|
| Status |
Public on Apr 11, 2015 |
| Title |
H3K9ac_42d_Input |
| Sample type |
SRA |
| |
|
| Source name |
mature fully-expanded rosette leaf tissue, 42d, input
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia (Col-0)
cell type: predominantly leaf mesophyll
age: 42d
chip antibody: none
|
| Treatment protocol |
N/A
|
| Growth protocol |
Sunshine LC-1 soil mix, weekly feedings with Gro-Power Liquid 4-8-2. Percival AR-60 growth chamber, 30 micromoles photons m^-2 sec^-1, 20 hours of light 4 hours of dark.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei extraction: Chromatin was fixed by vacuum infiltration with formaldehyde. Frozen tissue was ground in liquid nitrogen, filtered through Miracloth and subject to low speed centrifugation.
Chromatin Immunoprecipitation: Magnetic Dynabeads Protein G were coupled to antibodies and incubated with pre-cleared nuclei that had been sonicated in a BioRupter. Dynabeaks were washed, DNA was eluted and heated to reverse formaldehyde fixation. Histones were digested with proteinase K and DNA was precipitated and quantified using Pico-green.
H3K4me3 ChIP library construction: ChIP DNA was subject to end repair, dA was added to the 3' end, and Illumina adapters were ligated to the dA-tailed DNA. DNA was amplified by PCR and electrophoresed on a TAE gel to separate PCR products from the adaptor dimers. Eluted DNA was quantified using Pico-green. Multiplexing was not used for the H3K4me3 library.
H3K9ac ChIP library construction: The H3K9ac ChIP library used the Illumina TruSeq ChIP Sample Preparation Kit-Set A. Two samples were run per lane using multiplexing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H3K9ac input of 42d mature fully-expanded rosette leaf tissue.
|
| Data processing |
ChIP-seq library reads were mapped to the TAIR10 reference genome using bowtie-0.12.8 (Langmead et al., 2009).
The resultant mapped reads were collapsed to unique start sites and binned within 100bp windows along the genome.
Genome_build: TAIR10
Supplementary_files_format_and_content: BedGraph-formatted files contain ChIP-seq read counts (not normalized) within 100bp.
|
| |
|
| Submission date |
Apr 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Judy Brusslan |
| Organization name |
California State University Long Beach
|
| Department |
Department of Biological Sciences
|
| Lab |
MLSC-203
|
| Street address |
1250 Bellflower Blvd
|
| City |
Long Beach |
| State/province |
CA |
| ZIP/Postal code |
90840 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE67776 |
A Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence [ChIP-seq] |
| GSE67778 |
A Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence |
|
| Relations |
| BioSample |
SAMN03473652 |
| SRA |
SRX986844 |
