title: Patient derived xenograft for HPV+ HNSCC tumor MBD-Seq sample 20

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

data_processing:
XSQ Tools was used to convert XSQ to CSFASTA+QUAL files (default parameters)
SOLiD™ BioScope™ was used to generate alignments to hg19 (default parameters)
MACS-1.4.1 was used for peak calling, with parameters -s 50 --nomodel --shiftsize=90 -g hg19
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bed files for MACS peaks

extract_protocol:
Microdissected tumor tissue samples were cut on 0.35 mm thick frozen tissue sections. Those sections were digested in 1% Sodium Dodecyl Sulfate (SDS) solution (Sigma) and 50 μg/ml proteinase K (Invitrogen) solution at 48°C for 48–72 hours. DNA was purified by phenol-chloroform extraction and ethanol precipitation. DNA was resuspended in LoTE buffer, and DNA concentration was quantified using the NanoDrop spectrophotometer (Thermo Scientific).
DNA was sonicated, end-repaired, and ligated to SOLiD P1 and P2 sequencing adaptors lacking 5′ phosphate groups, using the NEBNext DNA Library Prep Set for SOLiD according to the manufacturer's recommended protocol (NEB). Libraries were then nick-translated with Platinum Taq polymerase and divided into two fractions: an enriched methylated fraction that was subjected to isolation and elution of CpG-methylated library fragments by using MBD2-MBD–bound magnetic beads, and a total input fraction that was left unenriched. These fractions were then amplified using 4–6 cycles for the total input, and 10–12 cycles for the enriched methylated fractions according to the NEBNext DNA Library Prep Set for SOLiD kit (NEB).
MBD-Seq. The libraries were subjected to emulsion PCR, bead enrichment, and sequencing on a SOLiD sequencer to generate on average approximately 25–50 million 50 bp single-end reads per sample according to the manufacturer's protocols (Life Technologies). The resulting color-space reads were aligned using Bioscope software (Applied Biosystems).
MACS peak identification software was used to identify regions of methylation by comparing the enriched versus total input libraries for each sample with a default cutoff of P < 10−6.

tag: sample type

value: Patient-derived HPV+ HNSCC xenograft

tag: patient id

tag: hpv integration

value: Non-integrated

tag: hpv type

tag: race

value: Caucasian

tag: smoking

value: Current smoker

tag: type of tobacco

value: Cigarette

tag: pack years

tag: alcohol use

value: Yes

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Patient derived xenograft for HPV+ HNSCC tumor MBD-Seq sample 37

status: Public on Mar 20 2018

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: sample type

value: Integrated

tag: age

tag: gender

value: Male

value: Former smoker


title: HPV+ HNSCC cell line SCC-047

value: HPV+ HNSCC cell line

tag: patient id

tag: hpv integration

tag: hpv type


title: HPV+ HNSCC cell line SCC-090

tag: race

tag: smoking

tag: type of tobacco


title: Y10117T

type: RNA

city: Seoul

first: Yong-Min

last: Huh

address: 50 Shinchon-ro

country: South Korea

institute: Yonsei University

description: SAMPLE 21

hyb_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for cRNA synthesis.

scan_protocol: Standard Illumina scanning protocol

data_processing: Genomestudio, quantile normalization

label: biotin

molecule: total RNA

source_name: Human gastric cancer

extract_protocol: RecoverAll™ total nucleic acid isolation kit (Ambion) or the mirVana RNA Isolation Labeling Kit (Ambion) were used. Quality control was performed with NanoDrop 2000 (Thermo Fischer Scientific) and RNA Nano 6000 chip (Agilent).

tag: tissue

value: gastric cancer

tag: Sex

value: female

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Y10119T

description: SAMPLE 22

label_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for cRNA synthesis.


title: 58: cell free DNA from plasma

type: other

city: Vilnius

first: Algimantas

last: Krisciunas

address: Sauletekio al. 7

country: Lithuania

institute: Vilnius University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing:
The sample data were processed using R package minfi (Aryee et al. 2014). Raw modification values were extracted using getM and preprocessRaw functions. At each of the 485,577 cytosines interrogated by the microarray, cytosine modification level was summarized by calculating the M value defined as log2 ( (M+100)/ (U+100)), where M and U are the methylated (M) and unmethylated (U) signal intensities (Du et al. 2010). Cytosines were annotated using the Illumina HumanMethylation450 manifest file (GEO GPL13534) and those from sex chromosomes were removed. In addition, polymorphic cytosines and cross-hybridizing probes were also removed (Chen et al. 2013) (total 382,378 cytosines). Outlying samples were identified from the obtained modification data using the following algorithm: first, a k-nearest neighbour imputation algorithm (impute.knn) was used to fill missing cytosine values. Next, using the raw data matrix each sample was projected into two-dimensional space using multidimensional scaling (cmdscale) that preserves sample distances while reducing dimensionality. For each sample, its mean distance to the 15 nearest samples was computed. The samples that deviated from the mean of the resulting distribution by more than three standard deviations were identified as outliers and removed from subsequent analysis (N=18)
minfi Quantile normalised Average Beta values. NAs inserted for outlier samples.
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: other

source_name: plasma

label_protocol: Standard Illumina Protocol

extract_protocol: cell free DNA was extracted and purified from plasma samples using QIAmp Circulating Nucleic Acid Kit according to manufacturer instructions

tag: diagnosis

value: prostrate cancer

value: plasma

tag: individual id

tag: visit

tag: center

value: BC

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Sensitive to AA treatment


title: Y10112T

description: SAMPLE 19

tag: age

value: male


title: Y10127T

description: SAMPLE 27

tag: tissue


title: Y10120T

description: SAMPLE 23

tag: Sex


title: Y10106T

description: SAMPLE 17

tag: ptstage


title: Normal UPPP control MBD-Seq sample 124

tag: sample type

value: Normal UPPP

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

tag: race

value: Caucasian

tag: smoking

value: Non-smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: No

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control MBD-Seq sample 125

tag: sample type

tag: patient id

tag: age

value: Female

value: African american


title: 57: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

value: BL

tag: center

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype


title: Y10103T

description: SAMPLE 16

tag: Sex

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Y10113T

description: SAMPLE 20

tag: age


title: Normal UPPP control MBD-Seq sample 123

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Y10098T

description: SAMPLE 15

tag: tissue

tag: age

tag: Sex

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: 55: cell free DNA from plasma

tag: diagnosis

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Resistant to AA treatment


title: Y10153T

description: SAMPLE 46

tag: tissue

value: gastric cancer


title: Normal UPPP control MBD-Seq sample 121

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

value: Male

tag: race

value: Other

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: 54: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype


title: Normal UPPP control MBD-Seq sample 122

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage


title: 56: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

value: FALSE


title: Y10111T

description: SAMPLE 18

tag: age

tag: Sex

value: male

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Normal UPPP control MBD-Seq sample 120

