|
| Status |
Public on Feb 26, 2019 |
| Title |
MG_2_5_2_H3K9me3-116174194 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
hours post fertilization: 2.5
developmental stage: embryo
chip antibody: H3K9me3 (Abcam ab8898, GR3176466-1)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells lysed using lysis buffer followed by chromatin shearing in Diagenode Bioruptor and histone-DNA complexes were isolated with antibody.
Illumina TruSeq ChIP
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed using Trimgalore version 4.0 and only reads greater than 20bp were retained. Parameters used trimgalore --length 20 --fastqc --gzip
Reads aligned using BWA version 0.7.15 algorithms algn and samse
Samtools 1.3.1 used to sort and index bam files
IGVtools 2.3.81 to create tdf files viewable in Integrated Genome Viewer. Parameters igvtools count -z 7 -w 100
HOMER version 4.8 create Tag Directories for downstream data analysis
HOMER version 4.8 call peaks using findpeaks style histone size 1000 against input file
HOMER version 4.8 annotatePeaks for metaplot and heatmap generation annotatePeaks parameters -hist 50 -ghist - size 10000
Rstudio for heatmap s
Genome_build: GCF_000002035.6_GRCz10_genomic
|
| |
|
| Submission date |
Apr 12, 2018 |
| Last update date |
Feb 26, 2019 |
| Contact name |
Mary Goll |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Georgia
|
| Department |
Genetics
|
| Lab |
Goll
|
| Street address |
120 E. Green Street
|
| City |
Athens |
| State/province |
Select State |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE113086 |
Developmental regulation of heterochromatin establishment at the maternal to zygotic transition |
|
| Relations |
| BioSample |
SAMN08923999 |
| SRA |
SRX3930992 |
