title: XRN1_degron_4h_r3

description: Library name: sample 63

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 XRN1-3V5-IAA7:KanMX8

value: IAA


title: WA09 cells, Day20, 100 ng/ml FGF8b, not DLX5 activated, rep 1

status: Public on Jul 29 2026

type: SRA

city: Helsinki

first: Shrinidhi

last: Madhusudan

state: Uusimaa

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: Library name: A10

library_source: transcriptomic

data_processing:
Raw reads (FASTQ) were quality-filtered using fastp; reads containing adapters, poly-N, or low-quality bases were removed to obtain clean reads. Q20, Q30, and GC content were calculated on the clean data.
Clean reads were aligned to the reference genome using HISAT2 v2.0.5
Gene-level read counts were quantified using featureCounts v1.5.0-p3, counting reads mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: Gene count matrices in Excel sheets (.xls, first column contains gene identifiers (Ensembl gene IDs)); each subsequent column contains the raw read counts for one sample, with column headers corresponding to the sample library names.

molecule: polyA RNA

organism: Homo sapiens

source_name: WA09 (WiCell)

growth_protocol: Human embryonic stem cells were differentiated to GnRH neurons using our previously established protocol, please refer those publications for details. PMID: 27426041, PMID: 31996360

extract_protocol:
Total RNA was extracted using NucleoSpin RNA (Machery-Nagel, Cat. 740955.250). Poly-T-oligo attached beads were used to isolate messenger RNA (mRNA) from total RNA. RNA integrity and quality were assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: For this publication, a DLX5 activation line was generated and this line was differentiated to GnRH neurons. For all conditions, cell were always DLX5 activated between Day10-Day20. Only for conditions stated, no FGF8b was given during Day10-Day20. Samples A and B are day20 all treated with 100 ng/ml FGF8b from day10-day20. Samples J and K are day25 neurons all treated with 100 ng/ml FGF8b from day10-day20. Samples B and K were additionally DLX5 activated from day10-day20. Samples, N#_A, F#_A and F#_C were all FACS-sorted day25 TdT positive GnRH neurons. Samples N#_A, F#_A were additionally DLX5 activated from day10-day20. Samples N#_A were NOT treated with FGF8b from day10-day20.

tag: cell line

value: WA09 (WiCell)

tag: cell type

value: human embryonic stem cells


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, Biological replicate 3

city: Boston

first: Yuko

last: Hasegawa

state: MA

address: 181 Longwood Ave.

country: USA

institute: Brigham and Women's Hospital

description:
Library name: Liver-day3-3
Liver_featureCounts.txt

data_processing:
Low-quality bases and the adaptors were trimmed using Trim Galore. The reads were mapped to the mouse reference genome (mm10) using STAR with default parameters, and the gene-level raw read count matrix was obtained using the featureCounts function in the subread using mouse GENCODE annotation M25 (GRCm38.p6)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was harvested by bead-beating the tissue in TRIzol
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: Mice were orally gavaged with 5 × 10⁹ Citrobacter rodentium

tag: tissue

value: Liver

tag: genotype

value: WT

tag: treatment

value: Cr infection

tag: time


title: CCL11-upregulated prostate cancer cells replicate 3

city: Bengbu

first: xingyu

last: chen

state: Anhui Province

address: Bengbu Medical University, 2600 Donghai Avenue, Longzihu District, Bengbu City, Anhui Province, P.R. China, 233030

country: China

institute: BBMC

description:
Library name: OE_3
CCL11-upregulated prostate cancer cells, biological replicate 3. Expression values are provided in columns FPKM.OE_3 and count.OE_3.

data_processing:
Raw reads were filtered using Cutadapt to remove reads containing adapters, polyA/polyG sequences, more than 5% unknown nucleotides, or more than 20% low-quality bases.
The quality of clean reads was evaluated using FastQC, including Q20, Q30, and GC content assessment.
Clean reads were aligned to the reference genome using HISAT2.
Mapped reads were assembled using StringTie, and transcriptomes from all samples were merged using gffcompare.
StringTie and ballgown were used to estimate transcript expression levels, and gene expression abundance was calculated as FPKM values.Differential expression analysis between groups was performed using DESeq2. Genes with FDR < 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: gene_count_matrix.txt: Tab-delimited text file containing gene-level raw read counts for all samples.
Supplementary files format and content: 1_genes_fpkm_expression.txt: Tab-delimited text file containing gene-level FPKM expression values for all samples.

source_name: prostate cancer

growth_protocol: PC3 prostate cancer cells were cultured under standard cell culture conditions before RNA extraction.

extract_protocol:
Total RNA was extracted using TRIzol reagent (ThermoFisher, 15596018) following the manufacturer's procedure. RNA quantity and purity were assessed using Thermo Fisher Qubit 3.0 and Agilent 5300 Fragment Analyzer. High-quality RNA samples with RIN values greater than 7.0 were used to construct sequencing libraries.
mRNA was purified from 2 μg total RNA using mRNA Capture Beads 2.0 with two rounds of purification. Purified mRNA was fragmented using magnesium ions at 94°C. The cleaved RNA fragments were reverse-transcribed to synthesize first-strand cDNA, followed by second-strand cDNA synthesis. After A-tailing, dual-index adapter ligation, PCR amplification, and purification, libraries with an average insert size of 400 ± 50 bp were generated. Paired-end sequencing was performed as 2 × 150 bp on an Illumina NovaSeq X Plus platform.

treatment_protocol: PC3 cells were divided into a negative control group and a CCL11-upregulation group. Cells in the CCL11-upregulation group were subjected to CCL11 upregulation, whereas cells in the negative control group received the matched control treatment. Cells were collected for RNA extraction after treatment.

value: prostate cancer

value: prostate cancer cell

value: CCL11 upregulation

tag: batch

value: batch 1


title: XRN1_degron_4h_r1

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: sample 61

data_processing:
FASTQ files were processed using the nf-core/rnaseq pipeline (version 3.10.1; 10.5281/zenodo.1400710), executed using Nextflow (v23.10.0) (Di Tommaso et al., 2017). Reads were aligned to the Saccharomyces cerevisiae strain SK1 reference genome (SK1_SGD_2018_NCSL00000000) using STAR (2.7.10a)47, and gene-level quantification was performed with RSEM (v1.3.1).  Differential expression analysis was carried out with DESeq2 (1.48.1) using a simple design formula (~ group). Wald tests were used to assess differential expression. Multiple-testing correction was performed using Independent Hypothesis Weighting (IHW)50; genes with an IHW-adjusted p-value below 0.05 were considered significant. ashr 51 was used for effect-size shrinkage.
Assembly: SK1-MvO-V1
Supplementary files format and content: txt and counts

organism: Saccharomyces cerevisiae

source_name: diploid

growth_protocol: Cells were arrested in early meiosis as described previously 9. Briefly, yeast cells were inoculated in yeast extract peptone dextrose (YPD) media [1% weight/volume (w/v) yeast extract, 2% w/v bacto peptone, 2% w/v glucose, uracil (24 mg/l) and adenine (12 mg/l)] for approximately 24 hours, before being diluted to OD600 0.4 in buffered, yeast extract, tryptone, acetate (BYTA, (1.0% w/v yeast extract, 2.0% w/v peptone, 1% potassium acetate, 50 mM potassium phthalate monobasic) and incubated for 16-18 hours. OD600 1.8 of yeast cells were then washed and transferred to SPO (0.3% Potassium acetate, Acetic acid to pH 7.0, 0.02% D-(+)-Raffinose pentahydrate).

extract_protocol:
24 OD units were collected by centrifugation, and snap frozen in liquid nitrogen. Per 10 OD units, RNA was extracted with Tris-EDTA-SDS (TES) buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and Acid Phenol:Chloroform:Isoamyl alcohol (125:24:1, Ambion) at 65°C for 45 minutes. Precipitation was carried out. rDNase (Machery-Nagel) treatment was carried out, before spin column purification (Machery-Nagel).
For degron strains, libraries from 100 ng of RNA were generated using the NEBNext Ultra II Directional PolyA mRNA Kit (modules K0105 and K0078), following the manufacturer’s protocols. Paired-end sequencing (100 bp) was performed on an Illumina NovaSeq X platform, with a minimum depth of 20 million reads per sample.

treatment_protocol: 3 hours after transfer to sporulation medium, copper (II) sulphate (CuSO4, 50 μM) and indole-3-acetic acid (IAA, 500 μM) were added to induce auxin-induced protein depletion. In all steps yeast were grown at 30°C at 300 rpm, and a 1:10 culture volume to flask total volume ratio was maintained.

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 XRN1-3V5-IAA7:KanMX6


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, Biological replicate 2

description:
Library name: Liver-day3-2
Liver_featureCounts.txt


title: 203977090025_R04C01_PD332_PFC

type: genomic

city: Exeter

first: Joshua

last: Harvey

state: Devon

address: RILD Building, RD&E, Barrack Road

department: Clinical and Biomedical Sciences

institute: University of Exeter

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina)

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

label: Cy3 & Cy5

molecule: genomic DNA

source_name: Prefrontal cortex

label_protocol: Standard Illumina Protocol

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Prefrontal cortex

tag: regiondescription

tag: plate

tag: centre

value: Imperial Brain Bank

tag: Sex

value: male

tag: thal

value: FALSE


title: RRP6_DMSO_4h_r3

description: Library name: sample 60

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RRP6-3V5-IAA7:KanMX11

value: DMSO


title: CCL11-upregulated prostate cancer cells replicate 2

description:
Library name: OE_2
CCL11-upregulated prostate cancer cells, biological replicate 2. Expression values are provided in columns FPKM.OE_2 and count.OE_2.


