title: gut_epith_interaction_low_diet_batch2_rep1

description:
Library name: INT_G_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: gut_epith_interaction_high_diet_semaglutide_batch2_rep1

status: Public on Jul 29 2026

type: SRA

city: St. Petersburg

first: Oscar

middle: E

last: Ospina

state: FL

address: 600 5th Street South

department: Health Informatics

country: USA

institute: Johns Hopkins All Children's Hospital

description:
Library name: INT_G_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.

library_source: transcriptomic

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.

molecule: polyA RNA

organism: Homo sapiens

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.

tag: cell type

tag: treatment

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

tag: batch


title: IL-1R1 nRestore_M_sham_72h_A106

city: Lexington

first: Joshua

middle: M

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

description:
Library name: A106
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 72h

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.

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: mouse brain

tag: strain

value: IL-1R1 nRestore

tag: Sex

value: Male

tag: surgery

value: sham

tag: timepoint

tag: age (months)

value: 7.67 months

tag: animal id

tag: experiment id


title: 1511_WT_R2

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: sample 2

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

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) 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

tag: genotype

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


title: 203973690015_R04C01_PD153_CNG

type: genomic

city: Exeter

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: Anterior cingulate

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: Anterior cingulate

tag: regiondescription

tag: plate

tag: centre

value: Imperial Brain Bank

value: female

tag: thal

value: FALSE


title: gut_epith_interaction_normal_diet_batch3_rep3

description:
Library name: INT_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 interaction (chip)


title: IL-1R1 nRestore_M_sham_24h_A135

description:
Library name: A135
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 24h

value: 5.0 months


title: CUP1-Pho92_R2

description: Library name: sample 5

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


title: 1511_WT_R1

description: Library name: sample 1


title: 203973690015_R03C01_PD969_CNG

value: male


title: gut_epith_interaction_normal_diet_batch2_rep3

description:
Library name: INT_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: IL-1R1 nRestore_M_sham_24h_A127

description:
Library name: A127
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 24h

value: 4.3 months


title: CUP1_Pho92_WT_3

description:
Library name: sample 39
A9

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 per gene


title: 203991410139_R08C01_PD1012_CNG


title: islet_interaction_high_diet_batch2_rep1

description:
Library name: INT_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.

source_name: pancreatic islet

value: pancreatic islet

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


title: IL-1R1 nRestore_M_sham_72h_A110

description:
Library name: A110
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 72h

value: mouse brain

value: IL-1R1 nRestore

value: 6.1 months


title: gut_epith_interaction_normal_diet_batch3_rep1

description:
Library name: INT_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: IL-1R1 nRestore_M_sham_24h_A125

description:
Library name: A125
Bulk RNA-seq, IL-1R1 nRestore, M, sham, 24h

value: Male

value: sham


title: CUP1_Pho92_WT_2

description:
Library name: sample 38
A8

value: diploid yeast cell


title: 203991410139_R03C01_20141901_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource


title: gut_epith_interaction_normal_diet_batch2_rep1

description:
Library name: INT_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: CUP1_Pho92_WT_1

description:
Library name: sample 37
A7


title: IL-1R1 nRestore_M_CHI_9h_A159

description:
Library name: A159
Bulk RNA-seq, IL-1R1 nRestore, M, CHI, 9h

value: CHI

value: 4.0 months


title: 203991410139_R02C01_20050099_CNG

value: FALSE


title: CUP1-Pho92-L38P_R1

description: Library name: sample 16

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


title: Liver, floxed control_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: m9582
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9582

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

tag: age

value: 16–18 months

value: Foxo3 floxed control (Cre-negative)

tag: diet

value: ad libitum

value: Fed


title: neuron_interaction_high_diet_batch3_rep1

description:
Library name: INT_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.

source_name: neuron

tag: cell type

value: neuron

tag: treatment

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


title: islet_interaction_high_diet_metformin_batch2_rep1

description:
Library name: INT_I_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: pancreatic islet

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

tag: batch


title: IL-1R1 nRestore_M_CHI_72h_A150

description:
Library name: A150
Bulk RNA-seq, IL-1R1 nRestore, M, CHI, 72h

tag: tissue

value: mouse brain

tag: strain

value: IL-1R1 nRestore

value: Male

value: 6.1 months


title: 203991390160_R05C01_20140411_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource

tag: Sex

value: male


title: Pho92_delete_3

description:
Library name: sample 36
A6

value: diploid yeast cell

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


title: 203991410139_R01C01_19870841_CNG

value: female

value: FALSE


title: neuron_interaction_high_diet_batch2_rep1

description:
Library name: INT_B_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: IL-1R1 nRestore_M_CHI_72h_A139

description:
Library name: A139
Bulk RNA-seq, IL-1R1 nRestore, M, CHI, 72h

tag: surgery

value: CHI

tag: timepoint

value: 5.9 months


title: 203991410064_R06C01_20185910_CNG


title: Pho92_delete_2

description:
Library name: sample 35
A5


title: neuron_interaction_high_diet_semaglutide_batch3_rep1

description:
Library name: INT_B_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: neuron

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


title: IL-1R1 nRestore_M_CHI_72h_A112

description:
Library name: A112
Bulk RNA-seq, IL-1R1 nRestore, M, CHI, 72h

tag: age (months)

value: 4.97 months

tag: animal id


title: CUP1_Pho92_28_52_130_155_delete_1

description:
Library name: sample 34
A40

tag: genotype

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-28-52 130-155delta


title: Liver, hepatocyte-specific Foxo3 KO_Fasted_rep3

description:
Library name: m9415
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9415

value: Liver

value: 16–18 months

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

value: ad libitum

value: overnight fasting


title: 203991410064_R03C01_PD936_CNG

value: Anterior cingulate

tag: regiondescription

value: Imperial Brain Bank


title: CUP1-Pho92-L35A_R1

description: Library name: sample 13

value: diploid yeast cell

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


title: neuron_interaction_high_diet_semaglutide_batch2_rep1

description:
Library name: INT_B_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: IL-1R1 nRestore_M_CHI_72h_A111

description:
Library name: A111
Bulk RNA-seq, IL-1R1 nRestore, M, CHI, 72h

value: mouse brain

value: IL-1R1 nRestore

value: Male

value: 5.3 months

tag: experiment id


title: Liver, hepatocyte-specific Foxo3 KO_Fasted_rep1

description:
Library name: m9408
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9408


title: Pho92_delete_1

description:
Library name: sample 33
A4

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


title: 203991410110_R07C01_20050022_CNG

tag: plate

tag: centre

value: Newcastle Brain Tissue Resource

value: female

value: FALSE


title: neuron_interaction_high_diet_metformin_batch3_rep1

description:
Library name: INT_B_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: neuron

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


title: CUP1_Pho92_110_155_delete_3

description:
Library name: sample 32
A39

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-110_155delta


title: 203991410110_R06C01_20163903_CNG

tag: thal


title: IL-1R1 nRestore_M_CHI_72h_A109

description:
Library name: A109
Bulk RNA-seq, IL-1R1 nRestore, M, CHI, 72h

value: CHI

value: 4.5 months


title: neuron_interaction_high_diet_metformin_batch2_rep1

description:
Library name: INT_B_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_CHI_72h_A105

description:
Library name: A105
Bulk RNA-seq, IL-1R1 nRestore, M, CHI, 72h

value: 7.67 months


title: neuron_interaction_low_diet_batch3_rep1

description:
Library name: INT_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.

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


title: CUP1_Pho92_110_155_delete_2

description:
Library name: sample 31
A38

value: diploid yeast cell


title: Liver, floxed control_Fasted_rep3

description:
Library name: m9478
Column name in RawCount_Matrix_ann.txt and TPM_Matrix_ann.txt: m9478

value: Liver

tag: age

value: 16–18 months

value: Foxo3 floxed control (Cre-negative)

tag: diet

value: ad libitum

value: overnight fasting


title: 203991410110_R04C01_C083_CNG

value: Anterior cingulate

value: Imperial Brain Bank


title: IL-1R1 nRestore_M_CHI_24h_A126

description:
Library name: A126
Bulk RNA-seq, IL-1R1 nRestore, M, CHI, 24h

value: mouse brain

value: IL-1R1 nRestore

value: Male

value: 4.3 months


title: 203977090026_R04C01_PD090_PFC

source_name: Prefrontal cortex

value: Prefrontal cortex

value: female

value: FALSE


title: 203991410110_R01C01_PDC112_CNG

value: male


title: CUP1_Pho92_110_155_delete_1

description:
Library name: sample 30
A37

tag: cell type

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-110_155delta


title: neuron_interaction_low_diet_batch2_rep1

description:
Library name: INT_B_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: neuron

tag: treatment

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

tag: batch


title: IL-1R1 nRestore_F_sham_9h_A165

description:
Library name: A165
Bulk RNA-seq, IL-1R1 nRestore, F, sham, 9h

tag: tissue

tag: strain

value: Female

value: sham

value: 4.0 months


title: CUP1_Pho92_28_52_130_155_delete_3

description:
Library name: sample 29
A36

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-28-52delta 130-155delta


title: 203991410066_R06C01_PD021_CNG

value: Anterior cingulate

value: Imperial Brain Bank

tag: Sex


title: CUP1_Pho92_28_52_130_155_delete_2

description:
Library name: sample 28
A35


title: neuron_interaction_normal_diet_batch3_rep3

description:
Library name: INT_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 interaction (chip)


title: 203991410066_R02C01_PDC092_CNG


title: neuron_interaction_normal_diet_batch2_rep3

description:
Library name: INT_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: IL-1R1 nRestore_F_sham_9h_A161

description:
Library name: A161
Bulk RNA-seq, IL-1R1 nRestore, F, sham, 9h

value: mouse brain

value: IL-1R1 nRestore

tag: surgery

tag: timepoint

value: 3.3 months


title: IL-1R1 nRestore_F_sham_9h_A156

description:
Library name: A156
Bulk RNA-seq, IL-1R1 nRestore, F, sham, 9h

tag: age (months)

value: 3.8 months

tag: animal id


title: CUP1_Pho92_W5AW18A_28_52_110_155_delete_3

description:
Library name: sample 27
A33

tag: genotype

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-28-52delta 110_155delta


title: 203973690079_R08C01_20000117_CNG

tag: regiondescription

value: Newcastle Brain Tissue Resource

value: male

value: FALSE


title: neuron_interaction_normal_diet_batch3_rep1

description:
Library name: INT_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.

