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Sample GSM1033545 Query DataSets for GSM1033545
Status Public on Dec 07, 2012
Title CMLPh-007T
Sample type SRA
 
Source name Atypical Chronic Myeloid Leukemia cells
Organism Homo sapiens
Characteristics genotype: wild type
Treatment protocol Leukemic cells were obtained by separation on a Ficoll-Paque Plus gradient (GE Healthcare, UK). The phenotype was evaluated by FACS analysis and myeloid cells (CD33, CD13, CD117) were >80% of total cells.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with TRIzol® (Invitrogen, Life technology, Grand Island, NY, USA) using the standard protocol.
2ug total RNA was processed according to Illumina TruSeqTM RNA Sample Preparation Kit (FC-122-1001) protocol modified for the time of fragmentation: mRNA was shared for 1 minute at 94°C and, after the ligation of the adapters, fragments of 400-500bp were selected on 2% agarose gel
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Data processing Image processing and basecall were performed using the Illumina Real Time Analysis Software RTA v1.9.35. Qseq files were deindexed and converted in the Sanger-FastQ file format using in-house scripts.
FastQ sequences were aligned to the human genome database (NCBI36/hg18) by using TopHat 1 vs 1.2.0 using default parameters and the gene and splice junctions models supplied by the Human Ensembl GTF annotation file vs54 (Homo_Sapiens.NCBI36.54.GTF) downloaded from the Ensembl FTP server (ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/).
The quantitative gene expression profile was estimated by SAMMate vs.2.6.1 by using the Human Ensembl GTF annotation file vs54 and the default parameters
To focus on the gene expression profile of known coding transcripts, a dataset of 20,907 protein-coding Ensembl Genes was selected from the whole transcriptome matrix of FPKM expression values for 36,655 unique Ensembl Gene obtained by SAMMate
A splice junction map for SETBP1-mutated and non-mutated cases was inferred by TopHat
Genome_build: Human genome database (NCBI36/hg18)
Supplementary_files_format_and_content: Tab-delimited text files include the chromosome, the Gene Name, the Ensembl Gene ID, Biotype, sum exon length of the gene, the gene reads counts and the normalized FPKM measurements of each protein_coding biotype for each sample generated by SAMMate using the Human GTF annotation file (vs54) and default parameters
 
Submission date Nov 08, 2012
Last update date May 15, 2019
Contact name Roberta Spinelli
E-mail(s) roberta.spinelli@unimib.it
Phone 0039-02-64488032
Fax 0039-02-6448-8260
URL http://www.dimep.medicina.unimib.it/personale_175.php?docente_id=32
Organization name University of Milano Bicocca
Department Department of Health Science
Lab Molecular Oncology Laboratory
Street address Via Cadore 48
City Monza
State/province MB
ZIP/Postal code 20900
Country Italy
 
Platform ID GPL10999
Series (1)
GSE42146 RECURRENT SETBP1 MUTATIONS IN ATYPICAL CHRONIC MYELOID LEUKEMIA
Relations
SRA SRX204126
BioSample SAMN01805352

Supplementary file Size Download File type/resource
GSM1033545_Gene_Expression_CMLPh-007T.txt.gz 392.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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