title: hMSCs, 3uM 3 days culture, Sample36

description: Library name: Gr5_3As_day3_S36

source_name: bone marrow

value: bone marrow

value: mesenchymal stromal cells

value: WT

value: male

value: iAsIII

value: sodium arsenite

tag: treatment

value: 3µM iAs

value: 3 days


title: Liver, tissue input, biol rep 2

status: Public on Jul 09 2025

type: SRA

city: Bethesda

first: Gennady

last: Margolin

state: MD

address: 9000 Rockville Pike

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
lcdb-wf pipeline (https://github.com/lcdb/lcdb-wf, v1.9rc)
zebrafish genome assembly version GRCz11/danRer11 and ENSEMBL gene annotation version 99.
R and packages DESeq2, clusterProfiler and GeneTonic
Assembly: danRer11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Danio rerio

source_name: liver

growth_protocol: Tg(kdrl:egfp-2a-rpl10a3xHA)y530 transgenic zebrafish were  housed in a large recirculating aquaculture facility.  Fry were fed rotifers and adults were fed Gemma Micro 300 (Skretting).

extract_protocol:
RNA from either total lysate or immunoprecipitated samples was harvested using RNeasy Micro Plus Kit (Qiagen #74034) with RNA-only ß-Mercaptoethanol supplementation in the RLT buffer
RNA libraries for RNA-seq were prepared by Novogene using SMART-seq V4 Ultra Low Input RNA kit & non-directional library

tag: tissue

value: liver

tag: genotype


title: R2

city: Hangzhou

first: wang

last: my

address: Cangqian Street, Cangxing Street

country: China

institute: BoYu Intelligent Health Innovation Laboratory, Hangzhou, 311100, P. R. China.

data_processing:
The sequences were aligned to the mouse mm10 genome using Bowtie2 and GENCODE database, and gene expression was quantified using HTSeq.
Assembly: mm10
Supplementary files format and content: xlsx file include TMM values for all samples

organism: Mus musculus

source_name: xenograft tumors

extract_protocol:
Total RNA isolation was performed using EASYspin reagent Kit (Aidlab Biotech, Beijing, China) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

value: xenograft tumors

value: treat with RGLS


title: MB166_10xRNA

city: Baden-Württemberg - Heidelberg

first: Piyush

last: Joshi

state: BW

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
Demultiplexing sequencing output was done by cellranger. Alignment to GRCh38 genome assembly was done by STARsolo for snRNA-seq reads.
Assembly: GRCh38, gencodegenes.org
Supplementary files format and content: Raw gene expression matrix for snRNA-seq data. Output of STARsolo alignment.

organism: Homo sapiens

source_name: Cerebellar tumor

extract_protocol:
Frozen tumor tissue was homogenized on ice in 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl (pH 8), 0.1% IGEPAL, 1 µM DTT, 0.4 U/µl Murine RNase Inhibitor. Cellular debris post homogenization was removed by pelleting at 100g for 1 min. Cloudy supernantant was again centrifuged at 400g for 4 minutes to pellet the nuclei. Pelleted nuclei were resuspended in homogenization buffer and pelleted again. Pellted nuclei was now resuspended in Nuclei buffer (10x genomics). Extracted nuclei were processed for single-cell multi-ome, RNA-seq or ATAc-seq run as per manufacturer's recommendation.
Single-cell multiome: Chromium Single Cell Multiome ATAC + Gene Expression. Single-cell RNA: Chromium Single Cell 3' Reagent Kits, V3.1.

value: Cerebellar tumor

tag: cell type

value: Brain tumor


title: OFC astrocytes, KD_GC4

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
KD_GFP_CON.peaks.annotated.txt
KD_GC4_A_S19_L001

library_source: genomic

data_processing:
Raw sequencing reads from mice were aligned to mm10 reference genome using HISAT2.
MACS was utilized to obtain sites of chromatin openness in samples.
diffReps was utilized to find differential sites between groups ZBT vs GFP in OE condition and ZBT-STRESS vs ZBT-CON, ZBT-STRESS vs GFP-STRESS, ZBT-CON vs GFP-CON, GFP-STRESS vs GFP-CON in KD condition.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing peaks

molecule: genomic DNA

source_name: OFC astrocytes

extract_protocol:
50,000 sorted nuclei were centrifuged at 500 ×g
for 10 min, 4°C. Pellets were resuspended in transposase reaction mix (25 μL 2x TD Buffer (Illumina Cat #FC-121-1030) 2.5 μL Tn5 Transposase (Illumina Cat #FC-121-1030) and 22.5 μL Nuclease Free H2O) on ice. Samples were incubated at 37°C for 30 min and then purified using the MinElute Reaction Cleanup kit (Qiagen Cat #28204) according to the manufacturer's instructions.
Following purification, library fragments were amplified using the Nextera index kit (Illumina Cat #FC-121-1011), under the following cycling conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute for a total of 5 cycles. In order to prevent saturation due to over-amplification, a 5µl aliquot was then removed and subjected to qPCR for 20 cycles to calculate the optimal number of cycles needed for the remaining 45 μL reaction. Libraries were amplified for a total of 13–19 cycles, followed by bead purification with Ampure XP beads (Beckman Coulter).

tag: condition

value: KD

tag: virus

value: GFP

tag: group

value: CON

value: OFC astrocytes


title: hMSCs, 3uM 3 days culture, Sample35

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: Gr5_3As_day3_S35

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 R package v1.38.0
Assembly: GRCh38 (hg38) (Homo_sapiens_assembly38)
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the RNA-Seq data alignments.

growth_protocol: human mesenchymal stromal cells from four male donors were expanded to an average population doubling level of 13.4, pooled, then seeded for long term culture and passaged whenever approaching confluence.

extract_protocol:
RNA was isolated using Rneasy mini kit (Qiagen). 1 ug of total RNA was used to construct sequencing libraries.
Library preparation for RNA sequencing was performed using the TruSeq® Stranded mRNA kit with the CD Index plate

treatment_protocol: Seeded cells were cultured for 24 hours to allow recovery, then treated with 0.12, 0.6, and 3.0 µM sodium arsenite and a vehicle control (water)

value: bone marrow

tag: Sex

tag: chemical

tag: chemical longname

tag: time


title: MB89_10xRNA


title: Liver, tissue input, biol rep 1


title: MB90_10xRNA


title: OFC astrocytes, KD_GC2

description:
KD_GFP_CON.peaks.annotated.txt
KD_GC2_A_S15_L001


title: MB5_10xRNA


title: hMSCs, 0.6uM 3 days culture, Sample32

description: Library name: Gr4_0-6As_day3_S32

value: mesenchymal stromal cells

value: 0.6µM iAs


title: hMSCs, 0.6uM 3 days culture, Sample33

description: Library name: Gr4_0-6As_day3_S33

value: WT

value: male


title: whole body, TCE treated, rep3

city: Beijing

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

data_processing:
For single-cell RNA-seq data: demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger software v4.0. For bulk RNA-seq: low-quality reads elimination, mapping and gene counting.
Assembly: GRCz11
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: whole body

extract_protocol:
For single-cell RNA-seq using 10x Genomics, RNA of cells from rostral half at 48 hpf were extracted by 10x Genomics controller following instructions. For bulk RNA-seq, Total RNA of zebrafish at 12 hpf were extracted using TRIzol reagents.
10x Genomics for single-cell RNA-seq following the standard protocol offered by 10x Genomics (single-cell, 3' V2) and bulk RNA-seq using service of Youji Technology Co. Ltd.

value: whole body

value: TCE


title: MB164_10xRNA


title: DKO (Bdh1-KO;shOxct1), day 7 post LmOVA infection, rep5

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Trim reads using TrimGalore! v0.6.0.
Align to mm10 and obtain gene counts based on Gencode vM24 gene annotations using STAR-2.7.8a.
Assembly: mm10
Supplementary files format and content: Tab-delimited files containing gene counts.

molecule: polyA RNA

source_name: CD8+ T cell

growth_protocol: In vitro-activated OT-I CD8+ T cells (Bdh1-WT or Bdh1-KO) were generated by stimulating naïve CD8+ T cells (1e6 cells/mL) with plate-bound anti-CD3ε (clone 2C11) and anti-CD28 (clone 37.51) antibodies (eBioscience, San Diego, CA) and 50 U/mL IL2 (PeproTech, Rocky Hill, NJ) for 24 h. Activated cells were transduced with shRNA contructs targeting firefly luciferase (shCtrl) or Oxct1 (shOxct1), then grown for 2 additional days in medium containing 50 U/ml IL-2. Cells were sorted based on Ametrine+, then transferred into naive C57BL/6 (CD45.1) mice. Mice were infected with LmOVA 1 day later. Cells were isolated by FACS sorting on CD45.2 and Ametrine+ on day 7 post infection.

extract_protocol:
Qiagen RNeasy Kit
Takara Smartseq v4 + Illumina Nextera Flex

value: CD8+ T cell

value: DKO (Bdh1-KO;shOxct1)

value: day 7 post LmOVA infection


title: whole body, TCE treated, rep2


title: hMSCs, 0.6uM 3 days culture, Sample31

description: Library name: Gr4_0-6As_day3_S31

value: iAsIII

value: sodium arsenite

value: 3 days


title: MB98_10xRNA

value: Cerebellar tumor

value: Brain tumor


title: whole body, TCE treated, rep1


title: MB96_10xRNA


title: hMSCs, 0.12uM 3 days culture, Sample30

description: Library name: Gr3_0-12As_day3_S30

value: 0.12µM iAs


title: DKO (Bdh1-KO;shOxct1), day 7 post LmOVA infection, rep4


title: whole body, untreated, rep3


title: DKO (Bdh1-KO;shOxct1), day 7 post LmOVA infection, rep3


title: hMSCs, 0.12uM 3 days culture, Sample29

description: Library name: Gr3_0-12As_day3_S29


title: OFC astrocytes, KD_GC3

description:
KD_GFP_CON.peaks.annotated.txt
KD_GC3_A_S17_L001

value: KD

value: GFP

value: CON

value: OFC astrocytes


title: DKO (Bdh1-KO;shOxct1), day 7 post LmOVA infection, rep2


title: MB272_10xRNA


title: hMSCs, 3uM 3 days culture, Sample34

description: Library name: Gr5_3As_day3_S34

value: bone marrow

value: mesenchymal stromal cells

value: WT

value: 3µM iAs


title: DKO (Bdh1-KO;shOxct1), day 7 post LmOVA infection, rep1

value: CD8+ T cell


title: whole body, untreated, rep1

value: whole body


title: hMSCs, vehicle 3 days culture, Sample27

description: Library name: Gr2_0As_day3_S27

value: male

value: untreated

value: vehicle (water)


title: MB296_10xRNA


title: MB248_10xRNA


title: whole body, untreated, rep2


title: hMSCs, 0.12uM 3 days culture, Sample28

description: Library name: Gr3_0-12As_day3_S28

value: iAsIII

value: sodium arsenite

value: 3 days


title: OFC astrocytes, KD_GC1

description:
KD_GFP_CON.peaks.annotated.txt
KD_GC1_A_S13_L001


title: Skin, tissue input, biol rep 2

source_name: skin

value: skin


title: rostral half, grem1a-dcas9

description: 10x Genomics

library_source: transcriptomic single cell

source_name: rostral half

value: rostral half


title: MB18_10xRNA

value: Cerebellar tumor

value: Brain tumor


title: hMSCs, vehicle 3 days culture, Sample26

description: Library name: Gr2_0As_day3_S26


title: Control (Bdh1-WT;shCtrl), day 7 post LmOVA infection, rep4

value: Control (Bdh1-WT;shCtrl)

