title: Whole blood, BN.N.NYU180.pre.1

tag: race

value: african american

tag: validation set


title: Whole blood, MN.N.NYU251.post.3451

status: Public on Aug 02 2020

type: RNA

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

hyb_protocol: Hybridized on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) or 3 time less than background signal in all samples were removed from further analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: amplified cRNA was generated from 100ng RNA using the TargetAmp Nano-g Biotin-aRNA Labeling Kit (Epicentre, Madison WI)

growth_protocol: Whole blood samples were collected in PAXgene Tubes (Qiagen) as recommended

extract_protocol: Total RNA was isolated using the PAXgene Blood miRNA Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: PAXgene tubes were transferred to Wistar Genomics facility for RNA extraction

tag: patient

tag: patient sample id

tag: nodule class

value: MN

tag: collection site

value: NYU

tag: cancer type

value: adenocarcinoma

tag: nodule histology

tag: gender

value: male

tag: age

value: caucasian

tag: smoking

value: quit

tag: packyears

tag: nodule size, mm

tag: cancer stage

tag: post treatment sample

value: yes

tag: post treatment days

tag: training set

value: no

tag: tissue

value: whole blood


title: Whole blood, MN.N.NYU1595.pre.2

value: squamous cell carcinoma

tag: race

value: smoker

tag: validation set


title: Whole blood, NN.N.NYU1499.pre.1

tag: patient

tag: patient sample id

value: NN

value: other


title: Whole blood, MN.N.NYU360.post.2122

tag: nodule class

tag: collection site

value: female


title: Whole blood, MN.N.NYU1559.post.183

tag: cancer type

tag: nodule histology


title: Whole blood, BN.N.NYU1484.pre.1

value: BN

value: solid

tag: gender

tag: age


title: Whole blood, BN.N.NYU99.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.N.NYU1612.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU377.pre.3

value: solid/ground glass opacity

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.N.NYU1476.post.619

value: MN

tag: training set

tag: tissue


title: Whole blood, MN.N.NYU755.post.172

value: NYU

value: other non-small cell

tag: race

tag: validation set


title: Whole blood, BN.N.NYU8.pre.2

tag: patient

tag: patient sample id

value: male


title: Whole blood, BN.N.NYU1614.pre.1

tag: nodule class

tag: collection site

value: caucasian


title: Whole blood, BN.N.NYU1240.pre.1

tag: cancer type

tag: nodule histology

value: african american

value: quit


title: Whole blood, BN.N.NYU1296.pre.1

tag: gender

tag: age

value: no

value: yes


title: Whole blood, BN.N.NYU317.pre.1

value: ground glass opacity

tag: smoking

tag: packyears

value: whole blood


title: Whole blood, BN.N.NYU994.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU1594.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.N.NYU1024.pre.2

value: smoker

tag: training set

tag: tissue


title: Whole blood, MN.N.NYU1559.post.118

value: adenocarcinoma

tag: race

tag: validation set


title: Whole blood, BN.N.NYU1539.pre.1

tag: patient

tag: patient sample id

value: female


title: Whole blood, MN.N.NYU1605.post.0

tag: nodule class

tag: collection site


title: Whole blood, MN.N.NYU524.post.67

tag: cancer type

tag: nodule histology


title: Whole blood, MN.N.NYU50.post.131

tag: gender

tag: age

value: other


title: Whole blood, BN.N.NYU823.pre.1

value: BN

tag: smoking

tag: packyears


title: Whole blood, NN.N.NYU1536.pre.1

value: NN

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU1593.pre.1

value: solid

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.N.NYU781.pre.1

value: NYU

value: solid/ground glass opacity

tag: training set

tag: tissue


title: Whole blood, MN.N.NYU1595.pre.1

value: MN

value: squamous cell carcinoma

value: male

tag: race

tag: validation set


title: Whole blood, BN.N.NYU1475.pre.2

tag: patient

tag: patient sample id

value: caucasian


title: Whole blood, BN.N.NYU712.pre.1

tag: nodule class

tag: collection site

value: no


title: Whole blood, BN.N.NYU663.pre.1

tag: cancer type

tag: nodule histology

value: yes


title: Whole blood, MN.N.NYU524.post.25

tag: gender

tag: age


title: Whole blood, BN.N.NYU1600.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.N.NYU1547.pre.1

value: never

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU1524.pre.1

tag: post treatment sample

tag: post treatment days

value: whole blood


title: Whole blood, BN.N.NYU1118.pre.1

value: quit

tag: training set

tag: tissue


title: Whole blood, BN.N.NYU1123.pre.1

tag: race

tag: validation set


title: Whole blood, MN.N.NYU524.pre.3

tag: patient

tag: patient sample id

value: adenocarcinoma

value: smoker


title: Whole blood, BN.N.NYU863.pre.1

tag: nodule class

tag: collection site

value: female


title: Whole blood, BN.N.NYU361.pre.2

value: BN

tag: cancer type

tag: nodule histology


title: Whole blood, BN.N.NYU83.pre.1

tag: gender

tag: age


title: Whole blood, BN.N.NYU1235.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.N.NYU1579.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU1414.pre.1

value: ground glass opacity

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.N.NYU1578.pre.1

value: solid

tag: training set

tag: tissue


title: Whole blood, MN.N.NYU1337.pre.1

value: NYU

tag: race

tag: validation set


title: Whole blood, BN.N.NYU1509.pre.1

tag: patient

tag: patient sample id


title: Whole blood, BN.N.NYU1592.pre.1

tag: nodule class

tag: collection site

value: solid/ground glass opacity


title: Whole blood, BN.N.NYU1591.pre.1

tag: cancer type

tag: nodule histology

value: african american


title: Whole blood, MN.N.NYU811.post.932

value: MN

value: squamous cell carcinoma

tag: gender

tag: age


title: Whole blood, BN.N.NYU678.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.N.NYU578.post.2227

value: caucasian

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU1575.pre.1

value: male

value: other

tag: post treatment sample

value: no

tag: post treatment days


title: Whole blood, BN.N.NYU683.pre.1

tag: training set

value: yes

tag: tissue

value: whole blood


title: Whole blood, BN.N.NYU1589.pre.1

tag: race

value: quit

tag: validation set


title: Whole blood, MN.N.NYU1055.post.101

tag: patient

tag: patient sample id

value: adenocarcinoma


title: Whole blood, BN.N.NYU556.pre.1

tag: nodule class

tag: collection site

value: female

value: smoker


title: Whole blood, BN.N.NYU1072.pre.1

value: BN

tag: cancer type

tag: nodule histology


title: Whole blood, BN.N.NYU1574.pre.1

value: solid

tag: gender

tag: age


title: Whole blood, MN.N.NYU1587.pre.1

value: NYU

tag: smoking

tag: packyears


title: Whole blood, NN.N.NYU488.pre.1

value: NN

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.N.NYU20.post.539

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.N.NYU1439.pre.1

value: ground glass opacity

tag: training set

tag: tissue


title: Whole blood, MN.N.NYU1476.post.521

value: MN

tag: race

tag: validation set


title: Whole blood, MN.N.NYU1452.post.558

tag: patient

tag: patient sample id

value: other non-small cell


title: Whole blood, MN.N.NYU3.pre.1

tag: nodule class

tag: collection site

value: caucasian


title: Whole blood, BN.N.NYU1477.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, BN.N.NYU169.pre.1

tag: gender

value: male

tag: age


title: Whole blood, NN.N.NYU1338.pre.1

value: african american

tag: smoking

tag: packyears


title: Whole blood, BN.N.NYU1572.pre.1

tag: nodule size, mm

tag: cancer stage

value: no


title: Whole blood, MN.N.NYU1559.pre.1

tag: post treatment sample

tag: post treatment days

value: yes


title: Whole blood, BN.N.NYU1564.pre.1

tag: training set

tag: tissue

value: whole blood


title: Whole blood, BN.N.NYU1157.pre.1

tag: race

value: quit

tag: validation set


title: Whole blood, MN.N.NYU674.post.918

tag: patient

tag: patient sample id

value: squamous cell carcinoma


title: Whole blood, MN.N.NYU697.post.860

tag: nodule class

tag: collection site

value: adenocarcinoma

value: female


title: Whole blood, BN.N.NYU267.pre.1

value: BN

tag: cancer type

tag: nodule histology

value: smoker


title: Whole blood, MN.N.NYU722.post.2862

value: NYU

tag: gender

tag: age


title: Whole blood, BN.N.NYU211.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.N.NYU1429.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU1603.pre.1

value: solid

value: other

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.N.NYU1551.pre.1

value: NN

tag: training set

tag: tissue


title: Whole blood, NN.N.NYU1495.pre.1

tag: race

tag: validation set


title: Whole blood, BN.N.NYU630.pre.2

tag: patient

tag: patient sample id

value: solid/ground glass opacity


title: Whole blood, BN.N.NYU1207.pre.1

tag: nodule class

tag: collection site


title: Whole blood, BN.N.NYU897.pre.1

tag: cancer type

tag: nodule histology

value: caucasian


title: Whole blood, BN.N.NYU203.pre.1

tag: gender

value: male

tag: age


title: Whole blood, BN.N.NYU377.pre.2

tag: smoking

tag: packyears


title: Whole blood, NN.N.NYU1550.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, NN.N.NYU770064.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.N.NYU202.pre.1

tag: training set

tag: tissue


title: Whole blood, NN.N.NYU1467.pre.1

tag: race

tag: validation set


title: Whole blood, BN.N.NYU1359.pre.1

tag: patient

tag: patient sample id


title: Whole blood, MN.N.NYU1476.pre.1

tag: nodule class

value: MN

tag: collection site


title: Whole blood, BN.N.NYU187.pre.1

tag: cancer type

tag: nodule histology

value: no


title: Whole blood, NN.N.NYU1549.pre.1

tag: gender

tag: age


title: Whole blood, BN.N.NYU1475.pre.1

tag: smoking

tag: packyears

value: yes


title: Whole blood, MN.N.NYU20.pre.1

tag: nodule size, mm

tag: cancer stage

value: whole blood


title: Whole blood, BN.N.NYU485.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.N.NYU811.post.295

value: quit

tag: training set

tag: tissue


title: Whole blood, MN.N.NYU697.post.174

tag: race

tag: validation set


title: Whole blood, BN.N.NYU1601.pre.1

tag: patient

tag: patient sample id


title: Whole blood, BN.N.NYU8.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.N.NYU674.post.240

tag: cancer type

value: squamous cell carcinoma

tag: nodule histology


title: Whole blood, BN.N.NYU730.pre.1

value: ground glass opacity

tag: gender

tag: age


title: Whole blood, BN.N.NYU261.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.N.NYU361.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU466.pre.1

value: female

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.N.NYU613.post.566

value: adenocarcinoma

tag: training set

tag: tissue


title: Whole blood, BN.N.NYU780.pre.1

value: BN

tag: race

tag: validation set


title: Whole blood, MN.N.NYU524.pre.2

tag: patient

tag: patient sample id

value: NYU


title: Whole blood, MN.N.NYU1311.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.N.NYU1055.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, BN.N.NYU630.pre.1

tag: gender

tag: age


title: Whole blood, MN.N.NYU697.pre.1

tag: smoking

value: smoker

tag: packyears


title: Whole blood, MN.N.NYU811.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.N.NYU1331.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.U.20443.pre.1

value: UPenn

tag: training set

tag: tissue


title: Whole blood, MN.U.20516.post.0

tag: race

tag: validation set


title: Whole blood, MN.N.NYU251.post.2337

tag: patient

tag: patient sample id


title: Whole blood, MN.U.20454.post.0

tag: nodule class

tag: collection site

value: african american


title: Whole blood, MN.N.NYU578.post.1225

tag: cancer type

tag: nodule histology


title: Whole blood, MN.U.20608.post.0

tag: gender

tag: age


title: Whole blood, MN.U.20498.post.0

tag: smoking

tag: packyears


title: Whole blood, MN.U.20443.post.0

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.N.NYU1452.pre.1

value: other non-small cell

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.U.20454.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.U.20499.post.0

tag: race

value: caucasian

tag: validation set


title: Whole blood, MN.U.20666.post.0

tag: patient

tag: patient sample id

value: male


title: Whole blood, MN.U.20448.post.0

tag: nodule class

value: MN

tag: collection site


title: Whole blood, BN.N.NYU1343.pre.1

tag: cancer type

tag: nodule histology

value: solid

value: no


title: Whole blood, MN.U.20608.pre.1

tag: gender

tag: age

value: yes

value: whole blood


title: Whole blood, BN.N.NYU377.pre.1

value: solid/ground glass opacity

tag: smoking

tag: packyears


title: Whole blood, MN.U.20582.post.0

value: squamous cell carcinoma

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20582.pre.1

value: female

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.U.20443.post.na

value: adenocarcinoma

tag: training set

tag: tissue


title: Whole blood, MN.U.20516.pre.1

tag: race

tag: validation set


title: Whole blood, MN.U.20448.pre.1

tag: patient

tag: patient sample id

value: quit


title: Whole blood, BN.U.20312.pre.2

tag: nodule class

value: BN

tag: collection site

value: granuloma


title: Whole blood, BN.U.20414.pre.2

value: UPenn

tag: cancer type

tag: nodule histology

value: never


title: Whole blood, BN.U.20282.pre.2

tag: gender

tag: age


title: Whole blood, MN.U.20499.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.U.20290.pre.2

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20666.pre.1

value: smoker

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.U.20497.pre.1

value: caucasian

tag: training set

tag: tissue


title: Whole blood, BN.U.20283.pre.2

value: other

tag: race

tag: validation set


title: Whole blood, MN.U.20498.pre.1

tag: patient

tag: patient sample id

value: MN


title: Whole blood, BN.U.20527.pre.1

tag: nodule class

tag: collection site

value: male


title: Whole blood, BN.U.20519.pre.1

tag: cancer type

tag: nodule histology

value: no


title: Whole blood, BN.U.20622.pre.1

tag: gender

tag: age

value: yes


title: Whole blood, BN.U.20475.pre.2

tag: smoking

tag: packyears

value: whole blood


title: Whole blood, BN.U.20576.pre.1

value: african american

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.U.20578.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.U.20524.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.U.20430.pre.1

tag: race

tag: validation set


title: Whole blood, MN.U.20438.pre.1

tag: patient

tag: patient sample id


title: Whole blood, BN.U.20277.pre.2

tag: nodule class

tag: collection site


title: Whole blood, BN.U.40175.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, BN.U.20302.pre.2

tag: gender

tag: age


title: Whole blood, BN.U.20612.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.U.20534.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20384.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.U.20590.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.U.20445.pre.1

tag: race

tag: validation set


title: Whole blood, NN.U.40215.pre.1

tag: patient

tag: patient sample id

value: NN


title: Whole blood, MN.U.20376.pre.2

tag: nodule class

tag: collection site


title: Whole blood, NN.U.40198.pre.1

tag: cancer type

tag: nodule histology

value: female


title: Whole blood, BN.N.NYU1024.pre.1

value: NYU

value: solid/ground glass opacity

tag: gender

tag: age


title: Whole blood, BN.U.20570.pre.1

value: BN

tag: smoking

value: quit

tag: packyears


title: Whole blood, BN.U.20656.pre.1

value: UPenn

value: granuloma

tag: nodule size, mm

tag: cancer stage


title: Whole blood, NN.U.40178.pre.1

value: smoker

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.U.20451.pre.1

value: adenocarcinoma

value: caucasian

tag: training set

tag: tissue


title: Whole blood, NN.U.40188.pre.1

tag: race

tag: validation set


title: Whole blood, MN.U.20394.pre.1

tag: patient

tag: patient sample id

value: MN

value: squamous cell carcinoma


title: Whole blood, NN.U.40179.pre.1

tag: nodule class

tag: collection site

value: no


title: Whole blood, MN.U.20496.pre.1

tag: cancer type

tag: nodule histology

value: male

value: yes


title: Whole blood, NN.U.40065.pre.1

tag: gender

tag: age

value: african american

value: whole blood


title: Whole blood, BN.U.40185.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.U.20601.pre.1

value: female

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20551.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.U.40217.pre.1

value: NN

tag: training set

tag: tissue


title: Whole blood, MN.U.20278.pre.1

tag: race

tag: validation set


title: Whole blood, NN.U.40202.pre.1

tag: patient

tag: patient sample id


title: Whole blood, NN.U.40117.pre.1

tag: nodule class

tag: collection site


title: Whole blood, NN.U.40214.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.U.20358.pre.1

tag: gender

tag: age


title: Whole blood, NN.U.40199.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.U.20460.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20361.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.N.NYU524.pre.1

value: NYU

tag: training set

tag: tissue


title: Whole blood, NN.U.40216.pre.1

tag: race

tag: validation set


title: Whole blood, BN.U.40221.pre.1

tag: patient

tag: patient sample id

value: BN


title: Whole blood, MN.U.20413.pre.1

tag: nodule class

tag: collection site

value: quit


title: Whole blood, BN.U.40182.pre.1

value: UPenn

tag: cancer type

tag: nodule histology


title: Whole blood, MN.U.20493.pre.1

tag: gender

tag: age


title: Whole blood, NN.U.40201.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.U.20403.pre.2

value: granuloma

tag: nodule size, mm

tag: cancer stage


title: Whole blood, NN.U.40220.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.U.40187.pre.1

value: smoker

tag: training set

tag: tissue


title: Whole blood, NN.U.40193.pre.1

tag: race

tag: validation set


title: Whole blood, MN.U.20450.pre.1

tag: patient

tag: patient sample id

value: adenocarcinoma


title: Whole blood, MN.U.20488.pre.1

tag: nodule class

tag: collection site

value: caucasian


title: Whole blood, MN.U.20416.pre.1

value: MN

tag: cancer type

tag: nodule histology


title: Whole blood, MN.U.20557.pre.1

tag: gender

tag: age

value: other


title: Whole blood, MN.U.20473.pre.1

tag: smoking

tag: packyears

value: no


title: Whole blood, MN.U.20562.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20449.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.U.40191.pre.1

value: male

tag: training set

tag: tissue


title: Whole blood, MN.U.20434.pre.1

value: squamous cell carcinoma

tag: race

value: yes

tag: validation set


title: Whole blood, MN.U.20484.pre.1

tag: patient

tag: patient sample id

value: whole blood


title: Whole blood, MN.U.20540.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.U.20471.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.U.20415.pre.1

tag: gender

value: female

tag: age

value: never


title: Whole blood, NN.U.40203.pre.1

value: NN

tag: smoking

tag: packyears


title: Whole blood, MN.U.20481.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.U.40183.pre.1

value: BN

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.U.40200.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.U.20368.pre.1

tag: race

tag: validation set


title: Whole blood, MN.U.20405.pre.1

tag: patient

tag: patient sample id

value: quit


title: Whole blood, BN.U.40184.pre.1

tag: nodule class

tag: collection site

value: UPenn


title: Whole blood, NN.U.40159.pre.1

tag: cancer type

tag: nodule histology

value: african american


title: Whole blood, MN.U.20378.pre.1

tag: gender

tag: age


title: Whole blood, NN.U.40177.pre.1

tag: smoking

value: smoker

tag: packyears


title: Whole blood, MN.U.20433.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, NN.U.40170.pre.1

tag: post treatment sample

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title: Whole blood, NN.U.40172.pre.1

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title: Whole blood, MN.U.20426.pre.1

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title: Whole blood, NN.U.40153.pre.1

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title: Whole blood, NN.U.40168.pre.1

tag: nodule class

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title: Whole blood, NN.U.40162.pre.1

tag: cancer type

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title: Whole blood, NN.U.40171.pre.1

tag: gender

tag: age


title: Whole blood, NN.U.40130.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.U.20479.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, NN.U.40131.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.U.40138.pre.1

tag: training set

tag: tissue


title: Whole blood, NN.U.40169.pre.1

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title: Whole blood, NN.U.40167.pre.1

tag: patient

tag: patient sample id


title: Whole blood, NN.U.40129.pre.1

tag: nodule class

tag: collection site


title: Whole blood, BN.U.20468.pre.1

tag: cancer type

tag: nodule histology

value: granuloma


title: Whole blood, NN.U.40122.pre.1

tag: gender

tag: age

value: caucasian


title: Whole blood, BN.U.20475.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.U.20403.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.U.20414.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.U.20392.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.U.20376.pre.1

value: MN

value: adenocarcinoma

tag: race

tag: validation set


title: Whole blood, MN.U.20380.pre.1

tag: patient

tag: patient sample id

value: no


title: Whole blood, MN.U.20377.pre.1

tag: nodule class

tag: collection site

value: male


title: Whole blood, MN.U.20342.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.U.20390.pre.1

tag: gender

tag: age


title: Whole blood, MN.U.20304.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.U.20428.pre.1

value: squamous cell carcinoma

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20340.pre.1

tag: post treatment sample

tag: post treatment days

value: yes


title: Whole blood, MN.U.20333.pre.1

tag: training set

tag: tissue

value: whole blood


title: Whole blood, MN.U.20369.pre.1

value: female

tag: race

tag: validation set


title: Whole blood, BN.U.20312.pre.1

tag: patient

tag: patient sample id


title: Whole blood, BN.U.20282.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.U.20281.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.U.20325.pre.1

tag: gender

tag: age


title: Whole blood, MN.U.20338.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.U.20069.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.U.20302.pre.1

tag: post treatment sample

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title: Whole blood, MN.U.20293.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.U.20280.pre.1

tag: race

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title: Whole blood, MN.U.20288.pre.1

tag: patient

tag: patient sample id


title: Whole blood, BN.U.20283.pre.1

tag: nodule class

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value: other


title: Whole blood, BN.U.20290.pre.1

tag: cancer type

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title: Whole blood, MN.U.20067.pre.1

tag: gender

tag: age


title: Whole blood, MN.U.20061.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.U.20273.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20553.pre.1

value: never

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.U.20296.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_4010.post.152

