|
Status |
Public on Jun 25, 2020 |
Title |
S2-DSRC AdMTase-seq (6 U Hia5) - rep2 |
Sample type |
SRA |
|
|
Source name |
S2-DSRC cells
|
Organism |
Drosophila melanogaster |
Characteristics |
cell line: S2-DSRC cells m6a-mtase conditions: 6 U Hia5 for 20min at 37C antibody: Millipore Sigma ABE572
|
Treatment protocol |
Nuclei were extracted using 0.05% IGEPAL in Buffer A (50 mM Tris-HCl, pH 8; 100mM NaCl; 1mM DTT) for 10 minutes at 4 degrees. Nuclei were treated with m6A-Mtase as above.
|
Growth protocol |
S2-DSRC cells were grown at room temerature to 90% confluency. K562 cells were grown at 37C to 5x10^5 cells/mL; Hela cells were grown at room temerature to 90% confluency
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Short DNA fragments were subjected to standard Illumina library construction
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
DS69048
|
Data processing |
Library strategy: AdMTase-seq Basecalling, RTA v1.13 Alignments to GRCh38, BWA v0.7.12 Read processing, Samtools v1.2 Read density, Bedops v2.4.15 Peak calling, Hotspot2 v2.1.1 Genome_build: dm6 Supplementary_files_format_and_content: 5% FDR peak calls as .bed file
|
|
|
Submission date |
Mar 13, 2020 |
Last update date |
Jun 25, 2020 |
Contact name |
John A Stamatoyannopoulos |
E-mail(s) |
jstam@altius.org
|
Organization name |
Altius Institute / University of Washington
|
Department |
Genome Sciences
|
Lab |
Stamatoyannopoulos
|
Street address |
2211 Elliott Avenue, 6th Floor
|
City |
SEATTLE |
State/province |
WA |
ZIP/Postal code |
98121 |
Country |
USA |
|
|
Platform ID |
GPL21306 |
Series (2) |
GSE146937 |
Single-molecule regulatory architectures captured by chromatin fiber sequencing [Dm AdMTase-seq] |
GSE146942 |
Single-molecule regulatory architectures captured by chromatin fiber sequencing |
|
Relations |
BioSample |
SAMN14374568 |
SRA |
SRX7909043 |