GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1033546 Query DataSets for GSM1033546
Status Public on Dec 07, 2012
Title CMLPh-008T
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 (
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
Phone 0039-02-64488032
Fax 0039-02-6448-8260
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)
SRA SRX204127
BioSample SAMN01805353

Supplementary file Size Download File type/resource
GSM1033546_Gene_Expression_CMLPh-008T.txt.gz 390.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap