GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1568712 Query DataSets for GSM1568712
Status Public on Aug 20, 2015
Title hDIS3_PIN_RNB_mut_RNA-seq
Sample type SRA
Source name HEK293 Flip-In T-Rex cell line
Organism Homo sapiens
Characteristics variant: DIS3D146N D487N + shRNA
Treatment protocol Expression of exogenous genes was induced by addition of doxycycline at a final concentration of 100ng/ml.
Growth protocol HEK293 Flp-In T-Rex cell lines were grown in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum (FBS; Gibco) and penicillin/streptomycin (Sigma-Aldrich) at 37°C in a 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA was isolated using TRI-Reagent (Sigma-Aldrich)
Total RNA was treated with Turbo-DNAse (Life Technologies), and then rRNA was removed from the samples using Ribo-Zero Kit (Epicentre), according to the manufacturer's protocols. As a control of experiment performance, external RNA (ERCC RNA Spike-In Mix; Life Technologies) was added to the samples. RNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Data processing Basecalls and demultiplexing were performed using CASAVA version 1.8.2
Adapters and reads shorter than 12 nt. and with quality lower than 20 were removed by cutadapt-1.2.1
Reads were mapped using RUMv2.05_05. The program requires left and right reads to be the same length, so reads has been striped adequately. The information about known transcripts was supplied to the program. It contained i) Gencode v18 transcript data ii) supplemented to Gencode v18 data tRNA coordinates from tRNA scan program iii) previously published PROMPT data which is a set 3kB upstream regions from the selected 2471 genes iv) snoRNA precursors defined by us for intronic snoRNA as regions from the end of the snoRNA to the beginning of the exon.
Only uniquely mapped reads have been counted.
New transcripts were assembled from deeply sequenced libraries from PIN RNB double mutant using Cufflinks v 2.1.1. Reads from three replicates were assembled separately. We applied all default parameters with exception of '--max-bundle-length' increased to 10^7 and '--max-bundle-frags' increased to 10^7. We used cuffmerge from cufflinks package to merge assemblies from the replicates.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each sample replicate; bedgraph files were generated using RUMv2.05_05; gtf file was generated using cuffmerge from Cufflinks v 2.1.1.
Submission date Dec 18, 2014
Last update date May 15, 2019
Contact name Andrzej Dziembowski
Phone +48 22 5922033
Organization name Institute of Biochemistry and Biophysics Polish Academy of Sciences
Lab Laboratory of RNA Biology and Functional Genomics
Street address Pawinskiego 5A
City Warszawa
ZIP/Postal code 02-106
Country Poland
Platform ID GPL18460
Series (1)
GSE64332 Human DIS3 shapes the RNA polymerase II transcriptome degrading variety of unwanted transcripts.
BioSample SAMN03268750
SRA SRX817374

Supplementary file Size Download File type/resource
GSM1568712_PIN_RNB_1.tsv.gz 3.2 Mb (ftp)(http) TSV
GSM1568712_PIN_RNB_2.tsv.gz 3.2 Mb (ftp)(http) TSV
GSM1568712_PIN_RNB_3.tsv.gz 3.2 Mb (ftp)(http) TSV
GSM1568712_PIN_RNBdeep_1.tsv.gz 3.3 Mb (ftp)(http) TSV
GSM1568712_PIN_RNBdeep_2.tsv.gz 3.3 Mb (ftp)(http) TSV
GSM1568712_PIN_RNBdeep_3.tsv.gz 3.3 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap