|
| Status |
Public on Aug 28, 2023 |
| Title |
H3.3 (HTR5-RFP) ChIP-seq in ddm1 biol Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
background: Col0 + pHTR5:HTR5-RFP
chip antibody: RFP-trap (ChromoTek; rtma-10)
genotype: ddm1-2
treatment: crosslinking
|
| Growth protocol |
Plants were grown under long day conditions at 22 °C. Seeds were grown on ½ Murashige and Skoog (MS) medium for 10 days, or transplanted to soil after 7days until pollen maturity.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Parent et al., 2021), starting with 1g of seedlings. In brief, after crosslinking in 1% formaldehyde for 10 min, the tissue was ground to a fine powder in liquid nitrogen, chromatin was extracted with 1% SDS Tris-based lysis buffer and sonicated to ~200bp fragments. Chromatin was cleared with protein A magnetic beads and incubated overnight with the antibody listed below. Immune complexes were eluted with low, and then high salt buffers, before reversing crosslinks and purifying DNA fragments with ChIP DNA clean and concentrator kit (Zymo Research). Low input ChIP for MGH3-GFP was performed with ~10e8 pollen grains. Fixation was for 15 min and subsequent grinding with acid-washed glass beads. DNA fragments underwent a preliminary phenol-chloroform and ethanol precipitation step before clean up.
NEBNext Ultra II DNA Library Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Compared to its H3 control in processed file (log2 fold change of normalized CPM)
ddm1_HTR5_IP_Rep2
|
| Data processing |
Adapter trimming with cutadapt
Genome alignement with Bowtie2-2.4.1
Deduplication with samtools
Bigwig made with Deeptools bamCompare with CPM normalization versus the corresponding control
Assembly: TAIR10
Supplementary files format and content: Bigwig files representating log2 fold change of count per million IP/Input or IP/H3(H4)
|
| |
|
| Submission date |
May 03, 2023 |
| Last update date |
Aug 28, 2023 |
| Contact name |
Jonathan Cahn |
| E-mail(s) |
cahnjonathan@gmail.com
|
| Organization name |
CSHL
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE231563 |
Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation [ChIP-seq] |
| GSE231565 |
Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. |
|
| Relations |
| BioSample |
SAMN34567959 |
| SRA |
SRX20209060 |
