title: AD_brain8_MeRIPseq

data_processing:
*library strategy: MeRIP-seq
RNA-seq data analysis: Basecalls were performed using bcl2fastq v2.19.0.316 for NextSeq 550 output.  We used FastQC to check the quality of RNA-seq raw reads.  RNA-seq clean reads were aligned to the human reference genome (hg19) from the UCSC database using HISAT2 with -k 1 --no-discordant --rna-strandness RF.  StringTie was implemented to assemble and quantify transcripts based on gencode.v19.annotation.gtf.
MeRIP-seq data analysis: Basecalls were performed using bcl2fastq v2.19.0.316 for NextSeq 550 output. We used FastQC to check the quality of RNA-seq raw reads.  RNA-seq clean reads were aligned to the human reference genome (hg19) from the UCSC database using HISAT2 with -k 1 --no-discordant --rna-strandness RF.  We used MACS3 with --nomodel --extsize 100 to call m6A peaks.The high-confidence m6A peaks were retained based on q value ≤ 10−5 and fold change ≥ 5. We used bedtools to get intersected m6A peaks detected in at least 3 samples. We used ChIPseeker to annotate the genomic region of a m6A peak as TSS, exon, 5′ UTR, 3′ UTR, intronic or intergenic. The ‘gencode.v19.annotation.gtf’ was used as the transcript database.
Assembly: hg19
Supplementary files format and content: bigwig. bigwig file incldue the coverage of reads in genome region

source_name: brain

value: brain

tag: subject status

value: individuals diagnosed with AD

value: no


title: GFP_liver_infected_Ec2

status: Public on May 20 2025

type: SRA

city: Morgantown

first: Gangqing

last: Hu

state: WV

address: 64 Medical Center Drive

country: USA

institute: West Virginia University

description: Library name: Robinson_3GEX_03_Ec2

library_source: transcriptomic single cell

data_processing:
Subsequent data QC, normalization, scaling, variable gene identification and clustering were performed using the Seurat R package v5 and custom R code. Cell data were quality controlled and filtered based on cellular complexity (number of genes per cell) and mitochondrial reads. Viable cells were selected by filtering for cells with UMI count comprised between 500 and 2500. Cells with over 200 genes, and mitochondrial percent reads less than 40 were kept for analysis. Following quality control analysis and data filtering, there were 622 control cells and 1,016 infected cells. After data normalisation and scaling, Principal-component (PC) analysis (RunPCA) was performed on the 2,000 most variable genes, identified by the function FindVariableFeatures. We used the RunHarmony function from the harmony R package for potential batch-effect correction.The Harmony embeddings were used to define the dimensionality of our dataset and the resulting number of PCs were used in the RunUMAP function for reduction into two dimensions as well as for nearest neighbor graph (SNN) creation (FindNeighbors). We used the Clustree R package to compute the optimal resolution for clustering (res=1.1),  number which was then supplied to the FindClusters function. Differential gene expression between infected and control cells was calculated with FindMarkers. Cluster specific gene signatures were obtained with the function FindAllMarkers. Cells were annotated using the Cell Typist with the Healthy_Mouse_Liver model and Majority Voting mode ON.
Assembly: GRCm38
Supplementary files format and content: *.filtered_feature_bc_matrix.h5 : Filtered feature barcode matrix stored as a Compressed Sparse Column (CSC) sparse matrix in hdf5 format. The rows consist of all the gene features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

molecule: polyA RNA

organism: Mus musculus

source_name: Liver, Male

extract_protocol:
Neonatal livers were dissociated using the same instrument with the “37C_m_LIDK_1” protocol and the Miltenyi Biotec murine liver dissociation kit. Following dissociation, tissues were pelleted at 350 x g for 5 min at 4˚C and ACK lysed for 4 min at room temperature. ACK was neutralized with 10% FBS in RPMI and pelleted at 350 x g for 5 min. Cell debris was removed by putting cells through 40 µm strainer in a 50 mL conical tube and pelleted. Cells were counted and assessed for viability using the ThermoFisher Scientific Countess 3 Automated Cell Counter (Waltham, MA, USA).
Downstream steps were performed according to the 10X Genomics manufacturer recommendations for the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (Product 1000269). The library was prepared using the 10X Genomics Chromium Controller available in the WVU FCSCCF by the WVU Genomics Core Facility.

tag: tissue

value: Liver

tag: Sex

value: Male

tag: genotype

tag: treatment

value: E. coli infected


title: Library 3 ref rep3

city: Boston

first: Wei-Chien

last: Yuan

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

library_source: genomic

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts
Paired-end reads were aligned to mm10 using bowtie or STAR.
Duplicate reads were removed using picard.
Peaks were called using MACS2
For the CRISPR screen, reads were trimmed and then mapped to a custom-built index of the library using bowtie 2. The mapped counts were first normalized within each library (total counts = 10E6 reads), averaged across experimental replicates, and then divided by the average normalized reads of the respective sequenced plasmid libraries (BC1-BC4) to calculate the final fold-enrichment for each guide in each mouse.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq, gene count was generted using featurecounts. For bulk ATAC-seq and ChIP-seq, algined reads are converted to bigwig tracks. For scATAC, peak-cell matrix is generated using ChromVAR. For the CRISPR-screening, processed data are tab separated text files for each mouse (biological replicate), showing, for each sgRNA, the fold enrichment over its abundance in the corresponding plasmid library (BC1-BC4).

molecule: genomic DNA

organism: Escherichia coli

source_name: plasmid

extract_protocol:
plamids exctrct from E coli
Plasmids were used as a template for a PCR using primers targeting the common sgRNA scaffold and containing Illumina TruSeq adapter sequences, with the following parameters: 98ºC 5’, 30 cycles of (98ºC 30’’, 58ºC 30’’, 72ºC 30’’). The number of cycles was optimized by DNA quantification to stop in the middle of the linear amplification phase. Illumina i5 and i7 adapters were added by performing an additional 10-12 PCR cycles with TruSeq adapter primers

value: plasmid


title: Library 4 ref rep1


title: Library 1 ref rep4


title: Library 3 ref rep2


title: Library 3 ref rep1


title: i3N_MAPTpaRNA_ASO1_RNAseq_rep2

city: Houston

first: Benxia

state: Texas

address: 431 Fannin

institute: University of Texas Health Science Center at Houston

library_source: transcriptomic

data_processing:
RNA-seq
RNA-seq data analysis: Basecalls were performed using bcl2fastq v2.19.0.316 for NextSeq 550 output.  We used FastQC to check the quality of RNA-seq raw reads.  RNA-seq clean reads were aligned to the human reference genome (hg19) from the UCSC database using HISAT2 with -k 1 --no-discordant --rna-strandness RF.  StringTie was implemented to assemble and quantify transcripts based on gencode.v19.annotation.gtf.
MeRIP-seq data analysis: Basecalls were performed using bcl2fastq v2.19.0.316 for NextSeq 550 output. We used FastQC to check the quality of RNA-seq raw reads.  RNA-seq clean reads were aligned to the human reference genome (hg19) from the UCSC database using HISAT2 with -k 1 --no-discordant --rna-strandness RF.  We used MACS3 with --nomodel --extsize 100 to call m6A peaks.The high-confidence m6A peaks were retained based on q value ≤ 10−5 and fold change ≥ 5. We used bedtools to get intersected m6A peaks detected in at least 3 samples. We used ChIPseeker to annotate the genomic region of a m6A peak as TSS, exon, 5′ UTR, 3′ UTR, intronic or intergenic. The ‘gencode.v19.annotation.gtf’ was used as the transcript database.
Assembly: hg19
Supplementary files format and content: bigwig. bigwig file incldue the coverage of reads in genome region

molecule: total RNA

organism: Homo sapiens

growth_protocol: WTC11-Ngn2 iPSCs were utilized to generate i3Neuron following a previously established protocol.  For pre-differentiation, WTC11-Ngn2 iPSCs were cultured with 2 μg ml−1 doxycycline in knockout DMEM/F12 medium supplemented with 1× N2, 1× NEAA, 1 μg ml−1 mouse laminin, 10 ng ml−1 brain-derived neurotrophic factor (BDNF) and 10 ng ml−1 NT3 for three days. ROCK inhibitor(10 μM) was included in the predifferentiation media for the first day, and the medium was replaced daily. During the maturation phase, predifferentiated neural cells were dissociated into single cells using accutase and plated on Poly-L-Ornithine-coated plates in maturation medium containing equal parts DMEM/F12 and Neurobasal-A with 2 μg ml−1 doxycycline, 0.5× B-27, 0.5× N-2, 1× NEAA, 0.5× GlutaMax, 1 μg ml−1 mouse laminin, 10 ng ml−1 BDNF and 10 ng ml−1 NT3. Doxycycline was only added to the maturation medium on the first day and omitted thereafter. Half of the medium was replaced weekly for the first 2 weeks, and the medium volume was doubled on week 3. Subsequently, one third of the medium was replaced weekly until 8 weeks for further treatment.

extract_protocol:
Total cellular RNAs were extracted by TRIzol (Thermo Fisher) or Zymo RNA miniprep kit (Zymo Research).  RNA-seq and MeRIP-seq were performed according to our previous report with some modifications (Xiong et al. 2021. PMID: 34108665). Total RNA (5 μg) was fragmented at 70 °C for 6 min in the fragmentation buffer (10 mM ZnCl2, 10 mM TrisHCl pH7.4), following precipitation the RNA were resuspended with ice-cold IP buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.1% NP-40, 20 U/mL Superase-In, 1× Protease Inhibitor) to a ﬁnal volume of 1050 μL. Of this, 50 μL of diluted RNA was utilized for RNA-seq (5% input for m6A IP) and the remaining 1000 μL was reserved for MeRIP-seq (Methylated RNA immunoprecipitation sequencing). To prepare anti-m6A antibody conjugated beads, 20 μL of Dynabeads Protein G beads (Thermo Fisher) was washed 3 times with 1ml IP buffer and then incubated with 1 μg of m6A antibody (Synaptic Systems, Cat 202-003) at room temperature for 30min. The conjugated anti-m6A-Dynabeads were washed in 1ml IP buffer 3 times. Subsequently, the RNA sample was mixed with the beads and rotated at 4 °C for 3 hours. The beads were then washed in the IP buffer 5 times. The immunoprecipitated RNAs were extracted from the beads by TRIzol-LS (Thermo Fisher). The extracted RNA was subjected to the next generation sequencing library preparation for RNA-seq and MeRIP-seq, as well as qPCR, to quantify the m6A levels.
RNA samples were collected by one of two methods: lysis in TRIzol reagent (Thermo Fisher) for RNA-seq and MeRIP-seq, followed by standard phenol-chloroform extraction methods; alternatively, lysis was performed using Zymo Research Quick-RNA MiniPrep kit (Genesee Scientific) for regular qPCR following the manufacturer protocol. Libraries for RNA-Seq and MeRIP-Seq were made with NEBNext Ultra Directional Library Prep Kit for Illumina (NEB, E7760) following the manufacturer’s instructions. Ribosome RNA was depleted with NEBNext rRNA Depletion Kit (NEB, E6301S). The generated libraries were quantified using the Qubit-3 system and/or qPCR. In some cases (such as Chip-seq), the libraries were examined by TBE PAGE gel and Bioanalyzer 2100. Sequencing of the libraries was performed using a NextSeq 550 platform (Illumina) with paired-end sequencing.

treatment_protocol: Knockdown experiments were performed using antisense oligonucleotides (ASOs) with modifications by Affinity Plus nucleic acids. ASOs were specifically designed and synthesized by IDT for the knockdown of MAPT-paRNA.  An unrelated scrambled ASO (Scr ASO) was used as a control.  ASOs was dissolved in TE buffer (10 mM Tris-HCl, pH 7.4, 1 mM EDTA) and directly added to the i3Neuron culture without any transfection reagent (termed gymnosis) at a final concentration of 10µM. After 3 days of ASOs treatment, cells were harvested for downstream analysis.

