|
| Status |
Public on Jan 12, 2020 |
| Title |
K562-pLV-miR-143-3_IgG |
| Sample type |
SRA |
| |
|
| Source name |
K562-pLV-miR-143_IgG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: multipotential, hematopoietic malignant cells
viral infection: pLV-miR-143 (Biosettia, mir-p114)
|
| Treatment protocol |
Cells were infected with pLV-miR-143 or control (Biosettia) PEG-concentrated viral particles followed by Puromycin selection. Purity of transduced cells was calculated using flow cytometry for expression of fluorescent markers. RNA Immunoprecipitation was performed according to the manufacturer's instructions (Sigma-Aldrich, RIP-12RXN)
|
| Growth protocol |
Cells were grown in RPMI-1640 medium without phenolred, 10% FBS, 1% Pen/Strep and 1µg/ml Puromycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol method according to the manufacturer's instructions
1µg of total RNA was subjected rRNA removal with Ribo-Zero Gold rRNA Removal Kit (Epicentre, RZG1224). RNA was enriched using random primer and reverse transcribed to double stranded cDNA (TargetAmp™-Nano Labeling Kit, Epicentre, TAN091096). The cDNA was end repaired, adenylated and ligated with PCR-indexes prior to 12 cycles of PCR. Sequencing was performed using 15pM hybridisation to a 2-100 paired end flow cell.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
processed data file:
143 IgG.txt
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence
reads were aligned to hg38 using TopHat
to assemlbe transcriptomes and analyze data from RNA-Seq we used Cufflinks suite (Trapnell, Rinn & Pachter)
Genome_build: hg38
Supplementary_files_format_and_content: text files include av. FPKM values for triplicates
|
| |
|
| Submission date |
Jan 12, 2017 |
| Last update date |
Jan 12, 2020 |
| Contact name |
Gerhard Behre |
| Organization name |
Leipzig University Hospital
|
| Department |
Division of Hematology and Oncology
|
| Street address |
Johannisallee 32A
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE93549 |
Identification of miR-143 mRNA-targets by AGO-RIP in the myeloid cell line K562 |
|
| Relations |
| BioSample |
SAMN06220152 |
| SRA |
SRX2488074 |
