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| Status |
Public on Dec 19, 2023 |
| Title |
Msn2DBD_Gcn4AD_lib_nativeloc_H08_2 |
| Sample type |
SRA |
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| Source name |
cultured yeast cells
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| Organism |
Saccharomyces cerevisiae BY4741 |
| Characteristics |
cell type: cultured yeast cells
type: Msn2DBD
fusion: Gcn4AD
loci: native
delta native tf: TRUE
promoter: synthetic
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| Growth protocol |
Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: Modified protocol of the nucleospin 96 RNA kit (Macherey-Nagel, Duren, Germany). Specifically, cell lysis was done in a 96 deep-well plate by adding 450 μl of lysis buffer containing 1 M sorbitol (Sigma-Aldrich), 100 mM EDTA, and 0.45 μl lyticase (10 IU/μl). The plate was incubated at 30°C for 30 minutes in order to break the cell wall and then centrifuged for 10 minutes at 2,500 rpm, and the supernatant was removed. From this point, extraction proceeded as in the protocol of nucleospin 96 RNA kit, only substituting β-mercaptoethanol with DTT 1M.
RNA libraries were created as described before (Chapal et al., 2019).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Demultiplexing with AdapterRemoval, --trim3p 0 21.
Identification of UMI with umi_tools extract, --bc-pattern=NNNNNNNNN.
Mapping the reads with bowtie2, -p8 --local --very-sensitive --trim-to 30 -x.
Sorting and indexing with samtools.
Deduplication of UMI with umi_tools dedup.
Calculation of coverage with bedtools coverage -counts -s -a.
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.txt: Processed data files contain counts mapped with bedtools coverage in format of (chromosome, chromosome location (start), chromosome location (stop), systemic name, number, strand, counts).
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| Submission date |
Jun 07, 2023 |
| Last update date |
Dec 19, 2023 |
| Contact name |
Naama Barkai |
| E-mail(s) |
naama.barkai@weizmann.ac.il
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| Phone |
+972-8-934-4429
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| Organization name |
Weizmann Institute of Science
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| Department |
Molecular Genetics
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| Lab |
Barkai Lab
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| Street address |
Herzl 234
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| City |
Rehovot |
| State/province |
HaMerkaz |
| ZIP/Postal code |
7630031 |
| Country |
Israel |
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| Platform ID |
GPL28475 |
| Series (2) |
| GSE234431 |
Activation domains and Coactivator direct genomic localization of fused DNA binding domains, defining the subset of activated promoters [RNA-seq] |
| GSE234433 |
Activation domains and Coactivator direct genomic localization of fused DNA binding domains, defining the subset of activated promoters |
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| Relations |
| BioSample |
SAMN35671699 |
| SRA |
SRX20636267 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7467824_Vova1_S12.H10_TGACGGA.txt.gz |
96.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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