|
| Status |
Public on Sep 13, 2019 |
| Title |
NKp46+ ILC3 Maf+/+ Il7rCre RNA-seq Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Maf WT NKp46+ ILC3
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl/6 (N5 backcross)
genotype/variation: Maf WT
age: adult
tissue: small intestine lamina propria
cell type: NKp46+ ILC3
|
| Growth protocol |
Mice were maintained under specific pathogen-free conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5,000-15,000 sort purified Nkp46+ ILC3 (CD3-CD19-CD127+CD90hiKLRG1-CCR6-NKp46+) and CCR6+ ILC3 (CD3-CD19-CD127+CD90hiKLRG1-CCR6+NKp46-) and approximately 17,000 ILC2 (CD3-CD19-CD127+KLRG1+) from Maf+/+Il7rCre and Maffl/flIl7rCre SILP were frozen in Trizol. RNA was purified from the aqueous phase using the RNeasy Plus Micro Kit (Qiagen).
Libraries were constructed from RNA using the Clontech SMARTer v3/v4 ultra-low input RNA-Seq kit (Takara Biosciences).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Nkp46_ILC3.rnaseq.Maf_WT.rep2
|
| Data processing |
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest mouse reference genome (GRCm38) using the aligner STAR v2.4.1a following the proposed 2-pass strategy, removing alignments containing non-canonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical)
Aligned reads were assigned to genes in the GENCODE vM13 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1). Briefly, raw counts were imported and filtered to remove genes with low or no expression, that is, keeping genes having two or more counts per million (CPMs) in two or more samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files with raw gene counts
|
| |
|
| Submission date |
Sep 12, 2019 |
| Last update date |
Sep 13, 2019 |
| Contact name |
Maria Ciofani |
| E-mail(s) |
maria.ciofani@duke.edu
|
| Organization name |
Duke University School of Medicine
|
| Department |
Integrative Immunobiology
|
| Street address |
207 Research Drive, 128 Jones Building
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE137321 |
c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program [RNA-seq] |
| GSE137322 |
c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program |
|
| Relations |
| BioSample |
SAMN12736167 |
| SRA |
SRX6835349 |
