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| Status |
Public on Feb 26, 2024 |
| Title |
Proliferating iMOPs, H3K4me3, CUT&Tag |
| Sample type |
SRA |
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| Source name |
iMOPs
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| Organism |
Mus musculus |
| Characteristics |
antibody: H3K4me3
cell line: iMOPs
cell type: Poliferating iMOPs
genotype: wild-type
treatment: none
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| Growth protocol |
Proliferating iMOPs: DMEM/F12, 1XB27, 25 µg/ml carbenicillin and 20 ng/ml bFGF. iMOP-derived neurons: Neurobasal media, 1XN21, 2 mM L-glutamine, and 1 µM K03861.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
500,000 cells were used for each CUT&Tag library prepration. Cells were incubated with primary antibodies against CHD4, H3K4me3, p300 and IgG (control). DNA libraries were amplified using PCR and purified using SPRI beads. Libraries were sequenced on illumina Hiseq 3000 platform (2X150bp).
pA-Tn5-transposomes mediated tagmentation using CUT&Tag-IT Assay kit (Active Motif).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Paired-end CUT&Tag reads were aligned to the mm10 genome assembly with bowtie2.
deepTools bamCoverage was used to remove duplicate reads and generate normalized bigiwigs files into reads per kilobase per million (RPKM) from individual samples.
Replicate bigiwig files were merged to generate the averaged bigwig files using deepTools bigwigCompare.
Peaks were called using SEACR under stringent conditions using IgG sample as the empirical background
Assembly: mm10
Supplementary files format and content: bigwig, averaged bigwig signals from two replicates
Supplementary files format and content: SEACR peaks (except for IgG control), consensus SEACR peaks from two replicates
Library strategy: CUT&Tag
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| Submission date |
Dec 12, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Kelvin Y. Kwan |
| E-mail(s) |
kelvin.kwan@rutgers.edu
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| Phone |
8484451781
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| Organization name |
Rutgers University
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| Department |
Cell Biology & Neuroscience
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| Street address |
604 Allison Rd.
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| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE250033 |
Chromatin Chromatin remodeling protein CHD4 regulates axon guidance of spiral ganglion neurons in developing inner ear |
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| Relations |
| BioSample |
SAMN38792714 |
| SRA |
SRX22870619 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7971696_P_CUTTag_H3K4me3_mean.bigwig |
38.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM7971696_P_CUTTag_H3K4me3_merged_peaks.bed.gz |
163.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
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