 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 01, 2016 |
| Title |
orer_wce_1 |
| Sample type |
SRA |
| |
|
| Source name |
orer embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 2-4 hr after egg deposition
genotype/variation: wild type
chip antibody: none
barcode kit: NEB-next-ChIP
library kit: NEB-next-ChIP
|
| Treatment protocol |
Embryos were dechorionated in 100% bleach for ~1 min, washed with water, fixed for 15 min shaking on a vortexer, speed 7 with 1.8% formaldehyde in heptane, washed with PBT-glycine and PBT, and frozen in liquid nitrogen until used.
|
| Growth protocol |
Fly stocks Toll10b (Meso) and gd7 (Ecto) were kind gifts from Mike Levine (UC Berkeley). gd7/gd7 females were crossed to gd7/+ males, and Toll10b, e /TM3, Sb, Ser, e females were crossed to Toll10b, e/TM3, Sb, Ser, e males. Offspring of these crosses were used for embryo collections. For Trl, Sna, Pc ChIPs wild type embryos (Oregon-R) were used. Embryos were collected on apple juice plates for 2 h and then matured at 25C for another 2 h (2-4h after egg deposition (AED)).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed according to He et al. (2011) with whole cell extract (WCE) derived from 100 mg embryos per ChIP
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to the UCSC dm3 reference genome using bowtie v1.1.1 retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base
|
| |
|
| Submission date |
May 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Zeitlinger Lab
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE68983 |
Genome-wide analysis of enhancers in Drosophila DV patterning |
|
| Relations |
| BioSample |
SAMN03700687 |
| SRA |
SRX1032405 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1689689_orer_wce_1.bw |
246.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
