|
| Status |
Public on May 31, 2021 |
| Title |
Effect of Cell cycle regulator CDK1 on Cell Differentiation (RNA-IP CDK1 inh KD) |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
We addressed the role of cell cycle regulator CDK1 during differentiation by either inhibiting its activity with the specific inhibitor RO3306 (10µM) or by knocking its expression down using specific shRNAs, during mesendoderm differentiation. Human pluripotent stem cells (H9 cells) were synchronized in their cell cycle and then induced to differentiate into mesendoderm for 24h. shRNAs against CDK1 were induced 4 days before starting the differentiation. The CDK1 inhibitor was added to the medium 8h after the induction of differentiation. At the end of the experiment, the cells were harvested and processed for total RNA extraction. RNA-IP was carried out using RiboCluster Profiler RIP-Assay Kit (MBL) following the manufacture’s recommendations.
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| Overall design |
Four different conditions were analyzed: Undifferentiated (UD), Mesendoderm (E24), Mesendoderm + CDK1 inhibityor (E24RO), Mesendoderm without induction of shRNA_CDK1 with tetracycline (E24woTET), and Mesendoderm plus induction of shRNA_CDK1 with tetracycline (E2TET). Two biological replicates were generated for each condition.
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| Contributor(s) |
Grandy R |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 07, 2019 |
| Last update date |
May 31, 2021 |
| Contact name |
Rodrigo Andres Grandy |
| Organization name |
University of Cambridge
|
| Department |
Surgery
|
| Lab |
Vallier Lab
|
| Street address |
Cambridge Stem Cell Institute/ Anne McLaren Laboratory West Forvie Building, Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0SZ |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (16)
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| This SubSeries is part of SuperSeries: |
| GSE130830 |
Effect of Cell Division on Cell Differentiation |
|
| Relations |
| BioProject |
PRJNA541529 |
| SRA |
SRP195817 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE130827_CDK1-KD_exomepeak_sig_diff_peak.bed.gz |
80.2 Kb |
(ftp)(http) |
BED |
| GSE130827_E24vsRO_exomepeak_sig_diff_peak.bed.gz |
78.2 Kb |
(ftp)(http) |
BED |
| GSE130827_GRCh38.84.gtf.gz |
43.6 Mb |
(ftp)(http) |
GTF |
| GSE130827_macs2_common_peaks_E24R1R2.bed.gz |
110.6 Kb |
(ftp)(http) |
BED |
| GSE130827_macs2_common_peaks_E24ROR1R2.bed.gz |
72.3 Kb |
(ftp)(http) |
BED |
| GSE130827_macs2_common_peaks_E24_iKD_TET_R1R2.bed.gz |
105.7 Kb |
(ftp)(http) |
BED |
| GSE130827_macs2_common_peaks_E24_iKD_woTET_R1R2.bed.gz |
201.3 Kb |
(ftp)(http) |
BED |
| GSE130827_rna-ip_ratio_7mG_Inp_E24R1_10.bw |
99.1 Mb |
(ftp)(http) |
BW |
| GSE130827_rna-ip_ratio_7mG_Inp_E24R2_10.bw |
74.9 Mb |
(ftp)(http) |
BW |
| GSE130827_rna-ip_ratio_7mG_Inp_E24ROR1_10.bw |
66.2 Mb |
(ftp)(http) |
BW |
| GSE130827_rna-ip_ratio_7mG_Inp_E24ROR2_10.bw |
83.0 Mb |
(ftp)(http) |
BW |
| GSE130827_rna-ip_ratio_7mG_Inp_iKD-CDK1_+TET_E24R1_10.bw |
81.3 Mb |
(ftp)(http) |
BW |
| GSE130827_rna-ip_ratio_7mG_Inp_iKD-CDK1_+TET_E24R2_10.bw |
78.4 Mb |
(ftp)(http) |
BW |
| GSE130827_rna-ip_ratio_7mG_Inp_iKD-CDK1_woTET_E24R1_10.bw |
86.0 Mb |
(ftp)(http) |
BW |
| GSE130827_rna-ip_ratio_7mG_Inp_iKD-CDK1_woTET_E24R2_10.bw |
73.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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