin_2
7C2KRB_17


title: PA1228-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1228.xlsx

value: PA1228 mutant


title: OC + Isoferulic acid-3

description: Library name: C71_3

value: Isoferulic acid


title: liver, DIO Rosuvastation 5

description: Library name: LY10

value: Rosuvastatin


title: ypk2D cells, caspofungin, rep1

description:
Library name: ypk2_caspofungin_1
7C2KRB_16

value: "KKY2001 ypk2D::HIS3MX6"


title: PA1228-1


title: OC + Isoferulic acid-2

description: Library name: C71_2

value: Ovary

value: Wildtype


title: liver, DIO Rosuvastation 4

description: Library name: LY9


title: ypk2D cells, pretreatment, rep3

description:
Library name: ypk2_pretreat_3
7C2KRB_15


title: liver, DIO Rosuvastation 3

description: Library name: LY8


title: OC + Isoferulic acid-1

description: Library name: C71_1


title: PA1210-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1210.xlsx

value: PA1210 mutant


title: ypk2D cells, pretreatment, rep2

description:
Library name: ypk2_pretreat_2
7C2KRB_14


title: OC + Vanillic acid-3

description: Library name: C70_3

value: Vanillic acid

value: BALB/c


title: liver, DIO Rosuvastation 2

description: Library name: LY7

value: Liver


title: PA1210-1

value: Pseudomonas aeruginosa PAO1


title: ypk2D cells, pretreatment, rep1

description:
Library name: ypk2_pretreat_1
7C2KRB_13


title: PA1208-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1208.xlsx

value: PA1208 mutant


title: liver, DIO Rosuvastation 1

description: Library name: LY6

value: WT


title: OC + Vanillic acid-2

description: Library name: C70_2


title: Wild-type cells, fluconazole, rep3

description:
Library name: WT_FLU_3
7C2KRB_12

value: his3::FRT leu2::FRT trp1::FRT


title: PA1208-1

value: grow until mid-log phase in LB


title: OC + Vanillic acid-1

description: Library name: C70_1

value: Batch 2


title: liver, DIO control (vehicle) 5

description: Library name: LY5

value: vehicle


title: Wild-type cells, fluconazole, rep2

description:
Library name: WT_FLU_2
7C2KRB_11


title: PA1206-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1206.xlsx

value: PA1206 mutant


title: OC + Gallic acid-3

description: Library name: C69_3

value: Gallic acid


title: liver, DIO control (vehicle) 4

description: Library name: LY4


title: Wild-type cells, fluconazole, rep1

description:
Library name: WT_FLU_1
7C2KRB_10


title: PA1206-1


title: OC + Gallic acid-2

description: Library name: C69_2


title: Wild-type cells, amphotericin B, rep3

description:
Library name: WT_AmB_3
7C2KRB_9


title: liver, DIO control (vehicle) 3

description: Library name: LY3


title: PA1197-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1197.xlsx

value: PA1197 mutant


title: OC + Gallic acid-1

description: Library name: C69_1


title: liver, DIO control (vehicle) 2

description: Library name: LY2


title: PA1197-1


title: Wild-type cells, amphotericin B, rep2

description:
Library name: WT_AmB_2
7C2KRB_8


title: OC + Rotundic acid-3

description: Library name: C68_3

value: Rutundic acid, Rotundic acid


title: liver, DIO control (vehicle) 1

description: Library name: LY1


title: Wild-type cells, amphotericin B, rep1

description:
Library name: WT_AmB_1
7C2KRB_7


title: PA1190-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1190.xlsx

value: PA1190 mutant


title: OC + Rotundic acid-2

description: Library name: C68_2

value: Ovary

value: Wildtype


title: Wild-type cells, caspofungin, rep3

description:
Library name: WT_Caspo_3
7C2KRB_6


title: PA1190-1


title: DG of mice at 14 days post random foot shocks

city: Shanghai

first: changfei

last: tang

address: No. 1 Banxia Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: Random-14d

data_processing:
All raw reads were processed using Cell Ranger (version 8.0.1) with default parameters and aligned to the standard mouse genome GRCm39 (mm39). Gene-barcode matrices were generated by counting UMIs and filtering non-cell associated barcodes. Downstream data analysis was conducted on Seurat (version 5.4.0). Cells with < 200 detected genes, < 0.8 log10GenesPerUMI, or > 5% mitochondrial gene expression were excluded. Potential doublets or multiplets were identified and further removed via DoubletFinder (version 2.0.4)1. Data were normalized and variable genes were identified. Data set integration across samples was performed using harmony (version 1.2.0)2. Dimensionality reduction was conducted using PCA (top 20 components) followed by UMAP and t-SNE visualization. Clustering was performed using the Louvain method on shared nearest neighbor graphs. Cell types were identified manually with known marker genes with Wilcoxon Rank-Sum Test for differential expression analysis. Astrocytes from scRNA-seq, granule cells and mossy cells from snRNA-seq were subsequently selected for further analysis.
Assembly: GRCm39
Supplementary files format and content: Processed data files include a gene expression matrix in Matrix Market format (matrix.mtx.gz), along with accompanying gene annotation (features.tsv.gz) and cell barcode (barcodes.tsv.gz) files for each sample.

source_name: DG area of the brain

extract_protocol:
For sc-RNA-seq, tissues were minced and dissociated using 0.1% Type I Collagenase (Sigma, C0130) and 10 μg/mL DNase I (Sigma, 11284932001) in PBS with 5% FBS at 37°C with shaking (50 r.p.m.) for 40 min, with intermediate collection every 20 min. Cell suspensions were filtered (40 μm) and treated with Red Blood Cell Lysis Solution (Thermo Fisher, 00-4333-57). For single nucleus sequencing, the nuclear fraction was isolated from frozen tissue specimens using the Shbio Nuclei Isolation Kit (SHBIO, #52009-10, China) following standardized procedures. Tissue samples were rapidly homogenized in chilled lysis buffer using a mechanical tissue disruptor until complete liquefaction was achieved. The resulting homogenate was filtered through a 40 μm nylon mesh to remove cellular debris and particulate matter, followed by centrifugation at 500 × g for 5 minutes at 4°C to pellet nuclei. Subsequent density gradient separation was performed by sequential addition of PB1, PB2, and PB3 solutions (as defined by the Shbio Nuclei Isolation Kit protocol), with intact nuclei accumulating at the PB2-PB3 interface. Isolated nuclei were gently resuspended in 50 μL of NB buffer using pipette mixing and quantified using an automated cell counting system (Thermo Fisher Scientific, USA).
For sc-RNA-seq, cDNA synthesis, barcoding, and library preparation were performed using the Chromium Next GEM Single Cell 3' Kit according to manufacturer's protocol (CG000731). Libraries were quantified using High Sensitivity DNA Chip (Agilent) and Qubit High Sensitivity DNA Assay (Thermo Fisher), then sequenced on NovaSeq 6000 (Illumina) with 2×150 bp chemistry.  For single-nucleus RNA sequencing, purified nuclei were processed immediately using the Chromium Single Cell 3' Library and Gel Bead Kit v3 (10X Genomics, USA) on a Chromium Controller instrument (10X Genomics, USA) for single-nucleus barcoding and cDNA synthesis. Library preparation was conducted according to the manufacturer's standardized protocol, with final sequencing performed on an Illumina NovaSeq 6000 platform (Illumina, USA) to generate high-throughput sequencing data.

value: DG area of the brain

value: random foot shocks


title: OC + Rotundic acid-1

description: Library name: C68_1

value: BALB/c


title: Wild-type cells, caspofungin, rep2

description:
Library name: WT_Caspo_2
7C2KRB_5


title: DG of mice at 14 days post-CFC training

description: Library name: CFC-14d

value: CFC training


title: PA1110-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1110.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA1110 mutant


title: OC + Asiatic acid-3

description: Library name: C67_3

value: Asiatic Acid


title: Wild-type cells, caspofungin, rep1

description:
Library name: WT_Caspo_1
7C2KRB_4

value: his3::FRT leu2::FRT trp1::FRT


title: DG of naive wild-type mice

description: Library name: WT-naïve

molecule: nuclear RNA

value: WT


title: PA1110-1

value: grow until mid-log phase in LB


title: DG of wild-type (WT) mice at 14 days post-CFC training

description: Library name: WT-CFC


title: PA1009-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1009.xlsx

value: PA1009 mutant


title: Wild-type cells, pretreatment, rep3

description:
Library name: WT_pretreat_3
7C2KRB_3


title: OC + Asiatic acid-1

description: Library name: C67_1

value: Batch 2


title: PA1009-1


title: Wild-type cells, pretreatment, rep2

description:
Library name: WT_pretreat_2
7C2KRB_2


title: Dentate gyrus (DG) of Csf2rb2-knockout mice at 14 days post-CFC training

description: Library name: KO-CFC


title: OC + Tetramethoxyflavanone7,3',4'5'-3

description: Library name: C66_4


title: Wild-type cells, pretreatment, rep1

description:
Library name: WT_pretreat_1
7C2KRB_1


title: scD3Blastoid

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway

institute: University of Texas at Austin

description:
Library name: scD3Blastoid
WT mouse ES, Gata3-Low, and Gata3-H aggregated to form synthetic embryos (blastoids) and cultured until Day 3. Blastoids were dissociated into FACS-sorted based on fluorescence markers

