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Sample GSM4073307 Query DataSets for GSM4073307
Status Public on Mar 01, 2020
Title Hypothalamus [JL405]
Sample type SRA
 
Source name hypothalamus
Organism Rattus norvegicus
Characteristics parent-of-origin: Paternal
time: P2
genotype/variation: Deletion
Sex: Female
tissue: Hypothalamus
Extracted molecule genomic DNA
Extraction protocol WGBS: Illumina TruSeq DNA Methylation Kit (Illumina EGMK81312).
RNA-seq: NEB NEBNext rRNA Depletion Kit (NEB E6310L) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB E7420S).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Description JL405
processed data file: DMRs.xlsx
processed data file: paternal_background_smoothed_methylation.txt
Data processing WGBS: CpG_me, DMRichR
RNA-seq: htstream, STAR
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: hypothalamus_counts.txt: Gene feature counts output from STAR aligner for each hypothalamus sample.
Supplementary_files_format_and_content: cortex_counts.txt: Gene feature counts output from STAR aligner for each cortex sample.
Supplementary_files_format_and_content: DMRs.xlsx: DMRs for each pair-wise group comparison output from DMRichR.
Supplementary_files_format_and_content: maternal_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for all maternal samples.
Supplementary_files_format_and_content: paternal_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for all paternal samples.
Supplementary_files_format_and_content: control_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for maternal and paternal wild-tpe samples.
 
Submission date Sep 10, 2019
Last update date Mar 01, 2020
Contact name Simon Jesse Lopez
E-mail(s) sjlop@ucdavis.edu
Phone 5307547840
Organization name UC Davis
Department MMI
Lab LaSalle
Street address One Shields Ave
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL24688
Series (1)
GSE137217 Imprinting effects of UBE3A loss on synaptic gene networks and Wnt signaling pathways
Relations
BioSample SAMN12723987
SRA SRX6828458

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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