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| Status |
Public on Mar 21, 2024 |
| Title |
batch2_rip_seq_Smyd5_KO_Input_rep1 |
| Sample type |
SRA |
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| Source name |
ES-E14
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| Organism |
Mus musculus |
| Characteristics |
cell line: ES-E14
cell type: Embryonic stem cells
genotype: Smyd5 KO
treatment: none
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected and washed with cold PBS once. Hela cells were spiked in as the internal control for normalization. 1 ml cold polysome lysis buffer (50 mM KCl, 25 mM Tris pH 7.4, 5 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 100 U/ml RNAase inhibitor, and 1× protease inhibitor cocktail) was added and incubated on ice for 10 min. Samples were cleaned by centrifugation at 14,000 rpm 4 °C for 10 min. 10% of the lysate was saved as the input sample. Others were incubated with Anti-DYKDDDDK G1 Affinity Resin beads (GenScript, Cat. #L00432) which were washed with NT2 buffer (50 mM Tris pH 7.4, 150 mM NaCl, 1 mM MgCl2, and 0.05% NP-40) at 4 °C for 4h. Beads were washed with NT2 buffer 5 times to remove unbound material. RNA was purified by Trizol reagent (Sangon Biotech, Cat. #B610409)
library preparation was done by RNA-seq library prep kit (VAHTS, Cat. #NR604)
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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 reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameters ‘-q 20 --paired’.
Trimmed reads were uniquely mapped to the mouse reference genome (mm9) using Bowtie2 (Langdon, 2015) (version 2.4.2).
PCR duplicates were removed using MarkDuplicates tool of Picard (version 2.23.3) (https://broadinstitute.github.io/picard/) with the parameter ‘--REMOVE DUPLICATES = true’.
Peaks were identified using MACS2 (Zhang et al., 2008) (version 2.2.7.1) with the parameters ‘–nomodel -f BAMPE -g mm’.
Genome coverage bigwig files were generated by deepTools (Ramirez et al., 2014) (version 3.5.0) bamCoverage with the parameter ‘--scaleFactor 1,000,000/(the number of reads mapped to hg19 genome)’.
Assembly: mm9
Supplementary files format and content: BigWig files
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| Submission date |
Aug 31, 2022 |
| Last update date |
Mar 21, 2024 |
| Contact name |
Dong Fang |
| E-mail(s) |
dfang@zju.edu.cn
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| Organization name |
Zhejiang University
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| Department |
Life Sciences Institute
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| Lab |
Fang lab
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| Street address |
866 Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE212422 |
FUS reads histone H3K36me3 to regulate alternative polyadenylation [RIP-seq] |
| GSE212425 |
FUS reads histone H3K36me3 to regulate alternative polyadenylation |
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| Relations |
| BioSample |
SAMN30616276 |
| SRA |
SRX17382793 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6531673_batch2_rip_seq_Smyd5_KO_Input_rep1.bw |
248.2 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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