|
| Status |
Public on Nov 20, 2016 |
| Title |
NSC_H3K27me3 |
| Sample type |
SRA |
| |
|
| Source name |
Neural stem cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Sca-Gal4/cyo;UAS-3xFLAG-blrp-mCherry-RanGap
tissue: Neural stem cells
Stage: 5-7h AEL
chip antibody: H3K27me3
chip antibody vendor: Abcam
chip antibody cat.: ab6002
|
| Treatment protocol |
Embryos were dechorionated with 50% solution of bleach for 3 minutes and were cross-linked in a 1:3 mix of ChIP-fixed buffer with 1.8% formaldehyde and heptane for 15 min on a shaker with speed at 300 rpm. The aqueous and organic phase was replaced with PBST plus 0.25 mM glycine to cease cross-linked reaction, and fixed embryos were rinsed by PBST for 3 times. Nuclei mixture were harvested by homogenizing the whole cross-linked Drosophila embryo, and nuclei of interest were isolated by anti-Flag M2 magnetic beads affinity purification.
|
| Growth protocol |
Embryos were collected on grape juice plates with yeast paste from embryo collection cages for 2 hr, and then allowed to develop for 3 and 10 additional hours before being harvested. So the collected embryos are 5–7h and and 12–14h old, respectively.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, then mapped to dm3 whole genome using bowtie v0.12.7 with parameters:–p 8 -t -v 2 -m 1 -5 1 --suppress 5,6
The uniquely mapped nucleosomal reads were used to identify genome-wide nucleosome positions through the peak-calling tool GeneTrack
Aligned histone modification reads were converted into Bedgraph format use bedtools genomecov, normalized by total mapped reads and sorted by their genomic location, then converted BedGraph format into Bigwig format.
Genome_build: dm3
Supplementary_files_format_and_content: Bigwig is a binary file. And bed.txt file for nucleosome positions includes nucleosome name, location (chromatin, start, end), the number of reads aligned on predicted nucleosme (rc), fuzziness of predicted nucleosme (fuzziness, the standard deviation of tag locations around the nucleosome dyad)
|
| |
|
| Submission date |
Apr 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Youqiong Ye |
| E-mail(s) |
youqye@gmail.com
|
| Phone |
+8613661565591
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
280 Chongqing south road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE80457 |
Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos [ChIP-seq] |
| GSE80458 |
Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos |
|
| Relations |
| BioSample |
SAMN04870944 |
| SRA |
SRX1715676 |