value: day 7 post LmOVA infection


title: Control (Bdh1-WT;shCtrl), day 7 post LmOVA infection, rep3


title: MB278_10xRNA


title: hMSCs, vehicle 3 days culture, Sample25

description: Library name: Gr2_0As_day3_S25

value: bone marrow

value: mesenchymal stromal cells


title: rostral half, dcas9

description: 10x Genomics


title: hMSCs, 3uM 30 days culture, Sample24

description: Library name: Gr9_3As_day30_S24

value: WT

value: 3µM iAs

value: 30 days


title: Combined_10xRNA


title: Control (Bdh1-WT;shCtrl), day 7 post LmOVA infection, rep2

value: CD8+ T cell


title: Neonatal rat ventricular myocytes, no doxorubicin, negative control mimic, replicate 2

city: Ann Arbor

first: Anthony

last: Rosenzweig

state: Michigan

address: 2800 Plymouth Rd, NCRC Building 25

department: Stanley and Judith Frankel Institute for Heart and Brain Health

institute: University of Michigan Medical Center

description:
Library name: U_Neg_2
U_Neg_2

data_processing:
Paired-end RNA-seq reads were trimmed of their adapter sequences and filtered for quality using the BBTools software package (executable: bbduk.sh;  parameters: ktrim=r k=21 mink=11 tbo tpe hdist=2 minlen=31). Adapter-trimmed reads were further filtered to remove low-quality bases at the 3’ ends of each read as well as ensure a reasonable overall read quality (executable: bbduk.sh;  parameters: qtrim=r trimq=10 maq=10).  Finally, low-complexity, homopolymer reads were removed (executable: bbduk.sh;  parameters: entropy=0.3 entropywindow=50 entropyk=5), as were reads matching PhiX sequences (executable: bbduk.sh;  parameters: ref=phix.fa k=31 hdist=1).
Trimmed, filtered reads were mapped to the reference transcriptome using the Salmon software package. (executable: salmon quant; parameters: --seqBias --gcBias -l A --numBootstraps=20 --validateMappings --allowDovetail).
Per-sample transcript-level quantifications were processed and aggregated to the gene level using tximport, a R/Bioconductor package. Gene-level counts were filtered to retain contributions from more useful biotypes - broadly these included: protein_coding, antisense, pseudogene, processed_pseudogene, processed_transcript, transcribed_processed_pseudogene, transcribed_unprocessed_pseudogene.  Genes were further filtered to remove those with no counts in any sample.
Per-sample gene-level read counts for genes surviving the above filters were normalized using the DESeq2 R/Bioconductor package.
Assembly: Rnor_6.0/Ensembl 98
Supplementary files format and content: Text file includes raw read counts for each sample

organism: Rattus norvegicus

source_name: Neonatal rat ventricular myocytes

growth_protocol: Isolated and purified neonatal rat ventricular cardiomyocytes (NRVMs) were plated at 1x10^6 cells/well in 6-well Primaria tissue culture dishes coated with 0.2% gelatin solution in DMEM (high glucose, with sodium pyruvate, Corning cat. #10-013-CV) supplemented with 10% horse serum, 5% fetal bovine serum  and 1% penicillin/streptomycin/L-glutamine

extract_protocol:
RNA was extracted with Trizol. Cleanup of RNA samples was performed by re-purification using the Zymo Quick-RNA MicroPrep kit. RNA was eluted in nuclease-free water.
Library construction was performed by Novogene (Durham, NC) according to their in-house protocol

treatment_protocol: The day after plating, cells were forward-transfected with miRNA mimics of miR-222-3p and/or miR-455-ep or Negative control mimic at 5nM each using Lipofectamine RNAiMax. 4uM doxorubicin or control treatment began 48h after transfection and lasted 24h.

value: Neonatal rat ventricular myocytes

value: Sprague-Dawley

value: no doxorubicin, negative control mimic


title: Neonatal rat ventricular myocytes, no doxorubicin, negative control mimic, replicate 3

description:
Library name: U_Neg_3
U_Neg_3


title: hMSCs, 3uM 30 days culture, Sample23

description: Library name: Gr9_3As_day30_S23

value: male

value: iAsIII

value: sodium arsenite


title: sample54_BIP_WT_CLP_1

city: Nanning

first: Maosen

last: Yang

state: Guangxi

address: No. 100, Daxue East Road

institute: Guangxi University

description: Library name: BIP_WT_CLP_1

data_processing:
Low-quality reads were removed and the Q20 and Q30 values and the GC content were calculated for the clean reads.
Clean data were mapped to the pig reference genome (Sscrofa11.1) using STAR software (v2.7.6a)
Kallisto (v0.44.0) was used to quantify gene expression in transcripts per kilobase per million mapped reads (TPM)
Assembly: Sscrofa11.1
Supplementary files format and content: CSV file containing counts values for each sample
Supplementary files format and content: CSV file containing TPM values for each sample

organism: Sus scrofa

source_name: muscle

extract_protocol:
Muscle tissue sample was homogenized in a tissue grinder for total RNA extraction using TRIzol (Invitrogen, USA) extraction method.
The purity of the total RNA was estimated using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The integrity and concentration of total RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 54 rRNA-depleted and random priming RNA-seq libraries were constructed.

value: muscle

tag: anatomical region

value: BIP


title: Neonatal rat ventricular myocytes, no doxorubicin, negative control mimic, replicate 1

description:
Library name: U_Neg_1
U_Neg_1


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-222 and miR-455 mimics, replicate 3

description:
Library name: U_639_3
U_639_3

value: no doxorubicin, miR-222 mimic, miR-455 mimic


title: sample53_BIP_WT_CLP_2

description: Library name: BIP_WT_CLP_2


title: hMSCs, 3uM 30 days culture, Sample22

description: Library name: Gr9_3As_day30_S22


title: hMSCs, 3uM 30 days culture, Sample21

description: Library name: Gr9_3As_day30_S21


title: T-2465, snRNA

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

description: 10X Genomics

data_processing:
Read alignment was performed using the CellRanger pipeline (v6.1.2−10X genomics) to reference GRCh38.p12 (refdata-cellranger-GRCh38-1.2.0 file provided by 10x Genomics). Count matrices were generated from BAM files using default parameters of the CellRanger pipeline
Filtering and QC was performed using DecontX, with default parameters, for the cingulate dataset, and CellBender for the SN dataset. CellBender (version 0.2.0) was run to remove ambient RNA with the addition of the '-cuda' flag to expedite the processing. Parameters were set with an expected cell count of 10,000, total droplets included at 30,000, FPR (false-positive rate) at 0.01, and a learning rate of 0.0001, utilizing 150 epochs. The total runtime for each sample ranged from 30 minutes to 1 hour, with acceleration achieved through the use of the NVIDIA A5000 GPU
Normalization of counts was done using the SCTransform function in Seurat, accounting for mitochondrial reads. Nuclei with percent reads aligning to mitochondrial genes >14% were excluded. Genes were filtered by keeping features with >500 counts per row in at least 100 cells. Doublets were identified using scDblFinder and then removed.
Assembly: GRCh38
Supplementary files format and content: .csv files of matrix that are gzipped

source_name: Cingulate Cortex

extract_protocol:
The tissue was homogenized in a Dounce homogenizer with 12–15 strokes of the loose pestle and 12–15 strokes of the tight pestle on ice in a Triton X-100 based, sucrose containing buffer. The suspension from each sample was filtered through a BD Falcon tubes with a cell strainer caps (Becton Dickinson, cat. no. 352235), washed, re-filtered, washed, followed by a cleanup step using iodixanol gradient centrifugation. The nuclear pellet was then re-suspended in 1% BSA in 545 nuclease-free PBS (containing RNAse inhibitors) and titrated to 600-1200 nuclei/μl.
Nuclear suspensions were processed by the Chromium Controller (10x Genomics) using single Cell 3′ Reagent Kit v2 or v3 (Chromium Single Cell 3′ Library & Gel Bead Kit v2/v3, catalog number PN-1000075; Chromium Single Cell A Chip Kit, 48 runs, catalog number: 120236; 10x Genomics). Sequencing and alignment: Sequencing of the snRNAseq libraries was done on Illumina NOVAseq 6000 platformV4 150 bp paired end reads.
snRNA (single-nuclei RNA sequencing)

value: Cingulate Cortex

value: F

tag: age

value: Control


title: sample52_BIP_WT_CLP_3

description: Library name: BIP_WT_CLP_3


title: T-4530, snRNA

description: 10X Genomics

source_name: Substantia Nigra

value: Substantia Nigra

value: M

value: PD


title: hMSCs, 0.6uM 30 days culture, Sample20

description: Library name: Gr8_0-6As_day30_S20

value: bone marrow

value: mesenchymal stromal cells

value: WT

value: 0.6µM iAs

value: 30 days


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-222 and miR-455 mimics, replicate 2

description:
Library name: U_639_2
U_639_2

value: Neonatal rat ventricular myocytes

value: Sprague-Dawley


title: sample51_BIP_ZBED6_KO_CLP_1

description: Library name: BIP_ZBED6_KO_CLP_1

value: ZBED6 knockout


title: T-5385, snRNA

description: 10X Genomics


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-222 and miR-455 mimics, replicate 1

description:
Library name: U_639_1
U_639_1


title: sample50_BIP_ZBED6_KO_CLP_2

description: Library name: BIP_ZBED6_KO_CLP_2

value: muscle


title: OJ5, snRNA

description: 10X Genomics


title: hMSCs, 0.6uM 30 days culture, Sample18

description: Library name: Gr8_0-6As_day30_S18

value: male

value: iAsIII

value: sodium arsenite


title: hMSCs, 0.6uM 30 days culture, Sample19

description: Library name: Gr8_0-6As_day30_S19


title: sample49_BIP_ZBED6_KO_CLP_3

description: Library name: BIP_ZBED6_KO_CLP_3

value: BIP


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-455 mimic, replicate 3

description:
Library name: U_455_3
U_455_3

value: no doxorubicin, miR-455 mimic


title: Control (Bdh1-WT;shCtrl), day 7 post LmOVA infection, rep1

value: CD8+ T cell

value: Control (Bdh1-WT;shCtrl)

value: day 7 post LmOVA infection


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-455 mimic, replicate 2

description:
Library name: U_455_2
U_455_2


title: hMSCs, 0.6uM 30 days culture, Sample17

description: Library name: Gr8_0-6As_day30_S17

value: bone marrow


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-455 mimic, replicate 1

description:
Library name: U_455_1
U_455_1


title: hMSCs, 0.12uM 30 days culture, Sample16

description: Library name: Gr7_0-12As_day30_S16

value: mesenchymal stromal cells

value: 0.12µM iAs


title: T-4210, snRNA

description: 10X Genomics

value: Cingulate Cortex

value: M

value: Control


title: sample48_EDL_WT_CLP_1

description: Library name: EDL_WT_CLP_1

value: EDL

value: WT


title: T-4424, snRNA

description: 10X Genomics

value: Substantia Nigra

value: PD


title: T-3799, snRNA

description: 10X Genomics

value: F


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-222 mimic, replicate 3

description:
Library name: U_222_3
U_222_3

value: Neonatal rat ventricular myocytes

value: Sprague-Dawley

value: no doxorubicin, miR-222 mimic


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-222 mimic, replicate 2

description:
Library name: U_222_2
U_222_2


title: T-5133, snRNA

description: 10X Genomics


title: Neonatal rat ventricular myocytes, no doxorubicin, miR-222 mimic, replicate 1

