|
| Status |
Public on Jan 01, 2018 |
| Title |
11225X17 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Loxodonta africana |
| Characteristics |
agent: Irradiated
time point: 5h
|
| 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_2Gy_5h_rep3
6_2Gy5h2
|
| 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 |
SRX3407591 |
| BioSample |
SAMN08045263 |
