|
| Status |
Public on Nov 13, 2017 |
| Title |
ILC2IL-33 Expand_ILC2 |
| Sample type |
SRA |
| |
|
| Source name |
lung innate lymphoid type-2 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: cells from mice injected with IL-33
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted and purified from lung (ILC2) or spleen (Treg) using the RNeasy Plus Mini Kit (Qiagen) per manufacturers instructions
Libraries of ILC2PBS and ILC2IL-33 samples were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech) as previously described. Briefly, the protocols for enzymatic fragmentation and ligation of the Ion Xpress Plus Fragment Library Kit (Life Technologies) were adjusted for our low-input total RNA of samples. Then resulting cDNA libraries were amplified onto Ion Sphere Particles with an Ion PI template OT2 200 Kit v3 (Life Technologies) and sequenced on an Ion Proton (Life Technologies) to generate an average depth of 20 million single-end 200bp reads, with less than 6.7% of the reads from ribosomal RNA and over 94% of the reads mapping to the mouse genome. Similarly, libraries of ILC2_act, ILC2_10, Treg_10- and Treg_10+ samples were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech), indexed using Nextera indices (Illumina) and sequenced on a NextSeq 500 (Illumina) using 75bp single-end sequencing kit per the manufacturer’s instructions. On average, about 10 million reads were generated from each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
cells from mice injected with IL-33
|
| Data processing |
The raw reads were were aligned by Tophat v2.1.0 to the mouse GRCm38assembly with GENCODE M9 annotations downloaded fromhttp://www.gencodegenes.org/. RPKM (Reads Per Kilobase of transcript perMillion mapped reads) values were calculated for lncRNA and protein codinggenes with Cufflinks 2.2.1 software. RPKM levels below 1.0 were set to a “floor”value of 1.0.
Genome_build: GRCm38 assembly with GENCODE M9 annotations
Supplementary_files_format_and_content: xlsx files include RPKM values for each Sample calculated by Cufflinks
|
| |
|
| Submission date |
May 25, 2016 |
| Last update date |
Oct 11, 2021 |
| Contact name |
AGCT Core |
| Organization name |
Cedars Sinai Medical Center
|
| Department |
BMS
|
| Street address |
8687 Melrose Ave, PDC B230
|
| City |
West Hollywood |
| State/province |
CA |
| ZIP/Postal code |
90069 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE81882 |
Identification of a distinct IL-10 producing subset of innate lymphoid type-2 effector cells with regulatory potential |
|
| Relations |
| BioSample |
SAMN05176202 |
| SRA |
SRX1799609 |
