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Sample GSM4278223 Query DataSets for GSM4278223
Status Public on Jan 31, 2020
Title SLX.14773.A011
Sample type SRA
 
Source name Drosophila Melanogaster Elav x 51D whole head homogenate treated with Normal Brain Homogenate, harvested at 30 days of age
Organism Drosophila melanogaster
Characteristics tissue: Whole head homogenate
fly line: Elav x 51D
age in days: 30
treatment: Normal Brain Homogenate
Treatment protocol Drosophila at were Drosophila at the larval stage of development were exposed to brain homogenates of cerebral cortex tissue from confirmed scrapie-positive or known scrapie-negative sheep. After hatching, Drosophila were transferred to inoculum-free tubes and allowed to develop normally. At 5 days and 30/40 days post hatching, the flies were euthanized and then decapitated for RNA extraction
Extracted molecule total RNA
Extraction protocol 15 fly heads was homogenised by manual grinding in an eppendorf tube with 50μl Trizol (Cat No. 15596-018; Invitrogen). A further 50μl of Trizol were mixed with the homogenate, which was then microfuged at 16,160 x g for 10 minutes and the supernatant transferred to RNAse-free tubes before adding a further 50μl Trizol and incubated for 5 minutes. RNA was isolated by conventional chloroform:isoamylalcohol:isopropanol extraction followed by ethanol precipitation. Air-dried RNA pellets were treated with DNAse 1 (Cat No. EN0521; Thermo Scientific) at 37 ̊C for 60 minutes, with the reaction halted by the addition of EDTA and incubation at 65 ̊C for 10 minutes. RNA samples were then subjected to the Qiagen RNeasy RNA Cleanup protocol according to the manufacturers’ instructions. The RNA samples were eventually eluted from RNeasy mini-spin columns, ethanol precipitated, re-suspended in RNAse-free water and stored at -80 ̊C.
A library of mRNA was prepared from 200 ng of total RNA, extracted as described above and that had been originally pooled from 15 fly heads from each experimental condition, using the Illumina TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description RNA from Drosophila Melanogaster Elav x 51D whole head homogenate treated with Normal Brain Homogenate, harvested at 30 days of age
Data processing Fastq reads were mapped to Drosophila Genome (built BDGP6) using Tophat V2.0.11
htseq-count 0.6.1p1 was used to generate gene level counts based on Ensembl V77 GTF
Differential gene expression was performed using edgeR
Genome_build: BDGP6
Supplementary_files_format_and_content: tab-delimited text containing raw gene-level count for each sample
 
Submission date Jan 21, 2020
Last update date Jan 31, 2020
Contact name Brian Yee Hong Lam
E-mail(s) yhbl2@cam.ac.uk
Organization name University of Cambridge
Department Metabolic Research Laboratories
Street address Box 289 Addenbookes Hospital, Hills Road
City Cambridge
ZIP/Postal code CB2 0QQ
Country United Kingdom
 
Platform ID GPL21306
Series (1)
GSE144028 Transcriptional signature of prion-induced neurotoxicity in a Drosophila model of transmissible mammalian prion disease
Relations
BioSample SAMN13898224
SRA SRX7587196

Supplementary file Size Download File type/resource
GSM4278223_SLX-14773.A011.count.txt.gz 64.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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