tag: cell line

tag: cell type

value: iPSC-derived Neurons


title: LN1A cells, rep 2

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description:
Library name: LN1A_2_1
LN1A_2_1_57956826

data_processing:
Libraries were run on the NextSeq2000 machine generating paired-end 50bp reads.
Raw reads were aligned to GRCm38.p6 mouse genome annotated with the GENCODE vM transcriptome via STAR (v2.7.6.a). Transcripts were counted with Salmon (v1.4.0).
Assembly: GRCm38.p6
Supplementary files format and content: tab delimited file contains raw counts for all samples

extract_protocol:
RNA was isolated from JH716-18, JH716-18-LN1A, and JH716-18-LN2A cell lines using the Quick-RNA MicroPrep kit (Zymo Research, R1051). Purified RNA was quantified using QuBit RNA BR Assay (Thermo Fisher, Q10210).
Libraries were made using Illumina TruSeq Stranded mRNA kit

tag: genetic background


title: Library 2 ref rep3


title: AD_brain6_MeRIPseq


title: Library 1 ref rep1


title: Citeseq, tumor day 2, HTO, L004

city: Toronto

first: Melanie

last: Girard

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

description:
Library name: TD2_HTO_L004
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Sequencing files were demultiplexed using Cellranger mkfastq
Demultiplexed mRNA data was processed using the Cellranger count pipeline and Cellranger aggr pipeline
ADT and HTO data was processed using CITE-seq-count (https://hoohm.github.io/CITE-seq-Count/Running-the-script/)
Assembly: mm10
Supplementary files format and content: CellRanger output files: LND1_mRNA_filtered_feature_bc_matrix_barcodes.tsv.gz, LND1_mRNA_filtered_feature_bc_matrix_features.tsv.gz, LND1_mRNA_filtered_feature_bc_matrix_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: TD2_mRNA_filtered_feature_bc_matrix_barcodes.tsv.gz, TD2_mRNA_filtered_feature_bc_matrix_features.tsv.gz, TD2_mRNA_filtered_feature_bc_matrix_matrix.mtx.gz
Supplementary files format and content: CITE-seq count output files: LND1_ADT_L001_umi_counts_barcodes.tsv.gz, LND1_ADT_L001_umi_counts_features.tsv.gz, LND1_ADT_L001_umi_counts_matrix.mtx.gz, LND1_ADT_L002_umi_counts_barcodes.tsv.gz, LND1_ADT_L002_umi_counts_features.tsv.gz, LND1_ADT_L002_umi_counts_matrix.mtx.gz, LND1_ADT_L003_umi_counts_barcodes.tsv.gz, LND1_ADT_L003_umi_counts_features.tsv.gz, LND1_ADT_L003_umi_counts_matrix.mtx.gz, LND1_ADT_L004_umi_counts_barcodes.tsv.gz, LND1_ADT_L004_umi_counts_features.tsv.gz, LND1_ADT_L004_umi_counts_matrix.mtx.gz
Supplementary files format and content: CITE-seq count output files: LND1_HTO_L001_umi_counts_barcodes.tsv.gz, LND1_HTO_L001_umi_counts_features.tsv.gz, LND1_HTO_L001_umi_counts_matrix.mtx.gz, LND1_HTO_L002_umi_counts_barcodes.tsv.gz, LND1_HTO_L002_umi_counts_features.tsv.gz, LND1_HTO_L002_umi_counts_matrix.mtx.gz, LND1_HTO_L003_umi_counts_barcodes.tsv.gz, LND1_HTO_L003_umi_counts_features.tsv.gz, LND1_HTO_L003_umi_counts_matrix.mtx.gz, LND1_HTO_L004_umi_counts_barcodes.tsv.gz, LND1_HTO_L004_umi_counts_features.tsv.gz, LND1_HTO_L004_umi_counts_matrix.mtx.gz
Supplementary files format and content: CITE-seq count output files: TD2_ADT_L001_umi_counts_barcodes.tsv.gz, TD2_ADT_L001_umi_counts_features.tsv.gz, TD2_ADT_L001_umi_counts_matrix.mtx.gz, TD2_ADT_L002_umi_counts_barcodes.tsv.gz, TD2_ADT_L002_umi_counts_features.tsv.gz, TD2_ADT_L002_umi_counts_matrix.mtx.gz, TD2_ADT_L003_umi_counts_barcodes.tsv.gz, TD2_ADT_L003_umi_counts_features.tsv.gz, TD2_ADT_L003_umi_counts_matrix.mtx.gz, TD2_ADT_L004_umi_counts_barcodes.tsv.gz, TD2_ADT_L004_umi_counts_features.tsv.gz, TD2_ADT_L004_umi_counts_matrix.mtx.gz
Supplementary files format and content: CITE-seq count output files: TD2_HTO_L001_umi_counts_barcodes.tsv.gz, TD2_HTO_L001_umi_counts_features.tsv.gz, TD2_HTO_L001_umi_counts_matrix.mtx.gz, TD2_HTO_L002_umi_counts_barcodes.tsv.gz, TD2_HTO_L002_umi_counts_features.tsv.gz, TD2_HTO_L002_umi_counts_matrix.mtx.gz, TD2_HTO_L003_umi_counts_barcodes.tsv.gz, TD2_HTO_L003_umi_counts_features.tsv.gz, TD2_HTO_L003_umi_counts_matrix.mtx.gz, TD2_HTO_L004_umi_counts_barcodes.tsv.gz, TD2_HTO_L004_umi_counts_features.tsv.gz, TD2_HTO_L004_umi_counts_matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: tumor

extract_protocol:
CD45+ cells sorted from tumors and tumor draining lymph nodes of IFNAR mixed bone marrow chimeric mice after intratumoral injection of ADU-S100 or vehicle control. Single cells were encapsulated in Gel-Beads in emulsion (GEMs) using the 10X Controller with a Chromium Singel Cell 3' GEM Library and Gel Bead Kit.
The CITE-seq and hashing protocol described by the New York Genome Center Technology Innovation Lab was used to generate an antibody-derived tag (ADT) sequencing library, a hashtag oligo (HTO) library, and a 3" gene expression library.

value: tumor

value: CD45+ cells

value: mixed bone marrow chimera (Ifnar +/+ CD45.1 and Ifnar-/- CD45.2)

value: mixed sample (ADU-S100 and vehicle)

tag: timepoint

value: day 2 post-treatment

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0301 anti-mouse Hashtag 1 (Vehicle), TotalSeq-A0302 anti-mouse Hashtag 2 (ADU-S100)


title: Citeseq, tumor day 2, HTO, L002

description:
Library name: TD2_HTO_L002
Hashtag-derived oligonucleotide (HTO)


title: Library 1 ref rep6


title: Library 2 ref rep1


title: Library 1 ref rep5


title: i3N_ASO_Control_RNAseq_rep2

value: ASO Control


title: Citeseq, tumor day 2, HTO, L001

description:
Library name: TD2_HTO_L001
Hashtag-derived oligonucleotide (HTO)


title: i3N_MAPTpaRNA_ASO1_RNAseq_rep1


title: AD_brain7_MeRIPseq


title: Library 1 ref rep3


title: JH716-18 cells, rep 3

description:
Library name: JH716-18_3_1
JH716-18_3_1_57956826


title: AD_brain4_RNAseq


title: AD_brain8_RNAseq


title: AD_brain2_MeRIPseq


title: Library 1 ref rep2


title: Normal_brain16_MeRIPseq

value: cognitively normal age-matched counterparts individual


title: Normal_brain16_RNAseq

value: brain


title: AD_brain6_RNAseq

value: individuals diagnosed with AD


title: AD_brain5_MeRIPseq

value: no


title: AD_brain5_RNAseq


title: AD_brain4_MeRIPseq


title: Citeseq, lymph node day 1, HTO, L004

description:
Library name: LND1_HTO_L004
Hashtag-derived oligonucleotide (HTO)

source_name: lymph node

value: lymph node

value: CD3- CD19- CD11b+ and/or MHCII+ cells

value: day 1 post-treatment


title: Citeseq, lymph node day 1, HTO, L003

description:
Library name: LND1_HTO_L003
Hashtag-derived oligonucleotide (HTO)


title: Normal_brain14_RNAseq


title: Normal_brain12_MeRIPseq


title: Citeseq, tumor day 2, ADT, L003

description:
Library name: TD2_ADT_L003
Antibody-derived oligonucleotide (ADT)

value: ADT

tag: adt

value: TotalSeq-A0880 anti-mouse GITR Ligand , TotalSeq-A0883 anti-mouse CD26 (DPP-4) , TotalSeq-A1042 anti-mouse CD88 (C5aR) , TotalSeq-A0202 anti-mouse CD64 (FcγRI) , TotalSeq-A0115 anti-mouse FcεRIα , TotalSeq-A0426 anti-mouse CD192 (CCR2) , TotalSeq-A0568 anti-mouse/rat XCR1 , TotalSeq-A0013 anti-mouse Ly-6C , TotalSeq-A0849 anti-mouse CD80 , TotalSeq-A0200 anti-mouse CD86 , TotalSeq-A0551 anti-mouse CD301a (MGL1) , TotalSeq-A0825 anti-mouse CD371 (CLEC12A) , TotalSeq-A0563 anti-mouse CX3CR1 , TotalSeq-A0422 anti-mouse CD172a (SIRPα) , TotalSeq-A0596 anti-mouse ESAM , TotalSeq-A0212 anti-mouse CD24 , TotalSeq-A0566 anti-mouse CD301b (MGL2) , TotalSeq-A0106 anti-mouse CD11c , Custom TotalSeq-A anti-mouse 4-1BBL , TotalSeq-A0014 anti-mouse/human CD11b


title: AD_brain7_RNAseq


title: Normal_brain10_MeRIPseq


title: Citeseq, tumor day 2, ADT, L004

description:
Library name: TD2_ADT_L004
Antibody-derived oligonucleotide (ADT)

value: tumor


title: AD_brain2_RNAseq


title: Citeseq, tumor day 2, HTO, L003

description:
Library name: TD2_HTO_L003
Hashtag-derived oligonucleotide (HTO)

value: CD45+ cells


title: Citeseq, tumor day 2, RNA

description:
Library name: TD2_RNA
polyA RNA

value: mixed bone marrow chimera (Ifnar +/+ CD45.1 and Ifnar-/- CD45.2)

value: mRNA


title: Citeseq, tumor day 2, ADT, L001

description:
Library name: TD2_ADT_L001
Antibody-derived oligonucleotide (ADT)

value: mixed sample (ADU-S100 and vehicle)

value: day 2 post-treatment


title: Normal_brain9_MeRIPseq


title: Citeseq, tumor day 2, ADT, L002

description:
Library name: TD2_ADT_L002
Antibody-derived oligonucleotide (ADT)


title: Normal_brain10_RNAseq


title: Normal_brain13_MeRIPseq


title: Citeseq, lymph node day 1, ADT, L001

description:
Library name: LND1_ADT_L001
Antibody-derived oligonucleotide (ADT)

value: TotalSeq-A0880 anti-mouse GITR Ligand , TotalSeq-A0883 anti-mouse CD26 (DPP-4) , TotalSeq-A1042 anti-mouse CD88 (C5aR) , TotalSeq-A0202 anti-mouse CD64 (FcγRI) , TotalSeq-A0115 anti-mouse FcεRIα , TotalSeq-A0426 anti-mouse CD192 (CCR2) , TotalSeq-A0568 anti-mouse/rat XCR1 , TotalSeq-A0013 anti-mouse Ly-6C , TotalSeq-A0849 anti-mouse CD80 , TotalSeq-A0200 anti-mouse CD86 , TotalSeq-A0551 anti-mouse CD301a (MGL1) , TotalSeq-A0825 anti-mouse CD371 (CLEC12A) , TotalSeq-A0563 anti-mouse CX3CR1 , TotalSeq-A0422 anti-mouse CD172a (SIRPα) , TotalSeq-A0596 anti-mouse ESAM , TotalSeq-A0212 anti-mouse CD24 , TotalSeq-A0566 anti-mouse CD301b (MGL2) , TotalSeq-A0106 anti-mouse CD11c , Custom TotalSeq-A anti-mouse 4-1BBL


title: Normal_brain14_MeRIPseq


title: C57BL/6J/mice, TG, HIIT, F, 5

city: Philadelphia

first: Sharlene

middle: M

last: Day

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania

description: Library name: Sample_63

data_processing:
Adapter sequences were trimmed using CutAdapt (v2.3)
Quality control was completed with FastQC (v0.11.8) and FastQ Screen. MultiQC (v1.7) was used to compile these results.
Reads were mapped to the GRCm38/mm10 reference genome (ENSEMBL) with STAR (v2.7.8a) and assigned counts using RSEM (v1.3.3.). Alignment options followed ENCODE standards.
Data were pre-filtered to remove genes with 0 counts in all samples.
Assembly: mm10
Supplementary files format and content: tab-delimieted text file with raw counts for each sample

source_name: heart

growth_protocol: Breeder mice were provided LabDiet 5008 mouse feed, and weaned mice were fed LabDiet 5L0D. Mice were group housed in plastic cages with metal tops, which included corn-cob bedding. Mice were provided free access to water administered in bottles. Mice were housed in ventilated cages that were changed every week. Housing room temperature was maintained within range of 21-23°C.

extract_protocol:
Total RNA was extracted from 7-9 samples per group for 64 samples total using the RNeasy Fibrous Tissue Mini Kit (Qiagen 74704) according to the manufacturer’s protocol. Complementary DNA (cDNA) was synthesized via reverse transcription using Omniscript RT Kit (Qiagen 205111) according to the manufacturer’s protocol.
Libraries were prepared using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) v2 and the xGen Broad-range RNA Library Prep according to the manufacturer’s protocol.

treatment_protocol: High intensity interval training (HIIT) mice: Mice subjected to HIIT were run on an Animal Treadmill Exer 3/6. Prior to the start of the training period, mice were placed on treadmills with the motor running, but with a stationary belt, for acclimation. Mice were also provided 3 days of running (Week 0) at 50% of the first week workload for additional acclimation. The total training period was 6 weeks. 3 days per week, mice participated in a single training session that lasted 31 minutes and included a warm-up, as well as low intensity (4) and high intensity (4) intervals. Intensity was determined as a percentage of the overall group average speed the mice achieved during graded exercise test (High Intensity: 85%; Low Intensity: 50%).  Speeds were progressively increased each week (1 m/min/wk for low intensity intervals, 2 m/min/wk for high intensity intervals) to account for physiologic adaptations from exercise training. Sedentary mice: Sedentary mice did not exercise.

value: heart

value: TG

value: HIIT

tag: biological replicate


title: Citeseq, lymph node day 1, HTO, L002

description:
Library name: LND1_HTO_L002
Hashtag-derived oligonucleotide (HTO)

value: HTO

value: TotalSeq-A0301 anti-mouse Hashtag 1 (Vehicle), TotalSeq-A0302 anti-mouse Hashtag 2 (ADU-S100)


title: Normal_brain13_RNAseq

value: brain

value: cognitively normal age-matched counterparts individual

value: no


title: Citeseq, lymph node day 1, HTO, L001

description:
Library name: LND1_HTO_L001
Hashtag-derived oligonucleotide (HTO)

value: lymph node

value: CD3- CD19- CD11b+ and/or MHCII+ cells

value: day 1 post-treatment


title: Citeseq, lymph node day 1, ADT, L004

description:
Library name: LND1_ADT_L004
Antibody-derived oligonucleotide (ADT)

value: ADT


title: Citeseq, lymph node day 1, ADT, L003

description:
Library name: LND1_ADT_L003
Antibody-derived oligonucleotide (ADT)

value: mixed bone marrow chimera (Ifnar +/+ CD45.1 and Ifnar-/- CD45.2)


title: C57BL/6J/mice, TG, Sed, F, 8

description: Library name: Sample_61

value: sedentary


title: Citeseq, lymph node day 1, RNA

description:
Library name: LND1_RNA
polyA RNA

value: mixed sample (ADU-S100 and vehicle)

value: mRNA


title: Normal_brain9_RNAseq


title: C57BL/6J/mice, TG, HIIT, F, 6

description: Library name: Sample_64


title: JHUBK7

city: Baltimore

first: Annie

last: Kathuria

state: Maryland

address: 400 N Broadway, Office 6029

department: Biomedical Engineering

institute: Johns Hopkins University

description:
Library name: Sample 14
Minimum of 20 million reads per sample
deseq2_star_salmon_length_scaled_counts.tsv

data_processing:
Base calling and demultiplexing were performed using Illumina’s DRAGEN Bio-IT platform. Raw sequencing reads were processed for quality control using FastQC and trimmed to remove adapters and low-quality bases using Trim Galore.
Assembly: Cleaned reads were aligned to the reference genome GRCh38.p14 using STAR.
Supplementary files format and content: data.zip
Supplementary files format and content: deseq2_star_salmon_length_scaled_counts.tsv

molecule: nuclear RNA

source_name: Human

extract_protocol:
Libraries were prepared using the NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs, Ipswich, MA), following the manufacturer's protocol. mRNA was enriched using poly(A) selection.
Library quality and size distribution were assessed using a Tapestation (Agilent) and quantified by Qubit (Thermo Fisher Scientific). Final libraries were pooled equimolarly and sequenced on an Illumina NovaSeq X Plus platform using a 25B lane configuration with paired-end 150 bp (PE150) reads with a minimum of 20M Reads per sample.

value: Human

value: NIBSC8 & WT4

value: Induced Pluripotent Stem Cell


title: JHUBK2

description:
Library name: Sample 10
Minimum of 20 million reads per sample
deseq2_star_salmon_length_scaled_counts.tsv


title: C57BL/6J/mice, TG, HIIT, F, 4

description: Library name: Sample_59

value: heart

value: TG

value: HIIT


title: C57BL/6J/mice, nTG, Sed, F, 8

description: Library name: Sample_60

value: nTG


title: JHUBK5

description:
Library name: Sample 13
Minimum of 20 million reads per sample
deseq2_star_salmon_length_scaled_counts.tsv


title: Normal_brain12_RNAseq

value: brain

value: cognitively normal age-matched counterparts individual


title: C57BL/6J/mice, nTG, HIIT, F, 9

description: Library name: Sample_58


title: C57BL/6J/mice, TG, Sed, F, 7

description: Library name: Sample_57


title: C57BL/6J/mice, nTG, HIIT, F, 10

description: Library name: Sample_62


title: JHUBK4

description:
Library name: Sample 12
Minimum of 20 million reads per sample
deseq2_star_salmon_length_scaled_counts.tsv


title: Citeseq, lymph node day 1, ADT, L002

description:
Library name: LND1_ADT_L002
Antibody-derived oligonucleotide (ADT)

value: lymph node

value: TotalSeq-A0880 anti-mouse GITR Ligand , TotalSeq-A0883 anti-mouse CD26 (DPP-4) , TotalSeq-A1042 anti-mouse CD88 (C5aR) , TotalSeq-A0202 anti-mouse CD64 (FcγRI) , TotalSeq-A0115 anti-mouse FcεRIα , TotalSeq-A0426 anti-mouse CD192 (CCR2) , TotalSeq-A0568 anti-mouse/rat XCR1 , TotalSeq-A0013 anti-mouse Ly-6C , TotalSeq-A0849 anti-mouse CD80 , TotalSeq-A0200 anti-mouse CD86 , TotalSeq-A0551 anti-mouse CD301a (MGL1) , TotalSeq-A0825 anti-mouse CD371 (CLEC12A) , TotalSeq-A0563 anti-mouse CX3CR1 , TotalSeq-A0422 anti-mouse CD172a (SIRPα) , TotalSeq-A0596 anti-mouse ESAM , TotalSeq-A0212 anti-mouse CD24 , TotalSeq-A0566 anti-mouse CD301b (MGL2) , TotalSeq-A0106 anti-mouse CD11c , Custom TotalSeq-A anti-mouse 4-1BBL


title: C57BL/6J/mice, nTG, Sed, F, 7

description: Library name: Sample_56


title: JHUBK3

description:
Library name: Sample 11
Minimum of 20 million reads per sample
deseq2_star_salmon_length_scaled_counts.tsv


title: WT4 Cerebral

description:
Library name: Sample 8
Minimum of 20 million reads per sample
data.zip
wt4-cerebral


title: NIBSC8 Mid/hindbrain

description:
Library name: Sample 7
Minimum of 20 million reads per sample
data.zip
nibsc8-auto


title: NIBSC8 Endothelial + Cerebral

description:
Library name: Sample 6
Minimum of 20 million reads per sample
data.zip
nibsc8-endo-cerebral


title: C57BL/6J/mice, nTG, HIIT, F, 8

description: Library name: Sample_55


title: NIBCS8 MRBO

description:
Library name: Sample 3
Minimum of 20 million reads per sample
data.zip
nibsc8-EAC


title: C57BL/6J/mice, nTG, Sed, F, 6

description: Library name: Sample_52


title: C57BL/6J/mice, TG, Sed, F, 6

description: Library name: Sample_53


title: NIBSC8 Endothelial + Mid/hindbrain

description:
Library name: Sample 5
Minimum of 20 million reads per sample
data.zip
nibsc8-endo-auto


title: C57BL/6J/mice, TG, HIIT, F, 3

description: Library name: Sample_51


title: NIBSC8 Cerebral + Mid/hindbrain

description:
Library name: Sample 2
Minimum of 20 million reads per sample
data.zip
nibsc8-cerebral-auto


title: C57BL/6J/mice, nTG, HIIT, F, 7

description: Library name: Sample_54


title: C57BL/6J/mice, TG, Sed, F, 5

description: Library name: Sample_49


title: C57BL/6J/mice, nTG, HIIT, F, 6

description: Library name: Sample_50


title: WT4 Endothelial

description:
Library name: Sample 9
Minimum of 20 million reads per sample
data.zip
wt4-endo


title: Genomic DNA from 208125290002_R06C01

type: genomic

city: Research Triangle Park

first: Zongli

last: xu

address: 111 TW Alexander Dr

department: Epidemiology Branch

institute: NIEHS

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hibridydzed to Illumina Mouse Methylation BeadChip using a standard Illumina protocol

scan_protocol: Illumina iScan

data_processing: ENmix package in R environment (1.44.0)

label: Cy3 and Cy5

source_name: Liver

label_protocol: Standard Illumina Protocol

extract_protocol: 50-100 mg of tissue from liver, muscle and adipose tissue were collected and DNA was isolated using Qiagen Allprep DNA/RNA/Protein Mini kit, as indicated by the manufacturer

treatment_protocol: liver, muscle and adipose tissue obtained from female and male offspring derived from either control or dKO females mated to WT males.

