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| Status |
Public on Feb 16, 2019 |
| Title |
WT_3 |
| Sample type |
SRA |
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| Source name |
Cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
growth conditions: saturated in YPD
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| Growth protocol |
Cells were grown overnight, shaking at 30C in YPD media (1% yeast extract, 2% peptone, 2% dextrose).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was purified using acid phenol extraction, and then treated with Turbo DNase and purified with a Qiagen RNeasy kit.
Illumina libraries were prepared from 800-900 ng of total RNA, using the Truseq Stranded mRNA Library Prep (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
sacCer3_genes.gff
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| Data processing |
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20), trimmed of adapter sequences, excluding read pairs in which either read was shorter than 28 bp after trimming.
Reads were mapped using bowtie2 2.2.3 using the parameter set --very-sensitive -X 500
The number of read pairs with a minimum MAPQ score of 30 that overlap each gene uniquely were counted using HTSeq-count.
genome build: sacCer3 or ScSu.fa
Supplementary_files_format_and_content: sacCer3_genes.gff are the gene annotations used for S. cerevisiae; ScSu_genes.gff are the annotations for S. cerevisiae x S. uvarum; tab-delimited text files ending in "counts.txt" include the number of read pairs mapping to each gene.
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| Submission date |
Feb 15, 2019 |
| Last update date |
Feb 17, 2019 |
| Contact name |
Seungsoo Kim |
| Organization name |
Stanford University
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| Department |
Chemical and Systems Biology
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| Lab |
Joanna Wysocka
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| Street address |
265 Campus Dr
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL19756 |
| Series (1) |
| GSE118118 |
A combination of transcription factors mediates inducible interchromosomal contacts |
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| Relations |
| BioSample |
SAMN10955727 |
| SRA |
SRX5383654 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3610398_WT_3.counts.txt.gz |
28.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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