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| Status |
Public on Apr 05, 2022 |
| Title |
5KO,DMSO,Inp,rep1 |
| Sample type |
SRA |
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| Source name |
#55
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| Organism |
Mus musculus |
| Characteristics |
cell line: #55
cell type: iMEFs
genotype: 5KO
treatment: DMSO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP DNA was fragmented by Picoruptor (Diagenode) for 10 cycles of 30 seconds on, 30 seconds off. Then, ChIP library was constructed by KAPA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit A (Roche) according to manufacturer instructions. The concentration of the ChIP-seq library was quantified by KAPA Library quantification kit (KAPA BIOSYSTEMS). ChIP sequencing was performed on a HiSeq X platform (Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Adaptor sequences and low quality bases in reads were trimmed using Trim Galore version 0.3.7
Then trimmed reads were aligned to the mouse GRCm38 genome assembly using bowtie version 0.12.7
Duplicated reads were removed using samtools version 0.1.18
BigWig files were produced by bamCoverage 2.5.4-1-eca29f6
RPKM value in each 10kb bin was calculated by featureCounts and house perl script, then Log2(FC) against input was calculated and quantile normalization was performed by house perl script
Assembly: mm10
Supplementary files format and content: wig or bigWIg
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| Submission date |
Apr 02, 2022 |
| Last update date |
Apr 07, 2022 |
| Contact name |
Kei Fukuda |
| E-mail(s) |
kefukuda8@gmail.com
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| Organization name |
RIKEN
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| Lab |
Cellular memory
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| Street address |
2-1 Hrosawa, Wakoshi
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| City |
Saitama |
| State/province |
Japan |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE200014 |
Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [HistoneLamin] |
| GSE200016 |
Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway |
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| Relations |
| BioSample |
SAMN27252709 |
| SRA |
SRX14708526 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6004847_5KO-Inp-rep1_L4_rmdup.bam.bw |
1.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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