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| Status |
Public on Aug 05, 2023 |
| Title |
BVSC_Input_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
chip antibody: none
genotype: Blimp1_mVenus_stella_ECFP
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
Cells were cultured on a shaker in the cell incubator for 5 days, 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 |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, ChIP was performed using a SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, #9005) .
Immunoprecipitated DNA were quantified using a Qubit 3.0 Fluorometer (Invitrogen) and qualified with an Agilent Bioanalyzer 2100 (Agilent Technologies). The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang.
Each sample was then amplified by PCR using P5 and P7 primers. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Using software Bcl2Fastq (v2.20.0.422) for image base recognition (Base Calling) on the original image data of sequencing results.
The quality evaluation of sequencing data was analyzed using software FastQC (v0.11.4).Use bowtie2 (Version: 2.2.6) alignment software to compare clean data to the reference genome sequence and calculate the alignment results.
Useing MACS2 software for peak extraction, and annotate Peaks using the R package ChIPseeker.
Detecting Significant Motif Sequences in Peaks Sequences Using MEME Software
Assembly: GRCm39.107
Supplementary files format and content: bigWig
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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) |
| GSE231661 |
NRF1 promotes primordial germ cell development, proliferation and survival [ChIP-seq] |
| GSE231663 |
NRF1 promotes primordial germ cell development, proliferation, and survival |
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| Relations |
| BioSample |
SAMN34591396 |
| SRA |
SRX20229348 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7295405_input_3.bw |
320.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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