title: post-vaccination blood sample from donor 2083

source_name: Blood sample from donor 2083

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: 201516350011_R01C01

status: Public on May 19 2020

type: genomic

city: London

first: Oliver

last: Robinson

state: London

address: St Mary's Campus, Norfolk Place

department: School of Public Health

country: United Kingdom

institute: IMPERIAL COLLEGE LONDON

description: normal blood sample

hyb_protocol: Then, bisulfite-converted DNA was used for hybridization on the Infinium HumanMethylation EPIC BeadChip, following the Illumina Infinium HD Methylation protocol. Briefly, a whole genome amplification step was followed by enzymatic end-point fragmentation and hybridization to HumanMethylation EPIC BeadChips at 48°C for 17 h, followed by single nucleotide extension. The incorporated nucleotides were labelled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP).

scan_protocol: the BeadChip was scanned using the Illumina HiScan SQ scanner. The intensities of the images were extracted using in-house software written for the R statistical computing environment. The methylation score for each CpG was represented as a β-value according to the fluorescent intensity ratio representing any value between 0 (unmethylated) and 1 (completely methylated).

data_processing:
DNA methylation (DNAm) data were pre-processed and normalized using in-house software written for the R statistical computing environment, including background and color bias correction, quantile normalization, and Beta MIxture Quantile dilation (BMIQ) procedure to remove type I/type II probes bias, as described elsewhere (Fiorito et al., 2017). DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values). Cross-reactive and polymorphic probes - with minor allele frequency greater than 0.01 in Europeans (Y. A. Chen et al., 2013) - were excluded. Methylation measures were set to missing if the detection p-value was greater than 0.01. Samples with the bisulfite conversion control fluorescence intensity lower than 10,000 for both type I and type II probes and those with total call rate lower than 95% were excluded. Finally, samples were excluded if the predicted sex (based on chromosome X methylation) did not match that self-reported.
DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values).

molecule: genomic DNA

organism: Homo sapiens

source_name: blood samples

extract_protocol: bisulphite conversion of 500 ng of each DNA sample was performed using the EZ DNA Methylation-Lightning Kit according to the manufacturer’s protocol (Zymo Research, Orange, CA).

tag: age

tag: Sex

value: F

tag: person id

tag: disease state

value: normal


title: 201516350011_R02C01

description: normal blood sample

label: biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP)

label_protocol: Illumina Infinium HD Methylation protocol

value: M


title: 201516350009_R08C01

description: normal blood sample


title: 201516350009_R06C01

description: normal blood sample


title: post-vaccination blood sample from donor 2061

type: RNA

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

country: USA

institute: Northwestern University

description: post-vaccination blood transcriptional profilling

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45oC with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: The data were analyzed with preprocessed in R using the RMA normalization method.

label: biotin

molecule: total RNA

source_name: Blood sample from donor 2061

label_protocol: Nugen amplification protocol

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: Blood

tag: donor set

tag: vaccination time

value: post-vaccination

tag: visit number

tag: hepatitis b average concentration (unit)

value: mIU/mL

tag: hepatitis b average concentration (pre-vax)

value: IU/mL

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

value: 1/dilution factor

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)

tag: gender


title: 201516350009_R07C01

description: normal blood sample


title: 201516350009_R05C01

description: normal blood sample


title: post-vaccination blood sample from donor 2063

source_name: Blood sample from donor 2063

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 2062

source_name: Blood sample from donor 2062

tag: donor set

tag: vaccination time

tag: age


title: post-vaccination blood sample from donor 2057

source_name: Blood sample from donor 2057

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)


title: post-vaccination blood sample from donor 2065

source_name: Blood sample from donor 2065

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)


title: post-vaccination blood sample from donor 2060

source_name: Blood sample from donor 2060

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 2059

source_name: Blood sample from donor 2059

tag: tissue

tag: donor

tag: gender


title: post-vaccination blood sample from donor 2055

source_name: Blood sample from donor 2055

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)


title: post-vaccination blood sample from donor 2058

source_name: Blood sample from donor 2058

tag: donor set

tag: vaccination time

tag: diphtheria average concentration (post-vax)


title: 201516350009_R04C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state


title: 201516350009_R02C01

description: normal blood sample


title: 201516350009_R03C01

description: normal blood sample


title: 201516350009_R01C01

description: normal blood sample


title: 201516350007_R07C01

description: normal blood sample


title: 201516350007_R08C01

description: normal blood sample


title: 201516350007_R06C01

description: normal blood sample


title: 201516350007_R05C01

description: normal blood sample


title: post-vaccination blood sample from donor 2051

source_name: Blood sample from donor 2051

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)


title: post-vaccination blood sample from donor 2052

source_name: Blood sample from donor 2052

tag: tissue

tag: donor

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)

tag: gender


title: 201516350007_R04C01

description: normal blood sample


title: 201516350007_R03C01

description: normal blood sample


title: 201516350007_R02C01

description: normal blood sample


title: post-vaccination blood sample from donor 2056

source_name: Blood sample from donor 2056

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 2053

source_name: Blood sample from donor 2053

tag: visit number

tag: hepatitis b average concentration (unit)

tag: age


title: post-vaccination blood sample from donor 2047

source_name: Blood sample from donor 2047

tag: hepatitis b average concentration (pre-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)


title: post-vaccination blood sample from donor 2050

source_name: Blood sample from donor 2050

tag: tissue

tag: donor

tag: tetanus average concentration (post-vax)


title: post-vaccination blood sample from donor 2054

source_name: Blood sample from donor 2054

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 2049

source_name: Blood sample from donor 2049

tag: donor set

tag: vaccination time

tag: gender


title: post-vaccination blood sample from donor 2044

source_name: Blood sample from donor 2044

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)


title: post-vaccination blood sample from donor 2048

source_name: Blood sample from donor 2048

tag: visit number

tag: hepatitis b average concentration (unit)

tag: diphtheria average concentration (post-vax)


title: 201516350007_R01C01

description: normal blood sample

source_name: blood samples

tag: age

tag: Sex

tag: person id

tag: disease state


title: 201516350006_R07C01

description: normal blood sample


title: 201516350006_R08C01

description: normal blood sample


title: post-vaccination blood sample from donor 2045

source_name: Blood sample from donor 2045

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)


title: post-vaccination blood sample from donor 2043

source_name: Blood sample from donor 2043

tag: donor set

tag: vaccination time

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)

tag: gender


title: post-vaccination blood sample from donor 2042

source_name: Blood sample from donor 2042

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 2046

source_name: Blood sample from donor 2046

tag: tissue

tag: donor

tag: age


title: post-vaccination blood sample from donor 2041

source_name: Blood sample from donor 2041

tag: hepatitis b average concentration (pre-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)


title: post-vaccination blood sample from donor 2040

source_name: Blood sample from donor 2040

tag: donor set

tag: vaccination time

tag: tetanus average concentration (post-vax)


title: 201516350006_R06C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2037

source_name: Blood sample from donor 2037

tag: visit number

tag: hepatitis b average concentration (unit)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)

tag: gender


title: 201516350006_R04C01

description: normal blood sample


title: post-vaccination blood sample from donor 2039

source_name: Blood sample from donor 2039

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 2036 technical replicate

source_name: Blood sample from donor 2036

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: age


title: 201516350006_R03C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516350003_R08C01

description: normal blood sample


title: 201516350006_R05C01

description: normal blood sample


title: 201516350006_R02C01

description: normal blood sample


title: 201516350003_R06C01

description: normal blood sample


title: 201516350006_R01C01

description: normal blood sample


title: 201516350003_R07C01

description: normal blood sample


title: 201516350003_R05C01

description: normal blood sample


title: post-vaccination blood sample from donor 2033

source_name: Blood sample from donor 2033

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: 201516350003_R04C01

description: normal blood sample


title: 201516350003_R03C01

description: normal blood sample


title: 201516350003_R02C01

description: normal blood sample


title: 201516350001_R08C01

description: normal blood sample


title: post-vaccination blood sample from donor 2035

source_name: Blood sample from donor 2035

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: gender


title: post-vaccination blood sample from donor 2034

source_name: Blood sample from donor 2034

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)


title: post-vaccination blood sample from donor 2030

source_name: Blood sample from donor 2030

tag: visit number

tag: hepatitis b average concentration (unit)

tag: age


title: 201516350001_R07C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2029

source_name: Blood sample from donor 2029

tag: tissue

tag: donor

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 2032

source_name: Blood sample from donor 2032

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: gender


title: post-vaccination blood sample from donor 2031

source_name: Blood sample from donor 2031

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)


title: post-vaccination blood sample from donor 2027

source_name: Blood sample from donor 2027

tag: tissue

tag: donor

tag: age


title: 201516350001_R06C01

description: normal blood sample

source_name: blood samples

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2026

source_name: Blood sample from donor 2026

tag: donor set

tag: vaccination time

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 2023

source_name: Blood sample from donor 2023

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: gender


title: 201516350001_R04C01

description: normal blood sample


title: 201516350003_R01C01

description: normal blood sample


title: 201516350001_R02C01

description: normal blood sample


title: 201516350001_R03C01

description: normal blood sample


title: post-vaccination blood sample from donor 2024

source_name: Blood sample from donor 2024

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)


title: 201516340039_R08C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state


title: 201516350001_R05C01

description: normal blood sample


title: 201516340039_R07C01

description: normal blood sample


title: 201516350001_R01C01

description: normal blood sample


title: 201516340039_R06C01

description: normal blood sample


title: 201516340039_R04C01

description: normal blood sample


title: post-vaccination blood sample from donor 2021

source_name: Blood sample from donor 2021

tag: donor set

tag: vaccination time

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: cholera normalized titer (post-vax)


title: 201516340039_R03C01

description: normal blood sample


title: post-vaccination blood sample from donor 2016

source_name: Blood sample from donor 2016

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: gender


title: post-vaccination blood sample from donor 2018

source_name: Blood sample from donor 2018

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)


title: post-vaccination blood sample from donor 2014

source_name: Blood sample from donor 2014

tag: donor set

tag: vaccination time

tag: age


title: post-vaccination blood sample from donor 2011

source_name: Blood sample from donor 2011

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 2022

source_name: Blood sample from donor 2022

tag: visit number

tag: hepatitis b average concentration (unit)

tag: cholera normalized titer (post-vax)


title: 201516340039_R01C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2013

source_name: Blood sample from donor 2013

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: gender


title: 201516340039_R02C01

description: normal blood sample


title: post-vaccination blood sample from donor 2019

source_name: Blood sample from donor 2019

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)


title: post-vaccination blood sample from donor 2017

source_name: Blood sample from donor 2017

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)

tag: age


title: post-vaccination blood sample from donor 2020

source_name: Blood sample from donor 2020

tag: tissue

tag: donor

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 2025

source_name: Blood sample from donor 2025

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)


title: 201516340035_R08C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516340035_R07C01

description: normal blood sample


title: 201516340035_R06C01

description: normal blood sample


title: post-vaccination blood sample from donor 2015

source_name: Blood sample from donor 2015

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: gender


title: post-vaccination blood sample from donor 2012

source_name: Blood sample from donor 2012

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)


title: 201516340035_R04C01

description: normal blood sample

source_name: blood samples

tag: age


title: 201516340035_R05C01

description: normal blood sample


title: post-vaccination blood sample from donor 2010

source_name: Blood sample from donor 2010

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: cholera normalized titer (post-vax)


title: 201516340035_R03C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2006

source_name: Blood sample from donor 2006

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: gender


title: 201516340035_R02C01

description: normal blood sample


title: 201516340035_R01C01

description: normal blood sample


title: post-vaccination blood sample from donor 2004

source_name: Blood sample from donor 2004

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 2007

source_name: Blood sample from donor 2007

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: age


title: post-vaccination blood sample from donor 2009

source_name: Blood sample from donor 2009

tag: donor set

tag: vaccination time

tag: cholera normalized titer (post-vax)


title: 201516340009_R08C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516340009_R07C01

description: normal blood sample


title: 201516340009_R05C01

description: normal blood sample


title: 201516340009_R06C01

description: normal blood sample


title: 201516340009_R04C01

description: normal blood sample


title: 201516340009_R03C01

description: normal blood sample


title: post-vaccination blood sample from donor 2001

source_name: Blood sample from donor 2001

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: gender


title: 201516340009_R02C01

description: normal blood sample


title: post-vaccination blood sample from donor 2003

source_name: Blood sample from donor 2003

tag: tissue

tag: donor

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 1071

source_name: Blood sample from donor 1071

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: age


title: post-vaccination blood sample from donor 1070

source_name: Blood sample from donor 1070

tag: visit number

tag: hepatitis b average concentration (unit)

tag: cholera normalized titer (post-vax)


title: 201516340009_R01C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1069

source_name: Blood sample from donor 1069

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: gender


title: post-vaccination blood sample from donor 1067

source_name: Blood sample from donor 1067

tag: donor set

tag: vaccination time

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 1072

source_name: Blood sample from donor 1072

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: age


title: 201516340003_R07C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1068

source_name: Blood sample from donor 1068

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1065

source_name: Blood sample from donor 1065

tag: donor set

tag: vaccination time

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: gender


title: post-vaccination blood sample from donor 1063

source_name: Blood sample from donor 1063

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: cholera normalized titer (pre-vax)


title: 201516340003_R06C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state


title: 201516340003_R08C01

description: normal blood sample


title: post-vaccination blood sample from donor 1062

source_name: Blood sample from donor 1062

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1066

source_name: Blood sample from donor 1066

tag: donor set

tag: vaccination time

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: gender


title: 201516340003_R04C01

description: normal blood sample

source_name: blood samples


title: 201516340003_R05C01

description: normal blood sample


title: 201516340003_R03C01

description: normal blood sample


title: 201516340003_R01C01

description: normal blood sample


title: post-vaccination blood sample from donor 1061

source_name: Blood sample from donor 1061

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: cholera normalized titer (pre-vax)


title: 201516330058_R07C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1064

source_name: Blood sample from donor 1064

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: cholera normalized titer (post-vax)


title: 201516330058_R06C01

description: normal blood sample


title: 201516330058_R05C01

description: normal blood sample


title: 201516330058_R04C01

description: normal blood sample


title: 201516340003_R02C01

description: normal blood sample


title: 201516330058_R02C01

description: normal blood sample


title: 201516330058_R01C01

description: normal blood sample


title: post-vaccination blood sample from donor 2005

source_name: Blood sample from donor 2005

tag: donor set

tag: vaccination time

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: gender


title: post-vaccination blood sample from donor 1059

source_name: Blood sample from donor 1059

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 1057

source_name: Blood sample from donor 1057

tag: tissue

tag: donor

tag: age


title: 201516330057_R08C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516330057_R07C01

description: normal blood sample


title: post-vaccination blood sample from donor 1058

source_name: Blood sample from donor 1058

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1054

source_name: Blood sample from donor 1054

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: gender


title: 201516330057_R06C01

description: normal blood sample


title: 201516330057_R05C01

description: normal blood sample


title: post-vaccination blood sample from donor 1060

source_name: Blood sample from donor 1060

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: cholera normalized titer (pre-vax)


title: 201516330058_R03C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 2036

source_name: Blood sample from donor 2036

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1050

source_name: Blood sample from donor 1050

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: gender


title: post-vaccination blood sample from donor 1055

source_name: Blood sample from donor 1055

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 1049

source_name: Blood sample from donor 1049

tag: donor set

tag: vaccination time

tag: age


title: post-vaccination blood sample from donor 1046

source_name: Blood sample from donor 1046

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (unit)


title: post-vaccination blood sample from donor 1045

source_name: Blood sample from donor 1045

tag: visit number

tag: hepatitis b average concentration (unit)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1051

source_name: Blood sample from donor 1051

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)


title: post-vaccination blood sample from donor 1044

source_name: Blood sample from donor 1044

tag: tissue

tag: donor

tag: gender


title: post-vaccination blood sample from donor 1048

source_name: Blood sample from donor 1048

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)


title: 201516330057_R03C01

description: normal blood sample

source_name: blood samples

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1052

source_name: Blood sample from donor 1052

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: cholera normalized titer (pre-vax)

tag: age


title: 201516330057_R04C01

description: normal blood sample


title: post-vaccination blood sample from donor 1056

source_name: Blood sample from donor 1056

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (post-vax)


title: 201516330057_R02C01

description: normal blood sample


title: post-vaccination blood sample from donor 1047

source_name: Blood sample from donor 1047

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)

tag: gender


title: 201516330057_R01C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1043

source_name: Blood sample from donor 1043

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: cholera normalized titer (pre-vax)