tag: sample type

value: Normal UPPP

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

tag: race

tag: smoking

value: Former smoker

tag: type of tobacco

value: Cigarette

tag: pack years

value: Unknown

tag: alcohol use

tag: t-stage

tag: n-stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Y10095T

description: SAMPLE 14

tag: tissue

tag: age

tag: Sex

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: HPV+ HNSCC cell line SCC-047 RNA-Seq

library_source: transcriptomic

data_processing:
Raw reads were trimmed to remove adapter sequences, and low quality reads using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The RNA sequencing data were normalized using the RSEM version 2 protocols as developed by TCGA.
The trimmed RNA-seq reads aligned to the GRCh37/hg19 genome assembly using MapSplice2 version 2.0.1.9 with default command line arguments
Fusion and junction expression were obtained from MapSplice and merged across samples. Junctions or fusions missing from a sample were assigned zero reads. Values were normalized per total number of reads in millions to obtain an RPM measure.
Gene expression values were quantified from RNA sequencing data using RSEM version 1.2.9 and upper quartile normalization according to the TCGA RSEM v2 normalization pipeline.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab delimited text files containing upper quartile normalized RSEM expression values and reads per million in junctions and fusions
Supplementary_files_format_and_content: tab delimited text file containing RPM values for fusions
Supplementary_files_format_and_content: tab delimited text file containing RPM values for junctions

extract_protocol:
The RNA was extracted from 0.35 mm thick frozen tissue sections using the mirVana miRNA Isolation Kit (Ambion, Forster City, CA) per manufacturer's recommendations. The concentration of RNA was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA). The RNA quality was assessed using an Agilent RNA 6000 Nano Kit (Santa Clara, CA). The samples were required to achieve an RNA Integrity Number (RIN) of at least 7.0.
A stranded RNA library was prepared using the Illumina TruSeq stranded total RNA-seq Gold kit (San Diego, CA) from 400 ng of total RNA following the manufacturer's recommendations. Next, a ribosomal RNA reduction was performed from total RNA and purified with AMPure XP magnetic beads. The purified RNA was fragmented, primed at 94°C for 8 min and stored at 4°C. The fragmented RNA was then converted to double-stranded cDNA, and the cDNA was 3’ adenylated and ligated with barcode adapters. The library was then enriched using PCR and AMPure XP bead purification. The quality and quantity of each library were assessed using the Agilent High Sensitivity DNA Analysis Kit.

tag: sample type

value: HPV+ HNSCC cell line

tag: patient id

tag: hpv integration

value: Integrated

tag: hpv type

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: anatomic tnm stage


title: Normal UPPP control MBD-Seq sample 119

value: Caucasian

value: Non-smoker

tag: pack years

tag: alcohol use

value: No

tag: t-stage

tag: n-stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Patient derived xenograft for HPV+ HNSCC tumor RNA-Seq sample 37

tag: sample type

value: Patient-derived HPV+ HNSCC xenograft

tag: patient id

tag: age

value: Yes


title: 53: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Resistant to AA treatment


title: HPV+ HNSCC cell line SCC-090 RNA-seq

tag: hpv integration

tag: hpv type

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy


title: 51: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: age

tag: individual id

tag: visit

tag: center

value: BC

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point


title: 52: cell free DNA from plasma

tag: outlier

value: FALSE

tag: phenotype


title: Normal UPPP control MBD-Seq sample 118

tag: sample type

value: Normal UPPP

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

value: Female

tag: race

value: African american

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control RNA-Seq sample 125

tag: age

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy


title: 50: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

value: BL

tag: center

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Sensitive to AA treatment


title: 49: cell free DNA from plasma

value: EoT


title: Normal UPPP control MBD-Seq sample 117

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

value: Male

tag: race

value: Caucasian

tag: smoking

value: Non-smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: No

tag: t-stage

tag: n-stage

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control MBD-Seq sample 116

tag: age

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy


title: Y10088T

description: SAMPLE 12

tag: tissue

value: gastric cancer

tag: Sex

value: male

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Y10094T

description: SAMPLE 13

value: female


title: Normal UPPP control RNA-Seq sample 123

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years


title: Normal UPPP control RNA-Seq sample 124

tag: age

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control MBD-Seq sample 115

tag: sample type

tag: patient id

value: Former smoker

value: Cigarette

value: Unknown

tag: primary surgical therapy


title: 48: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Resistant to AA treatment


title: 47: cell free DNA from plasma

tag: age

value: EoT

value: BC

value: TRUE


title: Normal UPPP control RNA-Seq sample 122

value: Normal UPPP

tag: hpv integration

tag: hpv type

tag: gender

value: Male

tag: race

value: African american

tag: smoking

value: Non-smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary chemotherapy


title: Normal UPPP control MBD-Seq sample 114

tag: sample type

tag: patient id

value: Female

value: Current smoker

value: No

tag: primary surgical therapy

tag: primary radiation therapy


title: Patient derived xenograft for HPV+ HNSCC tumor RNA-Seq sample 20

value: Patient-derived HPV+ HNSCC xenograft

tag: hpv integration

value: Non-integrated

tag: hpv type

tag: age

value: Caucasian

value: Cigarette

value: Yes


title: Normal UPPP control RNA-Seq sample 121

tag: gender

tag: race

value: Other

tag: smoking


title: Normal UPPP control RNA-Seq sample 120

value: Former smoker

tag: type of tobacco

tag: pack years

value: Unknown

tag: alcohol use


title: 45: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

value: BL

tag: center

value: BC

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Resistant to AA treatment


title: Normal UPPP control MBD-Seq sample 112

tag: sample type

value: Normal UPPP

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

value: Female

value: Non-smoker

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control MBD-Seq sample 113

tag: race

tag: smoking

value: Current smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: No


title: 44: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype


title: Normal UPPP control RNA-Seq sample 119

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

value: Male

value: Caucasian

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control RNA-Seq sample 118

tag: race

value: African american

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use


title: Normal UPPP control MBD-Seq sample 109

tag: sample type

tag: patient id

tag: hpv integration


title: Normal UPPP control MBD-Seq sample 111

tag: hpv type

tag: age

tag: gender

value: Cigarette

value: Yes


title: Normal UPPP control MBD-Seq sample 108

tag: t-stage

tag: n-stage

tag: anatomic tnm stage


title: Normal UPPP control MBD-Seq sample 110

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy


title: Normal UPPP control RNA-Seq sample 116

tag: race

tag: primary chemotherapy

tag: primary radiation therapy


title: 43: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype


title: Normal UPPP control RNA-Seq sample 117

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)


title: Normal UPPP control RNA-Seq sample 115

tag: race

value: Former smoker

value: Unknown

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: 42: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

