|
| Status |
Public on Jun 12, 2019 |
| Title |
B6.bead.beadPos.24.AD51617 |
| Sample type |
SRA |
| |
|
| Source name |
Alveolar macrophages
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Alveolar macrophages
strain/genotype: C57BL/6
infectious challenge: bead
infection status: beadPos
time infected (hrs): 24
library version: SMARTerPicoV2
experiment label: AD51617
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
cDNA libraries were constructed and amplified using the SMARTer Stranded Total RNA-Seq Kit (v1 or v2) - Pico Input Mammalian (Clontech) per the manufacturers instructions. Libraries were amplified and then sequenced on an Illumina NextSeq (2 x 75, paired-end).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Stranded paired-end reads of length 76 were preprocessed: The first three nucleotides of R1 (v1 kit) or R2 (v2 kit) were removed as described in the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian User Manual (v1: 112215, v2: 063017) and read ends consisting of 50 or more of the same nucleotide were removed.
The remaining read pairs were aligned to the mouse genome (mm10) + Mtb H37Rv genome using the gsnap aligner (v. 2016-08-24) allowing for novel splicing. (gsnap options: -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 )
Concordantly mapping read pairs (average 15-million / sample) that aligned uniquely were assigned to exons using the subRead program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
Genome_build: mm10 + Mtb H37Rv
Supplementary_files_format_and_content: rawCounts.tsv contains the raw counts for each sample generated by subRead, tab-separated
|
| |
|
| Submission date |
Jan 17, 2019 |
| Last update date |
Jun 12, 2019 |
| Contact name |
Aderem Lab |
| E-mail(s) |
alan.diercks@seattlechildrens.org
|
| 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 |
GPL19057 |
| Series (1) |
| GSE125287 |
Gene expression analysis of mouse alveolar macrophages infected with Mycobacterium tuberculosis |
|
| Relations |
| BioSample |
SAMN10767256 |
| SRA |
SRX5259281 |
