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Sample GSM1899799 Query DataSets for GSM1899799
Status Public on Oct 01, 2015
Title Rtf1_KD_rep2
Sample type SRA
Source name adenocarcinoma
Organism Homo sapiens
Characteristics cell line: HeLa cells
genotype: Rtf1 knockdown
Treatment protocol HeLa cells were infected with recombinant lentivirus expressing no shRNA or expressing one of functionally validated shRNAs and selected in the presence of 5 µg/ml Blasticidin for pLenti6-based vectors or 1 µg/ml Puromycin for pRSI9-based vectors.
Growth protocol DMEM+10%FCS
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared at 4 or 7 days post-infection using the AGPC method.
Following the removal of rRNA using the RiboMinus Eukaryote Kit (Life Technologies), libraries were constructed using the Ion Total RNA-Seq Kit (Life Technologies).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description Rtf1 knockdown: replicate 2
Data processing Basecalling and trimming of adaptor sequence were performed using Torrent Suite Software.
Sequenced reads were mapped to the human genome GRch37.p9 and reads per kilobase of transcript per million reads mapped (RPKMs) were calculated using CLC Genomics Workbench 6.5.1 with default settings.
Genome_build: GRch37.p9
Supplementary_files_format_and_content: an Excel file including RPKM values for all the samples
Submission date Sep 30, 2015
Last update date May 15, 2019
Contact name Yuki Yamaguchi
Organization name Tokyo Institute of Technology
Department Life Science and Technology
Street address 4259 Nagatsuta
City Yokohama
ZIP/Postal code 226-8501
Country Japan
Platform ID GPL17303
Series (1)
GSE73632 Comparative analysis of Rtf1- and PAF1C-regulated genes
BioSample SAMN04123927
SRA SRX1297545

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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