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Series GSE137448 Query DataSets for GSE137448
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
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.
 
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.
 
Contributor(s) Yildirim O, Damle M, Izgu E, Chalei V, Ji F, Sadrayev R, Szostak J, Kingston R
Citation(s) 32402276
Submission date Sep 13, 2019
Last update date Jul 20, 2020
Contact name Manashree Damle
E-mail(s) damle@molbio.mgh.harvard.edu
Organization name Massachusetts General Hospital
Department Molecular Biology
Lab Bob Kingston
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02155
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (96)
GSM4079475 WC_nascent_Async_rep1
GSM4079476 WC_nascent_Async_rep2
GSM4079477 WC_nascent_T0-2_rep1
Relations
BioProject PRJNA565450
SRA SRP221619

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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