title: 4252459024_R02C01

status: Public on Sep 30 2018

type: genomic

city: Hefei

first: Xuelei

last: Zhang

state: China

address: Science and teaching building, Meishan Road 81, Hefei230032, Anhui Province, China

department: Dermatology

country: China

institute: Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).

hyb_protocol: The whole genome genotyping was conducted at Chinese National Human Genome Center at Shanghai, China. Approximately 200ng of genomic DNA was used for genotyping analysis. Briefly, each sample was whole-genome amplified, fragmented, precipitated and resuspended in appropriate hybridization buffer.

scan_protocol: After hybridization, the BeadChip oligonucleotides were extended by a single labeled base,which was detected by fluorescence imaging with an Illumina Bead Array Reader.

label: not provided

molecule: genomic DNA

organism: Homo sapiens

source_name: Public control

label_protocol: not provided

extract_protocol: Genomic DNA was extracted from peripheral blood lymphocytes by standard procedures (Miller et al, 1988) using Flexi Gene DNA kits (QIAGEN, Germany)

tag: gender

value: Unknown

tag: tissue

value: Whole blood

tag: disease state

value: healthy control


title: 4252459023_R01C02

data_processing: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: 4252459002_R01C02


title: 4252459024_R01C01


title: 4252459024_R01C02


title: 4252459052_R02C02


title: 4252459002_R02C02


title: 4252459052_R01C01


title: 4252459002_R01C01


title: 4252459052_R02C01


title: 4252459023_R01C01


title: 4252459023_R02C02


title: 4252459054_R02C01


title: 4252459002_R02C01


title: 4252459054_R01C02


title: 4252459054_R01C01


title: 4252459024_R02C02


title: 4252459023_R02C01


title: 4252459052_R01C02


title: 4252459054_R02C02


title: 4252459055_R01C01


title: 4252459055_R01C02


title: 4252459055_R02C01


title: 4252459056_R01C02


title: 4252459056_R01C01


title: 4252459055_R02C02


title: 4252459056_R02C01


title: 4252459056_R02C02


title: 4252459057_R01C01


title: 4252459058_R01C01


title: 4252459058_R02C02


title: 4252459057_R02C01


title: 4252459058_R01C02


title: 4252459057_R01C02


title: 4252459057_R02C02


title: 4252459058_R02C01


title: 4252459059_R02C01


title: 4252459060_R02C01


title: 4252459060_R01C02


title: 4252459059_R02C02


title: 4252459059_R01C02


title: 4252459060_R01C01


title: 4252459059_R01C01


title: 4252459060_R02C02


title: 4252459067_R01C01


title: 4252459067_R01C02


title: 4252459067_R02C02


title: 4252459073_R02C01


title: 4252459073_R01C02


title: 4252459073_R01C01


title: 4252459067_R02C01


title: 4252459073_R02C02


title: 4252459075_R02C01


title: 4252459075_R02C02


title: 4252459075_R01C02


title: 4252459075_R01C01


title: 4252459079_R02C02


title: 4252459079_R01C01


title: 4252459080_R01C02


title: 4252459080_R01C01


title: 4252459080_R02C01


title: 4252459079_R02C01


title: 4252459080_R02C02


title: 4252459079_R01C02


title: 4252459081_R01C01


title: 4252459104_R01C01


title: 4252459100_R01C01


title: 4252459100_R02C02


title: 4252459100_R02C01


title: 4252459081_R02C02


title: 4252459081_R01C02


title: 4252459104_R01C02


title: 4252459100_R01C02


title: 4252459104_R02C01


title: 4252459081_R02C01


title: 4252459104_R02C02


title: 4252459106_R01C01


title: 4252459106_R01C02


title: 4252459106_R02C01


title: 4252459106_R02C02


title: 4252459107_R01C01


title: 4252459107_R02C01


title: 4252459107_R01C02


title: 4252459111_R01C02


title: 4252459114_R01C02


title: 4252459111_R02C02


title: 4252459114_R01C01


title: 4252459111_R02C01


title: 4252459107_R02C02


title: 4252459114_R02C01


title: 4252459111_R01C01


title: 4252459114_R02C02


title: 4252459116_R01C01


title: 4252459115_R01C02


title: 4252459115_R02C01


title: 4252459115_R01C01


title: 4252459116_R01C02


title: 4252459115_R02C02


title: 4252459116_R02C02


title: 4252459116_R02C01


title: 4252459117_R01C01


title: 4252459117_R01C02


title: 4252459117_R02C01


title: 4252459122_R01C01


title: 4252459117_R02C02


title: 4252459122_R01C02


title: 4252459128_R01C01


title: 4252459122_R02C02


title: 4252459128_R01C02


title: 4252459122_R02C01


title: 4252459131_R02C02


title: 4252459131_R01C02


title: 4252459132_R01C01


title: 4252459128_R02C01


title: 4252459131_R01C01


title: 4252459132_R02C01


title: 4252459131_R02C01


title: 4252459128_R02C02


title: 4252459132_R01C02


title: 4252459133_R01C01


title: 4252459133_R02C01


title: 4252459133_R01C02


title: 4252459132_R02C02


title: 4252459135_R01C01


title: 4252459133_R02C02


title: 4252459135_R02C01


title: 4252459135_R02C02


title: 4252459146_R01C01


title: 4252459135_R01C02


title: 4252459146_R01C02


title: 4252459146_R02C01


title: 4252459146_R02C02


title: 4252459152_R01C01


title: 4252459152_R01C02


title: 4252459152_R02C01


title: 4252459152_R02C02


title: 4252459155_R01C01


title: 4252459155_R01C02


title: 4252459160_R02C02


title: 4252459160_R01C02


title: 4252459160_R02C01


title: 4252459160_R01C01


title: 4252459155_R02C02


title: 4252459161_R01C02


title: 4252459161_R02C01


title: 4252459161_R01C01


title: 4252459155_R02C01


title: 4252459161_R02C02


title: 4252459162_R01C02


title: 4252459162_R01C01


title: 4252459162_R02C01


title: 4252459169_R01C01


title: 4252459169_R01C02


title: 4252459165_R01C01


title: 4252459165_R02C01


title: 4252459162_R02C02


title: 4252459165_R02C02


title: 4252459169_R02C01


title: 4252459169_R02C02


title: 4252459165_R01C02


title: 4252459170_R01C01


title: 4252459170_R01C02


title: 4252459170_R02C02


title: 4252459170_R02C01


title: 4252459178_R01C02


title: 4252459178_R01C01


title: 4252459171_R02C01


title: 4252459171_R01C01


title: 4252459172_R02C02


title: 4252459172_R02C01


title: 4252459171_R02C02


title: 4252459172_R01C02


title: 4252459172_R01C01


title: 4252459178_R02C02


title: 4252459183_R01C01


title: 4252459171_R01C02


title: 4252459183_R01C02


title: 4252459184_R01C02


title: 4252459185_R01C01


title: 4252459183_R02C02


title: 4252459184_R02C01


title: 4252459184_R02C02


title: 4252459183_R02C01


title: 4252459178_R02C01


title: 4252459185_R02C01


title: 4252459184_R01C01


title: 4252459185_R02C02


title: 4252459185_R01C02


title: 4252459186_R01C01


title: 4252459186_R01C02


title: 4252459186_R02C01


title: 4252459188_R01C01


title: 4252459186_R02C02


title: 4252459189_R01C02


title: 4252459189_R02C02


title: 4252459188_R01C02


title: 4252459189_R01C01


title: 4252459188_R02C02


title: 4252459188_R02C01


title: 4252459189_R02C01


title: 4252459191_R01C01


title: 4252459191_R02C01


title: 4252459191_R02C02


title: 4252459191_R01C02


title: 4252459192_R01C02


title: 4252459194_R01C01


title: 4252459195_R01C01


title: 4252459199_R01C02


title: 4252459192_R01C01


title: 4252459192_R02C02


title: 4252459195_R01C02


title: 4252459195_R02C01


title: 4252459192_R02C01


title: 4252459199_R01C01


title: 4252459195_R02C02


title: 4252459194_R02C01


title: 4252459199_R02C01


title: 4252459194_R01C02


title: 4252459194_R02C02


title: 4252459207_R02C01


title: 4252459207_R02C02


title: 4252459199_R02C02


title: 4252459211_R02C01


title: 4252459207_R01C01


title: 4252459211_R01C01


title: 4252459207_R01C02


title: 4252459211_R01C02


title: 4252459211_R02C02


title: 4252459215_R02C01


title: 4252459215_R01C02


title: 4252459215_R01C01


title: 4252459215_R02C02


title: 4252459224_R02C02


title: 4252459224_R02C01


title: 4252459229_R01C01


title: 4252459229_R01C02


title: 4252459217_R01C01


title: 4252459219_R01C01


title: 4252459219_R02C01


title: 4252459217_R01C02


title: 4252459218_R01C01


title: 4252459217_R02C01


title: 4252459216_R01C01


title: 4252459219_R02C02


title: 4252459219_R01C02


title: 4252459217_R02C02


title: 4252459224_R01C02


title: 4252459218_R02C01


title: 4252459229_R02C01


title: 4252459216_R01C02


title: 4252459218_R02C02


title: 4252459224_R01C01


title: 4252459216_R02C01


title: 4252459216_R02C02


title: 4252459218_R01C02


title: 4252459229_R02C02


title: 4252459234_R01C01


title: 4252459234_R01C02


title: 4252459234_R02C01


title: 4252459238_R01C01


title: 4252459239_R01C02


title: 4252459240_R01C01


title: 4252459239_R02C02


title: 4252459239_R01C01


title: 4252459257_R02C01


title: 4252459257_R01C01


title: 4252459265_R02C02


title: 4252459246_R02C02


title: 4252459272_R01C01


title: 4252459272_R01C02


title: 4252459234_R02C02


title: 4252459265_R02C01


title: 4252459238_R02C01


title: 4252459238_R01C02


title: 4252459272_R02C02


title: 4252459238_R02C02


title: 4252459240_R02C02


title: 4252459257_R01C02


title: 4252459240_R01C02


title: 4252459265_R01C02


title: 4252459240_R02C01


title: 4252459246_R02C01


title: 4252459246_R01C01


title: 4252459246_R01C02


title: 4252459273_R02C02


title: 4252459257_R02C02


title: 4252459273_R02C01


title: 4252459239_R02C01


title: 4252459265_R01C01


title: 4252459276_R01C01


title: 4252459276_R01C02


title: 4252459275_R02C02


title: 4252459275_R02C01


title: 4252459272_R02C01


title: 4252459276_R02C01


title: 4252459276_R02C02


title: 4252459283_R01C02


title: 4252459283_R01C01


title: 4252459273_R01C02


title: 4252459273_R01C01


title: 4252459275_R01C01


title: 4252459357_R01C01


title: 4252459348_R02C02


title: 4252459357_R02C01


title: 4252459357_R01C02


title: 4252459357_R02C02


title: 4252459283_R02C01


title: 4252459359_R02C02


title: 4252459359_R01C02


title: 4252459283_R02C02


title: 4252459359_R02C01


title: 4252459362_R02C02


title: 4252459362_R01C02


title: 4252459362_R01C01


title: 4252459275_R01C02


title: 4252459366_R01C01


title: 4252459366_R02C01


title: 4252459389_R01C01


title: 4252459389_R01C02


title: 4252459389_R02C01


title: 4252459389_R02C02


title: 4252459391_R01C01


title: 4252459391_R02C02


title: 4252459489_R01C01


title: 4252459391_R02C01


title: 4252459362_R02C01


title: 4252459391_R01C02


title: 4252459489_R01C02


title: 4252459359_R01C01


title: 4252459366_R02C02


title: 4252459851_R02C01


title: 4252459739_R01C01


title: 4252459489_R02C01


title: 4252459739_R02C02


title: 4252459851_R01C01


title: 4252459739_R02C01


title: 4252459489_R02C02


title: 4252459739_R01C02


title: 4252459851_R01C02


title: 4252459366_R01C02


title: 4254948034_R01C01


title: 4252459854_R02C02


title: 4252459854_R01C01


title: 4252459854_R01C02


title: 4254948034_R02C01


title: 4252459851_R02C02


title: 4254948034_R02C02


title: 4252459854_R02C01


title: 4254948134_R01C01


title: 4254948134_R01C02


title: 4254948134_R02C02


title: 4254948134_R02C01


title: 4254948034_R01C02


title: 4254948144_R01C02


title: 4254948144_R01C01


title: 4254948191_R01C02


title: 4254948171_R01C01


title: 4254948171_R01C02


title: 4254948191_R02C02


title: 4254948191_R02C01


title: 4254948191_R01C01


title: 4254948280_R01C02


title: 4254948171_R02C01


title: 4254948171_R02C02


title: 4254948282_R02C02


title: 4254948281_R02C02


title: 4254948281_R01C02


title: 4254948282_R01C02


title: 4254948281_R01C01


title: 4254948282_R02C01


title: 4254948292_R01C01


title: 4254948292_R01C02


title: 4254948280_R02C02


title: 4254948280_R02C01


title: 4254948144_R02C02


title: 4254948292_R02C02


title: 4254948281_R02C01


title: 4254948307_R01C01


title: 4254948144_R02C01


title: 4254948292_R02C01


title: 4254948282_R01C01


title: 4254948307_R01C02


title: 4254948307_R02C02


title: 4254948307_R02C01


title: 4254948308_R01C02


title: 4254948308_R01C01


title: 4254948313_R01C01


title: 4254948314_R01C02


title: 4254948313_R02C02


title: 4254948308_R02C01


title: 4254948313_R02C01


title: 4254948314_R01C01


title: 4254948313_R01C02


title: 4254948319_R01C01


title: 4254948314_R02C01


title: 4254948314_R02C02


title: 4254948308_R02C02


title: 4254948319_R01C02


title: 4254948330_R02C01


title: 4254948319_R02C01


title: 4254948332_R01C02


title: 4254948330_R02C02


title: 4254948330_R01C02


title: 4254948332_R02C01


title: 4254948330_R01C01


title: 4254948332_R02C02


title: 4254948332_R01C01


title: 4254948333_R01C01


title: 4254948333_R01C02


title: 4254948333_R02C02


title: 4254948337_R01C01


title: 4254948333_R02C01


title: 4254948337_R01C02


title: 4254948337_R02C01


title: 4254948341_R01C02


title: 4254948337_R02C02


title: 4254948341_R01C01


title: 4254948341_R02C02


title: 4254948342_R01C01


title: 4254948342_R02C02


title: 4254948342_R01C02


title: 4254948346_R02C02


title: 4254948346_R01C01


title: 4254948348_R01C01


title: 4254948342_R02C01


title: 4254948346_R01C02


title: 4254948341_R02C01


title: 4254948348_R01C02


title: 4254948348_R02C02


title: 4254948348_R02C01


title: 4254948319_R02C02


title: 4254948349_R01C02


title: 4254948349_R02C02


title: 4254948349_R02C01


title: 4254948354_R01C02


title: 4254948354_R01C01


title: 4254948355_R01C01


title: 4254948354_R02C01


title: 4254948355_R01C02


title: 4254948354_R02C02


title: 4254948355_R02C01


title: 4254948355_R02C02


title: 4254948356_R01C01


title: 4254948349_R01C01


title: 4254948356_R02C02


title: 4254948356_R02C01


title: 4254948346_R02C01


title: 4254948367_R01C02


title: 4254948363_R02C01


title: 4254948367_R01C01


title: 4254948367_R02C02


title: 4254948363_R01C01


title: 4254948368_R02C02


title: 4254948368_R01C01


title: 4254948367_R02C01


title: 4254948363_R02C02


title: 4254948369_R01C01


title: 4254948369_R01C02


title: 4254948369_R02C01


title: 4254948368_R02C01


title: 4254948369_R02C02


title: 4254948370_R01C01


title: 4254948370_R02C01


title: 4254948370_R02C02


title: 4254948370_R01C02


title: 4254948371_R01C01


title: 4254948371_R02C01


title: 4254948363_R01C02


title: 4254948356_R01C02


title: 4254948376_R01C01


title: 4254948376_R01C02


title: 4254948371_R02C02


title: 4254948376_R02C02


title: 4254948376_R02C01


title: 4254948377_R02C01


title: 4254948377_R01C02


title: 4254948378_R01C02


title: 4254948378_R02C01


title: 4254948378_R01C01


title: 4254948377_R02C02


title: 4254948378_R02C02


title: 4254948381_R01C02


title: 4254948381_R02C02


title: 4254948381_R02C01


title: 4254948382_R02C01


title: 4254948382_R01C01


title: 4254948381_R01C01


title: 4254948382_R02C02


title: 4254948382_R01C02


title: 4254948383_R01C01


title: 4254948383_R01C02


title: 4254948384_R01C02


title: 4254948384_R01C01


title: 4254948383_R02C01


title: 4254948384_R02C01


title: 4254948383_R02C02


title: 4254948368_R01C02


title: 4254948371_R01C02


title: 4254948385_R01C01


title: 4254948384_R02C02


title: 4254948385_R02C01


title: 4254948385_R02C02


title: 4254948386_R02C01


title: 4254948388_R02C01


title: 4254948389_R01C01


title: 4254948392_R01C01


title: 4254948386_R01C02


title: 4254948388_R01C01


title: 4254948392_R01C02


title: 4254948388_R02C02


title: 4254948389_R01C02


title: 4254948392_R02C01


title: 4254948392_R02C02


title: 4254948389_R02C02


title: 4254948393_R01C01


title: 4254948393_R02C02


title: 4254948393_R02C01


title: 4254948377_R01C01


title: 4254948386_R02C02


title: 4254948395_R01C01


title: 4254948385_R01C02


title: 4254948395_R01C02


title: 4254948389_R02C01


title: 4254948386_R01C01


title: 4254948395_R02C02


title: 4254948403_R01C01


title: 4254948403_R01C02


title: 4254948396_R02C02


title: 4254948396_R01C01


title: 4254948403_R02C01


title: 4254948406_R01C01


title: 4254948393_R01C02


title: 4254948406_R02C01


title: 4254948407_R02C02


title: 4254948407_R02C01


title: 4254948407_R01C01


title: 4254948407_R01C02


title: 4254948396_R01C02


title: 4254948406_R01C02


title: 4254948396_R02C01


title: 4254948409_R02C02


title: 4254948409_R01C02


title: 4254948395_R02C01


title: 4254948409_R02C01


title: 4254948410_R01C02


title: 4254948410_R02C01


title: 4254948410_R01C01


title: 4254948411_R01C01


title: 4254948410_R02C02


title: 4254948411_R01C02


title: 4254948411_R02C01


title: 4254948403_R02C02


title: 4254948406_R02C02


title: 4254948413_R01C01


title: 4254948412_R01C01


title: 4254948412_R01C02


title: 4254948412_R02C02


title: 4254948412_R02C01


title: 4254948411_R02C02


title: 4254948413_R01C02


title: 4254948409_R01C01


title: 4254948413_R02C02


title: 4254948413_R02C01


title: 4254948419_R01C01


title: 4254948418_R02C01


title: 4254948418_R02C02


title: 4254948418_R01C01


title: 4254948419_R01C02


title: 4254948419_R02C01


title: 4254948420_R02C01


title: 4254948420_R01C01


title: 4254948424_R01C01


title: 4254948424_R01C02


title: 4254948424_R02C01


title: 4254948424_R02C02


title: 4254948420_R02C02


title: 4254948388_R01C02


title: 4254948425_R01C01


title: 4254948425_R01C02


title: 4254948425_R02C01


title: 4254948418_R01C02


title: 4254948419_R02C02


title: 4254948420_R01C02


title: 4254948429_R01C02


title: 4254948430_R01C02


title: 4254948430_R01C01


title: 4254948427_R02C02


title: 4254948429_R02C01


title: 4254948431_R02C02


title: 4254948432_R02C01


title: 4254948432_R01C02


title: 4254948431_R02C01


title: 4254948431_R01C01


title: 4254948436_R02C01


title: 4254948436_R02C02


title: 4254948432_R01C01


title: 4254948427_R01C01


title: 4254948427_R01C02


title: 4254948437_R01C02


title: 4254948429_R01C01


title: 4254948427_R02C01


title: 4254948425_R02C02


title: 4254948429_R02C02


title: 4254948430_R02C02


title: 4254948430_R02C01


title: 4254948431_R01C02


title: 4254948437_R02C02


title: 4254948437_R02C01


title: 4254948438_R01C01


title: 4254948436_R01C02


title: 4254948438_R02C02


title: 4254948436_R01C01


title: 4254948432_R02C02


title: 4254948440_R02C02


title: 4254948439_R02C01


title: 4254948440_R01C02


title: 4254948438_R02C01


title: 4254948439_R02C02


title: 4254948443_R02C02


title: 4254948443_R02C01


title: 4254948440_R01C01


title: 4254948442_R02C02


title: 4254948437_R01C01


title: 4254948442_R02C01


title: 4254948458_R01C01


title: 4254948442_R01C01


title: 4254948442_R01C02


title: 4254948439_R01C01


title: 4254948439_R01C02


title: 4254948458_R01C02


title: 4254948440_R02C01


title: 4254948457_R01C01


title: 4254948443_R01C02


title: 4254948457_R01C02


title: 4254948443_R01C01


title: 4254948459_R01C01


title: 4254948459_R01C02


title: 4254948457_R02C01


title: 4254948457_R02C02


title: 4254948459_R02C01


title: 4254948460_R01C01


title: 4254948458_R02C01


title: 4254948438_R01C02


title: 4254948465_R02C02


title: 4254948458_R02C02


title: 4254948466_R01C01


title: 4254948460_R01C02


title: 4254948466_R02C01


title: 4254948460_R02C02


title: 4254948465_R01C02


title: 4254948465_R01C01


title: 4254948466_R01C02


title: 4254948467_R02C01


title: 4254948468_R01C02


title: 4254948468_R02C01


title: 4254948468_R02C02


title: 4254948467_R01C02


title: 4254948467_R01C01


title: 4254948460_R02C01


title: 4254948465_R02C01


title: 4254948467_R02C02


title: 4254948459_R02C02


title: 4254948477_R02C01


title: 4254948477_R01C01


title: 4254948479_R02C01


title: 4254948477_R02C02


title: 4254948478_R02C02


title: 4254948479_R01C01


title: 4254948478_R02C01


title: 4254948478_R01C02


title: 4254948478_R01C01


title: 4254948479_R02C02


title: 4254948479_R01C02


title: 4254948466_R02C02


title: 4254948480_R02C02


title: 4254948480_R01C02


title: 4254948480_R01C01


title: 4254948483_R01C01


title: 4254948468_R01C01


title: 4254948483_R02C02


title: 4254948483_R01C02


title: 4254948477_R01C02


title: 4254948484_R01C02


title: 4254948484_R02C02


title: 4254948484_R01C01


title: 4254948484_R02C01


title: 4254948485_R01C01


title: 4254948483_R02C01


title: 4254948485_R01C02


title: 4254948485_R02C01


title: 4254948486_R01C01


title: 4254948485_R02C02


title: 4254948486_R01C02


title: 4254948486_R02C01


title: 4254948480_R02C01


title: 4254948494_R02C02


title: 4254948494_R02C01


title: 4254948494_R01C01


title: 4254948494_R01C02


title: 4254948495_R01C01


title: 4254948495_R02C01


title: 4254948495_R02C02


title: 4254948495_R01C02


title: 4254948486_R02C02


title: 4254948499_R01C02


title: 4254948499_R01C01


title: 4254948499_R02C02


title: 4254948500_R01C01


title: 4254948500_R02C01


title: 4254948500_R02C02


title: 4254948500_R01C02


title: 4254948501_R01C01


title: 4254948501_R01C02


title: 4254948501_R02C02


title: 4254948505_R01C01


title: 4254948501_R02C01


title: 4254948505_R01C02


title: 4254948505_R02C01


title: 4254948506_R01C02


title: 4254948505_R02C02


title: 4254948506_R02C01


title: 4254948499_R02C01


title: 4254948506_R01C01


title: 4254948509_R01C01


title: 4254948506_R02C02


title: 4254948509_R02C01


title: 4254948510_R01C01


title: 4254948509_R01C02


title: 4254948510_R02C01


title: 4254948510_R01C02


title: 4254948509_R02C02


title: 4254948516_R01C01


title: 4254948515_R02C02


title: 4254948515_R01C01


title: 4254948516_R02C02


title: 4254948515_R01C02


title: 4254948516_R02C01


title: 4254948517_R01C02


title: 4254948517_R01C01


title: 4254948517_R02C02


title: 4254948517_R02C01


title: 4254948510_R02C02


title: 4254948516_R01C02


title: 4254948524_R02C01


title: 4254948528_R01C01


title: 4254948528_R02C01


title: 4254948524_R02C02


title: 4254948524_R01C02


title: 4254948528_R01C02


title: 4254948524_R01C01


title: 4254948531_R01C01


title: 4254948528_R02C02


title: 4254948531_R01C02


title: 4254948531_R02C01


title: 4254948550_R01C02


title: 4254948550_R02C01


title: 4254948550_R02C02


title: 4254948550_R01C01


title: 4254948551_R02C02


title: 4254948551_R01C01


title: 4254948551_R02C01


title: 4254948551_R01C02


title: 4254948552_R01C01


title: 4254948552_R01C02


title: 4254948552_R02C01


title: 4254948557_R02C01


title: 4254948557_R01C01


title: 4254948557_R02C02


title: 4254948557_R01C02


title: 4254948552_R02C02


title: 4254948568_R02C01


title: 4254948559_R01C02


title: 4254948559_R01C01


title: 4254948568_R01C02


title: 4254948559_R02C02


title: 4254948568_R01C01


title: 4254948559_R02C01


title: 4254948531_R02C02


title: 4254948568_R02C02


title: 4254948569_R01C02


title: 4254948569_R01C01


title: 4254948569_R02C01


title: 4254948569_R02C02


title: 4254948570_R01C01


title: 4254948570_R02C02


title: 4254948574_R02C02


title: 4254948575_R01C01


title: 4254948575_R01C02


title: 4254948570_R01C02


title: 4254948574_R01C02


title: 4254948574_R01C01


title: 4254948574_R02C01


title: 4254948575_R02C01


title: 4254948570_R02C01


title: 4254948582_R01C01


title: 4254948582_R01C02


title: 4254948575_R02C02


title: 4254948582_R02C01


title: 4254948582_R02C02


title: 4254948588_R01C02


title: 4254948588_R02C01


title: 4254948588_R01C01


title: 4254948592_R01C01


title: 4254948588_R02C02


title: 4254948592_R02C01


title: 4254948592_R02C02


title: 4254948593_R02C01


title: 4254948593_R02C02


title: 4254948593_R01C02


title: 4254948593_R01C01


title: 4254948605_R01C01


title: 4254948605_R01C02


title: 4254948605_R02C01


title: 4254948612_R02C01


title: 4254948612_R01C02


title: 4254948612_R02C02


title: 4254948615_R01C02


title: 4254948613_R01C01


title: 4254948592_R01C02


title: 4254948613_R02C02


title: 4254948612_R01C01


title: 4254948615_R02C01


title: 4254948615_R02C02


title: 4254948619_R02C02


title: 4254948619_R01C02


title: 4254948619_R02C01


title: 4254948605_R02C02


title: 4254948615_R01C01


title: 4254948619_R01C01


title: 4254948613_R01C02


title: 4254948613_R02C01


title: 4254948621_R01C02


title: 4254948621_R01C01


title: 4254948621_R02C02


title: 4254948621_R02C01


title: 4254948631_R02C01


title: 4254948631_R01C01


title: 4254948637_R01C02


title: 4254948637_R01C01


title: 4254948637_R02C01


title: 4254948631_R02C02


title: 4254948631_R01C02


title: 4254948644_R01C01


title: 4254948637_R02C02


title: 4254948644_R01C02


title: 4254948644_R02C02


title: 4254948645_R02C01


title: 4254948646_R01C01


title: 4254948644_R02C01


title: 4254948645_R01C01


title: 4254948647_R02C02


title: 4254948646_R02C01


title: 4254948646_R01C02


title: 4254948645_R01C02


title: 4254948647_R01C01


title: 4254948647_R02C01


title: 4254948646_R02C02


title: 4254948648_R01C01


title: 4254948647_R01C02


title: 4254948648_R01C02


title: 4263772516_R02C01


title: 4263772516_R01C01


title: 4263772516_R01C02


title: 4254948645_R02C02


title: 4270198616_R01C01


title: 4270198615_R01C02


title: 4270198616_R02C02


title: 4270198617_R01C01


title: 4270198616_R01C02


title: 4270198615_R02C02


title: 4263772516_R02C02


title: 4270198616_R02C01


title: 4270198617_R01C02


title: 4254948648_R02C01


title: 4270198617_R02C01


title: 4270198627_R01C01


title: 4270198617_R02C02


title: 4270198628_R02C02


title: 4270198627_R02C01


title: 4270198627_R01C02


title: 4270198628_R01C01


title: 4270198627_R02C02


title: 4270198628_R02C01


title: 4270198629_R01C01


title: 4270198629_R01C02


title: 4270198629_R02C01


title: 4270198629_R02C02


title: 4270198633_R01C01


title: 4270198633_R01C02


title: 4270198633_R02C01


title: 4270198633_R02C02


title: 4270198634_R01C01


title: 4270198634_R01C02


title: 4270198634_R02C01


title: 4270198634_R02C02


title: 4270198635_R01C02


title: 4270198628_R01C02


title: 4270198636_R01C01


title: 4270198635_R02C02


title: 4270198635_R02C01


title: 4270198636_R02C01


title: 4270198640_R01C01


title: 4270198639_R01C02


title: 4270198640_R01C02


title: 4270198639_R01C01


title: 4270198640_R02C02


title: 4270198641_R01C02


title: 4270198636_R02C02


title: 4270198639_R02C02


title: 4270198648_R01C02


title: 4254948515_R02C01


title: 4270198636_R01C02


title: 4270198648_R02C01


title: 4270198635_R01C01


title: 4270198639_R02C01


title: 4270198640_R02C01


title: 4270198641_R01C01


title: 4270198641_R02C01


title: 4270198641_R02C02


title: 4270198648_R01C01


title: 4270198650_R01C01


title: 4270198651_R01C02


title: 4270198650_R01C02


title: 4270198650_R02C01


title: 4270198649_R01C02


title: 4270198649_R01C01


title: 4270198651_R02C01


title: 4270198648_R02C02


title: 4270198651_R02C02


title: 4270198662_R01C01


title: 4270198652_R02C02


title: 4270198653_R02C02


title: 4270198653_R02C01


title: 4270198649_R02C02


title: 4270198653_R01C02


title: 4270198650_R02C02


title: 4270198662_R02C01


title: 4270198662_R01C02


title: 4270198651_R01C01


title: 4270198662_R02C02


title: 4270198675_R01C01


title: 4270198652_R01C01


title: 4270198653_R01C01


title: 4270198652_R02C01


title: 4270198675_R01C02


title: 4270198652_R01C02


title: 4270198699_R02C01


title: 4270198699_R01C01


title: 4270198676_R01C01


title: 4270198676_R02C01


title: 4270198699_R02C02


title: 4270198675_R02C01


title: 4270198676_R02C02


title: 4270198676_R01C02


title: 4270198675_R02C02


title: 4270198700_R01C01


title: 4270198700_R01C02


title: 4270198649_R02C01


title: 4270198700_R02C01


title: 4270198699_R01C02


title: 4270198701_R02C02


title: 4270198717_R01C01


title: 4270198701_R01C01


title: 4270198700_R02C02


title: 4270198717_R02C01


title: 4270198718_R02C02


title: 4270198717_R02C02


title: 4270198717_R01C02


title: 4270198718_R01C02


title: 4270198701_R01C02


title: 4270198718_R01C01


title: 4270198718_R02C01


title: 4270198719_R01C01


title: 4270198701_R02C01


title: 4270198725_R02C02


title: 4270198725_R01C01


title: 4270198719_R01C02


title: 4270198719_R02C01


title: 4270198723_R01C02


title: 4270198723_R01C01


title: 4270198725_R01C02


title: 4270198723_R02C01


title: 4270198719_R02C02


title: 4270198740_R02C01


title: 4270198740_R02C02


title: 4270198756_R01C01


title: 4270198756_R02C02


title: 4270198757_R01C02


title: 4270198757_R02C02


title: 4270198758_R02C01


title: 4270198758_R01C02


title: 4270198757_R02C01


title: 4270198758_R01C01


title: 4270198723_R02C02


title: 4270198725_R02C01


title: 4270198774_R01C02


title: 4270198774_R01C01


title: 4270198756_R02C01


title: 4270198740_R01C02


title: 4270198774_R02C01


title: 4270198776_R02C02


title: 4270198774_R02C02


title: 4270198775_R02C01


title: 4270198776_R01C02


title: 4270198775_R01C02


title: 4270198775_R01C01


title: 4270198775_R02C02


title: 4270198776_R02C01


title: 4270198740_R01C01


title: 4270198758_R02C02


title: 4270198778_R01C01


title: 4270198778_R01C02


title: 4270198757_R01C01


title: 4270198756_R01C02


title: 4270198778_R02C01


title: 4270198776_R01C01


title: 4270198779_R01C01


title: 4270198779_R01C02


title: 4270198780_R02C02


title: 4270198780_R02C01


title: 4270198778_R02C02


title: 4270198781_R01C01


title: 4270198781_R01C02


title: 4270198780_R01C01


title: 4270198780_R01C02


title: 4270198782_R01C02


title: 4270198781_R02C02


title: 4270198782_R01C01


title: 4270198781_R02C01


title: 4270198779_R02C02


title: 4270198779_R02C01


title: 4270198793_R02C01


title: 4270198794_R01C01


title: 4270198792_R02C01


title: 4270198782_R02C02


title: 4270198793_R01C02


title: 4270198792_R02C02


title: 4270198794_R02C01


title: 4270198793_R01C01


title: 4270198792_R01C01


title: 4270198794_R01C02


title: 4270198782_R02C01


title: 4270198800_R01C01


title: 4270198794_R02C02


title: 4270198792_R01C02


title: 4270198793_R02C02


title: 4270198800_R01C02


title: 4270198800_R02C01


title: 4270198801_R02C02


title: 4270198800_R02C02


title: 4270198802_R01C01


title: 4270198802_R01C02


title: 4270198801_R02C01


title: 4270198803_R01C01


title: 4270198801_R01C01


title: 4270198803_R01C02


title: 4270198802_R02C01


title: 4270198803_R02C01


title: 4270198802_R02C02


title: 4270198804_R01C01


title: 4270198803_R02C02


title: 4270198804_R02C01


title: 4270198804_R01C02


title: 4270198804_R02C02


title: 4270198805_R02C02


title: 4270198805_R01C01


title: 4270198806_R01C01


title: 4270198801_R01C02


title: 4270198805_R01C02


title: 4270198806_R01C02


title: 4270198805_R02C01


title: 4270198806_R02C01


title: 4270198806_R02C02


title: 4270198807_R01C02


title: 4270198808_R02C01


title: 4270198807_R01C01


title: 4270198808_R02C02


title: 4270198807_R02C01


title: 4270198808_R01C01


title: 4270198811_R01C01


title: 4270198808_R01C02


title: 4270198811_R02C01


title: 4270198811_R01C02


title: 4270198812_R01C01


title: 4270198812_R01C02


title: 4270198812_R02C01


title: 4270198812_R02C02


title: 4270198811_R02C02


title: 4270198813_R01C01


title: 4270198813_R01C02


title: 4270198813_R02C02


title: 4270198814_R01C02


title: 4270198813_R02C01


title: 4270198814_R02C01


title: 4270198814_R01C01


title: 4270198807_R02C02


title: 4270198815_R01C01


title: 4270198815_R02C01


title: 4270198814_R02C02


title: 4270198815_R01C02


title: 4270198816_R01C01


title: 4270198815_R02C02


title: 4270198817_R02C01


title: 4270198817_R01C02


title: 4270198818_R01C01


title: 4270198818_R01C02


title: 4270198822_R01C01


title: 4270198818_R02C02


title: 4270198816_R02C01


title: 4270198816_R02C02


title: 4270198817_R01C01


title: 4270198816_R01C02


title: 4270198817_R02C02


title: 4270198818_R02C01


title: 4270198822_R02C01


title: 4270198822_R02C02


title: 4270198822_R01C02


title: 4270198823_R01C01


title: 4270198823_R01C02


title: 4270198823_R02C01


title: 4270198823_R02C02


title: 4270198824_R01C01


title: 4270198824_R02C01


title: 4270198824_R01C02


title: 4270198828_R01C01


title: 4270198824_R02C02


title: 4270198828_R01C02


title: 4270198830_R01C02


title: 4270198830_R02C02


title: 4270198828_R02C02


title: 4270198829_R01C01


title: 4270198831_R01C02


title: 4270198828_R02C01


title: 4270198829_R01C02


title: 4270198831_R01C01


title: 4270198829_R02C01


title: 4270198829_R02C02


title: 4270198830_R01C01


title: 4270198832_R01C02


title: 4270198830_R02C01


title: 4270198831_R02C01


title: 4270198831_R02C02


title: 4270198832_R01C01


title: 4270198874_R01C02


title: 4270198837_R01C01


title: 4270198832_R02C01


title: 4270198832_R02C02


title: 4270198833_R01C01


title: 4270198833_R01C02


title: 4270198833_R02C02


title: 4270198833_R02C01


title: 4270198876_R02C02


title: 4270198876_R01C02


title: 4270198872_R01C02


title: 4270198877_R01C01


title: 4270198877_R01C02


title: 4270198874_R01C01


title: 4270198872_R02C02


title: 4270198874_R02C02


title: 4270198876_R02C01


title: 4270198874_R02C01


title: 4270198876_R01C01


title: 4270198877_R02C01


title: 4270198878_R01C01


title: 4270198879_R02C01


title: 4270198878_R01C02


title: 4270198879_R01C01


title: 4270198879_R01C02


title: 4270198877_R02C02


title: 4270198878_R02C02


title: 4270198878_R02C01


title: 4270198879_R02C02


title: 4270198880_R01C01


title: 4270198881_R01C02


title: 4270198880_R01C02


title: 4270198880_R02C02


title: 4270198881_R02C02


title: 4429411226_R01C01


title: 4429411226_R02C01


title: 4429411226_R02C02


title: 4429411226_R01C02


title: 4270198880_R02C01


title: 4270198881_R01C01


title: 4429411477_R02C01


title: 4429411477_R01C02


title: 4429411881_R01C02


title: 4429411477_R01C01


title: 4429411881_R01C01


title: 4429411881_R02C01


title: 4429411881_R02C02


title: 4270198881_R02C01


title: 4429411882_R01C01


title: 4429411882_R01C02


title: 4429411882_R02C02


title: uc0972

value: Female


title: uc0971


title: 4429411882_R02C01


title: uc1151


title: uc0970


title: uc1032


title: uc0993


title: uc0986


title: uc1040


title: uc1161


title: uc1251


title: uc1049


title: uc1210


title: uc1292


title: uc1326


title: 4429411477_R02C02


title: uc1368


title: uc1412


title: uc1697


title: uc1700


title: uc1446


title: uc1413


title: uc1701


title: uc1709


title: uc1275


title: uc1291


title: uc1710


title: uc1835


title: uc1828


title: uc1844


title: uc1829


title: uc1287


title: uc1855


title: uc1869


title: uc1874


title: uc1876


title: uc1908


title: uc1885


title: uc1901


title: uc1923


title: uc1890


title: uc1931


title: uc1880


title: uc1937


title: uc1933


title: UC3866


title: UC4272

value: Male


title: UC4273


title: uc1865


title: UC5114


title: UC5115


title: uc1917


title: UC5116


title: uc1924


title: UC5121


title: uc1934


title: UC4271


title: UC4270


title: UC5142


title: UC5145


title: UC5137


title: UC5138


title: UC5144


title: UC5140


title: UC5117


title: UC5119


title: UC5118


title: UC5149


title: UC5139


title: UC5146


title: UC5584


title: UC5583


title: UC5585


title: UC5587


title: UC5588


title: UC5589


title: L2158

source_name: Leprosy

value: granulomatous disease


title: L2483


title: uc1195


title: UC5147


title: UC5263


title: UC5148


title: L2536


title: UC4269


title: L2498


title: UC5582


title: L100


title: L10


title: L102


title: L1058


title: L1068


title: L1053


title: L1067


title: L103


title: L1069


title: L1072


title: L107


title: L1071


title: L1080


title: L1070


title: L1079


title: L1092


title: L1074


title: L1076


title: L1078


title: L1083


title: L1087


title: L1095


title: L1097


title: L109


title: L1114


title: L112


title: L1100


title: L1120


title: L110


title: L1099


title: L106


title: L1124


title: L101


title: L1128


title: L115


title: L114


title: L116


title: L1164


title: L1163


title: L119


title: L1179


title: L1191


title: L121


title: L123


title: L1171


title: L120


title: L124


title: L125


title: L126


title: L13


title: L127


title: L1127


title: L1298


title: L128


title: L1293


title: L14


title: L1305


title: L1300


title: L1129


title: L15


title: L154


title: L153


title: L117


title: L12


title: L156


title: L122


title: L1573


title: L155


title: L1579


title: L1580


title: L1571


title: L1584


title: L1578


title: L158


title: L1583


title: L129


title: L1581


title: L1585


title: L1303


title: L1586


title: L1588


title: L1590


title: L159


title: L1589


title: L1591


title: L1595


title: L1593


title: L1594


title: L1596


title: L16


title: L1598


title: L1600


title: L1599


title: L1601


title: L1576


title: L1602


title: L160


title: L1603


title: L1608


title: L1609


title: L1612


title: L1611


title: L1613


title: L1604


title: L161


title: L1615


title: L1618


title: L1619


title: L1617


title: L162


title: L1621


title: L1620


title: L1622


title: L1628


title: L1625


title: L1629


title: L163


title: L1632


title: L1635


title: L1605


title: L1644


title: L1638


title: L164


title: L1641


title: L1645


title: L1640


title: L1646


title: L1648


title: L1649


title: L1636


title: L1653


title: L1642


title: L165


title: L1652


title: L1655


title: L1658


title: L1650


title: L1657


title: L1659


title: L1637


title: L1661


title: L1662


title: L1663


title: L166


title: L1665


title: L1664


title: L1667


title: L1666


title: L167


title: L1671


title: L1669


title: L1670


title: L1680


title: L1675


title: L1672


title: L1685


title: L1684


title: L1677


title: L1687


title: L1681


title: L1689


title: L1688


title: L1690


title: L1692


title: L1699


title: L1697


title: L1693


title: L1698


title: L17


title: L1702


title: L1703


title: L1701


title: L1706


title: L1707


title: L1704


title: L1710


title: L1712


title: L1718


title: L1717


title: L1722


title: L1720


title: L1726


title: L1728


title: L1729


title: L1727


title: L1734


title: L1730


title: L1736


title: L1738


title: L1742


title: L1743


title: L1744


title: L1745


title: L1746


title: L1752


title: L1750


title: L1748


title: L1751


title: L1753


title: L1756


title: L1765


title: L1757


title: L1766


title: L1767


title: L1762


title: L1759


title: L1768


title: L1777


title: L1771


title: L1780


title: L1778


title: L1785


title: L1783


title: L1787


title: L1788


title: L1790


title: L1731


title: L1800


title: L1798


title: L1799


title: L1796


title: L1803


title: L1791


title: L1807


title: L1805


title: L1809


title: L1806


title: L1817


title: L1814


title: L1808


title: L1815


title: L1821


title: L1818


title: L1822


title: L1828


title: L1829


title: L1823


title: L1833


title: L1826


title: L1834


title: L1838


title: L1835


title: L1802


title: L1839


title: L1844


title: L1842


title: L1830


title: L1892


title: L1895


title: L1896


title: L1894


title: L1898


title: L1846


title: L1877


title: L1857


title: L1852


title: L1872


title: L1876


title: L1853


title: L1861


title: L1845


title: L1890


title: L1841


title: L1867


title: L1889


title: L1870


title: L1849


title: L1906


title: L1900


title: L1902


title: L1884


title: L1848


title: L1903


title: L1907


title: L1905


title: L1908


title: L1911


title: L1904


title: L1926


title: L1921


title: L1924


title: L1923


title: L1925


title: L1945


title: L1944


title: L1947


title: L1949


title: L1946


title: L1952


title: L1891


title: L1954


title: L1953


title: L1956


title: L1960


title: L1959


title: L1910


title: L1920


title: L1964


title: L1966


title: L1931


title: L1928


title: L1927


title: L1948


title: L1936


title: L1961


title: L1967


title: L1970


title: L1968


title: L1971


title: L1977


title: L1955


title: L1980


title: L1978


title: L1982


title: L1981


title: L2003


title: L1989


title: L2002


title: L1993


title: L2001


title: L1998


title: L2014


title: L2004


title: L2019


title: L2012


title: L1988


title: L2024


title: L2017


title: L1986


title: L1976


title: L1987


title: L1969


title: L2025


title: L1991


title: L2029


title: L2031


title: L2030


title: L2034


title: L2032


title: L2028


title: L2035


title: L2006


title: L2038


title: L2037


title: L2040


title: L2066


title: L2068


title: L2064


title: L2058


title: L2045


title: L2046


title: L2071


title: L2073


title: L2054


title: L2056


title: L2060


title: L2062


title: L2072


title: L2036


title: L2076


title: L2070


title: L2075


title: L2047


title: L2052


title: L2085


title: L2087


title: L2083


title: L2088


title: L2089


title: L2091


title: L2092


title: L2086


title: L2080


title: L2078


title: L2093


title: L2099


title: L2095


title: L2098


title: L2096


title: L2101


title: L2104


title: L2102


title: L2108


title: L2113


title: L2114


title: L2111


title: L2110


title: L2107


title: L2112


title: L2100


title: L2117


title: L2109


title: L2120


title: L2094


title: L2123


title: L2105


title: L2125


title: L2106


title: L2097


title: L2126


title: L2128


title: L2129


title: L2121


title: L2130


title: L2131


title: L2136


title: L2134


title: L2138


title: L2140


title: L2144


title: L2147


title: L2148


title: L2139


title: L2124


title: L2151


title: L2152


title: L2154


title: L2155


title: L2132


title: L2127


title: Vav-Control HSC H3K27me3-ChIP 1

type: SRA

city: St Louis

first: Hamza

last: CELIK

state: MO

address: 660 S Euclid Ave

department: Internal Medicine

country: USA

institute: Washington University in St Louis

library_source: genomic

data_processing:
For ChIP-seq reads were aligned to the mm10 using Bowtie2 v1.2.1.1
For ChIP-seq peak calling was performed with hiddenDomains v3.0
ChIPQC v3.6 was used for QC
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for H3K27me3

