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Sample GSM1062242

Query DataSets for GSM1062242

Status

Public on Dec 21, 2021

Title

NPM1+/FLT3+_49305

Sample type

SRA

Source name

Bone Marrow

Organism

Homo sapiens

Characteristics

diagnosis: acute myeloid leukemia (AML)
aml type: NPM1+/FLT3+
tissue: Bone Marrow

Growth protocol

none; primary patient sample

Extracted molecule

total RNA

Extraction protocol

RNA extraction were performed using Trizol reagents (Invitrogen).
Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

Sample 10

Data processing

Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters
Read counts per gene were obtained with the HTSeq package with htseq-count
The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.
Genome_build: GRCh37.61; GRCh37.p3
Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale

Submission date

Jan 10, 2013

Last update date

Dec 21, 2021

Contact name

Zeynep Kalender Atak

Organization name

KULeuven

Street address

Herestraat 49

City

Leuven