|
| Status |
Public on Apr 20, 2024 |
| Title |
MAP8.B6.Ly49h_WT_Hn_RNA |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Spleen
cell type: Natural killer cells
subset: Ly49H-
genotype: MAP8.B6.Ly49h_WT/Ly49KO
treatment: ex vivo
marker: singlet CD4-CD8-TCRBeta-CD19-NK1.1+NKp46+CD49a-CD49b+
|
| Treatment protocol |
Splenic NK cells were FACS-sorted from mice
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from sorted cells was extracted using Quick-RNA Microprep Kit (Zymo Research, R1050).
50-100 ng of total RNA was processed with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760) to generate mRNA-seq libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
singlet CD4-CD8-TCRβ-CD19-NK1.1+NKp46+CD49a-CD49b+
|
| Data processing |
STAR (v 2.5.4b) was used for alignment
“sambamba markdup” was used to remove PCR duplicates from paired-end libraries
reads with MAPQ < 30 were removed
"featureCounts -t exon --fracOverlap 0.5” from subread (v2.0.0) was used to count the number of reads overlapping the exons of each gene
Assembly: mm10
Supplementary files format and content: tsv: raw read counts for each gene in each sample
|
| |
|
| Submission date |
Mar 02, 2023 |
| Last update date |
Apr 20, 2024 |
| Contact name |
Changxu Fan |
| E-mail(s) |
fanc@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue, Room 5213
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE226497 |
Epigenetic evolution of the Ly49 gene family [RNA-seq] |
| GSE226502 |
Epigenetic evolution of the Ly49 gene family |
|
| Relations |
| BioSample |
SAMN33571788 |
| SRA |
SRX19551509 |