data_processing:
Data was processed with CellRanger from 10X genomics
Assembly: mm10
Supplementary files format and content: HDF5 (Hierarchical Data Format) and TAR/GZ (containing MEX format; matrix, barcodes, features)

source_name: Embryo

growth_protocol: Gata3-L, Gata3-H, and WT cells were aggregated. Blastoid was cultured for three days under continuous Dox treatment, then FACS sorted based on fluorescence tag (mCherry, GFP, mTagBFP2, respectively)

extract_protocol:
Samples were prepared using the 10X Genomics Chromium Single Cell Gene Expression Flex (Fixed RNA Profiling)
Library was prepared by University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF) following Chromium Next GEM Single Cell Gene Expression Flex user guide

value: Embryo

value: Mouse embryonic stem cell

value: WT mouse ES cells, Gata3-L, and Gata3-H cells with 1 day of pre-induction, followed by 2 days of post-induction upon aggregation


title: PA0952-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0952.xlsx

value: PA0952 mutant


title: OC + Tetramethoxyflavanone7,3',4'5'-2

description: Library name: C66_3

value: Ovary

value: Wildtype


title: PA0952-1


title: KKK_P12_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA78928

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-read mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.3.5.1.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1 .
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: retina

extract_protocol:
Freshly isolated mouse retinas were lysed in TRIzol Reagent for RNA extraction following the manufacturer's protocol.
RNA libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: retina

value: Panky-/-;Panky-like-/-;Nrl-/-


title: AJ CCR5/CG unt d15 3

city: Cleveland

first: Karen

last: Keslar

state: OH

address: 9500 Euclid Avenue NB30

institute: Cleveland Clinic

description: transplanted kidney

hyb_protocol: RNA was hybridized to the mouse Fibrosis panel following manufacturer's instructions

data_processing: Data was processed using the online Rosalind platform

source_name: kidney

extract_protocol: RNA was isolated with Qiagen RNeasy mini kit

tag: treatment group

value: AJ CCR5/CG unt d15


title: OC + Tetramethoxyflavanone7,3',4'5'-1

description: Library name: C66_2

value: BALB/c


title: KKK_P12_2

description: Library name: GA78927


title: PA0781-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0781.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA0781 mutant


title: OC + Riboflavin-3

description: Library name: C63_3

value: Riboflavin


title: AJ CCR5/CG unt d15 2

description: transplanted kidney


title: KKK_P12_1

description: Library name: GA78926


title: PA0781-1


title: OC + Riboflavin-2

description: Library name: C63_2


title: AJ CCR5/CG unt d15 1

description: transplanted kidney


title: HHK_P12_3

description: Library name: GA78925

value: Panky+/-;Panky-like+/-;Nrl-/-


title: PA0713-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0713.xlsx

value: PA0713 mutant

value: grow until mid-log phase in LB


title: AJ CCR5 unt d15 3

description: transplanted kidney

value: AJ CCR5 unt d15


title: 11_9h_CPG1

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

description: Library name: Sample11

data_processing:
Reads were quality-checked using FastQC v0.11.5 and trimmed using fastx_trimmer (FASTX Toolkit v0.0.14).
Adapter sequences, rRNA contamination, and ambiguous reads were removed using Trimmomatic v0.38, RNAdust v1.06, and removeN (Moirai).
Filtered reads were aligned to the UCSC mm39 genome assembly using BWA v0.7.10, and unmapped reads were subsequently aligned using HISAT2 v2.1.0.
CAGE peaks and transcription start sites (TSSs) were identified using PromoterPipeline (Kouno et al. 2019) and assigned to nearby genes (Deviatiiarov et al. 2023). Enhancers were predicted based on CAGE signal directionality and linked to promoters as described previously (Andersson et al. 2014).
Assembly: mm39
Supplementary files format and content: Tables with coordinates, assigned genes, and read counts (raw or TPM normalized) for promoters and enhancers

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow cells were isolated from femurs and tibias of C57BL/6 mice and cultured for 7 days in DMEM supplemented with 10% fetal calf serum (FCS), 1× non-essential amino acids, 1 mM sodium pyruvate, 100 U/mL penicillin–streptomycin, and 0.05 µM 2-mercaptoethanol. Macrophage differentiation was induced by macrophage colony-stimulating factor (M-CSF, 10 U/mL) supplied through conditioned medium from human M-CSF–expressing L929 cells. To induce M2-like polarization, BMDMs were treated with recombinant mouse IL-4 (50 ng/mL; Cat#574302) and IL-10 (50 ng/mL; Cat#575802) (BioLegend, San Diego, CA, USA) for 24 h.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
nAnTi-CAGE libraries were prepared from 5 µg total RNA according to the manufacturer’s protocol (DNAFORM, Yokohama, Japan)

treatment_protocol: For stimulation experiments, BMDMs were seeded at 5 × 10⁴ cells per well in 48-well plates and treated for 24 h with recombinant mouse IFN-γ (100 ng/mL; Cat#575308, BioLegend), CpG ODN-1826 (0.25 µg/mL; 5′-TCCATGACGTTCCTGACGTT-3′; Hokkaido System Science, Sapporo, Japan), or their combination.

value: bone marrow derived macrophages

tag: treatment time

value: CPG


title: OC + Riboflavin-1

description: Library name: C63_1

value: Batch 2


title: HHK_P12_2

description: Library name: GA78924


title: PA0713-1


title: AJ CCR5 unt d15 2

description: transplanted kidney


title: HHK_P12_1

description: Library name: GA78923


title: PA0625-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0625.xlsx

value: PA0625 mutant


title: OC + Aristolone-3

description: Library name: C62_3

value: Ovary

value: Aristolone


title: AJ CCR5 unt d15 1

description: transplanted kidney


title: TL1A 3

city: New York

first: Wei

last: Yang

address: Belfer Research Building,Room 760B,413 E. 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

description:
Library name: Reporter 6
10
Normalized counts_3.xlsx

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing.  After trimming the adaptors with cutadapt (version1.18) (https://cutadapt.readthedocs.io/en/v1.18/), RNA reads were aligned and mapped to the GRCm38 mouse reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR). and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/).  The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Assembly: GRCm38 mouse reference genome
Supplementary files format and content: excel file includes normalized counts for each sample

source_name: Intestine

extract_protocol:
RNA was extracted and purified using RNeasy Plus Micro Kit (Qiagen)
libraries were generated using SMART-Seq® v4 Ultra® Low Input RNA Kit

value: Intestine

value: stimulated in vitro with TL1A for 18hr


title: OC + Aristolone-2

description: Library name: C62_2

value: Wildtype


title: AJ-CCR5 CG CD20 d60 3

description: transplanted kidney

value: AJ-CCR5 CG CD20 d60


title: PA0625-1

value: Pseudomonas aeruginosa PAO1


title: OC + Aristolone-1

description: Library name: C62_1

value: BALB/c


title: TL1A 2

description:
Library name: Reporter 5
6
Normalized counts_3.xlsx


title: PA0586-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0586.xlsx

value: PA0586 mutant


title: AJ-CCR5 CG CD20 d60 2

description: transplanted kidney


title: OC + Pyrogallol-3

description: Library name: C61_3

value: Pyrogallol


title: TL1A 1

description:
Library name: Reporter 4
2
Normalized counts_3.xlsx


title: PA0586-1


title: AJ-CCR5 CG CD20 d60 1

description: transplanted kidney


title: OC + Pyrogallol-2

description: Library name: C61_2


title: un 3

description:
Library name: Reporter 3
9
Normalized counts_3.xlsx

value: stimulated in vitro without TL1A for 18hr


title: AJ CCR5 CG CD19 late d60

description: transplanted kidney

value: AJ CCR5 CG CD19 late d60


title: PA0581-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0581.xlsx

value: PA0581 mutant

value: grow until mid-log phase in LB


title: OC + Pyrogallol-1

description: Library name: C61_1


title: un 2

description:
Library name: Reporter 2
5
Normalized counts_3.xlsx


title: PA0581-1


title: OC + Butein-3

description: Library name: C60_3

value: Butein


title: un 1

description:
Library name: Reporter 1
1
Normalized counts_3.xlsx


title: AJ CCR5 CG unt d60 7

description: transplanted kidney

value: AJ CCR5 CG unt d60


title: PA0568-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0568.xlsx

value: PA0568 mutant


title: OC + Butein-2

description: Library name: C60_2

value: Ovary

value: Batch 2


title: AJ CCR5 CG unt d60 6

description: transplanted kidney


title: ChIPseq_Gata3Low_Dox2d_rep2

description:
Library name: g3Low_rep2
Gata3-Low mESCs with 2 days of dox induction were harvested for Gata3 ChIP seq.

library_source: genomic

data_processing:
All data reads were trimmed with Trim Galore (version 0.6.10) and mapped to the mm10 mouse reference genome using Bowtie2 (v2.3.5.1) with default parameters.
The alignments were further filtered with Samtools (version 1.10) with MAPQ >= 10.
PCR duplicates were subsequently eliminated with Picard Tools (version 2.27.5).
Peaks were detected utilizing MACS3 (version 3.0.2) with a false discovery rate (FDR) < 0.05.
RPGC-normalized bigwig files were produced using the deepTools bamCoverage (version 3.5.5).
Assembly: mm10
Supplementary files format and content: RPGC-normalized bigwig files

molecule: genomic DNA

extract_protocol:
ChIP were performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNAs were applied for the generation of sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (E7103L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.

value: Embryo

value: Mouse embryonic stem cells

value: Gata3-Low cells with 2 days of 0.5ug/mL Dox treatment


title: PA0568-1


title: AJ CCR5 CG unt d60 5

description: transplanted kidney


title: OC + Butein-1

description: Library name: C60_1

value: Wildtype


title: ChIPseq_Gata3Low_Dox2d_rep1

description:
Library name: g3Low_rep1
Gata3-Low mESCs with 2 days of dox induction were harvested for Gata3 ChIP seq.


title: PA0558-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0558.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA0558 mutant


title: OC + Naringenin chalcone-3

description: Library name: C59_3

value: Naringenin chalcone

value: BALB/c


title: AJ CCR5 CG unt d60 4

description: transplanted kidney


title: ChIPseq_Gata3High_Dox2d_rep2

description:
Library name: g3High_rep2
Gata3-High mESCs with 2 days of dox induction were harvested for Gata3 ChIP seq.

value: Gata3-High cells with 2 days of 0.5ug/mL Dox treatment


title: PA0558-1


title: AJ CCR5 CG CD19 late d60 4

description: transplanted kidney

value: AJ CCR5 CG CD19 late d60


title: OC + Naringenin chalcone-2

description: Library name: C59_2


title: ChIPseq_Gata3High_Dox2d_rep1

description:
Library name: g3High_rep1
Gata3-High mESCs with 2 days of dox induction were harvested for Gata3 ChIP seq.


title: PA1140-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1140.xlsx

value: PA1140 mutant


title: PA1575-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1575.xlsx

value: PA1575 mutant

value: grow until mid-log phase in LB


title: PA0813-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0813.xlsx

value: PA0813 mutant


title: PA1575-1


title: PA0805-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0805.xlsx

value: PA0805 mutant


title: PA0813-1


title: AJ CCR5 CG CD19 late d60 3

description: transplanted kidney


title: PA0545-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0545.xlsx

value: PA0545 mutant


title: OC + Naringenin chalcone-1

description: Library name: C59_1

value: Ovary

value: Batch 2


title: ChIPseq_Input

description:
Library name: g3_Input
Input DNA collected from not-induced chromatin for ChIP-seq normalization.

value: Embryo

value: Mouse embryonic stem cells

value: Cells under control conditions (mESC with no induction)


title: OC + (±)-Naringenin-3

description: Library name: C57_3

value: Wildtype

value: (±)-Naringenin

value: Batch 1


title: AJ CCR5 CG CD19 late d60 2

description: transplanted kidney


title: PA0545-1

value: Pseudomonas aeruginosa PAO1


title: Gata3Low_Dox5d_rep2

description:
Library name: Gata3Low_5d_rep2
Gata3-Low mESCs with 5 days of dox induction were harvested for Gata3 RNA seq.

data_processing:
All sequencing reads were trimmed using Trim Galore v0.6.10 and aligned to the mouse reference genome (mm10) with STAR (version 2.7.3a).
Alignments were then filtered using Samtools (version 1.10) with MAPQ score >= 10.
Raw counts were quantified using featureCounts from the Subread package (version v1.5.0-p1).
Assembly: mm10
Supplementary files format and content: Raw counts quantified using featureCounts

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen) (74136). The mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (E7490L).
The RNAs-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (E7770L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol. RNA-seq was conducted as paired-end sequencing on the NovaSeq 6000 (Illumina).

value: Mouse embryonic stem cell

value: Gata3-overexpressed mESC (Gata3-Low) with 5 day of induction


title: PA0495-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0495.xlsx

value: PA0495 mutant


title: AJ CCR5 CG CD19 late d60 1

description: transplanted kidney

value: AJ CCR5 CG CD19 late d60


title: Gata3Low_Dox3d_rep2

description:
Library name: Gata3Low_3d_rep2
Gata3-Low mESCs with 3 days of dox induction were harvested for Gata3 RNA seq.

value: Gata3-overexpressed mESC (Gata3-Low) with 3 day of induction


title: OC + (±)-Naringenin-2

description: Library name: C57_2

value: BALB/c


title: PA0495-1

value: grow until mid-log phase in LB


title: Gata3Low_Dox1d_rep2

description:
Library name: Gata3Low_1d_rep2
Gata3-Low mESCs with 1 day of dox induction were harvested for Gata3 RNA seq.

value: Gata3-overexpressed mESC (Gata3-Low) with 1 day of induction


title: OC + (±)-Naringenin-1

description: Library name: C57_1

value: Ovary


title: PA0454-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0454.xlsx

value: PA0454 mutant


title: AJ CCR5 CG CD19 early d60 3

description: transplanted kidney

value: AJ CCR5 CG CD19 early d60


title: OC + Linolenic acid-3

description: Library name: C56_3

value: Linolenic Acid


title: AJ CCR5 CG CD19 early d60 2

description: transplanted kidney


title: Gata3Low_noDox_rep2

description:
Library name: Gata3Low_noDox_rep2
Gata3-Low mESCs without dox induction were harvested for Gata3 RNA seq.

value: Embryo

value: Gata3-overexpressed mESC (Gata3-Low) with no induction


title: PA0454-1


title: AJ CCR5 CG CD19 early d60 1

description: transplanted kidney


title: Gata3Low_Dox5d_rep1

description:
Library name: Gata3Low_5d_rep1
Gata3-Low mESCs with 5 days of dox induction were harvested for Gata3 RNA seq.


title: OC + Linolenic acid-2

description: Library name: C56_2

value: Wildtype


title: PA0398-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0398.xlsx

value: PA0398 mutant


title: AJ CCR5 CG aCD20 d60 3

description: transplanted kidney

value: AJ CCR5 CG aCD20 d60


title: Gata3Low_Dox1d_rep1

description:
Library name: Gata3Low_1d_rep1
Gata3-Low mESCs with 1 day of dox induction were harvested for Gata3 RNA seq.

value: Mouse embryonic stem cell

value: Batch 1


title: Gata3Low_Dox3d_rep1

description:
Library name: Gata3Low_3d_rep1
Gata3-Low mESCs with 3 days of dox induction were harvested for Gata3 RNA seq.


title: PA0383-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0383.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA0383 mutant


title: AJ CCR5 CG aCD20 d60 2

description: transplanted kidney


title: OC + Linoleic acid-2

description: Library name: C55_2

value: Linoleic Acid


title: AJ CCR5 CG aCD20 d60 1

description: transplanted kidney


title: Gata3Low_noDox_rep1

description:
Library name: Gata3Low_noDox_rep1
Gata3-Low mESCs without dox induction were harvested for Gata3 RNA seq.


title: OC + Linolenic acid-1

description: Library name: C56_1

value: BALB/c


title: AJ B6 unt d60 4

description: transplanted kidney

value: AJ B6 unt d60


title: PA0383-1

value: grow until mid-log phase in LB


title: Gata3High_Dox5d_rep2

description:
Library name: Gata3High_5d_rep2
Gata3-High mESCs with 5 days of dox induction were harvested for Gata3 RNA seq.

value: Gata3-overexpressed mESC (Gata3-High) with 5 day of induction


title: OC + Linoleic acid-1

description: Library name: C55_1

value: Ovary


title: AJ B6 unt d60 3

description: transplanted kidney


title: PA0370-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0370.xlsx

value: PA0370 mutant


title: Gata3High_Dox3d_rep2

description:
Library name: Gata3High_3d_rep2
Gata3-High mESCs with 3 days of dox induction were harvested for Gata3 RNA seq.

value: Gata3-overexpressed mESC (Gata3-High) with 3 day of induction


title: PA0370-1


title: Gata3High_Dox1d_rep2

description:
Library name: Gata3High_1d_rep2
Gata3-High mESCs with 1 day of dox induction were harvested for Gata3 RNA seq.

value: Embryo

value: Gata3-overexpressed mESC (Gata3-High) with 1 day of induction


title: OC + Oleic acid-1

description: Library name: C54_2

value: Wildtype

value: Oleic Acid


title: Gata3High_noDox_rep2

description:
Library name: Gata3High_noDox_rep2
Gata3-High mESCs without dox induction were harvested for Gata3 RNA seq.

value: Gata3-overexpressed mESC (Gata3-High) with no induction


title: OC + Ethyl palmitate-3

description: Library name: C53_3

value: Ethyl palmitate, Palmitic acid ethyl ester


title: AJ CCR5 CG unt d60 3

description: transplanted kidney

value: AJ CCR5 CG unt d60


title: Gata3High_Dox5d_rep1

description:
Library name: Gata3High_5d_rep1
Gata3-High mESCs with 5 days of dox induction were harvested for Gata3 RNA seq.