description:
Library name: U_222_1
U_222_1


title: sample47_EDL_WT_CLP_2

description: Library name: EDL_WT_CLP_2

value: muscle


title: sample45_EDL_ZBED6_KO_CLP_1

description: Library name: EDL_ZBED6_KO_CLP_1

value: ZBED6 knockout


title: hMSCs, 0.12uM 30 days culture, Sample15

description: Library name: Gr7_0-12As_day30_S15

value: male

value: iAsIII

value: sodium arsenite

value: 30 days


title: hMSCs, 0.12uM 30 days culture, Sample14

description: Library name: Gr7_0-12As_day30_S14

value: bone marrow

value: mesenchymal stromal cells

value: 0.12µM iAs


title: T-5227, snRNA

description: 10X Genomics

value: M

value: Control


title: T-5259, snRNA

description: 10X Genomics

value: Substantia Nigra


title: hMSCs, 0.12uM 30 days culture, Sample13

description: Library name: Gr7_0-12As_day30_S13

value: WT


title: T-5547, snRNA

description: 10X Genomics

value: F


title: Neonatal rat ventricular myocytes, doxorubicin, negative control mimic, replicate 2

description:
Library name: D_Neg_2
D_Neg_2

value: Neonatal rat ventricular myocytes

value: doxorubicin, negative control mimic


title: sample43_EDL_ZBED6_KO_CLP_3

description: Library name: EDL_ZBED6_KO_CLP_3

value: EDL


title: hMSCs, vehicle 30 days culture, Sample12

description: Library name: Gr6_0As_day30_S12

value: untreated

value: vehicle (water)


title: T-5359, snRNA

description: 10X Genomics


title: sample44_EDL_ZBED6_KO_CLP_2

description: Library name: EDL_ZBED6_KO_CLP_2

value: muscle

value: ZBED6 knockout


title: Neonatal rat ventricular myocytes, doxorubicin, negative control mimic, replicate 3

description:
Library name: D_Neg_3
D_Neg_3

value: Sprague-Dawley


title: T-4116, snRNA

description: 10X Genomics


title: hMSCs, vehicle 30 days culture, Sample11

description: Library name: Gr6_0As_day30_S11

value: male

value: 30 days


title: Neonatal rat ventricular myocytes, doxorubicin, negative control mimic, replicate 1

description:
Library name: D_Neg_1
D_Neg_1


title: hMSCs, vehicle 30 days culture, Sample10

description: Library name: Gr6_0As_day30_S10

value: bone marrow

value: mesenchymal stromal cells


title: Neonatal rat ventricular myocytes, doxorubicin, miR-222 and miR-455 mimics, replicate 3

description:
Library name: D_639_3
D_639_3

value: doxorubicin, miR-222 mimic, miR-455 mimic


title: T-4839, snRNA

description: 10X Genomics

value: PD


title: sample42_GAS_WT_CLP_1

description: Library name: GAS_WT_CLP_1

value: GAS


title: sample41_GAS_WT_CLP_2

description: Library name: GAS_WT_CLP_2

value: WT


title: hMSCs, vehicle 30 days culture, Sample9

description: Library name: Gr6_0As_day30_S9


title: sample46_EDL_WT_CLP_3

description: Library name: EDL_WT_CLP_3


title: Neonatal rat ventricular myocytes, doxorubicin, miR-222 and miR-455 mimics, replicate 2

description:
Library name: D_639_2
D_639_2


title: T-2007, snRNA

description: 10X Genomics

value: Substantia Nigra

value: F


title: sample40_GAS_WT_CLP_3

description: Library name: GAS_WT_CLP_3


title: hMSCs, 3uM 3 days culture, Sample8

description: Library name: Gr5_3As_day3_S8

value: iAsIII

value: sodium arsenite

value: 3µM iAs

value: 3 days


title: T-4938, snRNA

description: 10X Genomics

value: M


title: Neonatal rat ventricular myocytes, doxorubicin, miR-222 and miR-455 mimics, replicate 1

description:
Library name: D_639_1
D_639_1

value: Neonatal rat ventricular myocytes


title: sample38_GAS_ZBED6_KO_CLP_2

description: Library name: GAS_ZBED6_KO_CLP_2

value: muscle

value: ZBED6 knockout


title: T-5498, snRNA

description: 10X Genomics


title: hMSCs, 0.12uM 3 days culture, Sample6

description: Library name: Gr3_0-12As_day3_S6

value: male

value: 0.12µM iAs


title: T-2791, snRNA

description: 10X Genomics

value: Control


title: Neonatal rat ventricular myocytes, doxorubicin, miR-455 mimic, replicate 2

description:
Library name: D_455_2
D_455_2

value: Sprague-Dawley

value: doxorubicin, miR-455 mimic


title: hMSCs, untreated 3 days before experiment, Sample4

description: Library name: Gr1_0As_dayminus7_S4

value: bone marrow

value: mesenchymal stromal cells

value: untreated

value: minus 3 days


title: sample37_GAS_ZBED6_KO_CLP_3

description: Library name: GAS_ZBED6_KO_CLP_3

value: GAS


title: Neonatal rat ventricular myocytes, doxorubicin, miR-455 mimic, replicate 1

description:
Library name: D_455_1
D_455_1


title: T-4934, snRNA

description: 10X Genomics

value: Substantia Nigra

value: PD


title: sample36_LD_WT_CLP_1

description: Library name: LD_WT_CLP_1

value: LD

value: WT


title: hMSCs, vehicle 3 days culture, Sample5

description: Library name: Gr2_0As_day3_S5

value: vehicle (water)

value: 3 days


title: T-0081, snRNA

description: 10X Genomics

value: F


title: Neonatal rat ventricular myocytes, doxorubicin, miR-222 mimic, replicate 2

description:
Library name: D_222_2
D_222_2

value: Neonatal rat ventricular myocytes

value: doxorubicin, miR-222 mimic


title: sample34_LD_WT_CLP_3

description: Library name: LD_WT_CLP_3

value: muscle


title: T-4515, snRNA

description: 10X Genomics

value: M


title: Neonatal rat ventricular myocytes, doxorubicin, miR-222 mimic, replicate 3

description:
Library name: D_222_3
D_222_3

value: Sprague-Dawley


title: hMSCs, untreated 3 days before experiment, Sample3

description: Library name: Gr1_0As_dayminus7_S3

value: bone marrow

value: male


title: sample35_LD_WT_CLP_2

description: Library name: LD_WT_CLP_2


title: hMSCs, untreated 3 days before experiment, Sample2

description: Library name: Gr1_0As_dayminus7_S2

value: mesenchymal stromal cells

value: untreated


title: Neonatal rat ventricular myocytes, doxorubicin, miR-222 mimic, replicate 1

description:
Library name: D_222_1
D_222_1


title: hMSCs, 0.6uM 3 days culture, Sample7

description: Library name: Gr4_0-6As_day3_S7

value: iAsIII

value: sodium arsenite

value: 0.6µM iAs


title: sample39_GAS_ZBED6_KO_CLP_1

description: Library name: GAS_ZBED6_KO_CLP_1

value: GAS

value: ZBED6 knockout


title: hMSCs, untreated 3 days before experiment, Sample1

description: Library name: Gr1_0As_dayminus7_S1

value: WT

value: minus 3 days


title: T-4235, snRNA

description: 10X Genomics

value: Substantia Nigra

value: F

value: Control


title: T-4815, snRNA

description: 10X Genomics

value: PD


title: HD.8-NDNs, NSCLC.5-NDNs/LDNs, NSCLC.6-NDNs/LDNs, scRNA-seq

city: Verona

first: Patrizia

last: Scapini

state: VR

address: strada le grazie,8

department: Medicine

country: Italy

institute: University of Verona

description:
Library name: HD8_NSCLC5_NSCLC6
BD-Rhapsody

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
FASTQ files obtained from sequencing were provided to the BD Rhapsody WTA Analysis Pipeline Targeted Multiplex Rhapsody Pipeline v1.0 or v2.0 with default settings
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence. Putative cells information were combined together with RSEC-adjusted molecules to generate a single-cell expression matrix.
Raw gene expression matrices were read into R (4.2) separately and converted to Seurat objects using the Seurat R package (4.1.1)
Assembly: Genome_build: hg38
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell
Library strategy: CITE-seq

source_name: Peripheral blood

extract_protocol:
Total CD66b+ neutrophils from the LDN and NDN fractions of peripheral blood from NSCLC patients and G-CSF-treated donors, and the NDN fraction of peripheral blood from healthy donors (HDs) as controls, were isolated by magnetic bead selection with fluorescence-conjugated anti-CD66b mAbs and processed with BD Rhapsody Single-Cell Analysis System for scRNA-seq.
cDNA Libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification kit and BD Single-Cell Multiplexing kit (BD Biosciences) following the manufacturer's protocol

value: Peripheral blood

tag: cell line

value: neutrophils

value: CD66b+ NDNs/LDNs

value: HD, NSCLC tumor

tag: batch


title: GD.5-NDNs/LDNs, GD.6-NDNs/LDNs, HD.7-NDNs, scRNA-seq

description:
Library name: GD5_GD6_HD7
BD-Rhapsody

value: HD, G-CSF administration


title: Neonatal rat ventricular myocytes, doxorubicin, miR-455 mimic, replicate 3

description:
Library name: D_455_3
D_455_3

value: Neonatal rat ventricular myocytes

value: Sprague-Dawley

value: doxorubicin, miR-455 mimic


title: KO_HX_2_smallRNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: KO fibroblasts / hypoxia

data_processing:
AB Small RNA pipeline v5.0 matching, normalization to 1.000.000 miRNAs count in each sample
Assembly: mmu9
Supplementary files format and content: Tab-delimited file include raw counts for each sample

source_name: mouse immortalized fibroblasts derived from mir210lox/lox mice

extract_protocol:
Total RNA was extracted using the RNA extraction kit (miRNeasy Qiagen) according to manufacturer’s instructions.
RNA libraries were generated with the NEB next small library prep set for SOLID.

treatment_protocol: Cells were cultured in normoxic (21% O2) or hypoxic (1% O2) for 24 hours

value: skin

value: mouse immortalized fibroblasts

value: C57BL/6 (mir210lox/lox)

value: hypoxia (Hx)


title: T-3998, snRNA

description: 10X Genomics

value: M


title: KO_HX_1_smallRNA

description: KO fibroblasts / hypoxia


title: sample30_PMM_WT_CLP_1

description: Library name: PMM_WT_CLP_1

value: muscle

value: PMM

value: WT


title: sample32_LD_ZBED6_KO_CLP_2

description: Library name: LD_ZBED6_KO_CLP_2

value: LD

value: ZBED6 knockout


title: KO_NX_1_smallRNA

description: KO fibroblasts / normoxia

value: normoxia (Nx)


title: sample29_PMM_WT_CLP_2

description: Library name: PMM_WT_CLP_2


title: sample28_PMM_WT_CLP_3

description: Library name: PMM_WT_CLP_3


title: sample31_LD_ZBED6_KO_CLP_3

description: Library name: LD_ZBED6_KO_CLP_3


title: sample33_LD_ZBED6_KO_CLP_1

description: Library name: LD_ZBED6_KO_CLP_1


title: KO_NX_2_smallRNA

description: KO fibroblasts / normoxia


title: sample27_PMM_ZBED6_KO_CLP_1

description: Library name: PMM_ZBED6_KO_CLP_1


title: T-3860, snRNA

description: 10X Genomics

value: Cingulate Cortex

value: PD


title: WT_NX_2_smallRNA

description: WT fibroblasts / normoxia

source_name: mouse immortalized fibroblasts derived from WT mice


title: T-4162, snRNA

description: 10X Genomics


title: HD.2-NDNs, GD.2-NDNs/LDNs, NSCLC.2-LDNs, scRNA-seq

description:
Library name: HD2_GD2_NSCLC2
BD-Rhapsody

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.422
FASTQ files obtained from sequencing were provided to the BD Rhapsody WTA Analysis Pipeline Targeted Multiplex Rhapsody Pipeline v1.0 or v2.0 with default settings
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence. Putative cells information were combined together with RSEC-adjusted molecules to generate a single-cell expression matrix.
Raw gene expression matrices were read into R (4.2) separately and converted to Seurat objects using the Seurat R package (4.1.1)
Assembly: Genome_build: hg38
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell

value: Peripheral blood

value: neutrophils

value: CD66b+ NDNs/LDNs

value: HD, G-CSF administration, NSCLC tumor


title: T-4857, snRNA

description: 10X Genomics

value: Substantia Nigra

value: Control


title: WT_HX_1_smallRNA

description: WT fibroblasts / hypoxia

value: skin

value: mouse immortalized fibroblasts


title: sample26_PMM_ZBED6_KO_CLP_2

description: Library name: PMM_ZBED6_KO_CLP_2


title: HD.1-NDNs, GD.1-NDNs/LDNs, NSCLC.1-LDNs, scRNA-seq

description:
Library name: HD1_GD1_NSCLC1
BD-Rhapsody


title: T-233, snRNA

description: 10X Genomics

value: M


title: KO_HX_2_RNA

description: KO fibroblasts / hypoxia

data_processing:
Reads were first filtered to remove SOLiD adaptors, SOLiD barcodes and rRNAs reads. Alignment was performed within Lifescope 2.5.1 software RNAseq pipeline using default parameters. Raw sequence reads were counts and rpkm was calculated by Lifescope 2.5.1
Assembly: mmu9
Supplementary files format and content: Tab-delimited file include raw counts for each sample

value: C57BL/6 (mir210lox/lox)

value: hypoxia (Hx)


title: sample25_PMM_ZBED6_KO_CLP_3

description: Library name: PMM_ZBED6_KO_CLP_3

value: muscle

value: PMM


title: T-1976, snRNA

description: 10X Genomics


title: T-4462, snRNA

description: 10X Genomics


title: sample24_RA_WT_CLP_1

description: Library name: RA_WT_CLP_1

value: RA

value: WT


title: WT_HX_2_smallRNA

description: WT fibroblasts / hypoxia


title: KO_NX_2_RNA

description: KO fibroblasts / normoxia

value: normoxia (Nx)


title: T-2017, snRNA

description: 10X Genomics

value: Cingulate Cortex


title: IL-18

city: Brno

first: Ioanna

last: Papatheodorou

address: Studentska

department: Center for Translational Medicine

country: Czech Republic

institute: International Clinical Research Center (ICRC), St.Anne’s Hospital

description: Library name: IL-18

data_processing:
Cellranger 8.0.1
Barcode processing, gene counting and aggregation were made using cellranger multi command
reference – refdata-gex-GRCh38-2024-A
probe-set – Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv
Assembly: GRCh38
Supplementary files format and content: Processed counts from filtered feature matrices are in MTX format with barcodes and gene names in tsv format and counts as mtx file.

source_name: human intestinal organoids & human monocytes

growth_protocol: IOs were differentiated from human induced pluripotent cells (hiPSCs) using an adapted protocol (Jose SS et al., 2020; McCracken KW et al., 2011). In brief, hiPSCs were differentiated to definitive endoderm (DE) using Activin A (100 ng/mL, R&D) in RPMI-1640 (Gibco) with increasing concentration of HyClone-defined fetal bovine serum (HC FBS) (GE Healthcare Bio-Sciences) (first day 0%, second day 0.2% and third and fourth day 2%). Next, the DE was differentiated to mid- and hindgut using RPMI-1640 supplemented with 15 mM HEPES, 2% HC FBS, FGF-4 (500 ng/mL, R&D), and WNT-3a (500 ng/mL, R&D) until 3D spheroids were observed. Spheroids were collected and seeded in Cultrex Membrane Extract, Type 2 (R&D). The spheroids were fed with IOs medium (Advanced DMEM F12 (Gibco) supplemented with 15 mM HEPES, B27 supplement (Thermo Fisher Scientific), GlutaMAX supplement (Thermo Fisher Scientific), P/S (500 U/mL), R-Spondin 1 (500 ng/mL, R&D), Noggin (100 ng/mL, R&D), and EGF (100 ng/mL, R&D)). The medium was changed twice a week. IOs that were at least 50 days old were used for the experiments.

extract_protocol:
Single cell suspensions were prepared via washing of IOs with cold Hank's balanced salt solution (HBSS, Gibco, Brooklyn, NY, USA), dissociation with TrypLE (Gibco, Brooklyn, NY, USA) and filtering through a 70-μm strainer. Dead cells and doublets were removed by use of the Dead cell removal kit (Miltenyi Biotec, Cologne, Germany) according to the manufacturer’s protocol.
Cells were fixed with Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit and hybridized with Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit according to the manufacturer’s guidelines (10X Genomics, Pleasanton, CA, USA). After the hybridization, cell suspensions were washed several times, passed through 30 µm filter and single-cell gel beads in emulsion (GEMs) were created by use of the Chromium Next GEM Single Cell Fixed RNA Gel Bead Kit and Chromium X instrument (10x Genomics, Pleasanton, CA, USA ). Single cell libraries were constructed with Chromium Next GEM Single Cell Fixed RNA Hybridization & Library Kit (10x Genomics, Pleasanton, CA, USA ). Libraries were equimolarly pooled and were sequenced using Illumina NovaSeq X.
single-cell RNAseq

treatment_protocol: IOs were co-cultivated with healthy donor monocytes and stimulated with IL-18 (50 ng/mL) and untreated controls were washed with cold PBS and the Cultrex was removed using Corning® Cell Recovery Solution (Corning) for 20 minutes at 4 °C.

value: induced pluripotent stem cells (iPSC)

value: IL-18 50ng/ml


title: GD.3-NDNs/LDNs, NSCLC.3-NDNs, NSCLC.4-NDNs/LDNs, scRNA-seq

description:
Library name: GD3_NSCLC3_NSCLC4
BD-Rhapsody

value: Peripheral blood

value: neutrophils

value: CD66b+ NDNs/LDNs

value: G-CSF administration, NSCLC tumor


title: T-4174, snRNA

description: 10X Genomics

value: Control


title: Time point T2 replicate 8

description: Library name: Ort7T2

data_processing:
Sequences were trimmed for adaptors/low quality sequences using Trim galore with default parameters.
Trimmed sequences were mapped to GRCh38-p10 (human genome) with HISAT2 using the default parameteres.
Read counts were determined with Htseq -count.
Raw gene counts were normalized following VST transformation by use of the package DESeq2 in the R v4.3.3. environment.
Differentially expressed genes were determined with DESeq2 in the R v4.3.3. enviroment.
Assembly: GRCh38-p10
Supplementary files format and content: The txt delimited file named Raw_counts_ORT_patients_bulkRNAseq.txt contains all the raw HTseq derived counts.
Supplementary files format and content: The txt delimited file named Normalized_counts_ORT_patients_bulkRNAseq.txt contains all the normalized counts following VST transformation.

source_name: peripheral blood

extract_protocol:
Cells were isolated from whole blood of orthopedic surgery patients using the negative selection RosetteSep kit (STEMCELL Technologies). Cells were lysed in of TRI Reagent®. The RNA was isolated using the RNeasy mini kit (Qiagen).
Libraries were constructed with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD using 250 ng of RNA as input
bulk RNAseq

value: peripheral blood

value: primary monocytes


title: sample23_RA_WT_CLP_2

description: Library name: RA_WT_CLP_2


title: HD.3-NDNs,  HD.4-NDNs, scRNA-seq

description:
Library name: HD3_HD4
BD-Rhapsody

value: CD66b+ NDNs

value: HD


title: sample22_RA_WT_CLP_3

description: Library name: RA_WT_CLP_3

value: muscle


title: Time point T1 replicate 8

description: Library name: Ort7T1


title: KO_NX_1_RNA

description: KO fibroblasts / normoxia

value: skin

value: mouse immortalized fibroblasts

value: C57BL/6 (mir210lox/lox)


title: T-1952, snRNA

description: 10X Genomics

value: M


title: sample21_RA_ZBED6_KO_CLP_1

description: Library name: RA_ZBED6_KO_CLP_1

value: RA

value: ZBED6 knockout


title: Time point T0 replicate 8

description: Library name: Ort7T0

value: WT


title: KO_HX_1_RNA

description: KO fibroblasts / hypoxia

value: hypoxia (Hx)


title: T-308, snRNA

description: 10X Genomics

value: Cingulate Cortex

value: PD


title: sample20_RA_ZBED6_KO_CLP_2

description: Library name: RA_ZBED6_KO_CLP_2


title: T-777, snRNA

description: 10X Genomics

value: F


title: WT_HX_2_RNA

description: WT fibroblasts / hypoxia


title: WT_NX_1_smallRNA

description: WT fibroblasts / normoxia

value: normoxia (Nx)


title: Time point T2 replicate 7

description: Library name: Ort40T2

value: peripheral blood


title: T-1619, snRNA

description: 10X Genomics

value: Control


title: sample19_RA_ZBED6_KO_CLP_3

description: Library name: RA_ZBED6_KO_CLP_3


title: Time point T1 replicate 7

description: Library name: Ort40T1

value: primary monocytes


title: WT_HX_1_RNA

description: WT fibroblasts / hypoxia


title: WT_NX_2_RNA

description: WT fibroblasts / normoxia


title: T-290, snRNA

description: 10X Genomics


title: sample18_SOL_WT_CLP_1

description: Library name: SOL_WT_CLP_1

value: SOL


title: Time point T0 replicate 7

description: Library name: Ort40T0


title: WT_NX_1_RNA

description: WT fibroblasts / normoxia


title: Time point T2 replicate 6

description: Library name: Ort36T2


title: T-257, snRNA

description: 10X Genomics


title: sample16_SOL_WT_CLP_3

description: Library name: SOL_WT_CLP_3

value: muscle


title: sample17_SOL_WT_CLP_2

description: Library name: SOL_WT_CLP_2


title: T-343, snRNA

description: 10X Genomics


title: AP61973

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description: Moderate-plane of nutrition

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS-UCD1.2) using the miRDeep2 package (version 2.00.8), the miRDeep2 quantifier module was used to quantify all expressed miRNAs in the sequence data, producing read counts for each individual sample.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: Anterior pituitary

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

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

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

value: Anterior pituitary

value: Holstein-Friesian

value: Moderate


title: sample15_SOL_ZBED6_KO_CLP_1

description: Library name: SOL_ZBED6_KO_CLP_1


title: GD.4-NDNs/LDNs, HD.5-NDNs, HD.6-NDNs, scRNA-seq

description:
Library name: GD4_HD5_HD6
BD-Rhapsody

value: Peripheral blood

value: neutrophils

value: CD66b+ NDNs/LDNs

value: HD, G-CSF administration


title: Time point T0 replicate 6

description: Library name: Ort36T0

value: WT


title: Time point T1 replicate 6

description: Library name: Ort36T1


title: AP61965

description: Moderate-plane of nutrition


title: T-362, snRNA

description: 10X Genomics

value: Cingulate Cortex


title: sample14_SOL_ZBED6_KO_CLP_2

description: Library name: SOL_ZBED6_KO_CLP_2

value: ZBED6 knockout


title: HUVECs, SFTSV infection, 12h, rep3

city: Nanjing

last: Jiang

address: Hankou Road

institute: Nanjing University

data_processing:
Cutadapt software (version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (version:hisat2-2.0.4) to map reads to the genome.
The mapped reads of each sample were assembled using StringTie (version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2,and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: Homo sapiens Ensembl v96
Supplementary files format and content: tab-delimited text file include raw counts for each Sample
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: HUVECs

growth_protocol: HUVECs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).1 ug of total RNA was used for the construction of sequencing libraries.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: HUVECs

value: Human Umbilical Vein Endothelial Cells


title: Time point T2 replicate 5

description: Library name: Ort35T2

value: peripheral blood


title: AP57867

description: Moderate-plane of nutrition


title: sample13_SOL_ZBED6_KO_CLP_3

description: Library name: SOL_ZBED6_KO_CLP_3


title: Time point T1 replicate 5

description: Library name: Ort35T1


title: HUVECs, SFTSV infection, 12h, rep2


title: Time point T0 replicate 5

description: Library name: Ort35T0


title: sample12_TA_WT_CLP_1

description: Library name: TA_WT_CLP_1

value: TA


title: T-551, snRNA

description: 10X Genomics

value: F

value: Control


title: AP51980

description: Moderate-plane of nutrition


title: AP57826

description: Moderate-plane of nutrition


title: HUVECs, SFTSV infection, 12h, rep1


title: Time point T2 replicate 4

description: Library name: Ort27T2

value: primary monocytes


title: sample11_TA_WT_CLP_2

description: Library name: TA_WT_CLP_2

value: muscle


title: HUVECs, control, 12h, rep3


title: Control

description: Library name: Control

value: human intestinal organoids & human monocytes

value: induced pluripotent stem cells (iPSC)

value: Untreated


title: AP73759

description: Moderate-plane of nutrition

value: Anterior pituitary

value: Holstein-Friesian

value: Moderate


title: sample10_TA_WT_CLP_3

description: Library name: TA_WT_CLP_3

value: WT


title: Time point T1 replicate 4

description: Library name: Ort27T1


title: AP47874

description: Moderate-plane of nutrition


title: HUVECs, control, 12h, rep2


title: sample9_TA_ZBED6_KO_CLP_1

description: Library name: TA_ZBED6_KO_CLP_1


title: AP87886

description: Moderate-plane of nutrition


title: HUVECs, control, 12h, rep1


title: Time point T0 replicate 4

description: Library name: Ort27T0


title: AP97854

description: Moderate-plane of nutrition


title: Time point T2 replicate 3

description: Library name: Ort23T2


title: sample8_TA_ZBED6_KO_CLP_2

description: Library name: TA_ZBED6_KO_CLP_2


title: TB, DONOR,Control [TB_Control_235]

