|
| Status |
Public on May 18, 2021 |
| Title |
ESCs, Ss18-KO.24h.RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells (mESCs)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: OG2 transgenetic mouse embryonic stem cells (OG2ES)
strain: 1/2 129SVJ+3/8 C57B6+1/8 CBA
genotype: c-Jun_TetOn_Ss18-KO_mESC
treatment: treated with doxycycline for 24h
passage: P12
|
| Treatment protocol |
Treated with 2µg/ml doxycycline
|
| Growth protocol |
Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol, according to the manufacturers instructions
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ss18-KO&WT.RNA-seq.merge.csv
|
| Data processing |
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM13) transcriptome using Bowtie2 (v2.2.5) and RSEM (v1.3.0)
Gene expression level was calculated using EDASeq (v2.4.1) GC-normalized method
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated value file containing GC-normalized RNA-seq data
|
| |
|
| Submission date |
Aug 05, 2019 |
| Last update date |
May 18, 2021 |
| Contact name |
kuang junqi |
| E-mail(s) |
kuangjunqi@westlake.edu.cn
|
| Organization name |
westlake University
|
| Street address |
No.18 Shilongshan Road
|
| City |
hangzhou |
| ZIP/Postal code |
310024 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE135397 |
SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [RNA-Seq] |
| GSE135451 |
SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation |
|
| Relations |
| BioSample |
SAMN12497442 |
| SRA |
SRX6657658 |
