|
| Status |
Public on Jan 27, 2021 |
| Title |
K17/3544 |
| Sample type |
SRA |
| |
|
| Source name |
Bone_Marrow_MNCs
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: JMML
age_months: 8.45901639344262
hemoglobin (%): 7.4
karyotype: 46,XX
mutation: PTPN11
bone_marrow_blasts%: 7
platelets (x 10^9/l): 79
Cause of death: /
survival from diagnosis (os) (years): 4.32580424366872
events_after_hsct: No event
survival from hsct (efs) (years): 3.7864476386037
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mononuclear cell preparations were isolated from bone marrow or peripheral blood using Ficoll density gradient (Axis-shield). Next, Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) in combination with on-column DNase I digestion (RNase-Free DNase set, Qiagen) according to manufacturer’s instructions. The quality of the extracted RNA was assessed using the RNA 6000 Nano and RNA 6000 PICO assays on an 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using a TruSeq Stranded Total RNA Kit adapted for long fragments (+/- 550 bp) with the Ribo-Zero Gold rRNA Removal Kit (Illumina), according to the manufacturer’s instructions. Prepared libraries were run on a HiSeq3000 high-throughput sequencing system (Illumina) and paired end reads were generated (average of 52 million reads per sample)
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
10
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 reference genome using STAR v2.4.2 using a 2-pass strategy for identification of novel transcripts
Known gene quantification was performed on gencode v25 during the first pass.
Differential expression analysis of known genes was performed in R with DESeq2 v1.14.1
Genome_build: hg38
Supplementary_files_format_and_content: normalizedCounts_Deseq2.txt
|
| |
|
| Submission date |
Mar 25, 2020 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Mattias Hofmans |
| E-mail(s) |
mattias.hofmans@ugent.be
|
| Organization name |
Ghent University Hospital
|
| Department |
Department of pediatrics
|
| Lab |
Pediatric Hematology-Oncology and Stem Cell Transplantation
|
| Street address |
C. Heymanslaan 10
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE147523 |
Total paired-end RNA sequencing of bone marrow and peripheral blood MNCs from patients with Juvenile myelomonocytic leukemia and age-matched controls |
|
| Relations |
| BioSample |
SAMN14446999 |
| SRA |
SRX7992750 |
