|
| Status |
Public on Nov 11, 2010 |
| Title |
E0-8_Kr-D2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
E0-8_Kr-D2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: E0-8
antibody: Kr-D2
antibody provider: White Lab
antibody lot/batch#: N/A
antibody catalog#: N/A
fly: iso1 (y; bw cn sp)
|
| Treatment protocol |
No Treatment
|
| Growth protocol |
1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.
|
| Label |
biotin
|
| Label protocol |
Affymetrix Labeling Protocol (TdT labeling)
|
| |
|
| Channel 2 |
| Source name |
input
|
| Organism |
Drosophila melanogaster |
| Characteristics |
antibody: none
|
| Treatment protocol |
No Treatment
|
| Growth protocol |
1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.
|
| Label |
biotin
|
| Label protocol |
Affymetrix Labeling Protocol (TdT labeling)
|
| |
|
| |
| Hybridization protocol |
Affymetrix Hybridization Protocol - Hybridizations were performed at the Functional Genomics Facility (FGF) at the University of Chicago.
|
| Scan protocol |
Affymetrix Protocol - Scans were performed at the Functional Genomics Facility (FGF) at the University of Chicago.
|
| Description |
input CEL file: extracted_E-0-8h_input_0-8h_Ctl1.CEL
input CEL file: extracted_E-0-8h_Input-0-8h-D_Ctl2.CEL
|
| Data processing |
.CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks.
.bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.
|
| |
|
| Submission date |
Nov 10, 2010 |
| Last update date |
Feb 02, 2015 |
| Contact name |
Kevin P. White |
| E-mail(s) |
kpwhite@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Institute for Genomics and Systems Biology
|
| Street address |
900 E. 57th STR. 10th FL.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platform ID |
GPL6629 |
| Series (2) |
| GSE23537 |
modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data |
| GSE25259 |
modENCODE_White Lab: genome-wide ChIP-chip data |
|
| Relations |
| Named Annotation |
GSM621326_extracted_MAT_Kr-D2_E-0-8h.Dm_tiling2_MR_v01_dm3.NR.bpmap_matscore.bar.txt_IGB.wig.gz |