value: Male

tag: group

value: case

value: Liver


title: Genomic DNA from 208100630026_R04C02

source_name: Muscle

value: Muscle


title: C57BL/6J/mice, nTG, Sed, F, 5

description: Library name: Sample_48

value: sedentary


title: C57BL/6J/mice, TG, HIIT, F, 2

description: Library name: Sample_47


title: NIBSC8 Cerebral

description:
Library name: Sample 1
Minimum of 20 million reads per sample
data.zip
nibsc8-cerebral


title: C57BL/6J/mice, nTG, HIIT, F, 5

description: Library name: Sample_46


title: Genomic DNA from 208125290037_R05C01

source_name: Fat

value: Female

value: Fat


title: Genomic DNA from 208125290037_R06C01


title: Genomic DNA from 208125290002_R05C01


title: Genomic DNA from 208100630026_R03C02


title: C57BL/6J/mice, nTG, Sed, F, 4

description: Library name: Sample_44


title: C57BL/6J/mice, TG, Sed, F, 4

description: Library name: Sample_45


title: Genomic DNA from 208125290002_R02C01


title: Genomic DNA from 208125290015_R02C01


title: C57BL/6J/mice, nTG, HIIT, F, 4

description: Library name: Sample_43


title: NIBSC8 Endothelial

description:
Library name: Sample 4
Minimum of 20 million reads per sample
data.zip
nibsc8-endo

value: Human


title: C57BL/6J/mice, TG, Sed, F, 3

description: Library name: Sample_42


title: C57BL/6J/mice, nTG, Sed, F, 3

description: Library name: Sample_41


title: Genomic DNA from 208125290037_R02C01


title: Genomic DNA from 208125290037_R01C01


title: C57BL/6J/mice, TG, HIIT, F, 1

description: Library name: Sample_40


title: Genomic DNA from 208125290002_R01C01


title: C57BL/6J/mice, nTG, HIIT, F, 3

description: Library name: Sample_39


title: Genomic DNA from 208125290015_R01C01


title: C57BL/6J/mice, TG, Sed, F, 2

description: Library name: Sample_38


title: Genomic DNA from 208100630026_R06C01


title: Genomic DNA from 207592480039_R06C01


title: C57BL/6J/mice, nTG, HIIT, F, 2

description: Library name: Sample_36


title: C57BL/6J/mice, nTG, HIIT, F, 1

description: Library name: Sample_35


title: C57BL/6J/mice, nTG, Sed, F, 2

description: Library name: Sample_37


title: Genomic DNA from 208100630026_R05C01


title: Genomic DNA from 208100630026_R02C01


title: C57BL/6J/mice, TG, Sed, F, 1

description: Library name: Sample_34


title: Genomic DNA from 207592480039_R05C01


title: Genomic DNA from 208100630021_R02C01


title: Genomic DNA from 208125290015_R03C02


title: Genomic DNA from 208125290015_R04C02


title: C57BL/6J/mice, TG, HIIT, M, 8

description: Library name: Sample_32


title: Genomic DNA from 208100630021_R01C01


title: C57BL/6J/mice, nTG, HIIT, M, 8

description: Library name: Sample_31


title: C57BL/6J/mice, TG, Sed, M, 9

description: Library name: Sample_30


title: C57BL/6J/mice, nTG, Sed, M, 7

description: Library name: Sample_29


title: C57BL/6J/mice, nTG, Sed, F, 1

description: Library name: Sample_33


title: Genomic DNA from 207592480039_R02C01


title: Genomic DNA from 207592480039_R01C01


title: Genomic DNA from 207592480039_R04C02


title: Genomic DNA from 208100630026_R01C01


title: Genomic DNA from 208100630021_R06C01


title: C57BL/6J/mice, TG, HIIT, M, 7

description: Library name: Sample_28


title: C57BL/6J/mice, nTG, Sed, M, 6

description: Library name: Sample_25


title: C57BL/6J/mice, TG, Sed, M, 8

description: Library name: Sample_26


title: C57BL/6J/mice, nTG, HIIT, M, 7

description: Library name: Sample_27


title: C57BL/6J/mice, nTG, HIIT, M, 6

description: Library name: Sample_23


title: Genomic DNA from 208125290015_R06C01


title: Genomic DNA from 207592480039_R03C02


title: Genomic DNA from 208125290015_R05C01


title: C57BL/6J/mice, TG, HIIT, M, 6

description: Library name: Sample_24


title: C57BL/6J/mice, nTG, Sed, M, 5

description: Library name: Sample_21


title: C57BL/6J/mice, TG, HIIT, M, 5

description: Library name: Sample_20


title: 384

first: Mathieu

last: Wimmer

address: 1701 N 13th Street

institute: Temple University

data_processing:
Evaluating quality of samples with FastQC ver  0.11.9
Remove adapters and unpaired reads using Trimmomatic ver 0.39
Mapping to the geonome by HISAT 2.2.0 release 2/6/2020
Making sorted bam files using SAMtools ver 1.11
Counting number of reads by Stringtie v2.1.2
Finding diffrenetinally expressed genes applying Deseq2 ver 1.28.1
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include log2 FPKM values for each Sample

organism: Rattus norvegicus

source_name: Periaqueductal grey brain tissue

extract_protocol:
Periaqueductal grey tissue was dissected and flash frozen on dry ice. RNA was extracted using trizol reagent followed by the Qiagen micro RNAeasy kit
Library preps were created using the NEBNext Ultra library prep kit for illumina

tag: brain region

value: Periaqueductal grey

tag: strain

value: Sprague Dawley

value: M

value: Moprhine-sired


title: Genomic DNA from 208125290037_R04C02


title: 313

value: Saline-sired


title: C57BL/6J/mice, TG, Sed, M, 6

description: Library name: Sample_18

value: heart

value: TG


title: Genomic DNA from 208125290002_R04C02


title: C57BL/6J/mice, nTG, Sed, M, 4

description: Library name: Sample_17

value: nTG


title: C57BL/6J/mice, TG, HIIT, M, 4

description: Library name: Sample_16

value: HIIT


title: Genomic DNA from 208100630021_R04C02

value: Male


title: 383

value: brain


title: C57BL/6J/mice, TG, Sed, M, 5

description: Library name: Sample_14


title: 312


title: Genomic DNA from 208100630021_R03C02

value: case

value: Liver


title: C57BL/6J/mice, nTG, HIIT, M, 4

description: Library name: Sample_15


title: C57BL/6J/mice, nTG, Sed, M, 3

description: Library name: Sample_13

value: sedentary


title: C57BL/6J/mice, TG, HIIT, M, 3

description: Library name: Sample_12


title: Genomic DNA from 208125290037_R03C02

value: Female

value: Muscle


title: C57BL/6J/mice, nTG, HIIT, M, 3

description: Library name: Sample_11


title: C57BL/6J/mice, TG, Sed, M, 4

description: Library name: Sample_10


title: Genomic DNA from 208100630021_R05C01


title: 298


title: C57BL/6J/mice, nTG, Sed, M, 2

description: Library name: Sample_9


title: Genomic DNA from 208125290037_R06C02

value: ctrl


title: Genomic DNA from 208125290002_R03C02

value: Fat


title: C57BL/6J/mice, TG, Sed, M, 3

description: Library name: Sample_6


title: C57BL/6J/mice, TG, Sed, M, 7

description: Library name: Sample_22


title: C57BL/6J/mice, TG, HIIT, M, 2

description: Library name: Sample_8


title: 297

value: Periaqueductal grey

value: Sprague Dawley


title: C57BL/6J/mice, nTG, Sed, M, 1

description: Library name: Sample_5


title: 372

value: M


title: C57BL/6J/mice, nTG, HIIT, M, 5

description: Library name: Sample_19


title: Genomic DNA from 208100630021_R06C02


title: 277

value: Moprhine-sired


title: C57BL/6J/mice, TG, HIIT, M, 1

description: Library name: Sample_4

value: heart


title: C57BL/6J/mice, nTG, HIIT, M, 1

description: Library name: Sample_3


title: C57BL/6J/mice, TG, Sed, M, 2

description: Library name: Sample_2

value: TG


title: Genomic DNA from 208125290037_R02C02


title: 359

value: Saline-sired


title: 373


title: C57BL/6J/mice, TG, Sed, M, 1

description: Library name: Sample_1


title: Genomic DNA from 208125290037_R05C02


title: Genomic DNA from 208125290037_R01C02


title: 358


title: 276


title: Genomic DNA from 208100630021_R05C02


title: Output IAPP 3B

city: Barcelona

first: Marta

last: Badia-Graset

address: Baldiri i Reixac, 14

country: Spain

institute: Institute for Bioengineering of Catalonia

description: From plasmid library

data_processing:
FastQ files from paired-end sequencing of each library replicate were processed using the DiMSum pipeline (https://github.com/lehner-lab/DiMSum)
Assembly: GRCh38
Supplementary files format and content: Processed data is in an Excel book. aa_seq = Amino acid sequence for a given IAPP variant, ID = Mutation identifier, dataset = Mutation type (WT, single substitutions, single insertions, single deletions, polymerase slip variants, multi-aa deletions and truncations), mean_count = Mean read counts of the input replicates normalized by the mean value of synonymous mutations, nscore_c = Merged nucleation score centered to WT,  nscore[1,2,3]_c = Nucleation score for [1,2,3] replicates, sigma = Merged error over nucletion score, category_fdr = FDR nucleation categories (NS_inc, WT-like, NS_dec).

molecule: other

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were transformed with the IAPP plasmid library in 3 biological replicates. A minimum of 100,000 yeast transformants were used for each replicate to ensure the coverage of the full library and reaching therefore a >50x coverage of each variant. Once the culture reached the exponential phase, cells were resuspended in 50 mL protein inducing medium (-URA, 2% glucose, 100uM Cu2SO4) at OD600=0.05. Selection was performed in 2 technical replicates for each biological replicate (biologial replicates 1-3, technical replicates A-B; see samples title). After 24h 10 ml input pellets were collected and stored at -20C for later DNA extraction (input pellets). In parallel, 135 million cells/replicate were plated on -ADE-URA selection medium in 145cm2 plates. Plates were incubated at 30 C for 7 days inside an incubator. Finally colonies were scraped off the plates with PBS 1x, harvested by centrifugation and stored at -20C for later DNA extraction (output pellets).

extract_protocol:
The input and output pellets (3 biological x 2 technical replicates x 2 conditions (input-output), 12 tubes in total) were thawed and resuspended in 0.5 ml extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris pH 8, 1mM EDTA pH 8), and underwent two cycles of freezing and thawing in an ethanol-dry ice bath (10 min) and at 62ºC (10min). Samples were then vortexed together with 0.5 ml of phenol:chloroform:isoamyl 25:24:1 and 0.5g of glass beads (sigma). The aqueous phase was recovered by centrifugation and mixed again with 0.5ml phenol:chloroform:isoamyl 25:24:1. DNA precipitation was performed by adding 1:10V of 3M NaOAc and 2.2V of 100% cold ethanol to the aqueous phase and incubating the samples at -20ºC for 1h. After a centrifugation step, pellets were dried overnight at room temperature. Pellets were resuspended in 0.3 ml resuspension buffer (10mM Tris pH 8, 1mM EDTA pH 8) and treated with 10 ul RNase A (Thermo Scientific) for 30min at 37ºC. The DNA was finally purified using 10 ul of silica beads (QIAEX II Gel Extraction Kit, Qiagen), washed and eluted in 30 ul elution buffer. Plasmid concentrations were measured by quantitative PCR with SYBR green (Merck) and primers annealing to the origin of replication site of the PCUP1-Sup35N-IAPP plasmid at 58 °C for 40 cycles.
PCR amplification in two steps using Q5 High-Fidelity DNA Polymerase (NEB). In step 1, 30 million plasmids were amplified for 15 cycles using frame-shifted adaptor primers with a partial homology to standard Illumina sequencing primers. PCR products from the first step were treatred with 2ul of ExoSAP-IT for 20 min at 37ºC and column purified (MinElute PCR Purification Kit, Qiagen). Purified products were used as templates in the second PCR step, where indexed Illumina primers were used for a 10 cycles amplification. All replicates were pooled together in an equimolar ratio. Finally, the pooled sequencing library was run on a 2% agarose gel, purified and sent for 125 bp paired-end Illumina sequencing.
The synthetic library was synthesized as an oligo pool by Twist Bioscience and with oligos consisting of IAPP variants region of 30 nt to 117 nt, flanked by 25 nt upstream and 21 nt downstream constant regions. 10 ng of the library were amplified by PCR (Q5 high-fidelity DNA polymerase, NEB) for 10 cycles with primers annealing to the constant regions (primers MB_01-02, Supplementary Table S3), following the manufacturer’s protocol. The product was treated with 2 ul of ExoSAP (Affymetrix) and then purified by column purification (MinElute PCR Purification Kit, Qiagen). The PCUP1-Sup35N plasmid was linearized by PCR (Q5 high-fidelity DNA polymerase, NEB) (primers MB_03-04, Supplementary Table S3). The product was treated with DpnI (ThermoFisher Scientific) and purified from a 1% agarose gel (QIAquick Gel Extraction Kit, Qiagen). The library was ligated to 100 ng of the linear vector with a ratio of 5:1 (library:vector) by a Gibson approach with 3 h of incubation. The reaction product was dialyzed for 30 minutes on a membrane filter (MF-Millipore 0,025 um membrane, Merck) and transformed into 10-beta Electrocompetent E.coli (NEB), by electroporation with 2.0kV, 200 Ω, 25 uF (BioRad GenePulser machine). Cells were recovered in SOC medium for 30 minutes and grown overnight in 50 ml of LB ampicillin medium. A number of cells were plated in LB ampicillin plates to calculate the transformation efficiency and confirm that each variant in the library would be represented at least 10 times. A total of 116.000 transformants were estimated. A total of 2 ml of overnight culture was harvested to obtain a miniprep of the IAPP library (NZYMiniprep kit, NZYTech).