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: GRCh38
Supplementary files format and content: Tab delimited file (txt) for raw hit counts

source_name: Human macrophages

extract_protocol:
RNA was isolated by using TRI reagent (Molecular Research Center, Cincinnati, OH, USA) according to manufacturer’s instructions.
polyA capture mRNA-seq

value: Human macrophages

value: Cultured human macrophages


title: sample7_TA_ZBED6_KO_CLP_3

description: Library name: TA_ZBED6_KO_CLP_3

value: ZBED6 knockout


title: AP97821

description: Moderate-plane of nutrition


title: Time point T1 replicate 3

description: Library name: Ort23T1


title: sample6_TIP_WT_CLP_1

description: Library name: TIP_WT_CLP_1

value: TIP


title: TB, DONOR,Control [TB_Control_234]


title: AP47825

description: Moderate-plane of nutrition


title: Time point T0 replicate 3

description: Library name: Ort23T0

value: peripheral blood


title: sample5_TIP_WT_CLP_2

description: Library name: TIP_WT_CLP_2


title: TB, DONOR,Control [TB_Control_228]


title: AP37865

description: Moderate-plane of nutrition


title: Time point T2 replicate 2

description: Library name: Ort21T2


title: AP41971

description: Moderate-plane of nutrition


title: sample4_TIP_WT_CLP_3

description: Library name: TIP_WT_CLP_3


title: Time point T1 replicate 2

description: Library name: Ort21T1


title: TB, DONOR,Control [TB_Control_223]


title: sample3_TIP_ZBED6_KO_CLP_1

description: Library name: TIP_ZBED6_KO_CLP_1


title: AP21978

description: Moderate-plane of nutrition


title: Time point T0 replicate 2

description: Library name: Ort21T0


title: sample2_TIP_ZBED6_KO_CLP_2

description: Library name: TIP_ZBED6_KO_CLP_2


title: Time point T2 replicate 1

description: Library name: Ort20T2


title: AP12937

description: Moderate-plane of nutrition


title: TB, DONOR,Treated [TB_235]

value: Infected with M. tuberculosis


title: TB, DONOR,Treated [TB_234]


title: TB, DONOR,Treated [TB_233]


title: Time point T1 replicate 1

description: Library name: Ort20T1


title: AP93760

description: High-plane of nutrition

value: High


title: CTL_0241

type: genomic

city: Washington

first: Kristen

last: Kocher

state: DC

address: 111 Michigan Ave NW

institute: Children's National Hospital

description:
n/a
nextseq550_w_beadchip_adapter

hyb_protocol: Illumina Methylation EPIC array (v1 and v2) kit

scan_protocol: iScan or NextSeq 550 with beadchip adapter

data_processing:
R/Rstudio (ChAMP, minfi, limma)
functional normalization of beta values extracted from raw idat files (XY, SNPs, cross-reactive probes filtered out)

label: other

source_name: buccal

label_protocol: cohort_patient ID

extract_protocol: buccal swabs were collected from newborns within the first month of life (using OC-175 pediatric buccal swabs, Genotek) and DNA was extracted using the L2Prep-It Kit (Genotek)

value: buccal

value: F


title: Time point T0 replicate 1

description: Library name: Ort20T0

value: primary monocytes


title: TB, DONOR,Treated [TB_228]


title: AP93744

description: High-plane of nutrition


title: AP92928

description: High-plane of nutrition


title: 281_Female_HFHSdiet_60wks

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

data_processing:
Sequencing was performed in an Illumina NextSeq 500 sequencing machine (Illumina) at a 2 × 74 bp paired-end resolution.
Sequence reads were mapped to the mouse reference genome (NCBI38/mm10) using Illumina RNA-Seq Alignment v2.0.2 software with default parameters in the Illumina BaseSpace environment.
Transcript abundance estimates (read counts) Illumina RNA-Seq Alignment v2.0.2 software with default parameters in the Illumina BaseSpace environment.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include read counts values for each Sample

source_name: Liver

extract_protocol:
Livers were removed and flash frozen on dry ice. Total RNA was extracted from liver tissue samples using miRNeasy Mini kits (Qiagen, Valencia, CA, USA).
RNA libraries for RNA-sequencing were prepared from 500 ng RNA using Illumina Stranded Total RNA Prep Ligation with Ribo-zero Plus library preparation kits as recommended in the manufacturer’s protocol.

treatment_protocol: Mice in the experimental group were maintained on the obesogenic high-fat and high-sucrose (HF/HS) diets (Teklad Custom Diet - TD.88137, Envigo, Madison, WI, USA) for 20, 40 and 60 weeks.  This diet contains 42% Kcal from milkfat high in palmitic acid, 0.2% of total cholesterol, and is high in sucrose (>30%).  Mice in the control group received an ingredient-matched low-fat and reduced sucrose diet (Teklad Custom Diet – TD.08485, Envigo).

value: Liver

value: tissue

value: HF/HS diet

value: Female

tag: time point

value: 60 weeks


title: TB, DONOR,Control [TB_control_233]

value: Control


title: TB, DONOR,Treated [TB_223]

value: WT


title: CTL_0222

description:
n/a
nextseq550_w_beadchip_adapter

value: M


title: AP81983

description: High-plane of nutrition

value: Anterior pituitary

value: Holstein-Friesian


title: Crypto,DONOR,Control [CryptoControl_new_23]

value: Human macrophages

value: Cultured human macrophages


title: CTL_0215

description:
n/a
nextseq550_w_beadchip_adapter


title: AP77860

description: High-plane of nutrition


title: 121_Female_HFHSdiet_60wks


title: AP47858

description: High-plane of nutrition


title: CTL_0214

description:
n/a
nextseq550_w_beadchip_adapter


title: sample1_TIP_ZBED6_KO_CLP_3

description: Library name: TIP_ZBED6_KO_CLP_3

value: muscle

value: TIP

value: ZBED6 knockout


title: CTL_0212

description:
n/a
nextseq550_w_beadchip_adapter

value: buccal

value: F


title: 111_Female_HFHSdiet_60wks

value: Liver


title: AP42931

description: High-plane of nutrition

value: High


title: AP37840

description: High-plane of nutrition


title: Crypto,DONOR,Control [Crypto_Control_228]


title: CTL_0209

description:
n/a
nextseq550_w_beadchip_adapter


title: 192_Female_Control_60wks

value: tissue


title: Crypto,DONOR,Control [Crypto_Control_223]


title: CTL_0207

description:
n/a
nextseq550_w_beadchip_adapter


title: 191_Female_Control_60wks

value: Female


title: Crypto,DONOR,Treated [Crypto_235]

value: Infected with C. neoformans


title: CTL_0227

description:
n/a
nextseq550_w_beadchip_adapter


title: AP37824

description: High-plane of nutrition


title: CTL_0205

description:
n/a
nextseq550_w_beadchip_adapter


title: 42_Female_Control_60wks

value: Control

value: 60 weeks


title: 122_Female_HFHSdiet_60wks

value: HF/HS diet


title: Crypto,DONOR,Treated [Crypto_234]

value: WT


title: CTL_0203

description:
n/a
nextseq550_w_beadchip_adapter

value: M


title: AP27864

description: High-plane of nutrition

value: Anterior pituitary

value: Holstein-Friesian


title: 32_Female_Control_60wks


title: AP27848

description: High-plane of nutrition


title: CTL_0202

description:
n/a
nextseq550_w_beadchip_adapter


title: 112_Female_HFHSdiet_60wks


title: 31_Female_Control_60wks


title: Crypto,DONOR,Control [Crypto_Control_23]

value: Human macrophages

value: Cultured human macrophages


title: Crypto,DONOR,Treated [Crypto_228]


title: CTL_0201

description:
n/a
nextseq550_w_beadchip_adapter


title: AP27823

description: High-plane of nutrition


title: Crypto,DONOR,Treated [Crypto_223]


title: 483_Female_HFHSdiet_40wks

value: 40 weeks


title: CTL_0189

description:
n/a
nextseq550_w_beadchip_adapter

value: buccal


title: 482_Female_HFHSdiet_40wks


title: AP17855

description: High-plane of nutrition


title: AP31979

description: High-plane of nutrition


title: CTL_0166

description:
n/a
nextseq550_w_beadchip_adapter

value: F


title: ACHN, DONOR,Control [ACHN_new_233]


title: cKO 3

city: Bunkyo-ku

first: Satoshi

last: Kofuji

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

description: Library name: Sample 4

data_processing:
DRAGEN
Adaptor sequence was not removed. Sequence reads were mapped to GRCm39 Release m28 using DRAGEN.
Read count extraction and normalization were performed using DRAGEN
Assembly: GRCm39 Release m28
Supplementary files format and content: Tab-delimited text files for both gene expression and transcript expression include TPM values and read counts in each sample.

source_name: Cerebral cortex

extract_protocol:
Total RNA was purified using TRIzol Reagent (15596018, Invitrogen) according to the manufacturer’s instructions. Extracted RNA was incubated with DNase I (2270B; Takara, Shiga, Japan) to degrade the genomic DNA and further purified using RNeasy Mini Kits (74104; QIAGEN). The quality of RNA was initially assessed by electrophoresis on a 1.5% agarose gel, and subsequently by absorption spectrophotometry.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input Kit following manufacturer's protocols.

value: Cerebral cortex

value: Mkk7flox/flox Emx1-Cre


title: N3

first: Xuedan

last: Han

address: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 639 Longmian Road. Nanjing , China.

institute: China Pharmaceutical University

description:
Library name: M23233455a
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10×Genomics Visium Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm 10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm 10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz:gene expression count data in Matrix Marker Exchange Fomat
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowers_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Normal tissue adjacent to bladder cancer

growth_protocol: BLCA and adjacent tissue samples were collected with the patients’ written informed consent and approved by the Human Research Ethics Committee of the Huashan Hospital, Fudan University (KY2011-009).

