|
| Status |
Public on Apr 13, 2020 |
| Title |
Input_wt_2 |
| Sample type |
SRA |
| |
|
| Source name |
Wild type (Hu2185)
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu2185
genotype: wild type
chip antibody: none
cell growth phase: mid-log exponential phase
|
| Treatment protocol |
Use final 1% formaldehyde to crosslink at room temperature for 30min and quench the fixation by adding glycine.The spinned down cell pellet was resuspended in ice code Lysis buffer(150mM NaCl, 50mM Hepes-KOH pH7.5, 0.1%SDS, 1%Triton X-100, 0.1% sodium deoxycholate, 1mM EDTA) with proteinase inhibitor (PI).Lyse cell in Fastprep machine 7 times during 30sec at max speed. Spin down the debris of yeast cells and keep the supernatant. The supernatant was then sent for sonication by Bioruptor Pico Sonicator (11 cycles of 30 sec on 30 sec off) to get the sheard chromatin. Spin down the debris again.
|
| Growth protocol |
Standard YES medium was used for cell culture. Standard fission yeast genetic techniques and media were used according to Moreno et al (1991). Yeast cells were grown to mid-logarithmic phase (5x10^6 cell/ml). Harvest 200x10^6 cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each IP, 30ul of sheard chromatin and 1ug of H3K9me2 antibody were prepared, and 10ul of protein A/G coated magnetic beads was used. After incubation and washing steps, final ChIP DNA was extracted through Qiagen PCR purification kit.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext® Ultra™ II DNA Library Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using Illumina bcl2fastq-1.8.4
ChIP-seq reads were aligned to the ASM294v2 genome assembly using STAR version 3.2 with configurations --alignIntronMax 1 --bamRemoveDuplicatesType UniqueIdenticalNotMulti
Genome_build: Schizosaccharomyces_pombe.ASM294v2
Supplementary_files_format_and_content: bedGraph files
|
| |
|
| Submission date |
Jan 30, 2019 |
| Last update date |
Apr 13, 2020 |
| Contact name |
Wenbo Dong |
| E-mail(s) |
[email protected]
|
| Phone |
0046769797414
|
| Organization name |
Karolinska Institutet
|
| Department |
Biosciences and Nutrition
|
| Lab |
Andreas Lennartsson
|
| Street address |
Hälsovägen 7C Neohuset
|
| City |
Hudidnge |
| State/province |
Sweden |
| ZIP/Postal code |
14183 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE125911 |
Abo1 is required for H3K9me2 to H3K9me3 transition in telomeric and centromeric heterochromatin [ChIP-seq] |
| GSE125912 |
Abo1 is required for H3K9me2 to H3K9me3 transition in telomeric and centromeric heterochromatin |
|
| Relations |
| BioSample |
SAMN10847887 |
| SRA |
SRX5311940 |
