|
| Status |
Public on Apr 25, 2018 |
| Title |
total RNA from bone marrow 16 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
disease state: adult mixed phenotype acute leukemia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After extraction of total RNA, we used Ribo-SPIA Technology (Nugen, CA) for cDNA synthesis as per the manufacture’s instruction. Synthesized cDNA library was sequenced by Illumina’s HiSeq 2000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw sequencing data from Illumina platform were converted to fastq files and aligned to the reference genome (hg19) using the Spliced Transcripts Alignment to a Reference (STAR) algorithm.
HTSeq-count was then utilized to generate the raw counts for each gene.
Raw counts were then analyzed by DESeq2 for data processing, normalization and differential expression analysis following standard procedures.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include normalized counts for each sample
|
| |
|
| Submission date |
Apr 24, 2018 |
| Last update date |
Apr 25, 2018 |
| Contact name |
Koichi Takahashi |
| Organization name |
UT MD Anderson Cancer Center
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE113601 |
RNA sequencing analysis of adult mixed phenotype acute leukemia (MPAL) |
|
| Relations |
| BioSample |
SAMN08976049 |
| SRA |
SRX3990350 |
