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| Status |
Public on Aug 11, 2015 |
| Title |
ChIP-exo RpoS pH5.5 1 |
| Sample type |
SRA |
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| Source name |
Immunoprecipitated DNA
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| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: K-12 MG1655
genotype: WT
chip antibody: anti-RpoS (neoclone, WP009)
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| Growth protocol |
E. coli K-12 MG1655 WT, GadE-8-myc, GadW-8-myc, and GadX-8-myc tagged strains were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| Data processing |
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters -S
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: ASM584v2
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).
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| Submission date |
Mar 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Donghyuk Kim |
| E-mail(s) |
dkim@unist.ac.kr
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| Organization name |
UNIST
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| Department |
Department of Chemical Engineering
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| Lab |
Systems Biology Lab
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| Street address |
50 UNIST-gil, Eonyang-eup, Ulju-gun
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| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
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| Platform ID |
GPL17439 |
| Series (2) |
| GSE66441 |
Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [ChIP-seq] |
| GSE66482 |
Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli |
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| Relations |
| BioSample |
SAMN03402346 |
| SRA |
SRX955681 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1633277_chipexo_rpoS_ph5.5_1.gff.gz |
31.7 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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