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Sample GSM2129691 Query DataSets for GSM2129691
Status Public on Jun 20, 2017
Title Primary diagnosis 053-010
Sample type SRA
 
Source name Density centrifuged bone marrow
Organism Homo sapiens
Characteristics sample type: Primary diagnosis
chemotherapy response: NA
npm1 mutation: No
flt-itd3: No
molecular risk group: NA
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the Qiagen miRNeasy kit and 500 ng was subject to library preparation using the Illumina Truseq small RNA kit. Molecules with the size of 40-200 nt were purified from a gel before sequencing.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiScanSQ
 
Description Human_AML_SnoRNA_Expression
Data processing Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
CASAVA BclToFastq was used to export fastq files
Illumina adapter sequences were removed using Cutadapt
Reads were mapped using Bowtie2 and further processed to BAM format using samtools
Regions with coverage were called from mapped reads using the bedtools genomeCoverageBed algorithm
Sequences from the extracted regions were compiled to a consensus sequence which was subject to BLAST against a custom small RNA database. Regions with a BLAST hit were further aggregated calculating the mean of the average coverages and further normalized to the total number of mapped reads by the identified hit name.
Genome_build: hg19 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Each processed file contains a column for the identified small nucleolar RNA (snoRNA) elements and the normalized average coverage for the respective sample.
 
Submission date Apr 21, 2016
Last update date May 15, 2019
Contact name Christian Rohde
E-mail(s) christian.rohde@uni-heidelberg.de
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 GPL15456
Series (2)
GSE80523 Expression profile of small nucleolar RNA (snoRNA) in acute myeloid leukemia.
GSE80602 AML1-ETO induces leukemia via C/D box snoRNA/RNPs.
Relations
BioSample SAMN04881243
SRA SRX1716950

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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