|
| Status |
Public on Mar 29, 2021 |
| Title |
gso30.IFNAR.N.N.4h.4 |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow Derived Macrophages
|
| Organism |
Mus musculus |
| Characteristics |
cell type: M-CSF differentiated bone marrow derived macrophages
experiment: gso30
genotype: IFNAR KO
treatment: Untreated
infection: Mock infected
hour post infection: 4
mouse identifier: 4
sequencing: Psomagen
|
| Treatment protocol |
Conditions had 2 possible interventions, treatment with either recombinant IFNbeta (500 U/mL) or media for four hours, and then infection with either live or heat-killed H37Rv (Mycobacterium tuberculosis strain) (at an MOI 10) or mock-infected for 4 or 24 hours before RNA collection.
|
| Growth protocol |
Bone marrow was harvested from femurs and bone marrow derived macrophages differentiated in RPMI + 50 ng/mL rM-CSF for 6 days before plating.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in TRIzol reagent and frozen at -80. TRIzol was thawed and total RNA extracted using Zymo Research Direct-zol extraction kits according to manufacturer's instruction, including an on-column DNase treatment.
For samples with sequencing characteristic "BGI": RNA samples were sent to BGI (bgi.com) for library preparation and sequencing. The BGI BV01 library prep was used and then the libraries were sequenced on their DNBSEQ-G400 platform. For samples with sequencing characteristic "Psomagen": RNA samples were sent to Psomagen (psomagen.com) for library preparation and sequencing. The Illumina TruSeq stranded kit was used for library prep and then the libraries were sequenced on an Illumina NovaSeq6000 S4.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Title code = experiment.genotype.treatment.infection.infectionTime.mouse
|
| Data processing |
Perform initial quality assessment using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) version 0.11.9
Read ends consisting of 50 or more of the same nucleotide were removed.
Reads were aligned to the mouse genome using GSNAP version 2018-07-04 (http://research-pub.gene.com/gmap/) called with args: gsnap.avx2 -N 1 -t 23 -D /gmapdb -d mm10ex_MTb -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 --format=sam
Feature counts were extracted from gsnap outputs using the featureCounts software (http://bioinf.wehi.edu.au/featureCounts/) part of Subread package v1.5.2
Differential expression of genes was calculated using edgeR (http://bioconductor.org/packages/edgeR/) version 3.26.8
Genome_build: mm10 + H37Rv Mtb
Supplementary_files_format_and_content: a .tsv with rows of raw counts of all genes (identified by MGI name in "gene" column and Ensembl stable ID in "Geneid" column) detected in at least 2 samples for each sample as columns (sample titles are column headers)
|
| |
|
| Submission date |
Dec 03, 2020 |
| Last update date |
Mar 29, 2021 |
| Contact name |
Aderem Lab |
| E-mail(s) |
[email protected]
|
| Organization name |
Seattle Children's Research Institute
|
| Lab |
Aderem Lab
|
| Street address |
307 Westlake Avenue North, Suite 500
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE162620 |
Gene expression analysis of WT, IFNAR KO, or STING KO bone marrow derived macrophages treated with IFNbeta and/or infected with live or heat killed Mycobacterium tuberculosis |
|
| Relations |
| BioSample |
SAMN16988837 |
| SRA |
SRX9627446 |
