|
| Status |
Public on Aug 11, 2021 |
| Title |
Aire-KO rep 3 (mouse) |
| Sample type |
SRA |
| |
|
| Source name |
Oral epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: Non-obese diabetic (NOD)
cell source: Tongue epithelium
age: 8 weeks
Sex: Male
genotype: Aire-/-
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted tongue epithelial cells were lysed in Trizol prior to extraction with the Norgen Biotek RNA Clean-up and Concentration Micro-Elute Kit (cat. # 61000)
Sequencing libraries were prepared by the Illumina Nextera method, following manufacturer's recommendations and sequenced in a NextSeq500 instrument in 150 bp end mode
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CPM_TMM_counts.txt
RawCountFile.txt
|
| Data processing |
Basecalls performed using Illumina’s RTA 2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.5.2a in single-pass mode. With the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.
|
| |
|
| Submission date |
Jul 01, 2019 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Michail Lionakis |
| E-mail(s) |
lionakism@niaid.nih.gov
|
| Phone |
3014435089
|
| Organization name |
National Institutes of Health
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE133603 |
Aberrant type 1 immunity drives mucosal fungal infection susceptibility |
|
| Relations |
| BioSample |
SAMN12172714 |
| SRA |
SRX6385430 |
