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Series GSE99594 Query DataSets for GSE99594
Status Public on Oct 05, 2022
Title Nuclear fractionation to identify chromatin associated RNA in interphase and M-phase cells [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The composition and dynamics of tightly bound chromatin associated RNAs during mitosis remains elusive. Here we report identification of chromatin enriched (cheRNAs) by biochemical nuclear fractionation coupled with RNA-seq in both interphase and mitotic phase of A549 and HeLaS3 cell lines. We show that highly abundant cheRNAs, mostly small noncoding RNAs, are largely maintained in mitotic chromatin, and constitute a substantial part of chromatin throughout cell cycle. We also show that the mitotic retained cheRNAs tend to be cell type nonspecific. We speculate that these cell type nonspecific cheRNAs might play roles in chromatin state and gene expression control. We anticipate the panoramic landscape of RNA composition of chromatin both in interphase and M-phase would shed light on understanding the structure and function of chromatin in M phase and would also help the understanding of some fundamental biological functions.
Overall design In this case, for each of A549 cells as well as HeLa-S3 cells, we performed RNA-seq on samples from two independent biological replicates of soluble nuclear extract (S) and chromatin pellet extract (P) both in asynchronized (with interphase accounting for ~95% of cells, we called these cells as “inter-phase cells” afterwards) and M-phase
Contributor(s) Zhang Y, Shi M, Li P, Ma Z, Shen W, Chen Y, Zhao Z
Citation(s) 36325053
Submission date Jun 02, 2017
Last update date Nov 17, 2022
Contact name Yan Zhang
Phone 861066948775
Organization name Beijing institute of Biotechnology
Street address Dongdajie street
City Beijing
State/province Not Applicable
ZIP/Postal code 100071
Country China
Platforms (1)
GPL17303 Ion Torrent Proton (Homo sapiens)
Samples (16)
GSM2648391 BC1_A549_IS_rep1
GSM2648392 BC2_A549_IP_rep1
GSM2648393 BC3_A549_MS_rep1
This SubSeries is part of SuperSeries:
GSE195694 Profiling and characterization of constitutive chromatin enriched RNAs
BioProject PRJNA388880
SRA SRP108471

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Supplementary file Size Download File type/resource
GSE99594_gene_info.tsv.gz 2.9 Mb (ftp)(http) TSV
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