|
| Status |
Public on Sep 26, 2019 |
| Title |
H2Aub-CtrlMO_2 |
| Sample type |
SRA |
| |
|
| Source name |
H2Aub-CtrlMO_whole embryo
|
| Organism |
Xenopus laevis |
| Characteristics |
Sex: female
animal id#: 2
embryonic stage: stage 12
frog type: pigmented
tissue: whole embryo
seq. of mo injected/embryo-ng: AGCTTTCGTTCATGTAACCTCCTCA-15
genotype/variation: control
chip antibody: H2AK199ub (Cell Signaling, D27C4, #8240)
|
| Treatment protocol |
Embryos were injected at the 1-cell stage with 15 ng of control MO or MO targeting Bap1 and maintained at 22oC until they reached stage 12.
|
| Growth protocol |
Embryos were obtained by in vitro fertilization of oocytes from 2 different females per condition
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed on 500 stage 12 embryos , according to a protocol from the Cold Spring Harbor Lab , with 35 minutes of crosslinking. Sodium N-lauroylsacrosine in Buffer E3 was replaced by 0.1% SDS,. Chromatin was sonicated to an average fragment size of 200 bp with a Diagenode Bioruptor® Pico before ChIP.
Libraries were prepared using the NEBNext® Ultra™ kit, and sequenced on the Illumia NextSeq 500 (1x75 bp).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed (if required) and aligned to the Xenopus laevis 9.1 genome using Novoalign (v3.04.06).
ChIP-Sequencing data was marked for duplicates using Picard (v1.128) and filtered for mapping quality using SAMtools (v1.2).
Bigwig files were created using THOR (10/5 Binning)
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Feb 14, 2019 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Michael Durante |
| E-mail(s) |
mdurante@med.miami.edu
|
| Phone |
2393575338
|
| Organization name |
University of Miami Miller School of Medicine
|
| Department |
Ophthalmology
|
| Lab |
Harbour
|
| Street address |
1501 NW 10th Ave., Ste 832
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL21248 |
| Series (2) |
| GSE126598 |
Loss of Bap1 leads to an increased global methylation and decrease in H3K27AC enhancer marks around key lineage commitment genes in Xenopus laevis embryos [ChIP-seq] |
| GSE126599 |
Loss of Bap1 in Xenopus laevis embryos |
|
| Relations |
| BioSample |
SAMN10941033 |
| SRA |
SRX5381441 |
