text: Anhui Normal University

characteristic: INSDC last update

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 5

text: not collected

text: not collected

characteristic: isolate

text: Odorrana tormota

text: biological replicate 2

text: not collected

text: not collected

text: gut


status: PUBLIC

characteristic: External Id

text: Anhui Normal University

characteristic: INSDC center name

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Model organism or animal

characteristic: NCBI submission model

characteristic: NCBI submission package

text: not collected

tag: attribute

characteristic: age

text: not collected

characteristic: breed

text: not collected

characteristic: cultivar

text: Treatment group 5

text: not collected

characteristic: ecotype

text: not collected

text: Odorrana tormota

characteristic: organism

text: biological replicate 3

characteristic: replicate

text: not collected

characteristic: sex

text: not collected

characteristic: strain

text: gut

characteristic: tissue

text: Model organism or animal sample from Odorrana tormota

characteristic: title


text: Anhui Normal University

characteristic: INSDC last update

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 6

text: not collected

text: not collected

characteristic: isolate

text: Odorrana tormota

text: biological replicate 1

text: not collected

text: not collected

text: gut


characteristic: External Id

text: Anhui Normal University

characteristic: INSDC center name

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 6

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 2

text: not collected

text: not collected

text: gut


text: Anhui Normal University

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 6

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 3

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

characteristic: NCBI submission model

characteristic: NCBI submission package

text: not collected

text: not collected

text: not collected

text: Treatment group 7

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 1

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

characteristic: age

text: not collected

characteristic: breed

text: not collected

text: Treatment group 7

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 2

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

characteristic: cultivar

text: Treatment group 7

text: not collected

characteristic: ecotype

text: not collected

text: Odorrana tormota

text: biological replicate 3

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 8

text: not collected

text: not collected

text: Odorrana tormota

characteristic: organism

text: biological replicate 1

characteristic: replicate

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 8

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 2

text: not collected

characteristic: sex

text: not collected

characteristic: strain

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 8

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 3

text: not collected

text: not collected

text: gut

characteristic: tissue

characteristic: title


text: Anhui Normal University

characteristic: INSDC last update

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 9

text: not collected

text: not collected

characteristic: isolate

text: Odorrana tormota

text: biological replicate 1

text: not collected

text: not collected

text: gut


characteristic: External Id

text: Anhui Normal University

characteristic: INSDC center name

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 9

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 2

text: not collected

text: not collected

text: gut


text: Anhui Normal University

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 9

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 3

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

characteristic: NCBI submission model

characteristic: NCBI submission package

text: not collected

text: not collected

text: not collected

text: Treatment group 10

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 1

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

characteristic: age

text: not collected

characteristic: breed

text: not collected

text: Treatment group 10

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 2

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

characteristic: cultivar

text: Treatment group 10

text: not collected

characteristic: ecotype

text: not collected

text: Odorrana tormota

text: biological replicate 3

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 11

text: not collected

text: not collected

text: Odorrana tormota

characteristic: organism

text: biological replicate 1

characteristic: replicate

text: not collected

text: not collected

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 11

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 2

text: not collected

characteristic: sex

text: not collected

characteristic: strain

text: gut


text: Anhui Normal University

text: live

text: Model organism or animal

text: not collected

text: not collected

text: not collected

text: Treatment group 11

text: not collected

text: not collected

text: Odorrana tormota

text: biological replicate 3

text: not collected

text: not collected

text: gut

characteristic: tissue

characteristic: title


text: Xinjiang Academy of Agricultural Sciences

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Plant

characteristic: SRA accession

text: Seedling stage

text: China: Xinjiang

text: Control Shangshu-9-1

characteristic: isolate

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Shangshu-9-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Seedling stage

text: China: Xinjiang

text: Control Shangshu-9-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Chaoshu-1-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Chaoshu-1-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Chaoshu-1-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xushu-22-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xushu-22-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xushu-22-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Z15-1-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Z15-1-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Z15-1-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Z15-1-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Z15-1-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Z15-1-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xushu-18-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xushu-18-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xushu-18-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Jishu-26-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Jishu-26-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Jishu-26-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xuzi-8-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xuzi-8-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xuzi-8-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xushu-18-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xushu-18-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xushu-18-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Jishu-26-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Jishu-26-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Jishu-26-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xuzi-8-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xuzi-8-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Control Xuzi-8-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Shangshu-9-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Shangshu-9-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Shangshu-9-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Chaoshu-1-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Chaoshu-1-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Chaoshu-1-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xushu-22-1

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xushu-22-2

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: live

text: Plant

text: Seedling stage

text: China: Xinjiang

text: Drought-treated Xushu-22-3

text: Ipomoea batatas

text: leaves

text: Plant sample from Ipomoea batatas


text: Shanghai Urban Construction Vocational College

text: live

text: Model organism or animal

characteristic: age

text: Shanghai Zoo

text: huahua

characteristic: breed

text: Shanghai

characteristic: ecotype

text: Panthera tigris

text: replicate=biological replicate 1

text: male

text: blood

text: Model organism or animal sample from Panthera tigris


text: live

text: Model organism or animal

text: Shanghai Zoo

text: congcong

text: Shanghai

text: Panthera tigris

characteristic: organism

text: replicate=biological replicate 2

characteristic: replicate

text: female

characteristic: sex

text: blood


text: live

text: Model organism or animal

text: Shanghai Zoo

text: guoguo

text: Shanghai

text: Panthera tigris

text: replicate=biological replicate 3

text: female

text: blood

characteristic: tissue

characteristic: title


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Model organism or animal

text: Shanghai Zoo

text: zhenzhen

text: Shanghai

text: Panthera tigris

text: replicate=biological replicate 4

text: female

text: blood


text: live

text: Model organism or animal

characteristic: SRA accession

text: Shanghai Zoo

text: lele

text: Shanghai

text: Panthera tigris

text: replicate=biological replicate 5

text: male

text: blood


characteristic: External Id

text: live

text: Model organism or animal

text: Shanghai Zoo

text: dudu

text: Shanghai

text: Panthera tigris

text: replicate=biological replicate 6

text: male

text: blood


characteristic: INSDC center name

text: live

text: Model organism or animal

text: Shanghai Zoo

text: feifei

text: Shanghai

text: Panthera tigris

text: replicate=biological replicate 7

text: female

text: blood


characteristic: INSDC first public

text: live

text: Model organism or animal

text: Shanghai Zoo

text: binbin

text: Shanghai

text: Panthera tigris

text: replicate=biological replicate 8

text: male

text: blood


text: live

characteristic: INSDC status

text: Model organism or animal

text: Shanghai Zoo

text: qiangqiang

text: Shanghai

text: Panthera tigris

text: replicate=biological replicate 9

text: male

text: blood


text: University of Iceland

text: live

characteristic: Latitude

characteristic: Longitude

text: AA

characteristic: MitochondrialClade

text: Invertebrate

characteristic: NCBI submission model

characteristic: altitude

text: Iceland:Thingvallavatn

characteristic: isolate

text: groundwater

text: Crangonyx islandicus

text: whole specimen

text: Invertebrate sample from Crangonyx islandicus


text: University of Iceland

text: live

text: AA

text: Invertebrate

characteristic: NCBI submission package

text: Iceland:Thingvallavatn

text: groundwater

text: Crangonyx islandicus

characteristic: organism

text: whole specimen


text: University of Iceland

text: live

text: E

text: Invertebrate

text: Iceland:Svartarvatn

text: groundwater

text: Crangonyx islandicus

text: whole specimen

characteristic: tissue


text: University of Iceland

text: live

text: E

text: Invertebrate

text: Iceland:Svartarvatn

text: groundwater

text: Crangonyx islandicus

text: whole specimen

characteristic: title


text: University of Iceland

characteristic: INSDC last update

text: live

text: F

text: Invertebrate

text: Iceland:Klapparos

text: groundwater

text: Crangonyx islandicus

text: whole specimen


text: University of Iceland

characteristic: INSDC secondary accession

text: live

text: F

text: Invertebrate

text: Iceland:Klapparos

text: groundwater

text: Crangonyx islandicus

text: whole specimen


Kg

text: University of Iceland

text: live

text: F

text: Invertebrate

characteristic: SRA accession

text: Iceland:Klapparos

text: groundwater

text: Crangonyx islandicus

text: whole specimen


Ki

characteristic: External Id

text: University of Iceland

text: live

text: F

text: Invertebrate

text: Iceland:Klapparos

text: groundwater

text: Crangonyx islandicus

text: whole specimen


Kk

text: University of Iceland

characteristic: INSDC center name

text: live

text: F

text: Invertebrate

text: Iceland:Klapparos

text: groundwater

text: Crangonyx islandicus

text: whole specimen


text: University of Iceland

characteristic: INSDC first public

text: live

text: E

text: Invertebrate

text: Iceland:Sandur

text: groundwater

text: Crangonyx islandicus

text: whole specimen


text: University of Iceland

text: live

characteristic: INSDC status

text: E

text: Invertebrate

text: Iceland:Sandur

text: groundwater

text: Crangonyx islandicus

text: whole specimen


text: Tianjin College University of Science and Technology Beijing

text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

characteristic: replicate

text: a nonamended control

text: Metagenome or environmental sample from soil metagenome


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: a nonamended control


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: a nonamended control


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

text: treatment 1


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: treatment 1


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: treatment 1


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

text: treatment 2


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: treatment 2


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: treatment 2


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

text: treatment 3


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: treatment 3


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: treatment 3


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

text: treatment G


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: treatment G


text: live

text: Metagenome or environmental

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: treatment G


text: University of California, San Francisco

text: live

text: Human

characteristic: age

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94158

text: RNA was isolated using the All-Prep Universal Kit, and clean-up was performed using the RNEasy Kit as needed (Qiagen). RNA sequencing libraries were generated using the Illumina TruSeq Stranded mRNA Library Prep Kit and sequenced on an Illumina HiSeq-4000 using the paired-end 100 protocol

characteristic: filename

text: fastq

characteristic: filetype

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

characteristic: platform

text: female

characteristic: sex

text: tumor


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: ILLUMINA

text: male

text: tumor


text: University of California, San Francisco

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94159

text: RNA was isolated using the All-Prep Universal Kit, and clean-up was performed using the RNEasy Kit as needed (Qiagen). RNA sequencing libraries were generated using the Illumina TruSeq Stranded mRNA Library Prep Kit and sequenced on an Illumina HiSeq-4000 using the single-end 50 protocol for HEI-193 schwannoma cells.

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: tissue

characteristic: title


characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Human

characteristic: SRA accession

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94160

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

text: live

characteristic: INSDC status

text: Human

characteristic: age

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94161

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94162

characteristic: filename

text: fastq

characteristic: filetype

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

characteristic: platform

text: male

text: cells


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94163

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

characteristic: sex

text: cells


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94164

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94165

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: tissue

characteristic: title


characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94166

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

text: live

characteristic: INSDC status

text: Human

characteristic: SRA accession

characteristic: age

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94167

text: fastq

text: Illumina HiSeq 4000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

text: live

text: Human

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94168

text: Flash frozen archived schwannoma specimens were minced with sterile Bard-Parker #10 surgical scalpels (Aspen Surgical) and mechanically dissociated with a Pestle Tissue Grinder (size A, Thomas Scientific) in ice cold lysis buffer consisting of 0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc2, 0.1 mM EDTA, 10 mM Tris-HCl, 1 mM DTT and 0.1% Triton X-100 in DEPC-treated water. Sucrose solution consisting of 1.8 M sucrose, 3 mM MgAc2, 1 mM DTT and 10 mM Tris-HCl in DEPC-treated water was added to the bottom of the lysis solution in ultracentrifuge tubes (Beckman Coulter) to form a gradient, which was ultracentrifuged at 107,000g for 2.5 hours at 4°C. Nuclei pellets were resuspended in phosphate buffered saline and sequentially filtered twice in 30 μm strainers (Miltenyi Biotec). Isolated nuclei were assessed with DAPI staining and loaded onto a 10x Chromium controller using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics).

characteristic: filename

text: fastq

characteristic: filetype

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: female

text: tumor


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94169

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

characteristic: platform

text: female

text: tumor


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94170

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

characteristic: isolate

text: Homo sapiens

text: ILLUMINA

text: female

characteristic: sex

text: tumor


text: University of California, San Francisco

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94171

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

characteristic: organism

text: ILLUMINA

text: female

text: tumor

characteristic: tissue


characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94172

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: female

text: tumor

characteristic: title


text: University of California, San Francisco

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Human

characteristic: SRA accession

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94173

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: female

text: tumor


text: University of California, San Francisco

text: live

text: Human

characteristic: age

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94174

characteristic: filename

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: tumor


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94175

text: fastq

characteristic: filetype

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: tumor


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94176

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

characteristic: isolate

text: Homo sapiens

text: ILLUMINA

characteristic: platform

text: male

text: tumor


text: University of California, San Francisco

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94177

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

characteristic: organism

text: ILLUMINA

text: female

characteristic: sex

text: tumor


characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94178

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: tumor

characteristic: tissue


text: University of California, San Francisco

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94179

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: female

text: tumor

characteristic: title


text: University of California, San Francisco

text: live

text: Human

characteristic: SRA accession

characteristic: age

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94180

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: female

text: tumor


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94181

text: Fresh schwannomas were minced with sterile Bard-Parker #10 surgical scalpels (Aspen Surgical) and incubated in 0.4% Collagenase Type 2 (Worthington) in pre-oxygenated Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) for 75 minutes at 37°C while rotating at 800 rotations per minute on a thermomixer. The suspension was sequentially filtered through 70 μm and 40 μm strainers (Thermo Fisher Scientific), centrifuged at 300g for 5 minutes, and resuspended in cold phosphate buffered saline. Single cell suspensions were loaded onto a 10x Chromium controller using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics). Libraries were sequenced on an Illumina NovaSeq (10X specific protocol) with >50,000 reads per cell. Library demultiplexing, read alignment to human genome GRCh38 and UMI quantification was performed in Cell Ranger version 1.3.1 (10X Genomics).

