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Series GSE199631 Query DataSets for GSE199631
Status Public on Nov 10, 2022
Title The nuclear granule Paraspeckles interacts with the chromatin remodeling SWI/SNF complex to regulate alternative splicing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary There are three major goals of the study 1) Understand if the differential effect of depletion of ARID1 paralogs on the trancriptome of HEK293FRT cells 2) Understand if NEAT1 depletion effects any alternative splicing pathways in HEK293FRT cells 3) Is the regulation of alternative splicing pathways by NEAT1 ARID1B dependent?
 
Overall design siRNA specific to either ARID1A, ARID1B or NEAT1 was used for experimental data sets. For both the controls, Wildtype or Parental a scrambled siRNA was used. In brief, 2 rounds of transfection with siRNA was employed with 24 hour interval in between each transfection. All the cells were harvested post 72 hours of first siRNA transfection and processed for RNA extraction.
 
Contributor(s) Reddy D, Gogol M, Workman J
Citation(s)
  • Reddy D, Bhattacharya S, Levy M, Zhang Y et al. Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep 2023 Jan 9;24(1):e55345. PMID: 36354291
Submission date Mar 28, 2022
Last update date Jan 24, 2023
Contact name Madelaine Gogol
Organization name Stowers Institute
Department Computational Biology Core
Street address 1000 E. 50th Street
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (15)
GSM5976484 ARID1A knockdown, replicate 1
GSM5976485 ARID1A knockdown, replicate 2
GSM5976486 ARID1A knockdown, replicate 3
Relations
BioProject PRJNA820871

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
GSE199631_counts.txt.gz 757.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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