 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 04, 2024 |
| Title |
EC-ATAC |
| Sample type |
SRA |
| |
|
| Source name |
EC
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: intestine
cell type: enterocyte
genotype: Myo1A-Gal4ts, UAS-GFP
|
| Treatment protocol |
100-150 guts for each sample were dissected in ice-cold DEPC-PBS within 2 hours, and were digested in 1mg/ml elastase solution (Sigma, cat. no. E0258) for 1 hour at room temperature. Cell suspension were then used to sort GFP+ cells via FASC. These sorted GFP+ cells were then used for library preperation for ATAC-seq
|
| Growth protocol |
All crosses were performed at 18℃, and 5-7d old adult F1 progenies with correct genotypes would be collected and transferred to 29 ℃ to induce gene expression.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each sample, around 40,000 PI- GFP+ (DAPI-; GFPweek ; mCherry+) cells were FACS sorted into ice-cold PBS and collected by centrifugation. Cell lysis, DNA Tagmentation by Tn5 were carried out using the ATAC-Seq Kit (Active motif, Catalog No. 53150), following the manufacturer’s instructions.
Tagmented DNA were amplified with N50x, N70x index to construct the sequencing library, also using the ATAC-Seq Kit (Active motif, Catalog No. 53150), following the manufacturer’s instructions. Amplified sequencing library is then purfied using 1.2x magnetic beads, and sequenced on a Hiseq platform.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw data were processed to remove low quality reads, and the clean data were then subjected to Cutadapt software to remove index sequences. These raw sequencing data were filtered and qualified reads were mapped to the D. melanogaster genome (BDGP6), using bowtie2 (version 2.2.4). PCR duplicates are removed by picard MarkDuplicates function, multimaped reads are removed by samtools, regions in blacklist are removed by bedtools intersect function.
bw files are generated by deepTools bamCoverage function using BPM normalization method, peaks are called by MACS3.
Assembly: D. melanogaster genome (BDGP6)
Supplementary files format and content: bigwig, narrowPeak
|
| |
|
| Submission date |
Jun 21, 2023 |
| Last update date |
Mar 04, 2024 |
| Contact name |
xi rongwen |
| E-mail(s) |
xirongwen@nibs.ac.cn
|
| Organization name |
National Institute of Biological Sciences, Beijing
|
| Street address |
No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL21306 |
| Series (1) |
| GSE235505 |
Efficient trans-differentiation/ de-differentiation of mature intestinal cells in adult Drosophila midgut by depleting a single transcription factor |
|
| Relations |
| BioSample |
SAMN35821869 |
| SRA |
SRX20741515 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7504080_EC.rmChrM.rmDup.rmMulti.sorted.rmBlacklist.BPM.bw |
94.6 Mb |
(ftp)(http) |
BW |
| GSM7504080_EC_peaks.narrowPeak.gz |
243.3 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
