|
| Status |
Public on Feb 24, 2015 |
| Title |
Heat Stress Sample 5 43oC |
| Sample type |
SRA |
| |
|
| Source name |
LMH Chicken Hepatocellular Carcinoma Cell Line
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: LMH Chicken Hepatocellular Carcinoma
treatment: heat stressed at 43oC
|
| Treatment protocol |
Cells were grown for 2.5 hours at either control (37oC) or heat stress (43oC) temperatures.
|
| Growth protocol |
LMH cells were grown according to the recommendations of ATCC.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were removed from the flask by trypsin digestions and collected by centrifugation at either control or heat stress temperatures. RNA was isolated using the Qiagen mini-prep protocol.
Libraries were constructed using the Illumina RNA-seq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Established cell line from a liver carcinoma in a male white leghorn chicken.
|
| Data processing |
CASAVA
Erange for RNA-SEQ alignment and qualitation
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Feb. 2004 (galGal2) assembly
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Feb 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Carl J Schmidt |
| Organization name |
University of Delaware
|
| Department |
Dept. of Animal and Food Sciences
|
| Street address |
531 South College Ave
|
| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
| |
|
| Platform ID |
GPL10223 |
| Series (1) |
| GSE55321 |
Transcriptome response to heat stress in the chicken hepatocellular carcinoma cell line |
|
| Relations |
| BioSample |
SAMN02664647 |
| SRA |
SRX475868 |