value: HFGCC

tag: race

tag: validation set


title: Whole blood, MN.U.20052.pre.1

tag: patient

tag: patient sample id

value: quit


title: Whole blood, MN.H.CCHS_1112.post.198

tag: nodule class

tag: collection site

value: other non-small cell


title: Whole blood, MN.U.20059.pre.1

value: UPenn

tag: cancer type

tag: nodule histology


title: Whole blood, MN.H.CCHS_1100.post.303

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_1086.post.351

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_4026.pre.1

value: small cell carcinoma

value: smoker

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.U.20054.pre.1

value: caucasian

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1101.post.304

value: MN

tag: training set

tag: tissue


title: Whole blood, MN.U.20060.pre.1

value: adenocarcinoma

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1105.post.349

tag: patient

tag: patient sample id

value: no


title: Whole blood, BN.H.CCHS_6040.pre.1

tag: nodule class

value: BN

tag: collection site

value: male

value: african american


title: Whole blood, MN.H.CCHS_1096.post.326

tag: cancer type

tag: nodule histology

value: yes

value: whole blood


title: Whole blood, MN.H.CCHS_1093.post.343

value: squamous cell carcinoma

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_1073.post.197

value: female

tag: smoking

value: never

tag: packyears


title: Whole blood, MN.H.CCHS_5003.post.0

value: HFGCC

value: quit

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.U.20063.pre.1

value: UPenn

value: granuloma

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_4024.pre.1

value: other non-small cell

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_4002.post.188

tag: race

tag: validation set


title: Whole blood, NN.H.CCHS_6039.pre.1

tag: patient

tag: patient sample id

value: NN

value: caucasian


title: Whole blood, MN.H.CCHS_4001.post.0

tag: nodule class

value: MN

tag: collection site


title: Whole blood, BN.H.CCHS_5005.pre.1

tag: cancer type

tag: nodule histology

value: no


title: Whole blood, MN.U.20048.pre.1

value: adenocarcinoma

tag: gender

tag: age

value: smoker


title: Whole blood, BN.U.40181.pre.1

value: BN

tag: smoking

tag: packyears


title: Whole blood, MN.U.20326.pre.1

value: african american

tag: nodule size, mm

tag: cancer stage

value: yes


title: Whole blood, NN.H.CCHS_6038.pre.1

tag: post treatment sample

tag: post treatment days

value: whole blood


title: Whole blood, BN.H.CCHS_5004.pre.1

value: solid/ground glass opacity

value: female

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_4007.pre.1

value: HFGCC

value: male

tag: race

value: other

value: never

tag: validation set


title: Whole blood, BN.H.CCHS_6029.pre.1

tag: patient

tag: patient sample id


title: Whole blood, NN.H.CCHS_6036.pre.1

tag: nodule class

tag: collection site

value: quit


title: Whole blood, BN.H.CCHS_6022.pre.1

tag: cancer type

tag: nodule histology

value: granuloma


title: Whole blood, NN.H.CCHS_6026.pre.1

value: NN

tag: gender

tag: age

value: caucasian


title: Whole blood, BN.H.CCHS_6032.pre.1

tag: smoking

tag: packyears

value: no


title: Whole blood, NN.H.CCHS_6028.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, NN.H.CCHS_6027.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.H.CCHS_6024.pre.1

tag: training set

tag: tissue


title: Whole blood, BN.H.CCHS_6037.pre.1

tag: race

tag: validation set


title: Whole blood, NN.H.CCHS_6030.pre.1

tag: patient

tag: patient sample id


title: Whole blood, BN.H.CCHS_6025.pre.1

tag: nodule class

tag: collection site


title: Whole blood, NN.H.CCHS_6023.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, NN.H.CCHS_6033.pre.1

tag: gender

tag: age


title: Whole blood, NN.H.CCHS_6034.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_4019.pre.1

value: MN

value: squamous cell carcinoma

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_4021.pre.1

value: adenocarcinoma

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.H.CCHS_6031.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_4023.pre.1

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_4022.pre.1

tag: patient

tag: patient sample id

value: smoker


title: Whole blood, MN.H.CCHS_4025.pre.1

tag: nodule class

tag: collection site

value: yes


title: Whole blood, NN.H.CCHS_6019.pre.1

tag: cancer type

tag: nodule histology

value: whole blood


title: Whole blood, MN.H.CCHS_1107.post.192

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_4016.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.H.CCHS_6035.pre.1

value: BN

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_4014.pre.1

value: female

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.H.CCHS_6021.pre.1

value: HFGCC

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_4018.pre.1

value: male

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1066.post.344

tag: patient

tag: patient sample id


title: Whole blood, MN.H.CCHS_4017.pre.1

tag: nodule class

tag: collection site


title: Whole blood, BN.H.CCHS_6018.pre.1

tag: cancer type

tag: nodule histology

value: african american


title: Whole blood, MN.H.CCHS_4020.pre.1

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_4009.pre.1

tag: smoking

tag: packyears


title: Whole blood, NN.H.CCHS_6017.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_4012.pre.1

value: other non-small cell

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1103.post.177

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_4013.pre.1

tag: race

value: quit

tag: validation set


title: Whole blood, MN.H.CCHS_1056.post.342

tag: patient

tag: patient sample id


title: Whole blood, NN.H.CCHS_6020.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.H.CCHS_4005.pre.1

tag: cancer type

value: small cell carcinoma

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tag: gender

tag: age


title: Whole blood, MN.H.CCHS_4008.pre.1

value: other

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1091.post.210

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_4010.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.H.CCHS_5002.pre.1

value: granuloma

tag: training set

tag: tissue


title: Whole blood, BN.U.20277.pre.1

value: UPenn

tag: race

value: caucasian

value: no

tag: validation set


title: Whole blood, MN.H.CCHS_4006.pre.1

tag: patient

tag: patient sample id

value: MN


title: Whole blood, MN.H.CCHS_4015.pre.1

tag: nodule class

tag: collection site

value: adenocarcinoma

value: never


title: Whole blood, MN.H.CCHS_1112.pre.1

tag: cancer type

tag: nodule histology

value: smoker

value: yes

value: whole blood


title: Whole blood, MN.H.CCHS_4011.pre.1

value: HFGCC

tag: gender

value: female

tag: age


title: Whole blood, NN.H.CCHS_6016.pre.1

value: NN

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1111.pre.1

value: male

value: african american

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_1106.pre.1

value: small cell carcinoma

tag: post treatment sample

tag: post treatment days


title: Whole blood, NN.H.CCHS_6013.pre.1

value: quit

tag: training set

tag: tissue


title: Whole blood, NN.H.CCHS_6015.pre.1

tag: race

tag: validation set


title: Whole blood, BN.H.CCHS_6012.pre.1

tag: patient

tag: patient sample id

value: BN


title: Whole blood, NN.H.CCHS_6007.pre.1

tag: nodule class

tag: collection site


title: Whole blood, NN.H.CCHS_6005.pre.1

tag: cancer type

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title: Whole blood, NN.H.CCHS_6011.pre.1

tag: gender

tag: age


title: Whole blood, BN.H.CCHS_6004.pre.1

tag: smoking

tag: packyears


title: Whole blood, NN.H.CCHS_6008.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_1109.pre.1

value: squamous cell carcinoma

tag: post treatment sample

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title: Whole blood, MN.H.CCHS_4002.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1055.post.204

tag: race

value: caucasian

tag: validation set


title: Whole blood, NN.H.CCHS_6001.pre.1

tag: patient

tag: patient sample id

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title: Whole blood, BN.H.CCHS_6010.pre.1

tag: nodule class

tag: collection site


title: Whole blood, NN.H.CCHS_6002.pre.1

tag: cancer type

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value: MN

tag: gender

tag: age


title: Whole blood, BN.H.CCHS_6009.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.H.CCHS_5001.pre.1

tag: nodule size, mm

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value: adenocarcinoma

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.H.CCHS_6006.pre.1

value: ground glass opacity

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_4004.pre.1

tag: race

value: smoker

tag: validation set


title: Whole blood, MN.H.CCHS_1073.pre.1

tag: patient

tag: patient sample id

value: never

value: yes


title: Whole blood, MN.H.CCHS_1110.pre.1

tag: nodule class

tag: collection site

value: HFGCC

value: whole blood


title: Whole blood, MN.H.CCHS_1071.post.201

tag: cancer type

tag: nodule histology


title: Whole blood, MN.H.CCHS_1052.post.215

tag: gender

tag: age


title: Whole blood, BN.H.CCHS_6003.pre.1

value: female

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1103.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.H.CCHS_2022.pre.1

value: male

tag: post treatment sample

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title: Whole blood, BN.H.CCHS_2024.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1043.post.194

tag: race

tag: validation set


title: Whole blood, BN.H.CCHS_3011.pre.1

tag: patient

tag: patient sample id


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tag: cancer type

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tag: age


title: Whole blood, MN.H.CCHS_1097.pre.1

value: other non-small cell

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tag: packyears


title: Whole blood, MN.H.CCHS_1104.pre.1

tag: nodule size, mm

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title: Whole blood, MN.H.CCHS_1100.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1102.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1099.pre.1

tag: race

value: african american

tag: validation set


title: Whole blood, MN.H.CCHS_1107.pre.1

tag: patient

tag: patient sample id

value: quit


title: Whole blood, MN.H.CCHS_1044.post.194

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title: Whole blood, MN.H.CCHS_2020.pre.1

tag: cancer type

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title: Whole blood, MN.H.CCHS_1054.post.233

tag: gender

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title: Whole blood, MN.H.CCHS_1101.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1027.post.272

value: other

tag: nodule size, mm

tag: cancer stage


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value: small cell carcinoma

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1096.pre.1

value: caucasian

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1046.post.180

tag: race

value: no

tag: validation set


title: Whole blood, BN.H.CCHS_3009.pre.1

tag: patient

tag: patient sample id

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title: Whole blood, MN.H.CCHS_1098.pre.1

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title: Whole blood, BN.H.CCHS_2021.pre.1

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tag: gender

tag: age


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value: squamous cell carcinoma

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value: HFGCC

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1006.post.305

tag: training set

tag: tissue

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title: Whole blood, MN.H.CCHS_1093.pre.1

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1091.pre.1

tag: patient

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title: Whole blood, MN.H.CCHS_1089.pre.1

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tag: cancer type

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tag: gender

tag: age


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value: ground glass opacity

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1088.pre.1

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tag: post treatment sample

tag: post treatment days


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value: other non-small cell

tag: training set

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title: Whole blood, BN.H.CCHS_2018.pre.1

tag: race

value: quit

tag: validation set


title: Whole blood, MN.H.CCHS_1085.pre.1

tag: patient

tag: patient sample id


title: Whole blood, MN.H.CCHS_1083.pre.1

tag: nodule class

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tag: cancer type

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title: Whole blood, MN.H.CCHS_1081.pre.1

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_1082.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1078.pre.1

tag: nodule size, mm

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value: NN

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1092.pre.1

value: small cell carcinoma

tag: training set

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title: Whole blood, MN.H.CCHS_1035.post.196

tag: race

value: caucasian

tag: validation set


title: Whole blood, MN.H.CCHS_1033.post.217

tag: patient

tag: patient sample id

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title: Whole blood, MN.H.CCHS_1051.pre.1

tag: nodule class

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title: Whole blood, MN.H.CCHS_1076.pre.1

