|
| Status |
Public on Jul 01, 2012 |
| Title |
THP1_mRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
THP1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP1
cell type: human monocytic leukemia
|
| Treatment protocol |
None
|
| Growth protocol |
Cells were cultured in RPMI 1640 media + 10% FBS + 2mM L-Glutamine + Pen/Strept + 0.05 mM betamercaptoethanol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 3x106 THP1 cells following Qiazol protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequence reads were filtered for low quality and mapped to the hg19 genome.
Supplementary_files_format_and_content: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following the protocol from Mortazavi et al, Nat Methods, 2008. Briefly, all reads falling in the exons of a given gene were counted and normalized by the length of the gene and the total reads of the run.
|
| |
|
| Submission date |
May 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Brown |
| E-mail(s) |
bdblab@gmail.com
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
1470 Madison Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE37769 |
mRNA profiling of THP1 cell line |
| GSE37771 |
miRNA sensor and decoy libraries permit high-throughput assessment of miRNA activity and function |
|
| Relations |
| SRA |
SRX146004 |
| BioSample |
SAMN00990957 |