value: neuron


title: IL-1R1 nRestore_F_sham_24h_A118

description:
Library name: A118
Bulk RNA-seq, IL-1R1 nRestore, F, sham, 24h

value: Female

value: 5.3 months

tag: experiment id


title: CUP1_Pho92_W5AW18A_28_52_110_155_delete_2

description:
Library name: sample 26
A32


title: neuron_interaction_normal_diet_batch2_rep1

description:
Library name: INT_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.


title: 203973690079_R03C01_20121032_CNG

tag: plate

tag: centre


title: CUP1_Pho92_W5AW18A_28_52_110_155_delete_1

description:
Library name: sample 25
A31


title: IL-1R1 nRestore_F_sham_24h_A117

description:
Library name: A117
Bulk RNA-seq, IL-1R1 nRestore, F, sham, 24h

value: sham


title: 203973690069_R06C01_P77/17_CNG

value: QSBB

tag: thal


title: adypocyte_interaction_high_diet_batch3_rep1

description:
Library name: INT_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 interaction (chip)


title: IL-1R1 nRestore_F_CHI_9h_A168

description:
Library name: A168
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 9h

value: CHI

value: 4.0 months


title: CUP1_Pho92_W5AW18A_28-52_delete_3

description:
Library name: sample 24
A30

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-W5A/W18A-28-52delta


title: gut_epith_interaction_high_diet_semaglutide_batch3_rep1

description:
Library name: INT_G_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: 203973690069_R05C01_20030007_CNG

value: Anterior cingulate

value: female


title: adypocyte_interaction_high_diet_batch2_rep1

description:
Library name: INT_A_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: IL-1R1 nRestore_F_CHI_9h_A167

description:
Library name: A167
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 9h

value: mouse brain

value: IL-1R1 nRestore


title: WT_3

description:
Library name: sample 23
A3

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


title: 203973690069_R04C01_PDC028_CNG

value: Imperial Brain Bank

value: FALSE


title: IL-1R1 nRestore_F_CHI_9h_A166

description:
Library name: A166
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 9h

value: Female


title: adypocyte_interaction_high_diet_semaglutide_batch3_rep1

description:
Library name: INT_A_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.


title: 203973690069_R03C01_PD918_CNG

value: male


title: adypocyte_interaction_high_diet_semaglutide_batch2_rep1

description:
Library name: INT_A_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: IL-1R1 nRestore_F_CHI_9h_A158

description:
Library name: A158
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 9h

value: 3.8 months


title: CUP1_Pho92_W5AW18A_28-52_delete_1

description:
Library name: sample 21
A28


title: 203973690069_R01C01_PD550_CNG


title: CUP1_Pho92_W5AW18A_28-52_delete_2

description:
Library name: sample 22
A29


title: 203976760069_R04C01_PD086_PFC

value: Prefrontal cortex


title: AB20829

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample 15
element screen

library_source: transcriptomic single cell

data_processing:
bases2fastq version 2.2.0.1940753917 arguments --legacy-fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Tumor

extract_protocol:
Tumors were finely minced on ice and enzymatically digested in RPMI containing 1 mg/mL Collagenase IV and 0.05 mg/mL DNase I at 37°C for three cycles of 8 minutes each. Between incubations, tissues were mechanically dissociated using a gentleMACS dissociator.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were inoculated with 1M MCA205-hTREM2 cell line. On day 7 received 4-5M armored CAR TREM2 cells (24h post cyclo treatment) . On day 15 tumors were collected.

value: Tumor

value: tumor-infiltrating CAR T cell

tag: sorting gate

value: CAR


title: WA09 cells, Day25, 100 ng/ml FGF8b, DLX5 activated, rep 4

city: Helsinki

first: Shrinidhi

last: Madhusudan

state: Uusimaa

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: Library name: K16

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.

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: IL-1R1 nRestore_F_CHI_9h_A157

description:
Library name: A157
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 9h

value: CHI


title: 203968030031_R01C01_C088_CNG

value: Anterior cingulate


title: AB20830

description:
Library name: Sample 16
element screen

tag: treatment

tag: batch


title: adypocyte_interaction_high_diet_metformin_batch3_rep1

description:
Library name: INT_A_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: adipocyte

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


title: CUP1_Pho92_28_52_delete_3

description:
Library name: sample 20
A27

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-28-52delta


title: adypocyte_interaction_high_diet_metformin_batch2_rep1

description:
Library name: INT_A_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: 203968030084_R07C01_PDC128_CNG

tag: tissue

value: Imperial Brain Bank

value: female


title: IL-1R1 nRestore_F_CHI_24h_A121

description:
Library name: A121
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 24h

value: mouse brain

tag: strain

value: IL-1R1 nRestore

tag: Sex

value: Female

value: 5.3 months


title: CUP1_Pho92_28_52_delete_2

description:
Library name: sample 19
A26


title: IL-1R1 nRestore_F_CHI_24h_A120

description:
Library name: A120
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 24h

tag: surgery

tag: timepoint

value: 4.4 months


title: adypocyte_interaction_low_diet_batch3_rep1

description:
Library name: INT_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 interaction (chip)


title: CUP1_Pho92_28_52_delete_1

description:
Library name: sample 18
A25


title: adypocyte_interaction_low_diet_batch2_rep1

description:
Library name: INT_A_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: 203968030084_R06C01_PD913_CNG

value: FALSE


title: IL-1R1 nRestore_F_CHI_24h_A119

description:
Library name: A119
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 24h

tag: age (months)

tag: animal id


title: CUP1_Pho92_1_70_delete_3

description:
Library name: sample 17
A24

tag: genotype

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-1-70delta


title: 203968030084_R05C01_PD1007_CNG

tag: regiondescription

value: male


title: adypocyte_interaction_normal_diet_batch3_rep3

description:
Library name: INT_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 interaction (chip)


title: 203968030084_R04C01_PD816_CNG

value: Anterior cingulate

tag: plate


title: IL-1R1 nRestore_F_CHI_24h_A022

description:
Library name: A022
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 24h

value: CHI

value: 7.07 months

tag: experiment id


title: IL-1R1 nRestore_F_CHI_24h_A020

description:
Library name: A020
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 24h

value: 7.2 months


title: adypocyte_interaction_normal_diet_batch2_rep3

description:
Library name: INT_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.

value: adipocyte


title: CUP1_Pho92_1_70_delete_1

description:
Library name: sample 15
A22

value: diploid yeast cell


title: CUP1_Pho92_1_70_delete_2

description:
Library name: sample 16
A23


title: adypocyte_interaction_normal_diet_batch3_rep1

description:
Library name: INT_A_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: IL-1R1 nRestore_F_CHI_24h_A018

description:
Library name: A018
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 24h

value: 5.7 months


title: 203968030060_R06C01_PD269_CNG

tag: centre

value: Imperial Brain Bank

tag: thal


title: adypocyte_interaction_normal_diet_batch2_rep1

description:
Library name: INT_A_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_W5A_W18A_3

description:
Library name: sample 14
A21

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-W5A/W18A


title: IL-1R1 gKO_M_sham_9h_A196

description:
Library name: A196
Bulk RNA-seq, IL-1R1 gKO, M, sham, 9h

value: mouse brain

value: IL-1R1 gKO

value: Male

value: sham

value: 4.47 months


title: si_YWHAZ_3

city: Urumqi

first: jie

last: wang

address: 152 Longquan Street, Tianshan District, Urumqi, Xinjiang Uygur Autonomous Region, China

country: China

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

description: Library name: Sample6

data_processing:
Raw reads with more than 2-N bases were discarded, and adaptors and low-quality bases were trimmed using FASTX-Toolkit (Version 0.0.13). Additionally, reads shorter than 16nt were removed.
Clean reads were then aligned to the GRCh38 genome using HISAT2, allowing for 4 mismatches. Uniquely mapped reads were utilized for gene read number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped).
The R Bioconductor package DESeq2 was employed to identify differentially expressed genes (DEGs), with a significance threshold set at a FDR < 0.05 and a fold change > 2 or < 0.5.
Alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between samples were defined and quantified using the ABLas pipeline as described previously[18]. Ten types of ASEs, including exon skipping (ES), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), mutually exclusive exons (MXE), mutually exclusive 5'UTRs (5pMXE), mutually exclusive 3'UTRs (3pMXE), cassette exon, A3SS&ES, and A5SS&ES, were detected based on splice junction reads. To assess lncRNA-regulated ASEs, Student’s t-test was applied, and events significant at a p-value cutoff corresponding to a false discovery rate cutoff of 5% were considered lncRNA-regulated ASEs.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM value for each Sample.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

