|
| Status |
Public on Dec 21, 2015 |
| Title |
Rib-GFP_fkh-Gal4_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Stage 11-16 embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: fkh-GAL4::UAS-rib-GFP
embryonic stages: Stage 11-16
|
| Growth protocol |
Embryos (fkh-GAL4::UAS-rib-GFP and sage-GAL4::UAS-rib-GFP) were collected for 8h at RT and allowed to age for 11 hours prior to their isloation using a COPAS Select embro sorter (Union Biometrica).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from three independent collections of stage 11-16 fkh:GAL4::UAS-rib-GFP and three of sage-GAL4::UAS-rib-GFP embryos were crosslinked at RT in 1.8% formaldehyde and homogenized for chromatin extraction. Anti-GFP antibody was used for immunoprecipitation.
Input and immunoprecipitated DNA were prepared for sequencing using the Illumina TruSeq ChIP Sample Preparation Kit per the manufacturer's instructions. Library construction was performed by the University of Minnesota Genomics Center.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
GFP-tagged rib transcription factor driven by fkh-Gal4 driver
merged replicates
|
| Data processing |
ChIP-seq reads were aligned to the dm6 genome assembly using BWA (Galaxy Tool Version 0.2.3) with default settings.
Replicates were merged using SamMerge (Galaxy Tool Version 1.1.2)
Peaks were called using MACS version 2.1.0.20140616 with the following setting: (P-value: 10e-5, mfold:10,32).
Genome_build: dm6
Supplementary_files_format_and_content: bed and bedgraph
|
| |
|
| Submission date |
Oct 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Joslynn Shannon Lee |
| Organization name |
University of Minnesota Medical School, Duluth campus
|
| Department |
Biomedical Sciences
|
| Street address |
1035 University Drive
|
| City |
Duluth |
| State/province |
MN |
| ZIP/Postal code |
55812 |
| Country |
USA |
| |
|
| Platform ID |
GPL9058 |
| Series (2) |
| GSE73780 |
ChIP-seq data from fkh-Gal4::UAS-rib-GFP and sage-Gal4::UAS-rib-GFP mid- through late-stage Drosophila embryos |
| GSE73781 |
Genome-wide Ribbon occupancy and gene expression profiling of wildtype and ribbon mutant Drosophila mid through late stage embryos |
|
| Relations |
| BioSample |
SAMN04147533 |
| SRA |
SRX1308480 |
