|
| Status |
Public on May 15, 2024 |
| Title |
MOLM14_untreated_3 |
| Sample type |
SRA |
| |
|
| Source name |
MOLM14
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MOLM14
cell type: leukemic cells
genotype: Control
treatment: Untreated
|
| Treatment protocol |
To induce knockdown of TRAF6 in human cells, the cells were cultured with doxycycline (1μg/mL) for 7 days. For knockout of Traf6 in murine AML cells, the leukemic cells were cultured with 1μM 4-hydroxytamoxifen for 4 days.
|
| Growth protocol |
The cells were cultured in RPMI1640 medium with 10% fetal bovine serum FBS and 1% penicillin and streptomycin . 10ng/mL of human IL-3 was added to the medium for culturing TF-1. MLL-AF9-expressing cells were cultured with IMDM) with 10% FCS, 10 ng/mL of SCF, 10 ng/mL of IL-3, and 10 ng/mL of IL-6.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Plus Mini Kit (Qiagen) following manufacturer's protocol
RNA libraries were prepared according to the protocol of QuantSeq 3'mRNA-Seq Library Prep Kit FWD (Lexogen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adaptor sequences were trimmed from the raw RNA-seq reads with fastp (v 0.23.1). Trimmed reads of each sample were mapped to the reference human genome hg38 and mouse genome mm10 by using STAR (v 2.3.1) and normalized to 1 million reads in the original library.
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: hg38 and mm10
Supplementary files format and content: The CSV file include raw read counts for each sample
|
| |
|
| Submission date |
Jan 30, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Kwangmin Choi |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Experimental Hematology & Cancer Biology
|
| Street address |
333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE254615 |
The effect of TRAF6 loss on the gene expression profiles in leukemia cells II |
| GSE254616 |
The effect of TRAF6 loss on the gene expression profiles in leukemia cells |
|
| Relations |
| BioSample |
SAMN39676498 |
| SRA |
SRX23453747 |