value: Mouse embryonic stem cell

value: Batch 1


title: AJ CCR5 CG unt d60 2

description: transplanted kidney


title: PA0351-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0351.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA0351 mutant


title: OC + Ethyl palmitate-2

description: Library name: C53_2

value: BALB/c


title: Gata3High_Dox3d_rep1

description:
Library name: Gata3High_3d_rep1
Gata3-High mESCs with 3 days of dox induction were harvested for Gata3 RNA seq.


title: PA0351-1

value: grow until mid-log phase in LB


title: Gata3High_Dox1d_rep1

description:
Library name: Gata3High_1d_rep1
Gata3-High mESCs with 1 day of dox induction were harvested for Gata3 RNA seq.


title: OC + Ethyl palmitate-1

description: Library name: C53_1


title: AJ CCR5 CG unt d60 1

description: transplanted kidney


title: AJ CCR5 CG unt d35 3

description: transplanted kidney

value: AJ CCR5 CG unt d35


title: PA0329-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0329.xlsx

value: PA0329 mutant


title: AJ CCR5 CG unt d35 2

description: transplanted kidney


title: PA0329-1


title: skeletal muscle cells MUT, at 7 days after induced damage. biological replicate 3

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

country: Italy

institute: IRCCS, Ospedale San Raffaele

description:
Library name: 95
10x Genomics

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files with the 'mkfastq' command in Cell Ranger (v6.1.2) with default setting.
The counts were generated using 10X Genomic Cellranger analysis pipelines (CellRanger v6.1.2), with the 'count' command, using the parameter --expect-cells 10000.
Assembly: mm10 (refdata-cellranger-mm10-2020-A)
Supplementary files format and content: barcode.tsv.gz: Barcode sequences correspond to column indices, single column with barcode Ids. Content of the Cellranger output folder "filtered_feature_bc_matrix".
Supplementary files format and content: features.tsv.gz: features correspond to row indices. Tab separeted file: first column is feature ID, second clumn feature name, third column feature type. Content of the Cellranger output folder "filtered_feature_bc_matrix".
Supplementary files format and content: matrix.mtx.gz: counts matrix. Content of the Cellranger output folder "filtered_feature_bc_matrix".

source_name: skeletal muscle

extract_protocol:
Freshly isolated quadriceps were minced into small pieces and enzymatically dissociated with 1.5mg/mL Dispase (Gibco, 17105-041) and 0.12% (w/v) Collagenase type I (Sigma-Aldrich, C0130) in two cycles of 30min at 37°C under constant 240 rpm agitation. The suspension was then passed through a 16G needle, followed by a 26G needle and filtered through a 40μm sterile strainer. Then cold CMF was added to inactivate enzymes and red blood cells lysed. To remove cell debris from the suspensions, Ficoll separation was performed. Cells were resuspended in 7 mL of pre-warmed DMEM High Glucose (Gibco, 41965-039) supplemented with 10% FBS (Gibco, 10270-106), in a 15 mL falcon, and 3.5 mL of Ficoll slowly layered on top. Samples were spined at 300g for 30min with no brake nor acceleration and the cell layer formed aspirated to another falcon and washed with cell medium.
Chromium Single Cell 3′ Reagent Kit v3.1 (10xGenomics)

value: skeletal muscle

tag: timepoint

value: 7 days

tag: genetic modification

value: FOP


title: AJ CCR5 CG unt d35 1

description: transplanted kidney


title: OC + Columbianadin-2

description: Library name: C51_2

value: Ovary

value: Columbianadin


title: OC + Columbianadin-1

description: Library name: C51_1

value: Wildtype


title: AJ CCR5 CG unt d17 3

description: transplanted kidney

value: AJ CCR5 CG unt d17


title: OC + Isofraxidin-3

description: Library name: C50_3

value: Isofraxidin


title: skeletal muscle cells MUT, at 7 days after induced damage. biological replicate 1

description:
Library name: 90
10x Genomics


title: AJ CCR5 CG unt d17 2

description: transplanted kidney


title: PA0318-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0318.xlsx

value: PA0318 mutant


title: PA0310-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0310.xlsx

value: PA0310 mutant


title: OC + Isofraxidin-2

description: Library name: C50_2

value: Batch 1


title: skeletal muscle cells WT, at 7 days after induced damage. biological replicate 3

description:
Library name: 112
10x Genomics

value: Ctr


title: PA3969-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3969.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA3969 mutant


title: PA0310-1

value: grow until mid-log phase in LB


title: AJ CCR5 CG unt d17 1

description: transplanted kidney


title: skeletal muscle cells WT, at 7 days after induced damage. biological replicate 2

description:
Library name: 109
10x Genomics


title: OC + Isofraxidin-1

description: Library name: C50_1

value: BALB/c


title: GFP_RIP_R2

first: qi

last: Tang

state: Shanghai

address: 复旦大学江湾校区生命科学学院

institute: Fudan University

description: Library name: GFP_RIP_R2

data_processing:
For sRNA-seq, raw reads was filtered by TrimGalore (version 0.4.1) to trim adaptors and remove low-quality sequences. Alignment was performed with the shortstack using TAIR10 reference genome from Ensembl Plants with default parameters.
For lariat RNA-seq, raw reads was filtered by using Fastp (v0.23.2) to remove adapter and low-quality reads with parameters “-z 4 -q 20 -n 10 -c -t 1”. Alignment was performed with the HISAT2 (v2.2.1) using TAIR10 reference genome from Ensembl Plants with default parameters, and duplicates were removed by Samtools markdup (v1.14). Subread featureCounts was used to obtain counts for intron and loop region with parameters “-p -C -O -M - -fraction - -fracOverlap 1”, tail region with parameters “-p -C -O -M - -fraction - -minOverlap 10”. To normalize expression, FPKM of loop region was calculated with custom R script, and those transcripts with FPKM≥5 and the ratio of loop/tail ((loop reads/loop length)/(tail reads/tail length))>2 in all three replicates were identified as lariat RNAs.
For mRNA-seq analysis, FPKM of parent genes was calculated by StringTie (v2.2.1) with parameters “-e -G”.
Assembly: Ensembl
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Arabidopsis tissue (0.4 g) was ground in liquid nitrogen with 1.25 ml cold PEB buffer (200 mM Tris-HCl, pH 9.0; 200 mM KCl; 35 mM MgCl2; 25 mM Na2EDTA; 5 mM DTT; 1 % Brij-35 ; 1 % IGEPAL® CA-630; 1 % Tween 20; 1 % Triton X-100; 1 % polyoxyethylene 10 tridecyl ether; 1 % DOC; 0.5 x Cocktail; 1 mM PMSF; 100 μg/ml CHX; 100 μg/ml Chl; 0.5 U / ml RRI, and 10 units/mL DNase I [Invitrogen AM2238]) and incubated on ice for 20 mins. After centrifugation twice at 16,000 g for 15 mins at 4 °C, lysate contains mainly monosomes which were layered onto a 12 ml 15 % to 60 % sucrose gradient, and centrifuged at 4 °C in a Beckman SW41Ti rotor at 35,000 r.p.m. for 7 h. Samples were peak fractionated by A260 absorption using the gradient station (Biocomp). polysome fractions were collected and subjected to RNA extraction with Trizol LS.
For sRNA sequencing (sRNA-seq),we prepared sRNA libraries using the NEBNext Small RNA Library Prep Set for Illumina.For lariat RNA-seq, 20 μg of total RNA were incubated at 37°C for 1 h in 50 μL reactions with RNase R (Epicentre, USA) at a final concentration of 1 U RNase R per μg total RNA. Then, RNAs were purified using the RNA Clean & Concentrator-5 (Zymo Research) following the manufacturer’s instructions. A Ribo-off kit (Vazyme, Nanjing, China) was used to remove rRNA from the above RNase Rtreated RNAs. 50 ng of RNA for each sample was fragmented with Frag/Prime Buffer (Vazyme) at 80°C for 1 min and used as the starting material for strand-specific RNA-seq library preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme). For lncRNAseq, 5 μg of total RNA for each sample was treated by the Ribo-off kit to remove rRNA and RNA. 50 ng of RNA for each sample was fragmentated at 94°C for 5 min for strand-specific RNA-seq library preparation using the above kit. For Ribo-seq,the ribosome footprint fragments were repaired via T4 PNK (NEB M0201S) in the absence of ATP and rRNA depletion was performed using Ribo-off kit (Yeason 12254ES). RNA 3' ligation, 5' ligation, reverse transcription and Library Amplification were performed using The QIAseq miRNA Library Kit (QIAGEN 331595). The PCR amplified cDNA construct was purified using a Monarch PCR & DNA Kit (NEB T1030S). The cDNA was separated via 6% (w/v) TBE-PAGE 10-well gel and and the library of the expected size (~180 bp) was selected and recovered.

