GSE210437
GSE GEO Potentially relatedEnhanced CLIP (eCLIP) identified differential UPF1 binding sites in mouse neural progenitor cells (NPCs) samples
Organism:
Mus musculus
Platform:
GPL24247
Samples:
2
Experiment Types:
Expression profiling by high throughput sequencing
Other
Submitted:
Aug 03 2022
Last Updated:
Apr 05 2024
Status:
Public on Apr 04 2024
Contact:
Gene,,Yeo (UCSD)
Relations
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA865731
Summary
As one of the key RNA regulation pathway, the NMD pathway plays a key role in the early brain development. The investigation of UPF1 specific binding transcript in mouse NPCs samples could give us a overall view of potential genes which are subjected to the NMD regulation. Among these genes we could identify how the NMD pathway shapes early mouse brian development.
Overall Design
eCLIP-seq with UPF1 specific antibody in mouse NPCs samples
Analysis (9 steps)
View Data Processing
Processing steps for GSE210437
- Data was processed using the eCLIP pipeline and available at: http://github.com/yeolab/eclip
- Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with umi_tools extract
- Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
- Trimmed reads were mapped against RepBase with STAR to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 30 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
- Remaining reads were mapped to the appropriate genome build (mm10) using STAR aligner (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
- Uniquely mapped reads were removed of PCR duplicates with umi_tools
- Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
- Clusters enriched over corresponding size-matched input (SMInput) were identified using a custom Perl script, available in the main eCLIP repository as: overlap_peakfi_with_bam.pl
Showing first 8 steps.
Supplementary Files (1)
GSE210437_RAW.tar
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GEO Samples (2)
SRA Experiments (2) and Runs (2)
Total: 687 MBGSM6430256: UPF1_MOCK; Mus musculus; RNA-Seq
Sample: SRS14430091
BioProject: PRJNA865731
BioSample: SAMN30124670
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: neural progenitor cells
genotype: Upf2fl/fl
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR20787440 | 9557398 | 965297198 | 291.87 | UPF1_MOCK_IP_S21_L002_R1_001.fastq.gz, SRR20787440, SRR20787440.lite | SRA |
GSM6430260: UPF1_MOCK_INPUT; Mus musculus; RNA-Seq
Sample: SRS14430094
BioProject: PRJNA865731
BioSample: SAMN30124667
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: neural progenitor cells
genotype: Upf2fl/fl
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR20787437 | 12929283 | 1305857583 | 395.43 | UPF1_MOCK_IN_S20_L002_R1_001.fastq.gz, SRR20787437, SRR20787437.lite | SRA |
Potentially Related Publications (1)
This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.