value: yeast cells

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)

tag: molecule type

value: PCR amplicon


title: C57BL/6J/mice, nTG, HIIT, M, 2

description: Library name: Sample_7

value: nTG

value: HIIT


title: mNPC cells , BCOR-TR2, Day0, rep2

first: Mitzi

middle: I

last: Kuroda

address: 77 Ave Louis Pasteur

department: Genetics and Medicine

institute: MGB

description: Library name: Sample29

data_processing:
Reads were processed for adapter contamination using cutadapt 4.1 and aligned to the mouse GRCm38 genome using STAR (version 2.7.9a) (Dobin et al. 2013). SAMTools was used to quality filter SAM files (Li et al. 2009). BigWig files were generated using Deeptools BamCoverage 3.5.0. Count matrix was generated using featuresCounts --countReadPairs -s 2 -T 6 -t exon (subread-2.0.6). Downstream processing of the data was carried out using R/Bioconductor (Ihaka and Gentleman 1996; Gentleman et al. 2004) and differential expression analysis was performed using the DESeq2 package. GO enrichment analysis with the org.Mm.eg.db annotation was done using clusterProfiler package.
Assembly: GRCm38
Supplementary files format and content: csv file contains raw counts of each samples

source_name: male

growth_protocol: Undifferentiated 129P2/OlaHsd -derived E14TG2a mouse ES cells (Iacovino et al. 2011; Mazzoni et al. 2011) were maintained on gelatin-coated plates supplemented with 15% embryonic stem-cell fetal bovine sera (GibcoTM, 10439), 1x nonessential amino acids (GibcoTM, 11140), 1x Glutamax (GibcoTM, 35050), 0.5 mM 2-mercaptoethanol (GibcoTM, 21985), and 10 ng/mL ESGRO® Recombinant Mouse LIF Protein (Sigma-Aldrich, ESG1107). Cells were passaged every 2 days using dissociation in 0.25% trypsin (GibcoTM, 25200).

extract_protocol:
Total RNA was isolated from 1x106 cells mES cells or mNPC derived from mES cells using the RNeasy Plus Mini Kit (Qiagen, 74134). mRNA was selected using PolyA enrichment (New England Biolabs, E7490S).
RNA quality was analyzed using RNA screen tape (Agilent Technologies, 5067-5576) on an Agilent Tape Station. Sequencing libraries were generated as per manufacturer protocol using the NEBNext Ultra II Directional RNA Library Preparation Kit (New England Biolabs, E7760). Library concentration and fragment sizes were analyzed with the D1000 Screen tape (Agilent Technologies, 5067-5582). Libraries were pooled and sequenced on the Illumina NovaSeq 6000 using the Harvard Medical School Biopolymers Facility.

treatment_protocol: Differentiation of mouse ES cells into neural progenitors was performed as described (Ying and Smith 2003). Briefly, mouse ES cells were plated onto 0.2% gelatin-coated tissue culture plastic at a density of 1.5x104/cm2 in ES cell media for 12-16 hr for attachment. For neural progenitor induction, mouse ES cell media was replaced with N2B27 medium and incubated for 6 days with medium changes daily for the first two days and then every 48 hours thereafter. N2B27 medium contains a 1:1 mix of Neurobasal medium (GibcoTM, 21103049), and DMEM/F12 (GibcoTM, 11330032), 1x nonessential amino acids (GibcoTM), 0.5 mM b-mercaptoethanol (GibcoTM), 0.5x Glutamax (GibcoTM), 1x N27 (GibcoTM, 17502048) and 1x B27 (GibcoTM, 17504044). On day 7, cells were harvested using trypsin for downstream analyses, including RNA sequencing and flow cytometry.

value: male

value: mNPC cells

value: 129P2/OlaHsd  E14Tg2a mES cells A2 Lox cre

value: Mutant  BCOR_TR_clone2

value: differentiated (day6)


title: mNPC cells , BCOR-TR1, Day0, rep3

description: Library name: Sample27

value: Mutant  BCOR_TR_clone1


title: mNPC cells , BCOR-TR2, Day0, rep3

description: Library name: Sample30


title: mNPC cells , BCOR-TR2, Day0, rep1

description: Library name: Sample28


title: mNPC cells , BCOR-ITD2, Day0, rep3

description: Library name: Sample24

value: Mutant  BCOR_ITD_clone2


title: Output IAPP 3A

description: From plasmid library


title: mNPC cells , BCOR-TR1, Day0, rep1

description: Library name: Sample25


title: mNPC cells , BCOR-ITD2, Day0, rep2

description: Library name: Sample23


title: Genomic DNA from 208125290037_R04C01

value: Female

value: ctrl

value: Liver


title: Genomic DNA from 208100630021_R02C02

value: Muscle


title: Output IAPP 2B

description: From plasmid library


title: mNPC cells , BCOR-ITD2, Day0, rep1

description: Library name: Sample22


title: Output IAPP 2A

description: From plasmid library


title: mNPC cells , BCOR-ITD1, Day0, rep1

description: Library name: Sample19

value: Mutant  BCOR_ITD_clone1


title: mNPC cells , WT, Day0, rep3

description: Library name: Sample18

value: Wild type BCOR


title: mNPC cells , BCOR-ITD1, Day0, rep3

description: Library name: Sample21


title: mNPC cells , WT, Day0, rep2

description: Library name: Sample17


title: mNPC cells , BCOR-ITD1, Day0, rep2

description: Library name: Sample20


title: Genomic DNA from 208125290002_R05C02

value: Fat


title: Genomic DNA from 208100630021_R01C02


title: Output IAPP 1A

description: From plasmid library

value: yeast cells

value: [psi-pin-] (MATa ade1-14 his3 leu2-3,112 lys2 trp1 ura3-52)

value: PCR amplicon


title: mNPC cells , WT, Day0, rep1

description: Library name: Sample16

value: male


title: Genomic DNA from 208125290037_R03C01


title: mES cells , BCOR-TR2, Day0, rep3

description: Library name: Sample15

value: mES cells


title: mNPC cells , BCOR-TR1, Day0, rep2

description: Library name: Sample26

value: mNPC cells

value: 129P2/OlaHsd  E14Tg2a mES cells A2 Lox cre


title: mES cells , BCOR-TR2, Day0, rep2

description: Library name: Sample14

value: Mutant  BCOR_TR_clone2


title: Genomic DNA from 208125290002_R06C02


title: Input IAPP 3B

description: From plasmid library


title: mES cells , BCOR-TR2, Day0, rep1

description: Library name: Sample13


title: Genomic DNA from 208100630026_R06C02


title: Input IAPP 3A

description: From plasmid library


title: Genomic DNA from 208125290002_R02C02


title: Input IAPP 2B

description: From plasmid library


title: mES cells , BCOR-TR1, Day0, rep2

description: Library name: Sample11

value: Mutant  BCOR_TR_clone1


title: mES cells , BCOR-TR1, Day0, rep3

description: Library name: Sample12


title: mES cells , BCOR-TR1, Day0, rep1

description: Library name: Sample10


title: Output IAPP 1B

description: From plasmid library


title: Input IAPP 2A

description: From plasmid library


title: mES cells , BCOR-ITD2, Day0, rep2

description: Library name: Sample8

value: Mutant  BCOR_ITD_clone2


title: mES cells , BCOR-ITD2, Day0, rep1

description: Library name: Sample7


title: mES cells , BCOR-ITD1, Day0, rep3

description: Library name: Sample6


title: Genomic DNA from 208100630026_R05C02

value: Female


title: Genomic DNA from 207592480039_R05C02

value: ctrl


title: mES cells , BCOR-ITD1, Day0, rep2

description: Library name: Sample5


title: Input IAPP 1B

description: From plasmid library


title: Input IAPP 1A

description: From plasmid library


title: mES cells , WT, Day0, rep3

description: Library name: Sample3


title: mES cells , BCOR-ITD1, Day0, rep1

description: Library name: Sample4


title: mES cells , WT, Day0, rep2

description: Library name: Sample2


title: Genomic DNA from 208125290002_R01C02

value: Liver


title: Genomic DNA from 208100630026_R02C02

value: Male


title: dsRED+ WT 4 dpf

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

description: 10x Genomics single-cell 3'RNA version3

data_processing:
Following sequencing, an average 25,000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ, aligned to Danio.rerio_genome and single-cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software (V7.0.1). The single-cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples, while anti-sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries.
Assembly: Zebrafish genome reference (GRCz10)
Supplementary files format and content: Tab-separated values files matrix files

organism: Danio rerio

source_name: 4 days post fertilization

extract_protocol:
WT and TKO embryos were collected at 4 dpf, and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells, a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol (DOI: 10.1016/j.mex.2018.10.009). 10,000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium.
10X Genomics’s Chromium instrument and Dual index Single-Cell 3′ Reagent kit (V3.1) were used to prepare the individually barcoded single-cell RNA-Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation-4200 traces (Agilent BioAnalyzer High Sensitivity Kit) and quantitated by the Qubit system.

value: 4 days post fertilization

value: hepatocytes and pancreatic endocrine beta-cells

value: WT- EK strain


title: Genomic DNA from 207592480039_R06C02

value: Fat


title: mES cells , BCOR-ITD2, Day0, rep3

description: Library name: Sample9


title: Genomic DNA from 208100630026_R04C01


title: GFP+ WT 4 dpf

description: 10x Genomics single-cell 3'RNA version3

value: neurons and pancreatic acinar cells


title: NC208, normoxic (6-months post-hypercapnia) control female

city: Nutley

first: Andy

last: Madrid

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health

description:
Library name: NC208
Processed data includes gene count estimate files from RSEM

data_processing:
Raw reads were assessed for quality using FastQC. Reads were aligned to the mm10 version of the mouse genome, using RSEM and STAR to quantify the number of reads aligned to each gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited file. Processed data includes tab-delimited files of expected counts per read and other read transformations: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: skeletal muscle

extract_protocol:
After specified timepoints, animals were euthanized. Then leg skin was dissected with tweezers and muscles exposed and under real time magnification using an illuminated magnifier (Omano, China) muscles were dissected individually, cutting first the distal tendon, and gently removing the entire muscle using dissecting scissors (Roboz RS-5840). After the proximal tendon was severed, the muscle was put in contact with a gauze under magnification to eliminate remaining blood, fat, and if needed also remaining tendon using scissors. Muscle was then weighed using an analytical balance (Sartorius Entris, Germany). Mass determination was performed on the tibialis anterior (TA), extensor digitorum longus (EDL), and soleus muscles.
RNA was sent to GENEWIZ for extraction, library preparation of poly A enrichment, and sequencing on an Illumina Novaseq 6000

value: skeletal muscle

value: female

value: WT

value: normoxic, 44 weeks aged

tag: age

value: 44 weeks


title: GFP+ TKO 4 dpf

description: 10x Genomics single-cell 3'RNA version3

tag: tissue

value: tfeb-tfe3a-tfe3a triple KO (TKO)