title: 201516340039_R05C01

description: normal blood sample

tag: age


title: 201516330054_R08C01

description: normal blood sample


title: 201516330054_R07C01

description: normal blood sample


title: 201516330054_R06C01

description: normal blood sample


title: 201516330054_R05C01

description: normal blood sample


title: 201516330054_R02C01

description: normal blood sample


title: 201516330054_R01C01

description: normal blood sample


title: 201516330053_R08C01

description: normal blood sample


title: 201516330053_R07C01

description: normal blood sample


title: 201516330054_R03C01

description: normal blood sample


title: 201516330053_R06C01

description: normal blood sample


title: 201516330054_R04C01

description: normal blood sample


title: post-vaccination blood sample from donor 1041

source_name: Blood sample from donor 1041

tag: visit number

tag: hepatitis b average concentration (unit)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1042

source_name: Blood sample from donor 1042

tag: tissue

tag: donor

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)

tag: gender


title: post-vaccination blood sample from donor 1039

source_name: Blood sample from donor 1039

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (pre-vax)


title: post-vaccination blood sample from donor 1040

source_name: Blood sample from donor 1040

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 1037

source_name: Blood sample from donor 1037

tag: visit number

tag: hepatitis b average concentration (unit)

tag: age


title: post-vaccination blood sample from donor 1032

source_name: Blood sample from donor 1032

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)


title: post-vaccination blood sample from donor 1035

source_name: Blood sample from donor 1035

tag: tissue

tag: donor

tag: cholera normalized titer (post-vax)


title: 201516330053_R04C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516330053_R05C01

description: normal blood sample


title: 201516330053_R02C01

description: normal blood sample


title: post-vaccination blood sample from donor 1033

source_name: Blood sample from donor 1033

tag: donor set

tag: vaccination time

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)

tag: gender


title: post-vaccination blood sample from donor 1036

source_name: Blood sample from donor 1036

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 1030

source_name: Blood sample from donor 1030

tag: tissue

tag: donor

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: age


title: post-vaccination blood sample from donor 1034

source_name: Blood sample from donor 1034

tag: donor set

tag: vaccination time

tag: cholera normalized titer (post-vax)


title: 201516330053_R03C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516330053_R01C01

description: normal blood sample


title: 201516330040_R08C01

description: normal blood sample


title: post-vaccination blood sample from donor 1031

source_name: Blood sample from donor 1031

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)

tag: gender


title: post-vaccination blood sample from donor 1029

source_name: Blood sample from donor 1029

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 1025

source_name: Blood sample from donor 1025

tag: donor set

tag: vaccination time

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: age


title: 201516330040_R07C01

description: normal blood sample

source_name: blood samples

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1026

source_name: Blood sample from donor 1026

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1024

source_name: Blood sample from donor 1024

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: gender


title: post-vaccination blood sample from donor 1028

source_name: Blood sample from donor 1028

tag: donor set

tag: vaccination time

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (pre-vax)


title: 201516330040_R06C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1023

source_name: Blood sample from donor 1023

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1021

source_name: Blood sample from donor 1021

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: gender


title: post-vaccination blood sample from donor 1027

source_name: Blood sample from donor 1027

tag: donor set

tag: vaccination time

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (pre-vax)


title: 201516330040_R05C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1022

source_name: Blood sample from donor 1022

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (post-vax)


title: 201516330040_R04C01

description: normal blood sample


title: post-vaccination blood sample from donor 1020

source_name: Blood sample from donor 1020

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: gender


title: post-vaccination blood sample from donor 1019

source_name: Blood sample from donor 1019

tag: donor set

tag: vaccination time

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (pre-vax)


title: 201516330040_R02C01

description: normal blood sample

tag: age

tag: Sex

tag: person id

tag: disease state


title: 201516330040_R01C01

description: normal blood sample


title: 201516330040_R03C01

description: normal blood sample


title: 201516330036_R08C01

description: normal blood sample


title: post-vaccination blood sample from donor 1017

source_name: Blood sample from donor 1017

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (post-vax)


title: 201516330036_R07C01

description: normal blood sample


title: 201516330036_R06C01

description: normal blood sample


title: 201516330036_R05C01

description: normal blood sample


title: 201516330036_R03C01

description: normal blood sample


title: 201516330036_R04C01

description: normal blood sample


title: 201516330036_R02C01

description: normal blood sample


title: post-vaccination blood sample from donor 1016

source_name: Blood sample from donor 1016

tag: tissue

tag: donor

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: gender


title: post-vaccination blood sample from donor 1014

source_name: Blood sample from donor 1014

tag: donor set

tag: vaccination time

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (pre-vax)


title: post-vaccination blood sample from donor 1015

source_name: Blood sample from donor 1015

tag: visit number

tag: hepatitis b average concentration (unit)

tag: age


title: post-vaccination blood sample from donor 1011

source_name: Blood sample from donor 1011

tag: hepatitis b average concentration (post-vax)

tag: diphtheria average concentration (unit)

tag: cholera normalized titer (unit)


title: post-vaccination blood sample from donor 1013

source_name: Blood sample from donor 1013

tag: tissue

tag: donor

tag: cholera normalized titer (post-vax)


title: post-vaccination blood sample from donor 1009

source_name: Blood sample from donor 1009

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)


title: post-vaccination blood sample from donor 1010

source_name: Blood sample from donor 1010

tag: donor set

tag: vaccination time

tag: gender


title: 201516330033_R06C01

description: normal blood sample

source_name: blood samples

tag: Sex

tag: person id

tag: disease state


title: 201516330033_R05C01

description: normal blood sample


title: fangf

type: SRA

city: Wenzhou

first: Zhao

last: Qiongya

address: Chashan Street

country: China

institute: Wenzhou Medical University

library_source: genomic

data_processing:
library strategy: Exome sequencing
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
The reads were first aligned to the GRCh37 build of the human reference genome using Burrows-Wheeler Aligner (BWA).
Variant calling was then performed on the realigned reads using ANNOVAR
Genome_build: Homo_sapiens_GRCh37/hg19
Supplementary_files_format_and_content: SNVs for each Sample

source_name: human blood

extract_protocol:
DNA was extracted from EDTA blood of each patient or their biological parents (trio) using a QIAamp DNA Mini Kit
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep for Illumina® (NEB, USA) following manufacturer’s recommendations

tag: genotype/variation

tag: source petient

value: blood


title: liu


title: post-vaccination blood sample from donor 1008

source_name: Blood sample from donor 1008

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (pre-vax)

tag: age


title: jia

tag: tissue


title: post-vaccination blood sample from donor 1007

source_name: Blood sample from donor 1007

tag: donor

tag: donor set

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (post-vax)


title: 201516330033_R04C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: post-vaccination blood sample from donor 1006

source_name: Blood sample from donor 1006

tag: vaccination time

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: gender


title: post-vaccination blood sample from donor 1053

source_name: Blood sample from donor 1053

tag: tissue

tag: donor

tag: tetanus average concentration (pre-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (pre-vax)

tag: age


title: 201516330033_R07C01

description: normal blood sample


title: post-vaccination blood sample from donor 1005

source_name: Blood sample from donor 1005

tag: donor set

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: cholera normalized titer (unit)


title: 201516330033_R02C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: fang

tag: genotype/variation

tag: source petient


title: 201516330033_R03C01

description: normal blood sample


title: 201516330033_R01C01

description: normal blood sample


title: H3_2 rep3

library_source: transcriptomic

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b)
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions(three biological replicates per condition) was performed using the DESeq2 R package (1.10.1). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package.
Genome_build: Homo_sapiens_Ensemble_90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: patient3_14487C_143B cells

growth_protocol: The cells were cultured in high glucose Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, St. Louis, MO, USA) containing 10% bovine calf serum (Sigma-Aldrich) at 37°C in a humidified CO2 incubator.