source_name: HaCaT cell

extract_protocol:
Total RNA was extracted using TRIzol Reagent and then treated with RQ1 DNase to remove DNA, followed by assessing its quality and quantity using a smartspec plus spectrophotometer (BioRad) and confirming integrity through 1.5% agarose gel electrophoresis. Each sample underwent mRNA capture using VAHTS mRNA capture Beads (Vazyme, N401), with an additional round of RQ1 DNase treatment.
Directional library preparation with the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (NR605) involved purifying, fragmenting, and converting polyadenylated mRNAs into double-stranded cDNA. This was followed by end repair, A tailing, and adaptor ligation (N323), with subsequent purification and size fractionation (300 - 500bps). Ligated products were then amplified, purified, quantified, and stored at -80℃ prior to sequencing, with strand-specific sequencing achieved by excluding amplification of the dUTP-marked strand. High-throughput sequencing was performed on an Illumina NovaSeq X Plus  system using 150nt paired-end sequencing, as per the manufacturer's instructions.

tag: cell line

value: HaCaT cell


title: 203968030060_R04C01_PD089_CNG

value: male

value: FALSE


title: CUP1_Pho92_W5A_W18A_1

description:
Library name: sample 11
A19

tag: cell type


title: 203968030060_R01C01_NP14/017_CNG

value: Anterior cingulate

value: Oxford Brain Bank


title: IL-1R1 gKO_M_sham_9h_A090

description:
Library name: A090
Bulk RNA-seq, IL-1R1 gKO, M, sham, 9h

value: 4.7 months


title: si_YWHAZ_1

description: Library name: Sample4


title: IL-1R1 gKO_M_sham_9h_A164

description:
Library name: A164
Bulk RNA-seq, IL-1R1 gKO, M, sham, 9h

value: 4.0 months


title: si_YWHAZ_2

description: Library name: Sample5


title: 203968030090_R08C01_PD714_CNG

value: female


title: WT_2

description:
Library name: sample 12
A2

value: diploid yeast cell

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


title: si_NC_3

description: Library name: Sample3


title: 203977090007_R06C01_PD294_PFC

value: Prefrontal cortex

value: Imperial Brain Bank


title: 203968030090_R07C01_PDC034_CNG


title: CUP1_Pho92_W18A_2

description:
Library name: sample 9
A17

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-W18A


title: si_NC_2

description: Library name: Sample2


title: IL-1R1 gKO_M_sham_72h_A037

description:
Library name: A037
Bulk RNA-seq, IL-1R1 gKO, M, sham, 72h

value: mouse brain

value: IL-1R1 gKO

value: 5.27 months


title: 203968030090_R06C01_PD502_CNG


title: si_NC_1

description: Library name: Sample1


title: CUP1_Pho92_W5A_3

description:
Library name: sample 7
A15

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-W5A


title: IL-1R1 gKO_M_sham_72h_A036

description:
Library name: A036
Bulk RNA-seq, IL-1R1 gKO, M, sham, 72h

value: Male

value: sham


title: 203991390061_R06C01_PD102_CNG

value: male

value: FALSE


title: A2780 cells, UB-sh2-3

city: Shanghai

first: Cuiping

last: Yang

address: No. 168 Wanghe Road, Fengxian District, Shanghai, China Welfare Association International Peace Maternity and Child Health Hospital, Fengxian Campus

department: Central Laboratory

description:
Library name: Sample9
Column name in all_samples_gene_Count.xlsx: UB-sh2-3

data_processing:
Raw data preprocessing: Raw data (FASTQ format) were first processed through in-house Perl scripts. Adapter sequences were removed, and low-quality reads (where bases with quality value ≤ 25 accounted for >60% of the read) and reads with >5% ambiguous bases ('N') were filtered out to obtain clean reads.
Alignment to reference genome: Clean reads were aligned to the reference genome using HISAT2 software (http://daehwankimlab.github.io/hisat2/) with default parameters.
Quantification of gene expression: FeatureCounts (http://subread.sourceforge.net/) was used to count the number of reads mapped to each gene. Gene expression levels were calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: GRCh38.p13 (Homo sapiens)
Supplementary files format and content: raw read counts for each gene across all samples (generated by FeatureCounts).
Supplementary files format and content: FPKM values for each gene across all samples.

growth_protocol: A2780 cells were maintained in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS) supplemented with 1% penicillin-streptomycin (P/S). Cells were kept at 37℃ in a humidified environment with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Magen) according to the manufacturer’s protocol. Chloroform and isopropanol (Sinopharm) were used for phase separation and RNA precipitation.  1.0 ug of total RNA was used for the construction of sequencing libraries.
Libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (ABclonal) following the manufacturer’s instructions. Magnetic beads (AMPure XP system, Beckman Coulter) were used for purification and size selection.

value: ovarian cancer cells

value: UBTD1 knockdown


title: CUP1_Pho92_W18A_1

description:
Library name: sample 8
A16


title: IL-1R1 gKO_M_sham_24h_A134

description:
Library name: A134
Bulk RNA-seq, IL-1R1 gKO, M, sham, 24h

value: 4.7 months


title: 203991390061_R05C01_20000064_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource


title: A2780 cells, UB-sh2-2

institute: International Peace Maternity and Child Health Hospital

description:
Library name: Sample8
Column name in all_samples_gene_Count.xlsx: UB-sh2-2


title: IL-1R1 gKO_M_sham_24h_A129

description:
Library name: A129
Bulk RNA-seq, IL-1R1 gKO, M, sham, 24h

value: 4.5 months


title: CUP1_Pho92_W5A_2

description:
Library name: sample 6
A14

value: diploid yeast cell


title: CUP1_Pho92_W5A_1

description:
Library name: sample 5
A13


title: 203977090067_R04C01_PD537_CNG

value: Imperial Brain Bank


title: A2780 cells, UB-sh2-1

description:
Library name: Sample7
Column name in all_samples_gene_Count.xlsx: UB-sh2-1


title: 203991390118_R06C01_PD077_CNG


title: IL-1R1 gKO_M_sham_24h_A027

description:
Library name: A027
Bulk RNA-seq, IL-1R1 gKO, M, sham, 24h

value: 5.3 months


title: 203991390118_R05C01_C020_CNG

value: female


title: IL-1R1 gKO_M_CHI_9h_A197

description:
Library name: A197
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 9h

value: mouse brain

value: IL-1R1 gKO

value: CHI

value: 4.47 months


title: CUP1_Pho92_W177A_2

description:
Library name: sample 3
A11

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


title: 203991400161_R04C01_20030129_CNG

value: male


title: A2780 cells, UB-sh1-2

description:
Library name: Sample5
Column name in all_samples_gene_Count.xlsx:  UB-sh1-2


title: CUP1_Pho92_W177A_3

description:
Library name: sample 4
A12


title: A2780 cells, UB-sh1-3

description:
Library name: Sample6
Column name in all_samples_gene_Count.xlsx: UB-sh1-3


title: IL-1R1 gKO_M_CHI_9h_A190

description:
Library name: A190
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 9h

value: Male

value: 4.67 months


title: CUP1_Pho92_W177A_1

description:
Library name: sample 2
A10


title: 203991400162_R08C01_PD967_CNG

value: FALSE


title: A2780 cells, UB-sh1-1

description:
Library name: Sample4
Column name in all_samples_gene_Count.xlsx:  UB-sh1-1

value: ovarian cancer cells

value: UBTD1 knockdown


title: IL-1R1 gKO_M_CHI_9h_A160

description:
Library name: A160
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 9h

value: 4.0 months


title: IL-1R1 gKO_M_CHI_9h_A155

description:
Library name: A155
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 9h

value: 3.8 months


title: A2780 cells, Vec-3

description:
Library name: Sample3
Column name in all_samples_gene_Count.xlsx: Vec-3

value: WT


title: 203991400162_R04C01_20040022_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource


title: S.cerevisae BY4741_Ty1, PostInd, Biol Rep3

city: Vancouver

first: Marjan

last: Barazandeh

state: BC

address: 6622-2405 Wesbrook Mall

department: Pharmaceutical Sciences

country: Canada

institute: University of British Columbia

description:
Library name: RP_Postind_R3
postind_rep_avg.bw

library_source: genomic

data_processing:
Adapters and low-quality bases were removed from paired-end reads with Trimmomatic (v0.39).
The reads were then mapped to the S. cerevisiae R64 reference genome using BWA-MEM (v0.7.18).
Only primary alignments with MAPQ ≥30 were retained, and unmapped, secondary, QC-fail, and supplementary reads were excluded.
PCR/optical duplicates were removed to generate de-duplicated, coordinate-sorted BAM files, which were indexed and summarized with SAMtools (v1.19.2).
dyad-centered coverage tracks were generated from de-duplicated BAMs using a 147-bp fragment shift, normalized to the genome-wide mean (excluding zero bins), Gaussian-smoothed (window = 3), and converted to bigWig.
Assembly: R64 (SacCer3)
Supplementary files format and content: bigWig