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, Biological replicate 1

description:
Library name: Liver-day3-1
Liver_featureCounts.txt


title: 203977090025_R01C01_20150061_PFC

value: Newcastle Brain Tissue Resource


title: CCL11-upregulated prostate cancer cells replicate 1

description:
Library name: OE_1
CCL11-upregulated prostate cancer cells, biological replicate 1. Expression values are provided in columns FPKM.OE_1 and count.OE_1.


title: RRP6_DMSO_4h_r2

description: Library name: sample 59

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RRP6-3V5-IAA7:KanMX10


title: Control prostate cancer cells replicate 3

description:
Library name: NC_3
Control prostate cancer cells, biological replicate 3. Expression values are provided in columns FPKM.NC_3 and count.NC_3.

value: control


title: RRP6_DMSO_4h_r1

description: Library name: sample 58

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RRP6-3V5-IAA7:KanMX9


title: C57BL/6J 8-10 weeks female, Liver, 1dpi, Biological replicate 3

description:
Library name: Liver-day1-3
Liver_featureCounts.txt

value: Liver

value: WT

value: Cr infection


title: Control prostate cancer cells replicate 2

description:
Library name: NC_2
Control prostate cancer cells, biological replicate 2. Expression values are provided in columns FPKM.NC_2 and count.NC_2.

value: prostate cancer

value: prostate cancer cell


title: RRP6_degron_4h_r3

description: Library name: sample 57

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RRP6-3V5-IAA7:KanMX8

value: IAA


title: C57BL/6J 8-10 weeks female, Liver, 1dpi, Biological replicate 2

description:
Library name: Liver-day1-2
Liver_featureCounts.txt


title: 203977090037_R02C01_PD908_PFC

value: Prefrontal cortex

value: Imperial Brain Bank


title: Control prostate cancer cells replicate 1

description:
Library name: NC_1
Control prostate cancer cells, biological replicate 1. Expression values are provided in columns FPKM.NC_1 and count.NC_1.

value: batch 1


title: RRP6_degron_4h_r2

description: Library name: sample 56

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RRP6-3V5-IAA7:KanMX7


title: 203977000009_R03C01_20152915_PFC

value: male

value: FALSE


title: RRP6_degron_4h_r1

description: Library name: sample 55

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RRP6-3V5-IAA7:KanMX6


title: 203977000009_R02C01_20140523_PFC

value: Newcastle Brain Tissue Resource


title: myoblast_epith_isolation_normal_diet_batch2_rep3

city: St. Petersburg

first: Oscar

middle: E

last: Ospina

state: FL

address: 600 5th Street South

department: Health Informatics

institute: Johns Hopkins All Children's Hospital

description:
Library name: ISO_M_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

data_processing:
Fastq files derived from Illumina sequencing were processed with the nf-core/rnaseq (v3.19) pipeline. Alignment performed with STAR (v2.7.11b) and quantification with salmon (v1.10.3). The quant files were then used as input for tximport (v1.34) and DESeq2 (v1.46). The untransformed count matrix was exported directly from the DESeq2 object. The normalized expression matrox for visualization was generated using VST normalization followed by batch correction with limma v3.62.2 (experiment batch - see manuscript for details).
Assembly: GRCh38.p14
Supplementary files format and content: Untransformed ("raw") RNAseq counts and normalized expression to replicate visualizations in the manuscript.

source_name: skeletal myoblast

extract_protocol:
RNA was isolated from harvested tissue compartments using the RNeasy Mini Kit (Qiagen, cat. no. 74106). Tissue lysates were prepared in RLT buffer supplemented with β-mercaptoethanol (Gibco, cat. no. 21985023) and stored at −80°C until RNA purification. RNA concentration and purity were assessed by NanoDrop spectrophotometry and Qubit fluorometry. RNA integrity was evaluated using Agilent RNA ScreenTape on an Agilent 4200 TapeStation prior to library preparation.
Total RNA samples passing quality control were submitted to Novogene for bulk mRNA-seq library preparation. Poly(A)+ mRNA was enriched from total RNA and used to generate non-directional Illumina-compatible sequencing libraries according to Novogene standard protocols. Libraries were sequenced on an Illumina NovaSeq X Plus platform using a paired-end 150 bp read configuration, with a target output of approximately 6 Gb raw data per sample.

value: skeletal myoblast

value: normal diet culture in isolation


title: C57BL/6J 8-10 weeks female, Liver, 0dpi, Biological replicate 3

description:
Library name: Liver-day0-3
Liver_featureCounts.txt

value: Liver

value: WT

value: Control (PBS)


title: 203977000009_R01C01_20174913_PFC


title: myoblast_epith_isolation_normal_diet_batch3_rep1

description:
Library name: ISO_M_C1_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: RAT1_DMSO_4h_r2

description: Library name: sample 53

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RAT1-3V5-IAA7:KanMX10

value: DMSO


title: 203977000030_R07C01_PD028_PFC


title: myoblast_epith_isolation_normal_diet_batch2_rep1

description:
Library name: ISO_M_C1_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: RAT1_DMSO_4h_r1

description: Library name: sample 52

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RAT1-3V5-IAA7:KanMX9


title: RAT1_DMSO_4h_r3

description: Library name: sample 54

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RAT1-3V5-IAA7:KanMX11


title: C57BL/6J 8-10 weeks female, Liver, 0dpi, Biological replicate 1

description:
Library name: Liver-day0-1
Liver_featureCounts.txt


title: 203977000030_R06C01_C094_PFC

value: Prefrontal cortex

value: Imperial Brain Bank

value: female


title: hepatocyte_isolation_high_diet_batch3_rep1

description:
Library name: ISO_L_W_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

source_name: primary hepatocyte

value: primary hepatocyte

value: high (western) diet culture in isolation


title: RAT1_degron_4h_r3

description: Library name: sample 51

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RAT1-3V5-IAA7:KanMX8

value: IAA


title: C57BL/6J 8-10 weeks female, Liver, 0dpi, Biological replicate 2

description:
Library name: Liver-day0-2
Liver_featureCounts.txt


title: miR_150overexpressing thrombocytes_bio_rep3

city: Geneva

first: Pierre

last: Fontana

state: Geneva

address: Rue Michel-Servet 1

department: Medicine

country: Switzerland

institute: University of Geneva

description:
Library name: sample 9
Column name in raw_counts_all_samples.txt: sample 9

data_processing:
Fastq reads were mapped to the Ensembl Danio rerio GRCz11 genome with STAR v.2.7.10b
Quantification of transcripts expression was performed with HTSeq v0.11.3 (htseq-count)
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR 1.34.1. with a multiple testing Benjamini and Hochberg correction FDR 5% and a fold change threshold of 2.
Assembly: Danio rerio GRCz11 genome
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

molecule: total RNA

organism: Danio rerio

source_name: thrombocytes

growth_protocol: Embryos obtained through natural matings were cultured at 28.5 °C in E3 medium. At 24-30 hours post fertilization the culture medium was supplemented with 0.003% (w/v) 1-phenyl 2-thiourea (PTU; Thermo Scientific Chemicals) to block the pigmentation and improve larval optical transparency.

extract_protocol:
Complete RNA was isolated from sorted thrombocytes using the miRNeasy Tissue/Cells Advanced Mini Kit (Qiagen) following the manufacturer’s protocol.
cDNA libraries were constructed using the SMARTer Ultra Low Input RNA kit (Clontech), combined with Nextera XT DNA Library preparation kit (Illumina) according to the manufacturers’ protocols.

treatment_protocol: Anesthetized larvae at 5 dpf were dissociated into single cells and GFP+/TagRFP+ cells were sorted and collected for RNAseq analysis.