characteristic: filename

text: BAM

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: tumor


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94182

text: BAM

characteristic: filetype

text: Illumina NovaSeq 6000

text: schwannoma

characteristic: isolate

text: Homo sapiens

text: ILLUMINA

text: male

text: tumor


text: University of California, San Francisco

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94183

text: BAM

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

characteristic: organism

text: ILLUMINA

characteristic: platform

text: male

text: tumor


characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

text: live

text: Human

text: HEI-193 schwannoma cells were dissociated in Trypsin-EDTA 0.25% (Thermo Fisher Scientific), passed through a 40 μm strainer, and washed/resuspended in phosphate buffered saline. Single cell suspensions were loaded onto a 10x Chromium controller using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics). Libraries were sequenced on an Illumina NovaSeq (10X specific protocol) with >50,000 reads per cell.

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

characteristic: sex

text: cells


text: University of California, San Francisco

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Human

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: tissue


text: University of California, San Francisco

text: live

text: Human

characteristic: SRA accession

characteristic: age

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: title


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94184

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94185

characteristic: filename

text: fastq

characteristic: filetype

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94186

text: HEI193_12_5Gy_3_S10_L002_R1_001.fastq.gz

text: HEI193_12_5Gy_3_S10_L002_R2_001.fastq.gz

text: HEI193_12_5Gy_3_S10_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: ILLUMINA

text: male

text: cells


characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94187

text: HEI193_5x1_8Gy_1_S5_L002_R1_001.fastq.gz

text: HEI193_5x1_8Gy_1_S5_L002_R2_001.fastq.gz

text: HEI193_5x1_8Gy_1_S5_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

characteristic: platform

text: male

text: cells


text: University of California, San Francisco

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94188

text: HEI193_5x1_8Gy_2_S6_L002_R1_001.fastq.gz

text: HEI193_5x1_8Gy_2_S6_L002_R2_001.fastq.gz

text: HEI193_5x1_8Gy_2_S6_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

characteristic: sex

text: cells


text: University of California, San Francisco

text: live

text: Human

characteristic: SRA accession

characteristic: age

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94189

text: HEI193_5x1_8Gy_3_S7_L002_R1_001.fastq.gz

text: HEI193_5x1_8Gy_3_S7_L002_R2_001.fastq.gz

text: HEI193_5x1_8Gy_3_S7_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: tissue


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94190

text: HEI-193 cells were transduced with the perturb-seq library at 1,000X coverage at an MOI of 0.1, corresponding to approximately 95% of cells with a single integration. 72 hours following transduction, sgRNA+ cells were FACS sorted (BFP+) and were recovered in DMEM 10% FBS. Sorted cultures were treated with either 0Gy, 1.8Gy x 5 daily fractions, or 12.5Gy x 1 fraction of radiotherapy using the X-Rad 320 irradiator (Precision X-Ray). 12 hours following the final fraction of radiotherapy, cells were trypsinized and harvested in single cell suspension on the 10x Chromium Controller (10x Genomics). Single-cell Perturb-seq libraries were processed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1with Feature Barcoding (10x Genomics), allowing direct capture of modified sgRNAs83, and sequenced on a illumina NovaSeq-6000.

text: VS_perturb_RNA_1_S7_L001_R1_001.fastq.gz

text: VS_perturb_RNA_1_S7_L002_R1_001.fastq.gz

text: VS_perturb_RNA_1_S7_L001_R2_001.fastq.gz

text: VS_perturb_RNA_1_S7_L002_R2_001.fastq.gz

text: VS_perturb_RNA_1_S7_L001_I1_001.fastq.gz

text: VS_perturb_RNA_1_S7_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: title


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94191

text: VS_perturb_RNA_2_S8_L001_R1_001.fastq.gz

characteristic: filename

text: VS_perturb_RNA_2_S8_L002_R1_001.fastq.gz

text: VS_perturb_RNA_2_S8_L001_R2_001.fastq.gz

text: VS_perturb_RNA_2_S8_L002_R2_001.fastq.gz

text: VS_perturb_RNA_2_S8_L001_I1_001.fastq.gz

text: VS_perturb_RNA_2_S8_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94192

