|
Status |
Public on Apr 11, 2015 |
Title |
H3K9ac_34d_ChIP |
Sample type |
SRA |
|
|
Source name |
mature fully-expanded rosette leaf tissue, 34d, H3K9ac ChIP
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Columbia (Col-0) cell type: predominantly leaf mesophyll age: 34d chip antibody: H3K9ac (Millipore 07-352)
|
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.
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
H3K9ac ChIP of 34d 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.
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|
|
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 |
SAMN03473645 |
SRA |
SRX986841 |