|
| Status |
Public on Jan 01, 2015 |
| Title |
AML Sample 11 |
| Sample type |
SRA |
| |
|
| Source name |
BM
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Acute Myeloid Leukemia
age: 70
Sex: female
race: White
eln_group: Favorable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from patient samples using the Trizol method
Total RNA (200 ng in 10 uL volume; RIN >4) was treated by Ribo-Zero Gold Subtraction reagents from TruSeq stranded total RNA (Illumina; RS-122-2201) to remove human cytoplasmic and mitochondrial rRNAs and for the subsequent construction of the RNA-seq library according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TRGRG100-V1T-1_S3_L001_STARout
|
| Data processing |
Basecalling with Illumina Casava version 1.8.2
Read demultiplexing done with bcl2fastq version 1.8.4
Adapter and quality trimming reads with CutAdapt version 1.6
Alignment with STAR version 2.4.0b
Quantified and annotated LncRNAs with HTSeq framework version 0.6.1
Raw data transformed into Reads Per Million (RPM) and quantiles normalized prior to statistical analysis; RNA-seq data were not thresholded
Hugo Gene Nomenclature Committee (HGNC) gene symbols were used to cross-reference RNA-seq and Arraystar lncRNAs measures.
Genome_build: hg19
Supplementary_files_format_and_content: RNAseqwithArraystarSymbols.NormalizedMatrix.xls; contains normalized expression data for LncRNAs
|
| |
|
| Submission date |
Nov 25, 2014 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Ayse Selen Yilmaz |
| E-mail(s) |
seleny75@yahoo.com
|
| Organization name |
OSU
|
| Department |
Biomedical Informatics
|
| Lab |
Bioinformatics shared Resource
|
| Street address |
1800 Cannon Drive
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE63646 |
Expression and Prognostic impact of LncRNAs in Acute Myeloid Leukemia |
|
| Relations |
| Reanalyzed by |
GSE122515 |
| BioSample |
SAMN03220457 |
| SRA |
SRX768416 |
