|
| Status |
Public on Jun 23, 2020 |
| Title |
Abhd11 OE-1 |
| Sample type |
SRA |
| |
|
| Source name |
mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
passage: passage 3
phenotype: Abhd11 over-expression
|
| Treatment protocol |
Control and Abhd11 KO ESCs were cultured in the absence of Doxycycline; Abhd11 RES ESCs were cultured in the presence of 1ng/ml Dox; Abhd11 OE ESCs were cultured in the presence of 1000ng/ml Dox.
|
| Growth protocol |
murine ESCs were on 0.2% gelatin-coated plates in ESC maintenance medium containing high glucose Dulbecco-modified Eagle medium (DMEM), 5% fetal bovine serum (FBS), 15% KnockOut Serum Replacement (KSR), 2mM Glutamax, 1mM sodium pyruvate, 0.1mM NEAA, 0.1mM b-mercaptoethanol, 100U/ml penicillin, 100U/ml streptomycin (all from Invitrogen) and 10ng/ml LIF (Millipore) at 37°C under 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent(Invitrogen,Cat:15596026) and a miRNeasy Micro Kit (QIAGEN,Cat:217084) according the manufacturer's manual. The RNA quality were measured using Agilent 4200 TapeStation.
RNA samples were send to Genminix Informatic Ltd. (Shanghai, China) for mRNA sequencing on Illumina Hiseq platform (Illumina, San Diego, California, USA) with 6Gbps.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Abhd11 OE ESCs cultured in the presence of 1000ng/ml Doxycyline
|
| Data processing |
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2(version:2.0.4).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after Hisat2 alignment, and then normalized by DESeq2 method. Finally, the count reads value of each gene was calculated.
Genome_build: mm10(GRCm38)
|
| |
|
| Submission date |
Dec 16, 2019 |
| Last update date |
Jun 26, 2020 |
| Contact name |
Rui Jian |
| E-mail(s) |
jianruilq2@aliyun.com
|
| Phone |
+8613627696789
|
| Organization name |
Third Military Medical University
|
| Department |
Department of Histology and Embryology
|
| Lab |
Laboratory of Stem Cell and Developmental Biology
|
| Street address |
Gaotanyan Street
|
| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE142067 |
Gene expression of Abhd11 knock-out or over-expression embryonic stem cells |
|
| Relations |
| BioSample |
SAMN13569004 |
| SRA |
SRX7376194 |