value: thrombocytes


title: 203977000030_R05C01_PD1075_PFC

value: FALSE


title: hepatocyte_isolation_high_diet_batch2_rep1

description:
Library name: ISO_L_W_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: RAT1_degron_4h_r2

description: Library name: sample 50

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RAT1-3V5-IAA7:KanMX7


title: XRN1_DMSO_4h_r3

description: Library name: sample 66

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 XRN1-3V5-IAA7:KanMX11


title: miR_150overexpressing thrombocytes_bio_rep2

description:
Library name: sample 8
Column name in raw_counts_all_samples.txt: sample 8


title: WA09 cells, Day20, 100 ng/ml FGF8b, not DLX5 activated, rep 3

description: Library name: A15

value: WA09 (WiCell)

value: human embryonic stem cells


title: 203977000030_R03C01_C088_PFC

value: male


title: 203977090004_R03C01_PD362_PFC


title: hepatocyte_isolation_low_diet_batch3_rep1

description:
Library name: ISO_L_F_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: low (fasting) diet culture in isolation


title: C57BL/6J 8-10 weeks female, Liver, 3dpi, Biological replicate 4

description:
Library name: Liver-day3-4
Liver_featureCounts.txt

value: Liver

value: WT

value: Cr infection


title: RAT1_degron_4h_r1

description: Library name: sample 49

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 RAT1-3V5-IAA7:KanMX6


title: 203977090025_R05C01_20130879_PFC

value: Prefrontal cortex

value: Newcastle Brain Tissue Resource


title: XRN1_degron_4h_r2

description: Library name: sample 62

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 XRN1-3V5-IAA7:KanMX7


title: miR_150overexpressing thrombocytes_bio_rep1

description:
Library name: sample 7
Column name in raw_counts_all_samples.txt: sample 7


title: 203977000069_R05C01_20163933_PFC


title: hepatocyte_isolation_low_diet_batch2_rep1

description:
Library name: ISO_L_F_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: primary hepatocyte


title: PAT1_DMSO_4h_r3

description: Library name: sample 48

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAT1-3V5-IAA7:KanMX11

value: DMSO


title: Control thrombocytes_nomiRNA_bio_rep3

description:
Library name: sample 3
Column name in raw_counts_all_samples.txt: sample 3

value: thrombocytes


title: 203977000069_R04C01_PD004_PFC

value: Imperial Brain Bank

value: FALSE


title: hepatocyte_isolation_normal_diet_batch3_rep3

description:
Library name: ISO_L_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: normal diet culture in isolation


title: Control thrombocytes_nomiRNA_bio_rep2

description:
Library name: sample 2
Column name in raw_counts_all_samples.txt: sample 2


title: PAT1_DMSO_4h_r2

description: Library name: sample 47

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAT1-3V5-IAA7:KanMX10


title: 203977000069_R01C01_PD061_PFC

value: male


title: C57BL/6J 8-10 weeks female, Liver, 1dpi, Biological replicate 4

description:
Library name: Liver-day1-4
Liver_featureCounts.txt

value: Liver


title: hepatocyte_isolation_normal_diet_batch2_rep3

description:
Library name: ISO_L_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: PAT1_DMSO_4h_r1

description: Library name: sample 46

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAT1-3V5-IAA7:KanMX9


title: Control thrombocytes_nomiRNA_bio_rep1

description:
Library name: sample 1
Column name in raw_counts_all_samples.txt: sample 1


title: 203973690061_R08C01_PD576_PFC

value: female


title: 203977090037_R08C01_PD898_PFC


title: 203977090037_R06C01_PD847_PFC


title: hepatocyte_isolation_normal_diet_batch3_rep1

description:
Library name: ISO_L_C1_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: PAT1_degron_4h_r3

description: Library name: sample 45

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAT1-3V5-IAA7:KanMX8

value: IAA


title: hir2-5 3, flg22

city: Tübingen

first: Hannah

middle: Lena

last: Weber

state: Baden-Württemberg

address: Auf der Morgenstelle 32

department: Biochemistry

country: Germany

institute: ZMBP Tübingen

description: Library name: hir257_treat_3

data_processing:
Bioinformatics analysis was performed by Eurofins Genomics. Mapping & Alignment; According to Eurofins: High quality sequence reads are aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference), run through Sentieon (Sentieon. 2021. Sentieon provides complete solutions for secondary dna/rna analysis for a variety of sequencing platforms, including short and long reads. Sentieon. Retrieved from https://www.sentieon.com/) framework, along with the known gene models. STAR (Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras. 2012. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 1 (October 2012), 15–21. DOI:https://doi.org/10.1093/bioinformatics/bts635) an aligner designed to specifically address many of the challenges of RNA-Seq data mapping using a strategy to account for spliced alignments. In general, STAR algorithm achieves highly efficient mapping by performing a two-step process – i) Seed searching, followed by ii) Clustering, stitching, and scoring. In seed searching step (i), for every read that STAR aligns, STAR will search for the longest sequence that exactly matches one or more locations on the reference genome. These longest matching sequences are called the Maximal Mappable Prefixes (MMPs). The different parts of the read that are mapped separately are called ‘seeds’. So the first MMP that is mapped to the genome is called seed1. STAR will then search again for only the unmapped portion of the read to find the next longest sequence that exactly matches the reference genome, or the next MMP, which will be seed2. This sequential searching of only the unmapped portions of reads underlies the efficiency of the STAR algorithm. STAR uses an uncompressed suffix array (SA) to efficiently search for the MMPs, this allows for quick searching against even the largest reference genomes. If STAR does not find an exact matching sequence for each part of the read due to mismatches or indels, the previous MMPs will be extended. If extension does not give a good alignment, then the poor quality or adapter sequence (or other contaminating sequence) will be soft clipped. In clustering, stitching, and scoring step (ii), the separate seeds are stitched together to create a complete read by first clustering the seeds together based on proximity to a set of ‘anchor’ seeds, or seeds that are not multi-mapping. Then the seeds are stitched together based on the best alignment for the read (scoring based on mismatches, indels, gaps, etc.).
For Gene Counts: According to Eurofins: Gene wise quantification is achieved by inspecting transcriptome alignments using RSEM (Bo Li and Colin N. Dewey. 2011. RSEM: Accurate transcript quantification from rna-seq data with or without a reference genome. BMC Bioinformatics 12, 1 (August 2011), 323. DOI:https://doi.org/10.1186/1471- 2105-12-323) tool. Using just the number of reads mapped to a transcript as a proxy for the transcript’s expression level, leads to the problem that the origin of some reads cannot always be uniquely determined. If two or more distinct transcripts in a particular sample share some common sequence (for example, if they are alternatively spliced mRNAs or mRNAs derived from paralogous genes), then sequence alignment may not be sufficient to discriminate the true origin of reads mapping to these transcripts. One approach to addressing this issue involves discarding these multiple-mapped reads (multireads for short) entirely. Another involves partitioning and distributing portions of a multiread’s expression value between all of the transcripts to which it maps (rescue-method). RSEM improves upon this approach, utilizing an Expectation-Maximization (EM) algorithm to estimate maximum likelihood expression levels accounting for multimapped reads generating near accurate expected counts for each gene annotated in the known gene model. Read counts are further normalized to account for sequencing depth and gene length biases, fragment per kilobase per million (FPKM) and Transcripts per million (TPM) values are generated and reported. Gene wise “expected counts” can then be used to identify differentially expressed genes.
For sign. Fold Changes: According to Eurofins; Genes receiving less than 10 reads on an average across the compared groups were removed. The abundance counts of each gene were then used to perform differential gene expression (DGE). DGE was performed using R/Bioconductor DESeq2 (Michael I. Love, Wolfgang Huber, and Simon Anders. 2014. Moderated estimation of fold change and dispersion for rna-seq data with deseq2. Genome Biology 15, 12 (December 2014), 550. DOI:https: //doi.org/10.1186/s13059-014-0550-8) package, which essentially normalizes the abundance counts to account for observed variance (due to differences in sequencing depths, sample groups and replicates) generating normalized gene counts. Statistical tests were performed for each gene to compare the distributions between conditions (treatment vs control) generating p-values for each gene. The final p-values were corrected by determining false discovery rates (FDR) using the Benjamin–Hochberg method. Using a FDR corrected p-value (adjusted p-value) <0.1 as a threshold, significantly differentially expressed genes between conditions were identified and reported.
Assembly: TAIR10 Genome
Supplementary files format and content: tsv file containing the sign. Fold changes. This files contains the genes which are classified as significantly differentially expressed between the conditions tested. Genes which have received >100 reads on an average across all samples, has > 1 log2Foldchange and FDR corrected p-value is <= 0.1, are classifed as “significant”. gene_id Gene identifier from gene models used in the analysis gene_name Corresponding gene name from refseq mean_counts Average of the normalized counts between the compared pair log2_foldChange FoldChange observed in treatment compared to control and is reported on a logarithmic scale to base 2. Positive values indicate upregulated genes in treatment and negative values indicate downregulated in the treatment compared to control sample. p_value Statistical test performed for each gene to void off any experimental variability adj_p_value False discovery rate (FDR) corrected P-value and is determined using a permutation test on treated versus control samples and corrected for multiple testing using the Benjamin–Hochberg method. FoldChange differences observed in genes below 0.1 FDR corrected p-value are considered significantly differ between treatment and control sample.
Supplementary files format and content: tsv file containig the gene count: Sample-wise, gene wise read counts, TPM value and FPKM value. The content is as follows - Column_ Description gene_id Gene identifier from gene models used in the analysis gene_name Corresponding gene name from refseq {sample}_counts sample wise read counts observed {sample}_TPM sample wise TPM observed {sample}_FPKM sample wise FPKM observed

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: For each sample, 7 seedlings grown for 10 days on ½ MS (short-day conditions) and pooled.

extract_protocol:
The RNA was extracted using the RNeasy Plant Kit (Qiagen) according to the manufacture's protocol and diluted to a concentration of 150 ng.
Strand-specific cDNA libraries were prepared by Eurofins Genomics from total RNA.

treatment_protocol: Samples were treated with either water (mock) or 1 µM flg22 for 10 min and then frozen in liquid N2.

