|
| Status |
Public on Dec 20, 2017 |
| Title |
WT_M1 |
| Sample type |
SRA |
| |
|
| Source name |
splenic NK cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Runx1WT
replicate: 2
ly49expression: HPOS
condition: MCMVD3
cell type: splenic NK cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted directly into Trizol and total RNA underwent amplification using SMART-seq V4 (Clontech) Ultra Low Input RNA kit.
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 47 million paired reads were generated per sample and the percent of mRNA bases was over to 72% on average.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RUNX1KOChimera_MCMV_F1M1M2_rawCounts_knownGene.txt
|
| Data processing |
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Genome_build: mm10
Supplementary_files_format_and_content: Text files are raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)
|
| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Colleen Lau |
| Organization name |
Cornell University
|
| Department |
Microbiology & Immunology
|
| Street address |
930 Campus Road
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE106138 |
Transcriptional regulation of adaptive NK and CD8 T cell responses [RNA-Seq] |
| GSE106139 |
Regulation of natural killer cells during MCMV infection |
|
| Relations |
| BioSample |
SAMN07833690 |
| SRA |
SRX3324183 |