value: seedlings


title: PA0234-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0234.xlsx

value: PA0234 mutant


title: OC + Scopoletin-3

description: Library name: C49_3

value: Scopoletin, Gelseminic acid, Chrysatropic acid, 6-Methylesculetin


title: skeletal muscle cells WT, at 7 days after induced damage. biological replicate 1

description:
Library name: 107
10x Genomics

value: skeletal muscle

value: 7 days


title: GFP_RIP_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: GFP_RIP_R1


title: OC + Scopoletin-2

description: Library name: C49_2

value: Ovary


title: PA0234-1


title: RDR6_RIP_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: RDR6_RIP_R3


title: skeletal muscle cells MUT, at 5 days after induced damage. biological replicate 3

description:
Library name: 96
10x Genomics

value: 5 days

value: FOP


title: PA0168-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0168.xlsx

value: PA0168 mutant


title: OC + Scopoletin-1

description: Library name: C49_1

value: Wildtype


title: RDR6_RIP_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: RDR6_RIP_R2


title: skeletal muscle cells MUT, at 5 days after induced damage. biological replicate 2

description:
Library name: 94
10x Genomics


title: OC + Bergaptol-3

description: Library name: C48_3

value: Bergaptol, 5-Hydroxyfuranocoumarin


title: skeletal muscle cells MUT, at 5 days after induced damage. biological replicate 1

description:
Library name: 92
10x Genomics


title: PA0045-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0045.xlsx

value: PA0045 mutant


title: OC + Bergaptol-2

description: Library name: C48_2

value: Batch 1


title: RDR6_RIP_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: RDR6_RIP_R1


title: skeletal muscle cells WT, at 5 days after induced damage. biological replicate 3

description:
Library name: 113
10x Genomics

value: Ctr


title: dbr1-3_lariats_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-3_lariats_R3


title: OC + Bergaptol-1

description: Library name: C48_1


title: skeletal muscle cells WT, at 5 days after induced damage. biological replicate 2

description:
Library name: 111
10x Genomics


title: dbr1-3_lariats_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-3_lariats_R2


title: OC + Decursinol-3

description: Library name: C47_3

value: Decursinol


title: dbr1-3_lariats_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-3_lariats_R1


title: OC + Decursinol-2

description: Library name: C47_2


title: Liver, MUP-uPA, HFD, TOFA, rep7

city: Berkeley

first: Chi

last: Zhu

state: CA California

address: Morgan Hall, Rm238

department: Department of Nutritional Sciences & Toxicology

institute: University of California, Berkeley

description: Library name: MUP-uPA_HFD_TOFA_liver_7

data_processing:
Transcriptome mapping was performed with STAR using the Ensembl annotation of the mm10 reference genome.
Read counts for individual genes were generated using HTSeq. Only genes with CPM > 1 for at least one sample were included in the analyses.
Analysis of differential expression was performed using only genes with normalized counts (CPM) >=1 for at least one sample
Assembly: mm10
Supplementary files format and content: Table with FPKM values in log2 for all samples

source_name: liver

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq

treatment_protocol: Major urinary protein (MUP)-urokinase-type plasminogen activator (uPA) transgenic mice were fed a 60% high fat diet for ten weeks followed by an oral dosing of vehicle control or 125 mg/kg TOFA, BID for six weeks

value: liver

value: TOFA


title: PA0168-1

value: Pseudomonas aeruginosa PAO1

value: grow until mid-log phase in LB


title: PA0398-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0398.xlsx

value: PA0398 mutant


title: OC + Linoleic acid-3

description: Library name: C55_3

data_processing:
Initial evaluation of the quality of raw RNA-seq fastq file was conducted utilizing FASTQC (v0.12.1).
The BBduk module within the bbmap toolkit (v39.80) was conducted with specific parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=t, trimq=10, and minlength=20 to eliminate adapter sequences and low-quality reads.
The cleaned reads were mapped to the mouse reference genome (build GRCm39, Ensembl release 115) through the STAR aligner (v2.7.10b)
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) along with the gene structure file (GRCm39.115.gtf).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

extract_protocol:
After four weeks of compound administration, a post-ovulatory state was induced by intraperitoneal injection of 5 IU PMSG followed 48 h later by 5 IU hCG. Ovaries were collected 16-18h after hCG administration, weighed, and immediately preserved in liquid nitrogen until RNA extraction.  Each ovary sample was immersed in 1 mL  TRIzol reagent (Invitrogen) and homogenized using a disposable grinder (Biomasher II; 890863; LMS Co., Tokyo, Japan).
Total RNA was isolated using Trizol reagent (Invitrogen). The quality of purity and integrity of the extracted RNA samples were analyzed using a NanoDrop ND-2000 Spectrophotometer (Thermo Inc., DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). RNA library was constructed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. The compound administration experiment was conducted in two independent animal experimental batches. Each batch included 14 compound-treated groups and corresponding young control (YC) and old control (OC) groups. Mice in both batches followed the same treatment schedule, post-ovulatory induction procedure, and ovary collection protocol. RNA extraction, library preparation, and sequencing were performed together for all samples. Batch assignment is indicated in the sample metadata.

value: Linoleic Acid

value: BALB/c


title: DBR1H85A_lariats_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: DBR1H85A_lariats_R3

value: seedlings


title: PA0012-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0012.xlsx

data_processing:
RNA-seq reads were mapped to the Pseudomonas aeruginosa (NC_002516.2) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Assembly: Pseudomonas aeruginosa (NC_002516.2)
Supplementary files format and content: xlsx files were generated from RNA-seq, containing the differential expressional genes.

extract_protocol:
The Pseudomonas aeruginosa PAO1 wild type strain and the HP mutants were inoculated into LB with corresponding antibiotics overnight cultured at 37 °C. Then the strains were one hundred times diluted into fresh LB. Before harvested, the P. aeruginosa strains were cultured for 3 h until OD600 to 0.6, at 37 °C with 220 rpm shaking. Then, 2 ml of bacterial cultures were collected by centrifugation (12,000 rpm, 4 °C). RNA extraction was performed by using the TianGen RNA extraction kit with the recommended DNase digestion. After removing rRNA by following the RiboRid protocol, mRNA was used to construct the cDNA library according to the NEBNext Ultra II RNA Library Prep Kit protocol (NEB), which was then sequenced using the HiSeq 2000 system (Illumina).
NEBNext UltraTM II RNA Library Prep Kit protocol

value: PA0012 mutant


title: PA0045-1


title: OC + Oleic acid-3

description: Library name: C54_4

value: Ovary

value: Oleic Acid


title: OC + Decursinol-1

description: Library name: C47_1

value: Wildtype


title: OC + Oleic acid-2

description: Library name: C54_3


title: PA0356-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0356.xlsx

value: PA0356 mutant


title: PA0039-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0039.xlsx

value: PA0039 mutant


title: Liver, MUP-uPA, HFD, TOFA, rep6

description: Library name: MUP-uPA_HFD_TOFA_liver_6


title: AJ B6 unt d60 2

description: transplanted kidney

value: AJ B6 unt d60


title: DBR1H85A_lariats_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: DBR1H85A_lariats_R2


title: AJ B6 unt d60 1

description: transplanted kidney


title: PA0012-1


title: skeletal muscle cells WT, at 5 days after induced damage. biological replicate 1

description:
Library name: 108
10x Genomics

value: skeletal muscle

value: 5 days

value: Ctr


title: OC + 7-Methoxycoumarin-3

description: Library name: C46_3

value: 7-Methoxycoumarin (Herniarin)

value: Batch 1


title: Liver, MUP-uPA, HFD, TOFA, rep5

description: Library name: MUP-uPA_HFD_TOFA_liver_5

value: liver

value: TOFA


title: DBR1H85A_lariats_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: DBR1H85A_lariats_R1


title: PA0356-1

value: Pseudomonas aeruginosa PAO1

value: grow until mid-log phase in LB


title: PA4611-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4611.xlsx

value: PA4611 mutant


title: Liver, MUP-uPA, HFD, TOFA, rep4

description: Library name: MUP-uPA_HFD_TOFA_liver_4


title: OC + 7-Methoxycoumarin-1

description: Library name: C46_1

value: BALB/c


title: PA4611-1


title: dbr1-2_dcl2-1_TuMV_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_mRNA_R2

value: seedlings


title: OC + 7-Methoxycoumarin-2

description: Library name: C46_2

value: Ovary


title: PA0039-1


title: PA4575-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4575.xlsx

value: PA4575 mutant


title: Liver, MUP-uPA, HFD, TOFA, rep3

description: Library name: MUP-uPA_HFD_TOFA_liver_3


title: OC + Scoparone-3

description: Library name: C45_3

value: Wildtype

value: Scoparone, 6,7-Dimethoxycoumarin


title: dbr1-2_dcl2-1_TuMV_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_mRNA_R1


title: PA4575-1


title: Liver, MUP-uPA, HFD, TOFA, rep2

description: Library name: MUP-uPA_HFD_TOFA_liver_2


title: OC + Scoparone-2

description: Library name: C45_2


title: dbr1-2_dcl2-1_mock_mRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_mRNA_R3


