|
| Status |
Public on Nov 23, 2022 |
| Title |
acute myeloid leukemia (AML)_DR04 |
| Sample type |
SRA |
| |
|
| Source name |
leukemia blast cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: leukemia blast cells
disease state: AML
aml status: de novo
fab type: M2
age: 88
Sex: m
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with miRNeasy Kits (NEB).
A total amount of 1µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for lliumina® (NEB, USA) following manufacturer 's recommendations.
Transcriptomic RNA-sequencing of poylA enrichmed molecules
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from Ensembl genome browser website. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package.
The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts, FPKMs
|
| |
|
| Submission date |
Sep 24, 2021 |
| Last update date |
Nov 23, 2022 |
| Contact name |
Christian Rohde |
| E-mail(s) |
[email protected]
|
| Organization name |
Heidelberg University
|
| Lab |
Molecular Hematology and Oncology
|
| Street address |
Im Neuenheimer Feld 410
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE184722 |
The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia [mRNA_primary_samples] |
| GSE184728 |
The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN21593338 |
| SRA |
SRX12326395 |
