|
| Status |
Public on Jul 08, 2021 |
| Title |
SEP3-AG(API-I) seq-DAP-seq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Sheared genomic DNA extracted from Arabidopsis thaliana.
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
protein epitope tags: 5XMyC
|
| Growth protocol |
Grow on 0.5 Murashige and Skoog medium in long-day conditions for 2-weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits
Illumina TruSeq adaptors with single end index
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Recombinant proteins were produced by TnT in vitro transcription translation system from Promega
|
| Data processing |
Alignment to genome is done by Bowtie2
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters (-q 0.001 --call-summits)
Peaks called where Control read coverage is too high are removed from analysis
replicates are treated by MSPC to create consensus peaks
Consensus peaks are reworked around maximum of peaks (+/-200 bp).
Consensus bedgraphs are computed by the mean of the replicates bedgraphs
Genome_build: TAIR10
Supplementary_files_format_and_content: Bed files contain position of consensus peaks centered around maximum
Supplementary_files_format_and_content: Bedgraphs files contain profiles of binding intensity (cpm)
|
| |
|
| Submission date |
Feb 04, 2021 |
| Last update date |
Jul 08, 2021 |
| Contact name |
Romain BLANC-MATHIEU |
| E-mail(s) |
romain.blancmathieu@cea.fr
|
| Organization name |
CEA
|
| Lab |
LPCV
|
| Street address |
17 Avenue des martyrs
|
| City |
Grenoble |
| ZIP/Postal code |
38000 |
| Country |
France |
| |
|
| Platform ID |
GPL17970 |
| Series (1) |
| GSE166205 |
sequential DNA affinity purification sequencing (seq-DAP-seq) data of SEP3-AGAPI |
|
| Relations |
| BioSample |
SAMN17799150 |
| SRA |
SRX10030835 |