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10×Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacture's construction


title: ACHN, DONOR,Control [ACHN_Control_new_2]


title: 481_Female_HFHSdiet_40wks

value: Liver

value: tissue


title: AP13745

description: High-plane of nutrition

value: High


title: Crypto,DONOR,Control [Crypto_Control_234]

value: Control


title: Crypto,DONOR,Treated [Crypto_233]

value: Infected with C. neoformans


title: ACHN, DONOR,Control [ACHN_Control_234]


title: N2

description:
Library name: M23229424a
Fresh frozen Spatial transcriptome sequencing

value: Normal tissue adjacent to bladder cancer


title: 473_Female_HFHSdiet_40wks

value: HF/HS diet

value: Female


title: ACHN, DONOR,Control [ACHN_Control_235]

value: WT


title: cKO 2

description: Library name: Sample 3


title: Control 3

description: Library name: Sample 2


title: ACHN, DONOR,Control [ACHN_Control_228]


title: Control 2

description: Library name: Sample 1


title: 462_Female_Control_40wks


title: ACHN, DONOR,Control [ACHN_Control_223]


title: T3

description:
Library name: M23229421a
Fresh frozen Spatial transcriptome sequencing

source_name: bladder cancer

value: bladder cancer


title: T2

description:
Library name: M23229419a
Fresh frozen Spatial transcriptome sequencing


title: 461_Female_Control_40wks


title: ACHN, DONOR,Treated [ACHN_235]

value: Human macrophages

value: Treated with cell-free conditioned medium from the cultures of the ACHN cell line


title: 453_Female_Control_40wks

value: 40 weeks


title: White, Replicate 2, sRNAseq

city: Kusatsu, Shiga

first: Midori

last: Tabara

address: 1-1-1, Noji-Higashi

institute: Ritsumeikan University

description: Library name: White 2

data_processing:
Adapter sequences was trimmed by the program “cutadapt” (Martin, 2011).
There is no available data of dahlia genome sequence, then we directly counted the read after adapter-trimming as total small RNAs.
Draft cDNA data was prepared from deposited HTS data with TRINITY.
Bowtie2 was used for counting conserved miRNA under the setting that allows only perfect matches against conserved miRNA sequence that was downloaded from miRbase (https://www.mirbase.org/).
Assembly: TRINITY processed file based on DRS137846 and matured miRNA sequence data (mature.fa) on miRbase.
Supplementary files format and content: xlsx file format including read count

organism: Dahlia pinnata

source_name: Petal

growth_protocol: Dahlia (D. variabilis) plants were grown on a commercially available compost soil (Akagi Engei Inc., Gunma, Japan) in a greenhouse at 24°C (Ohno et a., 2018).

extract_protocol:
Total RNA was extracted from the dissected dahlia petals, namely the pigmented (red) and unpigmented (white) regions of bicolor petals, using Trizol reagent according to the manufacturer’s protocol (Thermo Fisher Scientific).
The small RNA-sequencing library was prepared using a NEBNext Small RNA Library Prep kit (New England Biolabs Japan, Tokyo, Japan) according to the manufacturer’s instructions.

value: Petal

value: Yuino


title: White, Replicate 3,sRNAseq

description: Library name: White 3


title: T1

description:
Library name: M23229418a
Fresh frozen Spatial transcriptome sequencing


title: Pt30_T_2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

data_processing:
Sequencing was performed on HiSeq 2500 or NovaSeq 6000 platform in a 75-base or 101-base single-end mode.
Illumina RTA v1.18.64 or RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat (version 2.1.1).
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffdiff version 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: colorectal cancer

extract_protocol:
Total RNA was isolated with miRNeasy Mini or Micro Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared using SMART-Seq HT Kit (Takara Bio, Japan) and NexteraXT DNA Library Preparation Kit (Illumina); or TruSeq stranded mRNA Library Prep Kit (Illumina).

value: colorectal cancer


title: 452_Female_Control_40wks


title: White,  Replicate 1,sRNAseq

description: Library name: White 1


title: ACHN, DONOR,Treated [ACHN_234]

value: Cultured human macrophages


title: 471_Female_HFHSdiet_40wks

value: Liver


title: Pt30_T_1


title: Red, Replicate 3, sRNAseq

description: Library name: Red 3


title: N1

description:
Library name: M23229423a
Fresh frozen Spatial transcriptome sequencing


title: ACHN, DONOR,Treated [ACHN_223]


title: 463_Female_Control_40wks

value: tissue


title: 422_Female_HFHSdiet_20wks

value: 20 weeks


title: 421_Female_HFHSdiet_20wks


title: Red, Replicate 2, sRNAseq

description: Library name: Red 2


title: T47D, Normoxia Polysomes

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

institute: Univ of Alabama at Birmingham

data_processing:
Initial processing of the FASTQ-format sequencing outputs included adaptor sequence removal using Trimmomatic, alignment with HISAT2, and elimination of PCR duplicates via SAMtools, resulting in BAM or SAM files. These files were subsequently analyzed using the Partek Genomics Suite (PGS, St. Louis, MO, USA). Reads per Kilobase of transcript per Million mapped reads (RPKM) normalization was applied prior to statistical evaluations to identify differentially expressed genes based on fold change and significance levels.
Assembly: GRCh38/hg38
Supplementary files format and content: text file, gene symbol as ID and samples

source_name: Mammary

growth_protocol: SUM1315 cells (Asterand Bioscience) were cultured in DMEM-F12 medium with 5% heat-inactivated FBS, 10 μg/mL insulin, and 20 ng/mL EGF. T47D cells (ATCC) were grown in RPMI medium with 10% FBS and 10 μg/mL insulin. SkBr3 cells (ATCC) were maintained in McCoy’s 5A medium with 10% FBS.

extract_protocol:
Cells were exposed to hypoxic or normoxic conditions and then treated with cycloheximide before collection. After washing with cold PBS containing cycloheximide, the cells were lysed using a polysome lysis buffer. The lysates were incubated at 4°C and centrifuged to determine protein concentrations. Equal amounts of protein were applied to sucrose density gradients and centrifuged. The gradients were analyzed using the Brandel BR-188 system. RNA was isolated from the polysomes using the RNeasy Mini Kit, and 500 ng of total RNA was used for library construction and sequencing.
RNA library preparations and sequencing were performed using the NEBNext Ultra RNA Library Prep Kit. Libraries were validated on the Agilent TapeStation and quantified with the Qubit 2.0 Fluorometer and qPCR.

treatment_protocol: Cells were maintained at 37°C in a humidified environment with 5% CO2. For hypoxic conditions, cells were incubated at 37°C in a modular incubator chamber (Billups Rothenberg Inc.) with 1% O2, 5% CO2, and 94% N2. Cells were exposed to hypoxia for 8 hours.

value: Mammary

value: luminal A breast cancer cell line

value: Normoxic (21% O2) conditions


title: T47D, Hypoxia Polysomes

value: Hypoxic (1% O2) conditions


title: 302_Female_HFHSdiet_20wks

value: HF/HS diet

value: Female


title: SKBR3, Normoxia Polysomes

description: Sk-Norm

value: Luminal HER2+ breast cancer cell line

value: WT


title: 301_Female_HFHSdiet_20wks


title: V. fischeri, VF_2432-3XFLAG, Replicate 1 (iCLIP)

city: Madison

first: Jacob

middle: Alan

last: Vander Griend

state: Wisconsin

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: University of Wisconsin - Madison

description: Library name: Vibrio_fischeri_VF_2432_CLIP-seq_Bio_Rep1

library_source: other

data_processing:
Reads for the VF_2432 CLIP-seq output from the NextSeq sequencing run were first demultiplexed using Ultraplex V.1.1.5. Next, demultiplexed reads were analyzed using the nf-core/clipseq analysis pipeline V1.0.0 (https://github.com/nf-core/clipseq) against the V. fischeri ES114 genome (ENSEMBL_GCA_000011805) with manually appended information for the 10 currently known sRNAs (VF_2577 csrB2, VF_2578 ryhB, VF_2579 spf, VF_2593 csrB1, VF_2597 qrr1, VF_2599 ffs, VF_2639 ssrA, VF_2651 ssrS, VF_2654 rnpB, VF_A1194 psrN). Information on all unique tRNA and rRNA genes present in V. fischeri were provided as a separate file for smRNA pre-mapping. Within the nf-core/clip-seq pipeline, parameters for the STAR mapper were modified as previously described in Monti et al. (2024): "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outSAMattributes All --alignIntronMin 1000000 --outFilterScoreMin 10 --alignEndsType Extend5pOfRead1”. We opted to use --outFilterMultimapNmax set to 1 instead of 100 as used previously for more stringent mapping. Peakcaller iCount was invoked, and the adapter sequence “AGATCGGAAGAGCGGTTCAG” was provided to the pipeline.
Processed nf-core/clip-seq pipeline files are provided for the the crosslink positions and counts across the genome, and a further file produced from the iCount peakcaller for crosslink peaks is provided.
Assembly: ENSEMBL_GCA_000011805
Supplementary files format and content: xl.bedgraph.gz, Output crosslinks produced by the nf-core/clip-seq pipeline are provided with strand specificity. Score is the number of crosslinks at that position. Positive score indicates crosslink on positive strand, and negative score indicates crosslink on negative strand.
Supplementary files format and content: 3nt_3nt.peaks.bed.gz, BED file of iCount peaks using a 3 nt half window and a 3 nt merge window
Library strategy: iCLIP

molecule: other

organism: Aliivibrio fischeri

source_name: Strain MJM5029

growth_protocol: Single colonies of strain MJM5029 (rscS* dVF_2432 attTn7::VF_2432-3XFLAG) were grown for 16 hrs at 28 ˚C in LBS media with 220 RPM shaking, and the following morning subcultures were diluted 1/100 into 100 mL of fresh LBS media. Subcultures were grown at 28 ˚C until OD600 1.8, after which cultures were immediately placed on ice.

extract_protocol:
Both crosslinked aliquots were decanted into a 50 mL conical and centrifuged for 15 min at 6,000 x g and 4 ˚C. Supernatants were discarded and pellets were resuspended in 4 mL ice cold Lysis Buffer [50 mM Tris-HCl pH: 7.4, 100 mM NaCl, 1% IGEPAL CA-630, 0.1% SDS, 0.5% sodium deoxycholate, 1X cOmplete Protease Inhibitor cocktail (Roche)]. Resuspended pellets were mixed 1:1 with 0.1 mM glass beads (Cole-Parmer) in 2 mL screwcap tubes, and vortexed at max-speed on a Vortex-Genie 2 equipped with a MN bead tube holder (Macherey-Nagel) for 2.5 min at 4 ˚C, after which tubes were rested on ice for 2 min. This bead beating and cooling cycle was repeated 3X. After the final bead beating step, tubes were centrifuged for 2 min at 17,000 x g and 4 ˚C. The supernatants were collected, and lysate protein concentration was determined using the DC II protein kit (BioRad), using BSA to generate the protein standard curve. Lysates were diluted to a final protein concentration of 1 mg/mL in Lysis Buffer, and separated into four separate 1 mL aliquots. RNA ligands were trimmed using RNAse I (ThermoFisher) using either “high” (0.8U) or “low” (0.4U) doses, with both conditions receiving 2 uL of TURBO DNAse (Invitrogen), at 37 ˚C for 3 min with 1100 RPM shaking on a Thermomixer (Thermo Scientific). After this incubation, samples were cooled for 5 min on ice, before centrifugation at 21,000 x g for 10 min at 4 ˚C. Supernatants were then transferred to a Proteus Clarification Mini Spin column (Anatrace), and centrifuged at 13,000 RPM for 1 min at 4 ˚C. Final lysate samples were then applied to Dynabeads Protein G magnetic beads (Thermo) loaded with 4 ug of mouse M2 IgG anti-FLAG monoclonal antibody, or non-specific mouse IgG (Santa Cruz), and allowed to rock overnight at 4 ˚C. The following morning, the beads were dephosphorylated using PNK (NEB) and FastAP Alkaline Phosphatase (ThermoFisher) at 37 ˚C for 40 min with 1100 RPM shaking. After PNK and FastAP treatment, the 3’ pre-adenylated L3-IR-App adaptor was ligated onto the bead RNA-protein complexes using T4 RNA ligase I (NEB), PNK, and a final adaptor concentration of 0.1 µM. Beads were incubated at room temperature (23 ˚C) for 75 min, and tubes were flicked every 10 min to ensure mixing of beads with ligation mix. After ligation, unligated adaptors were removed with an enzyme mix of 5’ Deadenylase (NEB) and RecJf endonuclease (NEB), incubated at 30 ˚C for 1 hr, then for 30 min at 37 ˚C, shaking at 1100 RPM. RNA-protein complexes were eluted from beads using 1X NuPAGE loading buffer (Thermo) with 0.1 M DTT, and incubated at 70 ˚C for 1 min. Elutions were then loaded into 4-12% NuPAGE Bis-Tris acrylamide gels (Thermo), and run in 1X NuPAGE MOPS running buffer (Thermo) supplemented with NuPAGE antioxidant (Thermo) for 180V until the loading dye front reached the bottom of the gel, and the dye front was excised before transfer. Gels were then transferred to 0.45 µm Protran nitrocellulose membranes (Amersham) in 1X NuPAGE transfer buffer (Thermo), supplemented with 10% Methanol and NuPAGE Antioxidant, at 10 V for 1 hr. Membranes were then imaged using a LICOR Odyssey FC imager, and immediately frozen at -80 ˚C. All three complexes were harvested from the anti-FLAG samples treated with the lowest RNase digestion condition (0.4U) in both biological replicates.
RNA ligands were liberated from the VF_2432 complexes using Proteinase K treatment of membrane slices, followed by Phenol:Chloroform extraction. RNAs were then recovered following an overnight sodium acetate precipitation with GlycoBlue (ThermoFisher) and a selected reverse transcription primer, and reverse-transcribed using SuperScript IV (Invitrogen). RNAs were then degraded with NaOH treatment, and cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter). Circularization of cDNA was conducted using CircLigase II (LGC), after which a further bead cleanup was performed. Phusion HF polymerase (Thermo) was used for amplifying cDNA libraries using P3 and P5 Solexa primers with 22 cycles. Final libraries for two biological replicates were purified using bead cleanup, and submitted for sequencing at the University of Minnesota Genomics Center using an Illumina NextSeq 2000 platform.

treatment_protocol: Two 25 mL aliquots of the subculture were poured into sterile Nunc Omnitrays (Fisher Scientific), and subjected to 800 mJ/cm2 UV irradiation (254 nm) on a HL-2000 HybriLinker (Fisher Scientific).

value: Strain MJM5029

value: ES114 rscS* dVF_2432 attTn7::VF_2432-3XFLAG

value: 800 mJ/cm2 UV irradiation (254 nm), immunoprecipitation with Mouse M2 Anti-FLAG Sigma-F1804


title: V. fischeri, VF_2432-3XFLAG, Replicate 2 (iCLIP)

description: Library name: Vibrio_fischeri_VF_2432_CLIP-seq_Bio_Rep2


title: SKBR3, Hypoxia Polysomes

description: Sk-Hypox


title: Red, Replicate 1, sRNAseq

description: Library name: Red 1

value: Petal

value: Yuino


title: TLV_Control_5

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

description: Library name: 01T0071

data_processing:
The raw sequences were quality controlled using FastQC.
Fastp software was used to remove Illumina adapters and poly-A sequences. Reads shorter than 36 bp and reads with a quality lower thanthe default of 20 were removed from the dataset.
Cleaned sequences were aligned to the Sus scrofa genome (assembly Turkey_5.1.110) with reference annotation containing more than 16K genes listed in the Ensembl database.
Alignment and estimation of gene expression level were made using the RSEM package supported by STAR aligner.
Differentially expressed genes, gene isoforms and their corresponding p-values were determined using the statistical methods DESeq2
Assembly: GCA_000146605.4
Supplementary files format and content: genes_turkey_filtered.csv.gz
Supplementary files format and content: res-liver.tsv.gz
Supplementary files format and content: res-heart.tsv.gz

organism: Meleagris gallopavo

growth_protocol: Birds were kept on litter at a density of 4 individuals per pen; During the pre-experimental period (weeks 1-11), birds were fed Sal-free diets.  After the pre-experimental period (week 12-13), birds were selected and classified into two groups: the Sal-exposed and the control group and fed respective diets ad libitum.

extract_protocol:
Total RNA isolation was done by Maxwell RSC instrument (Promega, USA) using Maxwell® RSC simplyRNA Tissue Kit (Promega, USA).
The Hieff NGS Ultima Dual-mode mRNA Library Prep Kit (Yeasen Biotechnology, China) was used to construct libraries according to manufacturer's protocol.

treatment_protocol: The Sal-exposed group received an experimental diet with Sal ad libitum. Sal was administered in-feed at the concentration of 21 mg/kg feed during weeks 12-13. The estimated daily dose was 0.9 mg/kg b.w.

value: Control


title: SUM1315, Normoxia Polysomes

value: Triple negative breast cancer cell line


title: plt2/gPLT2C212S-GFP 5 nM RGF1 rep6

city: Tainan

first: Masashi

last: Yamada

address: No. 100, Sec. 1, Guiren 13th Rd., Guiren Dist.,

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
The sequencing reads were mapped to Arabidopsis genome TAIR10 using HISAT2 v2.1.0.
The read counts of genes were compared with the Araport11 genome annotation using featureCounts (subread v2.0.3).
The normalized expression values of genes were performed using DESeq (v1.34.0)
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

organism: Arabidopsis thaliana

source_name: Root meristematic zone

growth_protocol: Arabidopsis seeds were grown on MS plate for 6 days.

extract_protocol:
The seedings were aligned onto a 2% agarose plate for root tips collection. Using an ophthalmic scalpel (Feather), the meristematic zone of the seedlings were precisely dissected under a dissecting microscope (Axio Zoom, Zeiss). Total RNA was extracted from 50 root sections using the RNeasy Micro Kit (Qiagen). All total RNA samples were treated with DNaseI during RNA extraction.
RNA libraries were prepared using Universal RNA-Seq with NuQuant library preparation kit following manufacture's protocols

treatment_protocol: The seedings were transferred into 1/2 MS media and treated with mock, 0.3nM RGF1 or 5nM RGF1 for 24h.

value: Root meristematic zone

value: 24 hr

value: 5 nM RGF1


title: ACHN, DONOR,Treated [ACHN_228]

value: Human macrophages

value: Cultured human macrophages

value: Treated with cell-free conditioned medium from the cultures of the ACHN cell line


title: TLV_Control_4

description: Library name: 01T0070

value: Liver


title: 383_Female_Control_20wks

value: tissue

value: Female

value: 20 weeks


title: SUM1315, Hypoxia Polysomes

value: Mammary

value: WT

value: Hypoxic (1% O2) conditions


title: TLV_Control_3

description: Library name: 01T0069


title: plt2/gPLT2C212S-GFP 5 nM RGF1 rep4


title: plt2/gPLT2C212S-GFP 5 nM RGF1 rep3


title: SUM1315, Hypoxia 24 hr -3

data_processing:
Initial processing of the FASTQ-format sequencing outputs included adaptor sequence removal using Trimmomatic, alignment with HISAT2, and elimination of PCR duplicates via SAMtools, resulting in BAM or SAM files. These files were subsequently analyzed using the Partek Genomics Suite (PGS, St. Louis, MO, USA). Reads per Kilobase of transcript per Million mapped reads (RPKM) normalization was applied prior to statistical evaluations to identify differentially expressed genes based on fold change and significance levels.
Assembly: GRCh38/hg38
Supplementary files format and content: text file, ENST ID, RPKM counts

growth_protocol: SUM1315 cells (Asterand Bioscience) were cultured in DMEM-F12 medium with 5% heat-inactivated FBS, 10 μg/mL insulin, and 20 ng/mL EGF.

extract_protocol:
RNA isolation was performed using the RNeasy Mini Kit. For library construction and subsequent sequencing, 500 ng of total RNA was utilized.
RNA library preparations and sequencing were performed using the NEBNext Ultra RNA Library Prep Kit. Libraries were validated on the Agilent TapeStation and quantified with the Qubit 2.0 Fluorometer and qPCR.

treatment_protocol: Cells were maintained at 37°C in a humidified environment with 5% CO2. For hypoxic conditions, cells were incubated at 37°C in a modular incubator chamber (Billups Rothenberg Inc.) with 1% O2, 5% CO2, and 94% N2. Cells were exposed to hypoxia for 24 hours.

value: Triple negative breast cancer (TNBC) cell line


title: 382_Female_Control_20wks


title: TLV_Control_2

description: Library name: 01T0068


title: 292_Female_HFHSdiet_20wks

value: HF/HS diet


title: SUM1315, Hypoxia 24 hr -2


title: 381_Female_Control_20wks

value: Control


title: 203_Female_Control_20wks


title: plt2/gPLT2C212S-GFP 5 nM RGF1 rep1


title: SUM1315, Hypoxia 24 hr -1


title: TLV_SAL_exposed_6

description: Library name: 01T0054

value: SAL exposed


title: TLV_Control_6

description: Library name: 01T0072


title: TLV_Control_1

description: Library name: 01T0067


title: plt2/gPLT2C212S-GFP 5 nM RGF1 rep2

value: Root meristematic zone


title: 202_Female_Control_20wks


title: SUM1315, Normoxia 24 hr -3

value: Normoxic (21% O2) conditions


title: TLV_SAL_exposed_5

description: Library name: 01T0053


title: 252_Male_HFHSdiet_60wks

value: Male

value: 60 weeks


title: plt2/gPLT2C212S-GFP 0.3 nM RGF1 rep4

value: 24 hr

value: 0.3 nM RGF1


title: plt2/gPLT2C212S-GFP 0.3 nM RGF1 rep5


title: SUM1315, Normoxia 24 hr -2


title: TLV_SAL_exposed_4

description: Library name: 01T0052

value: Liver


title: plt2/gPLT2C212S-GFP 0.3 nM RGF1 rep3


title: SUM1315, Normoxia 24 hr -1


title: TLV_SAL_exposed_3

description: Library name: 01T0051


title: plt2/gPLT2C212S-GFP 0.3 nM RGF1 rep2


title: 92_Male_HFHSdiet_60wks

value: tissue


title: plt2/gPLT2C212S-GFP 0.3 nM RGF1 rep1


title: Control 2

city: San Diego

last: Foote

state: CA

address: 3381 Lebon Drive

department: Pediatrics

institute: UCSD

description:
Library name: AF03
10X Genomics

data_processing:
The CellRanger software package from 10X Genomics (v3.0.2) was used to align raw reads onto the mouse reference genome (GRCm38) and generate single-cell gene barcode matrices. CellBender (v0.3.0)63 was then used to remove technical artefacts and ambient RNA to produce improved estimates of gene expression.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Trachea/Larynx/Pharynx

extract_protocol:
Whole upper airway (larynx-trachea) was mechanically dissociated by mincing tissue with razor blades in solution containing 5 ml of RPMI 1640 (Thermo Scientific) with 10% fetal bovine serum, 1 mM HEPES (Life Technology), 1 mM MgCl2 (Life Technology), 1 mM CaCl2 (Sigma), 0.5 mg ml−1 collagenase D and type I/dispase (Roche), and 0.25 mg DNase I (Roche). Minced tissue was then digested by shaking at around 150 rpm for 30 min at 37 °C. Following incubation, upper airway pieces were mechanically dissociated further by straining through a MACS 70 μm filter. Red blood cells were removed by the addition of 1 ml of RBC lysis buffer (BioLegend) to each tube and incubation at room temperature for 1 min. Single-cell suspensions were pelleted (1,500 rpm, 4 °C, 5 min), counted with a hemocytometer and diluted to around 1 × 106 cells ml−1. Diluted cells were stained with Fc blocking antibody (5 mg ml−1, BD). Cells were then incubated with specific surface marker antibody at 1:1000 APC-FITC-conjugated anti-Epcam (BioLegend, no. 118214) to isolate epithelial lineage. Cells were then stained using live/dead dye (CD11b: Brilliant Violet 450, BioLegend, cat#75-0112-U025) before being resuspended in 2% FBS + 1:2000 DAPI. All FACS sorting was done on a BD FACSAria Fusion Sorter (BD Biosciences) analyzer with three lasers (405, 488 and 640 nm) at the Flow Cytometry Core at VA San Diego Health Care System and San Diego Veterans Medical Research Foundation.
Single cells were processed into complementary DNA libraries using Chromium Single Cell 3’ v3 kit (10X Genomics, Pleasanton, CA) and sequencing was carried out on the NovaSeq (Illumina) platform. The R package Seurat (v4.0)26 was then used to perform data quality control, normalization, principal components analysis, UMAP generation and differential gene expression testing.  Single cells with above 15% mitochondrial reads and between 200 and 7500 unique genes were considered high-quality cells and were filtered for further analyses. Additional filtering included a minimum UMI cutoff of 2 and minimum cell count cutoff of 10. LogNormalize global-scaling normalization method was applied with regressing variables cell cycle, S.Score, G2M.Score, and mitochondrial RNA level to remove confounding effect on downstream clustering. In addition, DoubletFinder (v2.0)64 was used to remove doublets and LogNormalize was again used to normalize feature expression. CCA65 was used to integrate dataset across two experimental batches for a total of n=8 mice (4 males, 4 females).

