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Status |
Public on Sep 26, 2019 |
Title |
H3K4me3-Bap1MO_1 |
Sample type |
SRA |
|
|
Source name |
H3K4me3-Bap1MO_whole embryo
|
Organism |
Xenopus laevis |
Characteristics |
Sex: female animal id#: 1 embryonic stage: stage 12 frog type: pigmented tissue: whole embryo seq. of mo injected/embryo-ng: AGCCTTTATTCATGTTGCCTCCTCC-15 genotype/variation: Bap1 depleted chip antibody: H3K4me3 (Active Motif, #39915)
|
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).
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|
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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
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|
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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 |
SAMN10941045 |
SRA |
SRX5381430 |