|
| Status |
Public on Oct 01, 2015 |
| Title |
Cytosol mRNA-seq 0.5 h Tg 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts, GADD34-/-
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic fibroblast
treatment: 0.5 h Tg
compartment: Cytosol
analysis: mRNA-seq
replicate: 2
|
| Treatment protocol |
Treatment with 1uM thapsigargin
|
| Growth protocol |
Cultured in DMEM + 10% FBS, 37C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pre-treatment with 180 uM cycloheximide for 30s. PBS wash. Release cytosol with digitonin. Extract remaining sample with dodecyl maltoside.
Ribosome profiling: Digest with Mnase (30 min 10 ug/ml, 37C), pellet ribosomes, extract RNA, PNK treat, gel isolation, library generation with NEB Directional Small RNA kit
mRNA-seq: RiboMinus, library prepataion using TruSeq RNA Sample Preparation Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Map reads to transcriptome with Bowtie (no mismatches)
Quantify translation as RPKM
Genome_build: hg19 (longest transcript isoform)
Supplementary_files_format_and_content: Excel spreadsheet indicating RPKM values
|
| |
|
| Submission date |
Jun 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
David Reid |
| Organization name |
Duke University
|
| Department |
Biochemistry
|
| Lab |
Nicchitta
|
| Street address |
436 Nanaline Duke Bldg., Box 3709 DUMC
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE69800 |
Ribosome profiling analysis of GADD34 null cells |
|
| Relations |
| BioSample |
SAMN03770651 |
| SRA |
SRX1056785 |
