title: GSS1376_222_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_119_F_BE

status: Public on Jul 20 2020

type: RNA

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

country: USA

institute: Procter and Gamble

description: batch_subjectID_gender_sampling site

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 microarray plates using the Affymetrix GeneTitan instrument

scan_protocol: ArrayPlates were scanned using the Affymetrix GeneTitan Instrument utilizing AGCC GeneTitan Instrument Control software version 4.2.0.1566

data_processing: The RMA algorithm was used as the processing protocol to normalize the data for subsequent analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: LCM-separated epidermis from human buttock

label_protocol: Biotinylated cRNA were prepared  using the Affymetrix HT 3’ IVT Express kit (Cat. #901253) on a Beckman Biomek FXp Laboratory Automation Workstation (Beckman Cat. #A31842).

extract_protocol: Total RNA from LCM samples was isolated utilizing the Pico Pure RNA Isolation Kit (Life Technologies, Grand Island, NY) according to manufacturer's recommendations

treatment_protocol: Punch biopsy samples were frozen in OCT media. Laser capture microdissection (LCM) was performed to isolate the epidermal compartments for gene expression profiling.

tag: tissue

value: LCM-separated epidermis

tag: collection time

tag: gender

value: female


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1376_223_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1403_105_F_AE

description: batch_subjectID_gender_sampling site

source_name: LCM-separated epidermis from human arm


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1376_242_F_BE

description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1376_262_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1376_210_F_BE

description: batch_subjectID_gender_sampling site


title: GSS1339_101_F_CE

description: batch_subjectID_gender_sampling site

source_name: LCM-separated epidermis from human cheek


title: GSS1376_272_F_BE

description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1339_262_F_CE

description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling time

source_name: LCM-separated epidermis from human forearm

value: male


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title: GSS0392_112 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_101 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_106 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_112 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_101 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_113 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_113 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_106 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_113 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_117 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_101 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_117 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_113 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_101 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_104 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_104 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_104 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_104 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_120 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_120 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_119 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_119 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_117 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_120 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_117 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_103 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_114 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_120 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_119 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_114 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_114 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_103 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_111 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_102 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_114 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_111 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_103 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_111 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_111 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_102 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_105 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_105 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_102 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_105 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_105 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_107 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_107 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_102 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_107 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_115 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_107 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_108 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_108 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_118 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_116 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_115 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_118 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_108 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_118 M_0

description: batch_subjectID_gender_sampling time


title: GSS0392_115 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_110 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_108 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_118 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_116 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1006 M_1200

description: batch_subjectID_gender_sampling time

source_name: LCM-separated dermis from human forearm

treatment_protocol: Punch biopsy samples were frozen in OCT media. Laser capture microdissection (LCM) was performed to isolate the dermal compartments for gene expression profiling.

value: LCM-separated dermis


title: GSS0392_110 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_110 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_116 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_116 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1006 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1006 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1008 M_1800

description: batch_subjectID_gender_sampling time


title: GSS0392_110 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1016 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1002 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1016 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1002 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1002 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1016 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1008 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1008 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1004 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1008 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1011 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1004 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1011 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1014 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1014 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1002 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1004 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1016 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1011 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1011 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1014 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1013 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1004 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1014 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1013 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1020 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1020 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1020 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1020 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1015 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1015 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1013 M_600

description: batch_subjectID_gender_sampling time


title: GSS0392_119 M_1200

description: batch_subjectID_gender_sampling time


title: GSS0392_103 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1019 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1019 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1019 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1018 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1018 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1018 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1019 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1012 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1012 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1012 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1017 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1013 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1018 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1017 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1015 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1006 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1012 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1017 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1017 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1010 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1010 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1005 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1010 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1005 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1005 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1003 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1010 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1003 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1003 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1005 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1003 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1009 M_600

