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Status |
Public on Dec 21, 2021 |
Title |
NPM1+/FLT3+_48792 |
Sample type |
SRA |
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Source name |
Bone Marrow
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Organism |
Homo sapiens |
Characteristics |
diagnosis: acute myeloid leukemia (AML) aml type: NPM1+/FLT3+ tissue: Bone Marrow
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Growth protocol |
none; primary patient sample
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
Sample 7
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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
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Submission date |
Jan 10, 2013 |
Last update date |
Dec 21, 2021 |
Contact name |
Zeynep Kalender Atak |
Organization name |
KULeuven
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Street address |
Herestraat 49
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City |
Leuven |
ZIP/Postal code |
3001 |
Country |
Belgium |
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Platform ID |
GPL11154 |
Series (1) |
GSE43417 |
Molecular characterization of t(2;14)(q22;q32) and t(6;14)(q25;q32) translocations in mixed myeloid/T lymphoid leukemia patients. |
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Relations |
SRA |
SRX216193 |
BioSample |
SAMN01885430 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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