value: Whole plant

value: HIR2 tDNA line


title: 203973690005_R07C01_20100359_PFC

value: Prefrontal cortex

value: Newcastle Brain Tissue Resource


title: hepatocyte_isolation_normal_diet_batch2_rep1

description:
Library name: ISO_L_C1_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: primary hepatocyte


title: PAT1_degron_4h_r2

description: Library name: sample 44

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAT1-3V5-IAA7:KanMX7


title: hir2-5 2, flg22

description: Library name: hir257_treat_2


title: 203973690005_R01C01_PD737_PFC

value: Imperial Brain Bank


title: islet_isolation_high_diet_batch3_rep1

description:
Library name: ISO_I_W_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

source_name: pancreatic islet

value: pancreatic islet

value: high (western) diet culture in isolation


title: PAT1_degron_4h_r1

description: Library name: sample 43

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAT1-3V5-IAA7:KanMX6


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, no FGF8b, DLX5 activated, rep 3

description: Library name: N21_A

value: WA09 (WiCell)

value: human embryonic stem cells


title: 203991450115_R08C01_PD746_PFC

value: FALSE


title: hir2-5 1, flg22

description: Library name: hir257_treat_1


title: islet_isolation_high_diet_batch2_rep1

description:
Library name: ISO_I_W_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: C57BL/6J 8-10 weeks female, Liver, 1dpi, Biological replicate 1

description:
Library name: Liver-day1-1
Liver_featureCounts.txt

value: Liver

value: WT

value: Cr infection


title: PAB1_DMSO_4h_r3

description: Library name: sample 42

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAB1-3V5-IAA7:KanMX11

value: DMSO


title: 203991450115_R07C01_20010025_PFC

value: Prefrontal cortex

value: male


title: myoblast_epith_isolation_normal_diet_batch3_rep3

description:
Library name: ISO_M_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: skeletal myoblast

value: normal diet culture in isolation


title: islet_isolation_low_diet_batch3_rep1

description:
Library name: ISO_I_F_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: low (fasting) diet culture in isolation


title: hir2-2 3, flg22

description: Library name: hir2org_treat_3

value: Whole plant

value: HIR2 tDNA line


title: PAB1_DMSO_4h_r2

description: Library name: sample 41

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAB1-3V5-IAA7:KanMX10


title: hir2-2 2, flg22

description: Library name: hir2org_treat_2


title: PAB1_DMSO_4h_r1

description: Library name: sample 40

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAB1-3V5-IAA7:KanMX9


title: islet_isolation_normal_diet_batch3_rep3

description:
Library name: ISO_I_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: pancreatic islet


title: C57BL/6J 8-10 weeks female, Liver, 0dpi, Biological replicate 4

description:
Library name: Liver-day0-4
Liver_featureCounts.txt

value: Control (PBS)


title: 203991450115_R06C01_PD340_PFC

value: Imperial Brain Bank

value: FALSE


title: PAB1_degron_4h_r3

description: Library name: sample 39

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAB1-3V5-IAA7:KanMX8

value: IAA


title: 203991450115_R03C01_20174954_PFC

value: Newcastle Brain Tissue Resource


title: Col-0 3, flg22

description: Library name: col_treat_3

value: WT


title: islet_isolation_low_diet_batch2_rep1

description:
Library name: ISO_I_F_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: hir2-2 1, flg22

description: Library name: hir2org_treat_1


title: Col-0 2, flg22

description: Library name: col_treat_2


title: PAB1_degron_4h_r2

description: Library name: sample 38

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAB1-3V5-IAA7:KanMX7


title: islet_isolation_normal_diet_batch3_rep1

description:
Library name: ISO_I_C1_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: islet_isolation_normal_diet_batch2_rep3

description:
Library name: ISO_I_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: PAB1_degron_4h_r1

description: Library name: sample 37

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 PAB1-3V5-IAA7:KanMX6


title: Col-0 1, flg22

description: Library name: col_treat_1


title: 203991460068_R06C01_PD759_PFC

value: Prefrontal cortex

value: female


title: 203991460068_R02C01_19920141_PFC

value: male


title: LSM1_DMSO_4h_r3

description: Library name: sample 36

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 LSM1-3V5-IAA7:KanMX11

value: DMSO


title: 203991460069_R05C01_C083_PFC


title: gut_epith_isolation_normal_diet_batch3_rep3

description:
Library name: ISO_G_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: normal diet culture in isolation


title: hir2-5 3, control (water)

description: Library name: hir257_mock_3

value: Whole plant

value: HIR2 tDNA line

value: Water


title: hir2-5 2, control (water)

description: Library name: hir257_mock_2


title: gut_epith_isolation_normal_diet_batch2_rep3

description:
Library name: ISO_G_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: LSM1_DMSO_4h_r1

description: Library name: sample 34

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 LSM1-3V5-IAA7:KanMX9


title: 203991460068_R01C01_PD992_PFC

value: Imperial Brain Bank

value: FALSE


title: islet_isolation_normal_diet_batch2_rep1

description:
Library name: ISO_I_C1_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: pancreatic islet


title: 203991410079_R08C01_C046_CNG

source_name: Anterior cingulate

value: Anterior cingulate


title: LSM1_degron_4h_r3

description: Library name: sample 33

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 LSM1-3V5-IAA7:KanMX8

value: IAA


title: gut_epith_isolation_normal_diet_batch3_rep1

description:
Library name: ISO_G_C1_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: LSM1_DMSO_4h_r2

description: Library name: sample 35

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 LSM1-3V5-IAA7:KanMX10


title: 203991460069_R04C01_PD050_PFC

value: Prefrontal cortex

value: female


title: hir2-5 1, control (water)

description: Library name: hir257_mock_1


title: 203991410079_R06C01_PD090_CNG


title: LSM1_degron_4h_r2

description: Library name: sample 32

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 LSM1-3V5-IAA7:KanMX7


title: 203991410079_R04C01_P64/09_CNG

value: QSBB

value: TRUE


title: hir2-2 3, control (water)

description: Library name: hir2org_mock_3

value: Whole plant


title: hir2-2 2, control (water)

description: Library name: hir2org_mock_2

value: HIR2 tDNA line


title: hir2-2 1, control (water)

description: Library name: hir2org_mock_1

value: Water


title: neuron_isolation_low_diet_batch3_rep1

description:
Library name: ISO_B_F_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

source_name: neuron

value: neuron

value: low (fasting) diet culture in isolation


title: 203991410122_R03C01_PD330_CNG

value: Imperial Brain Bank

value: FALSE


title: neuron_isolation_normal_diet_batch3_rep3

description:
Library name: ISO_B_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: normal diet culture in isolation


title: DCP2_DMSO_4h_r2

description: Library name: sample 29

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 DCP2-3V5-IAA7:KanMX10

value: DMSO


title: LSM1_degron_4h_r1

description: Library name: sample 31

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 LSM1-3V5-IAA7:KanMX6

value: IAA


title: gut_epith_isolation_normal_diet_batch2_rep1

description:
Library name: ISO_G_C1_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: neuron_isolation_normal_diet_batch2_rep3

description:
Library name: ISO_B_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: DCP2_DMSO_4h_r1

description: Library name: sample 28

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 DCP2-3V5-IAA7:KanMX9


title: DCP2_DMSO_4h_r3

description: Library name: sample 30

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 DCP2-3V5-IAA7:KanMX11


title: 203991410065_R08C01_PD834_CNG

value: Anterior cingulate

value: male


title: Col-0 1, control (water)

description: Library name: col_mock_1

value: Whole plant

value: WT


title: neuron_isolation_normal_diet_batch3_rep1

description:
Library name: ISO_B_C1_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: DCP2_degron_4h_r3

description: Library name: sample 27

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 DCP2-3V5-IAA7:KanMX8


title: RNA-seq_9dpg leaf epidermal cells, hdl, sample 2

city: Taipei

first: Chin-Min

last: Ho

address: A423, Institute of Plant and Microbial Biology, Academia Sinica

country: Taiwan

institute: Academia Sinica

description: Library name: hdl-1-2

data_processing:
The quality of RNA-seq raw reads was assessed by FastQC v0.11.9 and trimmed with Trimmomatic v0.33. Reads were then aligned to Arabidopsis_thaliana_TAIR10 using Bowtie2 (Galaxy Version 2.5.0+galaxy0); ~84% of reads mapped to the nuclear genome, and the remaining ~9% and ~7% of reads mapped to the mitochondrial and chloroplast genomes, respectively, and were filtered out. Run Samtools (version 1.16.1) sort and index the bam file; covert to bw with bamCoverage and ignore the reads of mitochondria and chloroplast. Calculations to identify differentially expressed genes (DEGs) were performed with DESeq2.
Assembly: TAIR10
Supplementary files format and content: bigWig files of WT and hdl
Supplementary files format and content: csv files include raw counts and  normalized counts for each sample

source_name: Leaf

growth_protocol: WT, hdl-1 seeds were startified in 4oC for 2 days and plants were grown in 1/2 MS media under long day condition for 9 days

extract_protocol:
9dpg WT and hdl seedlings with the AtML1pro:RCI2A-mcherry reporter were used for protoplast isolation and FACS. Approximately 20,000 mCherry-positive cells were sorted into 350 µl RNA extraction buffer, and total RNA was extracted from the samples using an RNeasy Micro kit (QIAGEN).
RNA-seq libraries were prepared using using an Illumina TruSeq RNA Library Preparation kit according to the manufacturer’s protocol. 10-20 ng RNA was used as starting material.