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tag: nodule histology

value: african american


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value: MN

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tag: age


title: Whole blood, MN.H.CCHS_1087.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1079.pre.1

tag: nodule size, mm

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value: BN

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1032.post.183

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1025.post.194

tag: race

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title: Whole blood, MN.H.CCHS_1080.pre.1

tag: patient

tag: patient sample id

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title: Whole blood, MN.H.CCHS_1001.post.303

tag: nodule class

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title: Whole blood, MN.H.CCHS_1012.post.233

tag: cancer type

value: squamous cell carcinoma

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title: Whole blood, MN.H.CCHS_1030.post.176

tag: gender

tag: age

value: smoker

value: yes


title: Whole blood, NN.H.CCHS_3003.pre.1

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value: female

tag: nodule size, mm

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value: male

tag: post treatment sample

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title: Whole blood, NN.H.CCHS_3004.pre.1

tag: training set

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title: Whole blood, NN.H.CCHS_3007.pre.1

tag: race

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title: Whole blood, BN.H.CCHS_3002.pre.1

tag: patient

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title: Whole blood, MN.H.CCHS_1071.pre.1

tag: gender

tag: age

value: quit


title: Whole blood, MN.H.CCHS_1070.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1065.pre.1

tag: nodule size, mm

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value: other

tag: post treatment sample

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title: Whole blood, BN.H.CCHS_2014.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_2015.pre.1

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1067.pre.1

tag: patient

tag: patient sample id


title: Whole blood, MN.H.CCHS_1060.pre.1

tag: nodule class

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title: Whole blood, MN.H.CCHS_1072.pre.1

tag: cancer type

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title: Whole blood, MN.H.CCHS_1052.pre.1

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_1015.post.178

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1069.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_1066.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1063.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1061.pre.1

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1055.pre.1

tag: patient

tag: patient sample id


title: Whole blood, MN.H.CCHS_1014.post.220

tag: nodule class

tag: collection site


title: Whole blood, BN.H.CCHS_2012.pre.1

tag: cancer type

tag: nodule histology

value: solid/ground glass opacity


title: Whole blood, BN.H.CCHS_2013.pre.1

tag: gender

tag: age

value: caucasian


title: Whole blood, MN.H.CCHS_1057.pre.1

tag: smoking

tag: packyears

value: no


title: Whole blood, MN.H.CCHS_1059.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.H.CCHS_2011.pre.1

value: ground glass opacity

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1054.pre.1

value: MN

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1056.pre.1

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1053.pre.1

tag: patient

tag: patient sample id


title: Whole blood, MN.H.CCHS_1062.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.H.CCHS_1045.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.H.CCHS_1048.pre.1

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_1046.pre.1

value: small cell carcinoma

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1049.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_1040.pre.1

value: african american

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1038.pre.1

value: adenocarcinoma

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1042.pre.1

value: squamous cell carcinoma

tag: race

value: smoker

tag: validation set


title: Whole blood, MN.H.CCHS_1035.pre.1

tag: patient

tag: patient sample id

value: HFGCC

value: yes


title: Whole blood, MN.H.CCHS_1050.pre.1

tag: nodule class

tag: collection site

value: female

value: whole blood


title: Whole blood, MN.H.CCHS_1031.pre.1

tag: cancer type

tag: nodule histology

value: male


title: Whole blood, MN.H.CCHS_1036.pre.1

tag: gender

tag: age

value: quit


title: Whole blood, MN.H.CCHS_1033.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1044.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_1005.post.197

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1039.pre.1

tag: training set

tag: tissue


title: Whole blood, BN.H.CCHS_2010.pre.1

value: BN

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1041.pre.1

tag: patient

tag: patient sample id


title: Whole blood, MN.H.CCHS_1020.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.H.CCHS_1024.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, NN.H.CCHS_2004.pre.1

value: NN

tag: gender

tag: age


title: Whole blood, BN.H.CCHS_2009.pre.1

value: caucasian

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1026.pre.1

tag: nodule size, mm

tag: cancer stage

value: no


title: Whole blood, BN.H.CCHS_2006.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1028.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1043.pre.1

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1032.pre.1

tag: patient

tag: patient sample id

value: other non-small cell


title: Whole blood, BN.H.CCHS_2008.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.H.CCHS_1029.pre.1

value: MN

tag: cancer type

tag: nodule histology


title: Whole blood, MN.H.CCHS_1023.pre.1

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_1034.pre.1

tag: smoking

tag: packyears


title: Whole blood, MN.H.CCHS_1030.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, NN.H.CCHS_3005.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1017.pre.1

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1022.pre.1

tag: race

tag: validation set


title: Whole blood, MN.H.CCHS_1021.pre.1

tag: patient

tag: patient sample id


title: Whole blood, MN.H.CCHS_1011.pre.1

tag: nodule class

tag: collection site


title: Whole blood, MN.H.CCHS_1018.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.H.CCHS_1016.pre.1

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_1027.pre.1

value: other

tag: smoking

value: never

tag: packyears


title: Whole blood, MN.H.CCHS_1015.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, BN.H.CCHS_2005.pre.1

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.H.CCHS_1012.pre.1

tag: training set

tag: tissue


title: Whole blood, BN.H.CCHS_2003.pre.1

tag: race

tag: validation set


title: Whole blood, BN.H.CCHS_2002.pre.1

tag: patient

tag: patient sample id

value: ground glass opacity


title: Whole blood, MN.H.CCHS_1006.pre.1

tag: nodule class

tag: collection site

value: squamous cell carcinoma


title: Whole blood, MN.H.CCHS_1010.pre.1

tag: cancer type

value: adenocarcinoma

tag: nodule histology


title: Whole blood, MN.H.CCHS_1008.pre.1

value: HFGCC

tag: gender

tag: age

value: smoker


title: Whole blood, MN.H.CCHS_1007.pre.1

value: female

tag: smoking

tag: packyears

value: yes


title: Whole blood, MN.H.CCHS_1014.pre.1

value: male

tag: nodule size, mm

tag: cancer stage

value: whole blood


title: Whole blood, MN.H.CCHS_1009.pre.1

value: quit

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.T.630W.pre.1

value: BN

value: Temple

value: african american

tag: training set

tag: tissue


title: Whole blood, MN.H.CCHS_1002.pre.1

value: other non-small cell

tag: race

value: caucasian

value: no

tag: validation set


title: Whole blood, MN.H.CCHS_1004.pre.1

tag: patient

tag: patient sample id

value: MN


title: Whole blood, MN.T.644W.post.62

tag: nodule class

tag: collection site


title: Whole blood, BN.T.646W.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.H.CCHS_1003.pre.1

tag: gender

tag: age


title: Whole blood, MN.H.CCHS_1005.pre.1

tag: smoking

tag: packyears


title: Whole blood, BN.T.618W.pre.1

tag: nodule size, mm

tag: cancer stage


title: Whole blood, MN.H.CCHS_1001.pre.1

tag: post treatment sample

tag: post treatment days


title: Sample Pool4_Gene_Expression

type: SRA

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
CITE-Seq hashed RNA library
Pool4.tar
feature_barcode_sheet.csv

library_source: transcriptomic

data_processing:
CITE-seq raw data were processed using 10x cellranger pipeline, version 3.1. 5' single cell RNA-seq and TCR data were processed using 10x cellranger pipeline version 2.1.1.
Genome_build: hg38
Supplementary_files_format_and_content: raw read counts per UMI, tab delimited

source_name: colon CD8 T cells

extract_protocol:
Chromium Single Cell V(D)J Reagent Kits with Feature Barcoding technology for Cell Surface Protein (CG000186 Rev A)
Cells were lysed within GEMs generated by the 10X platform to yield cell-specific transcriptomic, cell surface protein and TCR information.
Library preparation was performed as per the manufacturer instructions which differed slightly for the two batch runs (details above). Essentially, mRNA and cell-surface proteins were tagged with a unique cell-specific oligonucleotide (UMI). Size-based separation and targeted amplification were employed to define 3 different library types : Gene expression, TCR and cell surface protein (containing both cell surface protein and hashtag information). Sequencing was performed on either a HiSeq4000 (S21-S34) or Novaseq6000 (Pooled Sample 1-4) platform.
10x RNA-Seq, 10x feature barcoding, 10x VDJ

treatment_protocol: Biopsies were taken at endoscopy from patients and stored. Experiments were performed in two separate 'batches' - the first (S21-S34) with TCR and Gene expression information, and second (Sample Pools 1-4) with Gene expression and Surface Protein information (CITE-seq and Hashing). Following a collagenase tissue digest, the single-cell suspensions were stained for flurochrome tagged (FACS) antibodies for CD3 and CD8, and additionally for the 'Pooled sample' experiments, additional oligonucleotide tagged antibodies for 14 surface proteins that delienated key immune subsets and one of 5 hashing antibodies (to enable sample multiplexing). The cells were washed to remove excess antibody, then live CD8+ T cells were sorted at flow cytometry. For S21-S34, each sample was loaded separately into a different 10X well, and GEMs recovered and processed separately. For the Pooled samples, the CD8 cells from different samples were mixed in a 1:1 ratio prior to loading onto the 10X single-cell sequencing platform. As we recovered different numbers of CD8 cells from different samples at FACS, Pool 3 consists of the pooled cells left over in 3 samples after Pool 2 was generated.

tag: disease

value: Mixed UC and Control Pool


title: Sample Pool3_Gene_Expression

description:
CITE-Seq hashed RNA library
Pool3.tar
feature_barcode_sheet.csv


title: Sample Pool2_Feature_Barcoding

description:
CITE-seq hashing and protein expression library
Pool2.tar
feature_barcode_sheet.csv


title: RNA_AH31

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

description: RNA-seq in liver monocytes from human donnor with Acute on Chronic Liver Failure

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters : Truseq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:4
Annotation file Mus_musculus.GRCh38.90.gtf was obtained from the ftp.Ensembl.org server
Reads were aligned to GRCh38 by STAR_2.5.3a
Reads from the alignment were sorted and indexed according to chromosome positions
Duplicated reads were removed by using MarkDuplicates command from Picard tools.
Read counts in the alignment BAM-files that overlap with the gene features were obtained using HTSeq-0.9.1
Genes with no raw read count >=20 in at least 1 sample were filtered out with an R script
Raw read counts were normalized and differential expression analysis was performed with DESeq2 by applying a corrected p value FDR<0.05 and absolute log2-ratio larger than 1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file containing normalized reads counts and differential expression analysis results and  tab-delimited text files containing normalized read counts (such as total read count=20M) for each sample and gene

growth_protocol: PBMCs were isolated from sodium-heparinised whole blood by Ficoll (...) and 10-20 million PBMCs were frozen in FBS with 20% DMSO in liquid nitrogen. PBMCs were thawed and CD14hi monocytes were isolated by fluorescence-activated cells sorting (FACS) on a BD FACS Aria III

extract_protocol:
80000 to 100,000 CD14hi monocytes were isolated by FACS in RLT buffer and flash frozen. RNA extraction was performed using a RNeasy kit (Qiagen) and sample quality was tested on a 2100 Bioanalyzer (Agilent).
Truseq stranded mRNA Library preparation kit

tag: condition

value: Acute on Chronic Liver Failure

tag: tissue

value: Peripheral Blood

tag: cell type

value: monocyte CD14+


title: Sample Pool1_Feature_Barcoding

description:
CITE-seq hashing and protein expression library
Pool1.tar
feature_barcode_sheet.csv


title: Sample Pool1_Gene_Expression

description:
CITE-Seq hashed RNA library
Pool1.tar
feature_barcode_sheet.csv


title: Whole blood, BN.T.622W.pre.1

tag: patient

tag: patient sample id

tag: race

tag: training set

tag: validation set


title: Sample Pool2_Gene_Expression

description:
CITE-Seq hashed RNA library
Pool2.tar
feature_barcode_sheet.csv


title: Whole blood, BN.T.597W.pre.1

tag: nodule class

tag: collection site

tag: cancer type

tag: nodule histology

value: solid

tag: gender


title: Whole blood, BN.T.586W.pre.1

tag: age

tag: smoking

tag: packyears

tag: nodule size, mm

tag: cancer stage


title: RNA_AH30

source_name: monocytes from human donnor with Acute on Chronic Liver Failure

tag: condition

tag: tissue


title: RNA_AH21

description: RNA-seq in liver monocytes from human donnor with Severe Alcoholic Hepatitis

value: Severe Alcoholic Hepatitis

tag: cell type


title: RNA_AH17


title: RNA_AH19

source_name: monocytes from human donnor with Severe Alcoholic Hepatitis


title: Whole blood, MN.T.547W.pre.1

tag: patient

tag: patient sample id

value: adenocarcinoma

value: female

tag: post treatment sample

tag: post treatment days

value: yes


title: Whole blood, BN.H.CCHS_2007.pre.1

tag: nodule class

value: HFGCC

value: ground glass opacity

value: male

tag: race

value: smoker

tag: training set

tag: validation set

value: whole blood


title: Whole blood, BN.T.583W.pre.1

value: BN

tag: collection site

value: Temple

tag: cancer type

tag: nodule histology

tag: gender

value: african american

value: quit


title: Whole blood, BN.T.514W.pre.1

tag: age

value: caucasian

tag: smoking

tag: packyears

tag: nodule size, mm

value: no


title: Whole blood, MN.T.615W.post.84

value: MN

tag: cancer stage

tag: tissue


title: Whole blood, MN.T.575W.pre.1

tag: patient

tag: patient sample id


title: Whole blood, MN.H.CCHS_1047.pre.1

value: other

tag: post treatment sample

tag: post treatment days


title: Whole blood, BN.T.636W.pre.1

tag: nodule class

tag: race


title: RNA_AH37

tag: condition

value: Severe Alcoholic Hepatitis

value: Peripheral Blood

tag: cell type

value: monocyte CD14+


title: Whole blood, BN.T.567W.pre.1

tag: collection site

tag: cancer type

value: female

value: never

tag: training set

value: yes

tag: validation set


title: Sample Pool4_Feature_Barcoding

description:
CITE-seq hashing and protein expression library
Pool4.tar
feature_barcode_sheet.csv

tag: disease

value: Mixed UC and Control Pool


title: Whole blood, MN.T.533W.pre.1

value: adenocarcinoma

tag: nodule histology

tag: gender

tag: age

tag: smoking

tag: packyears


title: Sample Pool3_Feature_Barcoding

description:
CITE-seq hashing and protein expression library
Pool3.tar
feature_barcode_sheet.csv


title: RNA_AH15

tag: tissue


title: RNA_HC57

description: RNA-seq in liver monocytes from healthy human donnor

source_name: monocytes from healthy human donnor

value: Healthy control


title: RNA_HC50


title: RNA_HC40


title: RNA_HC47


title: RNA_HC56


title: RNA_HC38


title: ATAC_AH31

description: ATAC-seq in liver monocytes from human donnor with Acute on Chronic Liver Failure

library_source: genomic

data_processing:
Adapters were removed with Trimmomatic-0.36 with the following parameters : Nextera1.fa:1:25:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to GRCh38 by Bowtie2 with the following parameters : --X 2000 --fr --very-sensitive --no-discordant --no-mixed –non-deterministic
Reads from the alignment were sorted and indexed according to chromosome positions
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads mapping in chrM were removed with a custom script and samtools view
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal

molecule: genomic DNA

growth_protocol: PBMCs were isolated from sodium-heparinised whole blood by Ficoll and 10-20 million PBMCs were frozen in FBS with 20% DMSO in liquid nitrogen. PBMCs were thawed and CD14hi monocytes were isolated by fluorescence-activated cells sorting (FACS) on a BD FACS Aria III

extract_protocol:
20000 to 50000 sorted monocytes were washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl,3 mM MgCl2, 0.1% (v/v) Igepal CA-630).
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.

tag: subject status

value: Acute on Chronic Liver Failure


title: ATAC_AH37

description: ATAC-seq in liver monocytes from human donnor with Severe Alcoholic Hepatitis


title: ATAC_AH15


title: ATAC_AH17


title: ATAC_HC56

description: ATAC-seq in liver monocytes from healthy human donnor


title: ATAC_AH30


title: ATAC_AH19


title: ATAC_HC57


title: ATAC_AH21


title: ATAC_AH49


title: ATAC_HC50


title: ATAC_HC47


title: LizardC_H09

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis.
Genome_build: UCSC mm10 for mouse, and for Pogona vitticeps pvi1.1 from http://georges.biomatix.org/genomics-uc, For annotation a synthetic chromosom. composed of al of Pogona vitticepsl transcript models extracted from  “Pogona_vitticeps.male.cds"  from http://georges.biomatix.org/genomics-uc, extended with 200bp to the 5’ end separated by 20 bp spacers.
Supplementary_files_format_and_content: Tab-delimited file of UMI counts

molecule: polyA RNA

organism: Pogona vitticeps

source_name: brain

extract_protocol:
Fresh frozen and O.C.T (Tissue-Tek) embedded brains were sectioned and 14 μm thick sections collected on agarose membranes. A metal frame was then placed on the slide and used to make a well, filled with O.C.T and quickly frozen on dry ice. The glass slide was removed and
replaced with a second metal frame and the created well was filled with O.C.T and frozen.  In order to mount the sample at a predefined angle we first use a scalpel to remove the sample from the metal frames and then angled using a custom made positioning device. After mounting in the correct angle, he sample was repositioned on the cryostat and 70 μm strips were sliced, collected with a forceps and transferred in a 96-wells plate kept inside the cryostat. The angle of the cryostat sample holder was not changed between samples

tag: slice id (cutting angle and slice index)


