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| Status |
Public on Oct 03, 2024 |
| Title |
VOLIN_R1 |
| Sample type |
SRA |
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| Source name |
VOLIN
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| Organism |
Homo sapiens |
| Characteristics |
cell line: VOLIN
cell type: Multiple Myeloma
genotype: WT
replicate: biological replicate 1
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| Growth protocol |
MM cell lines were maintained in their original growth medium. The cell lines were cultured in human serum (HS) or fetal calf serum (FCS) in RPMI medium with 2nmol/l L-Glutamin. Specifically, URVIN was cultivated in 10% FCS in RPMI+IL-6 sup., FOLE in 10% HS in RPMI, IH-1, OH-2 and KJON in 10% HS in RPMI+IL-6 sup., VOLIN and JJN-3 in 10% FCS in RPMI, INA-6 and ANBL-6 in 10% FCS in RPMI+IL-6 (1ng/ml). IL-6 sup: IL-6 supernatant; isolated from peripheral blood leukocytes, an activity comparable to 2ng/ml used. . Low passages of the cell lines were used in the experiments.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using AllPrep DNA/RNA Mini prep (Qiagen).
RNA sequencing libraries were generated using 500 ng input RNA, using Lexogen SENSE mRNA-Seq library prep kit V2, according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
20 samples were sequenced on a NextSeq HO flowcell with 2 x 75 bp PE reads, giving an average output of ~28.3 M reads/sample (range 19.7 – 42.3).
Paired end FASTQ files were aligned using hisat2 v2.1.0 using pre-indexed hg37_tran (hg19) genome/transcriptome. Table with raw gene counts were generated using featureCounts v1.6.2 with Homo_sapiens.GRCh37.75.gtf (hg19) reference transcriptome, with options “’-t exon”, “-g gene_id”, “-O” (all overlapping features) and “-M --fraction” (assign multi-mapping reads using fractions).
Assembly: Hg19
Supplementary files format and content: text file includes raw gene counts for each sample
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| Submission date |
Dec 14, 2023 |
| Last update date |
Oct 03, 2024 |
| Contact name |
Kristine Misund |
| E-mail(s) |
kristinemisund@gmail.com
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| Organization name |
Norwegian University of Science and Technology
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| Department |
Department of Clincal and Molecular Medicine
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| Street address |
Prinsesse Kristinas gt 1
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| City |
Trondheim |
| ZIP/Postal code |
7030 |
| Country |
Norway |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE250236 |
Heterogeneous expression of cell surface markers in human myeloma cell lines: implications for disease modelling and therapeutic targeting |
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| Supplementary data files not provided |
| Raw data not provided for this record |
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