description: batch_subjectID_gender_sampling time


title: GSS2207_1001 M_1200

description: batch_subjectID_gender_sampling time


title: GSS2207_1001 M_600

description: batch_subjectID_gender_sampling time


title: GSS1404_177_F_AD

description: batch_subjectID_gender_sampling site


title: GSS2207_1007 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1001 M_0

description: batch_subjectID_gender_sampling time


title: GSS2207_1007 M_1800

description: batch_subjectID_gender_sampling time


title: GSS2207_1009 M_1800

description: batch_subjectID_gender_sampling time


title: GSS1404_207_F_AD

description: batch_subjectID_gender_sampling site


title: GSS2207_1009 M_1200

description: batch_subjectID_gender_sampling time


title: GSS1404_196_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_295_F_AD

description: batch_subjectID_gender_sampling site


title: GSS2207_1007 M_1200

description: batch_subjectID_gender_sampling time


title: GSS1404_262_F_AD

description: batch_subjectID_gender_sampling site


title: GSS2207_1007 M_600

description: batch_subjectID_gender_sampling time


title: GSS1404_272_F_AD

description: batch_subjectID_gender_sampling site


title: GSS2207_1009 M_0

description: batch_subjectID_gender_sampling time


title: GSS1404_147_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_176_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_144_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_216_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_215_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_211_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_187_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_194_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_153_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_259_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_155_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_133_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_124_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_152_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_132_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_318_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_138_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_314_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_179_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_258_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_118_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_213_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_148_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_160_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_271_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_170_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_168_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_269_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_251_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_105_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_161_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_108_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_277_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_250_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_242_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_131_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_151_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_208_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_218_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_281_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_101_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_121_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_162_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_143_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_243_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_282_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_214_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_175_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_252_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_110_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_172_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_227_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_192_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_188_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_321_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_300_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_185_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_191_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_238_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_158_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_284_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_222_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_308_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_114_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_237_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_141_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_224_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_265_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_199_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_233_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_171_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_134_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_154_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_317_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_260_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_221_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_248_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_190_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_103_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_130_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_203_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_137_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_119_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_313_F_AD

description: batch_subjectID_gender_sampling site


title: GSS2207_1001 M_1800

description: batch_subjectID_gender_sampling time


title: GSS1404_166_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_210_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_228_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_129_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_200_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_136_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_112_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_173_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_113_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_167_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_289_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_183_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_184_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_142_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_231_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_290_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_169_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_125_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_206_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_117_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_198_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_223_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_219_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_286_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_107_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_212_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_310_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_311_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_123_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_115_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_109_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_186_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_273_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_230_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_174_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_111_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_255_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_288_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_106_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_220_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_302_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_157_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_128_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_140_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_195_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_294_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_274_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_268_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_307_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_320_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1377_190_F_BD

description: batch_subjectID_gender_sampling site

source_name: LCM-separated dermis from human buttock


title: GSS1404_226_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_159_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_116_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_139_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_201_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_150_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_189_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1377_158_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1404_122_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1404_181_F_AD

description: batch_subjectID_gender_sampling site


title: GSS1377_153_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_189_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_129_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_148_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_282_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_289_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_284_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_114_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_151_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_127_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_170_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_144_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_186_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_231_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_318_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_116_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_155_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_184_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_130_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_181_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_103_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_243_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_110_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_188_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_147_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_314_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_224_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_133_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_210_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_221_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_169_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_195_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_200_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_311_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_136_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_238_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_219_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_259_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_295_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_125_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_162_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_206_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_140_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_154_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_137_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_216_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_222_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_308_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_177_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_150_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_288_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_183_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_157_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_271_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_269_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_118_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_262_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_119_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_174_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_242_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_196_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_141_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_101_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_161_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_167_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_258_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_201_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_213_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_211_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_109_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_160_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_159_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_124_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_142_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_248_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_138_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_123_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_277_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_302_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_307_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_132_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_111_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_260_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_321_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_199_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_166_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_112_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_227_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_226_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_313_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_122_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_272_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_191_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_107_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_139_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_252_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_113_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_223_F_BD

description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1377_115_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_215_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_172_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_320_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_131_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_249_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_317_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_208_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_283_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_205_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_105_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_273_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_274_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_108_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_121_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_152_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_220_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_187_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_212_F_BD

description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1377_230_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_218_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1340_310_F_CD

description: batch_subjectID_gender_sampling site

source_name: LCM-separated dermis from human cheek


title: GSS1377_265_F_BD

description: batch_subjectID_gender_sampling site


title: GSS1377_251_F_BD

description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1340_259_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_117_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_121_F_CD

description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1340_281_F_CD

description: batch_subjectID_gender_sampling site


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description: batch_subjectID_gender_sampling site


title: GSS1340_135_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_139_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_219_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_228_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_113_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_274_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_224_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_288_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_233_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_271_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_176_F_CD

description: batch_subjectID_gender_sampling site


title: GSS1340_194_F_CD

description: batch_subjectID_gender_sampling site


title: activated CD19+ cells metLN pt2

type: SRA

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing: Adapter trim with cutadapt, align with StarAligner, counts with Htseqcount, differential expression between groups with DESeq2. Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v3.1

source_name: metastatic lymph node

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. RNA was extracted using qiagen all-prep kits. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

tag: individual

tag: disease state

value: HPV+ HNSCC

tag: treatment

value: previously untreated disease

value: metastatic lymph node


title: activated CD19+ cells TIL pt1

source_name: primary tumor

value: primary tumor


title: activated CD19+ cells Flu PBMC

source_name: PBMC

value: healthy individual

value: healthy

value: seasonal Influenza vaccine 7 days prior

tag: cell type

value: PBMC


title: activated CD19+ cells TIL pt2


title: activated CD19+ cells metLN pt3


title: activated CD19+ cells metLN pt1


title: activated CD19+ cells TIL pt3


title: Metastatic lymph node antibody secreting cells [HPV22LN_ASC]

data_processing:
Reads were aligned to the human genome with HiSAT2
Reads were assigned to genes and counted with FeatureCounts
Differential expression analysis was performed with DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text with counts for each gene (FeatureCounts output)

source_name: Antibody secreting cells

growth_protocol: Cells were isolated from peripheral blood, tumor, or metastatic lymph node and frozen. Cells were thawed and sorted into RLT buffer.

extract_protocol:
RNA was extracted with the Qiagen Allprep DNA/RNA micro kit
poly(A) selection

tag: subject status

value: HPV+ HNSCC patient

tag: patient

value: Metastatic lymph node

value: Antibody secreting cells


title: Tumor infiltrating GC B cells [HPV29TIL_ABCpos]

source_name: GC B cells (CD71+ CD10+)

value: Tumor

value: GC B cells (CD71+ CD10+)


title: Tumor infiltrating GC B cells [HPV40TIL_ABCpos]


title: Metastatic lymph node GC B cells [HPV22LN_ABCpos]


title: Tumor infiltrating antibody secreting cells [HPV29TIL_ASC]


title: Metastatic lymph node naive B cells [HPV22LN_naive]

source_name: Naive B cells

value: Naive B cells


title: Tumor infiltrating activated B cells [HPV29TIL_ABCneg]

source_name: Activated B cells (CD71+CD10-)

value: Activated B cells (CD71+CD10-)


title: Metastatic lymph node antibody secreting cells [HPV4LN_ASC]


title: Tumor infiltrating antibody secreting cells [HPV40TIL_ASC]


title: Metastatic lymph node activated B cells [HPV4LN_ABCneg]


title: Metastatic lymph node GC B cells [HPV4LN_ABCpos]


title: Metastatic lymph node activated B cells [HPV22LN_ABCneg]


title: PBMC activated B cells (7 days post flu-vaccine) [EVC379_ABC]

source_name: Activated B cells (CD71+)