text: VS_perturb_RNA_3_S9_L001_R1_001.fastq.gz

text: VS_perturb_RNA_3_S9_L002_R1_001.fastq.gz

text: VS_perturb_RNA_3_S9_L001_R2_001.fastq.gz

text: VS_perturb_RNA_3_S9_L002_R2_001.fastq.gz

text: VS_perturb_RNA_3_S9_L001_I1_001.fastq.gz

text: VS_perturb_RNA_3_S9_L002_I1_001.fastq.gz

text: fastq

characteristic: filetype

text: Illumina NovaSeq 6000

text: schwannoma

characteristic: isolate

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94193

text: HEI-193 cells were transduced with the perturb-seq library at 1,000X coverage at an MOI of 0.1, corresponding to approximately 95% of cells with a single integration. 72 hours following transduction, sgRNA+ cells were FACS sorted (BFP+) and were recovered in DMEM 10% FBS. Sorted cultures were treated with either 0Gy, 1.8Gy x 5 daily fractions, or 12.5Gy x 1 fraction of radiotherapy using the X-Rad 320 irradiator (Precision X-Ray). 12 hours following the final fraction of radiotherapy, cells were trypsinized and harvested in single cell suspension on the 10x Chromium Controller (10x Genomics). Single-cell Perturb-seq libraries were processed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1with Feature Barcoding (10x Genomics), allowing direct capture of modified sgRNAs83, and sequenced on a illumina NovaSeq-6000.

text: VS_perturb_RNA_4_S10_L001_R1_001.fastq.gz

text: VS_perturb_RNA_4_S10_L002_R1_001.fastq.gz

text: VS_perturb_RNA_4_S10_L001_R2_001.fastq.gz

text: VS_perturb_RNA_4_S10_L002_R2_001.fastq.gz

text: VS_perturb_RNA_4_S10_L001_I1_001.fastq.gz

text: VS_perturb_RNA_4_S10_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

characteristic: organism

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94194

text: VS_perturb_sgRNA_1_S11_L001_R1_001.fastq.gz

text: VS_perturb_sgRNA_1_S11_L002_R1_001.fastq.gz

text: VS_perturb_sgRNA_1_S11_L001_R2_001.fastq.gz

text: VS_perturb_sgRNA_1_S11_L002_R2_001.fastq.gz

text: VS_perturb_sgRNA_1_S11_L001_I1_001.fastq.gz

text: VS_perturb_sgRNA_1_S11_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

characteristic: platform

text: male

text: cells


text: University of California, San Francisco

text: live

text: Human

characteristic: SRA accession

characteristic: age

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94195

text: VS_perturb_sgRNA_2_S12_L001_R1_001.fastq.gz

text: VS_perturb_sgRNA_2_S12_L002_R1_001.fastq.gz

text: VS_perturb_sgRNA_2_S12_L001_R2_001.fastq.gz

text: VS_perturb_sgRNA_2_S12_L002_R2_001.fastq.gz

text: VS_perturb_sgRNA_2_S12_L001_I1_001.fastq.gz

text: VS_perturb_sgRNA_2_S12_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

characteristic: sex

text: cells


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94196

text: HEI-193 cells were transduced with the perturb-seq library at 1,000X coverage at an MOI of 0.1, corresponding to approximately 95% of cells with a single integration. 72 hours following transduction, sgRNA+ cells were FACS sorted (BFP+) and were recovered in DMEM 10% FBS. Sorted cultures were treated with either 0Gy, 1.8Gy x 5 daily fractions, or 12.5Gy x 1 fraction of radiotherapy using the X-Rad 320 irradiator (Precision X-Ray). 12 hours following the final fraction of radiotherapy, cells were trypsinized and harvested in single cell suspension on the 10x Chromium Controller (10x Genomics). Single-cell Perturb-seq libraries were processed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1with Feature Barcoding (10x Genomics), allowing direct capture of modified sgRNAs83, and sequenced on a illumina NovaSeq-6000.

text: VS_perturb_sgRNA_3_S13_L001_R1_001.fastq.gz

text: VS_perturb_sgRNA_3_S13_L002_R1_001.fastq.gz

text: VS_perturb_sgRNA_3_S13_L001_R2_001.fastq.gz

text: VS_perturb_sgRNA_3_S13_L002_R2_001.fastq.gz

text: VS_perturb_sgRNA_3_S13_L001_I1_001.fastq.gz

text: VS_perturb_sgRNA_3_S13_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: tissue


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94197

text: VS_perturb_sgRNA_4_S14_L001_R1_001.fastq.gz

text: VS_perturb_sgRNA_4_S14_L002_R1_001.fastq.gz

text: VS_perturb_sgRNA_4_S14_L001_R2_001.fastq.gz

text: VS_perturb_sgRNA_4_S14_L002_R2_001.fastq.gz

text: VS_perturb_sgRNA_4_S14_L001_I1_001.fastq.gz

text: VS_perturb_sgRNA_4_S14_L002_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: title


text: University of California, San Francisco

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94198

text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

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text: fastq

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text: Illumina NovaSeq 6000

text: schwannoma

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characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94199