organism: Mus musculus

source_name: Hematopoietic Stem Cell (HSC)

extract_protocol:
1.0x104 HSCs were sorted into PBS+10% FBS, and then crosslinked at room temperature for 8 minutes using 1% paraformaldehyde (VWR #J531).  Chromatin was sheared using a Covaris E220 Focused-ultrasonicator until the DNA fragments were between 200 – 700 base pairs.  Chromatin samples were incubated overnight at 4°C with either the H3K27me3 antibody (Diagenode # pAb-195-050).  Following overnight incubation, protein G dynabeads (Life Technologies #130-099-508) were added for 2-hours at 4°C.  The beads were washed, and tagmented for 10-minutes at 37°C using the Nextera DNA Library Preperation Kit (Illumina #FC-121-1030).  After additional washes, an overnight decrosslinking was performed immunoprecipiated DNA was isolated using Ampure XP beads.
2xKapa HiFi HotStart Ready Mix (Kapa #KB KK2601), along with Nextera custom primers, was used for library amplification of the ChIP DNA(12 cycles of PCR as determined by qPCR).  Libraries were again purified with Ampure XP beads and run on an Illumina Hiseq 3000 (PE2X150).

tag: strain

tag: genotype

value: Wild-type

tag: age

tag: cre-driver

value: Vav-CRE

tag: chip antibody

value: H3K27me3 (Diagenode #pAb-069-050)

tag: cell type

value: Hematopoietic Stem Cell (HSC)

tag: indexes

value: TAAGGCGA


title: Vav-Jarid2-KO HSC H3K27me3-ChIP 1


title: Vav-Jarid2-KO MPP H3K27me3-ChIP 2

source_name: Multipotent Progenitor Cells (MPPs)

value: Multipotent Progenitor Cells (MPPs)

value: TCCTGAGC


title: Vav-Jarid2-KO HSC H3K27me3-ChIP 2


title: Vav-Control MPP H3K27me3-ChIP 1

value: AGGCAGAA


title: L2157


title: Vav-Jarid2-KO MPP H3K27me3-ChIP 1


title: L2156


title: Mx1-Jak2V617F - Jarid2KO HSC RNA-seq 2

library_source: transcriptomic

data_processing:
For RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4
For RNA-seq gene counts were derived with Subread:featureCount v1.4.5 as well as htseq-count v0.8.0
For RNA-seq QC was performed with RSeQC v2.3
For RNA-seq quantification and normalization of gene RPKM was performed using Partek Genomics Suite Software version 6.6
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with raw gene counts

molecule: total RNA

extract_protocol:
For RNA-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-) and MPPs (Lin-, cKit+, Sca1+, CD150-, CD48-) were sorted from a pooled sample of 5 male and 5 female 8-week old mice. HSCs and MPPs were purified from three biological replicates (composed of pooled WBM from three male and three female mice) of either control or tests cohorts.  Total RNA was isolated from the samples using the NucleoSpin RNA XS kit.
The SMARTer Ultra Low RNA kit (Clontech) was used to prepare the libraries from 3-5ng of total RNA.

value: Mx1-Jak2V617F - Jarid2KO

value: 10-weeks (2 months post-pIpC)

value: TACAGAC


title: Mx1-Jak2V617F - Jarid2KO  MPP RNA-seq 1

value: TCCCAGC


title: Mx1-Jak2V617F - Jarid2KO HSC RNA-seq 1

value: GCAACGC


title: Mx1-Jak2V617F - Jarid2KO  MPP RNA-seq 2

value: ATGACAG


title: Vav-Control MPP H3K27me3-ChIP 2


title: Mx1-Jak2V617F MPP RNA-seq 2

value: CTCCCGA


title: Mx1-Jak2V617F MPP RNA-seq 1

value: TGTTTGT


title: L2159

value: Male

value: Whole blood

value: granulomatous disease


title: L2161


title: Vav-Control HSC H3K27me3-ChIP 2

value: Wild-type

value: Vav-CRE

value: H3K27me3 (Diagenode #pAb-069-050)

value: CGTACTAG


title: L2163


title: Mx1-Jak2V617F HSC RNA-seq 2

value: Hematopoietic Stem Cell (HSC)

value: CCGGACC


title: Mx1-Jak2V617F HSC RNA-seq 1

value: GGTCCTC


title: Mx1-Control MPP RNA-seq 1

value: 10-weeks (2 months post-pIpC)

value: Multipotent Progenitor Cells (MPPs)

value: AGATACT


title: L2164

value: Female


title: Mx1-Control MPP RNA-seq 2

value: GCTTAGA


title: Mx1-Control HSC RNA-seq 2

value: GTCGATA


title: L2165


title: Mx1-Control HSC RNA-seq 1

value: GGGTCAA


title: Vav-Jarid2-KO MPP RNA-seq 3


title: L2168

value: Male


title: Vav-Jarid2-KO MPP RNA-seq 2

value: ACCCACT


title: L2174

value: Whole blood

value: granulomatous disease


title: L2182


title: L2171


title: L2175


title: L2183


title: Vav-Jarid2-KO MPP RNA-seq 1

value: Vav-CRE

value: TAACAAG


title: L2177


title: Vav-Jarid2-KO HSC RNA-seq 1


title: Vav-Jarid2-KO HSC RNA-seq 3

value: TCAACTG


title: L2172


title: Vav-Control HSC RNA-seq 3

value: Wild-type

value: Hematopoietic Stem Cell (HSC)

value: ACGTCTG


title: Vav-Control MPP RNA-seq 3

value: TGAGGTT


title: Vav-Control MPP RNA-seq 2

value: Multipotent Progenitor Cells (MPPs)

value: CAAGCCG


title: Vav-Jarid2-KO HSC RNA-seq 2


title: Vav-Control MPP RNA-seq 1

value: CGTCGCT


title: Vav-Control HSC RNA-seq 1

value: GAGGCGT


title: L2184


title: L2185


title: Vav-Control HSC RNA-seq 2

value: GTCTGAT


title: L2186


title: L2188


title: L2187

value: Female


title: sample.9_aloxe3

city: St. Louis

first: Brian

middle: Jesse

last: DeBosch

address: 660 S. Euclid Ave, Box 8208

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

description: run_2163_s_3_withindex_sequence.txt_TTTAACT_sample.9_aloxe3

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
To enhance the biological interpretation of the large set of transcripts, grouping of genes/transcripts based on functional similarity was achieved using the R/Bioconductor packages GAGE and Pathview.
GAGE and Path-view were also used to generate pathway maps on known signaling and metabolism pathways curated by KEGG.
Genome_build: NCBI GRCm38.p2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Primary murine hepatocytes were equilibrated in regular growth media (See DeBosch et al 2014 J Biol Chem) overnight following collagenase digestion.

extract_protocol:
Total RNA was extracted using Trizol Reagent precisely per manufacturer protocol.
Library preparation was performed with 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in buffer containing 40mM Tris Acetate pH 8.2, 100mM Potassium Acetate and 30mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags.  Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

treatment_protocol: Hepatocytes were transfected with adenovirus at approximately 10^6 viral particles per million cells for 24hr prior to RNA collection.

value: primary murine hepatocytes

tag: transfected with

value: adenovirus encoding ALOXE3

tag: time point

value: 24h after transfection


title: sample.7_aloxe3

description: run_2163_s_3_withindex_sequence.txt_ACGTCTG_sample.7_aloxe3


title: sample.8_aloxe3

description: run_2163_s_3_withindex_sequence.txt_TGAGGTT_sample.8_aloxe3


title: L2189

value: Male

value: Whole blood

value: granulomatous disease


title: L2178


title: sample.3_bgal

description: run_2163_s_3_withindex_sequence.txt_TTTTGTC_sample.3_bgal

value: adenovirus encoding beta galactosidase


title: L2194


title: sample.1_bgal

description: run_2163_s_3_withindex_sequence.txt_GAGGCGT_sample.1_bgal


title: L2190


title: sample.2_bgal

description: run_2163_s_3_withindex_sequence.txt_CGTCGCT_sample.2_bgal


title: L2191


title: Patient28 Monocytes

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

description: Monocytes purified from whole blood taken from Patient28

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.  Processed data file includes average Beta values.

label: Cy5 and Cy3

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was extracted from frozen whole blood samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

tag: patient number

value: blood

value: Monocytes


title: L2192


title: L2196


title: Patient28 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient28

value: CD4 T-cells


title: L2195


title: L2199


title: L2197


title: Patient28 B-cells

description: B-cells purified from whole blood taken from Patient28

value: B-cells


title: L2198


title: Patient27 Granulocytes

description: Granulocytes purified from whole blood taken from Patient27

value: Granulocytes


title: Patient27 Monocytes

description: Monocytes purified from whole blood taken from Patient27


title: Patient27 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient27

value: CD8 T-cells


title: L22


title: Patient28 Granulocytes

description: Granulocytes purified from whole blood taken from Patient28


title: L2227


title: Patient27 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient27


title: L2229


title: L2181


title: L2230


title: L2200


title: Patient26 Granulocytes

description: Granulocytes purified from whole blood taken from Patient26


title: L2232


title: Patient27 B-cells

description: B-cells purified from whole blood taken from Patient27


title: Patient28 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient28


title: L2233

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: L2234


title: L2235


title: Patient26 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient26


title: Patient26 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient26


title: Patient25 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient25


title: Patient26 B-cells

description: B-cells purified from whole blood taken from Patient26


title: Patient25 Monocytes

description: Monocytes purified from whole blood taken from Patient25


title: L2244


title: L2240


title: Patient25 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient25


title: L2245


title: Patient24 Granulocytes

description: Granulocytes purified from whole blood taken from Patient24


title: Patient25 Granulocytes

description: Granulocytes purified from whole blood taken from Patient25


title: L2248


title: L2238


title: L2247


title: Patient24 Monocytes

description: Monocytes purified from whole blood taken from Patient24


title: L2251


title: Patient25 B-cells

description: B-cells purified from whole blood taken from Patient25


title: L2252


title: Patient24 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient24


title: L2253


title: Patient23 Monocytes

description: Monocytes purified from whole blood taken from Patient23


title: L2255


title: Patient24 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient24


title: L2254


title: Patient24 B-cells

description: B-cells purified from whole blood taken from Patient24


title: Patient23 Granulocytes

description: Granulocytes purified from whole blood taken from Patient23


title: L2257


title: Patient23 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient23


title: L2256

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: L2258


title: Patient23 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient23


title: L2261


title: L2260


title: L2263


title: L2262


title: Patient22 Granulocytes

description: Granulocytes purified from whole blood taken from Patient22


title: L2264


title: Patient22 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient22


title: L2267


title: Patient23 B-cells

description: B-cells purified from whole blood taken from Patient23


title: L2269


title: Patient21 Granulocytes

description: Granulocytes purified from whole blood taken from Patient21


title: Patient22 B-cells

description: B-cells purified from whole blood taken from Patient22


title: L2270


title: L2271


title: Patient21 Monocytes

description: Monocytes purified from whole blood taken from Patient21


title: Patient21 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient21


title: L2272


title: Patient22 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient22


title: Patient21 B-cells

description: B-cells purified from whole blood taken from Patient21


title: Patient21 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient21


title: L2274


title: Patient22 Monocytes

description: Monocytes purified from whole blood taken from Patient22


title: L2266


title: L2276


title: Patient20 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient20


title: Patient20 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient20


title: L2277


title: Patient20 B-cells

description: B-cells purified from whole blood taken from Patient20


title: L2278


title: L2283


title: L2279


title: L2285


title: Patient19 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient19


title: Patient19 Granulocytes

description: Granulocytes purified from whole blood taken from Patient19


title: L2287

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: Patient19 Monocytes

description: Monocytes purified from whole blood taken from Patient19


title: Patient19 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient19


title: L2291


title: L2290


title: Patient20 Monocytes

description: Monocytes purified from whole blood taken from Patient20


title: L2293


title: L2294


title: Patient19 B-cells

description: B-cells purified from whole blood taken from Patient19


title: Patient18 Granulocytes

description: Granulocytes purified from whole blood taken from Patient18


title: Patient20 Granulocytes

description: Granulocytes purified from whole blood taken from Patient20


title: L2300


title: Patient18 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient18


title: L2301


title: L2303


title: Patient18 B-cells

description: B-cells purified from whole blood taken from Patient18


title: Patient17 Monocytes

description: Monocytes purified from whole blood taken from Patient17


title: Patient17 Granulocytes

description: Granulocytes purified from whole blood taken from Patient17


title: Patient18 Monocytes

description: Monocytes purified from whole blood taken from Patient18


title: L2314


title: Patient17 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient17


title: L2319


title: Patient16 Monocytes

description: Monocytes purified from whole blood taken from Patient16


title: L2320


title: Patient18 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient18


title: L2329


title: Patient16 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient16


title: L2323


title: Patient17 B-cells

description: B-cells purified from whole blood taken from Patient17


title: Patient17 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient17


title: Patient16 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient16


title: Patient15 Granulocytes

description: Granulocytes purified from whole blood taken from Patient15


title: Patient26 Monocytes

description: Monocytes purified from whole blood taken from Patient26


title: Patient16 B-cells

description: B-cells purified from whole blood taken from Patient16


title: L2343

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: L2341


title: L2346


title: L2304


title: L2356


title: Patient14 Monocytes

description: Monocytes purified from whole blood taken from Patient14


title: L2357


title: L2316


title: Patient15 B-cells

description: B-cells purified from whole blood taken from Patient15


title: Patient15 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient15


title: L2371


title: Patient16 Granulocytes

description: Granulocytes purified from whole blood taken from Patient16


title: L2340


title: L2381


title: L2383


title: Patient15 Monocytes

description: Monocytes purified from whole blood taken from Patient15


title: Patient14 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient14


title: Patient15 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient15


title: Patient14 B-cells

description: B-cells purified from whole blood taken from Patient14


title: Patient13 Monocytes

description: Monocytes purified from whole blood taken from Patient13


title: Patient13 Granulocytes

description: Granulocytes purified from whole blood taken from Patient13


title: L2390


title: L2392


title: L2386


title: Patient13 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient13


title: L2353


title: L2394


title: Patient14 Granulocytes

description: Granulocytes purified from whole blood taken from Patient14


title: Patient12 Granulocytes

description: Granulocytes purified from whole blood taken from Patient12


title: L2380


title: Patient12 Monocytes

description: Monocytes purified from whole blood taken from Patient12


title: Patient12 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient12


title: L2400


title: L2396


title: Patient14 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient14


title: L2398

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: Patient12 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient12


title: L2385


title: L2401


title: L2405


title: Patient12 B-cells

description: B-cells purified from whole blood taken from Patient12


title: L2403


title: Patient13 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient13


title: Patient11 Granulocytes

description: Granulocytes purified from whole blood taken from Patient11


title: Patient11 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient11


title: Patient11 B-cells

description: B-cells purified from whole blood taken from Patient11


title: Patient11 Monocytes

description: Monocytes purified from whole blood taken from Patient11


title: L2393


title: L2414


title: Patient10 Monocytes

description: Monocytes purified from whole blood taken from Patient10


title: Patient11 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient11


title: L2415


title: L2416


title: Patient10 Granulocytes

description: Granulocytes purified from whole blood taken from Patient10


title: Patient13 B-cells

description: B-cells purified from whole blood taken from Patient13


title: L2419


title: Patient10 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient10


title: L2410


title: Patient10 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient10


title: L2431


title: L2421


title: Patient9 Granulocytes

description: Granulocytes purified from whole blood taken from Patient9


title: Patient10 B-cells

description: B-cells purified from whole blood taken from Patient10


title: L2424


title: Patient9 Monocytes

description: Monocytes purified from whole blood taken from Patient9


title: L2443

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: L2445


title: Patient8 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient8


title: L2434


title: Patient9 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient9


title: Patient9 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient9


title: L2438


title: L2432


title: Patient9 B-cells

description: B-cells purified from whole blood taken from Patient9


title: L2440


title: L2448


title: Patient8 Monocytes

description: Monocytes purified from whole blood taken from Patient8


title: Patient8 Granulocytes

description: Granulocytes purified from whole blood taken from Patient8


title: L2451


title: L2417


title: Patient7 Monocytes

description: Monocytes purified from whole blood taken from Patient7


title: Patient8 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient8


title: L2444


title: Patient7 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient7


title: Patient7 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient7


title: Patient8 B-cells

description: B-cells purified from whole blood taken from Patient8


title: L2449


title: Patient7 Granulocytes

description: Granulocytes purified from whole blood taken from Patient7


title: L2420


title: L2446


title: L2465


title: Patient6 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient6


title: Patient7 B-cells

description: B-cells purified from whole blood taken from Patient7


title: Patient6 Monocytes

description: Monocytes purified from whole blood taken from Patient6


title: Patient6 Granulocytes

description: Granulocytes purified from whole blood taken from Patient6


title: Patient6 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient6


title: L2456

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: L2471


title: L2469


title: Patient5 Monocytes

description: Monocytes purified from whole blood taken from Patient5


title: Patient5 Granulocytes

description: Granulocytes purified from whole blood taken from Patient5


title: L2478


title: Patient6 B-cells

description: B-cells purified from whole blood taken from Patient6


title: L2453


title: Patient5 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient5


title: Patient5 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient5


title: L2484


title: L2458


title: L2459


title: L2481


title: Patient5 B-cells

description: B-cells purified from whole blood taken from Patient5


title: Patient4 Monocytes

description: Monocytes purified from whole blood taken from Patient4


title: L2473


title: L2474


title: L2499


title: L2493


title: L2487


title: L2500


title: L2489


title: L2490


title: L2496


title: L2488


title: L2492


title: L2497


title: L2504


title: Patient4 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient4


title: Patient3 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient3


title: Patient4 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient4


title: L2506


title: Patient4 Granulocytes

description: Granulocytes purified from whole blood taken from Patient4


title: L2505


title: Patient2 Granulocytes

description: Granulocytes purified from whole blood taken from Patient2


title: L2308


title: Patient2 Monocytes

description: Monocytes purified from whole blood taken from Patient2


title: Patient2 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient2


title: Patient3 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient3


title: Patient3 B-cells

description: B-cells purified from whole blood taken from Patient3


title: Patient3 Granulocytes

description: Granulocytes purified from whole blood taken from Patient3


title: Patient4 B-cells

description: B-cells purified from whole blood taken from Patient4


title: L2494

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).


title: Patient3 Monocytes

description: Monocytes purified from whole blood taken from Patient3


title: Patient2 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient2


title: L2508


title: Patient2 B-cells

description: B-cells purified from whole blood taken from Patient2


title: L2512


title: Patient1 Granulocytes

description: Granulocytes purified from whole blood taken from Patient1


title: L2517


title: L2515


title: L2509


title: Patient1 CD4 T-cells

description: CD4 T-cells purified from whole blood taken from Patient1


title: Patient1 CD8 T-cells

description: CD8 T-cells purified from whole blood taken from Patient1


title: L2522


title: L2523


title: Patient1 Monocytes

description: Monocytes purified from whole blood taken from Patient1


title: Patient1 B-cells

description: B-cells purified from whole blood taken from Patient1


title: Patient0 Granulocytes

description:
Granulocytes purified from whole blood taken from Patient1
This sample did not pass quality control. There is no processed data for this sample.


title: L2528


title: Patient0 CD8 T-cells

description:
CD8 T-cells purified from whole blood taken from Patient1
This sample did not pass quality control. There is no processed data for this sample.


title: L2527


title: L2530


title: Patient0 Monocytes

description:
Monocytes purified from whole blood taken from Patient1
This sample did not pass quality control. There is no processed data for this sample.


title: L2534


title: Patient0 B-cells

description:
B-cells purified from whole blood taken from Patient1
This sample did not pass quality control. There is no processed data for this sample.


title: L2533


title: L2539


title: L2540


title: L2538


title: L2548


title: L2552


title: Patient0 CD4 T-cells

description:
CD4 T-cells purified from whole blood taken from Patient1
This sample did not pass quality control. There is no processed data for this sample.


title: L2554


title: L2547


title: L2567


title: L2557


title: L2564


title: L2574


title: L2572


title: L2575


title: L2570


title: L2581


title: L2565


title: L2587


title: L2582


title: L2593


title: L2589


title: L2603


title: L2608


title: L2597


title: L2628


title: L2576


title: L2629


title: L2638


title: L2630


title: isotype_ctrl_ab_group_F_4_80_CD11b_m

type: RNA

city: Fukuoka

first: Hiroyuki

last: Takahashi

address: 7-45-1 Nanakuma, Jonan-ku

department: Department of Regenerative Medicine and Transplantation

country: Japan

institute: Faculty of Medicine, Fukuoka University

hyb_protocol: cRNA was hybridized to Affymetrix Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The data were analyzed with SST-RMA summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

label: biotin

source_name: hepatic macrophage without treatment

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: male

value: liver

value: macrophage

value: CRCLM model

tag: treatment

value: control


title: isotype_ctrl_ab_group_F_4_80_CD11b_p


title: anti_CCl3_ab_group_F_4_80_CD11b_p

source_name: hepatic macrophage with treatment

value: anti-CCl3 antibody


title: L2645


title: anti_CCl3_ab_group_F_4_80_CD11b_m


title: L2646


title: MG63_mineralized_rep3

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

country: Germany

institute: Charité - Universitätsmedizin Berlin

description:
min3
adhesive MG-63 cells, incubated on mineralized porcine tibia (72 hrs, 37 °C, 5% CO2)

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization.

source_name: MG-63, mineralized bone

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: MG-63 cells were incubated with Dulbecco´s Modified Eagle Medium (10% FBS, 5% penicillin/streptomycin, 5 % L-glutamine) at 37 °C, 5% CO2 and splitted (1:5 ratio) at 80-90% confluence every 3 days.

extract_protocol: Prior to total RNA extraction, Trizol (Sigma-Aldrich) was added to the cells. Subsequent RNA isolation was carried out using RNeasy Mini Kit (Qiagen), following the manual´s instructions (trizol dependent protocol).

tag: source gender

tag: source age

tag: source tissue

value: bone

tag: source tissue type

value: osteosarcoma

tag: cell line

tag: incubated on


title: L2640

tag: gender

value: Male

tag: tissue

value: Whole blood

tag: disease state


title: MG63_demineralized_rep2

description:
demin2
adhesive MG-63 cells, incubated on demineralized porcine tibia (72 hrs, 37 °C, 5% CO2)

source_name: MG-63, demineralized bone


title: MG63_demineralized_rep4

description:
demin4
adhesive MG-63 cells, incubated on demineralized porcine tibia (72 hrs, 37 °C, 5% CO2)


title: MG63_demineralized_rep3

description:
demin3
adhesive MG-63 cells, incubated on demineralized porcine tibia (72 hrs, 37 °C, 5% CO2)


title: L2672

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).

value: granulomatous disease


title: L2674


title: L2662


title: MG63_mineralized_rep2

description:
min2
adhesive MG-63 cells, incubated on mineralized porcine tibia (72 hrs, 37 °C, 5% CO2)


title: MG63_demineralized_rep1

description:
demin1
adhesive MG-63 cells, incubated on demineralized porcine tibia (72 hrs, 37 °C, 5% CO2)


title: MG63_mineralized_rep1

description:
min1
adhesive MG-63 cells, incubated on mineralized porcine tibia (72 hrs, 37 °C, 5% CO2)


title: MG63_mineralized_rep4

description:
min4
adhesive MG-63 cells, incubated on mineralized porcine tibia (72 hrs, 37 °C, 5% CO2)


title: L2677


title: 1 uM erlotinib

city: Taipei

first: Yi-Shuan

last: Sheen

address: 7 Chun-Shan South Road

country: Taiwan

institute: Natioanl Taiwan University Hospital

description: Gene expression after 1 uM erlotinib treatment.

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent-039494 SurePrint G3 Human V2 GE 8×60K Microarray (Agilent Technologies) at 65°C for 17 hours.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature Extraction 10.5.1.1 software (Agilent Technologies), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: 1 uM erlotinib-treated HMEC-1 cells

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, CA, USA) and labeled with Cy3 (CyDye, Agilent Technologies) during the in vitro transcription process. 0.6 μg of Cy3-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: HMEC-1s (American Type Culture Collection) were cultured in EGM-2MV BulletKit (Lonza) at 37℃, 5% (v/v) CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: HMEC-1 incubated with erlotinib at concentration of 0, 0.1 µM or 1 µM for 72 h.

value: 1 uM erlotinib


title: 0 uM erlotinib

description: Gene expression after 0 uM erlotinib treatment.

source_name: 0 uM erlotinib-treated HMEC-1 cells

value: 0 uM erlotinib


title: L2678


title: 0.1 uM erlotinib

description: Gene expression after 0.1 uM erlotinib treatment.

source_name: 0.1 uM erlotinib-treated HMEC-1 cells

value: 0.1 uM erlotinib


title: L2691


title: L2687


title: L2692

value: Female


title: L2696


title: L2701


title: L2682


title: L2705


title: L32


title: L30


title: L33


title: L332


title: L347


title: L372


title: L339


title: L35


title: L348


title: L34


title: L381


title: L384


title: L38


title: L373


title: L40


title: L390


title: L391


title: L448


title: L42


title: L43


title: L445


title: L39


title: L45


title: L476


title: L47


title: L336


title: L5


title: L51


title: L48


title: L490


title: L52


title: L57


title: L340


title: L418


title: L58


title: L59


title: L592


title: L60


title: L61


title: U266_mir10a_cell

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® human Gene 2.0 ST Array, and washed according to the protocol described in WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 2).

scan_protocol: GeneChips were and stained, and scanned by Scanner 3000 7G system according to the protocol described in WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 2).

data_processing: The data were analyzed with Command Console Software ver. 3.2 and Expression Console Software ver. 1.3.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Multiple Myeloma-derived cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA.

growth_protocol: Parental cells (RPMI8226, KMS-11, U266) were cultured in RPMI1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2. They were seeded at a density of 5 × 10^5 cells/ml, and transfected with 100 nM miR-10a mimic (Ambion), or 100 nM  scrambled control (Negative Control 1; Ambion) by using HiPerFect (Qiagen). At 48 hr after transfection,  cells were collected for subsequent cytogenetic analysis.

extract_protocol: QIAzol extraction of total RNA was performed according to the manufacturer's instructions.

value: Multiple Myeloma-derived cell line transfected with miR-10a mimic


title: L56


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 79)

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

description: Gene Expression in Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat

hyb_protocol: Hybridization of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: The raw data were pre-processed and normalized using the R/Bioconductor library gcrma

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix, as per the manufacturer's instructions.

growth_protocol: Male C57BL/6J mice were obtained from Charles River at three weeks of age and were maintained on normal lab chow. Mice were housed in pairs. At twelve weeks of age, all mice received control diet as a run-in for four weeks.

extract_protocol: Total RNA was extracted fwith TRIzol reagent (Invitrogen, Carlsbad, CA), treated with DNAse and purified on columns using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products.

treatment_protocol: Mice were maintained for 1 or 4 weeks on either a HFD (45% kCal from fat) or LFD (10% kCal from fat) ( composition based on D12451 and D12450B respectively Research Diets, NJ, US). The fat source in this experiment was palm oil instead of lard.  Diets were prepared by Research Diet Services (Wijk bij Duurstede, The Netherlands). Mice were then challenged with three intraperitoneal (IP) injections of recombinant mouse leptin (2 mg/kg body weight) (R&D Systems, Abingdon, UK) or vehicle at 24, 15 and approximately 3 hours prior to killing in the early morning.

tag: strain

tag: age

value: 16 week old

tag: week

value: lept

tag: diet

value: Low Fat

value: hypothalamus


title: L62


title: KMS11_mir10a_cell


title: L63


title: U266_nega_cell

value: Multiple Myeloma-derived cell line transfected with scramble-miR control


title: P0 Ovary ELAVL2 RIP-Seq

city: Mishima

first: Yuzuru

last: Kato

state: Shizuoka

address: 1111 Yata

department: Division of Mammalian Development

institute: National Institute of Genetics

data_processing:
Basecalls and Demultiplexing were performed using CASAVA version 1.8.2
Quality check of RIP-Seq reads was performed using FastQC version 0.11.2 and any duplicated reads were discarded
The RIP-Seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.8b with no-multiplehit option
Peakcalls performed using MACS2 version 2.1.0.20140616 with following options; nomodel,  q-value cutoff = 0.05, broad region calling is off
The peaks were annotated using ChIPpeakAnno and biomaRt; reference database is Ensembl
Genome_build: mm10
Supplementary_files_format_and_content: tsv files were generated using MACS2 and R; the peak file can be modified to load IGV
Supplementary_files_format_and_content: Elavl2_MACS2Out_16dec2015_peaks.tsv: Result of MACS2 peakcalls
Supplementary_files_format_and_content: elavl2.rip_narrow_peak.ENSMUSG-gene_id.tsv: Annotated peaks with ENSMUSG IDs

source_name: P0 ovary

growth_protocol: Mice were housed in special pathogen free room

extract_protocol:
One hundred newborn ovaries were homogenized in IP buffer (20 mM HEPES/KOH, pH7.5, 150 mM NaCl, 2.5 mM MgCl2, 0.1% NP-40, 1 mM dithiothreitol, 1× protease inhibitor cocktail (Roche), 100 U ml-1 RNase inhibitor (Takara)),and the debris was removed by centrifugation (10000 × g at 4°C for 10 min).The supernatants were incubated with magnetic beads conjugated to protein G (Invitrogen), which were pre-incubated with anti-ELAVL2 antibody (5 μg, Protein tech, 14008-1-AP) at 4°C for 2 hours.The lysate-bead mixtures were then incubated at 4°C for 6 hours with gentle rotation. The bead-antibody complexes were washed thrice with IP buffer and transferred to fresh 1.5 ml tubes. The complexes were washed again with IP buffer. The precipitated proteins and RNA were eluted by incubating the beads-antibody complex with the elution buffer (IP buffer containing 0.5% SDS) at 70°C for 5 min. Input samples (5% of starting materials) were taken from the centrifuged supernatants. Input and eluted samples were dissolved in TRIzol reagent (Invitrogen), and total RNAs were extracted according to the manufacture's protocol. The quality of RNAs was checked using the 2100 Bioanalyzer (Agilent).
Anti-sense RNAs were amplified by using TargetAmp 1-Round aRNA Amplification Kit 103 (Epicentre) according to the manufacture's protocol, and sequence libraries were then generated using the KAPA Stranded mRNA-Seq Kit Illumina platform (KAPA Biosystems) according to the manufacturer's protocol.  The resulting libraries were sequenced on the Illumina GAIIx (single end 36 base reads with TruSeq SBS kit v5 for GA., Illumina).

treatment_protocol: Newborn ovaries were disected in ice-cold PBS and were immeadiately frozen in liquid nitrogen. Frozen tissues were stored at -80 degree until the use.

value: ovary

tag: rip antibody

value: ELAVL2 (Protein tech, 14008-1-AP)


title: RNAseq_ENB_9T

city: Illkirch

first: Gabriel

middle: G

last: Malouf

address: 1 rue Laurent Fries

department: Cancer and functional genomics

country: France

institute: IGBMC

description: esthesineuroblastomas-rnase-profile-GM-02-normlizedData.txt

data_processing:
The raw reads in FASTQ format were aligned to the reference human genome, hg19, using MOSAIK alignment software. MOSAIK implemented Smith-Waterman algorithm to perform gapped alignment.
The overlaps between aligned reads and annotated genes were counted using HTSeq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). The gene counts were normalized using the scaling factor method.
If the number of overlapped read of any given gene is less than one per million total mapped read for all samples, this gene was excluded from further analysis.
ENB-14T is a outlier, which was excluded from the down-stream analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each Sample.

source_name: Primary tumor

extract_protocol:
RNA extraction was performed using the RNeasy Kit (Qiagen) according to the manufacturer’s instructions. Quality control of extracted nucleic acids was done using Agilent® bioanalyzer.
Total RNA for each sample was converted into a library of template molecules for sequencing on the Illumina HiSeq 2000 according to the NuGen Ovation RNA-Seq System V2 protocol.
Libraries were quantitated by qPCR (KAPA Systems), multiplexed and sequenced, 4 samples per lane, on the HiSeq2000 using 75 bp paired-end sequencing.

value: Esthesioneuroblastomas


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 78)

value: male


title: L65

value: Male


title: RPMI8226_mir10a_cell


title: P0 Ovary Input RNA


title: RNAseq_ENB_8T


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 75)

description: Gene Expression in Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 76)

description: Gene Expression in Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat

value: High Fat


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 77)


title: L66

value: Whole blood

value: granulomatous disease


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 74)


title: RPMI8226_nega_cell


title: KMS11_nega_cell


title: Old culture-activated HSCs PRI-724

city: Setagaya

first: Keisuke

last: Oboki

address: 2-1-6 Kamikitazawa

department: Center for Medical Research Cooperation

institute: TOKYO METROPOLITAN INSTITUTE of MEDICAL SCIENCE

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Gene 2.0 ST Array using the GeneChip WT PLUS Reagent Kit. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: CEL files converted by using the Expression Console Software (Affymetrix). Raw intensity values from each chip were normalized using the RMA algorithm and global scaling as normalization method.

source_name: Old culture-activated HSCs PRI-724

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA by using GeneChip WT PLUS Reagent Kit.

growth_protocol: Mouse primary HSCs were isolated and were pooled from five mice (8-11 week-old or 6-9 month-old) .The isolated HSCs were cultured in uncoated plastic dishes with DMEM high glucose supplemented with 10% fetal bovine serum, 10 mM sodium pyruvate, MEM Non-essential amino acids, 15 mM HEPES, and antibiotic solution at 37°C in 5% CO2.

extract_protocol: RNeasy Total RNA Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The quiescent HSCs were obtained from normal liver after plating the HSCs for 12 hours. Activated HSCs were obtained by continuous culture of quiescent HSCs for more than 20 days with replacement of medium in every 5 days. The activated HSCs were treated with or without C-82 (10 μM, Prism Pharma) dissolved in dimethyl sulfoxide (DMSO).

tag: developmental stage

value: old (6-9 month-old)

tag: activation status

value: culture activated


title: Young culture-activated HSCs PRI-724

source_name: Young culture-activated HSCs PRI-724

value: young (8-11 week-old)

tag: treatment


title: Old culture-activated HSCs vehicle

source_name: Old culture-activated HSCs vehicle

value: vehicle


title: Old HSCs quiescent

source_name: Old HSCs quiescent

value: quiescent

value: no


title: Young culture-activated HSCs vehicle

source_name: Young culture-activated HSCs vehicle


title: Young HSCs quiescent

source_name: Young HSCs quiescent


title: RNAseq_ENB_6T


title: L68

source_name: Leprosy


title: L69

value: Female


title: RNAseq_ENB_5T


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 73)

description: Gene Expression in Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat

value: 16 week old

value: ctrl

value: hypothalamus


title: RNAseq_ENB_59T


title: L7


title: RNAseq_ENB_52T


title: L70


title: L71


title: L73


title: RNAseq_ENB_4T


title: L74


title: RNAseq_ENB_23T


title: RNAseq_ENB_22T


title: RNAseq_ENB_21T


title: L76


title: L2544


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 69)

value: lept

value: Low Fat


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 71)

value: male


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 70)


title: L77

value: Male


title: RNAseq_ENB_24T

value: Esthesioneuroblastomas


title: L78

value: Whole blood


title: RNAseq_ENB_1T


title: L75

value: granulomatous disease


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 65)

description: Gene Expression in Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat

value: High Fat


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 66)


title: RNAseq_ENB_19T


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 68)


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: High Fat (sample 72)


title: L79


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 67)


title: RNAseq_ENB_17T


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 61)


title: RNAseq_ENB_20T


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 63)

description: Gene Expression in Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 62)


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: Low Fat (sample 60)


title: L797


title: RNAseq_ENB_15T


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 64)


title: RNAseq_ENB_14T


title: phyA-211_4 day_rep1

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: After Far-red light treatment

hyb_protocol: Following the standard Agilent protocols, labeled cRNA was hybridized to Agilent SurePrint G3 Arabidopsis 8x60K microarray chips containing 61,657 probes (Agilent, G4102A-031025).

scan_protocol: The hybridized chips were scanned with Agilent SureScan microarray scanner (Agilent, Santa Clara, CA). The array images were analyzed by Feature Extraction software (version 11.5.1.1; Agilent, Santa Clara, CA) to obtain the raw data.

data_processing: Quantile-normalization was performed for the log2-value of gMedianSignal

organism: Arabidopsis thaliana

source_name: the third and fourth leaves from 3-week-grown plants

label_protocol: The complementary RNA (cRNA) was generated using the Low input quick amp labeling kit (Agilent, 5190-2305) according to the standard Agilent One-Color microarray protocols. Re-verse transcription of the total RNA to double-stranded complementary DNA (cDNA) was per-formed, followed by synthesis of cRNA. cRNA was labeled with Cy3-dCTP.

growth_protocol: Arabidopsis thaliana plants were grown in an environmentally controlled growth room (Korea Instruments, Seoul, Korea) under long day (16 h light / 8 h dark) cycle at 22 ºC and 100 μmol m-2 s-1 of white light.

extract_protocol: Total RNA was obtained from detached leaves of Arabidopsis before and after FR light treat-ment (0 day and 4 days) using WelPrep total RNA isolation reagent (WELGENE, Daegu, Re-public of Korea). RNA purity and integrity were evaluated by NanoDrop 2000 (Thermo Fisher Scientific, NanoDrop Products, Wilmington, DE) and Bioanalyzer 2100 (Agilent, Santa Clara, CA), respectively, and the samples with their RNA integrity number ≥ 7 were used.

treatment_protocol: For light treatment, detached leaves and whole plants were incubated in growth chamber under continuous  far-red (730 nm) light with 1 μmol m-2 s-1 of LED.

tag: mutants

tag: days

value: 4 days

tag: replicates


title: L801


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 59)


title: L81


title: phyA-211_4 day_rep2

description: After Far-red light treatment


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 57)


title: phyB-9_0 day_rep2

description: Before Far-red light treatment

value: 0 day


title: L795


title: RNAseq_ENB_12T


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: High Fat (sample 58)


title: L83


title: phyB-9_4 day_rep2

description: After Far-red light treatment


title: phyB-9_4 day_rep1

description: After Far-red light treatment


title: L834


title: Col-0_4 day_rep1

description: After Far-red light treatment

value: Col-0 (Wild type)


title: Col-0_4 day_rep2

description: After Far-red light treatment


title: L835


title: RNAseq_ENB_13T


title: L85


title: pNET_Ser5P_mock_rep2

city: Guangzhou

first: Zhicheng

last: Dong

state: Guangdong

address: 230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Guangzhou University

description: nascent RNA

data_processing:
Library strategy: PNET-seq
After trimming of adapter and filtering of low quality data by Cutadapt v1.2.1, reads originating from rRNA were filtered by aligning against an index consisting of the 45S and 5S transcripts using STAR v2.5.3a and unmapped reads were subsequently aligned to the Arabidopsis genome TAIR10. Only uniquely mapped reads were retained, and the 5 coordinate of each read was used as the position of engaged polymerase.
genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include counts of engaged Pol II at each position on chromosome

source_name: seedling

growth_protocol: The Arabidopsis (Col-0 ecotype) seeds were germinated and grown in 1/2 MS for 12 days at 20°C under 16 hour light/8 hour dark.

extract_protocol:
The tissue powder was solubilized in 30 ml lysis buffer (50 mM HEPES, pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 10% glycerol, 5 mM 2-mercaptoethanol, 2 μg/ml pepstatin A, 2 μg/ml aprotinin, 1 mM PMSF), mixed well and filtrated through 110 μm nylon mesh and a 40 μm cell strainer.  The nuclei were spanned down at 3,200 g for 20 min at 4°C, followed by two washes with HBB buffer (25 mM Tris–HCl, pH 7.6, 0.44 M sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM 2-mercaptoethanol) and HBC buffer (20 mM Tris–HCl, pH 7.5, 352 mM sucrose, 8 mM MgCl2, 0.08% Triton-X, 8 mM 2-mercaptoethanol, 20% glycerol).
The obtained nuclei pellet were resuspended with 1 ml MNase buffer (20 mM Tris–HCl, pH 8.0, 5 mM NaCl, and 2.5 mM CaCl2) and digested with 20 U MNase (TaKaRa, 20U/μl) for 5 minutes at 37°C rotating at 1,400 rpm. Stopped the digestion by adding 40 μl 500 mM EDTA. Pol II-nascent RNA complex was released by mild sonication. Supernatants were collected by centrifuging at 16,000 g for 5 min at 4°C and Pol II complex were immunoprecipitated according to Nojima et al. [14]. The Pol II bond nascent RNAs were treated by T4 PNK on beads and extracted with 500μl TRIzol Reagent (Invitogen). The IP RNA was resolved on an 8% TBE-urea polyacrylamide gel and RNA with size from 35-100 nt was recovered. The 35-100 nt IP RNA was used to construct the NET-SEQ cDNA library with NEXTflex™ Small RNA-Seq Kit v3 (Bioo Scientific) according to the manual. The cDNA library was resolved in a non-denaturing 6% TBE polyacrylamide gel and size region 150-230 bp was recovered. cDNA library concentration was determined by Qubit QuantIT (Invitrogen) and kapa quantitative realtime PCR.

treatment_protocol: samples were treated with DMSO for one hour

tag: ecotype

value: seedling

value: 12 days

tag: antibody

value: name:CMA603; Clonality:Monoclonal; Supplier:MBL Life science; Catalog number:MABI0603


title: pNET_Ser5P_FP_rep1

description: nascent RNA

treatment_protocol: samples were treated with flavopyridol for one hour


title: pNET_Ser5P_FP_rep2

description: nascent RNA


title: L86


title: pNET_Ser2P_FP_rep2

description: nascent RNA

value: name:CMA602; Clonality:Monoclonal; Supplier:MBL Life science; Catalog number:MABI0602


title: pNET_Ser5P_mock_rep1

description: nascent RNA


title: Mouse hypothalamus,Week: 1,  Treament:  lept,  Diet: Low Fat (sample 56)

value: 16 week old


title: phyB-9_0 day_rep1

description: Before Far-red light treatment


title: L87


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 54)

value: hypothalamus


title: phyA-211_0 day_rep2

description: Before Far-red light treatment


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 53)

description: Gene Expression in Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat

value: ctrl


title: Col-0_0 day_rep2

description: Before Far-red light treatment


title: Mouse hypothalamus,Week: 4,  Treament:  ctrl,  Diet: Low Fat (sample 52)

value: Low Fat


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 55)

value: male

value: lept


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 51)


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: High Fat (sample 50)


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 49)

description: Gene Expression in Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat


title: phyA-211_0 day_rep1

description: Before Far-red light treatment


title: L886

description: Genomic DNA extracted from whole blood was genotyped using Human610-Quad BeadChip (Illumina).

value: Male


title: pNET_Ser2P_mock_rep2

description: nascent RNA


title: L888

value: Whole blood


title: pNET_Ser2P_mock_rep1

description: nascent RNA


title: pNET_Ser2P_FP_rep1

description: nascent RNA


title: L889

value: Female

value: granulomatous disease


title: L89


title: L88


title: pNET_unph_FP_rep1

description: nascent RNA

value: name:8WG16; Clonality:Monoclonal; Supplier:Abcam; Catalog number:Ab817


title: pNET_unph_FP_rep2

description: nascent RNA


title: Col-0_0 day_rep1

description: Before Far-red light treatment

value: 0 day


title: L9


title: Mouse hypothalamus,Week: 4,  Treament:  lept,  Diet: High Fat (sample 47)

value: High Fat


title: Mouse hypothalamus,Week: 1,  Treament:  ctrl,  Diet: Low Fat (sample 48)