GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM6705027 Query DataSets for GSM6705027
Status Public on Sep 10, 2023
Title 2h1wt3_coseg.BR1.input
Sample type SRA
Source name Arabidopsis seedlings
Organism Arabidopsis thaliana
Characteristics plant line: h1.2h1.2 segregant from the cross
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
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
BioSample SAMN31572508
SRA SRX18120881

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap