|
| Status |
Public on Aug 09, 2020 |
| Title |
Control 5 |
| Sample type |
SRA |
| |
|
| Source name |
MBH, control
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain/background: Sprague Dawley
gender: Female
age: 28 days
treatment: GFP (control)
tissue: MBH (medial basal hypothalamus)
|
| Treatment protocol |
Stereotaxically injected with EED-overexpressing lentiviral construct or GFP-expressing lentiviral construct at day 21 in MBH.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MBH tissue was removed, flash frozen on dry ice and chromatin prepared for RNA sequencing before sending it to the OHSU Massively Parallel Sequencing Shared Resource for library preparation and sequencing using a HiSeq 2500 instrument. Four samples per lane were sequenced with a target density of 300 million reads per lane using a single-read 100 cycle protocol.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
C5
28-day-old female rat stereotaxically injected with GFP-expressing lentiviral construct at day 21 in MBH.
Processed data file: EED_raw_counts.xlsx
|
| Data processing |
Initial basecalling using Illumina RTA 1.18.64.
Barcode and adapter sequence were removed using Trimmomatic v0.33 ILLUMINACLIP TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:10:34 HEADCROP:13
Alignment using Tophat2 v2.1 to rat rn6.
Splice junction mapping using Tophat2 v. 2.1.
Mapping to Ensembl build 83 using Bioconductor Rsubread package using default parameters except countMultiMappingReads = TRUE, AllowMultiOverlaps = TRUE.
Genome_build: rat rn6 (Rnor_6.0), Ensembl build 83 annotation
Supplementary_files_format_and_content: EED_raw_counts.xlsx: Excel file includes raw counts.
|
| |
|
| Submission date |
Aug 09, 2017 |
| Last update date |
Aug 09, 2020 |
| Contact name |
Hollis Wright |
| E-mail(s) |
wrighth@ohsu.edu
|
| Organization name |
ONPRC/OHSU
|
| Department |
DIvision of Neuroscience
|
| Lab |
Ojeda
|
| Street address |
505 NW 185th Avenue
|
| City |
Beaverton |
| State/province |
OR |
| ZIP/Postal code |
97006-3448 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE102471 |
Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression |
|
| Relations |
| BioSample |
SAMN07488195 |
| SRA |
SRX3083289 |
