|
| Status |
Public on Sep 16, 2013 |
| Title |
RAT_LVCP_Adult_3 |
| Sample type |
SRA |
| |
|
| Source name |
Adult lateral ventricular choroid plexus
|
| Organism |
Rattus norvegicus |
| Characteristics |
age: Adult
strain: Sprague-Dawley
|
| Treatment protocol |
No treatments, control animals only were used in the study.
|
| Growth protocol |
Both left and right lateral ventricular choroid plexuses were carefully dissected out as previously described (Liddelow et al., 2012) and placed in fresh ice-cold RNase-free PBS. Plexuses were pooled (n = 10 animals) and centrifuged at 1000rpm for 30 seconds and excess PBS removed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from pools of E15 and adult lateral ventricular choroid plexus (n = 3 for both ages) using the RNeasy Mini Kit, Qiashredder columns and gDNA removal columns (Qiagen, Valencia, CA, USA) according to standard supplier protocol. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina 1.5 phred score encoding used for basecalls
Trimmed reads mapped with Bowtie (v. 0.12.7) and mappen to Ensembl rat genome (release 61)
Number of reads mapped to nuclear genes determined with HTSeq (v. 0.4.7p4)
Differential expression (between embryonic and adult samples) detected using Bioconductor edgeR package (v. 2.4.0), with common dispersion used to estimate vairance between samples.
Genome_build: Ensembl (Hubbard et al., 2009) rat genome, release 61
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample
|
| |
|
| Submission date |
Feb 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shane A Liddelow |
| E-mail(s) |
shaneal@unimelb.edu.au
|
| Organization name |
The University of Melbourne
|
| Department |
Pharmacology
|
| Street address |
Level 8 Medical Building, Grattan Street
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE44072 |
Genome-wide analysis and comparison of E15 and adult rat lateral ventricular choroid plexus epithelial cells. |
|
| Relations |
| SRA |
SRX225356 |
| BioSample |
SAMN01911299 |