growth_protocol: overnight in SC-Ura+2% raffinose+ 0.1% dextrose, SC-Ura+2% galactose for 24 hours, SC-Ura+2% glucose for 24 hours, SC-Ura+2% galactose for 6 hours, SC-Ura+2% galactose for 12 hours,  SC-Ura+2% galactose for 24 hours, SC complete+2% glucose for 24 hours

extract_protocol:
Qiagen MinElute column
NEBNext Ultra™ II DNA Library Prep Kit

treatment_protocol: Minimal media with Raffinose, Galactose, glucose

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0

tag: treatment

value: BY4741+ Ty1 vector grown in SC complete+2% glucose for 24 hours


title: S.cerevisae BY4741_Ty1, PostInd, Biol Rep2

description:
Library name: RP_Postind_R2
postind_rep_avg.bw


title: 203991400139_R08C01_PDC005_CNG

value: Imperial Brain Bank

value: TRUE


title: A2780 cells, Vec-1

description:
Library name: Sample1
Column name in all_samples_gene_Count.xlsx: Vec-1


title: S.cerevisae BY4741_Ty1, PostInd, Biol Rep1

description:
Library name: RP_Postind_R1
postind_rep_avg.bw


title: 203991400139_R03C01_PD902_CNG

value: female


title: IL-1R1 gKO_M_CHI_9h_A101

description:
Library name: A101
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 9h

value: mouse brain

value: IL-1R1 gKO

value: CHI

value: 5.0 months


title: S.cerevisae BY4741_Ty1, Gal24h, Biol Rep3

description:
Library name: RP_24h_R3
24h_rep_avg.bw

value: BY4741+ Ty1 vector grown in SC-Ura+2% galactose for 24 hours


title: 203991400139_R01C01_PD295_CNG

value: male

value: FALSE


title: U-937-sgNS-Rep3

city: Duarte

first: Rui

last: Su

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

description:
Library name: U-937-sgNS-Rep3
sgNS.3

data_processing:
Paired-end RNA-seq reads were quality trimmed and adapter sequences were removed using cutadapt.
Cleaned reads were aligned to the human reference genome GRCh38 (hg38) using STAR.
Gene expression levels were quantified with RSEM using transcriptome-aligned reads and subsequently normalized using spike-in controls.
Assembly: GRCh38
Supplementary files format and content: txt
Supplementary files format and content: spike-in adjusted gene expressions

growth_protocol: Human U-937 cell line was grown in RPMI 1640 media supplemented with 10% FBS, 1% Penicillin-Streptomycin, 10 mM HEPES and 0.1% Plasmocin™ Prophylactic

extract_protocol:
Total RNA was extracted using TRIZOL reagent
RNA libraries for RNA-seq were prepared from 300 ng of total RNA using the KAPA mRNA HyperPrep Kit following the manufacturer’s protocols, with ERCC spike-in controls added according to Life Technologies’ guidelines.

treatment_protocol: U-937 cells were havested at approximately 8-10 days post lentivitus transduction.

value: AML

value: KMT2A-MLLT10 fusion


title: 203968030084_R02C01_20130827_CNG


title: S.cerevisae BY4741_Ty1, Gal24h, Biol Rep2

description:
Library name: RP_24h_R2
24h_rep_avg.bw


title: IL-1R1 gKO_M_CHI_72h_A137

description:
Library name: A137
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 72h

value: Male

value: 5.93 months


title: 203991400119_R07C01_P23/12_CNG

value: Anterior cingulate

value: QSBB


title: U-937-sgMETTL1.3-Rep2

description:
Library name: U-937-sgMETTL1.3-Rep2
sgM1.3.2


title: S.cerevisae BY4741_Ty1, Gal24h, Biol Rep1

description:
Library name: RP_24h_R1
24h_rep_avg.bw

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0


title: IL-1R1 gKO_M_CHI_72h_A136

description:
Library name: A136
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 72h

value: 5.87 months


title: 203991400119_R03C01_P02/14_CNG


title: IL-1R1 nRestore_F_CHI_24h_A017

description:
Library name: A017
Bulk RNA-seq, IL-1R1 nRestore, F, CHI, 24h

value: IL-1R1 nRestore

value: Female

value: 5.7 months


title: 203968030060_R05C01_20185962_CNG

value: Newcastle Brain Tissue Resource

value: female


title: CUP1_Pho92_W5A_W18A_2

description:
Library name: sample 13
A20

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-W5A/W18A


title: U-937-sgNS-Rep2

description:
Library name: U-937-sgNS-Rep2
sgNS.2


title: CUP1_Pho92_W18A_3

description:
Library name: sample 10
A18

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG trp1::hisG hyg::pho92 trp1::CUP1-HA-PHO92-W18A


title: IL-1R1 gKO_M_CHI_72h_A107

description:
Library name: A107
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 72h

value: mouse brain

value: IL-1R1 gKO

value: CHI

value: 4.6 months


title: S.cerevisae BY4741_Ty1, Gal12h, Biol Rep3

description:
Library name: RP_12h_R3
12h_rep_avg.bw

value: BY4741+ Ty1 vector grown in SC-Ura+2% galactose for 12 hours


title: U-937-sgMETTL1.3-Rep1

description:
Library name: U-937-sgMETTL1.3-Rep1
sgM1.3.1

value: AML

value: KMT2A-MLLT10 fusion


title: S.cerevisae BY4741_Ty1, Gal12h, Biol Rep2

description:
Library name: RP_12h_R2
12h_rep_avg.bw

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0


title: 203991390105_R03C01_RI95/1012_CNG

value: Anterior cingulate

value: Oxford Brain Bank

value: FALSE


title: IL-1R1 gKO_M_CHI_72h_A064

description:
Library name: A064
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 72h

value: Male

value: 6.1 months


title: IL-1R1 gKO_M_sham_72h_A108

description:
Library name: A108
Bulk RNA-seq, IL-1R1 gKO, M, sham, 72h

value: sham


title: U-937-sgNS-Rep1

description:
Library name: U-937-sgNS-Rep1
sgNS.1


title: 203991390105_R02C01_PD180_CNG

value: Imperial Brain Bank

value: female


title: IL-1R1 gKO_M_CHI_72h_A061

description:
Library name: A061
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 72h

value: 5.6 months


title: S.cerevisae BY4741_Ty1, Gal6h, Biol Rep3

description:
Library name: RP_6h_R3
6h_rep_avg.bw

value: BY4741+ Ty1 vector grown in SC-Ura+2% galactose for 6 hours


title: IL-1R1 gKO_M_CHI_24h_A131

description:
Library name: A131
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 24h

value: mouse brain

value: IL-1R1 gKO

value: 5.0 months


title: S.cerevisae BY4741_Ty1, Gal6h, Biol Rep2

description:
Library name: RP_6h_R2
6h_rep_avg.bw


title: 203991390076_R08C01_RI03/208_CNG

value: TRUE


title: 203991390076_R06C01_P83/16_CNG

value: QSBB


title: Static2

city: New Haven

first: Yibing

last: Qyang

address: 300 George St

institute: Yale University

description: Library name: Sample5

data_processing:
RNA-seq reads were aligned to the reference genome with STAR(version= 2.7.11a), gene counts were obtained using Subread/featureCounts(v2.0.3), and differential expression was analyzed in R (v4.4.1-foss-2022b) with DESeq2. GO enrichment was performed with clusterProfiler (org.Hs.eg.db, AnnotationDbi, enrichplot, DOSE), and KEGG pathways were analyzed using pathview. P-value less than 0.05 was considered significant.
Assembly: GRCh38
Supplementary files format and content: txt file including raw counts of each sample and gene IDs

source_name: Endothelial Cell

extract_protocol:
After conditioning, ECs from both flow and static grafts were lysed directly in TRIzol. Each RNA sample represented a pooled lysate from three independent batches derived from one HLHS patients. In total, iPSC-ECs from three HLHS patients were used for both flow and static graft conditions.
mRNA is purified, from a normalized input between 10-1000ng of total RNA, using mRNA capture beads prior to fragmentation (Watchmaker mRNA Library Prep Kit).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ T overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution is determined with the LabChip GX or Agilent TapeStation. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: iPSC-ECs were then seeded onto decellularized human umbilical arteries (dHUAs) and subjected to two hemodynamic conditions: (1) a shear preconditioning protocol designed to mimic IVC hemodynamics (ramping from 1 to 15 dynes/cm² over 36 h, maintaining 15 dynes/cm² for 48 h, then reducing to 5 dynes/cm² for 12 h), and (2) a static condition followed by abrupt exposure to 5 dynes/cm² for 6 h (static + abrupt flow).

