|
| Status |
Public on Dec 19, 2016 |
| Title |
RNAPII-CTDS2P_fft2Dfft3D_37C_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
S.pombe cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: fft2Dfft3D
antibody: ab5095; abcam
phase: mid-log phase
medium: YES (rich medium)
|
| Treatment protocol |
Final 1% formaldehyde fixation and 125mM glycine quencing were performed before cell harvest.
|
| Growth protocol |
Cell culture were inoculated twice. Cell cultures were inoculated with shaking for aeration at proper temperatures.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Every ChIP-seq cells were grown up to mid-log phase and harvested after final 1% formaldehyde fixation and 125mM glycine quencing. Cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. ChIP cells were disrupted by glass bead vortexing in ChIP lysis buffer and sonicated by Sonic Dismembrator Model 500, Fisher Scientific. Debris of the sonicate was excluded by centrifugation by 14,800rpm at 4 Celcius degree. IP samples were aliqouted from the sonicate and immunoprecipiated by proper amount of antibody and protein A/G beads, washed by ChIP lysis buffer for over-night at 4 Celcius degrees. IP samples were washed and eluted by proper buffers in Sigmaprep spin column. Proteins in both IP and input samples were degraded by 2hr 30ug proteinase K rxn and de-crosslinked at 65 Celcius degrees for at least 8hrs. The IP and input DNA were eluted by Quiagen PCR purification kit.
General Manual of Truseq ChIP library preparation kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNAPII_CTDS2P_fft2Dfft3D_mt-vs-wt_37C.bw
|
| Data processing |
The quality of fastq files were checked by fastqc and trimmed by trim_galore
The qualified fastq files were aligned to Spombe ASMv2 genome fa file using novoalign v3.03.02. Then, the aligned files were compressed and sorted by samtools v1.3.
The sorted BAM files of biological duplicates were compared by deeptools. If the duplicates were similar each other, they were merged and sorted by samtools v1.3.
The prepared merged BAM files were analyzed by deeptools to generate bigwig files and normalized values and profiles.
Genome_build: SpombeASMv2
Supplementary_files_format_and_content: bigwig files were generated by deeptools.
|
| |
|
| Submission date |
Dec 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Junwoo Lee |
| E-mail(s) |
junwoolee89@gmail.com
|
| Phone |
8328371831
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Epigenetics and Molecular Carcinogenesis
|
| Lab |
Blaine Barholomew Lab
|
| Street address |
2120 El Paseo Street, Apt.603
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL17225 |
| Series (1) |
| GSE83600 |
Chromatin remodeler Fun30-Fft3 disassembles nucleosomes to facilitate RNAPII elongation in fission yeast |
|
| Relations |
| BioSample |
SAMN06163573 |
| SRA |
SRX2435245 |