extract_protocol:
Total RNA was isolated from 3 biological triplicates of each cybrid cell by using an RNeasy Mini Extraction kit (Qiagen, Valencia, CA, USA), and mRNA from 20 μg of the total RNA was purified using poly-T-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

tag: cell type

value: human osteosarcoma 143B cell

tag: genotype


title: post-vaccination blood sample from donor 1009 technical replicate

tag: tissue

tag: donor

tag: vaccination time

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: cholera normalized titer (post-vax)

tag: gender


title: H3_2 rep2


title: 201516330030_R08C01

description: normal blood sample

tag: age

tag: Sex


title: 201516330030_R06C01

description: normal blood sample

tag: person id

tag: disease state


title: 201516330030_R07C01

description: normal blood sample


title: H3_1 rep3

tag: source petient


title: H3_2 rep1

tag: cell type


title: H3_1 rep2

tag: genotype


title: post-vaccination blood sample from donor 1001

source_name: Blood sample from donor 1001

tag: tissue

tag: donor set

tag: hepatitis b average concentration (pre-vax)

tag: diphtheria average concentration (unit)

tag: diphtheria average concentration (pre-vax)

tag: diphtheria average concentration (post-vax)

tag: tetanus average concentration (post-vax)

tag: cholera normalized titer (unit)

tag: cholera normalized titer (pre-vax)


title: 201516330030_R05C01

description: normal blood sample


title: H3_1 rep1


title: L3_2 rep3

source_name: patient3_14487T_143B cells


title: 201516330030_R04C01

description: normal blood sample


title: 201516330030_R03C01

description: normal blood sample


title: 201516330030_R02C01

description: normal blood sample


title: 201516330021_R08C01

description: normal blood sample


title: 201516330030_R01C01

description: normal blood sample


title: H2_2 rep3

source_name: patient2_14487C_143B cells


title: L3_2 rep2


title: 201516330021_R07C01

description: normal blood sample


title: H2_2 rep2


title: post-vaccination blood sample from donor 1004

source_name: Blood sample from donor 1004

tag: donor

tag: vaccination time

tag: visit number

tag: hepatitis b average concentration (unit)

tag: hepatitis b average concentration (post-vax)

tag: tetanus average concentration (unit)

tag: tetanus average concentration (pre-vax)

tag: cholera normalized titer (post-vax)

tag: gender


title: post-vaccination blood sample from donor 1038

source_name: Blood sample from donor 1038

tag: tissue

tag: donor set

tag: age


title: 201516330021_R06C01

description: normal blood sample

tag: Sex

tag: person id

tag: disease state


title: 201516330021_R05C01

description: normal blood sample


title: H2_2 rep1

tag: cell type

tag: genotype

tag: source petient


title: 201516330021_R04C01

description: normal blood sample


title: H2_1 rep2


title: L2_2 rep3

source_name: patient2_14487T_143B cells


title: H2_1 rep1


title: 201516330021_R02C01

description: normal blood sample


title: 201516330021_R01C01

description: normal blood sample


title: L2_2 rep2


title: L2_2 rep1


title: L2_1 rep3


title: 201516330018_R06C01

description: normal blood sample


title: L3_2 rep1


title: L2_1 rep1


title: 201516330018_R07C01

description: normal blood sample


title: L2_1 rep2


title: H2_1 rep3


title: H1_2 rep3

source_name: patient1_14487C_143B cells


title: H1_2 rep2


title: 201516330018_R05C01

description: normal blood sample


title: 201516330018_R03C01

description: normal blood sample


title: H1_2 rep1


title: 201516330018_R02C01

description: normal blood sample


title: 201516330018_R04C01

description: normal blood sample


title: fangm

tag: genotype/variation


title: 201516330021_R03C01

description: normal blood sample


title: H1_1 rep3


title: 201516330018_R01C01

description: normal blood sample


title: H1_1 rep2


title: 201516330013_R07C01

description: normal blood sample


title: 201516330013_R06C01

description: normal blood sample


title: L1_2 rep2

source_name: patient1_14487T_143B cells


title: 201516330018_R08C01

description: normal blood sample


title: 201516330013_R04C01

description: normal blood sample


title: L1_2 rep1


title: 201516330013_R03C01

description: normal blood sample


title: L1_1 rep3


title: L1_1 rep2


title: L1_1 rep1


title: 201516330013_R01C01

description: normal blood sample


title: 201516330013_R02C01

description: normal blood sample


title: 201516330010_R07C01

description: normal blood sample


title: RNA seq donor C plaque extracts + GSK

city: Dijon

first: David

last: MASSON

address: Bvd Jeanne D'Arc, UFR des sciences de santé

country: France

institute: INSERM

description: treated with plaque extracts (1/100 v/v) for 48h + GSK 2033 1µM

data_processing:
Libraries were sequenced with 2x150bp paired-end reads on an Illumina HiSeq.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: primary macrophages

growth_protocol: Mononuclear cells were isolated by Ficoll gradient centrifugation and monocyte negative selection was performed via magnetic activated cell sorting using the Monocyte Isolation Kit II (Miltenyi Biotec, Bergish Gladbach, Germany). Monocytes were differentiated into macrophages for 6 days with 100ng/mL of M-CSF into RPMI medium supplemented with 10% Fetal Bovine Serum (FBS) in 5% CO2 and 37°C.

extract_protocol:
Total RNAs were extracted using RNeasy Mini Kit (Qiagen, Hilden,Germany) according to the manufacturer's instructions.
mRNA purification from total RNA and library preparation were performed with the NEBNext Ultra RNA Library Preparation Kit with poly-A selection according to the manufacturer protocols.

tag: differentiation

value: peripheral blood monocytes derived macrophages

tag: donor

value: donor C

tag: treatment

value: plaque extracts + GSK2019


title: 201516330010_R06C01

description: normal blood sample

source_name: blood samples


title: 201516330010_R08C01

description: normal blood sample


title: RNA seq donor C ctrl

description: no treatment

value: No  treatment


title: 201516330010_R04C01

description: normal blood sample


title: 201516330036_R01C01

description: normal blood sample


title: 201516330013_R08C01

description: normal blood sample


title: RNA seq donor C plaque extracts

description: treated with plaque extracts (1/100 v/v) for 48h

value: plaque extracts


title: 201516330010_R03C01

description: normal blood sample


title: H1_1 rep1


title: RNA seq donor B plaque extracts + GSK

value: donor B


title: 201516330013_R05C01

description: normal blood sample


title: RNA seq donor B ctrl

description: no treatment


title: RNA seq donor A plaque extracts

value: donor A


title: RNA seq donor A plaque extracts + GSK


title: L1_2 rep3


title: 201516330010_R02C01

description: normal blood sample


title: 201516330010_R01C01

description: normal blood sample

value: F


title: RNA seq donor A ctrl

description: no treatment


title: 201516330007_R07C01

description: normal blood sample

value: normal


title: 201516330007_R08C01

description: normal blood sample

value: M


title: 201516330007_R06C01

description: normal blood sample


title: 201516330010_R05C01

description: normal blood sample


title: 201516330007_R05C01

description: normal blood sample


title: RNA seq donor B plaque extracts


title: 10wk_VipSCN_nuc094

city: Charlottesville

first: John

middle: N

last: Campbell

state: VA

address: 485 MCCORMICK RD, GILMER HALL ROOM 229 PO BOX 400328

department: Biology

institute: University of Virginia

description: 10wk old male (1 mouse)

data_processing:
Demultiplexing by bcl2fastq2 v2.20.0.
Alignment to mouse genome by HISAT2 v2.1.0 (using “-k 2”)
BAM conversion of aligned reads by SAMtools v1.8.063
Duplicate and low-quality read removal by Picard 2.17.0
Reads assigned to features (genes) using the feature Counts from the Subread package v1.6.0 (using recommended setting and a custom meta-annotation that merges overlapping isoforms)
Genome_build: Mus musculus, build: mm10, GRCm38
Supplementary_files_format_and_content: CSV of gene expression counts with rows of genes and columns of samples

molecule: polyA RNA

organism: Mus musculus

source_name: suprachiasmatic nucleus

growth_protocol: Six-week old (juvenile; n = 2) and 10 week-old (adult, n = 1) VIP-IRES-Cre::H2b-TRAP male siblings were bred from the same VIP-IRES-Cre x H2b-TRAP mouse line and raised on a 12 hrs light/dark cycle with food and water available ad libitum

extract_protocol:
The following morning, the RNAlater-preserved tissue samples were processed into single-nuclei suspensions according to the sNuc-Seq method of Habib et al.38. Briefly, the two SCN tissue samples (juvenile, adult) were dounce homogenized (Wheaton tissue grinders, catalog # 357538) and separated by density gradient centrifugation as described in the published protocol38. Each pellet was then re-suspended in 0.5 ml sNuc-Seq resuspension buffer38 and filtered through a 20 μm mesh (Miltenyi Biotec pre-separation filters, catalog # 130-101-812) to remove clumped nuclei and larger debris. Nuclei were counterstained with two drops of NucBlue Live ReadyProbes Reagent (ThermoFisher Scientific catalog # R37605) per ml of nuclei. Nuclei were sorted by MoFlo Astrios EQ cell sorter (Harvard Bauer core facility), gating for NucBlue+/mCherry+ singlets and distributing them individually to wells of 96-well plates containing 5 μl per well of nuclei capture buffer (1% beta-mercaptoethanol in Qiagen Buffer TCL; catalog # 1031576). Each plate was loaded with equal numbers of samples from juvenile and adult SCN tissue. Loaded plates were centrifuged for 5 min at 2,500 xg and 4degC to ensure nuclei reached the capture buffer and frozen at -80degC for up to 4 weeks until use.
Sample plates were transferred to an RNA-dedicated PCR cabinet, thawed quickly, and immediately purified with RNA-Clean XP (Beckman Coulter, catalog # A63987; 2.5:1 ratio of RNA-Clean XP to sample volume), eluting in 4μl Smart-seq2 buffer (2 μl Smart-seq2 cell lysis buffer, 1 μl 100 μM oligo-dT primer, and 1 μl 10 mM dNTP mix)61. cDNA was then generated and amplified as described in the Smart-Seq2 protocol61, except that 22 PCR cycles were used for the amplification step. After the PCR step, 10 μl of each sample was transferred to new 96-well plates for subsequent processing. Amplified cDNA was purified with two rounds of SPRIselect   (Beckman Coulter, catalog # B23318; 0.8:1 ratio of SPRIselect to sample volume), eluting in ultrapure water. cDNA concentration was measured by Qubit fluorometry in a microplate format, each well containing 2 μl of cDNA sample and 98 μl of Qubit working solution (ThermoFisher Scientific, catalog # Q32854). Qubit readings were collected with a fluorescence microplate reader (Molecular Devices SpectraMax M5; Harvard Medical School ICCB-Longwood core facility) and used to calculate DNA concentrations by comparing each sample’s Qubit reading to standards in a 50% dilution series (n=8 standards; range, 0.25 ng/μl to 0.01 ng/μl plus a negative control, 0.0 ng/μl). cDNA samples were then diluted to 0.15 ng/ μl with ultrapure water and processed into sequencing libraries with sample-specific indices using the Nextera DNA Sample Prep Kit and Nextera XT Index Kit v2 sets A-D (Illumina, catalog #s FC-131-1096, FC-131- 2001, FC-131-2002, FC-131-2003, FC-131-2004, respectively). Nextera XT was used at 1/4 reaction volumes but otherwise according to manufacturer’s instructions. Sequencing libraries were purified with two rounds of SPRIselect (0.8:1 ratio of SPRIselect to sample volume) and eluted in a single volume of ultrapure water. Library pool concentration was measured by Qubit according to the manufacturer’s instructions sized using Agilent BioAnalyzer high sensitivity kit, and then diluted with ultrapure water to a size-corrected concentration of 2 nM. The diluted library pool was denatured and further diluted to 2 pM loading concentration according to Illumina NextSeq recommendations, then sequenced with a NextSeq 500 v2 75cycle sequencing kit (Illumina, catalog # FC-404-2005).

treatment_protocol: One hour after light cycle onset, the VIP-IRES-Cre::H2b-TRAP mice were removed from their home cage and rapidly decapitated in order to minimize stress related changes in gene expression. Brains were extracted quickly, chilled briefly in ice cold DMEM/F12 media, and then sectioned coronally at 1 mm intervals in a chilled stainless-steel brain matrix. The brain sections containing and neighboring the SCN were collected in ice-cold RNAlater (Qiagen catalog # 76106). Each section was imaged by a fluorescence stereoscope (Zeiss Discovery V8) in order to visualize fluorescently labeled cells in the SCN for dissection. Dissected tissue was pooled across mice by age group (juvenile, adult) and placed into ice-cold RNAlater overnight in the dark at 4degC.

value: male

value: single mCherry+ cell nucleus

tag: sample time

value: sample collected at 7am


title: 201516330007_R03C01

description: normal blood sample


title: 10wk_VipSCN_nuc093

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc095

description: 10wk old male (1 mouse)


title: 201516330007_R02C01

description: normal blood sample


title: 201516330005_R08C01

description: normal blood sample


title: 201516330007_R01C01

description: normal blood sample


title: 201516330005_R05C01

description: normal blood sample


title: 10wk_VipSCN_nuc091

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc090

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc092

description: 10wk old male (1 mouse)


title: 201516330005_R03C01

description: normal blood sample


title: 201516330005_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc089

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc087

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc088

description: 10wk old male (1 mouse)


title: 201516330005_R06C01

description: normal blood sample


title: 10wk_VipSCN_nuc083

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc085

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc084

description: 10wk old male (1 mouse)


title: 201516330005_R01C01

description: normal blood sample


title: 10wk_VipSCN_nuc086

description: 10wk old male (1 mouse)


title: 201516330004_R08C01

description: normal blood sample


title: 10wk_VipSCN_nuc096

description: 10wk old male (1 mouse)

value: pool of 10 mCherry+ cell nuclei


title: 201516330007_R04C01

description: normal blood sample


title: 10wk_VipSCN_nuc082

description: 10wk old male (1 mouse)


title: 201516330004_R07C01

description: normal blood sample


title: 10wk_VipSCN_nuc081

description: 10wk old male (1 mouse)


title: 201516330004_R06C01

description: normal blood sample


title: 10wk_VipSCN_nuc080

description: 10wk old male (1 mouse)


title: 201516330004_R05C01

description: normal blood sample


title: 201516330004_R04C01

description: normal blood sample


title: 10wk_VipSCN_nuc078

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc079

description: 10wk old male (1 mouse)


title: 201516330005_R04C01

description: normal blood sample


title: 201516330004_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc077

description: 10wk old male (1 mouse)


title: 201516330004_R01C01

description: normal blood sample


title: 10wk_VipSCN_nuc076

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc075

description: 10wk old male (1 mouse)


title: 201516330003_R08C01

description: normal blood sample


title: 201516330004_R03C01

description: normal blood sample


title: 201516330003_R06C01

description: normal blood sample


title: 201516330003_R07C01

description: normal blood sample


title: 10wk_VipSCN_nuc074

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc072

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc073

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc071

description: 10wk old male (1 mouse)


title: 201516330003_R04C01

description: normal blood sample


title: 201516330003_R03C01

description: normal blood sample


title: 201516330003_R05C01

description: normal blood sample


title: 201516330003_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc070

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc068

description: 10wk old male (1 mouse)


title: 201516330003_R01C01

description: normal blood sample


title: 10wk_VipSCN_nuc066

description: 10wk old male (1 mouse)


title: 201516270056_R08C01

description: normal blood sample


title: 10wk_VipSCN_nuc065

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc064

description: 10wk old male (1 mouse)


title: 201516270056_R06C01

description: normal blood sample


title: 201516270056_R05C01

description: normal blood sample


title: 201516270056_R07C01

description: normal blood sample


title: 201516270056_R03C01

description: normal blood sample


title: 10wk_VipSCN_nuc063

description: 10wk old male (1 mouse)


title: 201516270056_R04C01

description: normal blood sample


title: 201516270042_R08C01

description: normal blood sample


title: 10wk_VipSCN_nuc062

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc060

description: 10wk old male (1 mouse)


title: 201516270056_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc061

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc059

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc058

description: 10wk old male (1 mouse)


title: 201516270042_R06C01

description: normal blood sample


title: 201516270056_R01C01

description: normal blood sample


title: 201516270042_R07C01

description: normal blood sample


title: 10wk_VipSCN_nuc069

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc067

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc056

description: 10wk old male (1 mouse)


title: 201516270042_R04C01

description: normal blood sample


title: 10wk_VipSCN_nuc055

description: 10wk old male (1 mouse)


title: 201516270042_R05C01

description: normal blood sample


title: 10wk_VipSCN_nuc054

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc053

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc052

description: 10wk old male (1 mouse)


title: 201516270042_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc051

description: 10wk old male (1 mouse)


title: 201516270038_R08C01

description: normal blood sample


title: 10wk_VipSCN_nuc049

description: 10wk old male (1 mouse)


title: 201516270038_R07C01

description: normal blood sample


title: 201516270038_R06C01

description: normal blood sample


title: 201516270038_R05C01

description: normal blood sample


title: 10wk_VipSCN_nuc057

description: 10wk old male (1 mouse)


title: 201516270038_R03C01

description: normal blood sample


title: 201516270038_R01C01

description: normal blood sample


title: 201516270038_R02C01

description: normal blood sample


title: 6wk_VipSCN_nuc096

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc094

description: 6wk old male (tissue pool from 2 mice)


title: 201516270031_R08C01

description: normal blood sample


title: 6wk_VipSCN_nuc095

description: 6wk old male (tissue pool from 2 mice)


title: 201516270042_R03C01

description: normal blood sample


title: 6wk_VipSCN_nuc091

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc089

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc090

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc093

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc092

description: 6wk old male (tissue pool from 2 mice)


title: 201516270031_R07C01

description: normal blood sample


title: 201516270031_R05C01

description: normal blood sample


title: 201516270042_R01C01

description: normal blood sample


title: 6wk_VipSCN_nuc088

description: 6wk old male (tissue pool from 2 mice)


title: 10wk_VipSCN_nuc050

description: 10wk old male (1 mouse)


title: 6wk_VipSCN_nuc086

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc087

description: 6wk old male (tissue pool from 2 mice)


title: 201516270031_R06C01

description: normal blood sample


title: 6wk_VipSCN_nuc085

description: 6wk old male (tissue pool from 2 mice)


title: 201516270038_R04C01

description: normal blood sample


title: 201516270031_R03C01

description: normal blood sample


title: 201516270031_R02C01

description: normal blood sample


title: 6wk_VipSCN_nuc083

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc082

description: 6wk old male (tissue pool from 2 mice)


title: 201516270031_R01C01

description: normal blood sample


title: 6wk_VipSCN_nuc081

description: 6wk old male (tissue pool from 2 mice)


title: 201516270021_R04C01

description: normal blood sample


title: 201516270021_R06C01

description: normal blood sample


title: 201516270021_R05C01

description: normal blood sample


title: 201516270021_R03C01

description: normal blood sample


title: 6wk_VipSCN_nuc079

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc077

description: 6wk old male (tissue pool from 2 mice)


title: 201516270031_R04C01

description: normal blood sample


title: 6wk_VipSCN_nuc078

description: 6wk old male (tissue pool from 2 mice)


title: 201516270021_R02C01

description: normal blood sample


title: 6wk_VipSCN_nuc076

description: 6wk old male (tissue pool from 2 mice)


title: 201516270021_R01C01

description: normal blood sample


title: 201516270015_R08C01

description: normal blood sample


title: 6wk_VipSCN_nuc075

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc074

description: 6wk old male (tissue pool from 2 mice)


title: 201516270015_R06C01

description: normal blood sample


title: 201516270015_R07C01

description: normal blood sample


title: 6wk_VipSCN_nuc084

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc073

description: 6wk old male (tissue pool from 2 mice)


title: 201516270015_R04C01

description: normal blood sample


title: 201516270015_R02C01

description: normal blood sample


title: 201516270021_R08C01

description: normal blood sample


title: 6wk_VipSCN_nuc071

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc070

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc072

description: 6wk old male (tissue pool from 2 mice)


title: 201516270021_R07C01

description: normal blood sample


title: 6wk_VipSCN_nuc080

description: 6wk old male (tissue pool from 2 mice)


title: 201516270015_R01C01

description: normal blood sample


title: 201516270011_R08C01

description: normal blood sample


title: 201516270011_R07C01

description: normal blood sample


title: 6wk_VipSCN_nuc066

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc067

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc065

description: 6wk old male (tissue pool from 2 mice)


title: 201516270011_R04C01

description: normal blood sample


title: 201516270011_R06C01

description: normal blood sample


title: 201516270011_R03C01

description: normal blood sample


title: 6wk_VipSCN_nuc063

description: 6wk old male (tissue pool from 2 mice)


title: 201516270011_R02C01

description: normal blood sample


title: 201516270011_R01C01

description: normal blood sample


title: 6wk_VipSCN_nuc064

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc062

description: 6wk old male (tissue pool from 2 mice)


title: 201516270001_R08C01

description: normal blood sample


title: 201516270001_R07C01

description: normal blood sample


title: 201516270011_R05C01

description: normal blood sample


title: 6wk_VipSCN_nuc061

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc059

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc069

description: 6wk old male (tissue pool from 2 mice)


title: 201516270001_R05C01

description: normal blood sample


title: 6wk_VipSCN_nuc057

description: 6wk old male (tissue pool from 2 mice)


title: 201516270001_R04C01

description: normal blood sample


title: 6wk_VipSCN_nuc058

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc056

description: 6wk old male (tissue pool from 2 mice)


title: 201516270001_R02C01

description: normal blood sample


title: 6wk_VipSCN_nuc054

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc068

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc055

description: 6wk old male (tissue pool from 2 mice)


title: 201516270001_R01C01

description: normal blood sample


title: 201516270001_R03C01

description: normal blood sample


title: 6wk_VipSCN_nuc053

description: 6wk old male (tissue pool from 2 mice)


title: 201516260034_R07C01

description: normal blood sample


title: 201516260034_R06C01

description: normal blood sample


title: 201516260034_R08C01

description: normal blood sample


title: 201516260034_R05C01

description: normal blood sample


title: 6wk_VipSCN_nuc060

description: 6wk old male (tissue pool from 2 mice)


title: 201516260034_R04C01

description: normal blood sample


title: 6wk_VipSCN_nuc050

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc051

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc049

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc052

description: 6wk old male (tissue pool from 2 mice)


title: 201516260034_R03C01

description: normal blood sample


title: 201516260034_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc048

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc047

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc046

description: 10wk old male (1 mouse)


title: 201516260006_R08C01

description: normal blood sample


title: 10wk_VipSCN_nuc044

description: 10wk old male (1 mouse)


title: 201516260006_R05C01

description: normal blood sample


title: 10wk_VipSCN_nuc045

description: 10wk old male (1 mouse)


title: 201516260006_R06C01

description: normal blood sample


title: 201516260034_R01C01

description: normal blood sample


title: 201516260006_R07C01

description: normal blood sample


title: 201516260006_R04C01

description: normal blood sample


title: 10wk_VipSCN_nuc042

description: 10wk old male (1 mouse)


title: 201516260006_R03C01

description: normal blood sample


title: 201516260006_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc040

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc039

description: 10wk old male (1 mouse)


title: 201516260006_R01C01

description: normal blood sample


title: 10wk_VipSCN_nuc041

description: 10wk old male (1 mouse)


title: 201516260005_R08C01

description: normal blood sample


title: 201516260005_R07C01

description: normal blood sample


title: 10wk_VipSCN_nuc038

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc035

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc036

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc034

description: 10wk old male (1 mouse)


title: 201516260005_R06C01

description: normal blood sample


title: 10wk_VipSCN_nuc037

description: 10wk old male (1 mouse)


title: 201516260005_R04C01

description: normal blood sample


title: 201516260005_R05C01

description: normal blood sample


title: 10wk_VipSCN_nuc033

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc032

description: 10wk old male (1 mouse)


title: 201516260005_R03C01

description: normal blood sample


title: 201516260005_R01C01

description: normal blood sample


title: 201516260005_R02C01

description: normal blood sample


title: 201516260004_R08C01

description: normal blood sample


title: 10wk_VipSCN_nuc030

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc029

description: 10wk old male (1 mouse)


title: 201516260004_R07C01

description: normal blood sample


title: 10wk_VipSCN_nuc031

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc027

description: 10wk old male (1 mouse)


title: 201516260004_R06C01

description: normal blood sample


title: 10wk_VipSCN_nuc025

description: 10wk old male (1 mouse)


title: 201516260004_R05C01

description: normal blood sample


title: 201516260004_R03C01

description: normal blood sample


title: 201516260004_R04C01

description: normal blood sample


title: 10wk_VipSCN_nuc043

description: 10wk old male (1 mouse)


title: 201516260004_R01C01

description: normal blood sample


title: 201506830111_R07C01

description: normal blood sample


title: 10wk_VipSCN_nuc026

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc024

description: 10wk old male (1 mouse)


title: Mulatta2TMR

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

description: V3 library prep protocol

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 3.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 3.1.0, 10X Genomics)
Genome_build: Mmul8
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples

organism: Macaca mulatta

source_name: Macaque trabecular meshwork, 10 y/o

extract_protocol:
Tissues were dissected in Ames' medium, digested in papain, and manually triturated into single cell suspensions in ovomucoid solution. The cells were resuspended in 0.04% non-acetylated BSA in Ames to solutions of ~1000 cells/uL and loaded into Chromium Single Cell Chips for a targeted recovery of 6,000 cells.
Single cell libraries were made with Chromium 3’ v3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v3 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: Eyes were enucleated immediately after the macaques were sacrificed. The eyes were transported on ice in Ames' medium (Sigma-Aldrich; equilibrated with 95% O2/5% CO2) for one hour.

value: Macaque trabecular meshwork


title: 201516260004_R02C01

description: normal blood sample


title: Mulatta1TML

description: V3 library prep protocol


title: 10wk_VipSCN_nuc021

description: 10wk old male (1 mouse)


title: 201506830111_R06C01

description: normal blood sample


title: 10wk_VipSCN_nuc022

description: 10wk old male (1 mouse)


title: 201506830111_R03C01

description: normal blood sample


title: 10wk_VipSCN_nuc020

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc028

description: 10wk old male (1 mouse)


title: 201506830111_R05C01

description: normal blood sample


title: H1650shSETD2-2

city: Changzhou

first: You

last: Zhou

state: Jiangsu

address: Juqian Rd No.185

institute: The Third Affiliated Hospital of Soochow University

data_processing:
Solexa pipeline version 1.8 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using Hisat2 with default parameters.
Fragments Per Kilobase of gene/transcript model per Million mapped reads (FPKM) were calculated using Ballgown. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent. Illumina KAPA Stranded RNA-Seq Library Prep Kit was used with 1 ug of purified RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Lung


title: H1650shSETD2-3


title: 201506830111_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc019

description: 10wk old male (1 mouse)


title: 201506830111_R01C01

description: normal blood sample


title: 10wk_VipSCN_nuc018

description: 10wk old male (1 mouse)


title: 201503670196_R08C01

description: normal blood sample


title: H1650shSETD2-1


title: 10wk_VipSCN_nuc017

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc023

description: 10wk old male (1 mouse)


title: 201503670196_R07C01

description: normal blood sample


title: 201506830111_R08C01

description: normal blood sample


title: 201503670196_R05C01

description: normal blood sample


title: 10wk_VipSCN_nuc016

description: 10wk old male (1 mouse)


title: H1650control-3

value: wild type


title: H1650control-2


title: 201503670196_R01C01

description: normal blood sample


title: 201503670196_R03C01

description: normal blood sample


title: H1650control-1


title: 10wk_VipSCN_nuc015

description: 10wk old male (1 mouse)


title: 201503670196_R02C01

description: normal blood sample


title: 10wk_VipSCN_nuc014

description: 10wk old male (1 mouse)


title: 201503670182_R08C01

description: normal blood sample


title: PC9-OE-NC3

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

data_processing:
Sequencing reads were trimmed using StringTie software.
Clean reads were mapped to human genome database (GRCh37) using the Hisat2 software.
Differential expression and normalized reads counts (FPKM, Fragments Per Kilobase of gene/transcript model per Million mapped fragments) were calculated using the Ballgown software.
Supplementary_files_format_and_content: FPKMs

source_name: Control cells

growth_protocol: Cells were cultured in DEME medium containing 10% FBS in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cells using the TRIzol Reagent.
RNA-seq libraries were prepared using the Illumina KAPA Stranded RNA-Seq Library Prep Kit.Sequencing was performed on an Illumina HiSeq 4000.

treatment_protocol: FTSJ1 plasmid or empty vector were transfected into PC9 cells using Lipofectamine 3000 transfection reagent.

value: Human adenocarcinoma tissue-derived cells

value: control


title: 201503670182_R06C01

description: normal blood sample


title: 201503670182_R07C01

description: normal blood sample


title: 10wk_VipSCN_nuc013

description: 10wk old male (1 mouse)


title: PC9-OE-NC2


title: 201503670182_R04C01

description: normal blood sample


title: 201503670182_R03C01

description: normal blood sample


title: 10wk_VipSCN_nuc011

description: 10wk old male (1 mouse)


title: PC9-OE-FTSJ3

source_name: FTSJ1-overexpression cells


title: 10wk_VipSCN_nuc010

description: 10wk old male (1 mouse)


title: 201503670196_R04C01

description: normal blood sample


title: 201503670181_R08C01

description: normal blood sample


title: 10wk_VipSCN_nuc012

description: 10wk old male (1 mouse)


title: 201503670181_R07C01

description: normal blood sample


title: 201503670182_R01C01

description: normal blood sample


title: PC9-OE-NC1


title: 201503670181_R05C01

description: normal blood sample


title: 201503670181_R06C01

description: normal blood sample


title: 10wk_VipSCN_nuc009

description: 10wk old male (1 mouse)


title: PC9-OE-FTSJ2


title: 201503670196_R06C01

description: normal blood sample


title: 201503670181_R04C01

description: normal blood sample


title: 201503670181_R01C01

description: normal blood sample


title: DB-38-A

city: New Haven

first: Elena

last: Tarabra

state: Connecticut

address: 330 cedar street

department: Endocrinology/Pediatrics

institute: Yale University - School of Medicine

data_processing:
RNA-seq reads were aligned to the human reference genome (hg38) using the HISAT2
Gene models were downloaded from the GENCODE project (v27).
read counts were extracted from StringTie outpout using the prepDE.py script (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq)
DESeq2 was used to determine differentially expressed genes
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited gene expression values (read counts from featureCounts)

source_name: adipose tissue

extract_protocol:
SAT and omVAT were removed, and homogenized into QIAzol Lysis Reagent. Total RNA was isolated using RNeasy Mini kit. Ribosomal depetion.  Illumina HI-Seq 4000  was used to sequencing 0.5 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Female

tag: tissue depot

value: abdominal subcutaneous adipose tissue

tag: tissue collection

value: during follow-up visit after weight loss


title: DB-39-A

tag: gender


title: 201503670182_R05C01

description: normal blood sample


title: 10wk_VipSCN_nuc007

description: 10wk old male (1 mouse)

tag: tissue


title: 201503670181_R03C01

description: normal blood sample

tag: age


title: 201503670182_R02C01

description: normal blood sample

tag: Sex


title: 201503670155_R08C01

description: normal blood sample

tag: person id


title: DB-37-A


title: 201503670155_R06C01

description: normal blood sample

tag: disease state


title: 10wk_VipSCN_nuc006

description: 10wk old male (1 mouse)


title: 201503670155_R07C01

description: normal blood sample


title: DB-35-A


title: 10wk_VipSCN_nuc005

description: 10wk old male (1 mouse)


title: 201503670155_R05C01

description: normal blood sample


title: 201503670155_R03C01

description: normal blood sample


title: 201503670155_R04C01

description: normal blood sample


title: 10wk_VipSCN_nuc004

description: 10wk old male (1 mouse)


title: PC9-OE-FTSJ1

tag: cell type


title: 10wk_VipSCN_nuc003

description: 10wk old male (1 mouse)

tag: genotype


title: 10wk_VipSCN_nuc008

description: 10wk old male (1 mouse)


title: 201503670181_R02C01

description: normal blood sample


title: 201503670154_R08C01

description: normal blood sample


title: 201503670155_R02C01

description: normal blood sample


title: BS-9_Sub

value: during sleeve gastrectomy


title: 201503670154_R07C01

description: normal blood sample


title: 201503670155_R01C01

description: normal blood sample


title: BS-8_Vis

value: omental-visceral adipose tissue


title: 10wk_VipSCN_nuc002

description: 10wk old male (1 mouse)


title: 10wk_VipSCN_nuc001

description: 10wk old male (1 mouse)


title: 6wk_VipSCN_nuc048

description: 6wk old male (tissue pool from 2 mice)


title: 201503670154_R05C01

description: normal blood sample


title: 201503670154_R06C01

description: normal blood sample


title: BS-8_Sub


title: 201503670154_R04C01

description: normal blood sample

value: F


title: 6wk_VipSCN_nuc047

description: 6wk old male (tissue pool from 2 mice)


title: BS-6_Vis


title: 201503670154_R02C01

description: normal blood sample

value: normal


title: 201503670154_R01C01

description: normal blood sample


title: BS-6_Sub


title: 6wk_VipSCN_nuc046

description: 6wk old male (tissue pool from 2 mice)


title: 201503670149_R08C01

description: normal blood sample


title: BS-9_Vis


title: BS-5_Vis


title: 201503670149_R05C01

description: normal blood sample

value: M


title: BS-5_Sub


title: 201503670149_R04C01

description: normal blood sample


title: 201503670149_R06C01

description: normal blood sample


title: BS-4_Vis


title: 201503670149_R03C01

description: normal blood sample


title: 201503670149_R02C01

description: normal blood sample


title: 6wk_VipSCN_nuc044

description: 6wk old male (tissue pool from 2 mice)

