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| Status |
Public on May 08, 2023 |
| Title |
PTBP2 knock-down RNA-seq from human iPSC-neurons |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To determine targets of PTBP2-dependent alternative splicing, we depleted PTBP2 in human neurons derived from induced-pluripotent stem cells (iPSC-neurons) using an LNA gapmer and performed RNA-seq on untreated, negative control-treated, and knock-down samples.
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| Overall design |
We performed differential gene expression and splicing analysis of RNA-seq data from untreated, negative control LNA gapmer-treated, and PTBP2 LNA gapmer-treated human iPSC-neurons.
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| Contributor(s) |
Dawicki-McKenna JM, Felix AJ, Waxman EA, Cheng C, Amado D, Ranum P, Bogush A, Dungan L, Heller EA, French DL, Davidson BL, Prosser BL |
| Citation(s) |
37149717 |
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| Submission date |
Jun 22, 2022 |
| Last update date |
May 09, 2023 |
| Contact name |
Jennine M Dawicki-McKenna |
| E-mail(s) |
[email protected]
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| Organization name |
University of Pennsylvania
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| Department |
Physiology
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| Street address |
700 CRB, 415 Curie Blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (9)
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| GSM6260210 |
iPSC-neurons, Untreated, rep1 |
| GSM6260211 |
iPSC-neurons, Untreated, rep2 |
| GSM6260212 |
iPSC-neurons, Untreated, rep3 |
| GSM6260213 |
iPSC-neurons, 5 µM PTBP2 gapmer, rep1 |
| GSM6260214 |
iPSC-neurons, 5 µM PTBP2 gapmer, rep2 |
| GSM6260215 |
iPSC-neurons, 5 µM PTBP2 gapmer, rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE206661 |
human iPSC-neurons and human cortex |
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| Relations |
| BioProject |
PRJNA851735 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE206660_GEO_RNAseq_gene-summarizedExperiment_counts.txt.gz |
834.3 Kb |
(ftp)(http) |
TXT |
| GSE206660_GEO_rMATS_output_cstat_0.01_SAMPLE1-None_SAMPLE2-PTBP2.tar.gz |
246.6 Mb |
(ftp)(http) |
TAR |
| GSE206660_RAW.tar |
3.5 Gb |
(http)(custom) |
TAR (of TAR) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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