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| Status |
Public on Jul 05, 2019 |
| Title |
Aplus |
| Sample type |
SRA |
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| Source name |
Infected_Bovinealveolarmacrophages
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| Organism |
Bos taurus |
| Characteristics |
animal: Animal 1
condition: Infected
timepoint: 24 HPI
cell type: Bovine alveolar macrophages
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| Treatment protocol |
2 x 10^6 macrophages were seeded in 60 mm tissue culture plates and challenged with M. bovis at an MOI of 10:1 (2 X 107 bacteria per plate) for 24 hours, parallel non-infected controls were prepared simultaneously.
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| Growth protocol |
Centrifuged cell pellet was resuspended in 15 ml of R10+ media and placed in a 75 cm [2] vented culture flask (CELLSTAR®, Greiner Bio-One Ltd., Stonehouse, UK) and incubated for 24 h at 37 °C, 5% CO2. After incubation, media was removed together with non-adherent cells and adherent cells were washed with 15 ml HBSS pre-warmed to 37 °C (Note: all pre-warmed media and solutions were heated to 37 °C prior to use). Adherent cells were dissociated by adding 10 ml pre-warmed 1× non-enzymatic cell dissociation solution (Sigma–Aldrich Ltd.) to each culture flask and incubating at room temperature for 10 min. Cells were then pelleted (200× g for 5 min at room temperature), resuspended in 10 ml pre-warmed R10+ media and the number of viable cells was counted using a Beckman Coulter® Vi-CELL™ XR Cell Viability Analyzer and reagent kit (Beckman Coulter Inc., High Wycombe, UK).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from infected (n = 4) and control (n = 4) bAM samples using the RNeasy Plus Mini Kit (Qiagen) as previously outlined (10.1095/biolreprod.111.094946). All RNA samples were of excellent quality (RIN >9).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
At each step of data processing, read quality was assessed via fastqc version 0.11.5
Sequenced reads were trimmed for adaptor sequence and the raw reads were aligned to the most recent build of the UMD 3.1.1 bovine transcriptome via salmon (version 0.8.1)
Aligned reads were also counted in Salmon and the resulting quantification files were annotated at gene level via tximport (version 3.7)
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Plain text, tab seperated quantification file denoting Name of sequence, Length, Effective Length, TPMs and the number of reads aligned
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| Submission date |
Jul 06, 2018 |
| Last update date |
Jul 05, 2019 |
| Contact name |
Thomas Hall |
| E-mail(s) |
[email protected]
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| Phone |
857168930
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| Organization name |
UCD
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| Department |
Vet sciences
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| Street address |
2, Taney Grove
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| City |
Dublin |
| State/province |
Select One |
| ZIP/Postal code |
D14 KW14 |
| Country |
Ireland |
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| Platform ID |
GPL23295 |
| Series (2) |
| GSE116732 |
Initial host response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes [RNA-seq] |
| GSE116734 |
Initial host response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes. |
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| Relations |
| BioSample |
SAMN09623382 |
| SRA |
SRX4348293 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3259599_Aplus_quant.sf.txt.gz |
331.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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