value: BL

tag: center

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype


title: 41: cell free DNA from plasma

tag: age

value: EoT

value: Sensitive

value: TRUE

value: Sensitive to AA treatment


title: Normal UPPP control RNA-Seq sample 114

tag: sample type

value: Normal UPPP

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

value: Female

tag: race

tag: smoking

value: Current smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: No

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)


title: 39: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

value: BC

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

value: Resistant to AA treatment


title: Normal UPPP control MBD-Seq sample 106

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

value: Male

tag: race

value: Caucasian

tag: smoking

value: Non-smoker

tag: type of tobacco

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: 46: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

tag: phenotype


title: 38: cell free DNA from plasma

tag: age

tag: psa amount

tag: visit time point

tag: outlier


title: Normal UPPP control RNA-Seq sample 112

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)


title: Normal UPPP control MBD-Seq sample 105

tag: age

value: African american

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: 37: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype


title: Normal UPPP control MBD-Seq sample 104

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)


title: 36: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: age

tag: individual id

tag: visit

value: BL

tag: center

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point


title: Normal UPPP control RNA-Seq sample 110

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control MBD-Seq sample 107

tag: age

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)


title: 35: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype


title: Normal UPPP control MBD-Seq sample 103

tag: sample type

value: Normal UPPP

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control RNA-Seq sample 108

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)


title: Normal UPPP control MBD-Seq sample 102

tag: sample type

tag: patient id

tag: hpv integration

value: Female

value: Cigarette


title: Normal UPPP control RNA-Seq sample 109

tag: hpv type

tag: age

tag: gender

value: No


title: 34: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

value: EoT

tag: center

value: BC

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype


title: Normal UPPP control MBD-Seq sample 101

tag: sample type

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control RNA-Seq sample 107

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender


title: 33: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Resistant to AA treatment


title: 31: cell free DNA from plasma


title: HPV+ HNSCC tumor MBD-Seq sample 49

tag: sample type

value: HPV+ HNSCC tumor

value: Non-integrated

value: Male

tag: race

value: Caucasian

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

value: Yes

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

value: AWD

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 50

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

value: Non-smoker

value: Unknown


title: 40: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Sensitive to AA treatment


title: Normal UPPP control RNA-Seq sample 113

tag: sample type

value: Normal UPPP

value: Female

tag: race

tag: smoking

value: Current smoker

tag: type of tobacco

value: Cigarette

tag: pack years

tag: alcohol use

value: No

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control RNA-Seq sample 106

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

value: Male


title: Normal UPPP control RNA-Seq sample 105

tag: sample type

tag: race

value: African american

tag: smoking


title: HPV+ HNSCC tumor MBD-Seq sample 48

value: HPV+ HNSCC tumor

value: Integrated

value: Caucasian

value: Former smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: Yes

value: NED


title: 32: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

value: BC

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Resistant to AA treatment


title: HPV+ HNSCC tumor MBD-Seq sample 47

tag: sample type

tag: patient id

tag: hpv integration

value: Non-integrated

tag: hpv type

tag: age

tag: gender

value: Other

value: Non-smoker

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: Normal UPPP control RNA-Seq sample 111

value: Normal UPPP

tag: race

tag: smoking

value: Current smoker

tag: type of tobacco

value: Cigarette

tag: pack years

tag: alcohol use


title: 29: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Sensitive to AA treatment


title: HPV+ HNSCC tumor MBD-Seq sample 46

tag: sample type

value: HPV+ HNSCC tumor

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

value: Male

value: Caucasian

value: Former smoker

value: Unknown

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

value: AWD

tag: primary surgical therapy

value: No

tag: primary chemotherapy

value: Yes

tag: primary radiation therapy


title: Normal UPPP control RNA-Seq sample 104

value: Female

tag: race

value: African american

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use


title: HPV+ HNSCC tumor MBD-Seq sample 45

tag: sample type

tag: patient id

tag: hpv integration

value: Non-integrated

value: Other

value: NED


title: Normal UPPP control RNA-Seq sample 103

value: Normal UPPP

tag: hpv type

tag: age

tag: gender

value: Non-smoker


title: HPV+ HNSCC tumor MBD-Seq sample 44

value: Current smoker

value: Cigarette

tag: t-stage

tag: n-stage

tag: anatomic tnm stage


title: Normal UPPP control RNA-Seq sample 101

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy


title: Normal UPPP control RNA-Seq sample 102

tag: race

tag: primary chemotherapy

tag: primary radiation therapy


title: 25: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Resistant to AA treatment