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characteristic: title


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text: University of California, San Francisco

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text: live

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text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

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text: HEI193_5x1_8_CROP_2_S13_L002_I1_001.fastq.gz

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text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

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text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94211

text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

text: HEI193_5x1_8_GEX_1_S4_L001_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_1_S4_L002_I1_001.fastq.gz

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text: fastq

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characteristic: organism

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94212

text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

text: HEI193_5x1_8_GEX_2_S5_L001_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L002_I1_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L003_I1_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L004_I1_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L001_I2_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L002_I2_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L003_I2_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L004_I2_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L002_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L003_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L004_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L001_R2_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L002_R2_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L003_R2_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L004_R2_001.fastq.gz

text: HEI193_5x1_8_GEX_2_S5_L001_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

characteristic: platform

text: male

text: cells


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94213

text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

text: HEI193_5x1_8_GEX_3_S6_L001_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L002_I1_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L003_I1_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L004_I1_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L001_I2_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L002_I2_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L003_I2_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L004_I2_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L002_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L003_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L004_R1_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L001_R2_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L002_R2_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L003_R2_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L004_R2_001.fastq.gz

text: HEI193_5x1_8_GEX_3_S6_L001_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

characteristic: sex

text: cells


text: University of California, San Francisco

characteristic: INSDC secondary accession

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94214

text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

characteristic: filename

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: tissue


characteristic: External Id

text: University of California, San Francisco

characteristic: INSDC center name

text: live

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94215

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells

characteristic: title


text: University of California, San Francisco

characteristic: INSDC first public

text: live

characteristic: INSDC status

text: Human

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94216

text: fastq

characteristic: filetype

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

text: live

text: Human

characteristic: SRA accession

characteristic: age

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94217

text: HEI193_5x1_8_ATAC_1_S4_L001_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L002_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L003_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L004_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L001_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L002_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L003_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L004_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L002_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L003_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L004_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L001_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L002_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L003_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L004_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_1_S4_L001_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

characteristic: isolate

text: Homo sapiens

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

text: live

text: Human

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94218

text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

text: HEI193_5x1_8_ATAC_2_S5_L001_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L002_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L003_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L004_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L001_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L002_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L003_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L004_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L002_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L003_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L004_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L001_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L002_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L003_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L004_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_2_S5_L001_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

characteristic: organism

text: ILLUMINA

text: male

text: cells


text: University of California, San Francisco

characteristic: INSDC last update

text: live

text: Human

characteristic: assembly

text: Raleigh Lab UCSF Helen Diller Family Comprehensive Cancer Center 1450 3rd Street, San Francisco 94219

text: sgRNA library was packaged into lentivirus using HEK-293T cells. HEI-193 cultures were transduced to an MOI of 0.1 and FACS sorted for sgRNA+ cells after 48 hours. Radiotherapy was then delivered to either 0Gy or 1.8Gy x 5 daily fractions using the X-Rad 320 irradiator (Precision X-Ray). Following completion of radiotherapy, cells were harvested with Trypsin and prepared following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing 10x Protocol (10x Genomics, CG000365 Rev C). Briefly, 1-2 105 cells were incubated in chilled Lysis Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, Digitonin 0.01%, BSA 1%, DTT 1mM, RNase inhibitor 1 U/µL) on ice for 4 minutes, washed with Wash Buffer (Tris-HCl (pH 7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/uL) 3 times, and resuspended in diluted nuclei buffer. Nuclei were counted and membrane integrity was evaluated by Trypan staining on the Countess II FL Automated Cell Counter (Thermo). Nuclei suspensions were diluted to approximately 3,000 nuclei/µL and processed according to the 10x Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338 Rev A). To recover sgRNA identities from single-nuclei RNA fractions, CROP-seq guides were amplified into dual-indexed Illumina libraries from the cDNA product of the 10x multiome protocol as described above with a three-round hemi-nested PCR as previously described85. 15 ng of full-length cDNA product was amplified with primers binding to the sgRNA constant region and 10x Genomics Read 1 Adaptor. Two subsequent PCR steps were performed to introduce i5 and i7 indices and Illumina P5 and P7 adaptors. After the first round of PCR, each product was size-selected using SPRI beads at 1.0x. Subsequent PCRs were conducted with 1 ng product. The final PCR product was size selected with 0.5x and then 1.0x SPRI beads and library quality was assessed by TapeStation high-sensitivity D1000 analysis (Thermo). CROP-seq libraries were pooled with gene expression libraries and sequenced on an Illumina NovaSeq 6000 using the paired end 100 bp protocol.

