Fructose and DHA multitissue RNAseq and RRBS in Meng et al., eBioMedicine, 2016: The RNA-Seq data was deposited to Gene Expression Ominbus (GEO) under accession numbers GSE59918 (control and fructose groups) and GSE 64815 (DHA). RRBS data was deposited to GEO under accession numbers GSE59893 (control and fructose groups) and GSE64816 (DHA).
TBI multitissue RNAseq and RRBS in Meng et al., eBioMedicine, 2017: The RNA-Seq data was deposited to Gene Expression Ominbus (GEO) with accession number GSE64978 (hippocampus) and GSE68207 (leukocytes). RRBS data was deposited to GEO with accession numbers GSE64984 (hippocampus) and GSE79270 and GSE83776 (leukocytes).
TBI hippocampal scRNAseq in Arneson et al., Nature Communications. 2018: The sequence data that support the findings of this study have been deposited in the Gene Expression Omnibus repository, with the series record GSE101901.
BPA multitissue RNAseq and RRBS in Shu et al., Endocrinology, 2019: RNA-seq and RRBS data have been submitted to the Gene Expression Omnibus (GEO) under accession numbers GSE121603 (for RNA-seq) and GSE121604 (for RRBS).
BPA liver RNAseq in Diamante et al., Environmental International, 2020: RNAseq data has been submitted to GEO under accession number GSE155845.
Omega-3 fatty acid DHA multitissue scRNAseq in Zhang et al. BBA – MMD, 2020: The datasets of RNAseq generated during the current study are available in Gene Expression Omnibus with series accession number GSE123896.
PAH scRNAseq in Hong et al., AJRCCM, 2020: http://mergeomics.research.idre.ucla.edu/PVDSingleCell/CellBrowser/
ALS scRNAseq in Liu et al., Neurobiology of Diseases, 2020: http://mergeomics.research.idre.ucla.edu/ALSsingleCell/ALS/; GEO: GSE178693
Supplemental Tables for Bgn study: Bgn_transcriptome_suppl_tables
Nanoparticle liver spheroids scRNAseq in Li et al., Nano Today, 2022: Raw sequencing reads were submitted to GEO under the accession number GSE201500
TBI multitissue multi-time point scRNAseq in Arneson et al. Cellular and Molecular Life Sciences, 2022: GEO accession number for the Drop-seq data is GSE180862.
SCING gene regulatory network code: Littman et al., iScience, 2023: https://github.com/XiaYangLabOrg/SCING
Multitissue scRNAseq for thyroid hormone T4 treatment in TBI in Zhang et al. BBA – MMD, 2024: Raw RNA-seq data used in this study have been deposited in the NCBI GEO data sets GSE247339 and GSE180862.
Adipose tissue scRNAseq in De Siqueira et al., Cell Reports, 2024: scRNA-seq and polysome RNA-seq data have been deposited at GEO: GSE267192 and GSE268057. All original code has been deposited at Zenodo at https://doi.org/10.5281/zenodo.13926724.
IAPP knockout vs wildtype RNAseq 6 wk vs 9wk comparison in Gurlo et al. Physiological Genomics, 2024: RNA-seq data have been deposited within GEO accession No. GSE256432.
Rat olfactory ensheathing cells scRNAseq in Phelps et al., eLife, 2024: Raw scRNA-seq data and expression matrix are available at GEO (accession number GSE215247). The scRNA-seq results also can be viewed interactively at the Single Cell Portal. OEC versus Leftovers: https://singlecell.broadinstitute.org/single_cell/study/SCP1237/leftovers-and-oecs. OEC subclusters: https://singlecell.broadinstitute.org/single_cell/study/SCP1489/oec-subcluster-batch-corrected.
Mouse liver, adipose, hypothalamus, small intestine scRNAseq for fructose diet and high fat high sucrose diet in Chen et al., Cell Reports, 2025: The raw scRNA-seq data fastq and gene expression count matrix were deposited in GEO (GEO: GSE208750). Interactive dataset visualization is available from the single cell portal (https://singlecell.broadinstitute.org/single_cell) under SCP1403 (intestine), SCP1404 (liver), SCP1405 (adipose), SCP1406 (hypothalamus), and SCP1407 (hypothalamus neurons).
Mouse aorta scRNAseq in Cheng et al. 2025: Single cell RNA sequencing data is accessible via GEO GSE208750.