|
| Status |
Public on Mar 16, 2017 |
| Title |
Ring1A-/-; Ring1B fl/fl; Rosa26 tg/+ ESCs (OHT-; Ring1A-/-)_S01670 |
| Sample type |
SRA |
| |
|
| Source name |
Ring1A-/-; Ring1B fl/fl; Rosa26 tg/+ ESCs (OHT-; Ring1A-/-)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: ESC
treatment: OHT-
genotype/variation: Ring1A-/-
|
| Treatment protocol |
Cells were cultured with complete, cysteine deficient, or valine deficient media with SCF and TPO for 24 hours.
|
| Growth protocol |
ES cells were cultured in standard condition
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Genomic DNA was isolated using QIAGEN All-prep kit
Library was prepared according to Illumina TruSeq protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
S01670
|
| 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 to relative expression using cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] plain text containig FPKM (fragments per kilobase exon per million reads) values.
|
| |
|
| Submission date |
Jul 16, 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 (2) |
| GSE84480 |
PCGF6-PRC1 suppresses premature differentiation of embryonic stem cells by silencing germ cell-related genes [RNA-Seq] |
| GSE87485 |
PCGF6-PRC1 suppresses premature differentiation of embryonic stem cells by silencing germ cell-related genes |
|
| Relations |
| BioSample |
SAMN05412426 |
| SRA |
SRX1954151 |
