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Series GSE267046 Query DataSets for GSE267046
Status Public on Jun 17, 2024
Title Global STARR-seq library profiling of open chromatin regions in livers of mice treated with the nuclear receptor CAR (Nr1i3) agonist ligand TCPOBOP, in livers of control male mice and in livers of control female mice. [G187_global]
Organisms Mus musculus; synthetic construct
Experiment type Other
Summary Massively parallel reporter assays (MPRA) are widely used to discover functional enhancers but have largely been limited to transfected cell models, which are confounded by vector-induced innate immune responses and lack the physiologically relevant cellular and endogenous hormonal context and chromatin environment of complex mammalian tissues. Here, we combine hydrodynamic injection with a modified STARR-seq-based MPRA to determine condition-specific enhancer activity in mouse liver at scale. Strong liver enhancer activity was observed with STARR-seq libraries containing an Albumin minimal promoter but not when using a Super Core promoter or an origin of replication promoter. Analysis of a global STARR-seq library, comprised of ~50,000 genomic sequences released by DNase-I digestion of mouse liver nuclei, identified condition-specific enhancers and revealed strong correlations between liver enhancer activity and the chromatin state of the corresponding endogenous genomic regions.
 
Overall design A global STARR-seq reporter library was prepared by cloning into a STARR-seq vector with a minimal Albumin promoter ~50,000 genomic regions released by limited DNase-I digestion of mouse liver nuclei. The global reporter library was delivered to mouse liver by hydrodynamic tail vein injection (HDI). Three types of Illumina sequencing libraries were prepared and are included in this GEO submission: the original global STARR-seq plasmid libraries used for HDI, global STARR-seq DNA libraries extracted from the transfected livers, and global STARR-seq RNA libraries prepared from STARR-seq reporter RNA extracted from each transfected liver. These libraries were all generated by PCR amplification carried out in parallel and under the same PCR conditions. The STARR-seq plasmid library is the same material used for HDI and indicates the relative abundance of each reporter sequence mapping to the ~50,000 genomic regions (DNase I-hypersensitive (DHS) regions) used for library preparation. The STARR-seq DNA plasmid library was prepared using DNA reporter-specific primers that amplify plasmid DNA extracted from the transfected livers. STARR-seq enhancer activity was calculated by dividing the Illumina sequencing read counts of each RNA reporter (numerator) by that of the corresponding STARR-seq plasmid or DNA library sequence reads (denominator). The STARR-seq RNA libraries were prepared from poly-adenylated RNA extracted from the HDI livers were reverse-transcribed followed by DNase treatment, and then amplified using RNA reporter-specific primers; these RNA libraries represent the self-transcribing activity of each DHS region included in the STARR-seq plasmid library.
 
Contributor(s) Chang T, Waxman DJ
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NIH grant(s)
Grant ID Grant title Affiliation Name
R01 DK121998 Growth Hormone Regulation of Sex Differences in Liver Metabolism BOSTON UNIVERSITY CHARLES RIVER CAMPUS David J Waxman
R01 ES024421 Xenobiotic-responsive hepatic long non-coding RNAs BOSTON UNIVERSITY CHARLES RIVER CAMPUS David J Waxman
Submission date May 08, 2024
Last update date Jun 17, 2024
Contact name David J. Waxman
E-mail(s) djw@bu.edu
Organization name Boston University
Department Department of Biology and Bioinformatics Program
Street address 5 Cummington Mall
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
Samples (15)
GSM8258924 TCPOBOP_1d_Male_STARRTYC6_RNA_replicate1
GSM8258925 TCPOBOP_1d_Male_STARRTYC6_RNA_replicate2
GSM8258926 TCPOBOP_1d_Male_STARRTYC6_RNA_replicate3
This SubSeries is part of SuperSeries:
GSE267205 STARR-seq reporter activity of plasmid libraries delivered to mouse liver by hydrodynamic injection: In vivo MPRA assay for enhancer activity
Relations
BioProject PRJNA1109401

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Supplementary file Size Download File type/resource
GSE267046_G187_global_processed_dataset.xlsx 11.3 Mb (ftp)(http) XLSX
GSE267046_STARR_seq_primer.txt.gz 618 b (ftp)(http) TXT
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