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| Status |
Public on Apr 07, 2023 |
| Title |
B.subtilis_RedC_rep2 |
| Sample type |
SRA |
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| Source name |
str. 168
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| Organism |
Bacillus subtilis |
| Characteristics |
strain: str. 168
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| Growth protocol |
E. coli DH5α and B. subtilis 168 strains were grown overnight in Luria-Bertani broth at 37 °C and 180 rpm to a final OD600 ~ 1.7.
T. adornatum 1910bT strain was grown on strictly anaerobic modified Pfennig medium supplemented with 0.1 g/L of yeast extract, 1/100 (v/v) of sterile culture broth filtrate of Desulfurococcus sp. 1910a and 1.0 g/L of glucose as the substrate under N2 in the gas phase at 80°C and pH 5.75 to a final growth yield of 3×10^7 cells/mL.
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| Extracted molecule |
other |
| Extraction protocol |
RedC uses custom oligos and adapters resulting in libraries ready for sequencing on the Illumina platform.
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For raw data processing RedClib pipeline was used (github: https://github.com/agalitsyna/RedClib)
Supplementary files format and content: Processed RedC data files are available as TSV files with individual mapped RNA-DNA contacts. Each row corresponds to an individual RNA-DNA contact that passed filtering steps. Columns represent information about 3' RNA, 5' RNA and DNA mapping position (chromosome, start, end, strand), CIGAR string and mapped sequence length.
Library strategy: RedC
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| Submission date |
Jul 27, 2022 |
| Last update date |
Apr 07, 2023 |
| Contact name |
Grigory Evko |
| E-mail(s) |
evko.grigory@gmail.com
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| Phone |
+79189668455
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| Organization name |
Institute of Gene Biology of the Russian Academy of Sciences
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| Lab |
Laboratory of Structural and Functional Organization of Chromosomes
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| Street address |
Vavilova str., 34/5
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| City |
Moscow |
| ZIP/Postal code |
119334 |
| Country |
Russia |
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| Platform ID |
GPL30886 |
| Series (1) |
| GSE209901 |
RNA-DNA interactome of a prokaryotic cell uncovered by proximity ligation |
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| Relations |
| BioSample |
SAMN29998384 |
| SRA |
SRX16694894 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6404256_Bsubtilis_RedC_rep2.tsv.gz |
77.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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