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| Status |
Public on Apr 26, 2021 |
| Title |
PVG_Untreated_Control_Saline_0_bone_marrow_rep1 |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: PVG
treatment group: Untreated
experimental group: virus: Control
experimental group: ova: Saline
experimental group: days post infection (dpi): 0
Sex: male
rna integrity number: 9.4
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions of bone marrow and lung tissue were resuspended in RNAlater (Ambion, Life Technologies, Mulgrave, VIC, Australia), and frozen at -80°C. Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (Qiagen Gmbh, Hilden, Germany). Total RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit, Illumina Inc, San Diego, CA. Sequencing was performed by the Australian Genome Research Facility (Illumina HiSeq2500, 50bp single-end reads, v4 chemistry).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
genecounts_bonemarrow.csv
RB48_HGMMWDMXX_ACCTTGGC.GGCCTCAT_L001_R1.fastq.gz
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| Data processing |
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.3.0 and Real Time Analysis (RTA) vv3.3.3, running on the instrument computer. RTA performs real-time base calling on the NovaSeq instrument computer.
Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data
Read libraries were mapped to the rat genome (rn6) using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Genome_build: rn6
Supplementary_files_format_and_content: genecounts_lung.csv and genecounts_bonemarrow.csv files contain a matrix of raw gene counts (unfiltered and un-normalised data)
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| Submission date |
Sep 03, 2020 |
| Last update date |
Apr 26, 2021 |
| Contact name |
Emma de Jong |
| E-mail(s) |
emma.dejong@telethonkids.org.au
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| Organization name |
Telethon Kids Institute
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| Street address |
15 Hospital Ave
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| City |
Nedlands, Perth |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE157441 |
Targeting IRF7 asthma phenotypes through immuno-modulation therapy |
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| Relations |
| BioSample |
SAMN16054055 |
| SRA |
SRX9070068 |
| 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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