title: URA5_dip

status: Public on Oct 31 2020

type: SRA

city: South San Francisco

first: Rebecca

middle: Y

last: Wang

state: CA

address: 1170 Veterans Blvd

country: USA

institute: Calico Life Science LLC

description:
MATa/α URA5/[barcode-URA3-Z3EVpr-URA5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

library_source: genomic

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)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: All BARseq, WGS, and RNAseq samples were grown using glutamate as a nitrogen source

extract_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)

tag: background strain

tag: time point

tag: media

value: SC+ClonNAT

tag: genotype

value: MATa/alpha URA5/[barcode-URA3-Z3EVpr-URA5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: URA4_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-URA4] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-URA4] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: YJU2

description:
MATa/α YJU2/[barcode-URA3-Z3EVpr-YJU2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha YJU2/[barcode-URA3-Z3EVpr-YJU2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: URA5_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-URA5] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-URA5] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: URA4_dip

description:
MATa/α URA4/[barcode-URA3-Z3EVpr-URA4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha URA4/[barcode-URA3-Z3EVpr-URA4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: URA2_dip

description:
MATa/α URA2/[barcode-URA3-Z3EVpr-URA2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha URA2/[barcode-URA3-Z3EVpr-URA2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: URA1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-URA1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-URA1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: URA2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-URA2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-URA2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: TUB1

description:
MATa/α TUB1/[barcode-URA3-Z3EVpr-TUB1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha TUB1/[barcode-URA3-Z3EVpr-TUB1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: TRP1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TRP1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TRP1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: TRP3_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TRP3] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TRP3] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: URA1_dip

description:
MATa/α URA1/[barcode-URA3-Z3EVpr-URA1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha URA1/[barcode-URA3-Z3EVpr-URA1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: TRP1_dip

description:
MATa/α TRP1/[barcode-URA3-Z3EVpr-TRP1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha TRP1/[barcode-URA3-Z3EVpr-TRP1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: TIP41_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TIP41] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TIP41] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: TIP41_dip

description:
MATa/α TIP41/[barcode-URA3-Z3EVpr-TIP41] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha TIP41/[barcode-URA3-Z3EVpr-TIP41] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: THR1_dip

description:
MATa/α THR1/[barcode-URA3-Z3EVpr-THR1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha THR1/[barcode-URA3-Z3EVpr-THR1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: THR1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-THR1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: SC+ClonNAT

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-THR1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: TAF7

description:
MATa/α TAF7/[barcode-URA3-Z3EVpr-TAF7] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha TAF7/[barcode-URA3-Z3EVpr-TAF7] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: SRS2_dip

description:
MATa/α SRS2/[barcode-URA3-Z3EVpr-SRS2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha SRS2/[barcode-URA3-Z3EVpr-SRS2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: SRS2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SRS2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SRS2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: SNF12_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SNF12] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-SNF12] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: SNF12_dip

description:
MATa/α SNF12/[barcode-URA3-Z3EVpr-SNF12] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha SNF12/[barcode-URA3-Z3EVpr-SNF12] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: RPB3

description:
MATa/α RPB3/[barcode-URA3-Z3EVpr-RPB3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha RPB3/[barcode-URA3-Z3EVpr-RPB3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: PRE2

description:
MATa/α PRE2/[barcode-URA3-Z3EVpr-PRE2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha PRE2/[barcode-URA3-Z3EVpr-PRE2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: POL3

description:
MATa/α POL3/[barcode-URA3-Z3EVpr-POL3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha POL3/[barcode-URA3-Z3EVpr-POL3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: POP8

description:
MATa/α POP8/[barcode-URA3-Z3EVpr-POP8] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha POP8/[barcode-URA3-Z3EVpr-POP8] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: RAD3

description:
MATa/α RAD3/[barcode-URA3-Z3EVpr-RAD3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha RAD3/[barcode-URA3-Z3EVpr-RAD3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: TRP4_dip

description:
MATa/α TRP4/[barcode-URA3-Z3EVpr-TRP4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha TRP4/[barcode-URA3-Z3EVpr-TRP4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ORC5

description:
MATa/α ORC5/[barcode-URA3-Z3EVpr-ORC5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ORC5/[barcode-URA3-Z3EVpr-ORC5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: MET8_dip

description:
MATa/α MET8/[barcode-URA3-Z3EVpr-MET8] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha MET8/[barcode-URA3-Z3EVpr-MET8] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: MET17_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET17] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET17] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: MET17_dip

description:
MATa/α MET17/[barcode-URA3-Z3EVpr-MET17] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha MET17/[barcode-URA3-Z3EVpr-MET17] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: MET13_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET13] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: SC+ClonNAT

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-MET13] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: MCM10

description:
MATa/α MCM10/[barcode-URA3-Z3EVpr-MCM10] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha MCM10/[barcode-URA3-Z3EVpr-MCM10] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: MAK5

description:
MATa/α MAK5/[barcode-URA3-Z3EVpr-MAK5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha MAK5/[barcode-URA3-Z3EVpr-MAK5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: MAK11

description:
MATa/α MAK11/[barcode-URA3-Z3EVpr-MAK11] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha MAK11/[barcode-URA3-Z3EVpr-MAK11] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: LYS2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LYS2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LYS2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: LYS5_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LYS5] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LYS5] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: LYS5_dip

description:
MATa/α LYS5/[barcode-URA3-Z3EVpr-LYS5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha LYS5/[barcode-URA3-Z3EVpr-LYS5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: SEC18

description:
MATa/α SEC18/[barcode-URA3-Z3EVpr-SEC18] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha SEC18/[barcode-URA3-Z3EVpr-SEC18] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: LYS2_dip

description:
MATa/α LYS2/[barcode-URA3-Z3EVpr-LYS2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha LYS2/[barcode-URA3-Z3EVpr-LYS2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: LEU4_dip

description:
MATa/α LEU4/[barcode-URA3-Z3EVpr-LEU4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha LEU4/[barcode-URA3-Z3EVpr-LEU4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: LYS1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LYS1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-LYS1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: LEU2_dip

description:
MATa/α LEU2/[barcode-URA3-Z3EVpr-LEU2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha LEU2/[barcode-URA3-Z3EVpr-LEU2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: KIN28

description:
MATa/α KIN28/[barcode-URA3-Z3EVpr-KIN28] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha KIN28/[barcode-URA3-Z3EVpr-KIN28] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ILV1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ILV1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ILV1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: NOP1

description:
MATa/α NOP1/[barcode-URA3-Z3EVpr-NOP1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha NOP1/[barcode-URA3-Z3EVpr-NOP1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: MET6_dip

description:
MATa/α MET6/[barcode-URA3-Z3EVpr-MET6] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha MET6/[barcode-URA3-Z3EVpr-MET6] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ILV1_dip

description:
MATa/α ILV1/[barcode-URA3-Z3EVpr-ILV1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: SC+ClonNAT

value: MATa/alpha ILV1/[barcode-URA3-Z3EVpr-ILV1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: HO_dip

description:
MATa/α HO/[barcode-URA3-Z3EVpr-HO] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha HO/[barcode-URA3-Z3EVpr-HO] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: HIS7_dip

description:
MATa/α HIS7/[barcode-URA3-Z3EVpr-HIS7] [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:
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)

value: MATa/alpha HIS7/[barcode-URA3-Z3EVpr-HIS7] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ILV2_dip

description:
MATa/α ILV2/[barcode-URA3-Z3EVpr-ILV2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ILV2/[barcode-URA3-Z3EVpr-ILV2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: HSK3

description:
MATa/α HSK3/[barcode-URA3-Z3EVpr-HSK3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha HSK3/[barcode-URA3-Z3EVpr-HSK3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: MCD1

description:
MATa/α MCD1/[barcode-URA3-Z3EVpr-MCD1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha MCD1/[barcode-URA3-Z3EVpr-MCD1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: HIS2_dip

description:
MATa/α HIS2/[barcode-URA3-Z3EVpr-HIS2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha HIS2/[barcode-URA3-Z3EVpr-HIS2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: TRP4_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TRP4] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-TRP4] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: HIS6_dip

description:
MATa/α HIS6/[barcode-URA3-Z3EVpr-HIS6] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha HIS6/[barcode-URA3-Z3EVpr-HIS6] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: HIS1_dip

description:
MATa/α HIS1/[barcode-URA3-Z3EVpr-HIS1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha HIS1/[barcode-URA3-Z3EVpr-HIS1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: HAS1