title: 28: cell free DNA from plasma

tag: age

value: Sensitive

value: Sensitive to AA treatment


title: 27: cell free DNA from plasma


title: HPV+ HNSCC tumor RNA-Seq sample 50

tag: sample type

value: HPV+ HNSCC tumor

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

value: Male

value: Caucasian

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

value: Unknown

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

value: AWD

value: No

value: Yes


title: HPV+ HNSCC tumor MBD-Seq sample 43

value: Integrated

tag: race

value: Non-smoker

value: NED

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 41

tag: sample type

tag: patient id

value: Non-integrated

tag: age

value: Female


title: HPV+ HNSCC tumor MBD-Seq sample 42

tag: hpv integration

tag: hpv type

tag: gender

value: Former smoker

value: Cigarette


title: 26: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

value: EoT

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype


title: HPV+ HNSCC tumor RNA-Seq sample 49

tag: sample type

value: HPV+ HNSCC tumor

value: Male

tag: race

value: Caucasian

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 47

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

value: Other

value: No


title: HPV+ HNSCC tumor RNA-Seq sample 48

tag: sample type

value: Integrated

tag: race

tag: smoking

value: Yes


title: 21: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

value: BC

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Sensitive to AA treatment


title: 24: cell free DNA from plasma

value: BL


title: 22: cell free DNA from plasma


title: 23: cell free DNA from plasma


title: 30: cell free DNA from plasma


title: HPV+ HNSCC tumor RNA-Seq sample 46

tag: patient id

tag: hpv integration

value: Non-integrated

tag: hpv type

value: Former smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: Unknown

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

value: AWD

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 45

tag: sample type

tag: age

tag: gender

tag: race

tag: smoking

value: Cigarette

value: NED


title: HPV+ HNSCC tumor MBD-Seq sample 39

value: HPV+ HNSCC tumor

tag: patient id

tag: hpv integration

tag: hpv type

value: Non-smoker


title: HPV+ HNSCC tumor MBD-Seq sample 40

value: Male

value: Caucasian

value: Current smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: DUC


title: HPV+ HNSCC tumor MBD-Seq sample 37

value: Integrated

value: Yes

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

value: No


title: HPV+ HNSCC tumor RNA-Seq sample 44

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy


title: HPV+ HNSCC tumor MBD-Seq sample 36

tag: sample type

value: Cigar

tag: primary chemotherapy

tag: primary radiation therapy


title: 19: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: age

tag: individual id

tag: visit

value: BL

tag: center

value: BC

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Sensitive to AA treatment


title: HPV+ HNSCC tumor MBD-Seq sample 35

value: HPV+ HNSCC tumor

tag: patient id

tag: hpv integration

value: Non-integrated

tag: hpv type

tag: gender

value: Female

tag: race

tag: smoking

value: Former smoker

tag: type of tobacco

value: Cigarette

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

value: NED


title: 17: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: age

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

value: Resistant to AA treatment


title: HPV+ HNSCC tumor RNA-Seq sample 41

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: gender

tag: race

value: Caucasian

tag: smoking

value: Non-smoker

tag: type of tobacco

tag: pack years

value: Yes

value: AWD

tag: primary surgical therapy

tag: primary chemotherapy

value: No

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 34

tag: age

value: Male

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup


title: HPV+ HNSCC tumor RNA-Seq sample 42

tag: sample type

tag: patient id

tag: hpv integration

value: Integrated


title: HPV+ HNSCC tumor RNA-Seq sample 40

tag: hpv type

tag: gender

tag: race

value: Current smoker

value: DUC


title: 16: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype


title: HPV+ HNSCC tumor MBD-Seq sample 33

tag: sample type

value: HPV+ HNSCC tumor

value: Unknown

tag: age

tag: smoking

value: Former smoker

tag: type of tobacco

value: Cigarette

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: 15: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

value: BC

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

value: Resistant to AA treatment


title: HPV+ HNSCC tumor MBD-Seq sample 38

tag: sample type

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

tag: race

value: Caucasian

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

value: NED

value: Yes


title: HPV+ HNSCC tumor RNA-Seq sample 38

value: Male

value: No

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 32

tag: sample type

tag: patient id

tag: hpv integration

value: Non-integrated

value: Cigar


title: 20: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

tag: age

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Sensitive to AA treatment


title: HPV+ HNSCC tumor RNA-Seq sample 36

value: HPV+ HNSCC tumor

tag: hpv type

tag: gender

tag: race

tag: smoking

value: Current smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy


title: HPV+ HNSCC tumor MBD-Seq sample 31

tag: sample type

tag: patient id

tag: hpv integration

tag: age

value: Non-smoker

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 30

tag: hpv type

tag: gender

tag: race

value: Unknown

value: AWD


title: HPV+ HNSCC tumor MBD-Seq sample 29

value: Integrated

tag: smoking

tag: type of tobacco

tag: pack years


title: HPV+ HNSCC tumor RNA-Seq sample 37

value: Former smoker

value: Cigarette

tag: alcohol use

tag: t-stage

tag: n-stage


title: HPV+ HNSCC tumor RNA-Seq sample 34

value: Caucasian

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

value: NED


title: HPV+ HNSCC tumor MBD-Seq sample 27

tag: sample type

value: Male

value: Yes

tag: primary surgical therapy

tag: primary chemotherapy


title: HPV+ HNSCC tumor MBD-Seq sample 28

tag: patient id

tag: hpv integration

value: Non-integrated

tag: age

value: Cigar+Cigarette

value: No


title: 13: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype


title: 18: cell free DNA from plasma

value: Resistant

value: Resistant to AA treatment


title: HPV+ HNSCC tumor RNA-Seq sample 43

tag: sample type

value: HPV+ HNSCC tumor

value: Integrated

tag: hpv type

tag: gender

tag: race

tag: smoking

value: Non-smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 26

tag: patient id

tag: hpv integration

tag: age

value: Caucasian

value: Current smoker

value: Cigarette

tag: primary surgical therapy

tag: primary chemotherapy


title: 10: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

value: EoT

tag: center

value: BC

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Sensitive to AA treatment


title: 14: cell free DNA from plasma


title: HPV+ HNSCC tumor RNA-Seq sample 31

tag: sample type

value: Non-integrated

tag: hpv type

tag: gender

value: Male

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

value: Yes

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

value: NED

value: No

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 32

tag: patient id

tag: hpv integration

tag: age

value: Former smoker

value: Cigar

tag: primary surgical therapy

tag: primary chemotherapy


title: 12: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

value: BL

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Resistant to AA treatment


title: 11: cell free DNA from plasma

value: Sensitive


title: 8: cell free DNA from plasma

value: BC


title: HPV+ HNSCC tumor MBD-Seq sample 25

tag: sample type

value: HPV+ HNSCC tumor

value: Integrated

tag: hpv type

tag: gender

tag: race

value: Caucasian

tag: smoking

value: Non-smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 35

tag: patient id

tag: hpv integration

value: Non-integrated

tag: age

value: Female

value: Cigarette

value: Yes

value: NED

tag: primary surgical therapy

tag: primary chemotherapy


title: 7: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Sensitive to AA treatment


title: HPV+ HNSCC tumor MBD-Seq sample 24

tag: sample type

tag: hpv type

tag: gender

value: Male

tag: race

tag: smoking

value: Current smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: No

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 23

tag: patient id

tag: hpv integration

tag: age

value: Former smoker

tag: primary surgical therapy

tag: primary chemotherapy


title: HPV+ HNSCC tumor RNA-Seq sample 29

tag: sample type

tag: hpv type

tag: gender


title: HPV+ HNSCC tumor RNA-Seq sample 30

tag: race

tag: smoking

tag: type of tobacco

value: Unknown

value: AWD


title: 5: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

tag: phenotype

value: Resistant to AA treatment


title: HPV+ HNSCC tumor RNA-Seq sample 28

tag: sample type

value: HPV+ HNSCC tumor

tag: patient id

tag: hpv integration

value: Non-integrated

tag: age

value: Caucasian

value: Cigar+Cigarette

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 26

value: Integrated

tag: hpv type

tag: gender

tag: race

tag: smoking

tag: type of tobacco

value: Cigarette

value: NED

value: Yes


title: HPV+ HNSCC tumor RNA-Seq sample 27

tag: sample type

tag: patient id

tag: hpv integration

value: Male

value: Non-smoker


title: HPV+ HNSCC tumor RNA-Seq sample 25

tag: age

tag: pack years

tag: alcohol use

value: No


title: HPV+ HNSCC tumor RNA-Seq sample 24

value: Current smoker

tag: t-stage

tag: n-stage

tag: anatomic tnm stage


title: 9: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: tissue

value: plasma

tag: individual id

tag: visit

tag: center

value: BC

tag: cohort

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Sensitive to AA treatment


title: HPV+ HNSCC tumor RNA-Seq sample 23

tag: sample type

value: HPV+ HNSCC tumor

tag: patient id

tag: hpv integration

tag: hpv type

tag: age

tag: gender

tag: race

tag: smoking

value: Former smoker

tag: type of tobacco

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

tag: primary radiation therapy


title: 6: cell free DNA from plasma

tag: diagnosis

tag: tissue

tag: individual id

tag: visit

value: EoT

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

value: FALSE

value: Resistant to AA treatment


title: 3: cell free DNA from plasma

tag: age

value: BL

tag: outlier

tag: phenotype


title: 1: cell free DNA from plasma


title: 2: cell free DNA from plasma


title: 4: cell free DNA from plasma


title: HPV+ HNSCC tumor RNA-Seq sample 22

tag: sample type

tag: patient id

tag: hpv integration

value: Non-integrated

tag: hpv type

tag: gender

value: Male

tag: race

value: Caucasian

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: t-stage

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

value: NED

value: Yes


title: HPV+ HNSCC tumor RNA-Seq sample 21

tag: age

value: Cigarette

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy

value: No

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 20

tag: sample type

tag: patient id

tag: hpv integration

value: Current smoker

value: AWD


title: HPV+ HNSCC tumor RNA-Seq sample 19

value: HPV+ HNSCC tumor

value: Integrated

tag: hpv type

tag: gender

tag: race


title: HPV+ HNSCC tumor RNA-Seq sample 18

tag: smoking

value: Former smoker

tag: type of tobacco

tag: pack years

value: Unknown


title: HPV+ HNSCC tumor RNA-Seq sample 13

value: Non-smoker

tag: alcohol use

tag: t-stage

tag: n-stage


title: HPV+ HNSCC tumor RNA-Seq sample 15

tag: age

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)


title: HPV+ HNSCC tumor MBD-Seq sample 18

tag: disease status at last clinical followup

tag: primary surgical therapy

tag: primary chemotherapy


title: HPV+ HNSCC tumor MBD-Seq sample 22

tag: sample type

tag: patient id

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 21

tag: hpv integration

tag: hpv type

tag: gender


title: HPV+ HNSCC tumor MBD-Seq sample 20

tag: race

tag: smoking

tag: type of tobacco


title: HPV+ HNSCC tumor RNA-Seq sample 14

tag: pack years

tag: alcohol use

tag: t-stage


title: HPV+ HNSCC tumor RNA-Seq sample 11

tag: age

tag: n-stage

tag: anatomic tnm stage


title: HPV+ HNSCC tumor MBD-Seq sample 19

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy


title: HPV+ HNSCC tumor MBD-Seq sample 17

tag: sample type

tag: patient id

tag: primary chemotherapy


title: HPV+ HNSCC tumor RNA-Seq sample 12

tag: hpv integration

tag: hpv type

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 17

tag: gender

tag: race

tag: smoking


title: HPV+ HNSCC tumor RNA-Seq sample 16

tag: type of tobacco

tag: pack years

tag: alcohol use


title: HPV+ HNSCC tumor RNA-Seq sample 10

tag: age

value: Female

tag: t-stage

tag: n-stage


title: HPV+ HNSCC tumor RNA-Seq sample 9

value: Cigar

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup


title: HPV+ HNSCC tumor RNA-Seq sample 7

tag: sample type

tag: patient id

tag: primary surgical therapy


title: HPV+ HNSCC tumor RNA-Seq sample 5

tag: hpv integration

tag: hpv type

tag: primary chemotherapy


title: HPV+ HNSCC tumor RNA-Seq sample 4

tag: gender

tag: race

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 2

tag: smoking

tag: type of tobacco

tag: pack years


title: HPV+ HNSCC tumor RNA-Seq sample 3

tag: age

tag: alcohol use

tag: t-stage


title: ∆tfb3

city: Copenhagen N

first: Xu

last: Feng

address: Ole Maaløes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

data_processing:
Raw reads produced from sequencing machines contain dirty reads which contain adapters, unknown or low quality bases.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S.L. Salzberg, 2012)
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was defined by setting FDR-value of 0.001 and log2 (Fold change) of 1 as the threshold.
Genome_build: S. islandicus REY15A (accession no. NC_017276)
Supplementary_files_format_and_content: Excel file with RPKM

organism: Saccharolobus islandicus REY15A

growth_protocol: The genetic host S. islandicus strain E233S1 and ∆tfb3 were cultured at 78 °C in SCVU medium (basic salts and 0.2% sucrose, 0.2% Casamino acids, 1% vitamin solution, 20 μg/mL uracil).

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols. rRNA was removed with kit after total RNA was collected from prokaryocyte. Fragmentation buffer was added for interrupting mRNA to short fragments.  Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized  using buffer, dATPs,dGTPs,dCTPs,dUTPs, RNase H and DNA polymerase I respectively after removing dNTPs. Short fragments were purified with QiaQuick  PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adapters.  Then, the UNG enzyme was used to degrade the second-strand cDNA, and the product was purified by MiniElute PCR Purification Kit before PCR amplification.  At last, the library was sequenced using Illumina HiSeq4000.

treatment_protocol: For NQO treatment, each strain was grown to an early exponential phase (OD600=0.20) at which NQO was supplemented to a concentration of 2 µM. Aliquots without the drug were used as control. Incubation was then continued. Cell samples for RNA extraction were taken 6 hours post NQO addition.

tag: genetic background

tag: genotype

value: delta tfb3


title: ∆tfb3_NQO

source_name: ∆tfb3 treated with NQO


title: E233S1_NQO

source_name: E233S1 treated with NQO

value: wildtype


title: HPV+ HNSCC tumor MBD-Seq sample 1

tag: sample type

value: Non-integrated

value: Male

tag: n-stage

tag: anatomic tnm stage

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup


title: HPV+ HNSCC tumor MBD-Seq sample 4

tag: patient id

tag: hpv integration

tag: hpv type

value: Caucasian

tag: primary surgical therapy

tag: primary chemotherapy


title: HPV+ HNSCC tumor MBD-Seq sample 6

tag: gender

tag: race

tag: smoking

tag: type of tobacco

value: NED

value: Yes

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 2

tag: age

tag: pack years

tag: alcohol use

tag: t-stage

value: No


title: HPV+ HNSCC tumor MBD-Seq sample 10

tag: sample type

value: Cigarette

tag: n-stage

tag: anatomic tnm stage


title: HPV+ HNSCC tumor MBD-Seq sample 8

tag: patient id

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup


title: HPV+ HNSCC tumor MBD-Seq sample 11

tag: hpv integration

tag: hpv type

tag: primary surgical therapy


title: HPV+ HNSCC tumor MBD-Seq sample 7

tag: gender

tag: race

tag: primary chemotherapy


title: HPV+ HNSCC tumor MBD-Seq sample 5

tag: smoking

tag: type of tobacco

tag: primary radiation therapy


title: HPV+ HNSCC tumor RNA-Seq sample 1

tag: age

tag: pack years

tag: alcohol use


title: E233S1

tag: genetic background

tag: genotype


title: HPV+ HNSCC tumor RNA-Seq sample 6

tag: sample type

tag: patient id

value: Current smoker

tag: t-stage

tag: n-stage

tag: anatomic tnm stage


title: HPV+ HNSCC tumor MBD-Seq sample 9

value: HPV+ HNSCC tumor

tag: hpv integration

tag: hpv type

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup

tag: primary surgical therapy


title: HPV+ HNSCC tumor MBD-Seq sample 3

tag: gender

tag: race

tag: smoking

tag: type of tobacco

value: AWD

tag: primary chemotherapy


title: HPV+ HNSCC tumor MBD-Seq sample 16

value: Integrated

tag: age

value: Former smoker

tag: pack years

tag: alcohol use

tag: primary radiation therapy


title: HPV+ HNSCC tumor MBD-Seq sample 13

tag: sample type

tag: patient id

value: Non-smoker

tag: t-stage


title: HPV+ HNSCC tumor MBD-Seq sample 12

tag: hpv integration

tag: n-stage

tag: anatomic tnm stage


title: HPV+ HNSCC tumor MBD-Seq sample 15

tag: hpv type

value: Unknown

tag: time to death or follow-up if alive (months)

