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| Status |
Public on Dec 28, 2020 |
| Title |
3C_Sis_transgene_suc_rep2 |
| Sample type |
SRA |
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| Source name |
Microorganism
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| Organism |
Sulfolobus islandicus |
| Characteristics |
genotype: DpyrEF DlacS DargD SiRe_0163::ParaS-lacS-argD
developmental stage: Log-phase cells supplied with sucrose and grown shaking
strain: REY15A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To prepare the material for 3C-seq library construction, cells were crosslinked, permeabilized, and treated with AluI. The DNA was then subjected to proximity ligation, crosslink reversal, and phenol extraction followed by isopropanol precipitation. Libraries were constructed using NEBNext Ultra DNA Library Prep Kit for Illumina.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
3C-seq reads were mapped to the genome of S. acidocaldarius DSM639 (GenBank ID: CP000077.1) or S. islandicus REY15A (GenBank ID: CP002425.1) using HiC-Pro version 2.9.0 (Servant et al., 2015) with default parameters. The genomic coordinates of each Sulfolobus species were re-defined so that they started from the first base of the AluI site in the original definition. Valid read were used to generate raw contact matrices. The intra-bin ligations were discarded by setting the values on the corresponding diagonal to zero. The raw contact matrices were iteratively corrected with MAX_ITER = 500 (and FILTER_LOW_COUNT_PERC = 0.01 for S. islandicus) to generate normalized contact matrices.
To calculate Transcripts Per Million (TPM), RNA-seq reads from each biological replicate were mapped in a strand-specific manner using Salmon version 0.8.2 (Patro et al., 2017). When gene expression was quantified at the operon level, reads were mapped to operons predicted by Operon-mapper (Taboada et al., 2018).
Genome_build: CP000077.1, CP002425.1
Supplementary_files_format_and_content: 3C-seq: tab-delimited tables. The first and second columns show genomic bins. The third column shows interaction scores (raw number of reads or normalized value) between bins in the first and second columns. RNA-seq: tab-delimited tables showing Transcripts Per Million (TPM) values for each genes.
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| Submission date |
Oct 19, 2020 |
| Last update date |
Dec 28, 2020 |
| Contact name |
Naomichi Takemata |
| Organization name |
Kyoto University
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| Department |
Synthetic Chemistry and Biological Chemistry
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| Street address |
Kyoto University, Katsura, Nishikyo-ku
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| City |
Kyoto |
| ZIP/Postal code |
615-8510 |
| Country |
Japan |
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| Platform ID |
GPL26275 |
| Series (1) |
| GSE159537 |
Multi-scale architecture of archaeal chromosomes |
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| Relations |
| BioSample |
SAMN16474859 |
| SRA |
SRX9296612 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4832116_Norm3C_Sis_transgene_suc_rep2.txt.gz |
10.8 Mb |
(ftp)(http) |
TXT |
| GSM4832116_Raw3C_Sis_transgene_suc_rep2.txt.gz |
4.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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