|
| Status |
Public on May 01, 2024 |
| Title |
Patid71 |
| Sample type |
SRA |
| |
|
| Source name |
BM/pB
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: BM/pB
cell type: mononuclear leukocytes
treatment: cytotoxic induction therapy with cytarabine/daunorubicin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq Stranded Total with Rebo Zero Gold library preparation kit following manufacturer's protocols.
Tumor derived RNA was subjected to 0.8x SPRI beadcleanup and size selection prior to DNase treatment and ribodepletion prior to using the NEBNext Ultra II Directional kit preparation. The library was constructed for whole transcriptome sequencing (RNA-seq). Paired-end 151-bp reads were generated on the Illumina NovaSeq (Illumina, Inc.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq data were processed using the EnFusion ensemble approach of seven fusion detection algorithms
Transcripts per million (TPM) values were generated from paired-end RNA sequence data using Salmon with bootstrapping set to 100
Assembly: Homo sapiens GRCh38.p12
Supplementary files format and content: Salmon TPM
|
| |
|
| Submission date |
Apr 29, 2024 |
| Last update date |
May 09, 2024 |
| Contact name |
Deedra R Nicolet |
| E-mail(s) |
nicolet.1@osu.edu
|
| Phone |
614-688-9749
|
| Organization name |
The Ohio State University
|
| Department |
CCC
|
| Street address |
1800 Cannon Drive, Rm 1250H
|
| City |
COLUMBUS |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE266099 |
Genomic profiles and survival prognosticators in African-American patients with acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN41112531 |
| SRA |
SRX24391987 |