title: LizardC_H12


title: ATAC_HC38


title: ATAC_HC40


title: LizardC_H10


title: LizardC_H07


title: LizardC_H08


title: LizardC_H04


title: LizardC_H03


title: LizardC_G12


title: LizardC_H01


title: LizardC_G08


title: LizardC_G04


title: LizardC_G06


title: LizardC_H11


title: LizardC_G09


title: LizardC_G07


title: LizardC_G05


title: LizardC_G01


title: LizardC_F09


title: LizardC_F10


title: LizardC_F06


title: LizardC_G03


title: LizardC_F08


title: LizardC_F05


title: LizardC_F11


title: LizardC_F07


title: LizardC_H06


title: LizardC_F12


title: LizardC_H02


title: LizardC_H05


title: LizardC_F04


title: LizardC_G11


title: LizardC_G10


title: LizardC_F03


title: LizardC_F02


title: LizardC_G02


title: Whole blood, MN.H.CCHS_1013.pre.1

tag: patient

tag: patient sample id

tag: nodule class

value: HFGCC

value: male

tag: nodule size, mm

tag: cancer stage

tag: post treatment sample

tag: post treatment days

value: whole blood


title: LizardC_E12


title: LizardC_E07


title: LizardC_E09


title: LizardC_E08


title: LizardC_E06


title: LizardC_E04


title: LizardC_E02


title: LizardC_E01


title: LizardC_D12


title: LizardC_E03


title: LizardC_D09


title: LizardC_E11


title: LizardC_D08


title: LizardC_D11


title: LizardC_D10


title: LizardC_D06


title: LizardC_D07


title: LizardC_D04


title: LizardC_D05


title: LizardC_D03


title: LizardC_F01


title: LizardC_D02


title: LizardC_D01


title: LizardC_C12


title: LizardC_C11


title: LizardC_C10


title: LizardC_E05


title: RNA_AH32

tag: condition

tag: cell type


title: LizardC_E10


title: LizardC_C07


title: LizardC_C09


title: LizardC_C06


title: LizardC_C08


title: LizardC_C04


title: LizardC_C03


title: LizardC_C02


title: LizardC_C01


title: LizardC_B10


title: LizardC_B11


title: LizardC_B09


title: LizardC_B12


title: LizardC_B08


title: LizardC_B06


title: LizardC_B07


title: LizardC_B05


title: LizardC_B03


title: LizardC_B01


title: LizardC_A11


title: LizardC_A12


title: LizardC_B02


title: LizardC_A10


title: LizardC_A09


title: LizardC_A08


title: LizardC_A06


title: LizardC_C05


title: LizardC_A07


title: LizardC_A05


title: LizardC_A04


title: LizardC_A03


title: LizardC_A01


title: LizardC_A02


title: ATAC_AH32


title: LizardE_H12


title: LizardE_H04


title: LizardE_H08


title: LizardE_H07


title: LizardE_H11


title: LizardC_B04


title: LizardE_H06


title: LizardE_H02


title: LizardE_H03


title: LizardE_G12


title: LizardE_H05


title: LizardE_H01


title: LizardE_H10


title: LizardE_G10


title: LizardE_G11


title: LizardE_G09


title: LizardE_G07


title: LizardE_G08


title: LizardE_G04


title: LizardE_G05


title: LizardE_G06


title: LizardE_G02


title: LizardE_G03


title: LizardE_G01


title: LizardE_F12


title: LizardE_F11


title: LizardE_H09


title: LizardE_F08


title: LizardE_F04


title: LizardE_F07


title: LizardE_F06


title: LizardE_F03


title: LizardE_F02


title: LizardE_E12


title: LizardE_F10


title: LizardE_E07


title: LizardE_E10


title: LizardE_E03


title: LizardE_E04


title: LizardE_E11


title: LizardE_E02


title: LizardE_E08


title: LizardE_F01


title: LizardE_E01


title: LizardE_E05


title: LizardE_E06


title: LizardE_F09


title: LizardE_D10


title: LizardE_D05


title: LizardE_D11


title: LizardE_D12


title: LizardE_D08


title: LizardE_D07


title: LizardE_D06


title: LizardE_D09


title: LizardE_D03


title: LizardE_F05


title: LizardE_C11


title: LizardE_E09


title: LizardE_C12


title: LizardE_C09


title: LizardE_C10


title: LizardE_C06


title: LizardE_C05


title: LizardE_C04


title: LizardE_C08


title: LizardE_C02


title: LizardE_C07


title: LizardE_C03


title: LizardE_B12


title: LizardE_B11


title: LizardE_C01


title: LizardE_B10


title: LizardE_D04


title: LizardE_B08


title: LizardE_B06


title: LizardE_B09


title: LizardE_B05


title: LizardE_B02


title: LizardE_D02


title: LizardE_B04


title: LizardE_B03


title: LizardE_B01


title: LizardE_D01


title: LizardE_A12


title: LizardE_A10


title: LizardE_A07


title: LizardE_A11


title: LizardE_A06


title: LizardE_A09


title: LizardE_A04


title: LizardE_A08


title: LizardE_A03


title: LizardB_H11


title: LizardB_H10


title: LizardE_A01


title: LizardB_H08


title: LizardB_H12


title: LizardB_H09


title: LizardE_B07


title: LizardB_H05


title: LizardB_H04


title: LizardB_H07


title: LizardB_H06


title: LizardB_H02


title: LizardB_G12


title: LizardB_H03


title: LizardB_G11


title: LizardB_G09


title: LizardB_G10


title: LizardB_G07


title: LizardE_A05


title: LizardB_G06


title: LizardB_G04


title: LizardB_G03


title: LizardE_A02


title: LizardB_G01


title: LizardB_F12


title: LizardB_F11


title: LizardB_F10


title: LizardB_G02


title: LizardB_F07


title: LizardB_F08


title: LizardB_F05


title: LizardB_F04


title: LizardB_F06


title: LizardB_F03


title: LizardB_G08


title: LizardB_H01


title: LizardB_E12


title: LizardB_F09


title: LizardB_F02


title: LizardB_E10


title: LizardB_E08


title: LizardB_E09


title: LizardB_E07


title: LizardB_E11


title: LizardB_E06


title: LizardB_G05


title: LizardB_E05


title: LizardB_E02


title: LizardB_E01


title: LizardB_E03


title: LizardB_D10


title: LizardB_D12


title: LizardB_E04


title: LizardB_D09


title: LizardB_D08


title: LizardB_D11


title: LizardB_D07


title: LizardB_F01


title: LizardB_D06


title: LizardB_D02


title: LizardB_D04


title: LizardB_D01


title: EDF1_ko_EM120_r3

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description:
combined_transcript_counts.tsv
combined_transcript_TPMs.tsv
combined_gene_counts.tsv
combined_gene_TPMs.tsv
EM120_vs_UN_inEDF1ko.tsv
EM120_vs_UN_EDF1ko_interaction.tsv

data_processing:
transcripts were quantified against GENCODE v31 transcript database using Salmon
transcript counts and TPMs for each gene were summed
Counts were rounded to nearest integer
fold changes and p values were computed with Deseq 2, using an interaction term for genotype and treatment condition
Genome_build: GRCh38 (hg38), Gencode release 30
Supplementary_files_format_and_content: Count and TPM (transcripts per million) tables. Fold changes aand p values from Deseq2

source_name: HEK293 cells

growth_protocol: HEK Cells were grown in DMEM with 10% FBS to ~70% confluency before harvest.

extract_protocol:
Media was removed and cells were resuspended in trizo, RNA was extracted with zymo directzol miniprep kit.
Zymo-Seq RiboFree™ Total RNA Library Kit

treatment_protocol: Cells were treated with emetine for 30 minutes or 2 hours, or left untreated for 2 hours.

tag: cell line

tag: genotype

tag: treatment

value: 1.8 microM emetine, 120 min

tag: zymo adapter name


title: LizardB_D03


title: EDF1_ko_EM30_r3

description:
combined_transcript_counts.tsv
combined_transcript_TPMs.tsv
combined_gene_counts.tsv
combined_gene_TPMs.tsv
EM30_vs_UN_inEDF1ko.tsv
EM30_vs_UN_EDF1ko_interaction.tsv

value: 1.8 microM emetine, 30 min


title: EDF1_ko_EM120_r1


title: LizardB_C10


title: LizardB_C09


title: LizardB_D05


title: LizardB_C11


title: EDF1_ko_EM30_r1


title: EDF1_ko_EM120_r2


title: EDF1_ko_UN120_r3

description:
combined_transcript_counts.tsv
combined_transcript_TPMs.tsv
combined_gene_counts.tsv
combined_gene_TPMs.tsv
EDF1ko_vs_WT_inUN.tsv

value: untreated


title: LizardB_C08


title: EDF1_ko_EM30_r2


title: LizardB_C07


title: LizardB_C05


title: LizardB_C06


title: WT_EM120_r2

description:
combined_transcript_counts.tsv
combined_transcript_TPMs.tsv
combined_gene_counts.tsv
combined_gene_TPMs.tsv
EM120_vs_UN_inWT.tsv
EM120_vs_UN_EDF1ko_interaction.tsv

value: WT


title: WT_EM30_r3

description:
combined_transcript_counts.tsv
combined_transcript_TPMs.tsv
combined_gene_counts.tsv
combined_gene_TPMs.tsv
EM30_vs_UN_inWT.tsv
EM30_vs_UN_EDF1ko_interaction.tsv


title: WT_EM120_r1


title: LizardB_C03


title: LizardB_C04


title: LizardB_C02


title: LizardB_B12


title: WT_EM30_r2


title: LizardB_B11


title: WT_UN120_r3


title: LizardB_C01


title: LizardB_C12


title: WT_UN120_r2


title: WT_EM30_r1


title: LizardB_B10


title: LizardB_B09


title: LizardB_B07


title: MOCK-48hr_2

city: singapore

first: justin

last: chu

state: SINGAPORE

address: 5 science drive 2

department: microbiology and immunology

country: Singapore

institute: national university of singapore

data_processing:
Base calls performed using FasTQC
The reads were alligned to mirBase 21
Count data was generated through HTSeq
EdgeR was used to compare the differential expression of miRNAs between the mock and infected samples
Genome_build: GRCh38
Supplementary_files_format_and_content: .edgeR file format with logFC, logCPM, Pvalue, FDR

source_name: Lonza C2517A (30019000) Human umbilical vein endothelial cells

growth_protocol: HUVEC cells were grown on T-75 flasks in EBM-2 growth media supplemented with growth factors and 10% FCS as per manufacture's protocol (Lonza)

extract_protocol:
Total RNA extraction was carried out according to Qiagene total RNA isolation kit
The libraries were constructed using Illumina's TruSeq RNA Library Prep Kit v2 kit protocol.

treatment_protocol: HUVEC cells were infected with DENV2  (strain Den2STp7c6) at MOI 10 or mock-infected with supernatant derived from uninfected C6/36 cells

value: endothelial cells

tag: passage

value: passage 3

tag: infected with

value: not infected

tag: time


title: WT_UN120_r1


title: LizardB_B08

tag: slice id (cutting angle and slice index)


title: EDF1_ko_UN120_r2


title: EDF1_ko_UN120_r1


title: WT_EM120_r3


title: LizardB_B05


title: LizardB_B06


title: DENV2-48hr_3

value: DENV2 (strain Den2STp7c6)


title: MOCK-48hr_1


title: DENV2-48hr_2


title: DENV2-48hr_1


title: LizardB_B04


title: LizardB_B03


title: MOCK-24hr_2


title: LizardB_B01


title: MOCK-24hr_1


title: MOCK-48hr_3


title: DENV2-24hr_1


title: LizardB_A12


title: DENV2-24hr_2


title: LizardB_A07


title: LizardB_A05


title: DGM-13471_sm (DropSeq_SingleCell_demographics)

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
'Technical' R1 read length: 20 and 'biological' R2 read length: 72.  The position of the barcodes in R1 reads are bases 1-12 and the UMI is 13-20.
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
The clustering algorithm was performed using Seurat, a R package for single cell analysis.  Raw digital expression matrices that contain integer counts of number of transcripts for each gene in each cell were generated separately for each sequence.
All the genes expressed in at least 10 cells and all the cells with at least 200 detected genes were analyzed. Cells were filtered out that had unique gene counts over 104 or <200 and the % mitochondrial genes for each cell >0.25.
The total 11,702 cells for the 6 samples were merged together in a matrix and normalized by the total number of unique molecular identifiers (UMIs) per cells, multiplying by a scale factor (104) and then log transformed. Cell-cell variation was regressed out in gene expression driven by number of detected molecules per cell as well as the % mitochondrial gene content.
Principal component analysis (PCA) was assessed on the datasets from 11,702 cells. Highly variable genes wereidentified and used as input to the PCA to ensure robust identification of the primary structure in the data. Twenty statistically significant PCs were calculated. The PCs were used to project cells onto a two dimensional map using t-Distributed Stochastic Neighbor Embedding with perplexity parameter set to 30, allowing cells with simi-lar expression signature genes and similar PCs loading to localize near each other. The clustering algorithm, K-nearest neighbor (KNN) graph based on the euclidean distance in PCA space was constructed to iteratively group cells together. The resolution parameter in FindClusters function in Seurat package was set to 0.5. With this approach, 11 district clusters were identified.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files include the Ensembl unique gene symbol and UMI values for all samples.

source_name: small airway epithelium brushing

extract_protocol:
Single cell capture, RNA extraction and cDNA preparation were performed on the Drop-seq system following the manufacturer’s protocol. In all cases, >80% of the cells were single cells, with 70 to 80% cell viability. Cell suspensions were filtered through a 35 µm nylon mesh cell strainer snap cap and loaded on an Influx™ cell sorter.  The single viable cells were sorted, resuspended in PBS/0.01% BSA and the sorted single cell suspension counted using Countess™ Automated Cell Counter adjusted to the final concentration of 100 to 120 cells/µl.
The single cell suspension, barcoded beads, and droplet generation oil were running through a microfluidics device to form droplets.  Droplets containing both a single cell and barcoded bead were immediately lysed and the released mRNA hybridized to the primers on the surface of the beads.
The single cell libraries were pooled and sequenced with paired end clustering and 101x2 cycles sequencing on the Illumina Hiseq 2500

tag: smoking status

value: smoker

tag: age

tag: gender

value: M

tag: ethnicity

value: Hispanic

value: small airway epithelium (SAE)


title: DGM-13451_sm (DropSeq_SingleCell_demographics)

value: nonsmoker

value: F

value: African


title: LizardB_A09


title: DGM-13460_sm (DropSeq_SingleCell_demographics)

value: Caucasian


title: LizardB_A06


title: LizardB_A04


title: DGM-13434_sm (DropSeq_SingleCell_demographics)

value: Asian-Pacificlslander


title: DGM-00384_sm (DropSeq_SingleCell_demographics)


title: DGM-13427_sm (DropSeq_SingleCell_demographics)


title: LizardB_A02


title: LizardB_A01


title: LizardB_A03


title: LizardB_B02


title: MT306: WT Ctrl

city: Bar Harbor

first: Maria

middle: A

last: Telpoukhovskaia

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
The RNA-seq read mapping and read count was performed using the Lexogen QuantSeq platform on the Bluebee cloud (https://www.bluebee.com/lexogen/) with GRCm38.84 reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: text files include raw gene counts for each sample

organism: Mus musculus

source_name: primary microglia

growth_protocol: Cortical culture was prepared from isolated cortex tissue of postnatal day 3 Grn WT and KO pups and grown in T75 PDL-coated flasks in DMEM supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 μg/mL streptomycin at 37° C with 5% CO2. After 10 days, the flasks were shaken for 2 hours at 200 rpm at 37° C, the media were collected in 25mL Falcon tubes, which were spun at 200 g for 15 minutes. Media were removed and microglia were resuspended in 1 mL (per 75T flask) and counted using a hemocytometer. Microglia were plated at 300,000 cells/well in 1 mL into 24-well plates for RNA-seq experiments.

extract_protocol:
The mRNA from cells was isolated using the Quick-RNA™ MiniPrep kit from Zymo Research (catalog No. R1055), and further purified and concentrated using RNA Clean&Concentrator™-25 kit from Zymo Research (catalog No. R1017). To measure RNA concentration and quality, NanoDrop and Agilent RNA Pico Chip on Bioanalyzer were used, respectively.
Samples with RIN # above 7 were considered to be good quality and their libraries were prepared in two batches following the protocol from Lexogen QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina. The library quality was assessed using Agilent High Sensitive DNA Chip on Bioanalyzer and the library concentrations were measured using Qubit dsDNA HS Assay kit.

treatment_protocol: The plated cells were incubated for 24 hours in media prior to media replacement with either growth media containing compounds (nor-BNI at 25 μM, DB-cAMP at 100 μM, final DMSO concentration 0.1%) or 0.1% DMSO vehicle control. After another 24 hours, the media was aspirated and the cells were washed with cold PBS three times.

tag: strain

tag: tissue

value: brain

value: post natal day 3

value: treated with vehicle


title: MT307: WT Ctrl

value: WT


title: MT302: KO Ctrl

value: Grn-/-


title: MT116: WT Ctrl


title: LizardA_H11


title: DENV2-24hr_3

value: endothelial cells

value: passage 3


title: LizardB_A08


title: LizardA_H09


title: MT113: KO nor

value: treated with nor


title: MT109: KO cAMP

value: treated with cAMP


title: LizardA_H08


title: LizardA_H06


title: MT107: KO cAMP


title: LizardA_H07


title: MT308: WT Ctrl


title: LizardA_H05


title: LizardA_H04


title: MT108: KO cAMP


title: LizardB_A10


title: LizardA_H03


title: LizardA_H02


title: MT101: KO Ctrl


title: MT105: KO Ctrl


title: LizardA_H12


title: MT104: KO Ctrl


title: LizardA_H01


title: LizardA_H10


title: LizardA_G12


title: S24_TCR

description: 10x TCR libraries

extract_protocol:
Chromium Single Cell V(D)J Reagent Kits (CG000086 Rev G)
Cells were lysed within GEMs generated by the 10X platform to yield cell-specific transcriptomic, cell surface protein and TCR information.
Library preparation was performed as per the manufacturer instructions which differed slightly for the two batch runs (details above). Essentially, mRNA and cell-surface proteins were tagged with a unique cell-specific oligonucleotide (UMI). Size-based separation and targeted amplification were employed to define 3 different library types : Gene expression, TCR and cell surface protein (containing both cell surface protein and hashtag information). Sequencing was performed on either a HiSeq4000 (S21-S34) or Novaseq6000 (Pooled Sample 1-4) platform.
10x RNA-Seq, 10x feature barcoding, 10x VDJ

tag: disease

value: UC


title: LizardA_G11


title: S33_TCR

description: 10x TCR libraries


title: MT115: KO nor


title: S23_TCR

description: 10x TCR libraries

value: Healthy Control


title: LizardA_G10


title: LizardA_G09


title: S21_TCR

description: 10x TCR libraries


title: LizardA_G08


title: LizardA_G06


title: LizardA_G07


title: S34

description: 10x gene expression libraries


title: S33

description: 10x gene expression libraries


title: S22

description: 10x gene expression libraries


title: S24

description: 10x gene expression libraries


title: LizardA_G05


title: LizardA_G04


title: S34_TCR

description: 10x TCR libraries


title: LizardA_G01


title: S21

description: 10x gene expression libraries


title: LizardA_F12


title: LizardA_G02


title: LizardB_A11


title: S22_TCR

description: 10x TCR libraries


title: LizardA_F10


title: LizardA_F11


title: hESC_9 [CLEVER-seq]

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

data_processing:
Library strategy: CLEVER-seq
Illumina CASAVA version 1.8 were used to the basecalling.
We used Trim Galore (v0.3.3) to remove adaptors and low quality bases.
Next, reads passed quality control were mapped to human reference genome (version: hg19) using Bismark (v0.13.0). After alignment, PCR duplicates were removed with the command ‘samtools rmdup’ (v0.1.18).
Genome_build: hg19
Supplementary_files_format_and_content: The processed bed files include chromosome, start position, end position, reference genotype, regular CpG ("0") or 5fCpG ("1"), strand.

source_name: Embryonic stem cell

extract_protocol:
The CLEVER-seq experiment was carried out according to the previous study with slight modification. The single cells of human early embryo were transferred into lysis buffer (20 mM Tris, 2 mM EDTA, 20 mM KCl, and 0.3% TritonX-100, 1 mg/ml QIAGEN protease) by mouth pipette. After centrifugation (1 min at 7,000 r.p.m., 4°C), the sample was incubated at 50°C for 3 hr to release the genomic DNA followed by 70°C for 30 min to inactive the protease. Then trace mount of spike-in oligo DNA contain 5fC modification was added into sample. In order to label the 5fC, 150 mM malononitrile (J&K) was used. Mineral oil (15 μl) was add onto the surface of the sample to prevent evaporation. The sample was incubated at 37°C for 20 hr with constant shaking at 850 r.p.m. in the Thermomixer (Eppendorf). Then the single cell genome was amplified by MALBAC (Yikon Genomics) according to the user guide.
The genomic DNA was fragment into ~300 by by covaris S2. The library construction was performed using KAPA Hyper Prep Kit (Kapa Biosystems). The libraries were sequenced on Illumina Hiseq 4000 platform in pair-end 150 bp model (Novogene).

tag: developmental stage

value: Inner cell mass


title: hESC_10 [CLEVER-seq]


title: hESC_11 [CLEVER-seq]


title: hESC_8 [CLEVER-seq]


title: LizardA_F09


title: hESC_12 [CLEVER-seq]


title: hESC_7 [CLEVER-seq]


title: LizardA_G03


title: LizardA_F05


title: LizardA_F06


title: S23

description: 10x gene expression libraries


title: LizardA_F07


title: hESC_3 [CLEVER-seq]


title: hESC_5 [CLEVER-seq]


title: hESC_2 [CLEVER-seq]


title: LizardA_F02


title: hESC_6 [CLEVER-seq]


title: LizardA_F01


title: LizardA_F03


title: LizardA_F04


title: hESC_4 [CLEVER-seq]


title: TE_embryo2_5 [CLEVER-seq]

source_name: Blastocyst

value: Trophoectoderm cells


title: hESC_1 [CLEVER-seq]


title: TE_embryo2_4 [CLEVER-seq]


title: LizardA_E11


title: TE_embryo2_2 [CLEVER-seq]


title: TE_embryo2_3 [CLEVER-seq]


title: LizardA_E08


title: TE_embryo2_1 [CLEVER-seq]


title: LizardA_E09


title: LizardA_E10


title: LizardA_E07


title: LizardA_F08


title: TE_embryo1_4 [CLEVER-seq]


title: LizardA_E06


title: TE_embryo1_2 [CLEVER-seq]


title: TE_embryo1_3 [CLEVER-seq]


title: LizardA_E04


title: LizardA_E05


title: ICM_embryo3_1 [CLEVER-seq]


title: TE_embryo1_1 [CLEVER-seq]


title: ICM_embryo3_2 [CLEVER-seq]


title: LizardA_E03


title: ICM_embryo2_5 [CLEVER-seq]


title: ICM_embryo2_6 [CLEVER-seq]


title: ICM_embryo2_4 [CLEVER-seq]


title: LizardA_D12


title: LizardA_E02


title: LizardA_E12


title: LizardA_E01


title: ICM_embryo2_3 [CLEVER-seq]


title: LizardA_D10


title: LizardA_D11


title: ICM_embryo2_1 [CLEVER-seq]


title: ICM_embryo1_3 [CLEVER-seq]


title: ICM_embryo2_2 [CLEVER-seq]


title: LizardA_D07


title: LizardA_D06


title: LizardA_D09


title: ICM_embryo1_2 [CLEVER-seq]


title: MOCK-24hr_3

tag: cell type

value: not infected


title: ICM_embryo1_1 [CLEVER-seq]


title: LizardA_D05


title: LizardA_D04


title: Morula_embryo3_4 [CLEVER-seq]

source_name: Morula blastomere

value: Morula


title: Morula_embryo3_3 [CLEVER-seq]


title: LizardA_D02


title: LizardA_D03


title: Morula_embryo3_1 [CLEVER-seq]


title: Morula_embryo2_3 [CLEVER-seq]


title: Morula_embryo3_2 [CLEVER-seq]


title: LizardA_C12


title: LizardA_C11


title: Morula_embryo2_4 [CLEVER-seq]


title: LizardA_C10


title: LizardA_C09


title: Morula_embryo2_2 [CLEVER-seq]


title: Morula_embryo2_1 [CLEVER-seq]


title: Morula_embryo1_2 [CLEVER-seq]


title: LizardA_C05


title: Morula_embryo1_1 [CLEVER-seq]


title: Morula_embryo1_3 [CLEVER-seq]


title: LizardA_C06


title: LizardA_C08


title: TE_embryo2_6 [CLEVER-seq]


title: 8cell_embryo2_4 [CLEVER-seq]

source_name: 8-cell blastomere

value: 8-cell embryo


title: 8cell_embryo2_3 [CLEVER-seq]


title: LizardA_C03


title: 8cell_embryo2_2 [CLEVER-seq]


title: Morula_embryo2_5 [CLEVER-seq]


title: LizardA_D01


title: 8cell_embryo1_6 [CLEVER-seq]


title: LizardA_C01


title: LizardA_B12


title: 8cell_embryo2_1 [CLEVER-seq]


title: 8cell_embryo1_4 [CLEVER-seq]


title: LizardA_B11


title: 8cell_embryo1_3 [CLEVER-seq]


title: LizardA_B10


title: LizardA_B08


title: 8cell_embryo1_2 [CLEVER-seq]


title: 8cell_embryo1_1 [CLEVER-seq]


title: LizardA_C07


title: LizardA_C04


title: LizardA_B07


title: 4cell_embryo3_1 [CLEVER-seq]

source_name: 4-cell blastomere

value: 4-cell embryo


title: LizardA_B06


title: 4cell_embryo2_4 [CLEVER-seq]


title: LizardA_B05


title: 4cell_embryo3_2 [CLEVER-seq]


title: 4cell_embryo2_3 [CLEVER-seq]


title: LizardA_B04


title: LizardA_B03


title: LizardA_C02


title: 4cell_embryo2_2 [CLEVER-seq]


title: LizardA_B02


title: 4cell_embryo2_1 [CLEVER-seq]


title: LizardA_B01


title: 8cell_embryo1_5 [CLEVER-seq]


title: LizardA_A12


title: LizardA_A10


title: 4cell_embryo1_3 [CLEVER-seq]


title: 4cell_embryo1_2 [CLEVER-seq]