value: Leaf

value: Leaf epidermal cells

value: hdl


title: 203991410065_R06C01_20174955_CNG

value: Newcastle Brain Tissue Resource

value: FALSE


title: 203991410065_R05C01_PD992_CNG

value: Imperial Brain Bank

value: female


title: RNA-seq_9dpg leaf epidermal cells, hdl, sample 1

description: Library name: hdl-1-1


title: adypocyte_isolation_high_diet_batch3_rep1

description:
Library name: ISO_A_W_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

source_name: adipocyte

value: adipocyte

value: high (western) diet culture in isolation


title: RNA-seq_9dpg leaf epidermal cells, WT, sample 3

description: Library name: WT-1-3


title: DCP2_degron_4h_r1

description: Library name: sample 25

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 DCP2-3V5-IAA7:KanMX6

value: IAA


title: 203991410052_R08C01_PDC078_CNG

value: Anterior cingulate


title: adypocyte_isolation_low_diet_batch3_rep1

description:
Library name: ISO_A_F_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: low (fasting) diet culture in isolation


title: RNA-seq_9dpg leaf epidermal cells, WT, sample 2

description: Library name: WT-1-2


title: NOT5_DMSO_4h_r3

description: Library name: sample 24

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 NOT5-3V5-IAA7:KanMX11

value: DMSO


title: adypocyte_isolation_normal_diet_batch3_rep3

description:
Library name: ISO_A_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: normal diet culture in isolation


title: 203991410052_R06C01_RI92/1020_CNG

value: Oxford Brain Bank


title: NOT5_DMSO_4h_r2

description: Library name: sample 23

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 NOT5-3V5-IAA7:KanMX10


title: RNA-seq_9dpg leaf epidermal cells, WT, sample 1

description: Library name: WT-1-1

value: Leaf

value: Leaf epidermal cells

value: WT


title: adypocyte_isolation_normal_diet_batch2_rep3

description:
Library name: ISO_A_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: 203991410052_R01C01_PD229_CNG

value: Imperial Brain Bank

value: FALSE


title: NOT5_DMSO_4h_r1

description: Library name: sample 22

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 NOT5-3V5-IAA7:KanMX9


title: 8dpg seedlings, hdl, H3K9me2,sample 2

description: Library name: hdl-H3K9me2-R2

library_source: genomic

data_processing:
The quality of ChIP-seq raw reads was assessed by FastQC v0.11.9 and trimmed with Trimmomatic v0.33. The cleaned data was then aligned to the Arabidopsis genome (TAIR10) by Bowtie 2 v2.3.5.1. Removal of mitochondria DNA, plastid DNA, and duplicated reads and the calculation of fragment length distributions were performed by deepTools.
Assembly: TAIR10
Supplementary files format and content: bigWig files of WT and hdl

source_name: seedlings

growth_protocol: WT, hdl-1 seeds were startified in 4oC for 2 days and plants were grown in 1/2 MS media under long day condition for 8 days

extract_protocol:
8dpg WT and hdl seedlings were fixed with 2% formaldehyde in 3C buffer for 1hr. After quenching and lysis, chromatin was sonicated using Bioruptor.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep kit (cat no. E7645). 10 ng DNA was used as starting material for input and ip samples. Libraries were amplified using 13-16 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using agencourt AMPure XP beads from Beckman Coulter.

value: seedlings

value: plant cells

value: hdl


title: NOT5_degron_4h_r3

description: Library name: sample 21

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 NOT5-3V5-IAA7:KanMX8

value: IAA


title: 8dpg seedlings, hdl, H3K9me2,sample 1

description: Library name: hdl-H3K9me2-R1


title: 203991410111_R08C01_PD844_CNG

value: Anterior cingulate

value: male


title: NOT5_degron_4h_r2

description: Library name: sample 20

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 NOT5-3V5-IAA7:KanMX7


title: 203991410111_R05C01_20185907_CNG

value: Newcastle Brain Tissue Resource


title: 8dpg seedlings, WT, H3, sample 2

description: Library name: Col-H3-R2


title: myoblast_interaction_high_diet_batch3_rep1

description:
Library name: INT_M_W_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: skeletal myoblast

value: high (western) diet culture in interaction (chip)


title: NOT5_degron_4h_r1

description: Library name: sample 19

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 NOT5-3V5-IAA7:KanMX6


title: 203991410122_R05C01_PD957_CNG

value: female


title: neuron_isolation_high_diet_batch3_rep1

description:
Library name: ISO_B_W_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: neuron

value: high (western) diet culture in isolation


title: 8dpg seedlings, WT, H3, sample 1

description: Library name: Col-H3-R1

value: WT


title: 203991410111_R04C01_C074_CNG

value: Imperial Brain Bank

value: FALSE


title: Col-0 3, control (water)

description: Library name: col_mock_3

value: Whole plant

value: Water


title: myoblast_interaction_high_diet_batch2_rep1

description:
Library name: INT_M_W_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: POP2_DMSO_4h_r3

description: Library name: sample 18

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 POP2-3V5-IAA7:KanMX11

value: DMSO


title: Col-0 2, control (water)

description: Library name: col_mock_2


title: 8dpg seedlings, WT, H3K9me2, sample 2

description: Library name: Col-H3K9me2-R2

value: seedlings

value: plant cells


title: 203991410122_R01C01_20110852_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource

value: male


title: 203991410028_R08C01_PD899_CNG


title: myoblast_interaction_high_diet_semaglutide_batch3_rep1

description:
Library name: INT_M_S_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: skeletal myoblast

value: high (western) diet culture in interaction (chip) with semaglutide 130 ng/mL


title: POP2_DMSO_4h_r2

description: Library name: sample 17

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 POP2-3V5-IAA7:KanMX10


title: 203991410028_R07C01_P21/17_CNG

value: QSBB


title: 8dpg seedlings, WT, H3K9me2, sample 1

description: Library name: Col-H3K9me2-R1

value: WT


title: myoblast_interaction_high_diet_semaglutide_batch2_rep1

description:
Library name: INT_M_S_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: POP2_DMSO_4h_r1

description: Library name: sample 16

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 POP2-3V5-IAA7:KanMX9


title: 9dpg leaf epidermal cells, hdl, sample 2

description: Library name: hdl-5

data_processing:
The quality of ATAC-seq raw reads was assessed by FastQC v0.11.9 and trimmed with Trimmomatic v0.33. The cleaned data was then aligned to the Arabidopsis genome (TAIR10) by Bowtie 2 v2.3.5.1.Removal of mitochondria DNA, plastid DNA, and duplicated reads, the calculation of fragment length distributions, and peak calling were performed by ATACgraph pipeline. To evaluate the quality of the ATAC-seq libraries, the Fraction of Reads in Peaks (FRiP) and Irreproducible Discovery Rate (IDR) were estimated following ENCODE ATAC-seq guidelines. The final alignment files were converted to bigwig format for visualization on the genome browser using deepTools v3.5.0. Post-alignment analysis and figures generation were conducted by R and Python scripts.
Assembly: TAIR10
Supplementary files format and content: bigWig files of WT and hdl

extract_protocol:
9dpg WT and hdl seedlings with the AtML1pro:RCI2A-mcherry reporter were used for protoplast isolation and FACS. Approximately 50,000-200,000 mCherry-positive cells were sorted into 300 µl PBS. Sorted cells were lysed and nuclei were collected for tagmentation according to the manufacturer’s protocol (TDE1, Illumina).
DNA was amplified by PCR using ATAC barcoded primers and NEB Next High-Fidelity PCR Master Mix. Libraries were amplified using 8-10 cycles on the thermocycler. Post amplification libraries were size selected 100-1000bp in length using agencourt AMPure XP beads from Beckman Coulter.

value: Leaf

value: Leaf epidermal cells

value: hdl


title: neuron_isolation_normal_diet_batch2_rep1

description:
Library name: ISO_B_C1_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: neuron

value: normal diet culture in isolation


title: DCP2_degron_4h_r2

description: Library name: sample 26

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 DCP2-3V5-IAA7:KanMX7

value: IAA


title: 203991410028_R02C01_20152915_CNG

value: Anterior cingulate

value: FALSE


title: myoblast_interaction_high_diet_metformin_batch3_rep1

description:
Library name: INT_M_M_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: high (western) diet culture in interaction (chip) with metformin 1 ug/mL


title: POP2_degron_4h_r3

description: Library name: sample 15

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 POP2-3V5-IAA7:KanMX8


title: 203991410028_R01C01_PD082_CNG

value: Imperial Brain Bank

value: male


title: myoblast_interaction_high_diet_metformin_batch2_rep1

description:
Library name: INT_M_M_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: skeletal myoblast


title: 9dpg leaf epidermal cells, hdl, sample 1

description: Library name: hdl-4


title: POP2_degron_4h_r2

description: Library name: sample 14

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 POP2-3V5-IAA7:KanMX7


title: 9dpg leaf epidermal cells, WT, sample 4

description: Library name: WT-5

value: WT


title: 203991390053_R07C01_20152906_CNG

value: Newcastle Brain Tissue Resource


title: myoblast_interaction_low_diet_batch3_rep1

description:
Library name: INT_M_F_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: low (fasting) diet culture in interaction (chip)


title: POP2_degron_4h_r1

description: Library name: sample 13

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 POP2-3V5-IAA7:KanMX6


title: 203991390089_R08C01_P17/16_CNG

value: QSBB

value: female


title: 9dpg leaf epidermal cells, WT, sample 3

description: Library name: WT-4

value: Leaf

value: Leaf epidermal cells


title: myoblast_interaction_low_diet_batch2_rep1

description:
Library name: INT_M_F_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: 9dpg leaf epidermal cells, WT, sample 2

description: Library name: WT-3


title: CAF40_DMSO_4h_r3

description: Library name: sample 12

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p555

value: DMSO


title: 203991390089_R05C01_PD758_CNG

value: Anterior cingulate

value: FALSE


title: myoblast_interaction_normal_diet_batch3_rep3

description:
Library name: INT_M_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: normal diet culture in interaction (chip)


title: CAF40_DMSO_4h_r2

description: Library name: sample 11

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p554


title: 9dpg leaf epidermal cells, WT, sample 1

description: Library name: WT-2


title: myoblast_interaction_normal_diet_batch2_rep3

description:
Library name: INT_M_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: skeletal myoblast


title: CAF40_DMSO_4h_r1

description: Library name: sample 10

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p553


title: 203977090067_R02C01_20185918_CNG

value: male


title: myoblast_interaction_normal_diet_batch3_rep1

description:
Library name: INT_M_C1_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: HDL:YFP-input 2

