|
| Status |
Public on Jun 29, 2017 |
| Title |
SJTALL022444_D1_COG study 0434 |
| Sample type |
SRA |
| |
|
| Source name |
COG study 0434
|
| 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 |
Illumina HiSeq 2000 |
| |
|
| Description |
181
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 |
| E-mail(s) |
[email protected]
|
| 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 |
GPL11154 |
| Series (2) |
| GSE71359 |
RNA sequencing of T-ALL (COG study) |
| GSE77741 |
Analyses of T-ALL (COG study) |
|
| Relations |
| BioSample |
SAMN03938695 |
| SRA |
SRX1118852 |
