|
| Status |
Public on Jul 20, 2017 |
| Title |
cKO4 |
| Sample type |
SRA |
| |
|
| Source name |
pre-selection DP thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: thymus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Before FACS staining, DN thymocytes were highly purified by depletion of CD4+ and CD8+ and DP thymocytes with AutoMACS. Then, DN NKT cells were FACS sorted using BD FACS Aria, and RNA was prepared using RNeasy Micro Plus kit containing gDNA eliminator columns (Qiagen). RNA was analyzed for quantity and quality using Agilent Bioanalyzer 2100 or Agilent 2200 TapeStation equipment, and 10 ng of total RNA was used with SMARTer Ultra Low Input RNA Kit v3 for Illumina Sequencing (Clontech) for cDNA synthesis.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina. Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
RNA-seq of Bcl11b+/+ CD24hiTCRblo pre-selection DP thymocytes
|
| Data processing |
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using tophat2 (version 2.8.0) with default parameters.
Aligned seqeunces were converted relative expression using cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.
|
| |
|
| Submission date |
Nov 22, 2016 |
| 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 |
GPL18480 |
| Series (1) |
| GSE90134 |
Transcriptome analysis of Bcl11b mutant CD4+CD8+ thymocytes |
|
| Relations |
| BioSample |
SAMN06047067 |
| SRA |
SRX2366842 |