description:
MATa/α HAS1/[barcode-URA3-Z3EVpr-HAS1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha HAS1/[barcode-URA3-Z3EVpr-HAS1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: MET13_dip

description:
MATa/α MET13/[barcode-URA3-Z3EVpr-MET13] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha MET13/[barcode-URA3-Z3EVpr-MET13] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: FAD1

description:
MATa/α FAD1/[barcode-URA3-Z3EVpr-FAD1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha FAD1/[barcode-URA3-Z3EVpr-FAD1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: DSN1

description:
MATa/α DSN1/[barcode-URA3-Z3EVpr-DSN1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha DSN1/[barcode-URA3-Z3EVpr-DSN1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: CDC45

description:
MATa/α CDC45/[barcode-URA3-Z3EVpr-CDC45] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha CDC45/[barcode-URA3-Z3EVpr-CDC45] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: LYS1_dip

description:
MATa/α LYS1/[barcode-URA3-Z3EVpr-LYS1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha LYS1/[barcode-URA3-Z3EVpr-LYS1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: HIS5_dip

description:
MATa/α HIS5/[barcode-URA3-Z3EVpr-HIS5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: SC+ClonNAT

value: MATa/alpha HIS5/[barcode-URA3-Z3EVpr-HIS5] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ILV2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ILV2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ILV2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: BAT1_1

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-BAT1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

library_source: transcriptomic

molecule: total RNA

value: SC+ClonNAT+estradiol

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-BAT1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ARO2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARO2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARO2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ARO7_dip

description:
MATa/α ARO7/[barcode-URA3-Z3EVpr-ARO7] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ARO7/[barcode-URA3-Z3EVpr-ARO7] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARO1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARO1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARO1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ARO2_dip

description:
MATa/α ARO2/[barcode-URA3-Z3EVpr-ARO2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ARO2/[barcode-URA3-Z3EVpr-ARO2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARG4_dip

description:
MATa/α ARG4/[barcode-URA3-Z3EVpr-ARG4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ARG4/[barcode-URA3-Z3EVpr-ARG4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: HIS4_dip

description:
MATa/α HIS4/[barcode-URA3-Z3EVpr-HIS4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha HIS4/[barcode-URA3-Z3EVpr-HIS4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARG3_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARG3] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARG3] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: FCF1

description:
MATa/α FCF1/[barcode-URA3-Z3EVpr-FCF1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha FCF1/[barcode-URA3-Z3EVpr-FCF1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARG2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARG2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARG2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ANY1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ANY1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ANY1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ARG1_dip

description:
MATa/α ARG1/[barcode-URA3-Z3EVpr-ARG1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ARG1/[barcode-URA3-Z3EVpr-ARG1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: CMD1

description:
MATa/α CMD1/[barcode-URA3-Z3EVpr-CMD1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha CMD1/[barcode-URA3-Z3EVpr-CMD1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARG1_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARG1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: SC+ClonNAT

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARG1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ANY1_dip

description:
MATa/α ANY1/[barcode-URA3-Z3EVpr-ANY1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ANY1/[barcode-URA3-Z3EVpr-ANY1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: CCT3

description:
MATa/α CCT3/[barcode-URA3-Z3EVpr-CCT3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha CCT3/[barcode-URA3-Z3EVpr-CCT3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: BRX1

description:
MATa/α BRX1/[barcode-URA3-Z3EVpr-BRX1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha BRX1/[barcode-URA3-Z3EVpr-BRX1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: BFR2

description:
MATa/α BFR2/[barcode-URA3-Z3EVpr-BFR2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha BFR2/[barcode-URA3-Z3EVpr-BFR2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ADE3_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ADE3] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ADE3] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ADE2_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ADE2] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ADE2] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: BAT1_10

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-BAT1] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
20190909_rawTPMtable.csv

value: SC+ClonNAT+estradiol

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-BAT1] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ARO7_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARO7] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARO7] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: ADE4_dip

description:
MATa/α ADE4/[barcode-URA3-Z3EVpr-ADE4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ADE4/[barcode-URA3-Z3EVpr-ADE4] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ADE2_dip

description:
MATa/α ADE2/[barcode-URA3-Z3EVpr-ADE2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ADE2/[barcode-URA3-Z3EVpr-ADE2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARO1_dip

description:
MATa/α ARO1/[barcode-URA3-Z3EVpr-ARO1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ARO1/[barcode-URA3-Z3EVpr-ARO1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARG4_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARG4] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ARG4] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 39_no_est_YNB_48h_3

description:
pooled library
ZEV_TOF_all_merge.txt

data_processing:
Library strategy: BAR-seq
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)

value: YNB+ClonNAT

value: pooled library


title: ACT1

description:
MATa/α ACT1/[barcode-URA3-Z3EVpr-ACT1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: SC+ClonNAT

value: MATa/alpha ACT1/[barcode-URA3-Z3EVpr-ACT1] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARG2_dip

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

value: MATa/alpha ARG2/[barcode-URA3-Z3EVpr-ARG2] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: ARG3_dip

description:
MATa/α ARG3/[barcode-URA3-Z3EVpr-ARG3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ARG3/[barcode-URA3-Z3EVpr-ARG3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: 35_no_est_YNB_24h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 38_no_est_YNB_48h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 34_no_est_YNB_24h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: ADE4_hap

description:
MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ADE4] [can1∆::STE2pr-SpHIS5] his3∆1 lyp1∆0 ura3∆0
zev_wgs_processeddata.csv

value: MATa [HAP1+::NatMX-ACT1pr-Z3EV-ENO2term] [barcode-URA3-Z3EVpr-ADE4] [can1delta::STE2pr-SpHIS5] his3delta1 lyp1delta0 ura3delta0


title: 33_no_est_YNB_12h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: ADE3_dip

description:
MATa/α ADE3/[barcode-URA3-Z3EVpr-ADE3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: MATa/alpha ADE3/[barcode-URA3-Z3EVpr-ADE3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: 31_no_est_YNB_12h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 30_est_YNB_48h_3

description:
pooled library
ZEV_TOF_all_merge.txt

value: YNB+ClonNAT+estradiol


title: 26_est_YNB_24h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 28_est_YNB_48h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 24_est_YNB_12h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 29_est_YNB_48h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 22_est_YNB_12h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 25_est_YNB_24h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 23_est_YNB_12h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 37_no_est_YNB_48h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 7_no_est_SC_18h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 36_no_est_YNB_24h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 5_no_est_SC_9h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 9_no_est_SC_18h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 8_no_est_SC_18h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 4_no_est_SC_9h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 6_no_est_SC_9h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 3_0hr_SC_3

description:
pooled library
ZEV_TOF_all_merge.txt

value: YPD


title: 3_0hr_YNB_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 2_0hr_SC_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 1_0hr_SC_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 20_est_SC_36h_2

description:
pooled library
ZEV_TOF_all_merge.txt

value: SC+ClonNAT+estradiol


title: 32_no_est_YNB_12h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 21_est_SC_36h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 2_0hr_YNB_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 27_est_YNB_24h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 1_0hr_YNB_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 19_est_SC_36h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 18_est_SC_18h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 17_est_SC_18h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 16_est_SC_18h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 15_est_SC_9h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 14_est_SC_9h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 13_est_SC_9h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: 12_no_est_SC_36h_3

description:
pooled library
ZEV_TOF_all_merge.txt


title: 11_no_est_SC_36h_2

description:
pooled library
ZEV_TOF_all_merge.txt


title: 10_no_est_SC_36h_1

description:
pooled library
ZEV_TOF_all_merge.txt


title: AD.CP2.23

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat (https://ccb.jhu.edu/software/tophat/index.shtml)
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

organism: Mus musculus

source_name: brain

extract_protocol:
Brains were removed, cross-sectional brain region encompassing hippocampal and cortical tissue was flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA isolation using miRNeasy (Qiagen cat. # 217004)  was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: NTG and APP/PS1 mice were treated with either vehilce or CP2 (25 mg/kg/day in 0.1% PEG dissolved in drinking water ad lib) or vehicle-containing water (0.1% PEG) starting at 9 months of age.

tag: treatment

tag: strain

tag: tissue

value: brain

tag: age

value: 23 months

value: APP/PS1 +/+


title: AD.CP2.21


title: AD.CP2.24


title: AD.20

value: non-treated


title: AD.CP2.25


title: AD.CP2.22


title: AD.19


title: AD.16


title: NTG.7

value: wild type; non-transgenic


title: NTG.10


title: NTG.8


title: Thy1LatNac_rep1_scRNA-seq

city: Stanford

first: Christina

middle: K

last: Kim

address: 318 Campus Drive West, Clark Center W080

institute: Stanford University

description: 10X Genomics 3' v2 kit

data_processing:
Data analyzed using 10X Genomics Cellranger 3.0 software to get counts
All 3 samples aggregated using cellranger_aggr, including normalization for sequencing depth
QC removed cells with <600 UMI counts, <1.2 UMIs per cell/genes per cell ratio, >0.4 percent mito UMIs
QC removed genes present in <20 cells or genes related to sex, neural activity or floating RNA
Additional data processing performed using cellranger_reanalyze and custon python3 scripts
Genome_build: mm10
Supplementary_files_format_and_content: Barcode, Gene name, and Counts aggregated across all 3 samples

source_name: Nucleus accumbens (NAc)

extract_protocol:
Dropviz.org for adult mammalian tissue
10x Genomics Single Cell 3' v2 kit

value: FLiCRE labeling during ChR2 opto-stim in NAc

value: 400um coronal brain dissection


title: Thy1LatNac_rep3_scRNA-seq

description: 10X Genomics 3' v2 kit


title: Human_blood - s29; Ramani et. al. + biotin-fillin

city: Novisibirsk

first: Veniamin

last: Fishman

address: Prospekt Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics The Siberian Branch of the Russian Academy of Sciences

data_processing:
Row fastq files were aligned by BWA-mem
Pairing and filtering were performed by our pipeline https://github.com/evgeniy240294/ExoC.
Genome_build: hg19
Supplementary_files_format_and_content: valid pairs files is tab-delimited text files, which include strand and genome coordinates of Hi-C pairs.
valid_pairs.tar contain valid pairs files from human private samples.

organism: Homo sapiens

extract_protocol:
DNAse Hi-C was performed as described in (Ramani. et. Al 2018) using biotin fillin strategy instead of biotinilated oligos (see the paper for detailed protocol)
DNase Hi-C

value: blood


title: Thy1LatNac_rep2_scRNA-seq

description: 10X Genomics 3' v2 kit


title: Prostate adenocarcinoma cell line - s31; Ramani et. al. + biotin-fillin

source_name: Prostate adenocarcinoma cell line

growth_protocol: LNCaP cells were grown in RPMI-1640 with 10% FBS and a penicillin/streptomycin mix (all from Invitrogen).

extract_protocol:
LNCaP cells were collected, washed from the trace of serum and resuspended in RPMI-1640 in the same concentration.
DNAse Hi-C was performed as described in (Ramani. et. Al 2018) using biotin fillin strategy instead of biotinilated oligos (see the paper for detailed protocol)
DNase Hi-C

tag: cell line

value: LNCaP cells


title: AD.17


title: Human_blood - s32; Ramani et al. this paper

extract_protocol:
DNAse Hi-C was performed as described in (Ramani. et. al 2018) using bridge and blunt adapter as in Ma. et. al 2018 (see the paper for detailed protocol)
DNase Hi-C


title: Human_blood - s28; Ramani et. al. + biotin-fillin


title: AD.18


title: NTG.9


title: Human_blood - s25; Ramani et. al. + biotin-fillin


title: Human_blood - s26; Ramani et. al. + biotin-fillin


title: Human_blood - s24; Ramani et. al. + biotin-fillin


title: Myelogenous leukemia cell line - K562; s30; Ramani et. al. + biotin-fillin

source_name: Myelogenous leukemia cell line

growth_protocol: K562 cells were grown in RPMI-1640 with 10% FBS and a penicillin/streptomycin mix (all from Invitrogen).

extract_protocol:
K562 cells were collected, washed from the trace of serum and resuspended in RPMI-1640 in the same concentration.
DNAse Hi-C was performed as described in (Ramani. et. Al 2018) using biotin fillin strategy instead of biotinilated oligos (see the paper for detailed protocol)
DNase Hi-C

value: K562 cells

value: As described in (Ma. et. al 2018) using biotin fillin strategy instead of biotinylated oligos (see the paper for detailed protocol)


title: Human_blood - s27; Ramani et. al. + biotin-fillin


title: Human_blood - s22; Ramani et. al. + biotin-fillin


title: Human_blood - s23; Ramani et. al. + biotin-fillin


title: Prostate adenocarcinoma cell line - s21; Ramani et. al. + long linker

extract_protocol:
LNCaP cells were collected, washed from the trace of serum and resuspended in RPMI-1640 in the same concentration.
DNAse Hi-C was performed as described in (Ramani. et. al 2018) using single linker (see the paper for detailed protocol)
DNase Hi-C


title: TRP3_dip

description:
MATa/α TRP3/[barcode-URA3-Z3EVpr-TRP3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3∆0/ura3∆0 [can1∆::STE2pr-SpHIS5]/CAN1 his3∆1/his3∆1 lyp1∆/LYP1
zev_wgs_processeddata.csv

value: SC+ClonNAT

value: MATa/alpha TRP3/[barcode-URA3-Z3EVpr-TRP3] [HAP1-NatMX-ACT1pr-Z3EV-ENO2term]/HAP1 ura3delta0/ura3delta0 [can1delta::STE2pr-SpHIS5]/CAN1 his3delta1/his3delta1 lyp1delta/LYP1


title: Prostate adenocarcinoma cell line - s18; Ramani et. al. + biotin-fillin


title: Pulmonary adenocarcinoma cell line - s20; Ramani et. al. + long linker

source_name: Pulmonary adenocarcinoma cell line

growth_protocol: A549 cells were grown in RPMI-1640 with 10% FBS and a penicillin/streptomycin mix (all from Invitrogen).

extract_protocol:
A549 cells were collected, washed from the trace of serum and resuspended in RPMI-1640 in the same concentration.
DNAse Hi-C was performed as described in (Ramani. et. al 2018) using single linker (see the paper for detailed protocol)
DNase Hi-C

value: A549 cells


title: Pulmonary adenocarcinoma cell line - s19; Ramani et. al. + long linker


title: Prostate adenocarcinoma cell line - s17; Ramani et. al. + biotin-fillin


title: Pulmonary adenocarcinoma cell line - s16; Ramani et. al. + biotin-fillin

extract_protocol:
A549 cells were collected, washed from the trace of serum and resuspended in RPMI-1640 in the same concentration.
DNAse Hi-C was performed as described in (Ramani. et. Al 2018) using biotin fillin strategy instead of biotinilated oligos (see the paper for detailed protocol)
DNase Hi-C


title: Pulmonary adenocarcinoma cell line - s15; Ramani et. al. + biotin-fillin


title: Human_blood - s11; Ma et. al. + new blunt

extract_protocol:
DNAse Hi-C was performed as described in (Ma. et. al 2018) modifing blunt adapter sequence and SDS treatment conditions (see the paper for detailed protocol)
DNase Hi-C


title: Human_blood - s13; Ma et. al. + long linker

extract_protocol:
DNAse Hi-C was performed as described in (Ma. et. al 2018) using single linker (see the paper for detailed protocol)
DNase Hi-C


title: Human_blood - s14; Ma et. al. + long linker


title: Human_blood - s8; Ma. et. al 2018 this paper

extract_protocol:
DNAse Hi-C was performed as described in (Ma. et. Al 2018)
DNase Hi-C


title: Human_blood - s4; Ma. et. al 2018 this paper


title: Human_blood - s6; Ma. et. al 2018 this paper


title: Myelogenous leukemia cell line - K562; s12; Ma et. al. + new blunt

extract_protocol:
K562 cells were collected, washed from the trace of serum and resuspended in RPMI-1640 in the same concentration.
DNAse Hi-C was performed as described in (Ma. et. al 2018) modifing blunt adapter sequence and SDS treatment conditions (see the paper for detailed protocol)
DNase Hi-C

value: As described in (Ma. et. al 2018) modifying blunt adapter sequence and SDS treatment conditions (see the paper for detailed protocol)


title: Human_blood - s2; Ma. et. al 2018 this paper


title: Human_blood - s1; Ma. et. al 2018 this paper


title: RNA-Seq-Ren1c-/-; Ren1cYFP_4

city: Charlottesville

first: Maria

middle: Florencia

last: Martinez

address: 409 Lane Rd. Rm 2006

institute: University of Virginia

description:
mm10_Ren1ckoRen1cyfp_BULK1to4_tpm.txt
BULK-LIB_2-N704

data_processing:
As4.1: The “TopHat” algorithm was used to align the reads to the mm10 genome, and 39 million aligned pairs were found.  The alignments in the BAM file were further analyzed using Cufflinks.
Native renin cells: We used FastQC to assess the quality of FASTQ file reads. Prior to alignment, we removed low quality reads and adapter sequences using Trimmomatic0.36. We aligned FASTQ reads to the GRCm38/ENSEMBL mouse genome using Salmon0.7.2. Samples with less than 300,000 total aligned reads were excluded from downstream analyses. Transcript-level estimates of expression were scaled up to gene level estimates using the Tximport 1.2.0 R package, with the “lengthScaledTPM” argument for abundance estimation.
Genome_build: mm10
Supplementary_files_format_and_content: 2746UV_As4.1_RNASeq_isoforms.fpkm_tracking
Supplementary_files_format_and_content: mm10_Ren1ckoRen1cyfp_BULK1to4_tpm.txt

source_name: renin cells

growth_protocol: The renin-expressing As4.1 cell line, harboring a Ren-2 5′-flanking sequence/SV40 T antigen hybrid transgene, was cultured in high glucose DMEM (Gibco #11965-092), 10% FBS at 37C in a humidified incubator containing 5% of CO2

extract_protocol:
Native Renin cells were isolated from the kidney cortex of adult animals using FACS sorting, utilizing our Ren1c-YFP reporter mice. Ren1c-YFP and Ren1c-/-; Ren1c-YFP mice were anesthetized with tribromoethanol and the kidneys were excised, decapsulated, demedullated. The kidney cortices from each animal were dissected and minced to a smooth consistency, and transferred into a 15 ml Falcon tube with 5 ml of enzymatic solution [0.3% collagenase A (Roche, Indianapolis, IN), 0.25% trypsin (Sigma- Aldrich, St. Louis, MO), and 0.0021% DNase I (Roche Applied Science)]. The tubes were placed flat inside a shaking incubator (80 RPM) for 15 minutes at 37℃. Then, the solution was pipetted up/down ten times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected with a plastic pipette and transferred to a fresh 15 ml tube on ice. The supernatants collected from the three digestions round were pooled and centrifuged in a Sorvall RT 6000 Refrigerated Centrifuge at 1,200 g for 4 minutes at 4°C. The cell pellet was resuspended with 25 ml of fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352360) and washed with an additional 3–5 ml of buffer 1. The flow-through was poured through a sterile 40 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352340) and washed with 3–5 ml of buffer 1. The flow-through was centrifuged at 1,200 g for 4 min at 4°C. After the centrifugation, the cell pellet was resuspended in 1ml of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Roche Applied Science)] and analyzed using a fluorescent-activated cell sorter (Influx Cell Sorter).
For As4.1 cells, libraries were prepared according to Active Motif protocol. Native renin cells samples underwent next-generation sequencing library preparation as described in the Fluidigm C1 manual using an Illumina NexteraXT library prep and index kits (Catalog Nos. FC-131-1096 and FC-131-1002). Briefly, cDNA samples were diluted, tagmented, and indexed with unique barcodes for downstream analyses. After the addition of indices and amplification, samples were multiplexed and cleaned using AMPure beads.

tag: cell type

value: primary kidney cells

value: Ren1c-/-; Ren1cYFP


title: Myelogenous leukemia cell line - K562; s5; Ma. et. al 2018 this paper

extract_protocol:
K562 cells were collected, washed from the trace of serum and resuspended in RPMI-1640 in the same concentration.
DNAse Hi-C was performed as described in (Ma. et. Al 2018)
DNase Hi-C

value: As described in (Ma. et. Al 2018)


title: Human_blood - s9; Ma. et. al 2018 this paper


title: RNA-Seq-Ren1cYFP

description: 2746UV_As4.1_RNASeq_isoforms.fpkm_tracking


title: RNA-Seq-Ren1c-/-; Ren1cYFP_1

description:
mm10_Ren1ckoRen1cyfp_BULK1to4_tpm.txt
BULK-LIB_2-N701


title: RNA-Seq-Ren1c-/-; Ren1cYFP_3

description:
mm10_Ren1ckoRen1cyfp_BULK1to4_tpm.txt
BULK-LIB_2-N703


title: Human_blood - s10; Ma et. al. + new blunt


title: Human_blood - s3; Ma. et. al 2018 this paper


title: Human_blood - s7; Ma. et. al 2018 this paper


title: pooled whole embryos 100 ng/L EE2 rep5

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

data_processing:
Raw files were trimmed using Trimmomatic v0.38
Trimmed fastq files were aligned to the fathead minnow reference genome NCBI Acc# WIOS00000000
Counting mapped reads were done using StringTie v1.3.4d
solvent1 was removed from the analysis. Features with less than 5 counts per million were removed. Significance of differentially expressed genes were assessed using edgeR v3.26.5, following the quasi-likelihood pipeline, with a cut-off FDR (Benjamini-Hochberg) < 0.05 and an effect size threshold |FC| > 1.5.
Genome_build: fathead minnow (Pimephales promelas) NCBI Acc# WIOS00000000
Supplementary_files_format_and_content: csv - raw counts of all samples
Supplementary_files_format_and_content: txt - differential expression with fold-change, log2fold-change, logCPM, P-value, and FDR

organism: Pimephales promelas

source_name: whole body tissue

growth_protocol: FHM embryos (<6 hhours post-fertilization) were exposed to graded concentrations (solvent control = 0.01% DMSO,  medium =  ng/L EE2,  high = 100 ng/L EE2) of EE2  in petridishes in a static renewal conditon

extract_protocol:
Total RNA was extracted using QIAGEN RNEasy plus universal mini kit following the manufacturer's protocol
Libraries were generated from 250 ng of total RNA. mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps were done using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Embryos were exposed from < 6 hours post-fertilization to 96 hours post-hatch

value: whole body

value: 4-days post-hatch

tag: exposure compound

tag: treatment/concentration

value: 100 ng/L EE2


title: RNA-Seq-Ren1c-/-; Ren1cYFP_2

description:
mm10_Ren1ckoRen1cyfp_BULK1to4_tpm.txt
BULK-LIB_2-N702


title: pooled whole embryos 100 ng/L EE2 rep3


title: pooled whole embryos 100 ng/L EE2 rep4


title: pooled whole embryos 100 ng/L EE2 rep2


title: pooled whole embryos 100 ng/L EE2 rep1


title: pooled whole embryos 20 ng/L EE2 rep4

value: 20 ng/L EE2


title: pooled whole embryos 20 ng/L EE2 rep2


title: pooled whole embryos 20 ng/L EE2 rep1


title: pooled whole embryos 20 ng/L EE2 rep5


title: pooled whole embryos 20 ng/L EE2 rep3


title: pooled whole embryos 0.01%DMSO rep4


title: pooled whole embryos 0.01%DMSO rep5


title: pooled whole embryos 0.01%DMSO rep3


title: pooled whole embryos 0.01%DMSO rep2


title: pooled whole embryos 0.01%DMSO rep1


title: Wild type on NF (WT_NF)

city: Varanasi

first: Subhash

middle: C

last: Lakhotia

state: UP

address: Cytogenetics Lab

department: Zoology

country: India

institute: Banaras Hindu UNiversity

description: S-15 S-21 S-27

data_processing:
The resulting sequencing Fastq files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie.
The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined.
Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples.
In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). A P-value ≤0.05 was taken to indicate significantly differentially expressing genes between different groups compared.
Genome_build: dm6
Supplementary_files_format_and_content: Cuffdiff 2.1.1 result showing differential gene expression between different samples in excel sheet

organism: Drosophila melanogaster

source_name: eye disc

extract_protocol:
RNA was isolated from 30 pairs of eye discs dissected out from wandering third instar larvae in PBS  using Trizol (Invitrogen, USA) reagent as per manufacture’s protocol. 1µg of the isolated RNA was subjected to DNAase treatment using 2U of TurboTM DNase (Ambion, Applied Biosystem) enzyme for 30 min at 37°C. The reaction was stopped using 15mM EDTA followed by incubation at 65°C for 5-7 min and purification on RNAeasy column (Qiagen). The purified RNA samples were processed for preparations of cDNA libraries using the TruSeq Stranded Total RNA Ribo-Zero H/M/R (Illumina) and sequenced on HiSeq-2500 platform (Illumina) using 50bp pair-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: eye disc

value: wandering third instar

value: OregonR+

tag: food supplement

value: NF


title: APP/PS1xRIPK1KD rep2

city: Boston

first: Chengyu

last: Zou

state: MA

address: 240 Longwood Ave

institute: Harvard medical school

description:
6-month-old male APP/PS1-RIPK1-KD mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 8
X8

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: nextseq_170608_rsem.genes.counts.matrix: Tab-delimited text file includes RPKM values for all samples. The column names 1, 2, 3, 4, 5, 6, 7, 8 and 9 represent Sample 1, Sample 2, Sample 3, Sample 4, Sample 5, Sample 6, Sample 7, Sample 8 and Sample 9, respectively.
Supplementary_files_format_and_content: APPPS1vsWT.txt: Differential gene expression of APP/PS1vs WT mice, calculated by edgeR (version 3.10.2).

source_name: Brain

extract_protocol:
Brain endothelial cells were isolated by FACS (CD31+CD45-) from brain homogenates.
20000 cells were collected and RNA was extracted from isolated cerebral ECs using Quick-RNA MiniPrep kit (Zymo Research) with the in-column DNase treatment. Each library was prepared using the Smart-seq2 protocol with a tagged oligo (dT) primer to make first strand cDNA from 1.5ng total RNA input.
Double-stranded cDNA was generated for library construction with 12 cycles of PCR and 0.075 ng of cDNA was used as input in a ¼ volume of standard NexteraXT (Illumina) reaction. Libraries were sequenced on an Illumina NextSeq500 instrument with 50 bases for read1 and 25 bases read2.

tag: genotype/variation

tag: Sex

value: Male

value: 6 months

value: Brain

value: Endothelial cells (CD31+CD45-)


title: IR72h20

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

country: China

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from mouse heart with I/R treated for 72 hours

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: Mouse with I/R treated for 72 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: 10-week-old male mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: All mice were euthanized by an overdose of pentobarbital on hours 6, 24 and 72 of  ischemia/reperfusion (I/R) treated. Total RNA was isolated with TRIzol (Invitrogen) from hearts at each time point according to manufacturer's instructions.

treatment_protocol: Wild-type male mice (10-week old) were subjected to 30 min of ligation of the left anterior descending coronary artery (LDA) followed by the reperfusion of 6, 24 and 72 hours.

tag: gender

value: Heart

value: I/R treated for 72 hours


title: APP/PS1xRIPK1KD rep3

description:
6-month-old male APP/PS1-RIPK1-KD mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 9
X9


title: IR24h14

description: Gene expression data from mouse heart with I/R treated for 24 hours

source_name: Mouse with I/R treated for 24 hours

value: I/R treated for 24 hours


title: Con3

description: Gene expression data from mouse heart with sham surgery

source_name: Mouse with sham surgery

value: sham


title: Con4


title: IR6h10

description: Gene expression data from mouse heart with I/R treated for 6 hours

source_name: Mouse with I/R treated for 6 hours

value: I/R treated for 6 hours


title: Con5


title: APP/PS1xRIPK1KD rep1

description:
6-month-old male APP/PS1-RIPK1-KD mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 7
X7


title: IR24h15


title: IR72h21


title: Con2


title: IR6h7


title: IR72h23


title: IR24h16


title: Wild type on RS (WT_RS)

description: S-14 S-20 S-26

value: RS


title: Wild type on AR (WT_AR)

description: S-13 S-19 S-25

value: AR


title: APP/PS1 group rep2

description:
6-month-old male APP/PS1 mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 5
X5


title: IR6h8


title: IR6h11


title: IR24h17


title: IR72h22


title: PolyQ on RS (PQ_RS)

description: S-11 S-17 S-23


title: PolyQ on AR (PQ_AR)

description: S-10 S-16 S-22


title: APP/PS1 group rep3

description:
6-month-old male APP/PS1 mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 6
X6


title: WT group rep3

description:
6-month-old male WT mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 3
X3

value: WT


title: WT group rep2

description:
6-month-old male WT mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 2
X2


title: WT group rep1

description:
6-month-old male WT mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 1
X1


title: PolyQ on NF (PQ_NF)

description: S-12 S-18 S-24


title: MDA networks

city: San Diego

first: Stephanie

middle: I

last: Fraley

address: 9500 Gilman Drive MC 0412

institute: UCSD

data_processing:
Count matrix for each sample was generated using cellRanger (10x Genomics)
Depth normalization was performed using cellRanger (10x Genomics)
Differential gene expression analysis was performed using Seurat (Stuart et al., 2019)
Genome_build: hg38, mm10
Supplementary_files_format_and_content: RDS files contain Seurat objects with raw and processed counts for each sample

extract_protocol:
Cells were collected using flow cytometry (FACS), and the Chromium Single Cell 3’ v3 kit (10x genomics, Pleasanton, CA) was used to extract the RNA
Chromium Single Cell 3’ v3 kit (10x genomics, Pleasanton, CA) was used for library construction

tag: phenotypic supervision status

value: yes

tag: phenotype

value: network


title: MDA spheroids

value: spheroid


title: BA1

city: Yangzhou

first: Jing

last: Zhang

address: 48 Wenhui Road

institute: Yangzhou university

data_processing:
Illumina Novaseq 6000 platform used for basecalling.
Clean reads were obtained by removing adapters, high contents of unknown bases reads and low quality reads
The clean reads were mapped to the reference genome of Chinese white pear deposited in the NCBI database (ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Pyrus_x_bretschneideri/) using Hisat2
Gene expression levels were estimated according to Fragments Per Kilobase of transcript sequence per Millions (FPKM)
Genome_build: Pyrus x bretschneideri (assembly Pbr_v1.0)
Supplementary_files_format_and_content: Excel files include genes read count and FPKM values for each sample (.xls)

organism: Pyrus pyrifolia

source_name: fruit bagging treated ‘Cuiguan’ pear fruit skin

growth_protocol: Six-year-old  ‘Cuiguan’ pears growing in an orchard in Yizheng, Jiangsu, China.

extract_protocol:
Total RNA was extracted by the ethyl ammonium bromide (CTAB) method using skin tissues collected from fruits with control and fruit bagging treatment 95 DAFB with three biological replicates.
RNA-Seq library was generated with NEB Next® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Half of the pear fruitlets were covered with Kobayashi paper bags. Single-layer white bags (F-PK2) were used 20 days after full bloom (DAFB) and double-layer yellow-white bags were used 40 DAFB. The other fruits without fruit bagging were set as control. Fruit samples were collected at  95 DAFB.

tag: cultivar

value: Cuiguan

value: pear fruit harvested 95 DAFB with fruit bagging treatment

value: fruit skin


title: CK3

source_name: untreated ‘Cuiguan’ pear fruit skin

value: pear fruit harvested 95 DAFB without treatment


title: CK2


title: BA3


title: Pooled non-asthma pcHi-C

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

description: gender: 2F-6M

data_processing:
HiCUP version 0.5.9 was used to map pcHi-C reads
CHiCAGO version 1.6.0 was performed on the pooled set of all reads from each sample
Genome_build: hg19
Supplementary_files_format_and_content: ibed

source_name: Primary ex vivo human bronchial epithelial cells

growth_protocol: ex vivo isolation

extract_protocol: Described in Montefiori, L. E. et al. A promoter interaction map for cardiovascular disease genetics. Elife 7, doi:10.7554/eLife.35788 (2018).