value: Trachea/Larynx/Pharynx

value: Epithelial


title: TLV_SAL_exposed_1

description: Library name: 01T0049


title: Control 1

description:
Library name: AF01
10X Genomics


title: plt2/gPLT2C212S-GFP mock rep5

value: Mock


title: 91_Male_HFHSdiet_60wks


title: iPSCs D10 , anti-IgG

city: Guangzhou

first: shuhui

last: xu

address: 190 Kaiyuan Avenue, Huangpu District

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: Library name: iPSCs D10 IgG

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 with the parameters: --end-to-end--very-sensitive--local--no-mixed--no-discordant--no-unal--phred33-I10-X700. Then, Sambamba was used to remove duplicate reads and samtools was used to sort the data. Peaks were called using MACS2 (v.2.2.7.1) with the following parameters: --SPMR--nomodel--extsize 200--keep-dup all--q 0.001. Reads that mapped to mitochondrial DNA or unassigned sequences were discarded. For paired-end sequencing data, only transformed into read coverage files (bigwig format) using deepTools with RPKM normalization. For the sample without repeats, differential binding region was analysis by manorm (v.1.3.0) with P-value <= 0.05.
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: iPSCs

extract_protocol:
For CUT&Tag library construction, NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit for Illumina (Novoprotein, N259-YH01) was used. Around 1×105 living cells were collected for each sample, and the CUT&Tag library was sequenced on a illumina nova6000, carried out by CNGB.
CUT&Tag

treatment_protocol: Around 100000 living cells were collected for each sample CUT&Tag library construction.

value: iPSCs

value: Tsc1 WT


title: THR_Control_6

description: Library name: 01T0060

source_name: Heart

value: Heart


title: 171_Male_Control_60wks


title: plt2/gPLT2C212S-GFP mock rep4


title: THR_Control_5

description: Library name: 01T0059


title: KOR , anti-RBBP4

description: Library name: KOR RBBP4

value: Tsc1 KO

value: 0.3nm Rapa+AAV-Cre


title: plt2/gPLT2C212S-GFP mock rep3


title: KO , anti-RBBP4

description: Library name: KO RBBP4

value: AAV-Cre


title: 23_Male_Control_60wks

value: Control


title: THR_Control_4

description: Library name: 01T0058


title: 22_Male_Control_60wks


title: plt2/gPLT2C212S-GFP mock rep2

value: Root meristematic zone


title: WT , anti-RBBP4

description: Library name: WT RBBP4


title: 101_Male_HFHSdiet_60wks

value: HF/HS diet

value: Male


title: TLV_SAL_exposed_2

description: Library name: 01T0050

value: SAL exposed


title: THR_Control_3

description: Library name: 01T0057


title: 21_Male_Control_60wks

value: 60 weeks


title: KOR , anti-TFE3

description: Library name: KOR TFE3


title: 11_Male_Control_60wks

value: Liver


title: THR_Control_1

description: Library name: 01T0055


title: plt2/gPLT2-GFP 5 nM RGF1 rep6

value: 24 hr

value: 5 nM RGF1


title: 523_Male_HFHSdiet_40wks

value: tissue

value: 40 weeks


title: plt2/gPLT2C212S-GFP mock rep1

value: Mock


title: KO , anti-TFE3

description: Library name: KO TFE3

value: iPSCs


title: WT , anti-TFE3

description: Library name: WT TFE3

value: Tsc1 WT


title: THR_SAL_exposed_6

description: Library name: 01T0042

value: Heart


title: plt2/gPLT2-GFP 5 nM RGF1 rep4


title: THR_SAL_exposed_5

description: Library name: 01T0041


title: plt2/gPLT2-GFP 5 nM RGF1 rep5


title: THR_SAL_exposed_4

description: Library name: 01T0040


title: 522_Male_HFHSdiet_40wks


title: plt2/gPLT2-GFP 5 nM RGF1 rep2


title: 513_Male_HFHSdiet_40wks


title: plt2/gPLT2-GFP 5 nM RGF1 rep3


title: WT.Tx_8989

city: Ann Arbor

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: Library name: Sample_8989

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v4.8.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCm38 (ENSEMBL) using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCm38
Supplementary files format and content: tab-delimited table with raw counts, filtered to remove genes with 0 counts in all samples.

source_name: liver

extract_protocol:
RNA was isolated using phenol/chloroform. 200 nanograms total RNA was used for the construction of sequencing libraries.
Library prep and sequencing were done at Innomics, Inc. Oligo dT beads were used  to enrich mRNA with poly A tail, then mRNA molecules were fragmented into small pieces. The fragmented mRNA was synthesized into first strand cDNA using random primers. The second strand cDNA was synthesized with dUTP instead of dTTP. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, then the fragments were PCR amplified. After quality control,  Libraries were circularized, then amplified to make DNA nanoball (DNB).

value: liver

value: female

value: Rescue


title: WT.Tx_8990

description: Library name: Sample_8990


title: WT.Tx_8958

description: Library name: Sample_8958


title: THR_Control_2

description: Library name: 01T0056

value: Control


title: plt2/gPLT2-GFP 5 nM RGF1 rep1

value: Root meristematic zone


title: THR_SAL_exposed_3

description: Library name: 01T0039


title: THR_SAL_exposed_2

description: Library name: 01T0038


title: WT.Veh_8997

description: Library name: Sample_8997

value: Vehicle


title: 503_Male_Control_40wks

value: Male


title: WT.Veh_699

description: Library name: Sample_699


title: plt2/gPLT2-GFP 0.3 nM RGF1 rep4

value: 0.3 nM RGF1


title: 251_Male_HFHSdiet_60wks

value: Liver

value: HF/HS diet

value: 60 weeks


title: 502_Male_Control_40wks

value: tissue


title: 521_Male_HFHSdiet_40wks

value: 40 weeks


title: THR_SAL_exposed_1

description: Library name: 01T0037

value: SAL exposed


title: plt2/gPLT2-GFP 0.3 nM RGF1 rep3

value: 24 hr


title: 501_Male_Control_40wks


title: IP_4_3_Blue_Putrescine

city: Budapest

first: István

last: Likó

address: Üllői út 26.

country: Hungary

institute: Semmelweis University

description: Library name: IP-4-3

data_processing:
The raw data from the sequencer, the reads collected in the fastq file (short sequencing reads), were subjected to qualitative analysis using the Fastqc (Babraham Bioinformatics) program.
The reads were trimmed using Trim Galore and Cutadapt to remove bases where the PHRED quality value was less than 20. Trimmed sequences were removed if they become shorter than 50 bases.
reads were aligned to wheat reference genome using Burrows‐Wheeler Aligner (BWA)
The analysis of the enriched methylated DNA locus was performed with bedtools and R statistical tools.
Assembly: GCF_018294505.1_IWGSC_CS_RefSeq_v2.1_genomic.fna     Triticum aestivum (bread wheat)
Supplementary files format and content: cvs, coverage count data by locus

organism: Triticum aestivum

source_name: leaf

extract_protocol:
The genomic DNA samples were isolated with NucleoSpin® Plant II Kit (MACHEREY-NAGEL GmbH, Düren, Germany) according to the manufacturer’s instructions.
The DNA sequencing library was prepared using immunoprecipitated (12 samples) and pooled, fragmented IP input DNAs (4 pooled samples) with xGen™ ssDNA & Low-Input DNA Library Preparation Kit (Integrated DNA Technologies (IDT), Inc., Coralville, IA, USA) according to the manufacturer's instructions.
The normalized, pooled, and denatured library samples were sequenced on the Illumina NextSeq platform (Illumina, Inc., San Diego, CA, United States) using 75 + 75 bp paired-end chemistry with NextSeq 500/550 HiOutput Kit v2.5 (150 Cycles)

value: leaf

value: variety Mv Beres


title: IP_4_2_Blue_Putrescine

description: Library name: IP-4-2


title: WT.Veh_493

description: Library name: Sample_493

value: liver


title: 493_Male_Control_40wks


title: plt2/gPLT2-GFP 0.3 nM RGF1 rep2


title: WT.Veh_491

description: Library name: Sample_491

value: female


title: IP_4_1_Blue_Putrescine

description: Library name: IP-4-1


title: 492_Male_Control_40wks


title: plt2/gPLT2-GFP 0.3 nM RGF1 rep1


title: 512_Male_HFHSdiet_40wks


title: WT.Veh_490

description: Library name: Sample_490


title: IP_3_3_Blue_Kontrol

description: Library name: IP-3-3


title: plt2/gPLT2-GFP mock rep5

value: Mock


title: plt2/gPLT2-GFP mock rep4


title: plt2/gPLT2-GFP 0.3 nM RGF1 rep5


title: WT.Veh_797

description: Library name: Sample_797


title: WT.Veh_482

description: Library name: Sample_482


title: KO.Veh_8976

description: Library name: Sample_8976


title: 271_Male_HFHSdiet_20wks

value: 20 weeks


title: 411_Male_HFHSdiet_20wks


title: IP_2_3_White_Putrescine

description: Library name: IP-2-3


title: plt2/gPLT2-GFP mock rep2

value: Root meristematic zone


title: plt2/gPLT2-GFP mock rep3


title: IP_3_1_Blue_Kontrol

description: Library name: IP-3-1


title: IP_2_2_White_Putrescine

description: Library name: IP-2-2


title: plt2/gPLT2-GFP mock rep1


title: KO.Veh_8966

description: Library name: Sample_8966

value: Vehicle


title: KO.Veh_8972

description: Library name: Sample_8972


title: 261_Male_HFHSdiet_20wks

value: Male


title: IP_2_1_White_Putrescine

description: Library name: IP-2-1


title: IP_1_3_White_Kontrol

description: Library name: IP-1-3


title: 373_Male_Control_20wks

value: Control


title: IP_3_2_Blue_Kontrol

description: Library name: IP-3-2


title: 413_Male_HFHSdiet_20wks

value: Liver


title: 372_Male_Control_20wks


title: KO.Veh_8960

description: Library name: Sample_8960


title: plt2 5 nM RGF1 rep4

value: 5 nM RGF1


title: plt2 5 nM RGF1 rep5


title: 371_Male_Control_20wks


title: 412_Male_HFHSdiet_20wks

value: HF/HS diet


title: IP_1_2_White_Kontrol

description: Library name: IP-1-2