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Series GSE111881 Query DataSets for GSE111881
Status Public on Oct 29, 2018
Title Transcriptome analysis of total RNA in human osteosarcoma cell line U2OS before and after inhibition of zinc finger protein ZNF768
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Inhibition of ZNF768 function was achieved by conditional over expression expression of the C-terminal zinc finger of ZNF768 for 12h. For preparation of total RNA cells were resuspended in TRIzol reagent (Life Technologies) at 0.9Mio/ml and snap-frozen. After thawing RNA was extracted from 0.4ml of TriZol lysate using the direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) as described in the manufacturer’s protocol. RNA was assessed for purity by UV-vis spectrometry (Nanodrop) and for integrity by Bioanalyzer (Agilent Bioanalyzer 2100, Agilent, Santa Clara USA)). RNA was of high purity (abs. 260/280 >1.9, abs 269/239>2.1) and integrity (Bioanalyzer RIN>9 ) and thus used for further processing. For production of RNA-seq libraries total RNA was DNAse treated (dsDNAse, Fermentas) and 100 ng of this RNA was processed with a strand-specific protocol (RNA-seq complete kit, NuGEN, San Carlos, USA). In brief the RNA was reverse transcribed to cDNA with a reduced set of hexamer primers, avoiding excessive representation of rRNA in the cDNA. Second strand cDNA synthesis was done in presence of dUTP. After ultrasonic fragmentation of the cDNA and end repair, Illumina-compatible adapter were ligated. Adapters contained uracil in one strand, allowing complete digestion of the second-strand derived DNA. After strand selection the libraries were amplified, assessed for correct insert size on the Agilent Bioanalyser and diluted to 10nM. Barcoded libraries were mixed in equimolar amounts and sequenced on an Illumina HiSeq1500 in single-read mode with a read length of 100 b.
Overall design ZNF768-deltaN
Contributor(s) Rohrmoser M, Kluge M, Yahia Y, Eber-Gruber A, Krebs S, Blum H, Greifenberg AK, Geyer M, Descostes N, Maqbool A, Andrau J, Friedel CC, Eick D
Citation(s) 30476274
Submission date Mar 15, 2018
Last update date Jan 28, 2019
Contact name Caroline Friedel
Organization name Ludwig-Maximilians-Universität München
Department Institut für Informatik
Street address Amalienstr. 17
City München
ZIP/Postal code 80333
Country Germany
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (8)
GSM3043277 U2OS cells ZNF768-DN (replicate 1)
GSM3043278 U2OS cells ZNF768-DN (replicate 2)
GSM3043279 U2OS cells ZNF768-DN (replicate 3)
BioProject PRJNA438476
SRA SRP135775

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Supplementary file Size Download File type/resource
GSE111881_Gencode_v25_U2OS.counts.txt.gz 546.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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