|
| Status |
Public on Oct 31, 2020 |
| Title |
TIP41_hap |
| Sample type |
SRA |
| |
|
| Source name |
TIP41_hap
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
background strain: S288C
time point: n/a
media: SC+ClonNAT
genotype: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TIP41] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0
|
| Growth protocol |
All BARseq, WGS, and RNAseq samples were grown using glutamate as a nitrogen source
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
BARSeq: pooled cultures were propagated at low density (OD < 0.05) and > 2 x 106 cells were collected at each time point. Genomic DNA was extracted using the YeaStar Genomic DNA kit (Zymo Research) and 5 ng of DNA were used to PCR amplify the uptag barcode region with custom primers
Whole Genome Sequencing: Genomic DNA was extracted using the YeaStar Genomic DNA kit (Zymo Research)
RNAseq: cells were frozen in lysis mastermix, then reverse transcription was done to obtain cDNA, which was then amplified and cleaned up with RNAClean Ampure XP beads
Libraries were constructed using the Nextera DNA Flex kit (Whole Genome Sequencing) and Nextera XT kit (RNAseq)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TIP41] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv
|
| Data processing |
Library strategy: Whole Genome Sequencing
RNAseq: Samples were demultiplexed using bcl2fastq, then fastq files were processed using Salmon and aligned using STAR
BARseq: Samples were demultiplexed using Barcas
Whole Genome Sequencing: Samples were demultiplexed using bcl2fastq and then BowTie2 was used to align the samples
Genome_build: SacCer3
Supplementary_files_format_and_content: 20190909_rawTPMtable.csv: csv file with raw TPMs from RNAseq
Supplementary_files_format_and_content: zev_wgs_processeddata.csv: csv file with sequencing information, rDNA coverage, copy number and gc content
Supplementary_files_format_and_content: ZEV_TOF_all_merge.txt: text file with normalized BARseq results (normalized to wild type, time 0, and read depth)
|
| |
|
| Submission date |
Sep 21, 2020 |
| Last update date |
Oct 31, 2020 |
| Contact name |
Rebecca Y Wang |
| E-mail(s) |
rebecca@calicolabs.com
|
| Organization name |
Calico Life Science LLC
|
| Street address |
1170 Veterans Blvd
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL27812 |
| Series (2) |
| GSE158318 |
A barcoded genome-scale library of inducible alleles reveals principles of synthetic gene control [Seq] |
| GSE158319 |
A barcoded genome-scale library of inducible alleles reveals principles of synthetic gene control |
|
| Relations |
| BioSample |
SAMN16233800 |
| SRA |
SRX9164870 |
