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Sample GSM4432533 Query DataSets for GSM4432533
Status Public on Jan 27, 2021
Title K17/3545
Sample type SRA
 
Source name Bone_Marrow_MNCs
Organism Homo sapiens
Characteristics disease state: JMML
age_months: 23.1803278688525
hemoglobin (%): 37
karyotype: 46,XY
mutation: PTPN11
bone_marrow_blasts%: 3.5
platelets (x 10^9/l): 25
Cause of death: /
survival from diagnosis (os) (years): 1.68925393566051
events_after_hsct: No event
survival from hsct (efs) (years): 1.3223819301848
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 11
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 SAMN14446998
SRA SRX7992751

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

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