|
| Status |
Public on Apr 30, 2015 |
| Title |
m6A-DpnII-dark |
| Sample type |
SRA |
| |
|
| Source name |
Algae cultured in constant dark
|
| Organism |
Chlamydomonas reinhardtii |
| Characteristics |
culture media: Tris-Acetate-Phosphate (TAP)
strain: CC 1609
|
| Growth protocol |
Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For enzyme digested samples, CviAII or DpnII are added to 10 U/ug and incubated overnight. Digested DNA is sonicated to ~500 bp segments which is subject to DNA library construction.
Standard DNA sequencing and Stranded RNA-seq protocol from Illumina
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
enzyme-treated
|
| Data processing |
After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1
Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01.
For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide.
Methylation ratios are determined by the the reads ends information.
Genome_build: Cre4
Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample.
|
| |
|
| Submission date |
Apr 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Guan-Zheng Luo |
| Organization name |
UChicago
|
| Department |
Chemistry
|
| Street address |
929 E 57th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL15922 |
| Series (1) |
| GSE62690 |
N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas |
|
| Relations |
| BioSample |
SAMN03567042 |
| SRA |
SRX1008141 |
