|
| Status |
Public on Jan 01, 2020 |
| Title |
pbmc_treated1 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pbmc
treatment: ganetispib for 24hr
|
| Treatment protocol |
cells were treated with either 0.1% DMSO or 500 nM ganetespib for 24 hrs
|
| Growth protocol |
heparinized blood was processed with Histopaque-1077 to isolated PBMCs which were cultured overnight in RPMI1640 with 20% autologous plasma in 60 mm tissue culture dishes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Qiagen Rneasy kit according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adapter sequence or low quality sequence then mapped to mm10
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
DEseq2 Bioconductor package was used for differential expression analysis
|
| |
|
| Submission date |
Apr 20, 2018 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Alex M Jaeger |
| E-mail(s) |
ajaeger@mit.edu
|
| Phone |
5136070067
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Koch Institute
|
| Lab |
Jacks
|
| Street address |
500 Main St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE113465 |
Evaluation of HSP90 inhibitor expsosure on Immune Cell Gene Expression |
|
| Relations |
| BioSample |
SAMN08964267 |
| SRA |
SRX3981594 |
