|
| Status |
Public on Apr 12, 2023 |
| Title |
RNA-Seq of AML patient (UD5), onset phase, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
phase: onset
disease state: AML
tissue: bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cryopreserved bone marrow (BM) mononuclear cells using QIAGEN’s AllPrep DNA/RNA kit.
RNAseq libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ud5_tum_rep1
|
| Data processing |
DNA from each of three pairs of matched AMLs was sequenced on the GridION X5 instrument with a run-time of 48h by using five or six individual R9.4 flow
The reads generated by each run were base-called using Guppy v2.0.2
The and quality assessment was performed with FastQC
To perform counts of transcripts from paired-end reads we used Salmon
DESeq2 was used to perform counts normalization and the statistical analysis
Assembly: hg19
Supplementary files format and content: Processed data files contain genes on each row and counts for each sample in the column
|
| |
|
| Submission date |
Sep 19, 2022 |
| Last update date |
Apr 12, 2023 |
| Contact name |
Gianluca Mattei |
| E-mail(s) |
gianluca.mattei@unifi.it
|
| Organization name |
Università degli Studi di Firenze
|
| Street address |
Via di S. Marta, 3
|
| City |
Firenze |
| State/province |
FI |
| ZIP/Postal code |
50139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE213684 |
High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias.[RNA-Seq] |
| GSE213686 |
High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias. |
|
| Relations |
| BioSample |
SAMN30822151 |
| SRA |
SRX17543808 |
