|
| Status |
Public on Aug 12, 2020 |
| Title |
Control NK cells Ctrl_3 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow NK cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
cell type: bone marrow NK cells
sorting markers: NK1.1+CD49b+
|
| Treatment protocol |
NK cells (NK1.1+CD9b+) were sorted from the bone marrow of Ncr1Cre Id2F/F (Id2KO), Ncr1Cre Tcf7F/F (Tcf1KO), Ncr1Cre Id2F/F Tcf7F/F (DKO) and Id2F/F (Ctrl) mice directly into RLT buffer. Three independent samples per genotype were assessed.
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNAeasy MicroKit (Qiagen) according to manufacturer’s recommendations.
Libraries were constructed using Nugen’s Ovation Ultralow Library systems and were subsequently subjected to 76 cycles of NextSeq500 sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Control NK cells
|
| Data processing |
Raw sequence reads were trimmed using Trimmomatic v 0.33 (TRAILING:30 MINLEN:20)
Trimmed reads were aligned to mouse genome assembly mm10 with Tophat v 2.1.0.
Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.
The R package EdgeR was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups. Genes were considered differentially expressed if the |fold change| >= 2 and FDR < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements provided as edgeR output files
|
| |
|
| Submission date |
Aug 11, 2020 |
| Last update date |
Aug 12, 2020 |
| Contact name |
Barbara L Kee |
| Organization name |
The University of Chicago
|
| Department |
Pathology
|
| Street address |
924 E57th st
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE156046 |
RNA-sequencing data from Ctrl (Id2F/F or Id2F/FTcf7F/F), Ncr1Cre Id2F/F, Ncr1Cre Tcf7F/F and Ncr1Cre Id2F/F Tcf7F/F bone marrow NK cells. |
|
| Relations |
| BioSample |
SAMN15791864 |
| SRA |
SRX8926330 |