title: LizardA_A09


title: LizardA_D08


title: 2cell_embryo2_1 [CLEVER-seq]

source_name: 2-cell blastomere

value: 2-cell embryo


title: LizardA_A08


title: LizardA_A07


title: LizardA_A06


title: 2cell_embryo1_1 [CLEVER-seq]


title: 2cell_embryo4_1 [CLEVER-seq]


title: 2cell_embryo5_2 [CLEVER-seq]


title: LizardA_A03


title: LizardA_A05


title: 2cell_embryo5_1 [CLEVER-seq]


title: 2cell_embryo3_2 [CLEVER-seq]


title: LizardD_H12


title: 2cell_embryo3_1 [CLEVER-seq]


title: LizardD_H11


title: malePN_embryo5

source_name: Male pronuclei

value: Zygote


title: LizardA_A02


title: LizardA_A11


title: 4cell_embryo1_1 [CLEVER-seq]


title: LizardA_A01


title: malePN_embryo8


title: malePN_embryo9


title: LizardD_H09


title: 2cell_embryo1_2 [CLEVER-seq]


title: malePN_embryo10


title: LizardD_H07


title: LizardA_B09


title: LizardD_H08


title: 2cell_embryo4_2 [CLEVER-seq]


title: LizardA_A04


title: malePN_embryo12


title: malePN_embryo2


title: malePN_embryo1


title: LizardD_H05


title: malePN_embryo7


title: malePN_embryo15


title: LizardD_H03


title: LizardD_H04


title: malePN_embryo13


title: LizardD_H02


title: LizardD_H01


title: malePN_embryo14


title: LizardD_H10


title: LizardD_G12


title: malePN_embryo11


title: LizardD_G11


title: femalePN_embryo3

source_name: Female pronuclei


title: LizardD_G10


title: femalePN_embryo6


title: LizardD_G09


title: femalePN_embryo9


title: femalePN_embryo10


title: femalePN_embryo4


title: LizardD_G08


title: LizardD_H06


title: LizardD_G07


title: femalePN_embryo12


title: LizardD_G06


title: femalePN_embryo1


title: LizardD_G05


title: LizardD_G04


title: LizardD_G03


title: LizardD_G02


title: femalePN_embryo7


title: femalePN_embryo2


title: femalePN_embryo15


title: femalePN_embryo13


title: LizardD_F12


title: LizardD_F11


title: femalePN_embryo14


title: LizardD_F10


title: LizardD_G01


title: 4cell_embryo1_4 [CLEVER-seq]


title: LizardD_F09


title: femalePN_embryo11


title: LizardD_F07


title: LizardD_F06


title: mice 9,3-3 (miRNA)

city: Shanghai

first: Zhenlin

last: Huang

state: Shanghai

address: 1200 Cailun Road, Zhangjiang High Tech Park

department: Institute of Chinese Materia Medica

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

scan_protocol: Slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating Median normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR)

source_name: 330mg/kg MCT group

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: Mice were supplied with standard laboratory diet and water ad libitum at a temperature 22±1 °C with a 12 h light–dark cycle (6:00–18:00) and 65±5% humidity. All mice were received humane care in compliance with the institutional animal care guidelines approved by the Experimental Animal Ethical Committee, Shanghai University of Traditional Chinese Medicine.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Twenty-four C57BL/6 male mice were randomly divided into 3 groups: (1) vehicle control (n=8), (2) 270 mg/kg MCT (n=8), (3) 330 mg/kg MCT (n=8). Mice were fasted for 12 h before orally given with different doses of MCT (270, 330mg/kg, intragastric administration), but allowed water ad libitum. Mice were allowed food and water ad libitum after MCT administration. Animals were sacrificed 48 h after MCT administration, and blood and livers were collected.

tag: Sex

value: male

value: 6 weeks

value: liver

tag: agent

value: Monocrotaline

tag: dose


title: LizardD_F05


title: mice 8,3-2 (miRNA)

institute: Shanghai University of Traditional Chinese Medicine


title: mice 7,3-1 (miRNA)


title: LizardD_F03


title: LizardD_F02


title: 1st-Pb_9 [CLEVER-seq]

source_name: 1st polar body

value: 1st polar body


title: LizardD_F04


title: LizardD_F01


title: LizardD_E12


title: 1st-Pb_7 [CLEVER-seq]


title: mice 3,1-3 (miRNA)

source_name: control group

value: saline

value: control


title: LizardD_E11


title: LizardD_F08


title: mice 2,1-2 (miRNA)


title: 1st-Pb_6 [CLEVER-seq]


title: LizardD_E10


title: mice 6,2-3 (miRNA)

source_name: 270mg/kg MCT group


title: 1st-Pb_10 [CLEVER-seq]


title: seedling_2

city: Hong Kong

first: Runsheng

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

data_processing:
The original raw data from Nanopore MinION are trasformed to sequenced reads by basecalling using Guppy basecaller (version 3.1.5).
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using porechop (V0.2.4), then mapped to to Arabidopsis thaliana genome (Araport11) using minimap2 (V2.17).
The mapping result are tranformed to bigGenPred format using scripts in TrackCluster package.
The isoform calling and quantification are carried out with TrackCluster.
Genome_build: Araport11
Supplementary_files_format_and_content: Two column table file containing the read count for each gene. The ".bb" file is the binary compression of the UCSC bed file with the "bigGenePred" format.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis thaliana col-0 seeds were surface sterilized with 50% commercial bleach and 0.01% Triton X-100 for 10 minutes, then washed 5 times with sterilized H2O. The sterilized seeds were sown on ½ MS plate with 1% sucrose and 0.6% Agar (sigma, cat#: A1296). Stratification at 4ºC for 48 hours, then placed in a growth chamber with 16h light/8h dark for 14 days. The 14-day seedlings were harvested (three biological replicates, each with one gram) for RNA extraction. Some seedlings were transplanted into soil for floral buds, the soil-based Arabidopsis seedlings were also treated with photoperiod of 16h light/8h dark. After another three-week growing, floral buds from plants equals to principal growth stage 6.0 to 6.1 were harvested, and they were immediately immersed in a foil boat full of liquid nitrogen in a relative larger liquid nitrogen container. Two Harvested biological replicates were frozen at -80 degree freezer till RNA isolation.

extract_protocol:
Total RNAs from Arabidopsis seedlings and floral buds were isolated with Trizol according to manufacturer’s instruction. The extracted total RNAs were then treated with Dnase I (NEB CAT#:M0303). The treated total RNAs were extracted with acidic phenol (125:24:1, pH4.5, ThermoFisher cat#: AM9720) and precipitated with LiCl. The purified RNAs were subjected to mRNA isolation with Dynabeads mRNA purification kit (ThermoFisher cat#: 61006).
Nanopore sequencing libraries were constructed using Direct RNA sequencing kit (cat# SQK-RNA002). The libraries were loaded onto Nanopore R9.4.1 flow cell (cat# FLO-MIN106) and sequenced on MinION acquired from Oxford Nanopore Technologies.

tag: Stage

value: 14-day seedlings

value: seedling


title: mice 4,2-1 (miRNA)


title: mice 1,1-1 (miRNA)


title: LizardD_E08

source_name: brain


title: 1st-Pb_5 [CLEVER-seq]


title: LizardD_E09


title: LizardD_E07


title: 1st-Pb_8 [CLEVER-seq]


title: LizardD_E06


title: LizardD_E04


title: floral_buds_2

source_name: floral bud

value: floral buds


title: 1st-Pb_4 [CLEVER-seq]


title: seedling_1


title: 1st-Pb_3 [CLEVER-seq]


title: LizardD_E03


title: LizardD_E05


title: LizardD_E02


title: floral_buds_1


title: 1st-Pb_2 [CLEVER-seq]


title: LizardD_E01


title: mice 5,2-2 (miRNA)


title: LizardD_D12


title: 1st-Pb_1 [CLEVER-seq]


title: LizardD_D11


title: Oocyte_11 [CLEVER-seq]

source_name: Oocyte

value: MII oocyte


title: LizardD_D10


title: LizardD_D09


title: LizardD_D08


title: RNA shopa_14d rep2

city: Pasadena

first: Theodora

last: Koromila

state: CA

address: 1200 E Califonia Blvd

institute: California Institute of Technology

data_processing:
ATAC-seq data, the raw 151bp paired-end fastq data were trimmed to before aligned to drosophila dm6 reference genome assembly using Bowtie2 aligner. Aligned bam files were subject to further sorting and duplicate removal using samtools before downstream analysis.
RNA-seq data, the raw 151bp paired-end fastq data were trimmed before aligned to drosophila dm6 reference genome/gene annotation using TOPHAT2. Aligned bam files were subject to gene quantification and differential analysis using cufflinks and cuffdiff pipelines.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for ATACseq, gene statistics table for RNAseq

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
Individual embryos were collected on agar plates from females of the following genotypes: wild-type/control (i.e y w females crossed to sh_opa males), mutant (i.e.MTD-Gal4 x sh_opa), or ectopically-expressing opa (i.e. MTD-Gal4 x UAS-opa). Nuclear morphology was observed under a compount microscope at 20x magnification.Single sh_opa and control embryos were assayed at nc14D (nc14+45’), whereas UAS-opa and control embryos were assayed at nc14B (nc14+20’).  Temperatures for sample collection were maintained at 26C to minimize variation in cell cycle timing. Under these conditions, cell cycle times were indistinguishable. Cell cycles were timed from the onset of anaphase of the previous cell cycle. Each embryo was hand-selected and hand-dechorionated for the analysis.
Fragmentation and amplification of ATAC-seq libraries were performed essentially as described previously (Buenrostro et al., 2015). RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770) following the manufacturer’s instructions.
Prepared libraries were subject to paired-end sequencing using an Illumina NovaSeq.

value: embryos

tag: age at harvest

tag: genotype

value: Opa shRNAi


title: Oocyte_10 [CLEVER-seq]


title: RNA shopa_14d rep1


title: LizardD_D07


title: RNA ctrl_14d rep3

value: wt


title: Oocyte_7 [CLEVER-seq]


title: Oocyte_9 [CLEVER-seq]


title: Oocyte_8 [CLEVER-seq]


title: LizardD_D06


title: LizardD_D02


title: LizardD_D01


title: ATAC opao_14b rep2

value: Opa overexpression (UAS opa)


title: Oocyte_6 [CLEVER-seq]


title: RNA ctrl_14d rep1


title: RNA ctrl_14d rep2


title: LizardD_D03


title: RNA shopa_14d rep3


title: LizardD_C12


title: LizardD_C11


title: ATAC opao_14b rep1


title: LizardD_C10


title: ATAC ctrl_14b rep2


title: LizardD_C08


title: LizardD_C09


title: LizardD_D04


title: LizardD_C07


title: Oocyte_4 [CLEVER-seq]


title: ATAC ctrl_14b rep1


title: LizardD_C06


title: LizardD_D05


title: LizardD_C05


title: LizardD_C04


title: Oocyte_3 [CLEVER-seq]


title: ATAC shOpa_14d rep3


title: Oocyte_2 [CLEVER-seq]


title: LizardD_C03


title: LizardD_C02


title: LizardD_C01