|
| Status |
Public on Mar 25, 2014 |
| Title |
3dpf_mtx-treated |
| Sample type |
SRA |
| |
|
| Source name |
danio rerio whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
Sex: na
treated with: 400 uM methotrexate applied at 1-cell stage
tissue: whole embryo
|
| Growth protocol |
Tubigen AB fish were crossed and embryos raised in embryo media until proper age was reached, with standard practices used
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos/tissue were flash frozen in Liquid Nitrogen and later gDNA was extracted with Gentra PureGene
ChIP-Seq DNA Sample Prep Kit was used
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Aligned with bwa 0.5.8c against zv9
Called peaks with macs2 2.0.10.20120703 (-g 1.4e9)
Used meRich as "-t" and mePoor as "-c l" sample for macs2 peak calls (matched by lane as indicated in the sample titles. Brain used for both lane4 and lane5 as control)
Took centers of peaks and added 100bp to each side with bedtools
Genome_build: zv9
Supplementary_files_format_and_content: bed file with areas of high methylation in the zebrafish tissues (methylation peak locations)
|
| |
|
| Submission date |
Nov 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
David McGaughey |
| E-mail(s) |
mcgaugheyd@mail.nih.gov
|
| Organization name |
NIH
|
| Department |
NEI
|
| Street address |
10 Center Dr
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE52110 |
Whole genome methylation profiling in developing and developed Zebrafish |
|
| Relations |
| BioSample |
SAMN02393723 |
| SRA |
SRX373357 |
