GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1832985 Query DataSets for GSM1832985
Status Public on Jun 29, 2017
Title rna_117_run193_001_COG study 0446
Sample type SRA
Source name COG study 0446
Organism Homo sapiens
Characteristics diagnosis: Newly diagnosed T-ALL patient
tissue: bone marrow
Treatment protocol COG study 9404/0434 (diagnostic samples)
Growth protocol Derived from bone marrow in newly diagnosed T-ALL patients
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols (14 samples; Truseq RNA Library Preparation kit ) or standard Ion Proton protocols (3 samples; Xpress Plus Fragment Library kit), respectively.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description 117
RNA sequencing data from primary T-ALL samples at diagnosis
Data processing Illumina mRNA-seq data (fastq files) were mapped using StrongArm pipeline
genomic rearrangements were identified using CICERO, a novel algorithm identifying fusion transcripts (Illumina data)
Ion Proton data (BAM files) were aligned with STAR (bases calling: IonTorrent Base Caller)
aligned data were analyzed using customized scripts written in R (for Ion Proton data)
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing results of identified fusion transcripts
Submission date Jul 27, 2015
Last update date May 15, 2019
Contact name Ksenia Matlawska
Phone 5052726177
Organization name University of New Mexico
Department Pediatrics
Lab BRF 140
Street address 915 Camino de Salud
City Albuquerque
State/province NM
ZIP/Postal code 87111
Country USA
Platform ID GPL17303
Series (2)
GSE71359 RNA sequencing of T-ALL (COG study)
GSE77741 Analyses of T-ALL (COG study)
BioSample SAMN03938685
SRA SRX1118841

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

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