tag: disease status at last clinical followup


title: HPV+ HNSCC tumor MBD-Seq sample 14

tag: gender

tag: race

tag: primary surgical therapy


title: CAD patient with RA 1

status: Public on Mar 19 2018

city: Lillehammer

first: Ingvild

last: Oma

address: Anders Sandviks gate 17

country: Norway

institute: Innlandet Hospital Trust

description: Gene expression data of the ascending aorta from CAD patient with RA

hyb_protocol: Labeled and fragmented single stranded cDNAs were hybridixed on GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix FS-450 Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett Packard Gene Array Scanner 3000

data_processing: The scanned images were prosessed using Affymetrix GeneChip Comand Console software. Robust microarray analysis (RMA) yielding normalized Log2 transformed signal intensities was applied for normalization. Gene transcripts with maximal signal values of less than 5 across the arrays were removed to filter for low and non-expressed genes. Differential expressed transcripts between groups were identified using ibe-way ANOVA as implemented in Partek Genomics Suite software.

source_name: CAD patient with RA, ascending aorta

label_protocol: 100ng of total RNA was subjected to cDNA and labeling kit (Affymetrix GeneChip HT One-cycle; and GeneChip HT IVT) according to the manufacturer's protocol for whole-genome gene expression analysis

extract_protocol: Total RNA was isolated from aortic specimens with TRI reagent (Sigma-Aldrich) and further purified and DNase treated using RNeasy Mini Kit (Qiagen)

value: Female

tag: disease state

value: CAD with RA

tag: tisue

value: Biopsy from the ascending aorta


title: CAD patient 2

description: Gene expression data of the ascending aorta from CAD patient

source_name: CAD patient, ascending aorta

value: CAD


title: CAD patient with RA 5


title: CAD patient 6


title: CAD patient with RA 8

value: Male


title: CAD patient 4


title: CAD patient 7


title: CAD patient 5


title: CAD patient with RA 2


title: CAD patient with RA 7


title: CAD patient with RA 3


title: CAD patient with RA 6


title: CAD patient with RA 4


title: CAD patient 8


title: CAD patient 3


title: genomic DNA whole blood [D_13D8341]

type: genomic

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Academic Medical Center Amsterdam

hyb_protocol: Bisulfite converted DNA was hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi (v1.16.0) for reading the data; MethylAid (v1.14.0) for quality control

label: CY3 and CY5

source_name: Down Syndrome_whole blood

label_protocol: Standard Illumina protocol

extract_protocol: Peripheral blood was drawn and stored in EDTA to prevent coagulation. Erythrocytes were lysed before proteins were aggregated out of the sample. Genomic DNA was extracted through ethanol precipitation, after which the DNA was dissolved in tris-ethylenediaminetetraacetic buffer (Tris-EDTA) and stored at 4°C.

value: M

tag: age

value: Postnatal_0-3 days

tag: group

value: Down Syndrome Newborn


title: G0015_2

city: Atlanta

first: Anna

middle: K

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

description: Human HT12-v4 - standard protocol

data_processing: BeadStudio

source_name: PBMC

extract_protocol: AllPrep RNA/DNA Mini Kit (Qiagen)

tag: Sex

value: African American

value: PBMC

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: CAD patient 1


title: G0020_2

description: Human HT12-v4 - standard protocol

tag: sample type


title: G0010_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0010_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: E0505_2

description: Human HT12-v4 - standard protocol

tag: sample type

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7


title: E0505_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0013_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: E0521_2

description: Human HT12-v4 - standard protocol

tag: sample type


title: G0019_1

description: Human HT12-v4 - standard protocol


title: genomic DNA whole blood [D_13D5279]

tag: gender

value: F

tag: age

tag: group


title: G0009_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: genomic DNA whole blood [N_13D6641]

source_name: control_whole blood

value: control


title: genomic DNA whole blood [D_13D7104]


title: genomic DNA whole blood [D_13D5554]


title: G0017_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection


title: G0009_1

description: Human HT12-v4 - standard protocol

tag: sample type

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: genomic DNA whole blood [D_13D4146]

tag: gender

tag: age

tag: group


title: G0001_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race


title: genomic DNA whole blood [D_13D4799]


title: genomic DNA whole blood [D_13D7350]


title: genomic DNA whole blood [N_13D7596]


title: genomic DNA whole blood [D_13D0929]


title: genomic DNA whole blood [D_13D2147]


title: genomic DNA whole blood [N_13D4806]


title: genomic DNA whole blood [D_13D6647]


title: genomic DNA whole blood [N_13D6284]


title: genomic DNA whole blood [N_13D5973]


title: G0054_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: G0006_2

description: Human HT12-v4 - standard protocol

tag: sample type

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0059_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race


title: G0003_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance


title: E0571_1

description: Human HT12-v4 - standard protocol


title: G0059_1

description: Human HT12-v4 - standard protocol


title: G0001_1

description: Human HT12-v4 - standard protocol


title: E0571_2

description: Human HT12-v4 - standard protocol


title: G0029_2

description: Human HT12-v4 - standard protocol


title: G0061_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0053_2

description: Human HT12-v4 - standard protocol

tag: sample type

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: G0029_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0006_1

description: Human HT12-v4 - standard protocol


title: G0061_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0041_1

description: Human HT12-v4 - standard protocol

tag: sample type


title: G0054_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: G0074_2

description: Human HT12-v4 - standard protocol

tag: race

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0049_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0596_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: sample type


title: G0049_2

description: Human HT12-v4 - standard protocol

tag: race

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: G0092_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2


title: G0003_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: sample type


title: G0039_1

description: Human HT12-v4 - standard protocol

tag: race

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0559_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance


title: G0165_2

description: Human HT12-v4 - standard protocol

tag: visit

tag: pregnancy complication


title: G0165_1

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection

tag: maternal age


title: E0596_2

description: Human HT12-v4 - standard protocol


title: G0039_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: G0092_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 12