value: Endothelial Cell

value: Static + abrupt flow


title: Static1

description: Library name: Sample4


title: IL-1R1 gKO_M_CHI_24h_A128

description:
Library name: A128
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 24h

value: CHI

value: 4.5 months


title: S.cerevisae BY4741_Ty1, Gal6h, Biol Rep1

description:
Library name: RP_6h_R1
6h_rep_avg.bw

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0


title: 203991390076_R05C01_PD705_CNG

value: Anterior cingulate

value: male

value: FALSE


title: Flow3

description: Library name: Sample3

value: Flow


title: IL-1R1 gKO_M_CHI_24h_A026

description:
Library name: A026
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 24h

value: Male

value: 5.3 months


title: S.cerevisae BY4741_Ty1, PreInd, Biol Rep3

description:
Library name: RP_Preind_R3
preind_rep_avg.bw

value: BY4741+ Ty1 vector grown overnight in SC-Ura+2% raffinose+ 0.1% glucose


title: 203991390076_R04C01_P82/15_CNG

value: female


title: S.cerevisae BY4741_Ty1, PreInd, Biol Rep2

description:
Library name: RP_Preind_R2
preind_rep_avg.bw


title: 203991390076_R03C01_20174918_CNG

value: Newcastle Brain Tissue Resource


title: Flow1

description: Library name: Sample1


title: S.cerevisae BY4741_Ty1, PreInd, Biol Rep1

description:
Library name: RP_Preind_R1
preind_rep_avg.bw


title: RCH-ACV TP53 WT Untreated 3

city: Utrecht

first: Frank

middle: van

last: Leeuwen

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

description:
Library name: Sample 24
WT_UT_R3

data_processing:
Raw data (raw reads) of FASTQ format were processed through fastp
alignment to reference genome (hg38) using the HISAT2 v2.0.5 algorithm program
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped of each gene.
FPKM of each gene was calculated
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: .xls file including FPKM values for each Sample
Supplementary files format and content: .xls file including count values for each sample

source_name: RCH-ACV

growth_protocol: Cells were grown in RPMI (Invitrogen, Thermo Fisher Scientific, Breda, the Netherlands), supplemented with 10% fetal bovine serum (FBS, Greiner Bio-One, Essen, Germany) and 1% penicillin/streptomycin solution (P/S) (Invitrogen) at a cell density between 0.25 and 3x106 cells per milliliter.

extract_protocol:
NucleoSpin RNA isolation kit  (Macherey-Nagel, 740955)
The NEBNext® UltraTM Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: 24-hour treatment with DMSO, 100 nM berzosertib, 4 nM orludodstat, or the combination thereof

value: RCH-ACV

value: BCP-ALL

value: TP53 WT

value: Untreated


title: S.cerevisae BY4741_empty vector, Dex24h, Biol Rep2

description:
Library name: RP_dex24_2
dex24_rep_avg.bw

value: BY4741+ empty URA3 vector grown in SC-Ura+2% glucose for 24 hours


title: 203968030087_R02C01_P20/14_CNG

value: QSBB


title: RCH-ACV TP53 WT Untreated 2

description:
Library name: Sample 23
WT_UT_R2


title: IL-1R1 gKO_F_sham_9h_A095

description:
Library name: A095
Bulk RNA-seq, IL-1R1 gKO, F, sham, 9h

value: mouse brain

value: IL-1R1 gKO

value: Female

value: sham

value: 4.7 months


title: IL-1R1 gKO_M_CHI_9h_A102

description:
Library name: A102
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 9h

value: CHI

value: 5.0 months


title: S.cerevisae BY4741_empty vector, Dex24h, Biol Rep1

description:
Library name: RP_dex24_1
dex24_rep_avg.bw

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0


title: RCH-ACV TP53 WT Untreated 1

description:
Library name: Sample 22
WT_UT_R1


title: S.cerevisae BY4741_empty vector, Gal24h, Biol Rep2

description:
Library name: RP_gal24_2
gal24_rep_avg.bw


title: 203968030003_R08C01_NP15/005_CNG

value: Anterior cingulate

value: Oxford Brain Bank

value: FALSE


title: IL-1R1 gKO_F_sham_72h_A080

description:
Library name: A080
Bulk RNA-seq, IL-1R1 gKO, F, sham, 72h

value: 6.53 months


title: RCH-ACV TP53 WT Combination treatment 3

description:
Library name: Sample 21
WT_CMB_R3

value: RCH-ACV

value: BCP-ALL

value: Combination


title: 203968030003_R07C01_20150061_CNG

value: Newcastle Brain Tissue Resource

value: male


title: RCH-ACV TP53 WT Combination treatment 2

description:
Library name: Sample 20
WT_CMB_R2

value: TP53 WT


title: S.cerevisae BY4741_empty vector, PreInd, Biol Rep2

description:
Library name: RP_preind2
preind1_rep_avg.bw

value: BY4741+ empty URA3 vector grown overnight in SC-Ura+2% raffinose+ 0.1% glucose


title: IL-1R1 gKO_F_sham_24h_A122

description:
Library name: A122
Bulk RNA-seq, IL-1R1 gKO, F, sham, 24h

value: mouse brain

value: IL-1R1 gKO

value: Female

value: 5.2 months


title: S.cerevisae BY4741_empty vector, PreInd, Biol Rep1

description:
Library name: RP_preind1
preind1_rep_avg.bw


title: RCH-ACV TP53 WT Berzosertib Single treatment 3

description:
Library name: Sample 18
WT_BER_R3

value: Berzosertib


title: IL-1R1 gKO_F_sham_9h_A181

description:
Library name: A181
Bulk RNA-seq, IL-1R1 gKO, F, sham, 9h

value: sham

value: 4.73 months


title: 203968030087_R08C01_PD727_CNG

value: Anterior cingulate

value: Imperial Brain Bank


title: Mettl1fl/fl; Mx1-Cre (M1)

description: Library name: Mettl1fl/fl; Mx1-Cre (M1)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger
Assembly: GRCm38
Supplementary files format and content: Helicobacter pylori ASM259984v1
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BM MNCs

extract_protocol:
Three female Mettl1+/+ Mx1-Cre mice (6 weeks old) and three female Mettl1fl/fl Mx1-Cre mice (6 weeks old) from the same litter were treated with poly (I:C) by intraperitoneal injection (10 mg/kg; every other day treatment for 7 treatments in total). 4 weeks after the final injection of poly (I:C) administration, BM cells were collected. For each group, cells from three mice were pooled into one sample and treated with ammonium chloride solution (07850, STEMCELL Technologies) to lyse red blood cells. Cells were then washed and resuspended in calcium- and magnesium-free 1× PBS containing 0.04% BSA (AM2616, Thermo Fisher Scientific).
A total number of exactly 20,000 cells per sample for 10 x Genomics single cell platform to generate single cell by partitioning and recovery within the 10 x Chromium chip, libraries were constructed according to the manufacturer’s instructions of Chromium GEM-X Single Cell 3' Reagent Kits v4.

value: BM MNCs

value: female

tag: age

value: 6 weeks old

value: Mettl1fl/fl; Mx1-Cre

value: poly (I:C)


title: IL-1R1 gKO_F_sham_24h_A116

description:
Library name: A116
Bulk RNA-seq, IL-1R1 gKO, F, sham, 24h

tag: tissue

value: 5.3 months


title: 203973690040_R06C01_RI95/1030_CNG

value: Oxford Brain Bank

value: male

value: FALSE


title: RCH-ACV TP53 WT Berzosertib Single treatment 2

description:
Library name: Sample 17
WT_BER_R2

value: RCH-ACV

value: BCP-ALL

value: TP53 WT


title: Mettl1+/+; Mx1-Cre (WT)

description: Library name: Mettl1+/+; Mx1-Cre (WT)

value: Mettl1+/+; Mx1-Cre

tag: strain


title: 203973690040_R03C01_20163928_CNG

value: Newcastle Brain Tissue Resource

tag: Sex


title: RCH-ACV TP53 WT Berzosertib Single treatment 1

description:
Library name: Sample 16
WT_BER_R1

value: Berzosertib


title: Cerebellum, 12-week-old, Cic-L-KO, rep8

city: Houston

first: Hamin

last: Lee

state: TX

address: 1 Baylor Plaza, Jan and Dan Duncan Neurological Research institute

institute: Baylor College of Medicine

description: Library name: CB-LKO-8

data_processing:
For each sample, the raw reads from multiple lanes were merged, and then were aligned to the Mus musculus reference transcriptome (GRCm38.p6, GENCODE M18) using STAR v2.7 with "-quantMode GeneCounts" to generate raw read counts
Assembly: GRCm38.p6, GENCODE M18
Supplementary files format and content: tsv file including raw counts of each sample

source_name: Cerebellum

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) from flash-frozen tissue
RNA libraries were prepared by Azenta Life Science using polyA selection and standard Illumina protocols

value: Cerebellum

value: Cic-L-KO

tag: time

tag: batch


title: 203973690063_R07C01_NP16/050_CNG

value: Anterior cingulate


title: RCH-ACV TP53 WT Orludodstat Single treatment 3

description:
Library name: Sample 15
WT_BAY_R3

value: Orludodstat


title: IL-1R1 gKO_F_CHI_9h_A174

description:
Library name: A174
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 9h

value: mouse brain

value: IL-1R1 gKO

value: Female

tag: surgery

value: CHI

tag: timepoint

tag: age (months)

value: 4.5 months


title: Cerebellum, 12-week-old, Cic-L-KO, rep7

description: Library name: CB-LKO-7

tag: genotype


title: IL-1R1 gKO_M_CHI_72h_A063

description:
Library name: A063
Bulk RNA-seq, IL-1R1 gKO, M, CHI, 72h

value: Male

value: 6.1 months

tag: animal id


title: 203973690063_R05C01_C087_CNG

tag: regiondescription

tag: plate

value: Imperial Brain Bank

value: female

value: FALSE


title: RCH-ACV TP53 WT Orludodstat Single treatment 2

description:
Library name: Sample 14
WT_BAY_R2

value: RCH-ACV

value: BCP-ALL

value: TP53 WT


title: IL-1R1 gKO_F_CHI_9h_A163

description:
Library name: A163
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 9h

