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| Status |
Public on Apr 13, 2023 |
| Title |
PTBP2 eCLIP from human iPSC-neurons and human cortex (Brodmann area 4) [CLIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To determine direct targets of PTBP2-dependent alternative splicing, we performed CLIP-seq analysis of PTBP2 binding in both human cortical tissue and human neurons derived from induced-pluripotent stem cells (iPSC-neurons), and we combine this with splicing analysis following PTBP2 depletion in iPSC-neurons.
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| Overall design |
We performed enhanced cross-linking immunoprecipitation (eCLIP) of PTBP2 in human cortex (Brodmann area 4) and 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 08, 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 (12)
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| GSM6260043 |
Human cortex, PTBP2 eCLIP, rep1 |
| GSM6260044 |
Human cortex, PTBP2 eCLIP, rep2 |
| GSM6260045 |
Human cortex, PTBP2 eCLIP, rep3 |
| GSM6260046 |
iPSC-neurons, Size-matched input, rep1 |
| GSM6260047 |
iPSC-neurons, Size-matched input, rep2 |
| GSM6260048 |
iPSC-neurons, Size-matched input, rep3 |
| GSM6260049 |
iPSC-neurons, PTBP2 eCLIP, rep1 |
| GSM6260050 |
iPSC-neurons, PTBP2 eCLIP, rep2 |
| GSM6260051 |
iPSC-neurons, PTBP2 eCLIP, rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE206661 |
human iPSC-neurons and human cortex |
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| Relations |
| BioProject |
PRJNA851722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE206650_GRChg38.BA4_realigned_10.narrow_peak.combined.bb |
705.4 Kb |
(ftp)(http) |
BB |
| GSE206650_GRChg38.IPS_realigned_10.narrow_peak.combined.bb |
705.4 Kb |
(ftp)(http) |
BB |
| GSE206650_RAW.tar |
490.1 Mb |
(http)(custom) |
TAR (of BW) |
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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