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Sample GSM2835478 Query DataSets for GSM2835478
Status Public on Dec 16, 2017
Title GEO-255
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: female
age (years): 46
response: sensitive
overall survival (days): 170
life status: dead
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 SAMN07843112

Supplementary file Size Download File type/resource
GSM2835478_GEO-255_htseq_counts.txt.gz 83.7 Kb (ftp)(http) TXT
Raw data not provided for this record
Processed data provided as supplementary file
Processed data are available on Series record

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