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| Status |
Public on Oct 01, 2021 |
| Title |
Δhfq RDM logarithmic rep 2 -RNA-seq |
| Sample type |
SRA |
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| Source name |
Culture lysate
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| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: K12 MG1661
genotype: {delta}hfq
media: M9 Rich Defined Media (RDM) + glucose
time of harvest: logarithmic phase
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples: NEBNext Ultra 2 Directional RNA kit
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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 |
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
After alignment to the U00096.3 genome, we performed gene-level quantitation with htseq-count, using union mode for scoring and all mode for non-unique assignments (appropriate for polycistronic mRNAs where a single read is often expected to span multiple genes). Differential expression calling was then performed using deseq2 with default settings.
Genome_build: E. coli U00096.3
Supplementary_files_format_and_content: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input V6rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text. Tsv files – differential expression calling from sleuth
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| Submission date |
Jan 13, 2021 |
| Last update date |
Dec 28, 2021 |
| Contact name |
Lydia Freddolino |
| E-mail(s) |
[email protected]
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| Organization name |
University of Michigan
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| Department |
Biological Chemistry
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| Lab |
Freddolino Lab
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| Street address |
1150 W. Medical Center Dr., MSRB 3 room 3315
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-0600 |
| Country |
USA |
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| Platform ID |
GPL18956 |
| Series (1) |
| GSE164796 |
IPOD-HR, ChIP-seq, RNA-seq of E. coli nucleoid associated protein deletions |
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| Relations |
| BioSample |
SAMN17310719 |
| SRA |
SRX9847195 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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