|
| Status |
Public on Apr 30, 2019 |
| Title |
H3K4me3 replicate 1 (tiling1) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K4me3 ChIP DNA from T. gondii
|
| Organism |
Toxoplasma gondii RH |
| Characteristics |
Stage: Tachyzoite
genotype: Wild type
|
| Treatment protocol |
Mnase-digestion
|
| Growth protocol |
Normal pH7 growth conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei extracted with high salt buffer and chromatin digested with micrococcal nuclease and digested DNA was incubated with antibodies against H3K4me3, H2AZ, H2AX or anti-Myc followed by protein G Dynabeads (Invitrogen). Immunoprecipitated DNA was amplified using Complete Whole Genome Amplification Kit (SIGMA ALDRICH)
|
| Label |
Cy5
|
| Label protocol |
1.2_g of Input and Experimental DNA sample were labelled with Cy3 and Cy5 dye respectively (NimbleGen Dual-Color DNA Labelling Kit) using Klenow Fragment 3->5 exo- (NEB) following manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
Input Mnase-digested DNA
|
| Organism |
Toxoplasma gondii RH |
| Characteristics |
Stage: Tachyzoite
genotype: Wild type
|
| Treatment protocol |
Input DNA
|
| Growth protocol |
Normal pH7 growth conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei extracted with high salt buffer and chromatin digested with micrococcal nuclease and digested DNA was incubated with antibodies against H3K4me3, H2AZ, H2AX or anti-Myc followed by protein G Dynabeads (Invitrogen). Immunoprecipitated DNA was amplified using Complete Whole Genome Amplification Kit (SIGMA ALDRICH)
|
| Label |
Cy3
|
| Label protocol |
1.2_g of Input and Experimental DNA sample were labelled with Cy3 and Cy5 dye respectively (NimbleGen Dual-Color DNA Labelling Kit) using Klenow Fragment 3->5 exo- (NEB) following manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
Cy3/5 labelled DNA (input/Experiment) were precipitated with 0.1 vol of 5M NaCl and 0.9 vol Isopropanol. Using NimbleGen Hybridization Kit, manufacturer's instructions were followed for hybridization reaction
|
| Scan protocol |
Arrays were scanned at wavelengths (532=cy3, 635=Cy5) with pixel size 5_m at 100% power using Agilent's DNA Microarray Scanner using Agilent scanner software
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. Following this a custom R-script was used to convert T. gondii genome version 4 data to version 11 and combine tiling 1 and 2 arrays. Processed files (_ratio.gff and ratio_peaks.gff) are in T. gondii version 11.
|
| |
|
| Submission date |
Oct 11, 2016 |
| Last update date |
Apr 30, 2019 |
| Contact name |
Kami Kim |
| E-mail(s) |
kami.kim@einstein.yu.edu
|
| Phone |
7184302611
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Medicine
|
| Lab |
Ullmann 1223
|
| Street address |
1300 Morris Park Avenue
|
| City |
Bronx |
| State/province |
New York |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL15563 |
| Series (1) |
| GSE87834 |
Genome-wide localisation of histone variants in Toxoplasma gondii implicates variant exchange in transcriptional control by demarcation of functional chromatin regions |
|