title: PA4543-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4543.xlsx

value: PA4543 mutant


title: OC + Scoparone-1

description: Library name: C45_1


title: Liver, MUP-uPA, HFD, ctrl, rep9

description: Library name: MUP-uPA_HFD_Ctrl_liver_9

value: control


title: dbr1-2_dcl2-1_mock_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_mRNA_R2


title: dbr1-2_dcl2-1_TuMV_mRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_mRNA_R3


title: PA4543-1


title: OC + 5,7-Dimethoxycoumarin-3

description: Library name: C44_3

value: Citropten (5,7-Dimethoxycoumarin)


title: Liver, MUP-uPA, HFD, ctrl, rep8

description: Library name: MUP-uPA_HFD_Ctrl_liver_8


title: dbr1-2_dcl2-1_mock_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_mRNA_R1


title: PA4539-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4539.xlsx

value: PA4539 mutant


title: Liver, MUP-uPA, HFD, ctrl, rep7

description: Library name: MUP-uPA_HFD_Ctrl_liver_7


title: OC + 5,7-Dimethoxycoumarin-2

description: Library name: C44_2


title: PA4539-1


title: dbr1-2_dcl2-1_TuMV_Ribo_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_Ribo_R3

data_processing:
For sRNA-seq, raw reads was filtered by TrimGalore (version 0.4.1) to trim adaptors and remove low-quality sequences. Alignment was performed with the shortstack using TAIR10 reference genome from Ensembl Plants with default parameters.
For lariat RNA-seq, raw reads was filtered by using Fastp (v0.23.2) to remove adapter and low-quality reads with parameters “-z 4 -q 20 -n 10 -c -t 1”. Alignment was performed with the HISAT2 (v2.2.1) using TAIR10 reference genome from Ensembl Plants with default parameters, and duplicates were removed by Samtools markdup (v1.14). Subread featureCounts was used to obtain counts for intron and loop region with parameters “-p -C -O -M - -fraction - -fracOverlap 1”, tail region with parameters “-p -C -O -M - -fraction - -minOverlap 10”. To normalize expression, FPKM of loop region was calculated with custom R script, and those transcripts with FPKM≥5 and the ratio of loop/tail ((loop reads/loop length)/(tail reads/tail length))>2 in all three replicates were identified as lariat RNAs.
For mRNA-seq analysis, FPKM of parent genes was calculated by StringTie (v2.2.1) with parameters “-e -G”.
Assembly: Ensembl
Supplementary files format and content: bigWig
Library strategy: Ribo-Seq


title: OC + 5,7-Dimethoxycoumarin-1

description: Library name: C44_1


title: OC + Ethyl gallate-3

description: Library name: C43_3

value: Ethyl gallate


title: PA4531-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4531.xlsx

value: PA4531 mutant


title: Liver, MUP-uPA, HFD, ctrl, rep5

description: Library name: MUP-uPA_HFD_Ctrl_liver_5

value: liver


title: dbr1-2_dcl2-1_TuMV_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_Ribo_R1


title: PA4531-1


title: OC + Ethyl gallate-2

description: Library name: C43_2

value: Batch 1


title: OC + Ethyl gallate-1

description: Library name: C43_1


title: PA4517-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4517.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA4517 mutant


title: PA4517-1

value: grow until mid-log phase in LB


title: TNFa + IFNg treated B6.Sst1S biological replicate 3

city: Dublin

first: Oleksii

middle: S

last: Rukhlenko

address: Systems Biology Ireland, University College Dublin

department: Systems Biology Ireland

country: Ireland

institute: University College Dublin

description: Library name: S12

data_processing:
R, Rsubread package
Raw sequence reads were mapped to GrCM38/mm10 using Rsubread package in R, raw counts were extracted
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow cells were isolated from the tibia and fibula of either B6 or B6.Sst1S mice. The bone marrow cell isolation, culture, and bone marrow-derived macrophage (BMDM) generation were performed according to the method previously described (Yabaji et al., 2022; DOI: 10.1016/j.xpro.2022.101241).

extract_protocol:
After the treatments, cells were washed with PBS and collected in TRIzol reagent. The total RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN), involving the DNase treatment using RNase-Free DNase (QIAGEN) following the recommended procedure. Total RNA integrity was verified using the High Sensitivity RNA Pico 6000 assay run on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). To enrich for mRNA, 150 ng of total RNA for each sample was incubated with magnetic Oligo-d(T)25 beads per the manufacturer’s instructions using NEB Next Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA).
Libraries were prepared using NEB Next Ultra II Directional RNA Library Kit for Illumina according to the manufacturer’s protocol. Briefly, after mRNA enrichment, the RNA was fragmented at 94oC for 15 min. First strand cDNA was generated, and incorporation of dUTP occurred during synthesis of second strand cDNA to indicate strandedness. Double-stranded cDNA then underwent end repair, A-tailing, adaptor ligation, and incorporation of sample-specific multiplex indices via PCR amplification (11 cycles) according to the manufacturer’s protocol (New England Biolabs, USA). Size distribution and molarity of amplified cDNA libraries were assessed via the Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies, USA).

treatment_protocol: B6 and B6.Sst1S BMDMs were treated with TNF (10 ng/mL), IFNg (5 U/mL), and in combination of both for 12 h.

value: Bone Marrow Derived Macrophages

value: TNF (10 ng/mL) + IFNg (5 U/mL) for 12 h


title: dbr1-2_dcl2-1_mock_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_Ribo_R2

value: seedlings


title: dbr1-2_dcl2-1_mock_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_Ribo_R1


title: Liver, MUP-uPA, HFD, ctrl, rep1

description: Library name: MUP-uPA_HFD_Ctrl_liver_1


title: TNFa + IFNg treated B6.Sst1S biological replicate 2

description: Library name: S11


title: dbr1-2_TuMV_Ribo_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_Ribo_R3


title: PA4141-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4141.xlsx

value: PA4141 mutant


title: Liver, CDAA-HFD, TOFA, rep5

description: Library name: WT_CDAA-HFD_TOFA_liver_5

treatment_protocol: C57BL/6J wild type mice were exposed to a choline-deficient, L-amino acid-defined, high-fat diet (CDAA-HFD) for eight weeks followed by an oral dosing regimen of vehicle control or 125 mg/kg TOFA, BID for four weeks

value: TOFA


title: dbr1-2_TuMV_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_Ribo_R2


title: PA4105-06-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4105-06.xlsx

value: PA4105-06 mutant


title: IFNg treated B6.Sst1S biological replicate 3

description: Library name: S9

value: IFNg (5 U/mL) for 12 h


title: dbr1-2_TuMV_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_Ribo_R1


title: PA4105-06-1


title: dbr1-2_mock_Ribo_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_Ribo_R3


title: PA4048-49-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA4048-49.xlsx

value: PA4048-49 mutant


title: IFNg treated B6.Sst1S biological replicate 1

description: Library name: S7


title: Liver, CDAA-HFD, TOFA, rep2

description: Library name: WT_CDAA-HFD_TOFA_liver_2


title: Liver, MUP-uPA, HFD, ctrl, rep4

description: Library name: MUP-uPA_HFD_Ctrl_liver_4

value: control


title: dbr1-2_mock_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_Ribo_R2


title: PA4048-49-1


title: TNFa treated B6.Sst1S biological replicate 3

description: Library name: S6

value: TNF (10 ng/mL) for 12 h


title: Liver, CDAA-HFD, TOFA, rep1

description: Library name: WT_CDAA-HFD_TOFA_liver_1


title: dbr1-2_mock_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_Ribo_R1


title: PA3142-44-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA3142-44.xlsx

value: PA3142-44 mutant


title: TNFa treated B6.Sst1S biological replicate 2

description: Library name: S5


title: Liver, CDAA-HFD, ctrl, rep4

description: Library name: WT_CDAA-HFD_ctrl_liver_4


title: Col-0_TuMV_Ribo_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_Ribo_R3


title: PA3142-44-1


title: TNFa treated B6.Sst1S biological replicate 1

description: Library name: S4


title: Liver, CDAA-HFD, ctrl, rep3

description: Library name: WT_CDAA-HFD_ctrl_liver_3


title: Col-0_TuMV_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_Ribo_R2


title: PA2072-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2072.xlsx

value: PA2072 mutant


title: Untreated B6.Sst1S biological replicate 3

description: Library name: S3

value: Control


title: Liver, CDAA-HFD, ctrl, rep2

description: Library name: WT_CDAA-HFD_ctrl_liver_2

value: liver


title: PA2072-1

value: Pseudomonas aeruginosa PAO1


title: Col-0_TuMV_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_Ribo_R1


title: Untreated B6.Sst1S biological replicate 2

description: Library name: S2


title: Liver, CDAA-HFD, ctrl, rep1

description: Library name: WT_CDAA-HFD_ctrl_liver_1


title: Col-0_mock_Ribo_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_Ribo_R3


title: PA2049-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA2049.xlsx

value: PA2049 mutant


title: Liver, PPARa-WT, HFD, TOFA, rep5

description: Library name: PPARa-WT_HFD_TOFA_liver_5

data_processing:
FASTQ reads were trimmed to 100 bases using Trimmomatic.
Transcriptome mapping was performed with STAR using the Ensembl annotation of the mm10 reference genome.
Read counts for individual genes were generated using HTSeq. Only genes with CPM > 1 for at least one sample were included in the analyses.
Analysis of differential expression was performed using only genes with normalized counts (CPM) >=1 for at least one sample
Assembly: mm10
Supplementary files format and content: Table with FPKM values in log2 for all samples

treatment_protocol: C57BL/6J wild type mice (Jax strain 000664)or PPARɑ whole body knockout mice (Jax strain 008154) were exposed to a 60% high fat diet for ten weeks followed by an oral, daily dosing regimen of vehicle control or 200 mg/kg TOFA for two weeks

value: wild type


title: Untreated B6.Sst1S biological replicate 1

description: Library name: S1

value: Bone Marrow Derived Macrophages


title: Liver, MUP-uPA, HFD, TOFA, rep1

description: Library name: MUP-uPA_HFD_TOFA_liver_1


title: PA2049-1

value: grow until mid-log phase in LB


title: Col-0_mock_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_Ribo_R2

value: seedlings


title: Liver, MUP-uPA, HFD, ctrl, rep6

description: Library name: MUP-uPA_HFD_Ctrl_liver_6


title: TNFa + IFNg treated B6 WT biological replicate 3

description: Library name: R12

value: B6 WT

value: TNF (10 ng/mL) + IFNg (5 U/mL) for 12 h


title: Liver, PPARa-WT, HFD, TOFA, rep4

description: Library name: PPARa-WT_HFD_TOFA_liver_4

value: TOFA


title: dbr1-2_dcl2-1_TuMV_Ribo_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_Ribo_R2


title: Col-0_mock_Ribo_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_Ribo_R1


title: Liver, MUP-uPA, HFD, ctrl, rep3

description: Library name: MUP-uPA_HFD_Ctrl_liver_3


title: PA1957-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1957.xlsx

value: PA1957 mutant


title: Liver, PPARa-WT, HFD, TOFA, rep3

description: Library name: PPARa-WT_HFD_TOFA_liver_3


title: TNFa + IFNg treated B6 WT biological replicate 2

description: Library name: R11


title: dbr1-3_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-3_sRNA_R3


title: dbr1-2_dcl2-1_mock_Ribo_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_Ribo_R3


title: PA1957-1


title: Liver, MUP-uPA, HFD, ctrl, rep2

description: Library name: MUP-uPA_HFD_Ctrl_liver_2


title: PA4141-2

value: PA4141 mutant


title: TNFa + IFNg treated B6 WT biological replicate 1

description: Library name: R10


title: IFNg treated B6 WT biological replicate 3

description: Library name: R9

value: IFNg (5 U/mL) for 12 h


title: dbr1-3_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-3_sRNA_R2


title: PA1941-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1941.xlsx

value: PA1941 mutant


title: Liver, PPARa-WT, HFD, TOFA, rep2

description: Library name: PPARa-WT_HFD_TOFA_liver_2


title: Liver, PPARa-WT, HFD, TOFA, rep1

description: Library name: PPARa-WT_HFD_TOFA_liver_1


title: dbr1-3_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-3_sRNA_R1


title: PA1941-1


title: TNFa + IFNg treated B6.Sst1S biological replicate 1

description: Library name: S10


title: IFNg treated B6 WT biological replicate 2

description: Library name: R8


title: Liver, PPARa-WT, HFD, ctrl, rep4

description: Library name: PPARa-WT_HFD_ctrl_liver_4

value: control


title: dbr1-2_dcl2-1_TuMV_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_sRNA_R2


title: PA1921-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1921.xlsx

value: PA1921 mutant


title: Liver, PPARa-WT, HFD, ctrl, rep3

description: Library name: PPARa-WT_HFD_ctrl_liver_3


title: dbr1-2_dcl2-1_TuMV_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_sRNA_R3


title: IFNg treated B6 WT biological replicate 1

description: Library name: R7


title: TNFa treated B6 WT biological replicate 3

description: Library name: R6

value: TNF (10 ng/mL) for 12 h


title: PA1921-1


title: Liver, PPARa-WT, HFD, ctrl, rep2

description: Library name: PPARa-WT_HFD_ctrl_liver_2

value: liver


title: dbr1-2_dcl2-1_TuMV_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_TuMV_sRNA_R1


title: Liver, CDAA-HFD, TOFA, rep4

description: Library name: WT_CDAA-HFD_TOFA_liver_4


title: OC + Columbianadin-3

description: Library name: C51_3

value: Ovary

value: Wildtype

value: Columbianadin

value: Batch 1

value: BALB/c


title: PA1891-97-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1891-97.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA1891-97 mutant

value: grow until mid-log phase in LB


title: IFNg treated B6.Sst1S biological replicate 2

description: Library name: S8

value: Bone Marrow Derived Macrophages


title: TNFa treated B6 WT biological replicate 2

description: Library name: R5

value: B6 WT


title: Liver, PPARa-WT, HFD, ctrl, rep1

description: Library name: PPARa-WT_HFD_ctrl_liver_1

value: wild type


title: dbr1-2_dcl2-1_mock_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_sRNA_R3

value: seedlings


title: PA1891-97-1


title: Liver, PPARa-KO, HFD, TOFA, rep5

description: Library name: PPARa-KO_HFD_TOFA_liver_5

value: PPARa-KO

value: TOFA


title: dbr1-2_dcl2-1_mock_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_sRNA_R2


title: PA1889-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1889.xlsx

value: PA1889 mutant


title: PA0318-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA0318.xlsx

value: PA0318 mutant


title: TNFa treated B6 WT biological replicate 1

description: Library name: R4

value: TNF (10 ng/mL) for 12 h


title: Untreated B6 WT biological replicate 3

description: Library name: R3

value: Control


title: Liver, CDAA-HFD, TOFA, rep3

description: Library name: WT_CDAA-HFD_TOFA_liver_3

value: liver


title: PA1889-1


title: Liver, PPARa-KO, HFD, TOFA, rep4

description: Library name: PPARa-KO_HFD_TOFA_liver_4


title: dbr1-2_dcl2-1_mock_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_mock_sRNA_R1


title: Untreated B6 WT biological replicate 2

description: Library name: R2


title: Liver, PPARa-KO, HFD, TOFA, rep3

description: Library name: PPARa-KO_HFD_TOFA_liver_3


title: DBR1_H85A_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: DBR1_H85A_sRNA_R3

source_name: Inflorescence

value: Inflorescence


title: PA1887-88-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1887-88.xlsx

value: PA1887-88 mutant


title: Liver, PPARa-KO, HFD, TOFA, rep2

description: Library name: PPARa-KO_HFD_TOFA_liver_2


title: DBR1_H85A_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: DBR1_H85A_sRNA_R2


title: Untreated B6 WT biological replicate 1

description: Library name: R1


title: PA1887-88-1


title: Liver, PPARa-KO, HFD, TOFA, rep1

description: Library name: PPARa-KO_HFD_TOFA_liver_1


title: Bhlhe40 KO_TL1A_3

description: Library name: ATAC-S12

data_processing:
In summary, reads were trimmed and aligned to the mouse reference genome (mm10) with Trimmomatic v0.39 51 and Bowtie2 v2.3.4.3 (https://doi.org/10.1038/nmeth.1923), respectively, and post alignment filtering was done with samtools v1.9 (https://doi.org/10.1093/bioinformatics/btp352) and Picard tools v2.20.7 (http://broadinstitute.github.io/picard/) to remove unmapped reads, improperly paired reads, nonunique reads, and duplicates. Peak calling was performed with MACS2 v2.2.4 52, blacklist regions being removed and only keeping peaks with adjusted P values smaller than 0.01. Consensus peak atlas was created keeping peaks that were found in three replicates within each condition
Assembly: mm10
Supplementary files format and content: Genome-wide enrichment tracks (bigWig) and peak calls (narrowPeak)

extract_protocol:
Genomic DNA was extracted from ~50,000 ILC3s  by detergent-mediated lysis followed by Tn5 transposase–mediated tagmentation (OMNI-ATAC protocol, adaped from Corces et al. Nature Methods 2017. ) and purified using  Zymo DNA Clean and Concentrator-5 kit.
ATAC-seq libraries were generated by Tn5 transposase–mediated tagmentation of accessible chromatin, followed by PCR amplification with indexed primers and size selection/cleanup to obtain sequencing-ready libraries.

value: Intestine


title: DBR1_H85A_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: DBR1_H85A_sRNA_R1


title: Bhlhe40 KO_TL1A_2

description: Library name: ATAC-S11


title: PA1885-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1885.xlsx

value: Pseudomonas aeruginosa PAO1

value: PA1885 mutant


title: Liver, PPARa-KO, HFD, ctrl, rep4

description: Library name: PPARa-KO_HFD_ctrl_liver_4

value: control


title: PA1885-1

value: grow until mid-log phase in LB


title: dbr1-2_dcl2-1_sRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_sRNA_R3


title: Bhlhe40 KO_TL1A_1

description: Library name: ATAC-S10


title: Liver, PPARa-KO, HFD, ctrl, rep3

description: Library name: PPARa-KO_HFD_ctrl_liver_3


title: dbr1-2_dcl2-1_sRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_sRNA_R2


title: Bhlhe40 Het_TL1A_3

description: Library name: ATAC-S9


title: PA1874-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1874.xlsx

value: PA1874 mutant


title: Liver, PPARa-KO, HFD, ctrl, rep1

description: Library name: PPARa-KO_HFD_ctrl_liver_1


title: Bhlhe40 Het_TL1A_2

description: Library name: ATAC-S8


title: PA1874-2


title: dbr1-2_TuMV_lariats_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_lariats_R3

tag: sample group


title: Bhlhe40 Het_TL1A_1

description: Library name: ATAC-S7


title: dbr1-2_dcl2-1_sRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_dcl2-1_sRNA_R1


title: Muscle, HFD, TOFA, rep8

description: Library name: WT_HFD_TOFA_muscle_8

treatment_protocol: C57BL/6J mice were exposed to a 60% high fat diet for seven weeks followed by an oral dosing regimen of vehicle control or TOFA (one week of loading dose of 125 mg/kg followed by maintenance dosing 62.5 mg/kg, BID) for a total of three weeks

value: skeletal muscle


title: dbr1-2_TuMV_lariats_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_lariats_R2

value: seedlings


title: PA1840-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1840.xlsx

value: PA1840 mutant


title: Liver, PPARa-KO, HFD, ctrl, rep2

description: Library name: PPARa-KO_HFD_ctrl_liver_2

value: PPARa-KO


title: Bhlhe40 KO_un_3

description: Library name: ATAC-S6


title: PA1840-1


title: Muscle, HFD, TOFA, rep7

description: Library name: WT_HFD_TOFA_muscle_7

value: TOFA


title: dbr1-2_TuMV_lariats_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_lariats_R1


title: PA1834-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1834.xlsx

value: PA1834 mutant


title: Bhlhe40 KO_un_2

description: Library name: ATAC-S5


title: Muscle, HFD, TOFA, rep6

description: Library name: WT_HFD_TOFA_muscle_6


title: dbr1-2_mock_lariats_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_lariats_R3


title: PA1834-1


title: Bhlhe40 KO_un_1

description: Library name: ATAC-S4


title: dbr1-2_mock_lariats_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_lariats_R2


title: Muscle, HFD, TOFA, rep5

description: Library name: WT_HFD_TOFA_muscle_5


title: PA1789-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1789.xlsx

value: PA1789 mutant


title: Bhlhe40 Het_un_3

description: Library name: ATAC-S3


title: dbr1-2_mock_lariats_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_lariats_R1


title: Muscle, HFD, TOFA, rep4

description: Library name: WT_HFD_TOFA_muscle_4


title: Muscle, HFD, TOFA, rep3

description: Library name: WT_HFD_TOFA_muscle_3


title: Bhlhe40 Het_un_2

description: Library name: ATAC-S2


title: Col-0_TuMV_lariats_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_lariats_R3


title: Bhlhe40 Het_un_1

description: Library name: ATAC-S1


title: PA1784-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1784.xlsx

value: PA1784 mutant


title: Muscle, HFD, TOFA, rep2

description: Library name: WT_HFD_TOFA_muscle_2


title: PA1784-1


title: Col-0_TuMV_lariats_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_lariats_R2


title: in vitro fertilization 32 days, sample 3

description:
Library name: 3_IVF_32d
IVF32_03:Counts

data_processing:
Quality control of raw reads (fastq files) was carried out using FastQC (v0.11.9)
Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! (v0.6.6)
Trimmed reads were aligned to the reference genome using STAR (v2.6.1d)
BAM file filtering and indexing was carried out using SAMtools (v1.9)
Duplicate reads were marked using Picard tools (v2.23.9)
Reads overlapping with exons were assigned to genes using featureCounts (v2.0.1)
Differential gene expression analysis was completed using DESeq2 (Galaxy Version 2.11.40.7+galaxy1)
Assembly: Bos taurus - assembly ARS-UCD1.2
Supplementary files format and content: tabular file include raw counts for each Sample

source_name: extracellular vesicles

growth_protocol: Non-lactating Nelore cows (Bos taurus indicus) with an average body condition score (BCS) of 3.0 ± 0.04 were selected and synchronized using a timed-AI protocol with estradiol benzoate. Artificial insemination (AI) and in vitro embryo production (IVF) were performed using semen from a single Angus bull (Bos taurus taurus).

extract_protocol:
Total RNA was extracted using the miRVana kit from Thermo Fisher Scientific Co.
Total RNA-Seq libraries were constructed from 150 ng of total RNA, using Zymo-Seq RiboFree Total RNA Library Kit according to manufacturer’s instructions.

treatment_protocol: On day 0, cows in the AI group were inseminated, while embryos were transferred to the IVF group on day 6.5. Slaughter took place on days 18 and 32 after AI and on days 12 and 26 post-embryo transfer (IVF group), representing key periods for maternal recognition (18 days) and early placental attachment (32 days). After slaughter, the reproductive tracts were immediately removed and kept on ice. On day 18, uterine horns were flushed with a saline solution to confirm pregnancy by embryo presence; on day 32, pregnancy was diagnosed via ultrasonography one day prior. Uterine fluid from 16 cows was collected and centrifuged to isolate extracellular vesicles, classified by size and concentration for AI and IVF on days 18 and 32. Samples from day 18 of the estrous cycle served as controls.

value: extracellular vesicles

value: in vitro fertilization


title: Muscle, HFD, TOFA, rep1

description: Library name: WT_HFD_TOFA_muscle_1


title: Col-0_TuMV_lariats_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_lariats_R1


title: PA1761-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1761.xlsx

source_name: Pseudomonas aeruginosa PAO1

value: PA1761 mutant


title: Muscle, HFD, ctrl, rep8

description: Library name: WT_HFD_ctrl_muscle_8


title: in vitro fertilization 32 days, sample 2

description:
Library name: 2_IVF_32d
IVF32_02:Counts


title: Col-0_mock_lariats_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_mock_lariats_R3


title: Muscle, HFD, ctrl, rep7

description: Library name: WT_HFD_ctrl_muscle_7


title: PA1753-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1753.xlsx

value: PA1753 mutant


title: in vitro fertilization 18 days, sample 3

description:
Library name: 3_IVF_18d
IVF18_03:Counts


title: Muscle, HFD, ctrl, rep6

description: Library name: WT_HFD_ctrl_muscle_6


title: PA1753-1

value: Pseudomonas aeruginosa PAO1


title: Muscle, HFD, ctrl, rep5

description: Library name: WT_HFD_ctrl_muscle_5


title: dbr1-2_TuMV_mRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_mRNA_R3


title: in vitro fertilization 18 days, sample 1

description:
Library name: 1_IVF_18d
IVF18_01:Counts


title: PA1749-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1749.xlsx

value: PA1749 mutant


title: dbr1-2_TuMV_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_mRNA_R2


title: artificial insemination 32 days, sample 3

description:
Library name: 3_AI_32d
AI32_03:Counts

value: artificial insemination


title: PA1749-1

value: grow until mid-log phase in LB


title: Muscle, HFD, ctrl, rep3

description: Library name: WT_HFD_ctrl_muscle_3

value: control


title: dbr1-2_TuMV_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_TuMV_mRNA_R1


title: PA1743-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1743.xlsx

value: PA1743 mutant


title: Muscle, HFD, ctrl, rep2

description: Library name: WT_HFD_ctrl_muscle_2

value: skeletal muscle


title: PA1743-1


title: Muscle, HFD, ctrl, rep1

description: Library name: WT_HFD_ctrl_muscle_1


title: artificial insemination 32 days, sample 1

description:
Library name: 1_AI_32d
AI32_01:Counts


title: dbr1-2_mock_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_mRNA_R2

value: seedlings


title: PA1679-2

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1679.xlsx

value: PA1679 mutant


title: Liver, HFD, TOFA, rep4

description: Library name: WT_HFD_TOFA_liver_4

value: liver

value: TOFA


title: artificial insemination 18 days, sample 3

description:
Library name: 3_AI_18d
AI18_03:Counts


title: dbr1-2_mock_mRNA_R1

address: 复旦大学江湾校区生命科学学院

description: Library name: dbr1-2_mock_mRNA_R1


title: artificial insemination 18 days, sample 2

description:
Library name: 2_AI_18d
AI18_02:Counts


title: PA1679-1


title: Liver, HFD, TOFA, rep3

description: Library name: WT_HFD_TOFA_liver_3


title: Col-0_TuMV_mRNA_R3

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_mRNA_R3


title: Liver, HFD, TOFA, rep2

description: Library name: WT_HFD_TOFA_liver_2


title: Col-0_TuMV_mRNA_R2

address: 复旦大学江湾校区生命科学学院

description: Library name: Col-0_TuMV_mRNA_R2


title: PA1126-1

description:
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1
PA1126.xlsx

value: PA1126 mutant