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| Status |
Public on May 31, 2024 |
| Title |
H929 cells, IGF2BP1 Clip-seq Input, rep 1 |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: H929
treatment: IGF2BP1 clip Input
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells lysis was performed in cold wash buffer (50mM Tris 7.4, 150mM NaCl, 2mM EDTA, 0.1% SDS, 0.5% NP-40, and 0.5% deoxycholate) supplemented with a 1% RNase inhibitor (Takara) and 2% protease inhibitor cocktail (Roche) for 30 min.After Ip,the protein-RNA complexes were cut from the gel and RNA was extracted with Trizol after digesting the proteins.
cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) according the manufacturer’s procedure.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq 6000 system for 150 nt paired-end sequencing.
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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 |
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Then randomly extract 250 thousand paired reads from clean data, use the blastn software to alignment with the NT database (ftp://ftp.ncbi.nih.gov/blast/db). And take the best result with evalue < 1e-10 and coverage > 80%.
Use the SortMeRNA software for ribosomal RNA reads removal. After discarded the rRNA reads, the remainly clean reads were mapped to the reference genome using HISAT2 with default parameters. Unique reads with high mapping quality were retained.
Assembly: hg38
Supplementary files format and content: bigWig
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| Submission date |
May 13, 2022 |
| Last update date |
May 31, 2024 |
| Contact name |
Jiadai Xu |
| E-mail(s) |
xu.jiadai@zs-hospital.sh.cn
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| Organization name |
Zhongshan Hospital, Fudan University
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| Department |
Hematology
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| Street address |
Fenglin Road 180, Shanghai, China
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE202973 |
IGF2BP1 regulate proliferation of multiple myeloma with chromosome 1q gain via CDC5L in a M6A way [CLIP-seq] |
| GSE202975 |
IGF2BP1 regulate proliferation of multiple myeloma with chromosome 1q gain via CDC5L in a M6A way |
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| Relations |
| BioSample |
SAMN28235467 |
| SRA |
SRX15263326 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6142365_Input_1.pos.bw |
12.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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