|
| Status |
Public on Aug 04, 2022 |
| Title |
P. falciparum 30-36 hpi (biol rep 5) |
| Sample type |
SRA |
| |
|
| Source name |
schizonts
|
| Organism |
Plasmodium falciparum |
| Characteristics |
cell type: schizonts
strain: 3D7
genotype: ORC1-3xHA + pTK-BSD
treatment: 24 uM Edu (7.5 min), 200 uM Brdu (7.5 min)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen MagAttract
SQK-LSK109
R9.4.1 MinION DNA sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Description |
R9.4.1 flowcells
|
| Data processing |
Basecalling (Guppy v5.0.11)
Genome alignment (Minimap2 v2.17-r941)
BrdU and EdU detection (DNAscent v3.0.2)
Fork, origin, and termination calling (DNAscent v3.0.2)
Assembly: P. falciparum 3D7 ASM276v2
Supplementary files format and content: bed files (fork, origin, and termination calls at 30 hpi and 36 hpi)
|
| |
|
| Submission date |
Jul 28, 2022 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Michael Boemo |
| E-mail(s) |
mb915@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Department of Pathology
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL32521 |
| Series (1) |
| GSE210010 |
Replication origin mapping in the malaria parasite P. falciparum |
|
| Relations |
| BioSample |
SAMN30031150 |
| SRA |
SRX16722867 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6413440_leftForks_DNAscent_forkSense.2021_11_15_FT_ONT_Plasmodium_BrdU_EdU_CellCycle.30hpi.bed.gz |
6.2 Kb |
(ftp)(http) |
BED |
| GSM6413440_leftForks_DNAscent_forkSense.2021_11_15_FT_ONT_Plasmodium_BrdU_EdU_CellCycle.36hpi.bed.gz |
105.7 Kb |
(ftp)(http) |
BED |
| GSM6413440_origins_DNAscent_forkSense.2021_11_15_FT_ONT_Plasmodium_BrdU_EdU_CellCycle.30hpi.bed.gz |
1.9 Kb |
(ftp)(http) |
BED |
| GSM6413440_origins_DNAscent_forkSense.2021_11_15_FT_ONT_Plasmodium_BrdU_EdU_CellCycle.36hpi.bed.gz |
26.3 Kb |
(ftp)(http) |
BED |
| GSM6413440_rightForks_DNAscent_forkSense.2021_11_15_FT_ONT_Plasmodium_BrdU_EdU_CellCycle.30hpi.bed.gz |
7.2 Kb |
(ftp)(http) |
BED |
| GSM6413440_rightForks_DNAscent_forkSense.2021_11_15_FT_ONT_Plasmodium_BrdU_EdU_CellCycle.36hpi.bed.gz |
105.8 Kb |
(ftp)(http) |
BED |
| GSM6413440_terminations_DNAscent_forkSense.2021_11_15_FT_ONT_Plasmodium_BrdU_EdU_CellCycle.30hpi.bed.gz |
1.6 Kb |
(ftp)(http) |
BED |
| GSM6413440_terminations_DNAscent_forkSense.2021_11_15_FT_ONT_Plasmodium_BrdU_EdU_CellCycle.36hpi.bed.gz |
25.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
