|
| Status |
Public on Jan 31, 2024 |
| Title |
mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1400] |
| Sample type |
SRA |
| |
|
| Source name |
CD138+ cells or bone marrow with CD138+ over 75%
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD138+ cells or bone marrow with CD138+ over 75%
subject status: plasmacell leukemia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using AllPrep Kit (Qiagen) according manufacturer instructions.
Library was generated using TruSeq RNA Exome Kit (Illumina) followed by sequencing on NextSeq (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads (Illumina) were aligned to reference genome hg38 (ENSEMBL) and Homo_sapiens.GRCh38.98.gtf.-transcriptome annotation release (ENSEMBL) using STAR two-pass mode ( star 2.7).
GRCh38.98.gtf.-transcriptome annotation release (ENSEMBL, release 98) was used for quantification, performed by RSEM 1.3.0, followed by TPM normalisation in RSEM-1.3.0.
Assembly: hg38
Supplementary files format and content: output of rsem package: txt table with normalized counts
|
| |
|
| Submission date |
Jan 12, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Anna Dolnik |
| E-mail(s) |
anna.dolnik@charite.de
|
| Organization name |
Charité Universitätsmedizin Berlin
|
| Department |
Campus Virchow-Klinikum (CVK)
|
| Lab |
Hämatologie, Onkologie und Tumorimmunologie
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE222727 |
Proteomic profiling Proteogenomic landscape of multiple myeloma reveals CDK6 upregulation as a targetable resistance mechanism for lenalidomide in multiple myeloma |
|
| Relations |
| BioSample |
SAMN32709413 |
| SRA |
SRX19015169 |
