|
Status |
Public on Jul 18, 2022 |
Title |
H3K9me3_Drosophila_embryo |
Sample type |
SRA |
|
|
Source name |
Drosophila melanogaster embryos
|
Organism |
Drosophila melanogaster |
Characteristics |
antibody: rabbit anti H3K9me3 (Active Motif 39062)
|
Treatment protocol |
isolated nuceli were treated for DiMeLo-seq with conditions described above
|
Growth protocol |
OregonR flies were maintained on standard molasses medium before transfer to embryo collection cages with apple-juice plates with yeast paste. Human cells grown in RPMI with 15% FBS, 1% penn/strep at 37C with 5% CO2
|
Extracted molecule |
genomic DNA |
Extraction protocol |
NEB HMW DNA extraction kit (T3050L) Oxford Nanopore sequencing libraries were generated with SQK-LSK110
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
MinION |
|
|
Data processing |
Megalodon (v2.3.4), Guppy (v5.0.15), using a Rerio res_dna_r941_min_modbases-all-context_v001.cfg basecalling model fast5s were aligned and modified bases were called using Megalodon (2.3.1 or 2.3.4) using the rerio all-context basecalling model (res_dna_r941_min_modbases-all-context_v001.cfg) with parameters --outputs mod_mappings and --mod-min-prob 0 Assembly: CHM13v1.1 reference genome or dm6 Supplementary files format and content: bam files with alignment and modification basecalling info Library strategy: DiMeLo-seq
|
|
|
Submission date |
Jul 13, 2022 |
Last update date |
Jul 18, 2022 |
Contact name |
Aaron Streets |
E-mail(s) |
astreets@berkeley.edu
|
Organization name |
University of California, Berkeley
|
Department |
Bioengineering
|
Street address |
Stanley Hall
|
City |
Berkeley |
State/province |
CA |
ZIP/Postal code |
94720 |
Country |
USA |
|
|
Platform ID |
GPL24622 |
Series (1) |
GSE208125 |
Protocol for Mapping Protein-DNA Interactions with Directed Methylation with Long-read Sequecing (DiMeLo-seq) |
|
Relations |
BioSample |
SAMN29486228 |
SRA |
SRX16028825 |