|
| Status |
Public on Nov 20, 2013 |
| Title |
WT_Undifferentiated |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype/variation: Wild type
treatment: KSR+LIF
|
| Growth protocol |
Differentiating embryonic stem cells are cultured on a gelatin-coated 100-mm dish with 10% serum for 2 days in the presence of 10 nM retinoic acid. Undifferentiated embryonic stem cells are maintained in the presence of KSR (15%), LIF (1,000U), serum (1%).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Isogen II reagent (Nippongene). The total RNA was further treated with DNase I and purified by aid of RNeasy Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA 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 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
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 |
Jun 28, 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) |
| GSE48419 |
Gene expression analysis of Ash1l mutant mouse embryonic stem cells. |
|
| Relations |
| BioSample |
SAMN02216977 |
| SRA |
SRX316678 |
