|
| Status |
Public on Jun 04, 2018 |
| Title |
Optix_GFP_Pos_Cell_5 |
| Sample type |
SRA |
| |
|
| Source name |
eye progenitor cells (Optix-GFP positive) from 3rd instar wandering larvae eye antennal disc
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: 3rd instar-wandering
treatment: Hand Dissections
treatment: FACS sorting
genotype: Optix2/3-GFP
cell type: eye progenitor cells
|
| Treatment protocol |
None
|
| Growth protocol |
Normal flyfood, 25 degrees
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Eye-antennal imaginal Disc were dissected from 3rd instar wandering larvae. The discs were dissociated with Trypsin 0.05% EDTA at 37'C for 45 minutes, filtered at 20µm and FACS soted based on GFP. Single cells were loaded into a Fluidigm C1 at a concentration of 1000 cells/µl. scATAC was performed as described previously (Buenrostro et al. 2015)
Tn5 and nextera library prep
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
scATAC-seq
Grh_regions_avgATAC_number_sc.tsv
|
| Data processing |
Cleaning (fastq-mcf)
Mapping to the dm6 genome using bowtie2
Single cells were deduplicated using picard tools
The number of cells with reads present in each DGRP peak was counted using custom scripts
Genome_build: Drosophila melanogaster FlyBase version 6.03
Supplementary_files_format_and_content: Grh_regions_avgATAC_number_sc.tsv contains a matrix indicating how many single cells have reads present within each peak from the bulk DGRP data
|
| |
|
| Submission date |
Aug 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jelle Jacobs |
| E-mail(s) |
jelle.jacobs9255@gmail.com
|
| Organization name |
Institute of molecular Pathology
|
| Department |
VBC
|
| Lab |
Stark lab
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE102441 |
The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes |
| GSE102544 |
The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [scATAC-seq] |
|
| Relations |
| BioSample |
SAMN07499296 |
| SRA |
SRX3088353 |
