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| Status |
Public on Oct 01, 2020 |
| Title |
THP1 + LF82 6h in growth medium replicat 1 |
| Sample type |
SRA |
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| Source name |
THP1 macrophages + LF82
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| Organisms |
Homo sapiens; Escherichia coli LF82 |
| Characteristics |
sample name: MB6-1
cell type: THP1 macrophages infected with E. coli LF82
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| Growth protocol |
Macrophages were infected and imaged as previously described (Demarre et al., 2017). Infections were performed at MOI 30 (measured by CFU), resulting in the observation of 3 LF82 bacteria per macrophage on average at 1 h P.I..
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted from THP1 macrophages infected by WT LF82 at 1 h and 6h P.I. Control experiments were performed with macrophages alone and bacteria alone cultivated for 1 h and 6 h in DMEM medium at 37°C and 5% CO2 without agitation. RNA extraction was performed as described before (Demarre et al, 2019).
Experiments were performed from biological duplicate. Human rRNAs were depleted using the Ribo-Zero kit, then strand-specific libraries were constructed using the TruSeq Stranded Total RNA kit (Illumina).
Paired-end sequencing (2 x 100 nt) was performed on a HiSeq 2500 sequencer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
hg19 and NC_011993.1
B120U7
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| Data processing |
Reads alignment was performed using Bowtie 2 (Langmead & Salzberg, 2012) and significant fold changes accessed with the DE-seq pipeline (Anders & Huber, 2010).
Genome_build: hg19 and NC_011993.1
Supplementary_files_format_and_content: Custom interface id, gene name, NCBI ID https://www.ncbi.nlm.nih.gov/nuccore/NC_011993.1, RPKM Condition 1, RPKM condition 2, Fold change (condition 2/condition 1), Deseq P value
Genome_build: hg19
Supplementary_files_format_and_content: gene_id (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25), gene type, gene name, RPKM Condition 1, RPKM condition 2, Fold change (condition 2/condition 1), Deseq P value
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| Submission date |
Jul 17, 2020 |
| Last update date |
Oct 01, 2020 |
| Contact name |
Olivier Espeli |
| E-mail(s) |
olivier.espeli@college-de-france.fr
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| Phone |
33144271249
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| Organization name |
College de France
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| Department |
CIRB
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| Street address |
11 place Marcelin Berthelot
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| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platform ID |
GPL28886 |
| Series (1) |
| GSE154648 |
Dual RNAseq analysis of THP1 macrophages infected by AIEC LF82 bacteria |
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| Relations |
| BioSample |
SAMN15569029 |
| SRA |
SRX8756195 |
| 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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