value: 3.3 months

tag: experiment id


title: 203973690063_R03C01_PD430_CNG

tag: centre

tag: thal


title: RCH-ACV TP53 WT Orludodstat Single treatment 1

description:
Library name: Sample 13
WT_BAY_R1

tag: cell line

tag: cell type

tag: treatment


title: IL-1R1 gKO_F_CHI_9h_A162

description:
Library name: A162
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 9h

tag: tissue

tag: strain


title: Cerebellum, 12-week-old, Cic-L-KO, rep5

description: Library name: CB-LKO-5

value: Cerebellum

value: Cic-L-KO

tag: time


title: Cerebellum, 12-week-old, Cic-L-KO, rep6

description: Library name: CB-LKO-6

tag: batch


title: 203973690063_R02C01_20150975_CNG

value: Anterior cingulate

value: Newcastle Brain Tissue Resource

tag: Sex

value: male


title: IL-1R1 gKO_F_CHI_9h_A152

description:
Library name: A152
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 9h

value: mouse brain

value: IL-1R1 gKO

value: Female

tag: surgery

tag: timepoint


title: RCH-ACV TP53 KO Untreated 3

description:
Library name: Sample 12
KO_UT_R3

tag: genotype

value: TP53 KO

value: Untreated


title: NT44_A, NBMI

city: Barcelona

first: Anna

last: Ramos-Triguero

address: C/ del Rosselló, 149

country: Spain

institute: FRCB-IDIBAPS

description:
Library name: NT44_A
150x2 bp

data_processing:
Quality control and preprocessing were performed using FastQC (v0.11.8), MultiQC (v1.9) and Trimmomatic (v0.39), alignment to Homo_sapiens.GRCh38.102 reference genome using STAR (v2.7.10.a) and quality control of alignment with Qualimap (v.2.2.2).
Gene counts were estimated using featureCounts (v1.6.4) and differentially expressed genes using DESeq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cord blood

extract_protocol:
Cord blood was collected at birth for transcriptomic analysis. 10 mL of whole blood were collected in BD Vacutainer® K3E 15% Aprotinin 250KIU (SGSH;BD361017). Peripheral blood mononuclear cells (PBMCs) were isolated by Blood Collection tube BD Vacutainer®, BD CPT™ (Avantor, BDAM362781). Total RNA was extracted with RNeasy Mini Kit (Qiagen,74106).
RNA samples were analyzed in Microomics Systems S.L. (Barcelona, Spain). Sequencing was performed using Illumina-NextSeq (150x2bp).

value: cord blood

value: PBMCs


title: IL-1R1 gKO_F_sham_24h_A045

description:
Library name: A045
Bulk RNA-seq, IL-1R1 gKO, F, sham, 24h

value: sham

tag: age (months)

value: 5.3 months

tag: animal id


title: Cerebellum, 12-week-old, Cic-L-KO, rep4

description: Library name: CB-LKO-4


title: 203973690063_R01C01_P11/11_CNG

tag: regiondescription

tag: plate

value: QSBB

value: FALSE


title: RCH-ACV TP53 KO Untreated 2

description:
Library name: Sample 11
KO_UT_R2

value: RCH-ACV

value: BCP-ALL


title: IL-1R1 gKO_F_CHI_9h_A086

description:
Library name: A086
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 9h

value: CHI

value: 4.7 months

tag: experiment id


title: Cerebellum, 12-week-old, Cic-L-KO, rep3

description: Library name: CB-LKO-3

value: Cerebellum

value: Cic-L-KO


title: 203977090045_R08C01_PDC059_CNG

value: Anterior cingulate

tag: centre

value: Imperial Brain Bank

value: female

tag: thal


title: RCH-ACV TP53 KO Untreated 1

description:
Library name: Sample 10
KO_UT_R1

tag: cell line

tag: cell type

value: TP53 KO


title: IL-1R1 gKO_F_CHI_9h_A183

description:
Library name: A183
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 9h

tag: tissue

value: mouse brain

value: IL-1R1 gKO

value: Female


title: IL-1R1 gKO_F_CHI_72h_A079

description:
Library name: A079
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 72h

tag: strain

value: 6.53 months


title: Cerebellum, 12-week-old, Cic-L-KO, rep2

description: Library name: CB-LKO-2

tag: time


title: 203977090045_R07C01_19970033_CNG

value: Newcastle Brain Tissue Resource


title: RCH-ACV TP53 KO Combination treatment 3

description:
Library name: Sample 9
KO_CMB_R3

tag: treatment

value: Combination


title: IL-1R1 gKO_F_CHI_72h_A077

description:
Library name: A077
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 72h

tag: Sex

value: 5.63 months


title: 203977090045_R04C01_PD659_CNG

value: male

value: FALSE


title: Cerebellum, 12-week-old, Cic-L-KO, rep1

description: Library name: CB-LKO-1

tag: batch


title: RCH-ACV TP53 KO Combination treatment 2

description:
Library name: Sample 8
KO_CMB_R2

value: RCH-ACV

value: BCP-ALL


title: IL-1R1 gKO_F_CHI_72h_A074

description:
Library name: A074
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 72h

tag: surgery

value: CHI

tag: timepoint

value: 5.8 months


title: Cerebellum, 12-week-old, Cic-S-KO, rep7

description: Library name: CB-SKO-8

value: Cerebellum

tag: genotype

value: Cic-S-KO


title: 203977090045_R03C01_PD357_CNG

value: Anterior cingulate

value: Imperial Brain Bank


title: RCH-ACV TP53 KO Combination treatment 1

description:
Library name: Sample 7
KO_CMB_R1

value: TP53 KO


title: IL-1R1 gKO_F_CHI_72h_A071

description:
Library name: A071
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 72h

value: mouse brain

value: IL-1R1 gKO

tag: age (months)

value: 6.17 months

tag: animal id


title: Cerebellum, 12-week-old, Cic-S-KO, rep6

description: Library name: CB-SKO-7


title: 203977090045_R02C01_P69/13_CNG

tag: regiondescription

tag: plate

value: QSBB

value: female


title: RCH-ACV TP53 KO Berzosertib Single treatment 3

description:
Library name: Sample 6
KO_BER_R3

value: Berzosertib


title: IL-1R1 gKO_F_CHI_72h_A069

description:
Library name: A069
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 72h

value: Female

tag: experiment id


title: Cerebellum, 12-week-old, Cic-S-KO, rep5

description: Library name: CB-SKO-6


title: 203977090021_R03C01_PDC093_CNG

tag: centre

tag: thal

value: FALSE


title: RCH-ACV TP53 KO Berzosertib Single treatment 2

description:
Library name: Sample 5
KO_BER_R2

tag: cell line

value: RCH-ACV

tag: cell type


title: IL-1R1 gKO_F_CHI_72h_A016

description:
Library name: A016
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 72h

tag: tissue

tag: strain

value: 7.2 months


title: Cerebellum, 12-week-old, Cic-S-KO, rep4

description: Library name: CB-SKO-5

tag: time


title: 203977090021_R01C01_PD099_CNG

tag: Sex

value: male


title: RCH-ACV TP53 KO Berzosertib Single treatment 1

description:
Library name: Sample 4
KO_BER_R1

value: BCP-ALL

tag: treatment


title: IL-1R1 gKO_F_CHI_24h_A048

description:
Library name: A048
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 24h

tag: surgery

value: CHI

value: 5.3 months


title: Cerebellum, 12-week-old, Cic-S-KO, rep3

description: Library name: CB-SKO-4

value: Cerebellum

value: Cic-S-KO

tag: batch


title: 203968030057_R08C01_PD125_CNG

value: Anterior cingulate

value: Imperial Brain Bank


title: RCH-ACV TP53 KO Orludodstat Single treatment 3

description:
Library name: Sample 3
KO_BAY_R3

tag: genotype

value: TP53 KO

value: Orludodstat


title: IL-1R1 gKO_F_CHI_24h_A047

description:
Library name: A047
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 24h

value: mouse brain

value: IL-1R1 gKO

tag: timepoint

tag: age (months)


title: Cerebellum, 12-week-old, Cic-S-KO, rep2

description: Library name: CB-SKO-3


title: 203968030057_R07C01_PD204_CNG

tag: regiondescription

value: female


title: IL-1R1 gKO_F_CHI_24h_A046

description:
Library name: A046
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 24h

value: Female

tag: animal id


title: RCH-ACV TP53 KO Orludodstat Single treatment 2

description:
Library name: Sample 2
KO_BAY_R2


title: adypocyte_isolation_normal_diet_batch2_rep1

description:
Library name: ISO_A_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.