title: NC210, normoxic (6-months post-hypercapnia) control female

description:
Library name: NC210
Processed data includes gene count estimate files from RSEM

tag: Sex


title: NC209, normoxic (6-months post-hypercapnia) control female

description:
Library name: NC209
Processed data includes gene count estimate files from RSEM

tag: genotype


title: Genomic DNA from 208125290002_R04C01

value: Muscle


title: NC206, normoxic (6-months post-hypercapnia) control female

description:
Library name: NC206
Processed data includes gene count estimate files from RSEM

tag: treatment


title: NC205, normoxic (acute) control female

description:
Library name: NC205
Processed data includes gene count estimate files from RSEM

value: normoxic, 20 weeks aged

value: 20 weeks


title: NC204, normoxic (acute) control female

description:
Library name: NC204
Processed data includes gene count estimate files from RSEM


title: Genomic DNA from 208125290015_R03C01

value: ctrl


title: NC203, normoxic (acute) control female

description:
Library name: NC203
Processed data includes gene count estimate files from RSEM


title: DPI-28_Caudal_3

city: Delhi

first: Jaidev

last: Sharma

state: Delhi

address: Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, near Govind Puri Metro Station, New Delhi, Delhi 110020

department: Computational Biology

country: India

data_processing:
Sequence reads were trimmed by using Fastp
Alignment was performed by using HISAT2
FeatureCount was used to generate the count matrix.
Assembly: rn6
Supplementary files format and content: tab delimited text files includes Raw values for each sample
Supplementary files format and content: tab delimited text files includes log2cpm values for each sample

source_name: Spinal Cord

extract_protocol:
Total RNA of these samples was extracted with Trizol as per manufacturer protocol.
The RNA libraries were constructed by using KAPA RNA HyperPrep Kit with RiboErase as per the manufacturer’s protocol.

value: Spinal Cord

tag: time

tag: region

value: Caudal


title: Genomic DNA from 208125290002_R03C01

value: Male


title: Genomic DNA from 208100630026_R03C01

value: Liver


title: DPI-28_Epicenter_3

institute: Indraprastha Institute of Information Technology

value: Epicenter


title: dsRED+ TKO 4 dpf

description: 10x Genomics single-cell 3'RNA version3

value: 4 days post fertilization

tag: cell type

value: hepatocytes and pancreatic endocrine beta-cells


title: NC110, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC110
Processed data includes gene count estimate files from RSEM

value: skeletal muscle

value: male


title: mES cells, WT, Day0, rep1

description: Library name: Sample1

tag: cell line

value: mES cells

value: 129P2/OlaHsd  E14Tg2a mES cells A2 Lox cre

value: Wild type BCOR


title: NC109, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC109
Processed data includes gene count estimate files from RSEM

value: WT

value: normoxic, 44 weeks aged

value: 44 weeks


title: Genomic DNA from 208125290015_R04C01

value: Female

value: Fat


title: NC202, normoxic (acute) control female

description:
Library name: NC202
Processed data includes gene count estimate files from RSEM

value: female

value: normoxic, 20 weeks aged

value: 20 weeks


title: NC108, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC108
Processed data includes gene count estimate files from RSEM


title: NC201, normoxic (acute) control female

description:
Library name: NC201
Processed data includes gene count estimate files from RSEM


title: DPI-28_Rostral_3

value: Spinal Cord

value: Rostral


title: NC107, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC107
Processed data includes gene count estimate files from RSEM


title: DPI-28_Caudal_1

value: Caudal


title: Genomic DNA from 208125290015_R06C02

value: ctrl

value: Muscle


title: NC207, normoxic (6-months post-hypercapnia) control female

description:
Library name: NC207
Processed data includes gene count estimate files from RSEM

value: skeletal muscle


title: NC106, normoxic (6-months post-hypercapnia) control male

description:
Library name: NC106
Processed data includes gene count estimate files from RSEM

value: male


title: Genomic DNA from 207592480039_R02C02

value: Liver


title: NC104, normoxic (acute) control male

description:
Library name: NC104
Processed data includes gene count estimate files from RSEM


title: DPI-28_Epicenter_1

value: Epicenter


title: Genomic DNA from 208125290015_R05C02

value: Male


title: DPI-14_Caudal_2


title: DPI-28_Rostral_1


title: DPI-14_Epicenter_2


title: NC103, normoxic (acute) control male

description:
Library name: NC103
Processed data includes gene count estimate files from RSEM

value: WT


title: HC210, 6-months post-hypercpania female

description:
Library name: HC210
Processed data includes gene count estimate files from RSEM

value: hypercapnia, 44 weeks aged

value: 44 weeks


title: Genomic DNA from 208100630021_R04C01

value: Fat


title: HC209, 6-months post-hypercpania female

description:
Library name: HC209
Processed data includes gene count estimate files from RSEM

value: female


title: DPI-14_Rostral_2


title: HC208, 6-months post-hypercpania female

description:
Library name: HC208
Processed data includes gene count estimate files from RSEM


title: DPI-14_Caudal_1


title: HC206, 6-months post-hypercpania female

description:
Library name: HC206
Processed data includes gene count estimate files from RSEM


title: Genomic DNA from 207592480039_R04C01


title: DPI-14_Epicenter_1


title: HC205, acute hypercapnia female

description:
Library name: HC205
Processed data includes gene count estimate files from RSEM

value: hypercapnia, 20 weeks aged


title: HC203, acute hypercapnia female

description:
Library name: HC203
Processed data includes gene count estimate files from RSEM

value: 20 weeks


title: HC204, acute hypercapnia female

description:
Library name: HC204
Processed data includes gene count estimate files from RSEM


title: Genomic DNA from 208125290015_R02C02


title: HC201, acute hypercapnia female

description:
Library name: HC201
Processed data includes gene count estimate files from RSEM


title: NC105, normoxic (acute) control male

description:
Library name: NC105
Processed data includes gene count estimate files from RSEM

value: normoxic, 20 weeks aged


title: DPI-14_Rostral_1

value: Spinal Cord

value: Rostral


title: HC202, acute hypercapnia female

description:
Library name: HC202
Processed data includes gene count estimate files from RSEM


title: NC102, normoxic (acute) control male

description:
Library name: NC102
Processed data includes gene count estimate files from RSEM


title: NC101, normoxic (acute) control male

description:
Library name: NC101
Processed data includes gene count estimate files from RSEM


title: DPI-1_Caudal_2

value: Caudal


title: Genomic DNA from 207592480039_R01C02

value: ctrl


title: HC109, 6-months post-hypercpania male

description:
Library name: HC109
Processed data includes gene count estimate files from RSEM

value: skeletal muscle


title: Genomic DNA from 208100630021_R03C01

value: Female


title: HC108, 6-months post-hypercpania male

description:
Library name: HC108
Processed data includes gene count estimate files from RSEM

value: male


title: HC207, 6-months post-hypercpania female

description:
Library name: HC207
Processed data includes gene count estimate files from RSEM


title: HC107, 6-months post-hypercpania male

description:
Library name: HC107
Processed data includes gene count estimate files from RSEM


title: DPI-1_Epicenter_2

value: Epicenter


title: Genomic DNA from 207592480039_R03C01

value: Muscle


title: HC106, 6-months post-hypercpania male

description:
Library name: HC106
Processed data includes gene count estimate files from RSEM

value: WT


title: DPI-1_Rostral_2


title: HC105, acute hypercapnia male

description:
Library name: HC105
Processed data includes gene count estimate files from RSEM


title: DPI-1_Caudal_1


title: HC103, acute hypercapnia male

description:
Library name: HC103
Processed data includes gene count estimate files from RSEM


title: AD 16, DART-Mut-treated

first: Junming

address: 75 E Concord St

institute: Boston University

description: Library name: A16-Mut

data_processing:
Raw FASTQ files were assessed for quality using FastQC (v0.12.1) to evaluate read quality, GC content, and adapter contamination
Adaptor sequences and low-quality bases were trimmed using Trimmomatic with default parameters
Trimmed reads were aligned to the human reference genome GRCh38.111 using STAR aligner (v2.7.9a) in single-pass mode, generating coordinate-sorted BAM files
C>U editing events indicative of m6A were identified using the Bullseye pipeline, which compares APOBEC1-YTH–treated (i.e., DART-WT) samples to YTHmut controls (i.e., DART-Mut) to detect m6A-proximal C>U conversions. Events were filtered based on editing ratio, coverage, and DRACH motif presence
Assembly: GRCh38.111 (Ensembl release 111)
Supplementary files format and content: Bullseye output files are in BED format. Each file lists m6A sites with chromosome, position, strand, gene name, editing level, and transcript region (e.g., CDS or 3′UTR). These files show where m6A was detected in each sample.

source_name: Dorsolateral prefrontal cortex (Broadmann area 9)

extract_protocol:
RNA was harvested using the Rneasy Plus Kit (Qiagen). 50ng of total RNA was used for the DART reaction. RNA was repurified using the RNeasy Micro Kit (Qiagen). 3ng of total RNA was used as input for cDNA library construction.
cDNA libraries were generated using the SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio) following the manufacturer’s protocol.

value: Alzheimer's disease

tag: dart treatment

value: Mutant


title: HC102, acute hypercapnia male

description:
Library name: HC102
Processed data includes gene count estimate files from RSEM


title: HC101, acute hypercapnia male

description:
Library name: HC101
Processed data includes gene count estimate files from RSEM


title: AD 15, DART-Mut-treated

description: Library name: A15-Mut

value: Dorsolateral prefrontal cortex (Broadmann area 9)


title: Genomic DNA from 208125290015_R01C02

value: Liver


title: DPI-1_Epicenter_1


title: HC110, 6-months post-hypercpania male

description:
Library name: HC110
Processed data includes gene count estimate files from RSEM

value: hypercapnia, 44 weeks aged

value: 44 weeks


title: DPI-1_Rostral_1


title: A205, aged female

description:
Library name: A205
Processed data includes gene count estimate files from RSEM

value: female

value: 72 weeks aged

value: 72 weeks


title: A204, aged female

description:
Library name: A204
Processed data includes gene count estimate files from RSEM


title: A203, aged female

description:
Library name: A203
Processed data includes gene count estimate files from RSEM


title: AD 13, DART-Mut-treated

description: Library name: A13-Mut


title: Sham3

value: Spinal Cord

value: Sham


title: A202, aged female

description:
Library name: A202
Processed data includes gene count estimate files from RSEM

value: skeletal muscle


title: A201, aged female

description:
Library name: A201
Processed data includes gene count estimate files from RSEM


title: A105, aged male

description:
Library name: A105
Processed data includes gene count estimate files from RSEM


