|
| Status |
Public on Aug 17, 2022 |
| Title |
UPNR_532 |
| Sample type |
SRA |
| |
|
| Source name |
Unsorted Bone Marrow Cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: T-ALL
cell type: Unsorted Bone Marrow Cells
chromothripsis status: negative
subtype: Not Available
age: 8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from bone marrow cells of patients using a QIAamp RNA Blood Mini Kit (Qiagen). Libraries were prepared at Novogene, (Cambridge, UK), following the NEBNext® Ultra™ RNA Library Prep Kit on polyA-enriched mRNA.
RNA libraries were prepared using manufacturer’s recommended protocol andsequenced on Illumina NovaSeq 6000 with 150bp paired-end read run (Illumina San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Low quality reads or reads with adapters were filtered out by using fastp software
Cleaned reads were aligned to the human genome (GRCh37/hg19) using STAR and processed with Samtools.
Read counts per gene were generated using HTseq package
Bioconductor/R DESeq2 package was used for normalization and differential expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts generated for each Sample
|
| |
|
| Submission date |
Jun 01, 2022 |
| Last update date |
Aug 17, 2022 |
| Contact name |
Cristina Mecucci |
| E-mail(s) |
cristina.mecucci@unipg.it
|
| Phone |
+39 075 5783808
|
| Organization name |
University of Perugia
|
| Department |
Department of Medicine, Hematology and Bone Marrow Transplantation Unit
|
| Lab |
Laboratory of Cytogenetics and Molecular Genetics
|
| Street address |
Piazzale Menghini n.9
|
| City |
Perugia |
| ZIP/Postal code |
06132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE205266 |
Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults [RNA-seq] |
| GSE205270 |
Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults |
|
| Relations |
| BioSample |
SAMN28813249 |
| SRA |
SRX15556933 |
