|
| Status |
Public on May 21, 2024 |
| Title |
scAIR001: scATAC-seq and interactome |
| Sample type |
SRA |
| |
|
| Source name |
Embryos nuclei
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Embryos nuclei
developmental stage: 0-24h
|
| Treatment protocol |
After collecting the eggs laid by adult female fruit flies, the embryos are carefully separated from the eggshell and transferred to a microcentrifuge tube. A lysis buffer is added to break down the cell membranes and release the nuclei. The embryos are gently squashed to further disrupt the cells, and the resulting mixture is centrifuged to separate the nuclei from cellular debris. The isolated nuclei are then subjected to crosslinking, a process that helps stabilize the nuclear proteins and DNA interactions
|
| Growth protocol |
To culture fruit flies for obtaining embryonic tissues, prepare a nutrient-rich culture medium by mixing cornmeal, yeast, sugar, and water. Transfer the fruit flies to vials containing the culture medium and seal them. Maintain the vials in a controlled environment with a 12-hour light-dark cycle. Allow the fruit flies to mate and lay eggs on the surface of the culture medium. After a few days, transfer the contents of the vials to a Petri dish. Use a stereomicroscope to collect the tiny embryos after 24 hours.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked cells were initially subjected to cell lysis and nuclei lysis to extract the nuclei. The lysed nuclei were then fragmented into smaller complexes using restriction enzymes, which cut the DNA at specific recognition sites. Following fragmentation, proximity ligation was performed to join the fragmented DNA ends together. This step helps generate smaller DNA fragments with proximity ligation, allowing for easier sequencing. The ligated nuclei were subsequently uploaded to the 10x Genomics platform for further processing and analysis.
The barcoded RNA and DNA by 10x genomics were performed library construction following the manual.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Raw sequencing data from scAIR are divided into 5 FASTQs: For scRNA-seq: (1) R1 corresponds to the cell barcode; (2) R2 corresponds to the sequencing reads from the cDNA molecule. For scATAC-seq: (1) R1 and R3 refer to the squencing reads from the DNA fragment; (2) R2 refers to the cell barcode.
Assembly: dm3
Supplementary files format and content: scRNA seq Matrix, scATAC seq Pairs
Library strategy: scAIR
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
May 21, 2024 |
| Contact name |
Tian (Simon) Zhongyuan |
| E-mail(s) |
simontian2020@outlook.com
|
| Phone |
+86 15001976248
|
| Organization name |
Southern University of Science and Technology (SUSTech)
|
| Department |
School of Life Sciences
|
| Lab |
Zheng Meizhen Lab
|
| Street address |
1088 Xueyuan Avenue
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE246674 |
Characterization of Transcriptome and Chromatin Interactome in Accessible Regions at Single-cell Resolution by scAIR |
|
| Relations |
| BioSample |
SAMN38052016 |
| SRA |
SRX22321704 |
