|
Status |
Public on Oct 31, 2020 |
Title |
ARG2_dip |
Sample type |
SRA |
|
|
Source name |
ARG2_dip
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
background strain: S288C time point: n/a media: SC+ClonNAT genotype: MATa/alpha ARG2/[barcode-URA3-Z3EVpr-ARG2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1
|
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)
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|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
MATa/α ARG2/[barcode-URA3-Z3EVpr-ARG2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1 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)
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|
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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 |
SAMN16234004 |
SRA |
SRX9164639 |