 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 15, 2014 |
| Title |
PA64s 5hmC |
| Sample type |
SRA |
| |
|
| Source name |
Panicle
|
| Organism |
Oryza sativa |
| Characteristics |
tissue type: panicle
passages: 3-4mm
strain: PA64s
chip antibody: anti-5-hydroxymethylytosine #39769, Active Motif
|
| Growth protocol |
Panicle materials in 3-4mm length were simultaneously collected from the super-hybrid rice group cultivars in a test field of China National Hybrid Rice R&D Center in Hunan Province, and DNA were extracted for Dot-blots assay.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs from panicle were denatured 95℃ for 10min and immediately chilled on ice for 5min. The Dot blot was performed on a bio-Dot Apparatus (#170-6545, Bio-Rad). The completely dried charged nylon-based membrane was baked for 2h at 80℃, after that 254 UV crosslink 10min and then blot Briefly with 5% non-fat milk at 1.5h room temperature. The primary rabbit anti-5-hydroxymethylytosine antibody (1:10k, #39769, Ative Motif) was applied to the membrane and incubated 1h at RT or overnight at 4℃, followed by peroxidase-conjugated anti-rabbit IgG secondary antibody. The signal was visualized by using ECL-Plus (Amersham Pharmacia Biotech).Purified genomic DNA should be sonicated into short fragments (200~300 bp) by Covaris DNA shearing with microTUBEs according to manufacturer’s instructions. Then 5hmC labeling reaction were performed in 75-ul solution containing 50mM HEPES buffer(PH7.9), 250 mM MgCl2, 100 µM UDP-6-N3-Glu, and 80 U βGT. The reactions were incubated for 2h at 37℃. After the reaction, The DNA substrates were purified and exchange buffer in H20 via Bio-rad micro bio spin according to the manufacturer’s instructions. The click chemistry was performed with the addition of 150µM biotin into the DNA solution and incubated 2h at 37℃.The DNA samples were then purified by Invitrogen DynabeadsMyOneTM Streptavidin C1 according to manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
chemical labeling
|
| Data processing |
The deep sequencing reads were stripped of the adaptor sequences with the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads that were less than 25 nt in length or contained an ambiguous nucleotide were discarded. The remaining reads were aligned to the TIGR rice genome Oryza sativa subsp. japornica (ver6.1), with up to two mismatches allowed, by the BWA 0.5.8 algorithm (Li and Durbin 2009). All non-redundant uniquely mapped reads were used for peaks calling using MACS (P-value<10-5) (Zhang et al. 2008). The location that peaks relative to a known transcript was determined based on the TIGR v6.1 database (Yuan et al. 2003; Ouyang et al. 2007).
Genome_build: TIGR ver6.1
|
| |
|
| Submission date |
Apr 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shuhui Song |
| E-mail(s) |
songshh@big.ac.cn
|
| Organization name |
Beijing Institute of Genomics, Chinese Academy of Sciences
|
| Street address |
No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China
|
| City |
Beijing |
| ZIP/Postal code |
86 |
| Country |
China |
| |
|
| Platform ID |
GPL13160 |
| Series (1) |
| GSE37242 |
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine in rice |
|
| Relations |
| SRA |
SRX141987 |
| BioSample |
SAMN00855331 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM914186_PA64s_peak.txt.gz |
51.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