text: HEI193_5x1_8_ATAC_3_S6_L001_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L002_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L003_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L004_I1_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L001_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L002_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L003_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L004_R3_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L002_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L003_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L004_R1_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L001_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L002_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L003_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L004_R2_001.fastq.gz

text: HEI193_5x1_8_ATAC_3_S6_L001_I1_001.fastq.gz

text: fastq

text: Illumina NovaSeq 6000

text: schwannoma

text: Homo sapiens

text: ILLUMINA

characteristic: platform

text: male

text: cells


text: PulseNet Next Generation Subtyping Methods Unit

characteristic: INSDC secondary accession

text: live

text: Pathogen.env

text: MO

text: shrimp

text: Vibrio metschnikovii

characteristic: strain

text: Vibrio metschnikovii


characteristic: External Id

text: live

text: Pathogen.env

text: MO

text: USA:MO

text: Salmon fillet

text: Vibrio metschnikovii

text: Vibrio metschnikovii


characteristic: INSDC center name

text: live

text: Pathogen.env

text: MO

text: USA:MO

text: shrimp

text: Vibrio metschnikovii

text: Vibrio metschnikovii


text: live

text: Pathogen.env

text: MO

text: USA:MO

text: shrimp

text: Vibrio parahaemolyticus

text: Vibrio parahaemolyticus

characteristic: title


characteristic: INSDC first public

text: live

text: Pathogen.env

text: MO

text: shrimp

text: Vibrio parahaemolyticus

text: Vibrio parahaemolyticus


text: live

characteristic: INSDC status

text: Pathogen.env

text: MO

text: USA:MO

text: shrimp

text: Vibrio brasiliensis

text: Vibrio brasiliensis


Mice lung tissues

text: The Third Affiliated Hospital of Guangzhou Medical University

text: live

text: Model organism or animal

text: postnatal day 14

text: RNA-seq on lung tissues from postnatal day 14 BPD mice which were treated with umbilical cord blood exosomes from very preterm infants with bronchopulmonary dysplasia or vehicle control.

characteristic: description

text: Mus musculus

text: female

characteristic: sex

text: FVB/NJ

text: Lung

characteristic: tissue

text: Model organism or animal sample from Mus musculus


McNabs Island

text: Dalhousie University

text: live

text: MIMARKS.survey

characteristic: SRA accession

characteristic: depth

text: Keywords: GSC:MIxS;MIMARKS:5.0

text: aquatic biome[ENVO_00002030]

text: marine tidal flow zone[ENVO_01001341]

text: marine water body[ENVO_00001999]|coastal water body[ENVO_02000049]

text: Canada: Halifax

text: 44.61 N 63.549 W

text: seawater metagenome


Georges Island

text: Dalhousie University

text: live

characteristic: NCBI submission model

text: MIMARKS.survey

characteristic: NCBI submission package

text: Keywords: GSC:MIxS;MIMARKS:5.0

text: aquatic biome[ENVO_00002030]

text: marine tidal flow zone[ENVO_01001341]

text: Canada: Halifax

text: 44.642 N 63.552 W

text: seawater metagenome


BIO

text: Dalhousie University

characteristic: INSDC last update

text: live

text: MIMARKS.survey

text: Keywords: GSC:MIxS;MIMARKS:5.0

text: aquatic biome[ENVO_00002030]

text: marine tidal flow zone[ENVO_01001341]

text: Canada: Halifax

text: 44.679 N 63.615 W

text: seawater metagenome

characteristic: organism


Tuffts Cove

text: Dalhousie University

text: live

text: MIMARKS.survey

text: Keywords: GSC:MIxS;MIMARKS:5.0

text: aquatic biome[ENVO_00002030]

text: marine tidal flow zone[ENVO_01001341]

text: Canada: Halifax

text: 44.675 N 63.595 W

text: seawater metagenome


Narrows

text: Dalhousie University

text: live

text: MIMARKS.survey

text: Keywords: GSC:MIxS;MIMARKS:5.0

text: aquatic biome[ENVO_00002030]

text: marine tidal flow zone[ENVO_01001341]

text: Canada: Halifax

text: 44.677 N 63.607 W

text: seawater metagenome


PreFilter

text: Dalhousie University

text: live

text: MIMARKS.survey

text: Keywords: GSC:MIxS;MIMARKS:5.0

text: aquatic biome[ENVO_00002030]

text: marine tidal flow zone[ENVO_01001341]