tag: subject status

value: non-asthma controls

value: pooled male and female


title: ChIP_input_iPax7-Dox_rep2

city: New York

state: New York

address: 522 First Avenue, Smilow Research Building, 1106

department: Pathology

institute: New York University School of Medicine

data_processing:
[Hi-C] All Hi-C datasets were uniformly pre-processed with the HiC-bench platform (Lazaris et al., 2017), outlined briefly as follows. First, all paired-end sequencing reads were aligned against the mouse genome version NCBIM37/mm9 with bowtie2 version 2.2.6 (Langmead and Salzberg, 2012) (specific settings: --very-sensitive-local --local). The aligned reads were further filtered using the GenomicTools (Tsirigos et al., 2012) gtools-hic filter command with the following parameters "--mapq 30 --min-dist 25000 --max-offset 500" (integrated in HiC-bench), which discards multi-mapped reads (“multihit”), read-pairs with only one mappable read (“single sided”), duplicated read-pairs (“ds.duplicate”), read-pairs with a low mapping quality of MAPQ <30, read-pairs resulting from self-ligated fragments and short-range interactions resulting from read-pairs aligning within 25kb (together called “ds.filtered”).
[pCHi-C] Raw sequencing reads from pCHi-C were processed using the HiCUP pipeline (Wingett et al., 2015), which maps the positions of di-tags against the mouse genome (NCBIM37/mm9), filters out experimental artifacts, such as circularized reads and re-ligations, and removes all duplicate reads. High-confidence interactions were identified by CHiCAGO as previously described (Score ≥ 5 in at least one condition) (Cairns et al., 2016).
[ChIP-seq] Raw reads were aligned to the mouse genome version NCBIM37/mm9 with bowtie2 version 2.3.4.1 (Langmead and Salzberg, 2012) (specific settings for paired-end reads: --local --no-mixed --no-discordant; specific settings for single-end reads: --local). Only uniquely mapped reads were selected for downstream analysis. PCR duplicates were removed using Picard-tools version 1.88. Peak-calling was done using MACS2 version 2.1.1 (Zhang et al., 2008) with a default q-value of 0.05.Replicate experiments were merged and the data were normalized per million total reads for visualization.
[ATAC-seq] Raw reads were aligned to the NCBIM37/mm9 reference genome with Bowtie2 version 2.2.6 using the options ‘--local --dovetail --minins 38 --maxins 2000 --no-mixed --no-discordant’. Only uniquely mapped reads were selected for downstream analysis. PCR duplicates were removed using Picard-tools version 1.88. Replicate experiments were merged, and the data were normalized per million total reads for visualization. Transposase-accessible regions were identified using the callpeak command of MACS2 version 2.1.1 with options ‘--nomodel --nolambda --keep-dup all --call-summits’ as described (Zhang et al., 2008).
Genome_build: mm9
Supplementary_files_format_and_content: [Hi-C] Text file with paired contacts from filtered Hi-C data.
Supplementary_files_format_and_content: [pCHi-C] Rds images of chicagoData objects.
Supplementary_files_format_and_content: bigWig and bed (narrowPeak) files for ChIP-seq and ATAC-seq.

source_name: Differentiating iPax7 myogenic progenitors

growth_protocol: ESCs containing the inducible Pax7 cassette were maintained in mouse ES medium. iPax7 muscle progenitors were grown on 0.1% gelatin-coated culture plates in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 1% Penicillin/streptomycin (Corning), 200 μg/ml bovine holo-transferrin (Sigma), 50 μg/ml L-ascorbic acid (Sigma), 4.5 mM 1-thioglycerol (Sigma), 5 ng/ml recombinant mouse bFGF (R&D systems), and 0.75 μg/ml doxycycline (Dox; Sigma) for the expression of Pax7. iPax7 progenitor cells lacking Dox were assessed 3 days after removing Dox from the culture media. Mouse wild-type and Myod1 knock-out primary myoblasts were grown in DMEM (cat #15-013-CV Corning) supplemented with 100 IU penicillin, 100 μg/ml streptomycin, 2 mM L-Glutamine and 10% fetal bovine serum.

extract_protocol:
Chromatin immunoprecipitation (ChIP) for CTCF (Cat. 07-729, Millipore) and Smc3 (Cat. ab9263, abcam) were performed as described previously (Lilja et al., 2017) with two biological replicates per factor per condition.
Sequencing libraries were prepared from purified DNA using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instruction and paired-end reads were obtained with the Illumina NextSeq 500 (75 cycles).

value: -Dox 3 days in iPax7 media

tag: antibody

value: input


title: Pooled asthma pcHi-C

description: gender: 2F-6M

value: asthma cases

value: Primary ex vivo human bronchial epithelial cells


title: ChIP_Smc3_iPax7-Dox_rep1

description:
iPax7-Dox_Smc3.merge.bigWig
iPax7-Dox_Smc3_peaks.narrowPeak

treatment_protocol: iPax7 progenitor cells lacking Dox were assessed 3 days after removing Dox from the culture media.

value: Differentiating iPax7 myogenic progenitors

tag: treatment


title: ChIP_Smc3_iPax7-Dox_rep2


title: ChIP_input_iPax7+Dox_rep2

source_name: iPax7 myogenic progenitors

value: iPax7 myogenic progenitors

value: 0.75ug/ml Dox in iPax7 media


title: BA2


title: ChIP_input_iPax7+Dox_rep1


title: ChIP_input_iPax7-Dox_rep1


title: ChIP_Smc3_iPax7+Dox_rep2

description:
iPax7+Dox_Smc3.merge.bigWig
iPax7+Dox_Smc3_peaks.narrowPeak


title: Etr1>Bra Rep2

city: Manhattan

first: Michael

last: Veeman

state: KS

address: 116 Ackert Hall

department: Division of Biology

institute: Kansas State University

data_processing:
base-calling by RTA (Real Time Analysis) v1.18.61
Sequenced reads were mapped to the Ciona KH2012 gene models using Tophat (v2.9.8b) with default parameters
The standard Deseq (v1.8.1) pipeline  was used to calculate read counts and test for differential expression
Genome_build: KH2012 gene models
Supplementary_files_format_and_content: excel worksheet containing counts normalized to library size and rlog transformed counts for all samples

organism: Ciona robusta

source_name: whole embryo stage 19.5

growth_protocol: Ciona embryos grown at 21 degrees Celsius in artificial seawater

extract_protocol:
400 embryos were collected at Hotta stage 19.5 into RNA lysis buffer and stored at -80C until RNA purification.RNA was purified with the Zymogen Quick-RNA miniprep kit (R1054) and eluted in 50 ul elution buffer. Final purified RNA concentration was 52-60 ng/ul.
Libraries were constructed with the TruSeq stranded mRNA library kit (Illumina) using standard protocols. Libraries were quality checked with an Agilent Tapestation and quantified by qPCR.

treatment_protocol: Fluorescently labeled by electroporation of reporter construct into fertilized eggs

tag: reporter construct

tag: developmental stage

value: embryo stage 19.5


title: Etr1>Bra Rep3


title: control Rep1

value: Bra>GFP


title: Tbx6-r.b>Bra Rep3


title: Tbx6-r.b>Bra Rep2


title: CK1

tag: tissue


title: control Rep2


title: ChIP_Smc3_iPax7+Dox_rep1


title: control Rep3


title: Tbx6-r.b>Bra Rep1


title: Etr1>Bra Rep1


title: Etr1>Bra/Foxa.a/Mnx rep3

data_processing:
base-calling by RTA (Real Time Analysis) v2.4.11
Sequenced reads were mapped to the Ciona KH2012 gene models using Tophat (v2.9.8b) with default parameters
The standard Deseq (v1.8.1) pipeline  was used to calculate read counts and test for differential expression
Genome_build: KH2012 gene models
Supplementary_files_format_and_content: excel worksheet containing counts normalized to library size and rlog transformed counts for all samples

extract_protocol:
300 embryos were collected at Hotta stage 19.5 into RNA lysis buffer and stored at -80C until RNA purification.RNA was purified with the Zymogen Quick-RNA miniprep kit (R1054) and eluted in 50 ul elution buffer. Final purified RNA concentration was 63-86 ng/ul.
Libraries were constructed with the NEBNext stranded mRNA library kit (Illumina) using standard protocols. Libraries were quality checked with an Agilent Tapestation and quantified by qPCR.

