|
| Status |
Public on Mar 06, 2015 |
| Title |
IgG_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
kernal
|
| Organism |
Zea mays |
| Characteristics |
developmental stage: 15 days after pollination
tissue: Endosperm
genotype: wildtype
chip antibody: rabbit IgG (Sigma, catalog# I5006, lot# SLBJ3775V, pack size 50MG)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Endosperm Lysates were clarified from sonicated nuclei. O2-DNA complexes were isolated with antibody and IgG serves as antibody control
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Catalog# IP-202-1012). ChIP DNA samples were subjected to end repair and A-base addition, followed by ligation with adapters. Barcode sequences of adapters correspond to the following: AGTCAA, ChIP of O2; AGTTCC, ChIP of IgG. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Illumina Genome Analyzer (GA) sequencing was performed by the OSUCCC Nucleic Acid Shared Resource-Illumina GA II Core.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CASAVA1.8.2 (Illumina) were used for image analysis and base calling.
Raw fastq data were trimmed using SolexaQA v2.5 program with Q20 (Phred score) and L40 (Length).
Cleaned data were then mapped to the maize reference genome using Bowtie2 with default parameters and allowing unique reads only.
[Ensembl plants release-15 zea_mays] Peak detection was done using MACS v2.0.10 using the indicated criteria.
[Ensembl plants release-26 zea_mays] Peak calling was performed s using MACS2 (v2.1.0) (band width = 300?model fold = [5, 50]; qvalue cutoff = 5.00e-02)
UCSC bedGraph files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: Ensembl plants release-15 zea_mays
Genome_build: Ensembl plants release-26 zea_mays
Supplementary_files_format_and_content: tab-delimited text file includes contains information about called peaks.
Supplementary_files_format_and_content: bed file includes the peak summits locations for every peaks.
|
| |
|
| Submission date |
Dec 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chaobin Li |
| E-mail(s) |
chaobinli@cau.edu.cn
|
| Phone |
+8613585766795
|
| Organization name |
China Agricultural University
|
| Lab |
National Maize Improvement Center of China
|
| Street address |
2 Yuanmingyuan West Road, NMICC Building
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL15463 |
| Series (1) |
| GSE63991 |
Genome-wide characterization of cis-acting DNA targets of Opaque2 in maize |
|
| Relations |
| BioSample |
SAMN03256351 |
| SRA |
SRX801129 |
