|
| Status |
Public on Dec 31, 2015 |
| Title |
NKT-3_5 |
| Sample type |
SRA |
| |
|
| Source name |
NKT stage-3
|
| Organism |
Mus musculus |
| Characteristics |
cell type: thymocyte
strain: C57BL/6
age: 6-to-8 wk old
|
| Growth protocol |
DN1eP thymocytes were cultured for 10 days on OP9/Dll-1 stromal monolayer in the presence of mouse IL-2 (5 ng/ml) and mouse IL-7 (5 ng/ml), both from R&D, in a complete RPMI1640 culture medium supplemented with 10% FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thymocyted were highly purified using standard methods, including MACS sorting followed by FACS sorting, and RNA was prepared using RNeasy Micro Plus kit containing gDNA eliminator columns. RNA was analyzed for quantity and quality using Agilent Bioanalyzer 2100 equipment. and around 10-to-100 ng of total RNA was used with SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech) or Illumina TruSeq RNA Sample Prep Kit v2 for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Surface Valpha14Jalpha18 TCR positive
|
| Data processing |
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
RNA-seq reads were aligned to mm9 genome using tophat2 (version 2.0.6) with default parameters.
Aligned reads were assigned to genes and counted using cufflinks version 2.1.1) with default parameters and annotation file of mouse Entrez genes.
Genome_build: mm9 (NCBI version 37.2)
Supplementary_files_format_and_content: FPKM (cufflinks output, tab-separated values)
|
| |
|
| Submission date |
Dec 09, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
takaho.endo@riken.jp
|
| Organization name |
RIKEN
|
| Department |
IMS
|
| Lab |
Laboratory for Integrative Genomics
|
| Street address |
1-7-22 Suehiro, Tsurumi
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE53150 |
RNAseq analysis of mature thymic NKT cells and immature thymic DN1eP cells |
|
| Relations |
| BioSample |
SAMN02439432 |
| SRA |
SRX389419 |
