|
| Status |
Public on Mar 18, 2016 |
| Title |
RNAseq-ALL-1 |
| Sample type |
SRA |
| |
|
| Source name |
Tumoral biospecimen, pre-B ALL patient
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: acute lymphoblastic leukemia
tissue: Bone marrow
age at diagnosis (years): 10
|
| Treatment protocol |
NA
|
| Growth protocol |
Cells were cultured in RPMI 1640 media supplemented with 10% Fetal Bovine Serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis for all patients using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. The Allprep DNA/RNA Mini kit (Qiagen) was used for all REH samples .Following a DNAse I treatment, total RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) and the Illumina TruSeq Stranded Total RNA kit (relapse samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System or the Illumina HiSeq 2500 System.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Description |
315_T
|
| Data processing |
AB SOLID data: Primary alignment with Lifescope software version 2.1
ILLUMINA data: Primary alignment with STAR
Mark duplicate with PICARD version 1.107
SplitNCigar with GATK version 3.2-2
Read counts using HTSeq version 0.6.1p1 with Ensembl GRCH37 version 75
Genome_build: hg19
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Mar 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Sinnett |
| E-mail(s) |
daniel.sinnett@umontreal.ca
|
| Organization name |
CHU Sainte-Justine
|
| Street address |
3175 Cote-Sainte-Catherine
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3T 1C5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16558 |
| Series (1) |
| GSE79373 |
CLIC5: a novel ETV6 target gene in childhood acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN04566688 |
| SRA |
SRX1640767 |
