|
| Status |
Public on Sep 21, 2022 |
| Title |
Ribosome profiling of Murine Embryonic Fibroblasts in the context of different Fbxo4 and hnRNPK status. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Background: SCF-Fbxo4 is suspected to regulate activity of RNA binding protein hnRNPK by non-degradive ubiquitylation. Research strategy: To determine the genomic output of SCF-Fbxo4 - hnRNPK interplay, murine embryonic fibroblasts (MEFs) with different status of hnRNPK/Fbxo4 were subjected to Ribosome profiling. Sequencing was performed on total RNA and RNA protected by ribosomes for each condition.
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| Overall design |
Applying RNAi strategy hnRNPK was depleted in either wild type MEFs or MEFs Fbxo(-/-). MEFs conditioned in 4 different ways: wt- control (I), Fbxo4 knock-out (II), Fbxo4 knock-out + hnRNPK RNAi knock-down (III) and RNAi hnRNPK knock-down only (IV) were subjected to sequencing of total RNA and Ribosome protected fragment.
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|
| Contributor(s) |
Diehl JA, Mucha B |
| Citation(s) |
36329064 |
| |
| Submission date |
Feb 10, 2022 |
| Last update date |
Dec 22, 2022 |
| Contact name |
J Alan Diehl |
| E-mail(s) |
jad283@case.edu
|
| Phone |
2163680268
|
| Organization name |
Case Western Reserve University
|
| Department |
Department of Biochemistry
|
| Lab |
Deihl Lab
|
| Street address |
2109 Adelbert Rd. SOM Wood/W402
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
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| Platforms (1) |
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| Samples (16)
|
| GSM5885014 |
S1: MEF_wt+non_targeting siRNA rep 1 [RNA] |
| GSM5885015 |
S2: MEF_wt+non_targeting siRNA rep 2 [RNA] |
| GSM5885016 |
S3: MEF_wt+hnRNPK siRNA rep 1 [RNA] |
| GSM5885017 |
S4: MEF_wt+hnRNPK siRNA rep 2 [RNA] |
| GSM5885018 |
S5: MEF_Fbxo4(-/-)+non_targeting siRNA rep 1 [RNA] |
| GSM5885019 |
S6: MEF_Fbxo4(-/-)+non_targeting siRNA rep 2 [RNA] |
| GSM5885020 |
S7: MEF_Fbxo4(-/-)+hnRNPK siRNA rep 1 [RNA] |
| GSM5885021 |
S8: MEF_Fbxo4(-/-)+hnRNPK siRNA rep 2 [RNA] |
| GSM5885022 |
rS1: MEF_wt+non_targeting siRNA rep 1 [RPF] |
| GSM5885023 |
rS2: MEF_wt+non_targeting siRNA rep 2 [RPF] |
| GSM5885024 |
rS3: MEF_wt+hnRNPK siRNA rep 1 [RPF] |
| GSM5885025 |
rS4: MEF_wt+hnRNPK siRNA rep 2 [RPF] |
| GSM5885026 |
rS5: MEF_Fbxo4(-/-)+non_targeting siRNA rep 1 [RPF] |
| GSM5885027 |
rS6: MEF_Fbxo4(-/-)+non_targeting siRNA rep 2 [RPF] |
| GSM5885028 |
rS7: MEF_Fbxo4(-/-)+hnRNPK siRNA rep 1 [RPF] |
| GSM5885029 |
rS8: MEF_Fbxo4(-/-)+hnRNPK siRNA rep 2 [RPF] |
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| Relations |
| BioProject |
PRJNA805181 |
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