|
| Status |
Public on Jun 23, 2023 |
| Title |
ATAC-seq in Lola-I mutant transheterozygous ORE50/ORC4 14-17hrs embryo Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: embryos
genotype: Lola-I transheterozygous mutant:ORE50/ORC4
developmental stage: 14-17h
|
| Treatment protocol |
Embryos were then dechorionated with 50% bleach solution for 2-3 minutes
|
| Growth protocol |
Drosophila melanogaster embryos OregonR were collected for 3 hours and aged for 14 hours on molasses agar plates at 25 degree celsius to get 14-17hr embryos(AED).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from Oregon-R embryos 2-4h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). Isolated nuclei were treated with Tn5 transposase((Illumina, #FC-121-1030).
Nextera index kit (Illumina, #FC-121-1011) was used to create libraries.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 50 bp each and aligned to the UCSC Drosophila melanogaster dm6 genome with Bowtie 2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
BigWig files contain per-base coverage of aligned read pairs of size 0-100bp.
Assembly: dm6
Supplementary files format and content: BigWig files contain counts of the aligned reads for each coordinate
|
| |
|
| Submission date |
Apr 15, 2022 |
| Last update date |
Jun 23, 2023 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE200867 |
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [ATAC-seq] |
| GSE200875 |
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development |
|
| Relations |
| BioSample |
SAMN27597125 |
| SRA |
SRX14868946 |
