|
| Status |
Public on May 01, 2015 |
| Title |
sample5_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: untreated
|
| 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 |
SAMN03366000 |
| SRA |
SRX885725 |
