|
| Status |
Public on Sep 10, 2023 |
| Title |
HM5_2h1trb123.BR1.input |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
plant line: h1.1h1.2trb1trb2trb3
antibody: input
developmental stage: 8 dpi (WT phenotypes) or 12 dpi (tiny phenotypes)
tissue: entire seedlings
|
| Treatment protocol |
Fresh seedlings of WT and mutant lines 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 5 daysunder 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).
Nextera DNA library prep Kit Illumina Cat #FC-121-1030
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
ChIP-DNA
|
| Data processing |
Reads were aligned against a genome that combines the Arabidopsis thaliana (TAIR10) and Drosophila melanogaster (dm6) genomes using bowtie2 v2.4.2 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.
Reads mapping to Drosophila genome were removed, together with unmapped reads, not primary alignments, supplementary alignments, duplicated reads and read mapping on regions with low mappability defined as in Quadrana L, et al., The Arabidopsis thaliana mobilome and its impact at the species level. Elife (2016) 3;5:e15716. doi: 10.7554/eLife.15716.
Read coverage was computed from the filtered bam files with Deeptools 3.5.1 bamCoverage, with the parameters "-bs 10 --scaleFactor". The sequencing depth was normalized using the scaling factor calculated as described above.
Assembly: TAIR10
Supplementary files format and content: bigwig files contaning normalized read coverage
|
| |
|
| Submission date |
Nov 02, 2022 |
| 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 |
GPL28290 |
| 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 |
SAMN31572500 |
| SRA |
SRX18120873 |
