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Status |
Public on Apr 20, 2020 |
Title |
S-phase enriched non-coding RNAs regulate gene expression and cell cycle progression |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
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Summary |
We infer that non-coding RNAs can function as key effectors during cell cycle, acting on distinct regulatory networks to ensure maintenance of gene expression programs and cell cycle progression.
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Overall design |
We performed nascent RNA-seq in asynchronized RPE-1 cells as well as synchronized RPE-1 cells at five different timepoints of S-phase of cell cycle progression. We also performed strand-specific RNAseq on control and three knockdown cell lines in which a lincRNA of interest was knocked down. We also performed histone ChIP-seq and Cut-n-run seq on asynchronized RPE1 cells.
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Contributor(s) |
Yildirim O, Damle M, Izgu E, Chalei V, Ji F, Sadrayev R, Szostak J, Kingston R |
Citation(s) |
32402276 |
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Submission date |
Sep 13, 2019 |
Last update date |
Jul 20, 2020 |
Contact name |
Manashree Damle |
E-mail(s) |
damle@molbio.mgh.harvard.edu
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Organization name |
Massachusetts General Hospital
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Department |
Molecular Biology
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Lab |
Bob Kingston
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Street address |
185 Cambridge Street
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02155 |
Country |
USA |
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Platforms (1) |
GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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Samples (96)
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Relations |
BioProject |
PRJNA565450 |
SRA |
SRP221619 |
Supplementary file |
Size |
Download |
File type/resource |
GSE137448_Control_LINC00704_RPKMs.txt.gz |
3.8 Mb |
(ftp)(http) |
TXT |
GSE137448_Control_LUCAT1_RPKMs.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
GSE137448_Control_Linc704_Async_RPKMs.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
GSE137448_Control_Lucat_Async_RPKMs.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
GSE137448_Control_MIAT_RPKMs.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
GSE137448_Control_Miat_Async_RPKMs.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
GSE137448_Nuclear_input_RPKMs.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
GSE137448_Nuclear_nascent_RPKMs.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
GSE137448_RAW.tar |
13.4 Gb |
(http)(custom) |
TAR (of BIGWIG) |
GSE137448_Whole_cell_input_RPKMs.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
GSE137448_Whole_cell_nascent_RPKMs.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |