|
| Status |
Public on Sep 13, 2017 |
| Title |
mRNA_Tbx21_KO_NK_IL15_48h_rpt1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse primary splenic NK cells
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Tbx21-/-
cell type: primary splenic NK cells
culture condition: 48 hour in vitro culture with IL-15.
|
| Growth protocol |
RNAseq IL-15 (version 2): 0.5-2 x 10^5 CD3- CD19- NKp46+ NK cells were purified from spleens of mice by cell sorting (>98% purity; FACSAria III; Becton Dickinson) and cultured for 48 hours in the presence of recombinant mouse IL-15 (20 ng/ml; eBioscience). These were then collected and resuspended in Trizol reagent (Invitrogen) for subsequent RNA isolation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 1% sodium pyruvate, 1% nonessential amino acids, 0.1% β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 0.2-0.5 million cells/ml in flat bottomed, 96 well tissue culture-treated plates (CoStar).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: Total RNA was extracted from 50-500K cells by phenol-chloroform method with GlycoBlue as co-precipitant (7 μg per sample; Life Technologies).
RNA-seq: Single-end libraries were prepared from 0.1-0.5 μg of total RNA using the TruSeq RNA Sample Preparation Kit V2 (Illumina).
RNA-seq: Indexed libraries were multiplexed and sequenced for 50 single read cycles on Illumina HiSeq 2000 or 2500 instruments according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sample20_RNA12
exp ID: 150224_212_213_s16
mRNA
Processed data file: Villarino JEM RPKM table.xlsx
|
| Data processing |
RNA-seq, alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to mouse genome mm9 using TopHat 2.0.8.
RNA-seq, RPKM: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *bw: bigWig files include ChIP-seq peaks.
Supplementary_files_format_and_content: JEM_RPKM_table.xlsx: Excel file includes RPKM values.
|
| |
|
| Submission date |
Jun 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuka Kanno |
| E-mail(s) |
kannoy@mail.nih.gov
|
| Phone |
301-402-3008
|
| Organization name |
NIH
|
| Department |
NIAMS
|
| Lab |
LCBS-MIIB
|
| Street address |
10 Center Drive, Rm13C120
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-1930 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE100674 |
Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells |
|
| Relations |
| BioSample |
SAMN07304812 |
| SRA |
SRX2975373 |
