|
| Status |
Public on Feb 27, 2022 |
| Title |
RNA-Seq - OCI-AML3 NPM1c degron2 cell line treated with 500nM dTag-13 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
OCI-AML3 NPM1c degron2 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
drug treatment: 500nM dTag-13 treatment for 24hr
genome type: DNMT3A;NPM1c;NRASmut
|
| Treatment protocol |
For dTag-13 treatment, OCI-AML3-NPM1c-degron cells were treated with DMSO or 500nM dTag-13 for 24 hrs. For Selinexor treatment, OCI-AML3 cells were treated with 25nM Selinexor for 24 hrs.
|
| Growth protocol |
All human leukemia cell lines are maintained in RPMI-1640 medium with 10% FBS and 1% Pen/Strep, mouse progenitor cell lines are maintained in RPMI-1640 medium with 1% CHO-SCF condidtion medium and 1uM betaestrodial
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen RNeasy micro
NEBNext Ultra II RNA-seq library kit was used to construct to library of mouse hematopietic progenitors. Swiftbio's rapid RNA-seq kit was used to construct the library for human AML cells.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
dTag2_(for_dTag）
|
| Data processing |
RNA-seq raw reads were mapped to the human genome (hg19) or mouse genome mm9 using STAR-2.6.1 with default parameters. Transcript levels were calculated as TPM and count using RSEM . Those genes having a count greater than 5 in at least 50% of the samples were kept for further examination. The DESeq2 R package was used to perform differential gene expression analysis between groups . Significantly differentially expressed genes were defined as those with a log2fold change (LFC) value of > 1 and a false discovery rate (FDR) of < 0.05.
Genome_build: hg19 mm9
Supplementary_files_format_and_content: RSEM transcript count
|
| |
|
| Submission date |
Feb 24, 2022 |
| Last update date |
Feb 28, 2022 |
| Contact name |
Xiaotian Zhang |
| E-mail(s) |
zxtzhangqian@gmail.com
|
| Organization name |
The University of Texas Health Science Center at Houston
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Zhang Lab
|
| Street address |
6431 Fannin St
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE197377 |
NPM1c hijacks the active trancription in leukemia development [RNA-Seq] |
| GSE197387 |
NPM1c hijacks the active trancription in leukemia development [ |
|
| Relations |
| BioSample |
SAMN26226138 |
| SRA |
SRX14276099 |
