|
| Status |
Public on Jul 01, 2012 |
| Title |
THP1_smallRNAseq |
| 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 |
Small RNA was extracted from 3x106 THP1 cells by using QIAGEN miRNeasy Mini Kit. Three different methods were used for the library construction (as in Jayaprakash, A. et al, Nucleic Acid Res, 2011):
"Illumina" protocol: Illumina TruSeq small RNA Sample Preparation Kit was used following manufacturer's instructions.
"Hannon" protocol: Adaptors containing the required sequences were ligated to each end, and then reverse transcribed and PCR amplified.
"Barcode" protocol: Pooled adaptors (to overcome ligation bias) containing the required sequences were ligated to each end, and then reverse transcribed and PCR amplified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
The 3' linker was identified and stripped out of the raw reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes read counts for each sequence of the three protocols used
|
| |
|
| Submission date |
May 04, 2012 |
| Last update date |
Jun 11, 2013 |
| 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) |
| GSE37770 |
smallRNA profiling of THP1 cell line |
| GSE37771 |
miRNA sensor and decoy libraries permit high-throughput assessment of miRNA activity and function |
|
| Relations |
| BioSample |
SAMN02197533 |