value: Etr1>Venus-Bra + Etr1>Foxa.a-Myc + Etr1>Mnx-HA

value: embryo stage E19.5


title: Etr1>Bra/Foxa.a/Mnx rep2


title: Etr1>Bra/Foxa.a/Mnx rep1


title: ChIP_CTCF_iPax7-Dox_rep2

description:
iPax7-Dox_CTCF.merge.bigWig
iPax7-Dox_CTCF_peaks.narrowPeak

value: CTCF


title: Etr1>Bra/Mnx rep3

value: Etr1>Venus-Bra + Etr1>Mnx-HA


title: ChIP_CTCF_iPax7-Dox_rep1


title: Etr1>Bra/Mnx rep1


title: Etr1>Bra/Mnx rep2


title: ChIP_CTCF_iPax7+Dox_rep2

description:
iPax7+Dox_CTCF.merge.bigWig
iPax7+Dox_CTCF_peaks.narrowPeak


title: Etr1>Bra/Foxa.a rep2

value: Etr1>Venus-Bra + Etr1>Foxa.a-Myc


title: Etr1>Bra/Foxa.a rep3


title: Etr1>Bra rep3


title: Etr1>Bra/Foxa.a rep1


title: pCHi-C_iPax7-Dox_rep2

description: pCHi-C

extract_protocol:
Approximately 30,000,000 iPax7 cells (+/-Dox) were cross-linked for 10 min by 2% formaldehyde in fresh media. Cross-linking was quenched by addition of 0.125M glycine. Cells were incubated at room temperature for 5 min and then centrifuged at 4°C for 5 min. Cross-linked cells were washed once in cold PBS, and the cell pellets were flash frozen in liquid nitrogen and stored at −80°C. Hi-C library generation was carried out with in-nucleus ligation as described previously (Nagano et al., 2015), with slight modifications. Briefly, chromatin was digested overnight at 37 °C with HindIII (NEB). Digested ends were filled in using biotinylated d-CTP and ligated in preserved nuclei. Cross-links were reversed by proteinase K treatment at 65 °C overnight and DNA was purified by phenol-chloroform extraction. DNA concentration was measured using Qubit 2.0 Fluorometer (Life Technologies). Biotin was removed from non-ligated restriction fragment ends by incubating the Hi-C library DNA with T4 DNA polymerase (NEB) for 4h at 20 °C in the presence of dATP and dGTP. After DNA purification with phenol:chloroform, 40 μg of DNA was sheared to an average size of 350 bp using Covaris LE220 following the manufacturer’s instructions. Double size selection of DNA was performed using AMPure XP beads (Beckman Coulter) and the sonicated DNA was end-repaired with T4 DNA polymerase, T4 DNA polynucleotide kinase, Klenow (all NEB) and dNTPs in 1× T4 DNA ligase reaction buffer (NEB). Biotin-marked ligation products were isolated using MyOne Streptavidin C1 DynaBeads (Invitrogen), adenine-tailed and ligated to paired-end adaptors (Illumina). The immobilized Hi-C products were amplified using SureSelect Primers from SureSelectXT Reagent kit, HSQ (Agilent Technologies) for pCHi-C-seq with 7 PCR amplification cycles with Phusion High-Fidelity DNA Polymerase (NEB). Capture Hi-C of promoters was carried out with SureSelect target enrichment (SureSelectXT Custom 3-5.9Mb library, Agilent Technologies), using the custom-designed biotinylated RNA bait library that overlap 25,747 Ensembl-annotated promoters of protein-coding, noncoding, antisense, snRNA, miRNA and snoRNA transcripts (Schoenfelder et al., 2015) and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies). 500 ng to 1 μg of Hi-C library were used for capture.
The enriched library was further amplified for pCHi-C-seq with 6 PCR amplification cycles using SureSelect primers (SureSelectXT Reagent kit, HSQ, Agilent Technologies) and Phusion High-Fidelity DNA Polymerase (NEB). Paired-end reads for pCHi-C libraries were obtained with Illumina NextSeq 500 (75 cycles).


title: ChIP_CTCF_iPax7+Dox_rep1


title: Etr1>Bra rep1


title: Etr1>Bra rep2


title: control rep 3


title: U0126 treatment 112cell rep3

source_name: whole embryo 112 cell stage

extract_protocol:
300 embryos were collected at indicated Hotta developmental stage into RNA lysis buffer and stored at -80C until RNA purification.RNA was purified with the Zymogen Quick-RNA miniprep kit (R1054) and eluted in 50 ul elution buffer. Final purified RNA concentration was 52-73 ng/ul.
Libraries were constructed with the NEBNext stranded mRNA library kit (Illumina) using standard protocols. Libraries were quality checked with an Agilent Tapestation and quantified by qPCR.

treatment_protocol: Treated with either 4mM U0126 or carrier control (DMSO 1:1000 dilution) at 32 cell stage.

tag: drug treatment

value: 4mM U0126 treatment

value: 112 cell stage


title: control rep 2


title: pCHi-C_iPax7+Dox_rep1

description: pCHi-C

tag: cell type


title: DMSO control 112cell rep3

value: DMSO control


title: U0126 treatment 112cell rep1


title: pCHi-C_iPax7+Dox_rep2

description: pCHi-C


title: pCHi-C_iPax7-Dox_rep1

description: pCHi-C

value: -Dox 3 days in iPax7 media


title: Robo1_Dox.4

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_Robo1_Dox-4-48074034

data_processing:
Reads were aligned to the mouse reference genome Mm10 using STAR
Gene feature counting was performed with RSEM
Transcripts with expression counts of 0 across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: gene filtered RSEM counts (txt, tab delimited)

source_name: 4T1 cell-line

growth_protocol: 3.5x10e4 4T1 K1 cells were seeded in 6-well plates in 4T1 media (RPMI 1640 (Gibco) supplemented with 10% (v/v) FBS (Thermo Fisher Scientific), 20mM HEPES (Gibco), 1mM sodium pyruvate (Gibco), and 0.25% (v/v) glucose (Gibco).

extract_protocol:
Total RNA was extracted from 1-3 million fresh frozen cells using the automated QiaSymphony magetic bead extraction.
Libraries were constructed according to Illumina’s instructions using the TruSeq Stranded mRNA library prep kit.

treatment_protocol: Dox (1 µg/mL) was added to the wells as indicated in the Characteristics section above at the time of seeding. siRNA (Non-targeting or Robo1) (Dharmacon) were transfected into the cells at the time of seeding according the Characteristics section above following the Dharmacon standard protocol for siRNA transfection. Following treatment cells were grown for 48 hours and then cells pellets were frozen for RNA extraction.

tag: cell line

value: 4T1 K1 cell line with dox-inducible shRNA targeting Id1 and Id3

tag: dox treatment

tag: sirna treatment

value: Robo1 siRNA

tag: genotype

value: Id1/3 + Robo1 knockdwon

tag: replicate


title: control rep 1


title: U0126 treatment 112cell rep2


title: DMSO control 112cell rep1


title: DMSO control 112cell rep2


title: Robo1_Dox.3

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_Robo1_Dox-3-48069038


title: U0126 treatment 64cell rep3

source_name: whole embryo 64 cell stage

value: 64 cell stage


title: Robo1_Dox.2

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_Robo1_Dox-2-48062030


title: U0126 treatment 64cell rep2


title: DMSO control 64cell rep3


title: U0126 treatment 64cell rep1


title: DMSO control 64cell rep2


title: Robo1_Dox.1

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_Robo1_Dox-1-48042132


title: Robo1.4

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_Robo1-4-48066035

value: Robo1 knockdown


title: DMSO control 64cell rep1


title: CrBra rep3

source_name: whole embryo stage 14

extract_protocol:
50-85 embryos were collected at Hotta stage 14 into RLT Plus buffer and stored at -80C until RNA purification.Half of the lysed sample was used for RNA purification with the Qiagen ALLPrep DNA/RNA Mini kit (Cat# 80204).
Libraries were constructed with the NEBNext stranded mRNA library kit (Illumina) using standard protocols. Libraries were quality checked with an Agilent Tapestation and quantified by qPCR.

treatment_protocol: Unfertilized eggs were injected with RNP mix (crRNA, tracrRNA, Cas9 protein) containing guide RNA specific to either Brachyury or GFP (control). Eggs were fertilized and grown to Hotta stage 14.