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.

value: adipocyte

value: normal diet culture in isolation


title: adypocyte_isolation_normal_diet_batch3_rep1

description:
Library name: ISO_A_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: Cerebellum, 12-week-old, Cic-S-KO, rep1

description: Library name: CB-SKO-1


title: U-937-sgMETTL1.3-Rep3

description:
Library name: U-937-sgMETTL1.3-Rep3
sgM1.3.3

value: AML

value: KMT2A-MLLT10 fusion


title: 203968030057_R05C01_P73/15_CNG

tag: plate

value: QSBB

value: FALSE


title: RCH-ACV TP53 KO Orludodstat Single treatment 1

description:
Library name: Sample 1
KO_BAY_R1

value: RCH-ACV

value: BCP-ALL


title: Cerebellum, 12-week-old, WT, rep8

description: Library name: CB-WT-8

value: Cerebellum

value: WT


title: IL-1R1 gKO_F_CHI_24h_A021

description:
Library name: A021
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 24h

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.

value: CHI

value: 7.07 months

tag: experiment id


title: 203968030057_R03C01_PD004_CNG

value: Anterior cingulate

tag: centre

value: Imperial Brain Bank

value: male

tag: thal


title: IL-1R1 gKO_F_CHI_24h_A019

description:
Library name: A019
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 24h

value: mouse brain

value: IL-1R1 gKO

value: 6.33 months


title: si3

city: Nanjing

first: Yuyu

last: Zhu

address: Xianlin

institute: Nanjing University of Chinese Medicine

description: Library name: si3

data_processing:
Basecalls performed using Illumina Casava 1.8
Index of the reference genome was built using Hisat2 v2.0.4 and pairedend clean reads were aligned to the reference genome using Hisat2 v2.0.4.
Data were filtered using the following specifications…
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: txt files including FPKM for each Sample

source_name: NCM460 cells

extract_protocol:
NCM460 cells were used for total RNA isolation with Trizol (Vazyme Biotech)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H ）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell line

value: NCM460 cells

tag: cell type

value: human normal colonic epithelial cells

value: HTRA2 knockdown

value: TNF-α


title: Cerebellum, 12-week-old, WT, rep7

description: Library name: CB-WT-7

tag: tissue


title: 203968030065_R08C01_PD306_CNG

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

value: FALSE


title: 203991390105_R05C01_20174936_CNG

value: Newcastle Brain Tissue Resource


title: si2

description: Library name: si2


title: IL-1R1 gKO_F_CHI_24h_A015

description:
Library name: A015
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 24h

source_name: mouse brain

tag: strain

value: Female

value: 7.4 months


title: Cerebellum, 12-week-old, WT, rep6

description: Library name: CB-WT-6

value: Cerebellum

value: WT

tag: time


title: 203968030065_R06C01_PD864_CNG

tag: Sex


title: IL-1R1 gKO_F_CHI_24h_A013

description:
Library name: A013
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 24h

tag: surgery

value: CHI


title: Cerebellum, 12-week-old, WT, rep5

description: Library name: CB-WT-5

tag: batch


title: si1

description: Library name: si1

tag: genotype

tag: treatment


title: 203968030065_R03C01_PDC123_CNG

value: Anterior cingulate


title: Bufotenidine3

description: Library name: Bufotenidine3

value: TNF-α+Bufotenidine


title: IL-1R1 gKO_F_CHI_24h_A011

description:
Library name: A011
Bulk RNA-seq, IL-1R1 gKO, F, CHI, 24h

tag: timepoint

tag: age (months)

value: 7.07 months


title: 203968030065_R02C01_RI04/099_CNG

tag: regiondescription

value: Oxford Brain Bank

value: male


title: Cerebellum, 12-week-old, WT, rep4

description: Library name: CB-WT-4


title: Bufotenidine2

description: Library name: Bufotenidine2


title: Cerebellum, 12-week-old, WT, rep3

description: Library name: CB-WT-3


title: IL-1R1 eRestore_M_sham_9h_A189

description:
Library name: A189
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 9h

value: mouse brain

value: IL-1R1 eRestore

value: Male

value: sham

value: 4.67 months

tag: animal id


title: 203968030034_R07C01_PDC026_CNG

tag: plate

value: Imperial Brain Bank

value: female

value: TRUE


title: Bufotenidine1

description: Library name: Bufotenidine1

value: NCM460 cells

value: human normal colonic epithelial cells


title: IL-1R1 eRestore_M_sham_9h_A188

description:
Library name: A188
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 9h

tag: experiment id


title: 203968030034_R04C01_20111135_CNG

tag: centre

value: Newcastle Brain Tissue Resource

tag: thal

value: FALSE


title: Cerebellum, 12-week-old, WT, rep2

description: Library name: CB-WT-2

value: Cerebellum

value: WT


title: IL-1R1 eRestore_M_sham_9h_A089

description:
Library name: A089
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 9h

value: 4.7 months


title: 203968030064_R07C01_P67/12_CNG

value: Anterior cingulate

value: QSBB


title: Cerebellum, 12-week-old, WT, rep1

description: Library name: CB-WT-1


title: TNFa2

description: Library name: TNFa2

tag: cell line

tag: cell type

value: TNF-α


title: TNFa3

description: Library name: TNFa3


title: IL-1R1 eRestore_M_sham_72h_A151

description:
Library name: A151
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 72h

tag: tissue

value: mouse brain

tag: strain

value: IL-1R1 eRestore

value: 5.87 months


title: Cortex, 12-week-old, Cic-L-KO, rep8

description: Library name: CTX-LKO-8

source_name: Cortex

value: Cortex

value: Cic-L-KO

tag: time


title: 203968030064_R03C01_PD973_CNG

source_name: Anterior cingulate

value: Imperial Brain Bank

tag: Sex

value: male


title: TNFa1

description: Library name: TNFa1

value: NCM460 cells


title: IL-1R1 eRestore_M_sham_72h_A062

description:
Library name: A062
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 72h

value: Male

tag: surgery

value: sham

value: 5.67 months


title: 203977090043_R06C01_RI95/1310_CNG

value: Oxford Brain Bank

value: female

value: TRUE


title: medium3

description: Library name: medium3

value: human normal colonic epithelial cells

tag: genotype

value: WT

value: medium


title: IL-1R1 eRestore_M_sham_72h_A060

description:
Library name: A060
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 72h

value: mouse brain

value: 6.13 months


title: Cortex, 12-week-old, Cic-L-KO, rep7

description: Library name: CTX-LKO-7

tag: batch


title: Cortex, 12-week-old, Cic-L-KO, rep6

description: Library name: CTX-LKO-6


title: 203977090043_R02C01_P47/11_CNG

value: Anterior cingulate

value: QSBB

value: FALSE


title: IL-1R1 eRestore_M_sham_24h_A130

description:
Library name: A130
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 24h

value: IL-1R1 eRestore

tag: timepoint

value: 4.5 months


title: medium2

description: Library name: medium2

value: NCM460 cells

tag: treatment


title: Cortex, 12-week-old, Cic-L-KO, rep5

description: Library name: CTX-LKO-5

value: Cortex

value: Cic-L-KO


title: 203977090066_R08C01_PD896_CNG

tag: regiondescription

value: Imperial Brain Bank

value: male


title: medium1

description: Library name: medium1


title: IL-1R1 eRestore_M_sham_24h_A029

description:
Library name: A029
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 24h

value: Male

value: sham

tag: age (months)

value: 4.93 months

tag: animal id


title: Cortex, 12-week-old, Cic-L-KO, rep4

description: Library name: CTX-LKO-4


title: 203977090066_R07C01_PD115_CNG

tag: plate


title: IL-1R1 eRestore_M_sham_24h_A023

description:
Library name: A023
Bulk RNA-seq, IL-1R1 eRestore, M, sham, 24h

value: 5.3 months

tag: experiment id


title: Control 4, biol rep 3

city: ANGERS CEDEX 01

first: Cléis

last: Beaulieu

address: 40 RUE DE RENNES

country: France

institute: UNIVERSITE D'ANGERS

description:
Library name: C4_C
T4C

data_processing:
An average of 33.4 million paired raw reads per sample were generated. Low quality bases and adapter sequences were trimmed using the fastp tool v.0.24.0. Filtered reads were aligned to the human reference genome GRCh38 using the STAR tool v.2.7.11b with default parameters. The average alignment of uniquely mapped reads was 30.4 million per sample, with 88% corresponding to mRNA. Gene-level counts matrix was generated using featureCounts/subread v.2.0.3
Prior to differentially expressed (DE) genes analysis, only genes annotated as protein-coding in the GTF annotation file (GENCODE v38), and with at least 10 counts in a sufficient number of samples within at least one condition, were retained for downstream analyses. DE genes were determined using DESeq2 v.1.44.0.
Assembly: GRCh38
Supplementary files format and content: .tsv file includes raw counts for each sample

source_name: Skin

growth_protocol: All cell lines (4 controls, 4 patients) were synchronized at the same passage and biological triplicates were obtained at 3 consecutive passages to ensure minimal physiological variation. Samples (n=24) were prepared in a randomized order throughout the entire procedure to minimize experimental bias.

extract_protocol:
Total RNA was extracted from all samples using the Rneasy Mini Kit (Qiagen), and residual DNA was removed using the Rnase-Free Dnase Set (Qiagen). mRNA were enriched from 250 ng of total RNA using a PolyA selection.
Library preparation was performed using the Illumina® Stranded mRNA Prep ligation kit (Illumina, 20040532), and samples were barcoded with index adapters from the Illumina® RNA UD Indexes (Illumina, 20091655) according to the manufacturer’s instructions. Libraries were normalized to 4nM, pooled, and sequenced on a NextSeq 550 Sequencing System (Illumina) in a paired-end (75 bp) mode using a High Output Flowcell v2.5 (Illumina, 20024907).

