|
| Status |
Public on May 06, 2024 |
| Title |
K1718-P-R1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
condition: B-cell
replicate: 2
phenotype: parental
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent
Total RNA samples were prepared for RNA-Seq with the NEBNext rRNA Depletion kit, the NEBNext Ultra Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR with default paramenters. Genes' Expression have been quantified using HT-Seq count using gencode v22 as gtf.
Read counts have been normalized with TMM algorithm, and converted into log2 counts per million of mapped reads (cpm)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (Raw_Counts sheet)
Supplementary files format and content: Matrix table with lcpm for every gene in every sample (Normalized lcpm)
|
| |
|
| Submission date |
Oct 05, 2023 |
| Last update date |
May 06, 2024 |
| Contact name |
Luciano Cascione |
| E-mail(s) |
luciano.cascione@ior.usi.ch
|
| Organization name |
IOR
|
| Department |
Lymphoma & Genomics Research Program
|
| Street address |
Via Chiesa 5
|
| City |
Bellinzona |
| State/province |
Ticino |
| ZIP/Postal code |
6500 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE173984 |
RNA-Seq of B-Cell Lines Clones, parental and resistant to Idelalisib or IMGN529 |
|
| Relations |
| BioSample |
SAMN37692567 |
| SRA |
SRX21997431 |
