|
Status |
Public on Mar 01, 2020 |
Title |
Hypothalamus [JL511] |
Sample type |
SRA |
|
|
Source name |
hypothalamus
|
Organism |
Rattus norvegicus |
Characteristics |
parent-of-origin: Paternal time: P9 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 |
JL511 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.
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|
|
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 |
SAMN12724012 |
SRA |
SRX6828473 |