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

institute: NTU, IPB

data_processing:
The raw sequence data were processed using the Illumina sequence data analysis pipeline GAPipeline 1.3.2. MACS2 was then employed to map the reads to the Arabidopsis genome (TAIR10).
To determine the correlation between biological repeats, Pearson correlation was computed using R statistical software on normalized signal intensity for ChIP binding peaks. The alignments were first converted to Wiggle (WIG) files. The data were then imported into the Integrated Genome Viewer (IGV) for visualization.
Assembly: TAIR 10
Supplementary files format and content: bigwig files

source_name: 10 days old plants

growth_protocol: The transgenic Arabidopsis seedlings were grown under Long-day conditions at 22°C and harvested after 10 days.

extract_protocol:
2 ng of DNA from ChIP was pooled to ensure that there are enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries.
End repair, adaptor ligation, and amplification were carried out using the NEB Genomic DNA Sample Prep kit according to the manufacturer's protocol.

tag: ecotype

tag: fraction

value: input


title: CAF40_degron_4h_r3

description: Library name: sample 9

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p552

value: IAA


title: CAF40_degron_4h_r2

description: Library name: sample 8

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p551


title: HDL:YFP-IP-2

value: IP


title: hepatocyte_interaction_high_diet_batch3_rep1

description:
Library name: INT_L_W_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: primary hepatocyte

value: high (western) diet culture in interaction (chip)


title: HDL:YFP-IP-1


title: CAF40_degron_4h_r1

description: Library name: sample 7

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550


title: 203973690024_R07C01_20060025_CNG

value: Newcastle Brain Tissue Resource


title: hepatocyte_interaction_high_diet_batch2_rep1

description:
Library name: INT_L_W_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: WT_TIRligase_DMSO_4h_r3

description: Library name: sample 6

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p555

value: DMSO


title: 203973690024_R01C01_20110403_CNG

value: Anterior cingulate

value: female

value: FALSE


title: Sample 14_F5A

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

description:
Library name: Sample 14
FF-EV_miRNAs_in_Rhino_CPM.xlsx

data_processing:
Raw FASTQ files were first subjected to quality control and adapter trimming using FASTp, with a minimum Phred quality score of 20, a required minimum read length of 15 nucleotides, and a maximum read length of 35 nucleotides. Filtered reads were then processed using the miRDeep2 Mapper module, discarding reads shorter than 15 nucleotides. miRNA quantification was performed with the miRDeep2 Quantifier tool using miRBase release 22.1 as the reference database. Reads were annotated against equine, bovine, and human precursor and mature miRNAs, allowing up to one mismatch.
Differential expression analysis was conducted using DESeq2 within Galaxy.
Assembly: miRBase release 22.1
Supplementary files format and content: xlsx file include CPM values for each sample

organism: Ceratotherium simum simum

source_name: Follicular fluid

extract_protocol:
For the GC ampless, total RNA, including miRNA, was isolated using the Qiagen miRNeasy Micro Kit (Qiagen, Germantown, MD) per the manufacturer’s instructions. Briefly, granulosa cells were incubated with Qiazol lysis reagent and vortexed to homogenize the cells. After 5 min, chloroform was added to the sample and centrifuged at 10,000 x g for 15 min to separate RNA and protein. The RNA phase was added to an elution column and eluted in water after multiple washes. For the follicular fluid (FF) samples, FF was centrifuged at 300 x g for 10 min, the supernatant was re-centrifuged at 2000 x g for 10 min, and again at 16,500 x g for 30 min. The final supernatant was passed through a 0.20-μm sterile syringe filter, removing particles larger than 200 nm in diameter. For the EV isolation, 2 ml of pre-centrifuged follicular samples were subjected to an ultracentrifugation procedure at 120,000 xg for 70 min at 4 C using the Beckman SWTi55 rotor. The EVs pellet was washed with sterile PBS and then centrifuged again at 120,000 xg for 70 min. The washed pellets were then resuspended in DPBS.  To precipitate EVs,  Exo-spin™ buffer was added to each sample and incubated overnight at 4°C. The precipitated EVs were purified using Exo-spin™ mini columns according to the manufacturer’s instructions. Final 180 µL EV aliquots were stored at −80°C for subsequent characterization and analysis. Total RNA including miRNAs was isolated from EVs using a Norgen Exosomal RNA Isolation kit (Norgen, Canada), according to the manufacturer’s instructions. On-column DNA digestion was performed to remove genomic DNA contaminants.
For GC samples library preparation kit was SMARTer smRNA-Seq Library Preparation Kit (Takara Bio) per manufacturer’s instructions. For FF-EV samples, Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Follicular fluid

value: Extracellular Vesicles

tag: corresponding oocyte_maturation

value: PB


title: 203973690002_R05C01_PD067_CNG

value: Imperial Brain Bank

value: male


title: WT_TIRligase_DMSO_4h_r2

description: Library name: sample 5

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p554


title: hepatocyte_interaction_high_diet_semaglutide_batch2_rep1

description:
Library name: INT_L_S_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: high (western) diet culture in interaction (chip) with semaglutide 130 ng/mL


title: WT_TIRligase_DMSO_4h_r1

description: Library name: sample 4

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p553


title: Sample 12_F4A

description:
Library name: Sample 12
FF-EV_miRNAs_in_Rhino_CPM.xlsx

value: NoPB


title: 203973690002_R04C01_PD368_CNG


title: hepatocyte_interaction_high_diet_metformin_batch3_rep1

description:
Library name: INT_L_M_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: primary hepatocyte

value: high (western) diet culture in interaction (chip) with metformin 1 ug/mL


title: Sample 11_F4

description:
Library name: Sample 11
FF-EV_miRNAs_in_Rhino_CPM.xlsx


title: 203973690002_R01C01_PD683_CNG


title: hepatocyte_interaction_high_diet_metformin_batch2_rep1

description:
Library name: INT_L_M_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: Sample 10_F2A

description:
Library name: Sample 10
FF-EV_miRNAs_in_Rhino_CPM.xlsx


title: WT_TIRligase_degron_4h_r2

description: Library name: sample 2

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p551

value: IAA


title: hepatocyte_interaction_low_diet_batch3_rep1

description:
Library name: INT_L_F_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: low (fasting) diet culture in interaction (chip)


title: 203991400112_R06C01_20152920_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource


title: WT_TIRligase_degron_4h_r1

description: Library name: sample 1

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550


title: Sample 8_F1A

description:
Library name: Sample 8
FF-EV_miRNAs_in_Rhino_CPM.xlsx

value: Follicular fluid

value: Extracellular Vesicles


title: 203991390103_R07C01_PD544_CNG

value: Imperial Brain Bank

value: FALSE


title: 133B2_VORA_R3

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

description:
Library name: Sample 6
6G63S6_6
Processed_Data_File_GEO_Vorasidenib.txt

data_processing:
FastQ generation and demultiplexing were performed using BCL Convert v4.3.6 and fqtk v0.3.1.
Read filtering was performed using FastP v0.24.0, including poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length of 50 bp.
Reads were aligned to the GRCm39_114 mouse reference genome using STAR aligner v2.7.
BAM files were coordinate-sorted using samtools v1.21.
PCR and optical duplicates were removed by UMI-based deduplication using UMICollapse v1.1.0.
Mapping QC was assessed using RustQC v0.2.1.
Gene expression was quantified using featureCounts (subread v2.1.1), strand-specific, with fractional assignment of multi-mapping reads, using exons and 3' UTR as feature identifiers, grouped by gene_id.
Differential expression was performed using edgePython v0.2.5.
Assembly: GRCm39_114
Supplementary files format and content: tab delimited raw counts with genes in rows and samples in columns

source_name: glioma tumor cells

growth_protocol: Primary murine cell lines were grown in NeuroCult basal medium containing 10% NeuroCult Proliferation Supplement (Stemcell Technologies, #05702) and supplemented with 2µg/mL heparin (Stemcell Technologies #07980) plus growth factors (Shenandoah Biotech #PB-500-20) including 20ng/mL Epidermal Growth Factor (EGF; #200-53), 20ng/mL Fibroblast Growth Factor-basic (FGF; #200-12), 10ng/mL PDGF-AA (#200-54) and 10ng/mL PDGF-BB (#200-58). Cultures were grown as adherent monolayer in T25 laminin coated flasks.

