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Sample GSM2598436 Query DataSets for GSM2598436
Status Public on Oct 30, 2017
Title tDNA2334_rep2
Sample type SRA
Source name tDNA2334
Organism Saccharomyces cerevisiae
Characteristics strain: W303
media: YPD
Treatment protocol Yeast cells were fixed with 3% formaldehyde for 10 min, and quenched with 125 mM glycine for 5 min. Cells were pelleted and spheroplasted with Zymolyase. The spheroplasts were washed by PBS, subjected to long-crosslinker fixation for 40min, and quenched with 250 mM glycine for 5 min. Cells were pelleted again, washed with PBS, and treated with a level of MNase yielding >95% mononucleosomes. After stopping MNase, chromatin pellet and supernatant was dephosphorylated using rSAP separately. Crosslinked chromatin was subject to T4 DNA polymerase / T4 PNK enzyme mix solution to generate blunt ends. Chromatin was diluted into 2.5 mL and treated with T4 DNA ligase. Ligated products were treated with 100U of exonuclease III for 5 min to eliminate biotinylated ends of unligated DNA. Proteinase K was then added and incubated at 65 C overnight.
Growth protocol The 100mL yeast cultures were grown to midlog phase ~OD 0.55 in indicated media at 30 C.
Extracted molecule genomic DNA
Extraction protocol DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis.
Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~10-12 cycles of PCR using Illumina paired-end primers.
Amplified library was purified and subject to Illumina Nextseq 500 paired end sequencing with 42 x 42 bp reads.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing Library strategy: Micro-C
OLB 1.9/CASAVA_v1.8.2 were used for base calling.
Barcoded libraries were demultiplexed autmatically by Illumina Basespace platform.
Paired reads were mapped to reference genome separately by Bowtie2.
Parse SAM files and remove duplicate reads.
Mate unique paired reads and generate BED file for all valid interactions.
Triplet sparse conact matrix with various resolutions (e.g., 100bp, 200bp, 1kb, and 5kb) were generated, in which the first two columns are bin numbers and the third colum is interaction count.
Genome_build: S288C (sacCer3)
Supplementary_files_format_and_content: BED (Chr1, Pos1, Strand1, Chr2, Pos2, Strand2), contact matrix
Submission date May 04, 2017
Last update date May 15, 2019
Contact name Xavier Darzacq
Phone 510-642-0884
Organization name University of California, Berkeley
Department Molecular and Cell Biology
Lab Darzacq Lab
Street address 475D Li Ka Shing Center
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platform ID GPL19756
Series (1)
GSE98543 Transfer RNA Genes Affect Chromosome Architecture and Function
BioSample SAMN06891113
SRA SRX2783779

Supplementary file Size Download File type/resource
GSM2598436_tDNA2334-2_contact-matrix.tar.gz 122.4 Mb (ftp)(http) TAR
GSM2598436_tDNA2334_2_allValidPairs.bed.gz 147.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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