|
| Status |
Public on May 24, 2024 |
| Title |
MBT Flav input DNA |
| Sample type |
SRA |
| |
|
| Source name |
Flavopiridol treated MBT zebrafish embryo
|
| Organism |
Danio rerio |
| Characteristics |
strain: Tubingen
tissue: embryo
developmental stages: sphere stage
chip antibody: none
|
| Treatment protocol |
4 datasets were generated from flavopiridol treated emrbyos. Embryos were dechorinated immediately after fertilization, and closely monitored for the development stages. Flavopiridol (Sigma-Aldrich F3055) were added to the embryo water to a final concentration of 10uM to inhibit transcription elongation at 3.75hpf, and the embryos then were collected at sphere stage.
|
| Growth protocol |
Zebrafish embryos (strain Tübingen) were incubated at 28C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei from formaldehyde crosslinked (1%; 10min at room temperature) embryos were isolated and chromatin was fragmented using sonicator (Branson). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and Dynabeads. DNA fragments were purified and libraries were prepared by NEBnext DNA Library Prep Kit (NEB, E7370L). Adapter ligated DNA was purified using AMPure XP beads (Beckman Coulter, A63881) and sequenced by illumina HiSeq 2500.
NEBnext DNA Library Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MBT_flav_input.bw
|
| Data processing |
Raw reads were aligned to zv10 using Novoalign ( v2.8 novocraft) with the options [-r None -k -Q 13 -o SAM]
Sam files were converted to bam files using samtools.
Sorted bam files of replicates were then merged using MergeSamFiles.jar from Picard tools (v 1.100)
Peaking calling, relative to paired input, was performed using MACS2 (v2.1.0.20140616), using the following parameters: -f BAM -g 1.4e9 -B --fix-bimodal --extsize 250 -q 0.01
treat_pileup.bdg files from macs2 were then converted to bigWig files using bedGraphtoBigWig
Genome_build: zv10
Supplementary_files_format_and_content: text files are peak profiles generated from MACS2, and bigWig files represent the genome-wide protein occupancy
|
| |
|
| Submission date |
May 24, 2021 |
| Last update date |
May 24, 2024 |
| Contact name |
Bradley R Cairns |
| E-mail(s) |
candice.wike@hci.utah.edu
|
| Organization name |
Huntsman Cancer institute/HHMI
|
| Department |
oncological Sciences
|
| Street address |
2000 Cir of Hope Dr
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE175444 |
Distinctive roles for the chromatin remodeling ATPases Brg1 and Brm in early zebrafish embryos [ChIP-seq] |
| GSE175447 |
Distinctive roles for the chromatin remodeling ATPases Brg1 and Brm in early zebrafish embryos |
|
| Relations |
| BioSample |
SAMN19317930 |
| SRA |
SRX10973777 |
