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| Status |
Public on Dec 01, 2019 |
| Title |
ZEV_miseq_uninduced_9 |
| Sample type |
SRA |
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| Source name |
Synthetic promoter reporter gene assay
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| Organism |
synthetic construct |
| Characteristics |
plasmid type: Synthetic promoter driving reporter gene
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| Growth protocol |
Cells were grown in yeast nitrogen base media with 2 percent dextrose, lacking uracil, for three passages after library transformation. Passages were always at least 10 OD600*mL units.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
PCR amplicons from random oligonucleotide pools, joined by Golden Gate assembly at constant regions encoding transcription factor binding sites based on the PZEV artificial promoter system.
After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
Plasmid DNA and barcodes to assign an artificial promoter to an expression bin
filtered_read_table_miseq_ZEV.txt
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| Data processing |
Library strategy: FACS-seq
Base-calling: default FASTQ output from Illumina bcl2fastq
Paired-end alignment (Miseq data only): PEAR 0.9.6 with flags -j 8 -v 1 -g 2 -n 20
Consensus sequence extraction (Miseq only): scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/build_table_align.py)
Read table construction (Nextseqs and validation Miseq): scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/build_table_exact.py)
Mean extraction: scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/mean_fitting_likelihood_cuda.py)
Genome_build: not applicable – artificial sequence
Supplementary_files_format_and_content: means_nextseq_*.csv: comma-delimited table. No header – first column sequence, second column promoter activity in replicate A (GPD) or uninduced condition (others), third column activity in replicate B (GPD) or induced condition (others).
Supplementary_files_format_and_content: filtered_read_table_miseq_*.txt: comma-delimited table. No header – first column sequence, second column group identifier (from intermediate processing steps), following columns read counts in each bin, as assigned by ‘barcode_miseq_*.csv’ key tables in deposited code
Supplementary_files_format_and_content: final_means_ids_added.csv: comma-delimited table. “Seqs”: sequence. “Means_A”: promoter activity, uninduced. “Means_B”: promoter activity, induced. “Experiment”: numerical ID of artificial promoter set this sequence is part of (cf. text Supplementary Tables 1 and 2), “None” if a mutant/mis-assembled sequence. “Design”: numerical ID of sequence within its “Experiment”, -1 if “Experiment” is None.
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| Submission date |
Aug 06, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Christina Smolke |
| Organization name |
Stanford University
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| Department |
Bioengineering
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| Lab |
Smolke lab
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| Street address |
443 Via Ortega
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL17769 |
| Series (1) |
| GSE135464 |
Model-driven generation of artificial yeast promoters |
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| Relations |
| BioSample |
SAMN12505121 |
| SRA |
SRX6660437 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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