|
| Status |
Public on May 19, 2014 |
| Title |
Scm3-GFP ChipSeq |
| Sample type |
SRA |
| |
|
| Source name |
Scm3-GFP ChipSeq
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: 5929
genotype/variation: expressing GFP-tagged Scm3
cell type: asynchronous haploid cells
chip antibody: GFP
chip antibody vendor: Molecular Probes
chip antibody cat.#: A-11122
|
| Growth protocol |
Cells were grown in an asynchronous culture of YES media to a density of 1x10^7 cells/ml
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed for 15 min in 1% formaldehyde (Sigma) and lysed with 0.4 mg/ml Zymolase (AMS Biotechnology Europe) in PEMS for 1 hour at 36°C. Samples were sonicated for 20 minutes in a Bioruptor (Diagenode). The samples were incubated overnight with 7.5 µl αGFP antibody and 125 µl Protein G dynabeads. The samples were washed and incubated with 1% SDS for 4 hours at 65°C. The DNA was purified with a Qiagen PCR purification kit and centromeric enrichment was verified by qPCR.
Illumina libraries were prepared following the TruSeq Nano DNA kit guidelines (Illumina) using NEXTflex (Bioo Scientific) adapters with internal barcodes. Multiplexed libraries were sequenced on an Illumina HiSeq2000 (Ark Genomics, Edinburgh, UK).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GCTCGGTA
|
| Data processing |
Reads were aligned to the S. pombe EF2 genome using Bowtie2 with parameters --non-deterministic --no-mixed -X 300 -5 20 -3 20
Sorted bam files were generated using samtools
Coverage was calculated using MACS with parameters -w -S -g 12570000 --keep-dup=1000000 --space=1
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: wig files
|
| |
|
| Submission date |
Feb 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas Toda |
| E-mail(s) |
ntoda03@gmail.com
|
| Organization name |
University of Edinburgh
|
| Department |
Institute of Cell Biology
|
| Lab |
Allshire Lab
|
| Street address |
6.34 Michael Swann Building
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE54685 |
Eic1 links Mis18 with the CCAN/Mis6/Ctf19 complex to promote CENP-A assembly |
|
| Relations |
| BioSample |
SAMN02628351 |
| SRA |
SRX464903 |
