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| Status |
Public on Sep 30, 2022 |
| Title |
5KO,DMSO,RNA,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 |
polyA RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen)
500 ng of total RNA was used for RNA-seq library construction. RNA-seq library was constructed by KAPA mRNA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit (Roche) according to manufacturer instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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
Mapping reads to genome or transcript by TopHat v2.1.1
BigWig files were produced by bamCoverage 2.5.4-1-eca29f6
Assembly: mm10
Supplementary files format and content: bigWIg
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| Submission date |
Sep 30, 2022 |
| Last update date |
Sep 30, 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) |
| GSE200015 |
Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [RNA-Seq] |
| 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 |
SAMN31111927 |
| SRA |
SRX17767700 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6612277_5KO-DMSO-rep1.bam.bw |
14.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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