|
| Status |
Public on Jan 01, 2024 |
| Title |
CUTandTag_Insm1_mouse_E18.5_mTEC_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
medullary thymic epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wt
target: Insm1
strain: CD1
developmenta stage: E18.5 embryo
cell type: medullary thymic epithelial cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
mTECs were isolated using UEA1 coupled Dynabeads from wildtype 6-8weeks old mice. 0.5ul of Insm1 or 2ul of IgG (DIA.AN, Q6008) antibody was incubated with 5x104 mTEC cells in a volume of 100ul first antibody buffer for overnight at 4°C. Then, the Donkey anti-guinea pig antibody (Jackson ImmunoResearch,706-005-148) was used and incubated with the mTEC for 45 minutes in 100ul secondary antibody buffer at room temperature. After washing away the unbound antibodies, the ChiTag transposon was incubated with mTECs for one hour at room temperature. The fragmentation, DNA purification and library construction were performed according to the product protocol.
The fragmentation, DNA purification and library construction were performed according to the instruction of the manufactory (Novoprotein, N259-YH01)
Nextera index-kit adapter primers were used for library construction, 16x cycles were used for PCR amplification
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
library strategy: Cut&Tag
Raw CUT&Tag sequencing data was trimmed adopters using fastp and aligned to mouse genome (mm10) using Bowtie2 with the parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -X 700”.
BigWig files were generated using deepTools bamCoverage under default parameters.
Assembly: mm10
Supplementary files format and content: BigWig
|
| |
|
| Submission date |
Jan 09, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Shiqi Jia |
| E-mail(s) |
shiqijia@jnu.edu.cn
|
| Organization name |
Jinan University
|
| Street address |
Huangpu Avenue West 613
|
| City |
Guangzhou |
| ZIP/Postal code |
510613 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE193926 |
Insm1 regulates the expression of thymic tissue-restricted antigens and the immune tolerance [CUT&Tag] |
| GSE193929 |
Insm1 regulates the expression of thymic tissue-restricted antigens and the immune tolerance |
|
| Relations |
| BioSample |
SAMN32644421 |
| SRA |
SRX18981162 |
