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Sample GSM2446265 Query DataSets for GSM2446265
Status Public on Oct 07, 2017
Title HiC cut3
Sample type SRA
Source name cut3
Organism Schizosaccharomyces pombe
Characteristics strain: SPO25
culture condition: 36C 2hour
mutation: cut3-477
Growth protocol The fission yeast Schizosaccharomyces pombe strains were cultured in Yeast-Extract Adenine.
Extracted molecule genomic DNA
Extraction protocol The in situ Hi-C experiment was performed as previously reported (Rao et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell 159, 1665–80 (2014).) Total RNA was extracted from cells as previously described (Alfa et al. Experiments with fission yeast. (Cold Spring Harbor Laboratory Press, 1993).)
Hi-C samples were prepared for sequencing using NEBNext Multiplex Oligos for Illumina kit. RNA libraries were prepared for sequencing using NEBNext ultra NDA library prep kit
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Data processing Library strategy: HiC-seq
HiC-seq: The 76 bp paired reads were separately aligned to the fission yeast genome (version ASM294v2.19) using Bowtie2.2.5. Partial alignment was judged by the CIGAR string. Unaligned bases were trimmed, and a remaining sequence was realigned. If alignable locations were not identified across the genome, either upstream or downstream 5 bases were trimmed. Reads were again evaluated by the CIGAR string, and the trimming step was repeated until the truncated reads became less than 25 bp. Mapped reads were assigned to MboI fragments.
HiC-seq: Redundant paired reads mapped to exactly the same genomic positions were discarded to remove a potential PCR bias. When reads were aligned to repetitive sequences or have low mapping quality (MAPQ < 30), they were also removed. Subsequently, paired reads aligned to two loci positioned less than 20 kb apart and potentially derived from self-ligation and undigested products were discarded.
HiC-seq: Contact matrices were generated at three resolutions such as 5, 10, and 20 kb. The entire fission yeast genome was divided into 5, 10, or 20 kb sections. A raw contact matrix was first constructed by counting paired reads assigned to two genomic sections. Note that reads belong to MboI fragments.
Biases in *raw *contact matrices were corrected by *ICE* method (*Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999 1003 (2012)*). The *ICE* normalization was repeated 10 times, and an average score of bias corrected matrix was adjusted to 1 , resulting in contact scores.
Genome_build: ASM294v2.19
Supplementary_files_format_and_content: HiC-seq: tab-deliminated text files of normalized scores. First row and column indicate the location of the genome in following format, "<chromosome name>:<start position>:<end position>"
Submission date Jan 05, 2017
Last update date May 15, 2019
Contact name Hideki Tanizawa
Organization name University of Oregon
Department Institute of Molecular Biology
Street address 1370 Franklin Blvd
City Eugene
State/province OR
ZIP/Postal code 97403
Country USA
Platform ID GPL13988
Series (1)
GSE93198 Architectural alterations of the fission yeast genome across the cell cycle
BioSample SAMN06208970
SRA SRX2467295

Supplementary file Size Download File type/resource
GSM2446265_HiC_cut3_10kb.txt.gz 11.3 Mb (ftp)(http) TXT
GSM2446265_HiC_cut3_20kb.txt.gz 2.9 Mb (ftp)(http) TXT
GSM2446265_HiC_cut3_5kb.txt.gz 37.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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