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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 11, 2018 |
| Title |
ORF1_2_IPTG |
| Sample type |
SRA |
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| Source name |
E. coli MG1655 / pORF1
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| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
induction: induced 50 µM IPTG
replicates: ORF1 replicate 2 / induced
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| Treatment protocol |
The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics.
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| Growth protocol |
Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol. The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated. The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing.
TruSeq
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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 |
BGI inhouse software “filter_fq” for basecalling and trimming
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline.
Genome_build: NC_000913
Supplementary_files_format_and_content: The columns in the processed files are the following in order: GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process
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| Submission date |
Dec 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dan I. Andersson |
| E-mail(s) |
[email protected]
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| Organization name |
Uppsala University
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| Department |
Department of Medical Biochemistry and Microbiology
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| Street address |
Box 582
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| City |
Uppsala |
| ZIP/Postal code |
SE-751 23 |
| Country |
Sweden |
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| Platform ID |
GPL18956 |
| Series (1) |
| GSE92601 |
A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function. |
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| Relations |
| BioSample |
SAMN06166431 |
| SRA |
SRX2436327 |
| 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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