tag: surrogate variable 13


title: E0520_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0033_2

description: Human HT12-v4 - standard protocol


title: E0525_1

description: Human HT12-v4 - standard protocol


title: G0027_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 14

tag: surrogate variable 15


title: G0027_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 10

tag: surrogate variable 11


title: G0030_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 12

tag: surrogate variable 13


title: E0510_1

description: Human HT12-v4 - standard protocol


title: G0028_2

description: Human HT12-v4 - standard protocol


title: G0018_1

description: Human HT12-v4 - standard protocol


title: G0028_1

description: Human HT12-v4 - standard protocol


title: G0033_1

description: Human HT12-v4 - standard protocol


title: G0023_1

description: Human HT12-v4 - standard protocol


title: G0023_2

description: Human HT12-v4 - standard protocol


title: G0030_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 14

tag: surrogate variable 15


title: G0026_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type


title: G0025_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 10

tag: surrogate variable 11


title: G0026_2

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: E0526_1

description: Human HT12-v4 - standard protocol


title: G0025_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 12

tag: surrogate variable 13


title: G0014_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: surrogate variable 14

tag: surrogate variable 15


title: E0538_2

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 10

tag: surrogate variable 11


title: G0022_2

description: Human HT12-v4 - standard protocol


title: G0014_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 12

tag: surrogate variable 13


title: G0022_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit


title: E0543_2

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 14

tag: surrogate variable 15


title: G0034_1

description: Human HT12-v4 - standard protocol


title: E0569_2

description: Human HT12-v4 - standard protocol


title: E0538_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: E0542_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: surrogate variable 12

tag: surrogate variable 13


title: E0543_1

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 14

tag: surrogate variable 15


title: E0556_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: E0528_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit


title: G0044_2

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: E0542_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0551_2

description: Human HT12-v4 - standard protocol

tag: Sex


title: E0566_1

description: Human HT12-v4 - standard protocol

tag: race


title: E0553_2

description: Human HT12-v4 - standard protocol

tag: sample type

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: E0556_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 3


title: E0553_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0549_1

description: Human HT12-v4 - standard protocol

tag: sample type


title: E0566_2

description: Human HT12-v4 - standard protocol

tag: experienced labor


title: E0548_1

description: Human HT12-v4 - standard protocol

tag: fetal intolerance


title: E0569_1

description: Human HT12-v4 - standard protocol

tag: visit


title: G0044_1

description: Human HT12-v4 - standard protocol

tag: pregnancy complication


title: E0548_2

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection


title: E0549_2

description: Human HT12-v4 - standard protocol

tag: maternal age


title: G0015_1

description: Human HT12-v4 - standard protocol


title: E0547_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: G0042_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race


title: E0541_2

description: Human HT12-v4 - standard protocol

tag: sample type


title: E0546_2

description: Human HT12-v4 - standard protocol

tag: experienced labor


title: E0547_2

description: Human HT12-v4 - standard protocol

tag: fetal intolerance

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0042_2

description: Human HT12-v4 - standard protocol

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: E0540_2

description: Human HT12-v4 - standard protocol


title: E0541_1

description: Human HT12-v4 - standard protocol


title: E0535_2

description: Human HT12-v4 - standard protocol


title: E0539_2

description: Human HT12-v4 - standard protocol


title: E0536_1

description: Human HT12-v4 - standard protocol


title: G0067_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: E0535_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance


title: E0531_1

description: Human HT12-v4 - standard protocol

tag: visit


title: G0067_1

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0530_2

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9


title: G0035_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit


title: E0523_2

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: E0527_2

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 14

tag: surrogate variable 15


title: E0534_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit


title: E0530_1

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: E0524_2

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection

tag: maternal age


title: E0524_1

description: Human HT12-v4 - standard protocol


title: E0527_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0523_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: surrogate variable 3


title: E0528_2

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection

tag: maternal age


title: 11b_GR

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

country: France

institute: CEA-Institut de Genomique, Centre National de Genotypage

description: Granulocyte DNA from pedigree 11 twin b

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline.  of bisulfite-treated DNA was analyzed using the Infinium  Human Methylation 450 K bead arrays spanning approximately  over 480,000 CpG sites/sample (Illumina Inc., San  Diego, CA). Processing was done according to the manufacturer’s  protocol using an automated pipeline, and the  arrays were scanned on an Illumina iScan platform (Illumina  Inc., San Diego, CA) established at the Life & Brain  Center (Bonn, Germany)

data_processing: Subset quantile normalization, revised version of Touleimat & tost, Epigenomics 2012

label: Cy5, Cy3

source_name: Twin 11b granulocytes

extract_protocol: Peripheral blood was processed using density gradient centrifugation and the granulocyte fraction was preserved. Serial cell sorting was performed on the mononuclear cell fraction using a RoboSep device (StemCell Technologies), using first a CD14 positive selection, then a CD4 positive selection and finally a B cell enrichment. Genomic DNA was extracted and purified from monocytes, CD4+ T-cells, B-cells and granulocytes using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) following the manufacturer's instructions

tag: status

value: Co-twin

tag: cell type

value: Granulocytes

tag: gender

tag: zygosity

value: Opposite-sex dizygotic


title: G0060_2

description: Human HT12-v4 - standard protocol


title: 11a_GR

description: Granulocyte DNA from pedigree 11 twin a

scan_protocol: the arrays were scanned on an Illumina iScan platform

source_name: Twin 11a granulocytes

value: Systemic lupus erythematosus (SLE)


title: 15b_GR

description: Granulocyte DNA from pedigree 15 twin b

source_name: Twin 15b granulocytes

value: Same-sex dizygotic


title: 13a_GR

description: Granulocyte DNA from pedigree 13 twin a

source_name: Twin 13a granulocytes

value: Female


title: 10b_GR

description: Granulocyte DNA from pedigree 10 twin b

source_name: Twin 10b granulocytes

value: Monozygotic


title: 14b_GR

description: Granulocyte DNA from pedigree 14 twin b

source_name: Twin 14b granulocytes


title: 14a_GR

description: Granulocyte DNA from pedigree 14 twin a

source_name: Twin 14a granulocytes


title: 15a_GR

description: Granulocyte DNA from pedigree 15 twin a

source_name: Twin 15a granulocytes


title: E0522_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: G0060_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: 13b_GR

description: Granulocyte DNA from pedigree 13 twin b

source_name: Twin 13b granulocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: G0047_1

