|
| Status |
Public on Dec 16, 2017 |
| Title |
GEO-248 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow or peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Acute Myeloid Leukemia
tissue: bone marrow or peripheral blood mononuclear cells
gender: male
age (years): 47
response: sensitive
overall survival (days): 1992
life status: alive
predicted ps29mrc group: predicted sensitive
runx1-runx1t1_fusion: No
runx1_mutation: No
|
| Treatment protocol |
Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mononuclear cells from peripheral blood (PB) or bone marrow (BM) were enriched by Ficoll gradient centrifugation.
RNAseq libraries were prepared using the Sense mRNA Seq Library Prep Kit V2 (Lexogen, n=238) and the TruSeq RNA Library Preparation V2 Kit (Illumina, n=12, GEO-1 to 12) following the manufractur´s instruction. Between 500-1000 ng total RNA (RNA integrity number [RIN] >7) were used as input material. All sequencing was paired end and performed using polyadenylated-selected and, in case of the Lexogen libraries, stranded RNA sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
STAR v2.5.1b used for sequence alignment with hg19 genome build
STAR v2.5.1b used for second pass alignment with hg19 genome build along with pooled splice junciton information
Picard v1.136.0 used for merging properly paired and discordant paired reads
HTSeq Count v0.6.0 used for gene counts
All gene expression variables were scaled to a mean value of 0 and variance equal to 1
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including gene counts
Supplementary_files_format_and_content: Raw data: German law does not allow raw data to be submitted for public access
|
| |
|
| Submission date |
Oct 27, 2017 |
| Last update date |
Mar 21, 2018 |
| Contact name |
Tobias Herold |
| E-mail(s) |
tobias.herold@med.uni-muenchen.de
|
| Organization name |
University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)
|
| Department |
Department of Internal Medicine III
|
| Street address |
Marchioninistr. 15
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE106291 |
A 29-Gene and Cytogenetic Score for the Prediction of Resistance to Induction Treatment in Acute Myeloid Leukemia |
|
| Relations |
| BioSample |
SAMN07843119 |
