|
Status |
Public on Jan 01, 2018 |
Title |
11225X8 |
Sample type |
SRA |
|
|
Source name |
Blood
|
Organism |
Loxodonta africana |
Characteristics |
agent: Untreated time point: 24h
|
Extracted molecule |
total RNA |
Extraction protocol |
PureLink RNA mini kit, RNeasy MinElute Cleanup Kit Illumina TruSeq Stranded RNA Kit with Ribo Zero Gold
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Af_Elephant_NT_24h_rep3 4_NT24h2
|
Data processing |
Reference Creation: p53 retrogenes not present in Ensembl annotation were added manually. USeq_8.8.9beta MakeTranscriptome was to create splices. Set max splices to 10K. Created index using novoindex 2.08.03. Reads were aligned to the LoxAfr3 transcriptome index using pysano Spliced alignments were converted back to genomic space using USeq's SamTranscriptomeParser Normalized coverage tracks were created using USeq's Sam2USeq and USeq2UCSCExe application Differential expression was determined using USeq's DefinedRegionDifferentialSeq application Genome_build: loxAfr3 Supplementary_files_format_and_content: TXT, Differential expression
|
|
|
Submission date |
Nov 19, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Chris Gregg |
E-mail(s) |
chris.gregg@neuro.utah.edu
|
Organization name |
University of Utah
|
Department |
Neurobiology and Anatomy
|
Lab |
Chris Gregg Lab
|
Street address |
20 South 2030 East
|
City |
Salt Lake City |
State/province |
UT |
ZIP/Postal code |
84112 |
Country |
USA |
|
|
Platform ID |
GPL24284 |
Series (1) |
GSE107117 |
DNA Damage Response in Elephant Cells |
|
Relations |
SRA |
SRX3407584 |
BioSample |
SAMN08045330 |