NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1616547 Query DataSets for GSM1616547
Status Public on May 01, 2015
Title sample21_IR
Sample type SRA
 
Source name Primary CLL MNCs
Organism Homo sapiens
Characteristics treatment: irradiation
cell type: Primary CLL MNCs
tp53 status: TP53wt
del11q and/or atmmut: no
patient treatment status: previously treated
Treatment protocol CLL cells were irradiated with 5 Gy (IR) or left untreated (NT) and harvested after 24h.
Growth protocol CLL cells were cultured for 24h in RPMI supplemented with 10% human serum.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol reagent.
Small RNA libraries were constructed using the NEBNext Small RNA Library Prep Set for Illumina following the manufacturer's instructions. Nucleic acids of approximately 15-35 nt length were gel purified during library preparation.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description MatureMiRNA_readcounts_DESeq2_normalized.xlsx
ncRNA.excludingMatureMiRNA_readcounts_DESeq2_normalized.xlsx
mRNA_readcounts_DESeq2_normalized.xlsx
Data processing Basecalling was performed with Illumina RTA 1.13.48, CASAVA 1.8.2.
Sequencing reads were trimmed for adaptor sequences with cutadapt v1.2.1.
Sequencing reads were quality artifact filtered with FastX.
Reads of 17-25 nt length were selected for mature miRNA analyses.
Reads ≥15 nt were selected for non-coding RNA and mRNA analyses (excluding mature miRNA).
Reads were aligned using Bowtie with the following configurations: -v -a --best --strata --norc.
Reads were normalized by standardizing read counts by a sample-specific size factor using DESeq2 1.0.19 in R 3.0.1.
Genome_build: For mature miRNA analyses, reads were aligned to miRBase v19 hsa sequences.
Genome_build: For non-coding RNA (excluding mature miRNA sequences) and mRNA analyses, hsa sequences of Ensembl 71, GtRNAdb, Rfam 11.0, piRNA cluster database were used as reference.
Supplementary_files_format_and_content: Excel files containing normalized read counts.
 
Submission date Feb 23, 2015
Last update date May 15, 2019
Contact name Thorsten Zenz
E-mail(s) [email protected]
Organization name German Cancer Research Center (DKFZ)
Department Department of Translational Oncology
Street address Im Neuenheimer Feld 460
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL11154
Series (1)
GSE66186 smRNA sequencing analysis to identify p53-dependent non-coding RNA networks in Chronic Lymphocytic Leukemia
Relations
BioSample SAMN03366028
SRA SRX885759

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

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