value: Influenza PBMC

value: Activated B cells (CD71+)


title: PBMC antibody secreting cells (7 days post flu-vaccine) [EVC379_ASC]


title: Food, rep4

city: Chicago

first: Wanhao

last: Chi

state: IL

address: 947 E. 58th Street

department: Neurobiology

institute: University of Chicago

data_processing:
Illumina software bcl2fastq was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, examined for sequencing quality using fastqc (v 0.11.5), and then mapped to dmel (r6.22) whole genome using STAR (2.6.1b) with parameters --sjdbOverhang 99 --twopassMode Basic
Each bam files was processed using Aspli to obtain differentially expressed genes
Two sequencing bam files from the sample sample were merged using samtools
Alternative splice varients were analyzed using Leafcutter
Genome_build: dmel (r6.22)
Supplementary_files_format_and_content: a tab-delimited text file that includes gene counts from ASpli
Supplementary_files_format_and_content: gene_counts.txt: outputs from ASpli
Supplementary_files_format_and_content: alternative_splicing.Rdata: outputs from Leafcutter

organism: Drosophila melanogaster

source_name: adult head

extract_protocol:
Total RNA was extracted from fly heads using RNA extraction kits (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: head

tag: developmental stage

value: adult

tag: Sex

value: male


title: Starvaton, rep1


title: Starvaton, rep2


title: Starvaton, rep3


title: Food, rep3


title: Food, rep2


title: Tumor infiltrating activated B cells [HPV40TIL_ABCneg]


title: Food, rep1


title: KO (BAT) rep1

city: Wuhan

first: Chengyu

last: Liu

address: No.13, Hangkong Road

country: China

institute: Huazhong University of Science and Technology

description: BAT KO.xls

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference  genome  and  gene  model  annotation  files  were  downloaded  from  genome website  directly.  Index  of  the  reference  genome  was  built  using  Bowtie  v2.2.3  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
Quantification of gene expression level: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.  FPKM,  expected  number  of  Fragments  Per  Kilobase  of  transcript  sequence  per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis:  Differential  expression  analysis  of  two conditions/groups (two biological replicates per condition) was performed using the DESeq R  package  (1.18.0).  DESeq  provide statistical  routines  for  determining  differential expression in digital gene expression data using a model based on the negative binomial distribution.  The  resulting  P-values  were  adjusted  using  the Benjamini  and  Hochberg’s approach  for  controlling  the  false  discovery  rate. Genes  with  an  adjusted  P-value  <0.05 found by DESeq were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes: Gene  Ontology  (GO)  enrichment  analysis  of  differentially  expressed  genes  was implemented by the GOseq R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG  is  a  database  resource  for  understanding  high-level  functions  and  utilities  of  the biological system, such as the cell, the organism and the ecosystem, from molecular-level information,  especially  large-scale  molecular  datasets  generated  by  genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways.
PPI analysis of differentially expressed genes: PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions. For the species existing in the database, we  construct  the  networks  by  extract  the  target  gene  list  from  the  database;  Otherwise, Blastx  (v2.2.28)  was  used  to  align  the  target  gene  sequences  to  the  selected  reference protein sequences, and then the networks was built according to the known interaction of selected reference species.
Genome_build: Mus_musculus, GRCm38, ensembl 79
Supplementary_files_format_and_content: Changed mRNA between two group samples including WT and Mecp2 Adi KO

organism: Mus musculus

source_name: brown adipose tissue

growth_protocol: Mice were maintained in a specific-pathogen-free, temperature controlled (22 ± 1°C) animal facility with a 12-hr light/dark cycle, and free access to water/food.

extract_protocol:
Total RNA from inguinal white adipose tissue or brown adipose tissue of each mouse was extracted individually using RNAiso Plus (Takara Biotechnology, Dalian, China). An equal amount of RNA (n = 6) from the same group was combined into 2 samples/group for RNA sequencing. RNA-Sequencing was performed by Novogene (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: brown adipose tissue

tag: age

tag: genotype

value: Mecp2 Adi KO


title: WT (BAT) rep2

description: BAT WT.xls

value: floxed


title: WT (BAT) rep1

description: BAT WT.xls


title: KO (BAT) rep2

description: BAT KO.xls


title: WT (iWAT) rep1

description: iWAT WT.xls

source_name: inguinal adipose tissue

value: inguinal adipose tissue


title: Starvaton, rep4


title: GN_NTB_5 [GN-7_S22]

city: South San Francisco

first: Joshua

last: Lichtman

state: CA

address: 333 Oyster Point Boulevard

department: Translational Science

institute: NGM Biopharmaceuticals

description: processed data file: allSamples_WAT_GN_Genes_ReadCounts.txt

data_processing:
For brown adipose QuantSeq data, the unique molecular identifiers (UMI) were trimmed from the start of the reads using umi2index tools (Lexogen).
Both brown adipose (QuantSeq), white adipose (bulk RNA-seq), and gastrocnemius muscle  (bulk RNA-seq) data raw reads were filtered using Trim Galore! to remove low quality and adaptor bases. Reads shorter than 20nt were discarded.
Filtered reads were mapped to UCSC mm9 genome sequences using STAR (v2.6.0a). The mapped reads of QuantSeq data were collapsed to UMI reads using collapse_UMI_bam tool (Lexogen).
At last, counts of all samples were generated using featureCounts (v1.6.2), and edgeR (v3.22.3) was used to get normalized counts and perform differential gene expression analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression raw read counts in tabular data format (txt)

source_name: non-tumor brearing control_Gastrocnemius Muscle

extract_protocol:
Gastrocnemius muscle (GN), white and brown adipose were flash frozen prior to RNA isolation.  RNA was prepared using the Qiagen RNAeasy kit with on column DNAse treatment.
Brown adipose RNA was prepared for sequencing using the UMI second strand synthesis module for QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and sequenced on an Illumina NovaSeq 6000 (100bp single-end reads and 5-10 million reads were generated for each sample). White adipose and gastrocnemius muscle RNA were prepared for sequencing using the TailorMix Directional RNA Sample Preparation Kit (SeqMatic) and sequenced on an Illumina NovaSeq 6000 (100bp single-end reads and 30-50 million reads were generated for each sample).

treatment_protocol: Tissues from non-tumor bearing (NTB) and HT1080 tumor bearing animals treated with IgG1 or 3P10 (3mg/kg, weekly starting Day 0) were harvested 21 days post inoculation.

tag: strain background

tag: mouse group

value: non-tumor bearing

value: non-tumor brearing control

value: Gastrocnemius Muscle


title: GN_NTB_3 [GN-16_S30]


title: GN_NTB_4 [GN-4_S20]


title: Basophil-depleted ILC2s

city: Newark

first: Juan

middle: C.

last: Inclan Rico

state: New Jersey

address: 205 South Orange Avenue, Rutgers Cancer Institute of New Jersey at University Hospital

department: Medicine/CII

institute: Rutgers New Jersey Medical School

description: BILCs

data_processing:
Demultiplexing with cellranger v3.1.0 mkfastq, bcl2fastq v2.20.0.422
Barcode and UMI deconvolution, mapping with cellranger v3.1.0 count
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files (HDF5) for cellranger of deconvoluted gene expression matrix

source_name: Lung-resident sort-purified ILC2s

growth_protocol: Wildtype or basophil-depleted mice were infected with the hookworm Nippostrongylus brasiliensis 5 days prior sort-purification

extract_protocol:
NA
10X 3' gene expression
Single cell RNA-seq

treatment_protocol: 10,000 lung-resident ILC2s from control and basophil-depleted mice were sort-purified on live CD45+CD3-CD19-CD11b-CD11c-NK1.1-B220-CD5-Ter-119-gdTCR-FceR1–CD90+CD127+ cells from six biological replicates and pooled into two samples per group. Purity for all cell populations were determined to be 98% or greater.

tag: condition

value: Basophil-depleted

tag: infection

value: hookworm Nippostrongylus brasiliensis

value: Lung-resident ILC2s


title: GN_3P10_5 [GN-9_S24]

source_name: Ht1080 tumor model_3P10 antibody treatment_Gastrocnemius Muscle

value: Ht1080 tumor model

value: 3P10 antibody treatment

tag: tissue


title: GN_NTB_2 [GN-10_S25]


title: KO (iWAT) rep2

description: iWAT KO.xls


title: wildtype ILC2s

description: WILCs

value: control


title: GN_3P10_1 [GN-12_S27]


title: GN_3P10_3 [GN-3_S19]


title: GN_3P10_2 [GN-15_S29]


title: GN_IgG1_4 [GN-23_S31]

source_name: Ht1080 tumor model_IgG1 antibody treatment_Gastrocnemius Muscle

value: IgG1 antibody treatment


title: GN_IgG1_5 [GN-8_S23]


title: GN_IgG1_3 [GN-2_S18]


title: GN_IgG1_2 [GN-14_S28]


title: WAT_NTB_5 [WAT-7_S7]

source_name: non-tumor brearing control_WAT

value: White Adipose Tissue


title: GN_IgG1_1 [GN-11_S26]


title: KO (iWAT) rep1

description: iWAT KO.xls


title: WAT_NTB_4 [WAT-4_S5]


title: WT (iWAT) rep2

description: iWAT WT.xls


title: GN_NTB_1 [GN-1_S17]


title: WAT_NTB_3 [WAT-16_S15]


title: GN_3P10_4 [GN-6_S21]


title: WAT_NTB_2 [WAT-10_S10]


title: WAT_NTB_1 [WAT-1_S2]


title: WAT_3P10_4 [WAT-6_S6]

source_name: Ht1080 tumor model_3P10 antibody treatment_WAT


title: WAT_3P10_1 [WAT-12_S12]


title: WAT_IgG1_5 [WAT-8_S8]

source_name: Ht1080 tumor model_IgG1 antibody treatment_WAT


title: WAT_3P10_3 [WAT-3_S4]


title: WAT_IgG1_2 [WAT-14_S13]


title: WAT_IgG1_3 [WAT-2_S3]


title: WAT_IgG1_4 [WAT-23_S112]


title: WAT_3P10_2 [WAT-15_S14]


title: BAT_NTB_5 [bat5_S23_L007]

description: processed data file: allSamples_BAT_Genes_ReadCounts.txt

source_name: non-tumor brearing control_BAT

value: Brown Adipose Tissue


title: BAT_3P10_6 [bat18_S35_L007]

source_name: Ht1080 tumor model_3P10 antibody treatment_BAT


title: WAT_IgG1_1 [WAT-11_S11]


title: BAT_NTB_4 [bat4_S22_L007]


title: BAT_3P10_4 [bat16_S33_L007]


title: BAT_NTB_1 [bat1_S19_L007]


title: BAT_NTB_2 [bat2_S20_L007]


title: BAT_3P10_3 [bat15_S32_L007]


title: BAT_3P10_2 [bat14_S31_L007]


title: WAT_3P10_5 [WAT-9_S9]


title: BAT_3P10_1 [bat13_S30_L007]


title: BAT_IgG1_5 [bat11_S29_L007]

source_name: Ht1080 tumor model_IgG1 antibody treatment_BAT


title: BAT_IgG1_3 [bat9_S27_L007]


title: BAT_IgG1_4 [bat10_S28_L007]


title: BAT_IgG1_1 [bat7_S25_L007]


title: BAT_NTB_3 [bat3_S21_L007]


title: Surface_PBS_R1

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline (version3.0). Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using cavefish genome astMex1, ensembl 87 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Genome_build: astMex1
Supplementary_files_format_and_content: cellranger output raw count matrix in hdf5 format

organism: Astyanax mexicanus

source_name: headkidney single cells

extract_protocol:
Single cell suspension from freshly dissected headkidney tissue from cave and surface morphotypes of A. mexicanus were produced by forcing tissue through 40 µM cell strainer into L-15 media (Sigma), containing 10 % water and 5 mM HEPES buffer (pH 7.2) and 20 U/mL heparin (L-90). The strainer was washed once with L-90 and cells were washed once by spinning cells at 500 x g at 4 ºC for 5 mins. Supernatant was discarded and cells were resuspended in 1 mL of L-90 media (L-15 containing 10 % water, 5 mM HEPES (7.2 pH), 5 % fetal calf serum, 4 mM L-glutamin, Penicillin-Streptomycin mix with 10000 U/mL each). Mature Erythrocytes were reduced via flowcytometric sorting (Influx System) of hematopoietic tissue based on scatter characteristics. Sorted cells were washed once in L-90 media  and run again on Influx system to ensure removal of mature erythrocyte cluster and measure cell viability (percentage live cells after sorting: surface fish 82.2 % and cavefish 88.9 %).
Single Cell 3' Reagent kits v2 User Guide Rev D (10X Genomics)

tag: morphotype

value: Surfacefish

value: PBS

value: headkidney

value: Adult


title: Surface_PBS_R2


title: BAT_NTB_6 [bat6_S24_L007]


title: Surface_LPS_R1

value: LPS


title: Pachon_PBS_R1

value: Pachon Cavefish


title: Pachon_LPS_R2


title: BAT_3P10_5 [bat17_S34_L007]


title: Shannon.HMU

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

library_source: genomic

data_processing:
Library strategy: WGS
All gibbon genomic shot-gun data were aligned to the gibbon genome reference (Nleu3.0) using BWA
MELT v2.1.3 was used to predict de novo LAVA insertions and deletions (indels) from each of the 23 whole genome shot-gun alignments
We characterized all LAVA inserts based on information such as genomic location, length, and insertion position relative to closest gene [intergenic, exonic, intronic, promoter (<3Kb upstream of gene) or terminator (<3Kb downstream of gene)]
The initial set of LAVA predictions was next filtered to remove: 1) low quality inserts, as assessed by MELT, 2) single copy inserts in the population, 3) inserts shorter than 290bp (the minimum length required to discriminate a composite LAVA from its non-SVA subunits), and 4) inserts found on unplaced Nleu3.0 contigs.
We generated binary LAVA genotype profiles for all gibbon individuals (heterozygous or homozygous LAVA insertion=1, homozygous absence of LAVA= 0)
Genome_build: Nleu3.0
Supplementary_files_format_and_content: an excel spreadsheet containing position, genomic and genotype information for all LAVA insertions across 23 gibbons

molecule: genomic DNA

organism: Hylobates muelleri

source_name: blood

extract_protocol:
Total gDNA was extracted from blood of gibbons and randomly sheared
sheared gDNA was used to generate illumina libraries using the NEBNext Ultra II library contruction kit (NEB)

value: blood


title: Victor.NGA

organism: Nomascus gabriellae


title: BAT_IgG1_2 [bat8_S26_L007]


title: non-CAD3

city: Dongguan

first: weipeng

last: Wu

state: Guangdong

address: Xin Cheng Avenue 1#, Songshan Lake

institute: Guangdong Medical University

data_processing:
illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38/hg38 using HISAT2 with parameters HWI-ST1276 71 C1162ACXX  1 1101 1208 2458 1 N CGATGT
Transcripts Per Million (TPM) were calculated using a protocol from Zhou et al.,  PLoS One, 2010.
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was harvested from the plasma of  CAD patients and non-CAD controls using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: non-CAD control

value: Plasma

value: none; untreated

tag: molecule subtype

value: ribosomal RNA-depleted total RNA


title: non-CAD2


title: non-CAD1


title: CAD3

value: coronary artery disease (CAD)


title: Surface_LPS_R2


title: Pachon_PBS_R2


title: Pachon_LPS_R1


title: CAD2


title: CAD1


title: small RNA-Seq MIR21 KO_rep2

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

description: MIR21 KO_rep2

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 16
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.3.2) with parameters  -p 6 -N 1
aligned reads were sorted using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 1-T 6  -t miRNA -g ID and miRBase annotations (v21)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including CPM, log2 fold change and false discovery rate values for each sample

source_name: lung cancer derived cell line

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Small RNA-seq libraries and sequencing was performed by Novogene (Hong Kong)

treatment_protocol: 48 hours upon seeding cells were harvested for RNA extraction.

tag: cell line

tag: genomic knockout

value: MIR21 knockout

tag: passages

value: harvested 48h upon seeding


title: small RNA-Seq Ctrl_rep3

value: Control


title: small RNA-Seq MIR21 KO_rep1

description: MIR21 KO_rep1


title: small RNA-Seq Ctrl_rep2


title: small RNA-Seq Ctrl_rep1


title: MIR21 KO_rep3

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Poly-A RNA was enriched using oligo(dT) beads. RNAs are fragmented randomly by adding fragmentation buffer. cDNA is synthesized by using random hexamers primer followed by second stramd synthesis. Strand-specific double-stranded cDNA libraries are completed by size selection (250-300bp) and PCR enrichment. Completed libraries are sequenced on an Illumina HiSeq platform by Novogene (Hong Kong).


title: MIR21 KO_rep2


title: small RNA-Seq MIR21 KO_rep3

description: MIR21 KO_rep3


title: MIR21 KO_rep1


title: Ctrl_rep3


title: Ctrl_rep2


title: Ctrl_rep1


title: HV65_CD19 [H36]

city: Amsterdam

first: Brendon

middle: P.

last: Scicluna

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC Locatie AMC

description:
CD19_20161336
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt

data_processing:
Sequence read quality was assessed by means of the FastQC methods and Trimmomatic was used to trim the Illumina adapters containing, poor-quality bases and ambiguous nucleotide-containing sequences.
Reads were used to align against the Genome Reference Consortium Human Genome Build 38 patch release 7 (GRCh38.p7)  (GRCh38.p7) using TopHat 2(vrsion 2.1.1), Count data were generated by means of the featureCounts method.
Sequence reads were analyzed by Mapsplice2. circRNA was called if it was supported by at least four back-spliced reads in at least two different samples.
Genome_build: Genome Reference Consortium Human Genome Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: tab-delimited text files including DESeq2 normalized values for each cell type.

extract_protocol:
Total RNA was isolated from each cell-type by means of the miRNeasy RNA isolation kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions. RNA quality was assessed by bioanalysis (Agilent), with all samples having RNA integrity numbers (RINs) > 7. Total RNA concentrations were determined by Qubit® 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA).
Sequencing libraries were prepared by means of the Ovation® RNA-Seq System V2 (NuGEN) kit as per manufacturer’s instructions

tag: subject status

value: Healthy

tag: gender

value: female

tag: cell type


title: HV62_CD19 [H35]

description:
CD19_20161335
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt

value: male


title: HV55_CD19 [H34]

description:
CD19_20161334
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt


title: HV81_CD19 [H33]

description:
CD19_20161333
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt


title: 3938_CD19 [S32]

description:
CD19_20161332
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt

value: Patient


title: 3919_CD19 [S31]

description:
CD19_20161331
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt


title: 4028_CD19 [S29]

description:
CD19_20161329
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt


title: 6641_CD19 [S28]

description:
CD19_20161328
processed data file:
CD19-circRNA-normalized.txt
CD19-linear-normalized.txt