title: Sham1


title: AD 11, DART-Mut-treated

description: Library name: A11-Mut


title: AD 12, DART-Mut-treated

description: Library name: A12-Mut


title: AD 18, DART-Mut-treated

description: Library name: A18-Mut


title: CHIPseq, CFAP20/CCNC-dKO, rep1

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

data_processing:
For all sequencing data, a sequencing quality profile was generated using FastQC (Version 0.11.9). Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the Human Genome 38 using bwa-mem tools (BWA (Version 0.7.17) and reference genome GCA_000001405.15_GRCh38 (Li, 2013). In parallel reads were aligned to the D.melanogaster genome BDGP6 to quantify spike-in counts. Only uniquely mapping and high-quality reads (> q30) were included in the analyses. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2). Example genome tracks were generated in IGV (Version 2.4.3).
OK-seq data in untreated RPE1 cells was downloaded from Chen et al. 2019 (datasets GSM3130725 and GSM3130726). Sequences were trimmed using TrimGalore (Version 0.6.5), and aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Replication initiation zones were subsequently defined using the replication fork directionality analysis R toolkit (OKseqHMM; available on https://github.com/CL-CHEN-Lab/OK-Seq), with read coverage threshold 6 for GSM3130725 and 1 for GSM3130726, and smoothing window size 15 kb. Initiation zones present in both datasets were identified using mergePeaks of HOMER tools (Version 4.8.2), with -d given. Origins were defined as the center of initiation zones. For all origins, their nearest TSS was defined using annotatePeaks of HOMER tools, together with the distance between the TSS and the origin. Here, a negative distance represents an origin upstream of the TSS (co-directional transcription relative to replication), while a positive distance represents an origin downstream of a TSS (head-on transcription relative to replication). To allow for clean transcription versus replication analyses, we further selected only origins for which their nearest TSS was not preceded by another gene within 5kb upstream of the TSS. This resulted in a list of 2,040 origins.  A list of 49,948 gene-coordinates was obtained from the UCSC genome database selecting the “knownCanonical” table containing the canonical transcription start sites per gene (Karolchik et al., 2004). To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected by calculating gene size-corrected read-densities of BrU-seq data in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings. These 3,000 actively transcribed genes were used in downstream analyses, unless stated otherwise.
Read-density profiles around origin or TSS/TTS coordinates were defined using the AnnotatePeaks.pl tool of HOMER using normalization to 10M reads (for profiles around origins), or to the number of identified Drosophila spike-in reads (for profiles around TSSs of transcribed genes). Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423) (Team, 2019). Where indicated, average profiles were trimmean 0.1 (0.05 from top, 0.05 from bottom) to remove extreme values.
Assembly: Hg38
Supplementary files format and content:
TSScoordinates_InclBrUseqInWTmock.txt: tab-delimited text file containing coordinates of 9944 TSSs, including associated BrUseq signal in WT cells
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_WT_mock_rep1.txt: tab-delimited text file containing the spike-normalized read-density at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_CFAP20KO_mock_rep1.txt: tab-delimited text file containing the spike-normalized read-density at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
ChIPseq_ReadDensityAroundTSS_Hg38_10kbWindow_SpikeNormalized_CFAP20-CCNC-dKO_mock_rep1.txt: tab-delimited text file containing the spike-normalized read-density at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
OriginCenter_OKseq_Select5kbUpstreamTSSempty.txt: tab-delimited text file containing coordinates of origins identified as described.
ChIPseqRPB1_ReadDensityAroundOKseqOrigins_200KbWindow_WT_rep*.txt: tab-delimited text file containing read-density/10M reads at the indicated distance from a set of origins

source_name: RPE1 iCas9 p53/puro-dKO CFAP20/CCNC-dKO

growth_protocol: All cell lines were cultured at 37°C with 5% CO2 in DMEM GlutaMAX (Gibco), supplemented with 10% fetal calf serum (Avantor, VWR) and penicillin/streptomycin (Sigma).

extract_protocol:
Attached cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed once with PBS followed by incubation with 1% FA for 20 min at RT. Fixation was stopped by the addition of glycine in PBS to a final concentration of 0.1 M for 3 min at RT. This was followed by washing with cold PBS and collection of the cells in 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), and 20 mM Hepes (pH 7.6) in miliQ. Chromatin was pelleted by centrifugation for 5 min at 400 × g and incubated in 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) in miliQ for 10 min at 4 °C. Chromatin was again pelleted by centrifugation and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6) in miliQ) to a final concentration of 15 × 10^6 cells/mL. Chromatin was sonicated to approximately one nucleosome using the Bioruptor Pico (Diagenode), 15 cycles of 30s ON/30 s OFF in a 4°C water bath. ChIP was performed using 28 μg of chromatin (22 μg for CFAP20/CCNC-KO) + 40 ng of Drosophila spike-in chromatin (32.6 ng for CFAP20/CCNC-KO; Active Motif, 53083) with 3 μl of RNAPII antibody (Active Motif, 61686) and 1 μg spike-in antibody (Active Motif, 61686) by overnight incubation at 4 °C. Protein-chromatin-pull down followed with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D, 10003D). ChIP samples were extensively washed and purified using Qiagen MinElute kit.
Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters or xGen UDI-UMI adapters. Samples were sequenced using an Illumina NextSeq500 or HiSeq X, using paired-end sequencing with 42 or 151 bp from each end.

treatment_protocol: Cells were grown to 80-90% confluency

value: RPE1 iCas9 p53/puro-dKO CFAP20/CCNC-dKO

tag: genome used_to_map_to

value: Hg38 | BDGP6 (spike-in)

value: untreated

tag: pulldown antibody

value: Rabbit anti-RPB1 (Bethyl, A304-405A) | anti-D.Melanogaster H2Av (Active Motif, 61686)

tag: type of_material

value: ChIP DNA


title: HC104, acute hypercapnia male

description:
Library name: HC104
Processed data includes gene count estimate files from RSEM

value: male

value: WT

value: hypercapnia, 20 weeks aged

value: 20 weeks


title: AD 10, DART-Mut-treated

description: Library name: A10-Mut

value: Dorsolateral prefrontal cortex (Broadmann area 9)

tag: group

value: Alzheimer's disease

value: Mutant


title: CHIPseq, CFAP20-KO, rep1

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO


title: AD 8, DART-Mut-treated

description: Library name: A8-Mut


title: A102, aged male

description:
Library name: A102
Processed data includes gene count estimate files from RSEM

value: 72 weeks aged

value: 72 weeks


title: A101, aged male

description:
Library name: A101
Processed data includes gene count estimate files from RSEM


title: Genomic DNA from 208100630026_R01C02

value: Male

value: ctrl

value: Fat


title: AD 6, DART-Mut-treated

description: Library name: A6-Mut


title: AD 5, DART-Mut-treated

description: Library name: A5-Mut


title: BPTES-2

city: changzhi

first: Pu

last: wang

state: shanxi

address: jiefang road 163

country: China

institute: changzhi medical college

description: BPTES

data_processing:
Quality assessment using Q30 score ensured high-quality sequencing data. Triming of 3’ adaptors and removal of low-quality reads were performed using cutadapt software (version 1.9.3). The clean reads were aligned to the reference human genome (UCSC HG19) with the help of Hisat2 software (version 2.0.4). the cluster analysis were performed using Metascape (https:// metascape.org).
The analysis of macrophage quantity employed the X-CELL algorithm.
Assembly: MM10
Supplementary files format and content: RAW DATA FOR EVERY SAMPLE
Supplementary files format and content: raw and normalized counts

source_name: LIVER

extract_protocol:
Total RNA was extracted from whole liver using Trizol reagent (Thermo Fisher) following the manufacturer’s instructions.
The isolated RNA was then used to create an RNA-seq library with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: 12-month-old C57 mice were randomly divided into two groups and received BPTES via intraperitoneal injection at a dose of 12.5 mg/kg, three times a week for two months.

value: LIVER

value: aging and treated with BPTES

tag: age at start of experiment

value: 12 months


title: BPTES-1

description: BPTES

tag: strain


title: CHIPseq, WT, rep1

source_name: RPE1 iCas9 p53/puro-dKO WT

value: RPE1 iCas9 p53/puro-dKO WT

value: Hg38 | BDGP6 (spike-in)

value: untreated

value: Rabbit anti-RPB1 (Active Motif, 61686) | anti-D.Melanogaster H2Av (Active Motif, 61686)

value: ChIP DNA


title: Heated seeds

city: Fukuoka

first: Yushi

last: Ishibashi

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Department of Bioresource Sciences

country: Japan

institute: Kyushu University, Faculty of Agriculture

data_processing:
The raw sequence reads are filtered based on quality using FastQC (http://bioinformatics.babraham.ac.uk/projects/fastqc/). The adapter sequences are also   trimmed off the raw sequence reads by trimmomatic (v0.38).
The trimmed reads are mapped to reference genome IRGSP-1.0 with Bismark (v0.22.3) and HISAT2 (v2.1.0) program.
The methylation ratio of every single cytosine location is extracted from the mapping results after the deduplication, using 'bismark_methylation_extractor' script. And the differentially methylation regions (DMRs) are calculated by DSS (v2.36.0) package on Bioconductor.
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: tsv including chr, start, end, methylated pacentage, count of methylated and count of unmethylated

organism: Oryza sativa

source_name: seed

extract_protocol:
Rice DNA was harvested using Dneasy plant mini kit (QIAGEN)
The genomic DNA were treated with bisulfite by using EZ DNA Methylation-Gold Kit (ZYMO RESEARCH). Then bisulfite sequencing libraries were prepared with Accel-NGS Methyl-Seq DNA Library Kit (Swift BioScience) according to the manufacturer's instructions.

value: seed

value: Nipponbare

value: incubate at 30 ℃


title: PVT_WT5

city: Chengdu

first: Peiwen

last: Jian

state: Sichuan

address: 9F, B2, Tianfu Life Science Park, Second Research Building, West China Hospital, Sichuan University, Chengdu，China

institute: West China Hospital of Sichuan University

description:
Library name: Sample5
Column name in Processed data.txt: PVT_WT5:fpkm

data_processing:
1. Quality control Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
2. Reads mapping The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
3. Expression analysis: we used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
4. Differential expression analysis: Then difference expression of genes was analyzed by DESeq (v1.38.3) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, we used R language Pheatmap (v1.0.12) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
5. Enrichment analysis: we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO (v2.50.0) to perform GO enrichment analysis on the differential genes (all DEGs / up DEGs / down DEGs), calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. ClusterProfiler (v4.6.0) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value <0.05. Gene Set Enrichment Analysis (GSEA) (v4.1.0) tool was used for GSEA enrichment analysis of all genes, and GSEA enrichment analysis pathway map was drawn. 6. New transcript analysis On the basis of the existing reference genome, using the software StringTie (v2.2.1) to assemble the mapped reads, and comparing the splicing results with the known transcripts to obtain no annotations Transcripts of information. 7. Differential variable shear analysis Using rMATS (v4.0.1) software to analyze differential variable shear events. The main types of variable shear events analyzed are mainly SE, RI, MXE, A5SS, A3SS. 8. SNP and InDel analysis The Varscan (v2.3.9) software was used to obtain SNP and InDel sites, and the filtering criteria were: 1) SNP site base Q>20; 2) The number of Reads covering the site> 8; 3) The number of Reads supporting the mutation site> 2; 4) The p-value of SNP locus is <0.01. Analysis of variant sites. 9. Transcription factor family analysis The prediction of transcription factors is to compare plants and animals with PlantTFDB (Plant Transcription Factor Database) and AnimalTFDB (Animal Transcription Factor DataBase) databases respectively to predict the transcription factor and the family information to which the transcription factor belongs. Then the DEGs that were predicted to be transcription factors were statistically. 10. Exon difference analysis Using the DEXSeq (v1.44.0) package to analyze the difference in exon usage in RNA-seq experimental data, where the difference in exon usage refers to the relatively different exon usage due to experimental conditions. 11. Interaction Analysis of Differential Gene Protein Network The STRING database (https://string-db.org/) is used for protein interaction analysis to reveal the relationship between target genes.
Assembly: Ensembl GRCm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. 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 and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) Shanghai Personal Biotechnology Cp. Ltd.

value: brain

value: WT


title: PVT_WT6

description:
Library name: Sample6
Column name in Processed data.txt: PVT_WT6:fpkm


title: AD 4, DART-Mut-treated

last: Hu

description: Library name: A4-Mut

value: Dorsolateral prefrontal cortex (Broadmann area 9)

value: Alzheimer's disease

value: Mutant


title: Control seeds

value: incubate at 25 ℃


title: PVT_WT4

description:
Library name: Sample4
Column name in Processed data.txt: PVT_WT4:fpkm


title: AGING-3

description: AGING

value: LIVER

value: aging


title: A103, aged male

description:
Library name: A103
Processed data includes gene count estimate files from RSEM

value: skeletal muscle

value: male

value: 72 weeks aged

value: 72 weeks


title: AGING-2

description: AGING

value: 12 months


title: sp-PJI03

city: Fuzhou

first: Xinyu

last: Fang

address: Chazhong road

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
Pass filter data of fastq format were processed by Cutadapt[1](version 1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Bowtie2 (v2.2.6) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2(v2.2.6).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1p1) estimated gene expression levels from the pair-end clean data.
Assembly: Staphylococcus aureus (ID 154) - genome - NCBI (NIH. Gov)

organism: Staphylococcus aureus

source_name: MSSA

extract_protocol:
RNA was harvested using TRIzol.
RNA libraries for RNA-seq were prepared using VAHTS Total RNA-seq (Bacteria) Library Prep Kit for Illumina following manufacturer's protocols.

