|
| Status |
Public on Jan 25, 2024 |
| Title |
Tongue CCL28 Candida-infected_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
tongue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: CCL28-/-
infection: Candida albicans, strain CAF2-1
day after infection: 1
tissue: whole tongue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
tongues were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy mini kit. The concentration was measured with Nanodrop 2000c. RNA samples then were sent on dry ice to Novogene for library preparation and sequecing. Contract ID is H202SC20072776 . Batch ID is X202SC20072776-Z01-F001. Illumina TruSeq RNA Sample Prep Kit (Cat# FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
After enrichment, mRNAs are fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand is subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules are purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs are ligated with P5/P7 sequencing adapters to prepare for hybridization. In order to select the insert fragment of preferentially 150~200 bp in length, the modified libraries are purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library is ready after PCR amplification and products purification by AMPure XP beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
deseq/Differential_Expression__DESeq2__compare_2_groups__on_CCL28_Infected_on_CCL28_Sham.diffexpr.w_symbols.txt
deseq/Differential_Expression__DESeq2__compare_2_groups__on_CCL28_Infected_on_WT_infected.diffexpr.w_symbols.txt
|
| Data processing |
(1) Remove reads containing adapters.
(2) Remove reads containing N > 10% (N represents the base cannot be determined).
(3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Original image data file from high-throughput sequencing is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality
Genome_build: mm10
|
| |
|
| Submission date |
Jan 26, 2021 |
| Last update date |
Jan 25, 2024 |
| Contact name |
Anna R Huppler |
| Organization name |
Medical College of Wisconsin
|
| Department |
Pediatrics
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE165545 |
Tongue RNA expression after oropharyngeal candidiasis in mice deficient in CCL28 |
|
| Relations |
| BioSample |
SAMN17577816 |
| SRA |
SRX9940223 |
