|
| Status |
Public on Feb 13, 2022 |
| Title |
RNA_MM1S_CO2 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line derived from human plasma cell myelom
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MM.1S (ATCC, CRL-2974)
cell type: Human myeloma cell line
culture condition: in the lower chamber from a transwell coculture with HS5
repeat: r2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from approximately 10^5 sorted cells for each sample using Qi-agen kit (RNeasy Plus Mini Kit, 74134) according to manufacturer’s instructions.
250-500ng of total RNA was used for each sample as a starting material for RNA-Seq library prep using KAPA mRNA HyperPrep Kit (Roche Diagnostics, 08098123702) according to manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Reads were aligned to mouse genome (hg38) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by RPKM (PMID: 18516045) with an in-house script.
Genome_build: hg38
Supplementary_files_format_and_content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.
|
| |
|
| Submission date |
Jan 13, 2022 |
| Last update date |
Feb 13, 2022 |
| Contact name |
Gangqing Hu |
| E-mail(s) |
michael.hu@hsc.wvu.edu
|
| Organization name |
West Virginia University
|
| Department |
MicroBiology, Immunology, and Cell Biology
|
| Lab |
2072A, HSC North, Floor 2
|
| Street address |
64 Medical Center Drive
|
| City |
Morgantown |
| State/province |
West Virginia |
| ZIP/Postal code |
26506-9177 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE193656 |
Bone Marrow Stroma-induced Transcriptome and Regulome Signatures of Multiple Myeloma [RNA-seq] |
| GSE193658 |
Bone Marrow Stroma-induced Transcriptome and Regulome Signatures of Multiple Myeloma |
|
| Relations |
| BioSample |
SAMN25026067 |
| SRA |
SRX13799879 |
