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| Status |
Public on Jun 30, 2020 |
| Title |
RNA-seq in murine acute myeloid leukemia (AML) cells with and without knockdown of Tet1 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To explore the global targets and dissect the mechanism underlying the oncogenic function of TET1 in AML, we performed deep sequencing for mRNA isolated from mouse MLL-ENL-ERtm cells with and without knockdown of Tet1.
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| Overall design |
We transduced pGFP-V-RS-based retroviral shRNA targeting Tet1 (i.e., shTet1) as reported in Huang H et al., PNAS, 2013 (reported as shTet1-a+b), or scramble shRNA (i.e., shNS), into mouse MLL-ENL-ERtm cells. After puromycin selection (1 µg/mL) for three passages and SILAC adaption, cells were collected and RNA was extracted using miRNeasy kit (Qiagen). PolyA RNA was subsequently purified from 50-100 ng total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module. NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) was used for library preparation. Each group was sequenced in triplicate by Illumina Hiseq 1000 with single end 51-bp read length.
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| Contributor(s) |
Chen J, Weng H, Huang H |
| Citation missing |
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| Submission date |
Jul 02, 2018 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Jianjun Chen |
| E-mail(s) |
jianchen@coh.org
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| Phone |
6262185591
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| Organization name |
Beckman Research Institute of City of Hope
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| Department |
Systems Biology
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| Lab |
Chen Lab
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| Street address |
1218 S. 5th Ave., Room 2062
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| City |
Monrovia |
| State/province |
CA |
| ZIP/Postal code |
91016 |
| Country |
USA |
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| Platforms (1) |
| GPL15103 |
Illumina HiSeq 1000 (Mus musculus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE116551 |
RNA-seq and 5hmC-seq in acute myeloid leukemia (AML) cells with and without knockdown of Tet1 |
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| Relations |
| BioProject |
PRJNA479002 |
| SRA |
SRP151818 |
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