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Sample GSM1077483 Query DataSets for GSM1077483
Status Public on Sep 16, 2013
Title RAT_LVCP_E15_2
Sample type SRA
Source name Embryonic (E15) lateral ventricular choroid plexus
Organism Rattus norvegicus
Characteristics age: Embryonic day 15 (E15)
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
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.
SRA SRX225352
BioSample SAMN01911295

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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