value: MSSA

tag: isolate

value: severe pain PJI (sp-PJI)


title: CCI3

description:
Library name: Sample3
Column name in Processed data.txt: CCI3:fpkm

value: CCI


title: Control 19, DART-Mut-treated

description: Library name: C19-Mut

value: Control/non-AD


title: A104, aged male

description:
Library name: A104
Processed data includes gene count estimate files from RSEM

tag: age


title: AGING-1

description: AGING

tag: tissue


title: Control 18, DART-Mut-treated

description: Library name: C18-Mut


title: sp-PJI01


title: sp-PJI02


title: BPTES-3

description: BPTES

value: aging and treated with BPTES


title: Control 17, DART-Mut-treated

description: Library name: C17-Mut


title: CCI1

description:
Library name: Sample1
Column name in Processed data.txt: CCI1:fpkm

value: brain

value: WT


title: mp-PJI03

value: mild pain PJI (mp-PJI)


title: Control 16, DART-Mut-treated

description: Library name: C16-Mut

value: Dorsolateral prefrontal cortex (Broadmann area 9)

value: Mutant


title: mp-PJI02


title: LU_RAS_KD_SNF5_D10_WT_IP

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

description:
Library name: Sample48
antibody SNF5

data_processing:
Raw data :The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format, which contains sequence information and the corresponding sequencing quality information.
Evaluation of data (Data quality control) Sequence artifacts, including reads containing adapter contamination, low-quality and unrecognizable nucleotide (N), undoubtedly set the barrier for the subsequent reliable bioinformatics analysis. Hence quality control is an essential step and applied to guarantee the meaningful downstream analysis. we used fastp to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read;   (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Clean sequencing datasets were aligned to the human reference genome (hg19) using Bowtie2 (v2.3.4.3) and processed with Samtools (v1.2). The resulting BAM files were converted into BigWig format using the bamCoverage tool from deepTools (v3.3.2.0.0)
Enriched binding peaks were identified by MACS2 (v2.1.1) after filtering against input controls
Assembly: hg19
Supplementary files format and content: bigwig

source_name: primary fibroblasts cells

growth_protocol: MEM, 10% fetal bovine serum, 1× penicillin/streptomycin. Cells were maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
2 ug of total RNA was used for the construction of sequencing libraries.For ChIP-seq, cells were fixed with 1% formaldehyde for 10 minutes.Then terminate crosslinking with glycine. Add Micrococcal Nuclease to each IP preparation, mix by turning the tube several times and incubate at 37°C for 20 minutes with frequent stirring to digest the DNA to approximately 150-900 bp in length.
The ChIP-Seq library preparation was proceeded as follows: (1) The DNA fragments were end-repaired and A-tailed. (2) The DNA fragments with A tail were ligated with sequencing adaptors. (3) The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system（Agilent, USA）and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150, according to the effective library concentration and data amount required

treatment_protocol: The cells overexpressing Tet-on RASG12V were continuously induced with doxycycline for 0, 2, 4, 6, 8, and 10 days to induce senescence.  Crosslinked chromatin complexes were isolated from 1,6-Pr2GalNAz metabolically labeled cells and biotinylated. DNA was then purified using the MiniBEST DNA Fragment Purification Kit.

value: primary fibroblasts cells

value: Immortalized cells by hTERT

value: indece senescent D10,shGATAD2A, shJUN


title: LU_RAS_KD_HAJUN_D10_WT_IP

description:
Library name: Sample46
antibody HA


title: Control 15, DART-Mut-treated

city: Boston

description: Library name: C15-Mut


title: Control 12, DART-Mut-treated

description: Library name: C12-Mut


title: mp-PJI01


title: LU_RAS_KD_HAJUN_D10_AA_IP

description:
Library name: Sample45
antibody HA


title: TEX_Exhaustion, RNA, Day32, rep4

first: Shelley

middle: L.

last: Berger

department: Penn Epigenetics Institute

description: Library name: Cl13_P14_Day32_RNA_Rep4_S16

data_processing:
FASTQ files were aligned using STAR 2.7.1a using mm10 Gencode reference genome.
Read counts of genes were quantified by featureCounts.
Normalized read counts were generated using DESeq2.
Genome tracks were created based on STAR processd bam files using bamCoverage.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count and normalized read count by DESeq2 values for each Sample

source_name: Splenocytes

extract_protocol:
Total RNA (~30-120 ng) was extracted using RNA Clean & Concentrator-5 (ZYMO R1013) following manufacturer's instruction. mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760L) and following manufacturer's instructions.

value: Splenocytes

value: P14 CD8 T cells

value: LCMV clone 13 infection


title: liver, RD5

city: Shanghai

first: Ziyun

last: Wu

state: Shanghai

address: 800 Dongchuan RD

department: Food Science and Engineering

institute: Shanghai Jiao Tong University

description:
Library name: FKRN230065060-1A
35

data_processing:
FASTQ output files were aligned to Mus musculus GRCh39 reference genomes using STAR with a 2-pass procedure. Genes (Aligned.sortedByCoord.out.bam file from STAR outputs) were quantified using RSEM.
Assembly: Mus musculus GRCh39 reference genomes
Supplementary files format and content: tab-delimited text files include gene-id, expected_count, TPM, FPKM for each sample

source_name: liver

growth_protocol: Seven-week-old C57BL/6J male mice (n = 60) underwent a 20-hours fasting period (with free access to water) after a one-week acclimatization feeding. The animals were then divided into eight fiber diet groups, one AIN-93G regular diet (RD) group, and one calorie restriction (CR) group. After switching to the customized diet ad libitum, food and water intake were measured hourly over the next 4 hours (from 18:00 to 22:00).

extract_protocol:
Approximately 10 mg of liver tissue (left lobe) was immersed in 600 μl TRIzol, homogenized thoroughly, snap-frozen in liquid nitrogen, and stored at -80°C for RNA extraction the following day. All samples were ground using a high throughput tissue grinder at 300 g for 30 s (repeated three times). Following centrifugation at 14,000 g at 4°C for 10 min. RNA was extracted using M5 HiPer Universal Plus RNA Mini Kit (Mei5 Biotech, Beijing, China) according to manufacturer instructions. All RNA samples used had a RIN >8.
All RNA samples were sent to Novogene Co., Ltd (Beijing, China) for quality control (Sample QC). After RNA library preparation, cDNA libraries are sequenced on Illumina NovaSeq platforms using a paired-end 150 bp sequencing strategy. Approximately 6 G clean data and a >75% uniquely mapped reads rate for each sample were obtained for each sample. Six biological replicates were included.

treatment_protocol: Over the following 13 days, the CR group was fed the AIN-93G diet but was restricted to eating only during the most active 2-h period (18:00-20:00) of the circadian rhythm, while the other 9 groups were fed ad libitum. Water was provided ad libitum throughout the study. Food intake, water intake, and body weight were measured daily at 18:00. On Day 13 and 14, the same fasting and 4-h intake test protocol as on Day 0 and 1 was repeated. All mice were sacrificed, and hepatectomy was performed.

value: liver

tag: tissue region

value: left lobe

value: AIN-93G regular diet

tag: batch


title: liver, RD3

description:
Library name: FKRN230065058-1A
33

tag: genotype

tag: treatment


title: liver, RD6

description:
Library name: FKRN230065061-1A
36


title: liver, RD4

description:
Library name: FKRN230065059-1A
34


title: LU_RAS_KD_HAJUN_D0_WT_IP

description:
Library name: Sample44
antibody HA

value: shGATAD2A, shJUN


title: Control 11, DART-Mut-treated

description: Library name: C11-Mut

value: Control/non-AD


title: CCI2

description:
Library name: Sample2
Column name in Processed data.txt: CCI2:fpkm

value: CCI


title: Control 10, DART-Mut-treated

description: Library name: C10-Mut


title: LU_RAS_KD_HAJUN_D10_WT_input

description:
Library name: Sample42
none


title: TEX_Exhaustion, RNA, Day32, rep3

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Cl13_P14_Day32_RNA_Rep3_S15


title: Control 8, DART-Mut-treated

description: Library name: C8-Mut


title: LU_RAS_KD_HAJUN_D0_AA_IP

description:
Library name: Sample43
antibody HA


title: liver, RD2

description:
Library name: FKRN230065057-1A
32


title: TEX_Exhaustion, RNA, Day32, rep2

description: Library name: Cl13_P14_Day32_RNA_Rep2_S14


title: liver, RD1

description:
Library name: FKRN230065056-1A
31


title: LU_RAS_KD_SNF5_D10_AA_IP

description:
Library name: Sample47
antibody SNF5


title: TEX_Exhaustion, RNA, Day32, rep1

description: Library name: Cl13_P14_Day32_RNA_Rep1_S13


title: Control 7, DART-Mut-treated

description: Library name: C7-Mut


title: LU_RAS_KD_HAJUN_D10_AA_input

description:
Library name: Sample41
none


title: Control 5, DART-Mut-treated

description: Library name: C5-Mut


title: LU_RAS_KD_HAJUN_D0_WT_input

description:
Library name: Sample40
none


title: liver, IF5

description:
Library name: FKRN230065054-1A
29

value: Inulin Fiber Diet


title: TMEM_Memory, RNA, Day30, rep3

description: Library name: Arm_P14_Day30_RNA_Rep3_S7

value: LCMV Armstrong infection


title: LU_RAS_KD_HAJUN_D0_AA_input

description:
Library name: Sample39
none


title: AD 19, DART-WT-treated

description: Library name: A19-WT

value: Alzheimer's disease

value: Wildtype


title: liver, IF4

description:
Library name: FKRN230065053-1A
28


title: TMEM_Memory, RNA, Day30, rep2

description: Library name: Arm_P14_Day30_RNA_Rep2_S6


title: LU_RAS_KD_MBD2_D10_WT_IP

description:
Library name: Sample38
antibody MBD2


title: TMEM_Memory, RNA, Day30, rep1

description: Library name: Arm_P14_Day30_RNA_Rep1_S5


title: liver, IF2

description:
Library name: FKRN230065051-1A
26


title: LU_RAS_KD_MBD2_D10_AA_IP

description:
Library name: Sample37
antibody MBD2


title: AD 18, DART-WT-treated

description: Library name: A18-WT

value: Dorsolateral prefrontal cortex (Broadmann area 9)


title: AD 17, DART-WT-treated

description: Library name: A17-WT


title: liver, IF3

description:
Library name: FKRN230065052-1A
27


title: TN_Naive, RNA, Day32, rep4

description: Library name: Naive_P14_Day32_RNA_Rep4_S12

value: Naive wild type


title: LU_RAS_KD_FlagGATAD2A_D10_WT_IP

description:
Library name: Sample36
antibody Flag

value: primary fibroblasts cells

value: Immortalized cells by hTERT


title: AD 15, DART-WT-treated

description: Library name: A15-WT


title: TN_Naive, RNA, Day32, rep3

description: Library name: Naive_P14_Day32_RNA_Rep3_S11

value: Splenocytes


title: liver, IFm6

description:
Library name: FKRN230065049-1A
24

value: Inulin Fiber Diet modified


title: LU_RAS_KD_FlagGATAD2A_D10_AA_IP

description:
Library name: Sample35
antibody Flag

value: indece senescent D10,shGATAD2A, shJUN


title: liver, IF6

description:
Library name: FKRN230065055-1A
30

value: liver