value: Skin

value: Fibroblasts

value: WT

tag: sample id

tag: sample id_2

tag: patient id_ctrl

value: Control


title: 203977090066_R05C01_PD945_CNG

tag: tissue

value: Anterior cingulate

tag: centre

tag: thal


title: Cortex, 12-week-old, Cic-L-KO, rep3

description: Library name: CTX-LKO-3

tag: time


title: Control 4, biol rep 2

description:
Library name: C4_B
T4B

tag: cell type

tag: Sex


title: IL-1R1 eRestore_M_CHI_9h_A187

description:
Library name: A187
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 9h

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.]

value: mouse brain

tag: strain

tag: surgery

value: CHI

value: 4.67 months


title: Cortex, 12-week-old, Cic-L-KO, rep2

description: Library name: CTX-LKO-2

tag: genotype

tag: batch


title: 203977090066_R04C01_20185913_CNG

tag: regiondescription

value: Newcastle Brain Tissue Resource

value: FALSE


title: Control 4, biol rep 1

description:
Library name: C4_A
T4a


title: IL-1R1 eRestore_M_CHI_9h_A177

description:
Library name: A177
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 9h

value: IL-1R1 eRestore

tag: timepoint

tag: age (months)

tag: animal id


title: Cortex, 12-week-old, Cic-L-KO, rep1

description: Library name: CTX-LKO-1

value: Cortex

value: Cic-L-KO


title: 203977090066_R03C01_PD739_CNG

tag: plate

value: Imperial Brain Bank

value: male


title: Control 3, biol rep 3

description:
Library name: C3_C
T3c

tag: sample id

tag: sample id_2


title: IL-1R1 eRestore_M_CHI_9h_A170

description:
Library name: A170
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 9h

tag: tissue

value: Male

tag: experiment id


title: Cortex, 12-week-old, Cic-S-KO, rep7

description: Library name: CTX-SKO-8

value: Cic-S-KO


title: 203991400140_R08C01_C075_CNG

tag: centre

tag: thal


title: Control 3, biol rep 2

description:
Library name: C3_B
T3B

value: Skin

tag: cell type

tag: patient id_ctrl


title: IL-1R1 eRestore_M_CHI_9h_A100

description:
Library name: A100
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 9h

tag: strain

tag: Sex

value: 5.0 months


title: Cortex, 12-week-old, Cic-S-KO, rep6

description: Library name: CTX-SKO-7

tag: genotype

tag: time


title: 203991400140_R05C01_20163918_CNG

tag: regiondescription

value: female


title: Control 3, biol rep 1

description:
Library name: C3_A
T3a

value: Fibroblasts

value: WT

value: Control

tag: batch


title: IL-1R1 eRestore_M_CHI_9h_A099

description:
Library name: A099
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 9h

value: mouse brain

tag: surgery

value: CHI

tag: timepoint

tag: age (months)

value: 5.17 months


title: 203991400140_R04C01_PD294_CNG

value: Anterior cingulate

tag: plate

value: FALSE


title: Cortex, 12-week-old, Cic-S-KO, rep5

description: Library name: CTX-SKO-6

value: Cortex


title: IL-1R1 eRestore_M_CHI_9h_A091

description:
Library name: A091
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 9h

value: IL-1R1 eRestore

value: 4.7 months

tag: animal id


title: Control 2, biol rep 3

description:
Library name: C2_C
T2C

tag: tissue

tag: sample id

tag: sample id_2


title: Cortex, 12-week-old, Cic-S-KO, rep4

description: Library name: CTX-SKO-5


title: Sample 9_F2

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

description:
Library name: Sample 9
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: NoPB


title: 203991400140_R03C01_P58/10_CNG

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.

tag: centre

value: QSBB

tag: thal


title: Control 2, biol rep 2

description:
Library name: C2_B
T2B

value: Skin

tag: cell type

tag: patient id_ctrl


title: Cortex, 12-week-old, Cic-S-KO, rep3

description: Library name: CTX-SKO-4

tag: genotype

value: Cic-S-KO


title: IL-1R1 eRestore_M_CHI_72h_A146

city: Lexington

last: Morganti

address: 789 S. Limestone St

institute: University of Kentucky

description:
Library name: A146
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 72h

tag: strain

tag: Sex

value: Male

value: 5.67 months

tag: experiment id


title: Control 2, biol rep 1

description:
Library name: C2_A
T2A

value: Fibroblasts

value: WT

value: female

value: Control

tag: batch


title: 203991400140_R01C01_PD020_CNG

value: Anterior cingulate

tag: regiondescription

value: Imperial Brain Bank

value: male


title: IL-1R1 eRestore_M_CHI_72h_A059

description:
Library name: A059
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 72h

value: mouse brain

value: IL-1R1 eRestore

tag: surgery

value: CHI

tag: timepoint

tag: age (months)

value: 6.13 months


title: Cortex, 12-week-old, Cic-S-KO, rep2

description: Library name: CTX-SKO-3

tag: tissue

value: Cortex

tag: time


title: 203991400117_R04C01_20150242_CNG

tag: plate

value: Newcastle Brain Tissue Resource

value: FALSE


title: IL-1R1 eRestore_M_CHI_72h_A058

description:
Library name: A058
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 72h

tag: animal id


title: Control 1, biol rep 3

description:
Library name: C1_C
T1c

value: Skin

tag: sample id

tag: sample id_2


title: Cortex, 12-week-old, Cic-S-KO, rep1

description: Library name: CTX-SKO-1

value: Cic-S-KO


title: 203991400117_R03C01_P14/14_CNG

tag: centre

value: QSBB

tag: thal


title: Control 1, biol rep 2

description:
Library name: C1_B
T1B

tag: cell type

value: Fibroblasts

tag: genotype

tag: patient id_ctrl


title: Cortex, 12-week-old, WT, rep8

description: Library name: CTX-WT-8

value: WT


title: Control 1, biol rep 1

description:
Library name: C1_A
T1a

tag: Sex

value: female


title: IL-1R1 eRestore_M_CHI_72h_A040

description:
Library name: A040
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 72h

tag: strain

value: Male

value: 4.93 months

tag: experiment id


title: 203991400117_R05C01_PD411_CNG

value: Anterior cingulate

tag: regiondescription

value: Imperial Brain Bank


title: IL-1R1 eRestore_M_CHI_72h_A039

description:
Library name: A039
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 72h

value: mouse brain

tag: surgery

tag: timepoint

value: 4.9 months


title: 203991400152_R08C01_NP14/133_CNG

tag: tissue

value: Oxford Brain Bank

value: male


title: Cortex, 12-week-old, WT, rep7

description: Library name: CTX-WT-7

value: Cortex

tag: time

tag: batch


title: Infantile Cerebellar-Retinal Degeneration, patient 2, biol rep 3

description:
Library name: ICRD2_C
ICCc

value: ROAc

value: ROA

value: Patient

value: Non syndromic


title: IL-1R1 eRestore_M_CHI_72h_A038

description:
Library name: A038
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 72h

value: IL-1R1 eRestore

value: CHI

tag: age (months)

tag: animal id


title: Cortex, 12-week-old, WT, rep6

description: Library name: CTX-WT-6

value: WT


title: 203991400152_R05C01_PD765_CNG

tag: plate

value: female

value: FALSE


title: Infantile Cerebellar-Retinal Degeneration, patient 2, biol rep 2

description:
Library name: ICRD2_B
ICCb

value: Skin

value: Fibroblasts

tag: sample id

value: ROAB

tag: sample id_2


title: IL-1R1 eRestore_M_CHI_24h_A030

description:
Library name: A030
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 24h

value: mouse brain

value: Male

value: 4.93 months


title: Cortex, 12-week-old, WT, rep5

description: Library name: CTX-WT-5


title: 203991400152_R04C01_PD970_CNG

value: Anterior cingulate

tag: centre

value: Imperial Brain Bank

value: male

tag: thal


title: Infantile Cerebellar-Retinal Degeneration, patient 2, biol rep 1

description:
Library name: ICRD2_A
ICCa

tag: cell type

tag: genotype

value: ROAa

tag: patient id_ctrl

value: ROA


title: IL-1R1 eRestore_M_CHI_24h_A028

description:
Library name: A028
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 24h

tag: strain

tag: Sex

tag: experiment id


title: Cortex, 12-week-old, WT, rep4

description: Library name: CTX-WT-4

value: Cortex


title: 203991400152_R02C01_20196910_CNG

tag: regiondescription

value: Newcastle Brain Tissue Resource


title: Infantile Cerebellar-Retinal Degeneration, patient 1, biol rep 3

description:
Library name: ICRD1_C
I19c

tag: tissue

value: ICCc

value: Patient

value: Syndromic

value: ICRD


title: Cortex, 12-week-old, WT, rep3

description: Library name: CTX-WT-3

value: WT

tag: time


title: 203991400160_R08C01_PDC091_CNG

value: FALSE


title: IL-1R1 eRestore_M_CHI_24h_A025

description:
Library name: A025
Bulk RNA-seq, IL-1R1 eRestore, M, CHI, 24h

value: IL-1R1 eRestore

tag: surgery

value: CHI

tag: timepoint

value: 5.3 months