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| Status |
Public on Feb 03, 2018 |
| Title |
naïve-2 |
| Sample type |
SRA |
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| Source name |
naïve, spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: CB57BL/6NCrl
agent: naïve
tissue: spleen
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| Treatment protocol |
SLRs were complexed to in vivo-jetPEI® (Polyplus transfection) according to manufacturer’s instructions, with N/P ratio = 8. 25 µg of RNA in a 200 µl volume was injection per mouse intravenous
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues collected into RNAlater were blotted dry and transferred into Trizol (Thermo Fisher Scientific) in a Lysing Matrix D tube (MP Biomedical) for homogenization. Supernatant was collected for chloroform phase separation and RNA was precipitated using isopropyl alcohol. The RNA pellet was then washed with 75% ethanol and redissolved in water.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequenced reads were checked for quality control using the FastQC tool (Babraham Bioinformatics, Babraham Institute, Cambridge, UK). Good quality reads were mapped to the reference genome (GRCm38/mm10) using the software package Tophat v 2.0.6. Default settings were used, except for the mean inner mate distance between the pairs that was set to 150bp. A maximum of two mismatches and a minimum length of 36 bp per segment were allowed.
The BAM files from Tophat were then converted to SAM format by Samtools (v 1.4) and raw counts estimated by the Python script HTSeq count. Reference GTF file for gene annotation was downloaded from iGenomes website.
EdgeR was used to calculate normalized gene expression levels, represented as counts per million (CPM). CPMs were calculated for 39,169 transcripts from the Ensembl database.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file contains CPM values for annotated transcripts for all samples
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| Submission date |
Nov 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Marie Pyle |
| E-mail(s) |
anna.pyle@yale.edu
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| Organization name |
Yale University
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| Street address |
219 Prospect St.
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE106229 |
Gene expression changes upon activation of RIG-I by a minimal potent RIG-I ligand |
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| Relations |
| BioSample |
SAMN08024440 |
| SRA |
SRX3389692 |
| 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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