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Sample GSM1322114 Query DataSets for GSM1322114
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
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
BioSample SAMN02628351
SRA SRX464903

Supplementary file Size Download File type/resource
GSM1322114_1180N0004_4_GCTCGGTA_L001_R1_001.wig.gz 27.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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