|
| Status |
Public on Jan 01, 2020 |
| Title |
Histone H3 Hydra Replicate I |
| Sample type |
SRA |
| |
|
| Source name |
Complete Polyp
|
| Organism |
Hydra vulgaris |
| Characteristics |
strain: Hydra vulgaris Ind-Pune
chip antibody: Histone H3 (Ab1791, abcam)
|
| Treatment protocol |
None
|
| Growth protocol |
Hydra vulgaris were grown using standard protocol.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone H3-DNA and RNA polymerase II-DNA complexes were isolated with antibody.
Standard ChIP protocols was followed to obatin chromatin from Hydra vulgaris. The ChIP-seq libraries have been prepared according to the Life Technologies protocol, SOLiD ChIP-seq kit guide (A12066). The quality of the libraries has been checked with the Bioanalyser DNA High sensitivity and by ChIP-qPCR. The sequencing was performed with the AB SOLiD 4 System sequencer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
Chromatin IP using specific antibody
|
| Data processing |
For the SOLiD 4 System, high-quality reads were matched to individual samples based on the barcode tag and using default parameters in SOLiD Experimental Tracking Software (SETS) v4.0.1.
Reads were mapped using the Bowtie, color-space program.
Bed files were generated using BedTools
Genome_build: Hydra_vulg_ind_pune, h7
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Nov 18, 2014 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Krishanpal Karmodiya |
| E-mail(s) |
[email protected]
|
| Organization name |
Indian Institute of Science Education and Research
|
| Department |
Center of Excellence in Epigenetics
|
| Street address |
Dr. Homi Bhabha Road
|
| City |
Pune |
| State/province |
Maharashtra |
| ZIP/Postal code |
411008 |
| Country |
India |
| |
|
| Platform ID |
GPL19432 |
| Series (1) |
| GSE63414 |
Genome-wide maps RNA Polymerase II and Histone H3 of Hydra vulgaris |
|
| Relations |
| BioSample |
SAMN03199344 |
| SRA |
SRX762923 |
