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| Status |
Public on Jan 08, 2024 |
| Title |
CLIP2 |
| Sample type |
SRA |
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| Source name |
testis
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| Organism |
Mus musculus |
| Characteristics |
tissue: testis
clip antibody: SRSF1 antibody (sc-33652, Santa Cruz Biotechnology)
strain: C57BL/6N
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total cells were isolated from adult WT C57BL/6N mouse testes, and then the cells were cross-linked by ultraviolet light (254 nm) to maintain the covalent binding of RBPs to their cognate RNA. Subsequently, SRSF1 and cross-linked RNAs were immunoprecipitated with an anti-SRSF1 antibody and digested with micrococcal nuclease (EN0181, Thermo Fisher Scientific). An IR800-biotin adapter was ligated to the 3′ ends of the RNA fragments. Then, the SRSF1/RNA complexes were separated by SDS‒PAGE and transferred to a nitrocellulose membrane (HATF00010, Millipore). These RNA and protein complexes from approximately 47 to 62 kDa were extracted from the nitrocellulose membrane, after which proteinase K (9034, Takara) digestion was performed. RNA was isolated with saturated phenol (AM9712, Ambion),
RNA ligated with adaptors, and converted to cDNA with a SuperScript III First-Strand Kit (18080-051, Invitrogen). The cDNA was amplified by PCR to prepare the corresponding libraries and then sequenced on illumina NovaSeq 6000.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For the analyses of CLIP-seq data, the adaptor sequences were first removed from the reads by Trimmomatic (version 0.36)
Subsequently, Bowtie 2 (version 2.1.0) was applied for mapping of clean reads to the mm10 reference genome with the parameters "-p 10 -L 15 -N 1 -D 50 -R 50 --phred33 --qc-filter --very-sensitive --end-to-end."
CLIP-seq peaks were identified by Piranha (version 1.2.1) with the following parameters: "-s -b 20 -d Zero Truncated Negative Binomial -p 0.05."
Homer (version 4.9.1) was used for peak annotation based on the mm10 genome assembly and for analyses of SRSF1-binding motifs
Assembly: mm10
Supplementary files format and content: bigWig (track)
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| Submission date |
Mar 14, 2023 |
| Last update date |
Jan 08, 2024 |
| Contact name |
Jiali Liu |
| E-mail(s) |
liujiali@cau.edu.cn
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| Phone |
86-10-62732277
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| Organization name |
China Agricultural University
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| Street address |
2 West Yuanmingyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE227303 |
SRSF1 is crucial for male meiosis through alternative splicing during homologous pairing and synapsis in mice [CLIP-seq] |
| GSE227422 |
SRSF1 is crucial for male meiosis through alternative splicing during homologous pairing and synapsis in mice |
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| Relations |
| BioSample |
SAMN33755559 |
| SRA |
SRX19674189 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7094521_SRSF1_rep2.bowtie.map.rmDup.bigwig |
41.0 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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