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| Status |
Public on Apr 06, 2021 |
| Title |
NCM3722 |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Escherichia coli |
| Characteristics |
strain: NCM3722
growth medium: M9 + 0.5% glucose
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| Growth protocol |
Pre-cultures were diluted to OD600=0.003 in 250 mL fresh media. The culture was kept in 2.8 L flask at 37C with aeration (220 rpm) until OD600 reached 0.3.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction was performed as described in detail previously (Li et al., Cell 2014). 250 mL of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 mL canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C.
To multiplex cDNA library preparation with other experiments, ribosome protected mRNA fragments were pooled 1:1 with B. subtilis ribosome protected fragments (demultiplexing is possible & unambiguous downstream by read alignment). Ribosome protected mRNA fragments were size selected via gel purification, dephosphorylated at the 3’ end and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ribosome protected mRNA
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| Data processing |
Base calls performed using Casava version 1.7.
Trimmed reads were aligned to CP011495.1 and CP011496.1 using Bowtie v1.0.1 with options -v 1 -k 2 -m 2. To deal with non-template addition during reverse transcription, reads with a mismatch at their 5' end had their 5' end re-assigned to the immediate next downstream position. The footprint reads with size between 15 to 42 nucleotides in length were mapped to the genome using the center-weighted approach; for each footprint read, the center residues that are at least 10 nucleotides away from either ends were given a weight of one over the length of the fragment (minus the 10 nucleotides on both ends) to generate the wig file.
genome build: CP011495.1
genome build: CP011496.1
Base calls performed using Casava version 1.7.
Supplementary_files_format_and_content: wiggle file with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).
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| Submission date |
Nov 05, 2019 |
| Last update date |
Apr 09, 2021 |
| Contact name |
Jean-Benoit Lalanne |
| E-mail(s) |
lalannej@uw.edu
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| Organization name |
University of Washington
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| Department |
Genome Sciences
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| Lab |
Jay Shendure
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platform ID |
GPL21222 |
| Series (1) |
| GSE139983 |
From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions |
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| Relations |
| BioSample |
SAMN13218655 |
| SRA |
SRX7101497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4151082_NCM3722_CP011495.1_ribo_pool_v1m2k2_f.wig.gz |
2.9 Mb |
(ftp)(http) |
WIG |
| GSM4151082_NCM3722_CP011495.1_ribo_pool_v1m2k2_r.wig.gz |
3.1 Mb |
(ftp)(http) |
WIG |
| GSM4151082_NCM3722_CP011496.1_ribo_pool_v1m2k2_f.wig.gz |
43.5 Kb |
(ftp)(http) |
WIG |
| GSM4151082_NCM3722_CP011496.1_ribo_pool_v1m2k2_r.wig.gz |
23.6 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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