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| Status |
Public on Dec 01, 2021 |
| Title |
eluturation-arrest-release-exp190911_large-60min_bio-rep1 |
| Sample type |
SRA |
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| Source name |
cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: A17896
treatment: eluturation-arrest-release
cell size: large
time point: 60 min
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
cell pellets were lysed in 300 µL TRI Reagent (Zymo Research) by bead beating using a Fastprep 24 (4°C, settings: 5.0 m/s, 1 x 30 seconds). Cell debris was pelleted (13 krpm, 5 minutes) and the supernatant recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research).
mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina® (NEB, #E7775) was then used to prepare libraries for paired-end (2x150 bp) Illumina sequencing
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
eluturation-arrest-release-exp190911_large-60min_bio-rep1
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| Data processing |
read alignment, ChIP-seq Bowtie 1.0.1
read alignment, RNA-seq STAR-2.5.3a
custom code
Genome_build: custom
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM
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| Submission date |
Feb 26, 2021 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Georgi Kolev Marinov |
| Organization name |
STANFORD UNIVERSITY
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| Department |
Genetics
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| Street address |
279 Campus Drive West, Beckman Center, B-257A/259
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5101 |
| Country |
USA |
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| Platform ID |
GPL27812 |
| Series (1) |
| GSE167842 |
Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size |
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| Relations |
| BioSample |
SAMN18079085 |
| SRA |
SRX10182765 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5113903_eluturation-arrest-release-exp190911_large-60min_bio-rep1.bigWig |
41.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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