extract_protocol:
RNA was isolated using the Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, #D7003)
RNA libraries were prepared for 3' end counting bulk RNA sequencing by Plasmidsaurus. Total RNA was reverse transcribed into cDNA using a poly(dT)VN primer, followed by second-strand synthesis, tagmentation, library indexing, and amplification. Libraries incorporate unique molecular identifiers (UMIs) for PCR duplicate removal and unique dual indices (UDIs) to prevent index hopping. Sequencing was performed single-end on Illumina instruments, ~90 bp reads, biased toward the 3' end of transcripts.

treatment_protocol: Cells were treated with 1 μM Vorasidenib or DMSO vehicle. Media with drug or DMSO control was replaced every 2 days. Cells were passaged as needed and collected for RNA on Day 14.

value: glioma tumor cells

value: IDH1R132H+PIK3CAE545K+sgRNA Cic, Fubp1, Cdkn2a

value: Vorasidenib 1μM


title: 203977090074_R08C01_RI94/1335_CNG

value: Oxford Brain Bank

value: male


title: myoblast_interaction_normal_diet_batch2_rep1

description:
Library name: INT_M_C1_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: skeletal myoblast

value: normal diet culture in interaction (chip)


title: 203973690024_R08C01_PD681_CNG

value: female


title: HDL:YFP-input 1

value: input


title: hepatocyte_interaction_normal_diet_batch3_rep3

description:
Library name: INT_L_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: primary hepatocyte


title: 133B2_VORA_R2

description:
Library name: Sample 5
6G63S6_5
Processed_Data_File_GEO_Vorasidenib.txt


title: Sample 7_F1

description:
Library name: Sample 7
FF-EV_miRNAs_in_Rhino_CPM.xlsx

value: PB


title: 203991390103_R05C01_20152936_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource


title: Pho92_del_R3

description: Library name: sample 24

data_processing:
FASTQ files were processed using the nf-core/rnaseq pipeline (version 3.10.1; 10.5281/zenodo.1400710), executed using Nextflow (v23.10.0) (Di Tommaso et al., 2017). Reads were aligned to the Saccharomyces cerevisiae strain SK1 reference genome (SK1_SGD_2018_NCSL00000000) using STAR (2.7.10a)47, and gene-level quantification was performed with RSEM (v1.3.1).  Differential expression analysis was carried out with DESeq2 (1.48.1) using a simple design formula (~ group). Wald tests were used to assess differential expression. Multiple-testing correction was performed using Independent Hypothesis Weighting (IHW)50; genes with an IHW-adjusted p-value below 0.05 were considered significant. ashr 51 was used for effect-size shrinkage.
Assembly: SK1-MvO-V1
Supplementary files format and content: tsv and read counts

treatment_protocol: 3 hours after transfer to sporulation medium, copper (II) sulphate (CuSO4, 50 μM) was added. In all steps yeast were grown at 30°C at 300 rpm, and a 1:10 culture volume to flask total volume ratio was maintained.

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG pho92::HYG


title: hepatocyte_interaction_normal_diet_batch2_rep3

description:
Library name: INT_L_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: 133B2_VORA_R1

description:
Library name: Sample 4
6G63S6_4
Processed_Data_File_GEO_Vorasidenib.txt


title: hepatocyte_interaction_high_diet_semaglutide_batch3_rep1

description:
Library name: INT_L_S_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: high (western) diet culture in interaction (chip) with semaglutide 130 ng/mL


title: 203991390103_R04C01_PD612_CNG

value: Imperial Brain Bank

value: FALSE


title: hepatocyte_interaction_normal_diet_batch3_rep1

description:
Library name: INT_L_C1_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: 133B2_DMSO_R3

description:
Library name: Sample 3
6G63S6_3
Processed_Data_File_GEO_Vorasidenib.txt

value: glioma tumor cells

value: IDH1R132H+PIK3CAE545K+sgRNA Cic, Fubp1, Cdkn2a

value: DMSO vehicle control


title: Pho92_del_R2

description: Library name: sample 23


title: 203991390103_R02C01_20174954_CNG

value: male


title: 133B2_DMSO_R2

description:
Library name: Sample 2
6G63S6_2
Processed_Data_File_GEO_Vorasidenib.txt


title: hepatocyte_interaction_normal_diet_batch2_rep1

description:
Library name: INT_L_C1_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: Pho92_del_R1

description: Library name: sample 22


title: 203991390158_R08C01_PD706_CNG


title: WT_TIRligase_degron_4h_r3

description: Library name: sample 3

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p552

value: IAA


title: 203977090024_R04C01_PD1007_PFC

value: Prefrontal cortex


title: mIMCD3 cells, NFAT5-DMSO

city: Tianjin

first: xudan

last: dou

state: Tianjin

address: No.22 Qixiangtai Road

institute: Tianjin Medical University

data_processing:
The Bowtie2 algorithm was employed to align paired-end reads obtained from ChIP-seq and ATAC-seq experiments to the mouse reference genome mm10. To eliminate PCR duplicates and reads aligned to mtDNA, the "mark duplicates" command from Picard (http://broadinstitute.github.io/picard/) was utilized. Subsequently, ChIP-seq and ATAC-seq peaks were identified using HOMER's findPeaks algorithm. Bigwig files were generated based on the deepTools output5. Statistical differences in normalized read counts across peaks between sets of ChIP-seq experiments were determined using HOMER's getDifferentialPeaks.pl, which leverages the statistical modeling functions of DESeq2. ChromHMM algorithm was then applied to define chromatin states, while the AnnotatePeaks.pl algorithm was utilized to analyze the distribution of peaks around the transcription start site (TSS). Additionally, the FindMotifsGenome.pl algorithm was employed to assess motif enrichment.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
mIMCD3 cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was halted by adding 150 mM of glycine for 5 minutes at room temperature.mIMCD3 cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was halted by adding 150 mM of glycine for 5 minutes at room temperature.
Library construction was effected with a VAHTS Universal DNA Library Prep Kit for Illumina V3, and sequencing was carried out on the Illumina platform.

tag: chip antibody

value: anti-Nfat5 (Abcam, ab3446)

value: Mouse inner medullary collecting duct

value: DMSO


title: islet_interaction_high_diet_batch3_rep1

description:
Library name: INT_I_W_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: pancreatic islet

value: high (western) diet culture in interaction (chip)


title: Embryo, 30DPA, biol rep 3

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

description: Library name: Embryo_30DPA_R3

data_processing:
Raw reads quality filtering and trimming for adapter contaminants with Trimmomatic v0.39 (Bolger et al., 2014)
High quality reads were mapped to the Triticum durum cv. Svevo Rel 2.0 genome and annotation using STAR 2.7.10b (Dobin et al., 2013).
Read counts and transcripts per million TPM were calculated per gene using RSEM v1.3.3 (Li and Dewey, 2011).
Assembly: Svevo Rel2.0 genome assembly
Supplementary files format and content: tab delimited text file including rawcounts for each sample
Supplementary files format and content: tab delimited text file including TPM values for each sample

organism: Triticum turgidum subsp. durum

source_name: Embryo sampled at 30DPA

growth_protocol: Durum wheat seeds (Triticum turgidum L. ssp. durum) cv. Svevo were pre-germinated in Petri dishes with wet filter paper, at 4 °C for 5 days to obtain a synchronous germination. Germinating seeds were then transferred into pots filled with loam-based potting soil, plus 1/3 of sand and perlite (in 1:1 volume ratio) in a controlled environment starting with a 14/10 hours day/night length at 14/8 °C and progressively reaching 16/8 hours day night length at 24/20 °C

extract_protocol:
Total RNA was extracted from 100 mg fresh weight material; the Direct-Zol RNA Miniprep Kits Zymo Research) was used for leaf, root, meristem and ovary samples, while the RNeasy Plant Mini Kit (Qiagen) was used for seed samples. In both protocols genomic DNA contamination was removed using the on-column DNase treatment
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

value: Embryo

tag: Stage

tag: cultivar

value: Svevo


title: 133B2_DMSO_R1

description:
Library name: Sample 1
6G63S6_1
Processed_Data_File_GEO_Vorasidenib.txt

tag: cell type


title: CUP1-Pho92-W177A_R3

description: Library name: sample 21

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-W177A


title: 203991390158_R02C01_PDC085_CNG

tag: tissue

value: Anterior cingulate

value: Imperial Brain Bank

value: female

value: FALSE


title: EPN_and_Brain_Samples

description:
Library name: EPN_BBB_raw_scRNA
10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were carried out in Cell Ranger v9.0.0 (10X Genomics, https://www.10xgenomics.com/support/software/cell-ranger/latest)
Samples were multiplexed using GEM-X Flex chemistry. Raw sequencing files are shared across multiple samples; sample identity is resolved via probe barcode as indicated in supplemental file.
Assembly: Mus musculus mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain or tumor tissue

extract_protocol:
Cells were isolated using the GEM-X Flex Sample Preparation v2 kit (10x Genomics, #PN-1000781).
Libraries were prepared using the 10x Genomics Chromium GEM-X Flex platform. Sequencing was performed in paired-end mode. Read 1 contains cell barcode and UMI sequences, while Read 2 contains cDNA inserts representing captured transcripts.

