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Sample GSM2454482 Query DataSets for GSM2454482
Status Public on Jan 12, 2020
Title K562-pLV-control-3_IgG
Sample type SRA
 
Source name K562-pLV-control_IgG
Organism Homo sapiens
Characteristics cell line: K562
cell type: multipotential, hematopoietic malignant cells
viral infection: pLV-control (Biosettia, mir-p000)
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:
control 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 SAMN06220158
SRA SRX2488067

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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