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| Status |
Public on Aug 05, 2023 |
| Title |
bv_negtive_NRF1_OE_3 |
| Sample type |
SRA |
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| Source name |
Embryoidbody
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| Organism |
Mus musculus |
| Characteristics |
tissue: Embryoidbody
cell line: BVSC
cell type: pluripotent stem cells
genotype: NRF1 overexpression
treatment: Induced differentiation
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| Treatment protocol |
The embryoid body (EB) were generated from 1.5 x10e6 PSCs in 10cm petri dishes with differentiation medium including IMDM with 15% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C
For p20 vector-based gene expression induction, 1.5 μg/ml doxycycline were added during differentiation of day 2 to 5.Cells were cultured on a shaker in the cell incubator, with the medium changed every 2 days.
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| Growth protocol |
PSCs were cultured in DMEM (Gibco) with 1 μM PD0325901(Stemgent), 3 μM CHIR99021 (Stemgent), 1,000 units/ml LIF (Gibco),15% FBS (Gibco), 0.05 mM β-mercaptoethanol, 2 mM L-Glu, 0.1 mM NEAA, 100 units/ml penicillin, 0.1mg/ml streptomycin on feeder free wells coated with 0.2% gelatin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested with RNAiso plus kit(Takara).1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers.
First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends.
Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Evaluating the quality of sequencing dataFastQC（v0.10.1）
Sequencing data filtering（version 1.9.1） Remove the adapter sequence;Remove bases with a mass value of less than 20 or containing N at the 5 'or 3' end; Sequences with reads length less than 75 bp after removing trim.
Use Hisat2 (v2.0.1) software for short reads comparison, with default parameters.
Normalization were performed using Htseq software (V0.6.1)
Assembly: GRCm39.107
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample
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| Submission date |
May 04, 2023 |
| Last update date |
Aug 05, 2023 |
| Contact name |
wang pengxiang |
| E-mail(s) |
pxwang@bio.ecnu.edu.cn
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| Organization name |
ECNU
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| Street address |
No.500, Dongchuan Road
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| City |
shanghai |
| ZIP/Postal code |
200241 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE231662 |
NRF1 promotes primordial germ cell development, proliferation, and survival [RNA-seq] |
| GSE231663 |
NRF1 promotes primordial germ cell development, proliferation, and survival |
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| Relations |
| BioSample |
SAMN34586423 |
| SRA |
SRX20220671 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7295410_bv_negtive_NRF1_OE_3.txt.gz |
462.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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