value: brain or tumor tissue


title: CUP1-Pho92-W177A_R2

description: Library name: sample 20

source_name: diploid

tag: genotype


title: 203991390146_R08C01_PD746_CNG


title: islet_interaction_high_diet_semaglutide_batch3_rep1

description:
Library name: INT_I_S_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

tag: treatment

value: high (western) diet culture in interaction (chip) with semaglutide 130 ng/mL


title: Liver, hepatocyte-specific Foxo3 KO_Fed_rep3

city: Nagasaki

first: Toshimitsu

last: Komatsu

state: Nagasaki

address: 1-12-4 Sakamoto

department: Biomedical Research Support Center

country: Japan

institute: Nagasaki University School of Medicine

description:
Library name: m9606
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9606

data_processing:
Base calling and conversion from BCL to FASTQ format were performed using Illumina Real-Time Analysis (RTA, v4.6.7) and bcl2fastq (v2.19) with default settings.
Adapter sequences and low-quality bases (Phred score <20) were removed using Trimmomatic (v0.38). The trimming was performed with the following parameters: ILLUMINACLIP:adapter.fa:2:30:10, LEADING:20, TRAILING:20, SLIDINGWINDOW:4:15, and MINLEN:36.
Trimmed reads were aligned to the reference genome (mm10) using HISAT2 (v2.1.0).
Gene-level read counts were quantified from the aligned reads using featureCounts (v1.6.3). Only uniquely mapped reads were counted, and strand-specific assignment was performed based on the library preparation protocol.
Raw read counts were normalized and differential expression analysis was performed using DESeq2 (v1.24.0) based on the relative log expression (RLE) method.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with gene-level raw counts (rows: genes, columns: samples).
Supplementary files format and content: Tab-delimited text file with gene-level TPM values (rows: genes, columns: samples).

source_name: Liver

extract_protocol:
Total RNA was isolated from frozen liver tissues using ReliaPrep™ RNA tissue miniprep system (Promega). Quality and quantity of total RNA were evaluated using a Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Strand-specific RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), according to the manufacturer’s instructions.

value: Liver

value: Male

tag: age

value: 16–18 months

value: Hepatocyte-specific Foxo3 knockout (Foxo3^flox/flox, Alb-cre positive)

tag: diet

value: ad libitum

value: Fed


title: 203991390146_R05C01_PDC081_CNG

tag: regiondescription


title: CUP1-Pho92-W177A_R1

description: Library name: sample 19


title: islet_interaction_high_diet_semaglutide_batch2_rep1

description:
Library name: INT_I_S_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: pancreatic islet

tag: batch


title: Liver, hepatocyte-specific Foxo3 KO_Fed_rep2

description:
Library name: m9605
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9605


title: CUP1-Pho92-L38P_R3

description: Library name: sample 18

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-L38P


title: 203991390146_R03C01_C084_CNG

tag: plate

tag: centre


title: 203991400112_R01C01_PD493_CNG

tag: Sex

tag: thal


title: hepatocyte_interaction_low_diet_batch2_rep1

description:
Library name: INT_L_F_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: primary hepatocyte

value: low (fasting) diet culture in interaction (chip)


title: islet_interaction_high_diet_metformin_batch3_rep1

description:
Library name: INT_I_M_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: high (western) diet culture in interaction (chip) with metformin 1 ug/mL


title: Liver, hepatocyte-specific Foxo3 KO_Fed_rep1

description:
Library name: m9604
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9604


title: 203991410053_R06C01_19970075_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource


title: 203991390146_R02C01_20130879_CNG

value: male


title: CUP1-Pho92-L38P_R2

description: Library name: sample 17

value: diploid yeast cell


title: islet_interaction_low_diet_batch3_rep1

description:
Library name: INT_I_F_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: CUP1-Pho92-L35A_R3

description: Library name: sample 15

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-L35A


title: islet_interaction_low_diet_batch2_rep1

description:
Library name: INT_I_F_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: Liver, floxed control_Fed_rep2

description:
Library name: m9581
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9581

value: Foxo3 floxed control (Cre-negative)


title: Liver, floxed control_Fed_rep1

description:
Library name: m9580
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9580

value: Liver


title: 203991390160_R04C01_C094_CNG

value: Imperial Brain Bank

value: female

value: FALSE


title: CUP1-Pho92-L35A_R2

description: Library name: sample 14


title: islet_interaction_normal_diet_batch3_rep3

description:
Library name: INT_I_C3_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: normal diet culture in interaction (chip)


title: 203991390160_R03C01_PD055_CNG


title: 203991390146_R01C01_NP10/011_CNG

value: Oxford Brain Bank


title: islet_interaction_normal_diet_batch2_rep3

description:
Library name: INT_I_C3_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: pancreatic islet


title: Liver, hepatocyte-specific Foxo3 KO_Fasted_rep2

description:
Library name: m9413
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9413

value: Male

value: 16–18 months

value: Hepatocyte-specific Foxo3 knockout (Foxo3^flox/flox, Alb-cre positive)

value: ad libitum

value: overnight fasting


title: CUP1-Pho92-I39A_R3

description: Library name: sample 12

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-L39A


title: 203991390160_R01C01_PD086_CNG

value: Anterior cingulate


title: islet_interaction_normal_diet_batch3_rep1

description:
Library name: INT_I_C1_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: CUP1-Pho92-I39A_R2

description: Library name: sample 11

value: diploid yeast cell


title: 203991390151_R08C01_PD759_CNG


title: islet_interaction_normal_diet_batch2_rep1

description:
Library name: INT_I_C1_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: CUP1-Pho92-I39A_R1

description: Library name: sample 10


title: 203991390151_R07C01_PD576_CNG


title: gut_epith_interaction_high_diet_batch3_rep1

description:
Library name: INT_G_W_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: high (western) diet culture in interaction (chip)


title: Liver, floxed control_Fasted_rep2

description:
Library name: m9477
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9477

value: Foxo3 floxed control (Cre-negative)


title: 203991390151_R05C01_PD980_CNG

value: male


title: CUP1-Pho92-35-42_del_R3

description: Library name: sample 9

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-L35-42delta


title: gut_epith_interaction_high_diet_batch2_rep1

description:
Library name: INT_G_W_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: CUP1-Pho92-35-42_del_R2

description: Library name: sample 8


title: Liver, floxed control_Fasted_rep1

description:
Library name: m9474
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9474

value: Liver


title: 203991390151_R03C01_20160475_CNG

value: Newcastle Brain Tissue Resource

value: FALSE


title: IL-1R1 nRestore_M_sham_9h_A154

city: Lexington

middle: M

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

description:
Library name: A154
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 9h

data_processing:
Quality assessment of raw reads with FastQC
Read alignment with STAR to mouse genome
Transcript quantification with Salmon
Gene-level count aggregation with tximeta
Differential expression analysis with DESeq2
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level read counts (salmon.merged.gene_counts.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.
Supplementary files format and content: Tab-delimited text file with Salmon-quantified gene-level TPM values (salmon.merged.gene_tpm.tsv). Columns are sample IDs, rows are Ensembl gene IDs with gene names.

source_name: mouse brain

growth_protocol: 14:10 (light:dark), ad lib food access

extract_protocol:
RNeasy Mini with genomic dna depletion
RNA library preparation was performed by Novogene (Project X202SC24077443-Z01-F001). [Add library prep kit info, e.g., Illumina Stranded mRNA Prep, polyA selection, etc.]

treatment_protocol: Mice underwent closed head injury (CHI) or sham surgery. Brain tissue was collected at 9h, 24h, or 72h post-injury.

value: mouse brain

tag: strain

value: IL-1R1 nRestore

tag: surgery

value: sham

tag: timepoint

tag: age (months)

value: 3.8 months

tag: animal id

tag: experiment id


title: CUP1-Pho92-35-42_del_R1

description: Library name: sample 7

tag: cell type


title: 203991390151_R02C01_PDC023_CNG

tag: tissue

value: Imperial Brain Bank

value: female


title: IL-1R1 nRestore_M_sham_72h_A147

description:
Library name: A147
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 72h

value: Male

value: 4.7 months


title: 203973690007_R06C01_PD362_CNG

value: Anterior cingulate


title: CUP1-Pho92_R3

description: Library name: sample 6

value: diploid yeast cell

tag: genotype

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 Trp1::CUP1-HA-PHO92-WT


title: gut_epith_interaction_high_diet_metformin_batch3_rep1

description:
Library name: INT_G_M_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

tag: treatment

value: high (western) diet culture in interaction (chip) with metformin 1 ug/mL


title: IL-1R1 nRestore_M_sham_72h_A138

description:
Library name: A138
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 72h

value: 5.9 months


title: 203973690007_R05C01_P10/15_CNG

value: QSBB


title: gut_epith_interaction_high_diet_metformin_batch2_rep1

description:
Library name: INT_G_M_EX2
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.


title: IL-1R1 nRestore_M_sham_72h_A113

description:
Library name: A113
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 72h

value: 4.97 months


title: CUP1-Pho92_R1

description: Library name: sample 4


title: 203973690015_R08C01_PD334_CNG

value: male


title: gut_epith_interaction_low_diet_batch3_rep1

description:
Library name: INT_G_F_EX3
Poly(A)-enriched, non-directional mRNA-seq library prepared from total RNA isolated from human tissue compartments cultured in the MOTIVE-6 six-organ MPS or matched isolation controls under nutrient or drug-treatment conditions.

value: low (fasting) diet culture in interaction (chip)


title: 1511_WT_R3

description: Library name: sample 3

value: MATa/alpha ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: 203973690015_R07C01_20150159_CNG

value: Newcastle Brain Tissue Resource

value: FALSE