tag: crispr target

value: Brachyury


title: Robo1.3

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_Robo1-3-48063027


title: CrBra rep1


title: Robo1.2

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_Robo1-2-48069035


title: CrBra rep2


title: CrGFP control rep3

value: GFP


title: CrGFP control rep2


title: Robo1.1

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_Robo1-1-48069033


title: NT_Dox.3

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_NT_Dox-3-48073029

value: Non-targeting siRNA

value: Id1/3 knockdown


title: NT_Dox.4

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_NT_Dox-4-48072030


title: NT_Dox.2

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_NT_Dox-2-48065026


title: NT.4

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_NT-4-48066026

value: Control


title: NT.3

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_NT-3-48064023


title: NT_Dox.1

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_NT_Dox-1-48073026


title: NT.2

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_NT-2-48062020


title: CrGFP control rep1


title: RNA-Seq-As4.1

description: 2746UV_As4.1_RNASeq_isoforms.fpkm_tracking

source_name: As4.1 cells

value: As4.1 Tumoral cell

tag: passages


title: NT.1

description:
ID1_Robo1.genes.counts.filtered.txt
ID1_NT-1-48062018


title: 4_2746UV, Input DNA

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
The two peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009)
Genome_build: mm10
Supplementary_files_format_and_content: wig

extract_protocol:
Native Renin cells were isolated from the kidney cortex of adult animals using FACS sorting, utilizing our Ren1c-YFP reporter mice. Ren1c-YFP and Ren1c-/-; Ren1c-YFP mice were anesthetized with tribromoethanol and the kidneys were excised, decapsulated, demedullated. The kidney cortices from each animal were dissected and minced to a smooth consistency, and transferred into a 15 ml Falcon tube with 5 ml of enzymatic solution [0.3% collagenase A (Roche, Indianapolis, IN), 0.25% trypsin (Sigma- Aldrich, St. Louis, MO), and 0.0021% DNase I (Roche Applied Science)]. The tubes were placed flat inside a shaking incubator (80 RPM) for 15 minutes at 37℃. Then, the solution was pipetted up/down ten times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected with a plastic pipette and transferred to a fresh 15 ml tube on ice. The supernatants collected from the three digestions round were pooled and centrifuged in a Sorvall RT 6000 Refrigerated Centrifuge at 1,200 g for 4 minutes at 4°C. The cell pellet was resuspended with 25 ml of fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352360) and washed with an additional 3–5 ml of buffer 1. The flow-through was poured through a sterile 40 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352340) and washed with 3–5 ml of buffer 1. The flow-through was centrifuged at 1,200 g for 4 min at 4°C. After the centrifugation, the cell pellet was resuspended in 1ml of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Roche Applied Science)] and analyzed using a fluorescent-activated cell sorter (Influx Cell Sorter).  .Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Active Motif protocol

value: Tumoral cell line As4.1


title: 3R_2746UV, Pol II_ChIPSeq

tag: chip antibody

value: Pol II


title: 1R_2746UV, Med1_ChIPSeq

value: Med1 (Bethyl Laboratories, cat# A300-793A)


title: 2_2746UV, H3K27ac_ChIPSeq


title: APP/PS1 group rep1

description:
6-month-old male APP/PS1 mouse was sacrificed for isolating endothelial cells. The mRNA of isolated endothelial cells was extracted for next-generation sequencing.
mRNA
Sample 4
X4

tag: strain

tag: genotype/variation

tag: Sex

value: Male

tag: age

value: 6 months

value: Brain

value: Endothelial cells (CD31+CD45-)


title: UOK268WT

type: genomic

city: Bethesda

first: Christopher

middle: James

last: Ricketts

state: Maryland

address: Building 10

department: Urologic Oncology Branch

institute: National Cancer Institute

description: HLRCC-derived RCC cell line with wild-type FH re-expression

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human methylation450k Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: GenomeStudio

label: Cy5 and Cy3

source_name: Primary renal tumor derived cell line

label_protocol: Standard Illumina Protocol

growth_protocol: All cell lines were maintained in DMEM with High Glucose (4500 mg/L), L-glutamine (4.0mM), and Phenol Red (Thermo Fisher, 11965167) and 10% Fetal Bovine Serum

extract_protocol: DNA for the tumors and normal kidney was obtained from FFPE blocks.  Characteristic tumor or normal histomorphology samples were needle microdissected and microdissected FFPE tissue was lysed in a cocktail containing mineral oil (for deparaffinization), proteinase K, and ATL lysis buffer (Qiagen), and resultant lysates were filter-purified by Qiagen DNA enrichment columns. Purified DNAs were treated with FFPE DNA restoration solution (Illumina).  Cell line genomic DNA was extracted from ~1 million cells using the Maxwell 16 System with a Maxwell 16 Cell DNA Purification Kit (Promega, Madison, WI). DNA quantification was performed using a ThermoScientific NanoDrop 1000 (Wilmington, DE)

tag: disease state

value: Hereditary leiomyomatosis and renal cell carcinoma (HLRCC)

tag: sample type

value: Patient-derived RCC cell line


title: SDHB-RCC3

description: Primary SDHB-RCC renal tumor

source_name: Primary renal tumor

value: Succinate dehydrogenase deficient renal cell carcinoma (SDHB-RCC)

value: Primary renal tumor


title: 4_01T2, Input DNA


title: 3_01T0, H3K27ac_ChIPSeq


title: SDHB-RCC3 N

description: SDHB-RCC associated normal kidney

source_name: Normal Kidney

value: Associated normal kidney


title: SDHB-RCC4 N

description: SDHB-RCC associated normal kidney


title: VHL7

description: Primary VHL renal tumor

value: von Hippel-Lindau disease (VHL)


title: HPRC4

description: Primary HPRC renal tumor

value: Hereditary papillary renal cell carcinoma (HPRC)


title: HLRCC2

description: Primary HLRCC renal tumor


title: HPRC3

description: Primary HPRC renal tumor


title: HLRCC2 N

description: HLRCC associated normal kidney


title: SDHB-RCC4

description: Primary SDHB-RCC renal tumor


title: HPRC1

description: Primary HPRC renal tumor


title: HLRCC7

description: Primary HLRCC renal tumor


title: VHL8

description: Primary VHL renal tumor


title: VHL2 N

description: VHL associated normal kidney


title: VHL5

description: Primary VHL renal tumor


title: BHD3

description: Primary BHD renal tumor

value: Birt-Hogg-Dubé syndrome (BHD)


title: HLRCC6 Rt

description: Primary HLRCC renal tumor


title: VHL3 N

description: VHL associated normal kidney


title: VHL4

description: Primary VHL renal tumor


title: BHD4

description: Primary BHD renal tumor


title: HPRC2

description: Primary HPRC renal tumor


title: VHL6

description: Primary VHL renal tumor


title: HLRCC8

description: Primary HLRCC renal tumor


title: 2_01S2, Input DNA

source_name: renin cells

value: Ren1c-/-; Ren1c-YFP


title: BHD1

description: Primary BHD renal tumor


title: 1_01S1, H3K27ac_ChIPSeq


title: VHL3

description: Primary VHL renal tumor


title: 2_2892UV, Input DNA


title: BHD2

description: Primary BHD renal tumor


title: VHL9

description: Primary VHL renal tumor


title: SL332964

data_processing:
Peaks identified using the MACS2 peak caller with a q value threshold of 0.01, were merged with DiffBind. Coverage values were calculated using bedtools multicov. In short, the coverage values were normalized using the estimate SizeFactors function from the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: wig files

extract_protocol:
Native Renin cells were isolated from the kidney cortex of adult animals using FACS sorting, utilizing our Ren1c-YFP reporter mice. Ren1c-YFP and Ren1c-/-; Ren1c-YFP mice were anesthetized with tribromoethanol and the kidneys were excised, decapsulated, demedullated. The kidney cortices from each animal were dissected and minced to a smooth consistency, and transferred into a 15 ml Falcon tube with 5 ml of enzymatic solution [0.3% collagenase A (Roche, Indianapolis, IN), 0.25% trypsin (Sigma- Aldrich, St. Louis, MO), and 0.0021% DNase I (Roche Applied Science)]. The tubes were placed flat inside a shaking incubator (80 RPM) for 15 minutes at 37℃. Then, the solution was pipetted up/down ten times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected with a plastic pipette and transferred to a fresh 15 ml tube on ice. The supernatants collected from the three digestions round were pooled and centrifuged in a Sorvall RT 6000 Refrigerated Centrifuge at 1,200 g for 4 minutes at 4°C. The cell pellet was resuspended with 25 ml of fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352360) and washed with an additional 3–5 ml of buffer 1. The flow-through was poured through a sterile 40 µm nylon cell strainer (Falcon™ Cell Strainers, Corning, Inc. 352340) and washed with 3–5 ml of buffer 1. The flow-through was centrifuged at 1,200 g for 4 min at 4°C. After the centrifugation, the cell pellet was resuspended in 1ml of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Roche Applied Science)] and analyzed using a fluorescent-activated cell sorter (Influx Cell Sorter).
We collected 50,000 cells for As4.1 and from chronically recruited mice, and 17,000 juxtaglomerular cells and cells from acutely recruited mice. Cells were washed with PBS and treated with Lysis Buffer. Then, cells were re-suspended in a transposition reaction mix (Illumina, cat # FC-121-1030) followed by DNA purification, before PCR amplification with 12-16 cycles with barcode primers (Illumina, cat # FC-121-1011). PCR products were purified with AmpureXP beads (Beckman Coulter, cat # A63881)

value: Ren1c-YFP_Low Na+ Cap


title: VHL2

description: Primary VHL renal tumor


title: SL332963


title: VHL1 N

description: VHL associated normal kidney