text: Canada: Halifax

text: seawater metagenome

text: PF


text: Fudan University

text: live

text: Human

text: WYM Lab

text: Homo sapiens

text: not determined

text: cell line

text: Human sample from Homo sapiens

characteristic: value


text: Nanchang University

characteristic: INSDC secondary accession

text: live

text: Model organism or animal

text: matured fish

characteristic: isolate

text: Siganus canaliculatus

text: female

text: fin

text: Model organism or animal sample from Siganus canaliculatus


characteristic: External Id

text: Nanchang University

text: live

text: Model organism or animal

text: matured fish

text: Siganus canaliculatus

text: male

text: fin


text: Tianjin College University of Science and Technology Beijing

characteristic: INSDC center name

text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

characteristic: replicate

text: a nonamended control

text: Metagenome or environmental sample from soil metagenome


characteristic: INSDC first public

text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: a nonamended control

characteristic: title


text: live

characteristic: INSDC status

text: Metagenome or environmental

text: bacteria

characteristic: description

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: a nonamended control


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

text: treatment 1


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: treatment 1


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: treatment 1


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

text: treatment 2


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: treatment 2


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: treatment 2


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

text: treatment 3


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: treatment 3


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: treatment 3


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 1

text: treatment G


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 2

text: treatment G


text: live

text: Metagenome or environmental

text: bacteria

text: China:Tianjin

text: coastal saline soil

text: 39.12 N 117.53 E

text: soil metagenome

text: biological replicate 3

text: treatment G


text: Korea University Guro Hospital

text: live

text: MIMS.me

text: MIGS/MIMS/MIMARKS.human-gut

characteristic: PCDAI

characteristic: SES-CD

text: Keywords: GSC:MIxS;MIMS:5.0

text: host-associated

text: human gut

text: feces

text: Fistula

characteristic: fistula

text: Korea

text: Homo sapiens

characteristic: host

text: CD

text: male

text: not collected

characteristic: location

text: metagenome

text: MIMS Environmental/Metagenome sample from metagenome


text: Korea University Guro Hospital

characteristic: INSDC last update

text: live

text: MIMS.me

characteristic: NCBI submission model

text: MIGS/MIMS/MIMARKS.human-gut

characteristic: NCBI submission package

characteristic: SRA accession

characteristic: antiTNFa

text: Keywords: GSC:MIxS;MIMS:5.0

text: host-associated

text: human gut

text: feces

text: No Fistula

text: Korea

text: Homo sapiens

text: CD

text: male

text: not collected

text: metagenome


characteristic: External Id

text: Korea University Guro Hospital

characteristic: INSDC secondary accession

text: live

text: MIMS.me

text: MIGS/MIMS/MIMARKS.human-gut

text: Keywords: GSC:MIxS;MIMS:5.0

text: host-associated

text: human gut

text: feces

text: No Fistula

text: Korea

text: Homo sapiens

text: CD

text: male

text: not collected

text: metagenome

characteristic: organism


characteristic: EEN

text: Korea University Guro Hospital

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: MIMS.me

text: MIGS/MIMS/MIMARKS.human-gut

characteristic: calprotectin

text: Keywords: GSC:MIxS;MIMS:5.0

text: host-associated

text: human gut

text: feces

text: No Fistula

text: Korea

text: Homo sapiens

text: CD

text: male

text: not collected

text: metagenome


text: Korea University Guro Hospital

text: live

characteristic: INSDC status

text: MIMS.me

text: MIGS/MIMS/MIMARKS.human-gut

characteristic: PCDAI

text: Keywords: GSC:MIxS;MIMS:5.0

characteristic: description

text: host-associated

text: human gut

text: feces

text: Fistula

text: Korea

text: Homo sapiens

text: CD

text: female

text: not collected

text: metagenome

characteristic: title


text: Korea University Guro Hospital

text: live

text: MIMS.me

text: MIGS/MIMS/MIMARKS.human-gut

text: Keywords: GSC:MIxS;MIMS:5.0

text: host-associated

text: human gut

text: feces

text: No Fistula

characteristic: fistula

text: Korea

text: Homo sapiens

characteristic: host

text: CD

text: female

text: not collected

text: metagenome


text: Korea University Guro Hospital

characteristic: INSDC last update

text: live

text: MIMS.me

characteristic: NCBI submission model

text: MIGS/MIMS/MIMARKS.human-gut

text: Keywords: GSC:MIxS;MIMS:5.0

text: host-associated

text: human gut

text: feces

text: No Fistula

text: Korea

text: Homo sapiens

text: CD

text: male

text: not collected

text: metagenome


text: Korea University Guro Hospital

text: live

text: MIMS.me

text: MIGS/MIMS/MIMARKS.human-gut

characteristic: NCBI submission package

characteristic: SES-CD

characteristic: SRA accession

text: Keywords: GSC:MIxS;MIMS:5.0

text: host-associated

text: human gut

text: feces

text: No Fistula

text: Korea

text: Homo sapiens

text: CD

text: male

text: not collected

characteristic: location

text: metagenome