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Series GSE139914 Query DataSets for GSE139914
Status Public on Dec 09, 2020
Title The genomic underpinnings of oscillatory biomarkers supporting successful memory encoding in humans
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Brain oscillations are remarkable components of brain activity that support memory encoding. However, it remains a major challenge to determine the molecular mechanisms underlining this activity in humans. Here, we used direct intracranial electroencephalography recordings from patients performing free recall tasks of verbal memory encoding in temporal cortex. Using resected tissue transcriptomics from the same patients, we linked gene expression with brain oscillations, identifying genes correlated with oscillatory signatures of memory formation across six frequency bands. Co-expression analysis isolated biomarker-specific modules associated with neuropsychiatric disorders as well as ion channel activity. Using single-nuclei transcriptomic data from resected tissue, we further revealed that biomarker-specific modules are enriched for both excitatory and inhibitory neurons. This unprecedented dataset of patient-specific brain oscillations coupled to genomics unlocks new insights into the genetic mechanisms that support memory encoding. By linking brain expression of these genes to oscillatory patterns, our data help overcome limitations of phenotypic methods to uncover genetic links to memory performance.
Overall design Transcriptomic data obtained from resected human Brodmann Area 38 tissue were integrated with intracranial electroencephalography (iEEG) data from the same subjects to link memory-related oscillations with gene expression in 16 subjects. Matched post-mortem tissues from healthy and epileptic individuals were used for cross-validations. Single-nuclei RNA-sequencing and single-nuclei chromatin accessibility obtained from similar Brodmann Area 38 samples were used to define the cell-type composition of genes and coexpressed gene expression modules associated with memory oscillation. Resected tissues were obtained from living donors.
Contributor(s) Berto S, Fontenot M, Ayhan F, Caglayan E, Douglas C, Konopka G
Citation(s) 33686299
Submission date Nov 04, 2019
Last update date Mar 10, 2021
Contact name Genevieve Konopka
Organization name UT Southwestern Medical Center
Department Neuroscience
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (56)
GSM4148707 Lega_06
GSM4148708 Lega_07
GSM4148709 Lega_09
BioProject PRJNA587524
SRA SRP228565

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Supplementary file Size Download File type/resource
GSE139914_RAW.tar 112.3 Mb (http)(custom) TAR (of H5)
GSE139914_Within_Subject_CPM.txt.gz 5.7 Mb (ftp)(http) TXT
GSE139914_Within_Subject_RawCounts.txt.gz 1.3 Mb (ftp)(http) TXT
GSE139914_Within_Subject_scATACseq_matrix.h5.gz 165.3 Mb (ftp)(http) H5
GSE139914_Within_Subject_snRNAseq_Counts.txt.gz 5.6 Mb (ftp)(http) TXT
GSE139914_Within_Subject_snRNAseq_Counts_NewBatch.txt.gz 57.6 Mb (ftp)(http) TXT
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