|
| Status |
Public on May 05, 2017 |
| Title |
RNAseq_PMA_THP1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1 cells, + PMA exposure
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
pma exposure: 72 hr PMA exposure
|
| Treatment protocol |
For differentiation of THP-1 cells, non-adherent cells were diluted to 2 x 105 cells/mL and grown overnight, and a final concentration of 100 nM PMA was added the following morning. THP-1 derived macrophages were collected after 72 hr exposure to PMA by aspirating media and any non-adherent cells, and incubating adherent cells with TrypLE (ThermoFisher) for 15 minutes followed by cell wash in phosphate buffer saline (PBS) buffer.
|
| Growth protocol |
THP-1 cells were obtained from ATCC (Lot # 62454382) and grown for multiple passages in T-75 flasks between 2-8 x 105 cells/mL in growth medium containing RPMI-1640 (Corning), 10% fetal bovine serum, and 1% penicillin streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 5 million treated or untreated THP-1 cells were collected and washed with 1x ice cold PBS. RNA was extracted using the Dynabeads mRNA Direct kit according to manufacturer directions. Sequencing libraries were prepared using the Epicenter ScriptSeq V2 kit according to manufacturer supplied protocol. The resulting libraries were quantified by Qubit, mixed in equal concentrations, and assayed by Bioanalyzer prior to sequencing using Illumina HiSeq 2500 technology.
libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PMA THP-1 cells RNA-seq technical replicate 2
|
| Data processing |
All samples were sequenced together on an Illumina HiSeq2500 (paired-end, 100), and sequencing reads trimmed using trim galore v. 0.4.0, prior to downstream sequence alignment and analyses
Trimmed RNA sequencing reads were mapped to gencode v19 transcripts using kallisto. For analysis of differential genes, kallisto outputs were processed using tximport. Genes with less than 2 counts per million were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: Statistical significance was determined using the glmTreat function in edgeR with a fold change cutoff of 2.
|
| |
|
| Submission date |
May 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Van Bortle |
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Michael Snyder
|
| Street address |
3165 Porter Dr
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94043 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE96800 |
Transcription and chromatin profiling in differentiating THP-1 monocytes and THP-1 derived macrophages |
|
| Relations |
| BioSample |
SAMN06891925 |
| SRA |
SRX2785186 |
