|
| Status |
Public on Sep 10, 2023 |
| Title |
Input_WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
8-day-old Arabidopsis seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
plant line: WT
antibody: input
tissue: entire seedlings
|
| Treatment protocol |
Fresh seedlings of the WT Col-0 or the 2h1 mutant line were crosslinked for 15 min using 1% formaldehyde.
|
| Growth protocol |
Arabidopsis seeds were surface-sterilized, plated on half strength Murashige and Skoog (MS) medium 0.9% agar and cultivated under long-day (16h/8h) light/dark and 23/19°C periods
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed as in Nassrallah et al., eLife (2018; doi: 10.7554/eLife.37892).
ChIP-Seq TruSeq kit was used, SE 50bp reads were produced
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP-DNA
|
| Data processing |
Reads were trimmed using Trimmomatic 0.36 with the following command "java -jar trimmomatic-0.36.jar SE -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Trimmed read were aligned against a genome that combines the Arabidopsis thaliana (TAIR10) and Drosophila melanogaster (dm6) genomes using bowtie2 v2.3.3 and the setting "--very-sensitive". The reads mapping to Drosophila genome were first normalized according to the number of input reads and then used to obtain a normalization factor for each sample.
Duplicated mapped reads were removed with sambamba 0.7.1 markdup and reads with mapping quality lower than MAPQ 10 discarded with sambamba 0.7.1 and the command [view -F "mapping_quality >= 10"].
Read coverage was computed from the filtered bam files with Deeptools 3.4.0 bamCoverage. The sequencing depth was normalized using the scaling factor calculated as described above.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Oct 29, 2020 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Fredy BARNECHE |
| E-mail(s) |
barneche@ens.fr
|
| Organization name |
CNRS
|
| Department |
IBENS
|
| Street address |
Rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE160410 |
Linker histones mediate sequence-specific regulation of chromosomal organization and H3K27me3 enrichment over genes and telomeric repeats (ChIP-RX) |
| GSE160414 |
Linker histones mediate sequence-specific regulation of chromosomal organization and H3K27me3 enrichment over genes and telomeric repeats |
|
| Relations |
| BioSample |
SAMN16595328 |
| SRA |
SRX9398761 |
