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| Status |
Public on Aug 18, 2023 |
| Title |
5'UTRm, embryonic DRG |
| Sample type |
SRA |
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| Source name |
none
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| Organism |
Mus musculus |
| Characteristics |
tissue: none
cell type: Cultured primary dorsal root ganglion neurons
strain: CD-1
genotype: Wild type
developmental stage: embryonic stage E13
treatment: none
in vivo_viral_gene_delivery: none
in vitro_viral_gene_delivery: LV-5'UTRmut
ip antibody: Anti-CSDE1(ab201688)
molecule subtype: CSDE1-IP product, RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
For CSDE1-IP or HA-IP sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-CSDE1 or anti-HA antibody, and the RNA from the immunoprecipitated product was extracted using Rneasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB109))
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
MinION |
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| Data processing |
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts
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| Submission date |
Jul 10, 2023 |
| Last update date |
Aug 18, 2023 |
| Contact name |
Yongcheol Cho |
| E-mail(s) |
[email protected]
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| Phone |
82-53-785-6190
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| Organization name |
DGIST
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| Department |
Department of Brain Sciences
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| Lab |
Axon Regeneration and Degeneration
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| Street address |
333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun
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| City |
Dalseonggun, Daegu |
| State/province |
Daegu |
| ZIP/Postal code |
42988 |
| Country |
South Korea |
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| Platform ID |
GPL24973 |
| Series (1) |
| GSE236910 |
Sciatic nerve injury-responsive differential CSDE1 association efficiency of ribosomal protein coding mRNAs |
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| Relations |
| BioSample |
SAMN36381069 |
| SRA |
SRX20960076 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7585181_eDRG.ex.1.2.3.tsv.gz |
917.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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