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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
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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?
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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.
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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
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Submission date |
Mar 28, 2022 |
Last update date |
Jan 24, 2023 |
Contact name |
Madelaine Gogol |
Organization name |
Stowers Institute
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Department |
Computational Biology Core
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Street address |
1000 E. 50th Street
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City |
Kansas City |
State/province |
MO |
ZIP/Postal code |
64110 |
Country |
USA |
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Platforms (1) |
GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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Samples (15)
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GSM5976487 |
ARID1B knockdown, replicate 1 |
GSM5976488 |
ARID1B knockdown, replicate 2 |
GSM5976489 |
ARID1B knockdown, replicate 3 |
GSM5976490 |
Wild type control for ARID kd, replicate 1 |
GSM5976491 |
Wild type control for ARID kd, replicate 2 |
GSM5976492 |
Wild type control for ARID kd, replicate 3 |
GSM5976493 |
RNAi knockdown of NEAT1, replicate 1 |
GSM5976494 |
RNAi knockdown of NEAT1, replicate 2 |
GSM5976495 |
RNAi knockdown of NEAT1, replicate 3 |
GSM5976496 |
Parental control for NEAT1 knockdown, replicate 1 |
GSM5976497 |
Parental control for NEAT1 knockdown, replicate 2 |
GSM5976498 |
Parental control for NEAT1 knockdown, replicate 3 |
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Relations |
BioProject |
PRJNA820871 |
Supplementary file |
Size |
Download |
File type/resource |
GSE199631_counts.txt.gz |
757.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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