|
| Status |
Public on Mar 15, 2021 |
| Title |
15H013 |
| Sample type |
SRA |
| |
|
| Source name |
BCLQ (http://bclq.org)
|
| Organism |
Homo sapiens |
| Characteristics |
expansion: RNA Extraction from 2 million blasts directly obtained from BCLQ
blast percentage at extraction: 90
tissue of origin at extraction: Peripheral blood
cell type: Acute myeloid leukemia blasts
|
| Treatment protocol |
No treatment applied
|
| Growth protocol |
Except for 14H124 (expansion in NSG mice), all samples were not expanded.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA RNA Hyperprep Stranded PolyA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities using Trimmomatic 0.35 and then mapped to the reference transcriptome using kallisto 0.43.0, taking into account that libraries are stranded.
TPM values were computed by kallisto 0.43.0 using a transcriptome index built on human genome GRCh38 along with Ensembl 88 annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression files are tab delimited with columns 1) Ensembl transcript identifier, 2) transcript length , 3) effective transcript length, 4) estimated counts, and 5) transcript per million reads sequenced (TPM).
|
| |
|
| Submission date |
Mar 25, 2020 |
| Last update date |
Mar 15, 2021 |
| Contact name |
Claude Perreault |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Research in Immunology and Cancer
|
| Street address |
2950, Chemin de Polytechnique
|
| City |
Montréal |
| State/province |
Québec |
| ZIP/Postal code |
H3C 3J7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE147524 |
Discovery of tumor specific antigens in acute myeloid leukemia. |
|
| Relations |
| BioSample |
SAMN14447008 |
| SRA |
SRX7992768 |