value: male


title: 201503670149_R01C01

description: normal blood sample


title: 6wk_VipSCN_nuc043

description: 6wk old male (tissue pool from 2 mice)

value: single mCherry+ cell nucleus


title: BS-4_Sub


title: 201503670145_R08C01

description: normal blood sample


title: 201503670154_R03C01

description: normal blood sample


title: 201503670145_R07C01

description: normal blood sample


title: 201503670145_R06C01

description: normal blood sample


title: BS-3_Vis


title: BS-3_Sub


title: 201503670145_R05C01

description: normal blood sample


title: 201503670145_R04C01

description: normal blood sample


title: 6wk_VipSCN_nuc040

description: 6wk old male (tissue pool from 2 mice)

value: sample collected at 7am


title: 201503670145_R02C01

description: normal blood sample


title: 6wk_VipSCN_nuc039

description: 6wk old male (tissue pool from 2 mice)


title: BS-2_Vis


title: 201503670149_R07C01

description: normal blood sample


title: 6wk_VipSCN_nuc045

description: 6wk old male (tissue pool from 2 mice)


title: 201503670145_R01C01

description: normal blood sample


title: BS-2_Sub


title: 6wk_VipSCN_nuc041

description: 6wk old male (tissue pool from 2 mice)


title: 201503590073_R07C01

description: normal blood sample


title: 6wk_VipSCN_nuc042

description: 6wk old male (tissue pool from 2 mice)


title: 201503590073_R08C01

description: normal blood sample


title: BS-1_Vis


title: 6wk_VipSCN_nuc037

description: 6wk old male (tissue pool from 2 mice)


title: 201503590073_R06C01

description: normal blood sample


title: 6wk_VipSCN_nuc038

description: 6wk old male (tissue pool from 2 mice)


title: BS-1_Sub


title: 6wk_VipSCN_nuc036

description: 6wk old male (tissue pool from 2 mice)


title: 201503590073_R05C01

description: normal blood sample


title: 201503590073_R03C01

description: normal blood sample


title: 201503590073_R04C01

description: normal blood sample


title: 201503590073_R02C01

description: normal blood sample


title: BS-11-VIS


title: 201496860105_R08C01

description: normal blood sample


title: 6wk_VipSCN_nuc035

description: 6wk old male (tissue pool from 2 mice)


title: 201503590073_R01C01

description: normal blood sample


title: 6wk_VipSCN_nuc034

description: 6wk old male (tissue pool from 2 mice)


title: 201496860105_R07C01

description: normal blood sample


title: BS-10_Vis


title: 6wk_VipSCN_nuc033

description: 6wk old male (tissue pool from 2 mice)


title: 201496860105_R04C01

description: normal blood sample


title: 201496860105_R06C01

description: normal blood sample


title: BS-10_Sub


title: 6wk_VipSCN_nuc032

description: 6wk old male (tissue pool from 2 mice)


title: 201496860105_R03C01

description: normal blood sample


title: WTCHG_260153

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

description:
2 lanes
WTCHG_345854_260153
WTCHG_348065_260153

data_processing:
Fastq quality was evaluated using FastQC (0.11.2) and contamination by other organisms was excluded using FastQ Screen (0.4.4). Files were not trimmed.
Transcripts per million (TPM) and counts tables were obtained using Salmon (0.8.2 [40]) with kmer size option 31 and index option fmd. Salmon results were imported into R using tximport (1.10.0 [41]).
Genome_build: hg38
Supplementary_files_format_and_content: TPM tables from salmon

source_name: iPSC-derived motor neurons

growth_protocol: iPSCs were grown on Matrigel until confluency, then neural induction was started using DMEM/F12:Neurobasal 1:1, N2, B27,  ascorbic acid (0.5 mM), 2-mercaptoethanol, compound C (3 µM) and Chir99021 (3 µM). After 4 days in culture, RA (1 µM) and SAG (500 nM) were added to the medium. On the next day, Chir99021 and compound C were removed from the medium, and the cells were cultured for another 4–5 days. After that, cells were split 1:3 on approximately day 10. Subsequently, the medium was supplemented with growth factors BDNF (10 ng/ mL), GDNF (10 ng/mL), N-[N-(3,5-Difluorophenacetyl)-L-ala- nyl]-S-phenylglycine t-butyl ester (DAPT) (10 mM), and laminin (0.5 mg/mL). After 7 days, DAPT and laminin were removed from the medium, and the neurons were allowed to mature until day 25-30.

extract_protocol:
RNA was extracted from whole iPSMN cultures at day 30.
Library preparation was carried out using the Illumina TruSeq RNA Sample Prep Kit v2 by the Oxford Centre for Human Genomics. RNA sequencing was performed on the Illumina HiSeq4500 platform over 75 cycles. Sequences were paired-end. Fastq files were generated from the sequencing platform using the manufacturer’s proprietary software.

value: iPSC-derived motor neurons

tag: cell type background

value: iPSC line derived from a C9orf72-HR positive ALS patient

value: hexanucleotide expansion

tag: date

value: MAR

tag: operator


title: 6wk_VipSCN_nuc031

description: 6wk old male (tissue pool from 2 mice)


title: 201496860105_R01C01

description: normal blood sample


title: 201496860042_R08C01

description: normal blood sample


title: 201496860042_R07C01

description: normal blood sample


title: 6wk_VipSCN_nuc030

description: 6wk old male (tissue pool from 2 mice)


title: WTCHG_268152

description:
2 lanes
WTCHG_345854_268152
WTCHG_348065_268152

tag: genotype/variation

value: OCT


title: BS-11-SC


title: 6wk_VipSCN_nuc029

description: 6wk old male (tissue pool from 2 mice)


title: 201496860042_R05C01

description: normal blood sample


title: WTCHG_257189

description:
2 lanes
WTCHG_345854_257189
WTCHG_348065_257189

value: AUG


title: 6wk_VipSCN_nuc028

description: 6wk old male (tissue pool from 2 mice)


title: 201496860042_R02C01

description: normal blood sample


title: 201503670145_R03C01

description: normal blood sample


title: WTCHG_290173

description:
2 lanes
WTCHG_345854_290173
WTCHG_348065_290173

value: control patient sample


title: 201496860041_R08C01

description: normal blood sample


title: 201496860042_R01C01

description: normal blood sample


title: WTCHG_261141

description:
2 lanes
WTCHG_345854_261141
WTCHG_348065_261141

value: edited samples


title: 6wk_VipSCN_nuc026

description: 6wk old male (tissue pool from 2 mice)


title: 201496860105_R02C01

description: normal blood sample


title: 201496860041_R07C01

description: normal blood sample


title: WTCHG_258177

description:
2 lanes
WTCHG_345854_258177
WTCHG_348065_258177


title: 201496860041_R05C01

description: normal blood sample


title: 6wk_VipSCN_nuc025

description: 6wk old male (tissue pool from 2 mice)


title: WTCHG_269140

description:
2 lanes
WTCHG_345854_269140
WTCHG_348065_269140


title: 201496860041_R04C01

description: normal blood sample


title: 201496860042_R06C01

description: normal blood sample


title: 201496860041_R03C01

description: normal blood sample


title: 201496860041_R01C01

description: normal blood sample


title: 201496860041_R02C01

description: normal blood sample


title: 201496860040_R07C01

description: normal blood sample


title: 201496860042_R04C01

description: normal blood sample


title: 201496860040_R08C01

description: normal blood sample


title: 6wk_VipSCN_nuc022

description: 6wk old male (tissue pool from 2 mice)


title: WTCHG_259165

description:
2 lanes
WTCHG_345854_259165
WTCHG_348065_259165


title: 6wk_VipSCN_nuc024

description: 6wk old male (tissue pool from 2 mice)


title: WTCHG_263117

description:
2 lanes
WTCHG_345854_263117
WTCHG_348065_263117


title: 6wk_VipSCN_nuc023

description: 6wk old male (tissue pool from 2 mice)


title: WTCHG_289185

description:
2 lanes
WTCHG_345854_289185
WTCHG_348065_289185


title: WTCHG_267164

description:
2 lanes
WTCHG_345854_267164
WTCHG_348065_267164


title: 201496860041_R06C01

description: normal blood sample


title: 201496860040_R04C01

description: normal blood sample


title: 201496860040_R06C01

description: normal blood sample