|
| Status |
Public on Jan 24, 2023 |
| Title |
AP2XII-2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ME49:TIR1
|
| Organism |
Toxoplasma gondii |
| Characteristics |
cell line: ME49:TIR1
cell type: tachyzoite
genotype: Me49[delta]hxgprt::TUB1:Firefly Luciferase;[delta]ku80::SAG1:CAT,TUB1:TIR1-3FLAG,AP2XII-2^HA-AID
|
| Growth protocol |
Freshly lysed tachyzoites were innoculated on confluent HFFs, grown for 24 hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
monolayers were syringe lysed and filtered, cell pellets rinsed with PBS twice
As per manufacturer: CUT&TAG-IT Assay kit, Anti-Rabbit, Active motif, Cat no. 53160
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
AP2XII-2_CUTnTAG_peaks.bed
AP2XII-2.bigwig
|
| Data processing |
map to Toxoplasma genome (ME49 v52) with bowtie2 allowing for mate pair dovetailing
call peaks with MACS2 using default settings (without control)
Assembly: ME49 v52 (toxodb.org)
Supplementary files format and content: AP2XII-2 peak file (BED)
Supplementary files format and content: AP2XII-2 binding sites (bigiwig)
Library strategy: CUT&TAG
|
| |
|
| Submission date |
Nov 03, 2022 |
| Last update date |
Jan 24, 2023 |
| Contact name |
Michael James Holmes |
| E-mail(s) |
holmesmi@iu.edu
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Pharmacology & Toxicology
|
| Street address |
635 Barnhill Drive
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL23377 |
| Series (1) |
| GSE217220 |
AP2XII-2 binding sites in Toxoplasma gondii |
|
| Relations |
| BioSample |
SAMN31592290 |
| SRA |
SRX18157905 |
