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Series GSE212159 Query DataSets for GSE212159
Status Public on Nov 23, 2022
Title De novo enhancer function in divergent hominin haplotypes
Organisms Mus musculus; synthetic construct
Experiment type Expression profiling by high throughput sequencing
Summary Identifying functional changes in gene regulatory elements in the human lineage is essential to understanding how humans emerged as a species. We performed genome-wide comparative genomic analysis of humans and great apes to identify 1581 Human Ancestor Quickly-Evolved Regions (HAQERs), which we identify as the fastest-evolved regions of the human genome (hg38). To detect how rapid sequence divergence contributed to divergent gene regulatory functionality in HAQERs, we designed in vivo STARR-seq as a multiplex single-cell assay of enhancer activity in the developing mouse brain. We tested multiple haplotypes from hominins (Human/Neanderthal/Denisova) and non-hominins (Chimpanzee and the inferred Human-Chimpanzee ancestor) for 13 HAQERs to assess their enhancer activity in the developing brain. We found significant differences in enhancer activity between hominins and non-hominins in 8 of these sequences.
Overall design In this assay, STARR-seq plasmids along with an EGFP transfection reporter plasmid are delivered to the developing mouse cerebral cortex via in utero electroporation. Following 18 hours of incubation, mouse brains are harvested and GFP+ cells are isolated via Fluorescent Activated Cell Sorting. Single cell sequencing is then performed to recover gene expression, EGFP transfection reporter plasmid expression, and STARR-seq reporter expression. We performed two independent STARR-seq experiments (V4.2 = E14.5 injection, V4.1 = E15.5 injection)  with the same input library, which we sequenced for input normalization.
Contributor(s) Lowe CB, Mangan RJ
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Submission date Aug 26, 2022
Last update date Nov 25, 2022
Contact name Craig Barrett Lowe
Organization name Duke University School of Medicine
Department Molecular Genetics and Microbiology
Street address 213 Research Dr
City Durham
State/province North Carolina
ZIP/Postal code 27710
Country USA
Platforms (2)
GPL17769 Illumina MiSeq (synthetic construct)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (3)
GSM6510409 Output mouse scSTARR-seq, E15.5 Injection; scRNA-seq
GSM6510410 Output mouse scSTARR-seq, E14.5 Injection; scRNA-seq
GSM6510411 Input library sequencing; RNA-seq
BioProject PRJNA874114

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE212159_RAW.tar 65.0 Mb (http)(custom) TAR (of MTX, TSV)
GSE212159_constructList.txt.gz 10.5 Kb (ftp)(http) TXT
GSE212159_featureCountAndInputNormalization.txt.gz 2.8 Kb (ftp)(http) TXT
GSE212159_haqerOverlaps.txt.gz 25.8 Kb (ftp)(http) TXT
GSE212159_pooledClusterCounts.txt.gz 4.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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