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| Status |
Public on Mar 21, 2024 |
| Title |
batch1_Fus_Fus_KO1_rep2 |
| 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: Fus KO
treatment: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
105 cells were collected in NE buffer (20 mM HEPES pH 7.5, 0.5 mM spermidine, 10 mM KCl, 0.1% TritonX-100, 10% Glycerol, and 1 mM PMSF) and kept on ice for 10 min.
10 µl ConA beads which were pre-washed by binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2) were added to each sample and incubated at room temperature for 10 min. After being washed with washing buffer (20 mM HEPES pH 7.5, 0.5 mM spermidine, 150 mM NaCl, and 0.1% BSA) once, beads were incubated with blocking buffer (20 mM HEPES pH 7.5, 0.5 mM spermidine, 150 mM NaCl, 0.1% BSA, and 2 mM EDTA) at room temperature for 5 min. Samples were incubated with diluted primary antibodies (1:100 dilution in washing buffer) at room temperature for 2 h. After washing with washing buffer once, secondary antibodies were added at a 1:100 dilution and incubated at room temperature for 30 min. PA-Tn5 transposons were then added and incubated at room temperature for 30 min. Beads were washed with washing buffer twice and incubated with 10 mM MgCl2 in washing buffer at 37 °C for 1h. The 30 μl tagmentation reaction was stopped by adding 2.25 μl 0.5 M EDTA, 2.75 μl 10% SDS, and 0.5 μl 20 mg/ml Proteinase K and incubated at 55 °C for 30 min, and then 70 °C for 20 min. DNA was purified by 0.9X of VAHTS DNA clean beads (VAHTS, Cat. #N411-03).
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| Library strategy |
OTHER |
| Library source |
genomic |
| 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).
Peaks were identified using MACS2 (Zhang et al., 2008) (version 2.2.7.1) with the parameters ‘–nomodel -f BAMPE -g mm’. For H3K27me3 and H3K36me3 modifications, parameter ‘--broad’ was added.
Genome coverage bigwig files were generated by BEDtools (Quinlan, 2014) (version 3.5.0) genomecov and bedGraphToBigWig (version 4) (https://www.encodeproject.org/software/bedgraphtobigwig/) with the parameter ‘-scale 10,000,000/mapped_reads_number’.
Assembly: mm9
Supplementary files format and content: BigWig files
Library strategy: CUT&Tag
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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) |
| GSE212423 |
FUS reads histone H3K36me3 to regulate alternative polyadenylation [CUT&Tag] |
| GSE212425 |
FUS reads histone H3K36me3 to regulate alternative polyadenylation |
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| Relations |
| BioSample |
SAMN30616273 |
| SRA |
SRX17382706 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6531683_batch1_Fus_Fus_KO1_rep2.bw |
7.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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