|
| Status |
Public on Sep 07, 2020 |
| Title |
SEP3_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
3-Sep
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 2-weeks old seedlings
primary protein epitope tags: SEP3-3FLAG
molecule subtype: PCR amplified genomic DNA
|
| Growth protocol |
2-weeks old seedlings of Arabidopsis thaliana
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Recombiant proteins were produced by TnT in vitro transcription translation system from Promega
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 |
| |
|
| Data processing |
library strategy: sequential DNA affinity purification sequencing [DAP-seq]
Image data generated by Miseq is transferred into raw reads through base calling software (BCL2FASTQ v2.17)
Alignement to genome is done by Bowtie2 with parameters:
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters
Peaks called where Control read coverage is too high are removed from analysis
Genome_build: TAIR10
Supplementary_files_format_and_content: NarrowPeaks representing peaks positions and p-values
Supplementary_files_format_and_content: Bedgraphs are whole genome profile of reads
|
| |
|
| Submission date |
May 13, 2020 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Jérémy LUCAS |
| E-mail(s) |
jeremy.lucas@cea.fr
|
| Organization name |
CNRS
|
| Street address |
17 avenue des Martyrs
|
| City |
Grenoble |
| ZIP/Postal code |
38000 |
| Country |
France |
| |
|
| Platform ID |
GPL17970 |
| Series (1) |
| GSE150528 |
Genome-wide binding of SEPALLATA3 (SEP3) and AGAMOUS (AG) complexes determined by sequential DNA-affinity purification sequencing |
|
| Relations |
| BioSample |
SAMN14916584 |
| SRA |
SRX8339615 |