description: Human HT12-v4 - standard protocol


title: 9b_GR

description: Granulocyte DNA from pedigree 9 twin b

source_name: Twin 9b granulocytes


title: 12b_GR

description: Granulocyte DNA from pedigree 12 twin b

source_name: Twin 12b granulocytes


title: G0016_1

description: Human HT12-v4 - standard protocol


title: 12a_GR

description: Granulocyte DNA from pedigree 12 twin a

source_name: Twin 12a granulocytes


title: 10a_GR

description: Granulocyte DNA from pedigree 10 twin a

source_name: Twin 10a granulocytes


title: E0513_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 14

tag: surrogate variable 15


title: G0047_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: E0517_1

description: Human HT12-v4 - standard protocol


title: E0513_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: 7b_GR

description: Granulocyte DNA from pedigree 7 twin b

source_name: Twin 7b granulocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: 9a_GR

description: Granulocyte DNA from pedigree 9 twin a

source_name: Twin 9a granulocytes


title: 7a_GR

description: Granulocyte DNA from pedigree 7 twin a

source_name: Twin 7a granulocytes


title: 6b_GR

description: Granulocyte DNA from pedigree 6 twin b

source_name: Twin 6b granulocytes


title: 8a_GR

description: Granulocyte DNA from pedigree 8 twin a

source_name: Twin 8a granulocytes


title: 8b_GR

description: Granulocyte DNA from pedigree 8 twin b

source_name: Twin 8b granulocytes


title: E0511_2

description: Human HT12-v4 - standard protocol

source_name: PBMC

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance


title: 5b_GR

description: Granulocyte DNA from pedigree 5 twin b

source_name: Twin 5b granulocytes


title: 6a_GR

description: Granulocyte DNA from pedigree 6 twin a

source_name: Twin 6a granulocytes


title: E0509_1

description: Human HT12-v4 - standard protocol

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0055_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 14

tag: surrogate variable 15


title: E0518_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: E0518_1

description: Human HT12-v4 - standard protocol

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4


title: E0504_2

description: Human HT12-v4 - standard protocol


title: 3b_GR

description: Granulocyte DNA from pedigree 3 twin b

source_name: Twin 3b granulocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: E0504_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor


title: E0521_1

description: Human HT12-v4 - standard protocol

tag: fetal intolerance


title: E0508_2

description: Human HT12-v4 - standard protocol

tag: visit


title: E0522_2

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0508_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: weeks gestation at sample collection

tag: maternal age


title: 14b_CD4T

description: CD4+ T-cell DNA from pedigree 14 twin b

source_name: Twin 14b CD4+ T-cells

tag: status

tag: cell type

value: CD4+ T-cells

tag: gender

tag: zygosity


title: 5a_GR

description: Granulocyte DNA from pedigree 5 twin a

source_name: Twin 5a granulocytes


title: 1b_GR

description: Granulocyte DNA from pedigree 1 twin b

source_name: Twin 1b granulocytes


title: E0506_2

description: Human HT12-v4 - standard protocol

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication


title: G0055_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12


title: E0502_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: weeks gestation at sample collection

tag: maternal age


title: E0502_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication


title: E0503_2

description: Human HT12-v4 - standard protocol


title: 13a_CD4T

description: CD4+ T-cell DNA from pedigree 13 twin a

source_name: Twin 13a CD4+ T-cells

tag: status

tag: cell type

tag: gender

tag: zygosity


title: 11a_CD4T

description: CD4+ T-cell DNA from pedigree 11 twin a

source_name: Twin 11a CD4+ T-cells


title: 1a_GR

description: Granulocyte DNA from pedigree 1 twin a

source_name: Twin 1a granulocytes


title: 3a_GR

description: Granulocyte DNA from pedigree 3 twin a

source_name: Twin 3a granulocytes


title: 15a_CD4T

description: CD4+ T-cell DNA from pedigree 15 twin a

source_name: Twin 15a CD4+ T-cells


title: 15b_CD4T

description: CD4+ T-cell DNA from pedigree 15 twin b

source_name: Twin 15b CD4+ T-cells


title: 12a_CD4T

description: CD4+ T-cell DNA from pedigree 12 twin a

source_name: Twin 12a CD4+ T-cells


title: 10b_CD4T

description: CD4+ T-cell DNA from pedigree 10 twin b

source_name: Twin 10b CD4+ T-cells


title: E0586_2

description: Human HT12-v4 - standard protocol


title: 11b_CD4T

description: CD4+ T-cell DNA from pedigree 11 twin b

source_name: Twin 11b CD4+ T-cells


title: 10a_CD4T

description: CD4+ T-cell DNA from pedigree 10 twin a

source_name: Twin 10a CD4+ T-cells


title: G0053_1

description: Human HT12-v4 - standard protocol

source_name: PBMC

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0008_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: 14a_CD4T

description: CD4+ T-cell DNA from pedigree 14 twin a

source_name: Twin 14a CD4+ T-cells

tag: status

tag: cell type

tag: gender

tag: zygosity


title: E0584_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12


title: E0584_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: 13b_CD4T

description: CD4+ T-cell DNA from pedigree 13 twin b

source_name: Twin 13b CD4+ T-cells

tag: status

tag: cell type

tag: gender

tag: zygosity


title: 9b_CD4T

description: CD4+ T-cell DNA from pedigree 9 twin b

source_name: Twin 9b CD4+ T-cells


title: E0564_1

description: Human HT12-v4 - standard protocol


title: E0586_1

description: Human HT12-v4 - standard protocol


title: G0161_1

description: Human HT12-v4 - standard protocol


title: 9a_CD4T

description: CD4+ T-cell DNA from pedigree 9 twin a

source_name: Twin 9a CD4+ T-cells


title: E0511_1

description: Human HT12-v4 - standard protocol


title: 7a_CD4T

description: CD4+ T-cell DNA from pedigree 7 twin a

source_name: Twin 7a CD4+ T-cells


title: 8b_CD4T

description: CD4+ T-cell DNA from pedigree 8 twin b

source_name: Twin 8b CD4+ T-cells


title: 7b_CD4T

description: CD4+ T-cell DNA from pedigree 7 twin b

source_name: Twin 7b CD4+ T-cells


title: 6a_CD4T

description: CD4+ T-cell DNA from pedigree 6 twin a

source_name: Twin 6a CD4+ T-cells


title: E0622_2

description: Human HT12-v4 - standard protocol


title: 6b_CD4T

description: CD4+ T-cell DNA from pedigree 6 twin b

source_name: Twin 6b CD4+ T-cells


title: 5b_CD4T

description: CD4+ T-cell DNA from pedigree 5 twin b

source_name: Twin 5b CD4+ T-cells


title: 5a_CD4T

description: CD4+ T-cell DNA from pedigree 5 twin a

source_name: Twin 5a CD4+ T-cells


title: G0002_1

description: Human HT12-v4 - standard protocol


title: G0128_1

description: Human HT12-v4 - standard protocol


title: G0184_2

description: Human HT12-v4 - standard protocol


title: G0184_1

description: Human HT12-v4 - standard protocol


title: G0087_1

description: Human HT12-v4 - standard protocol


title: G0161_2

description: Human HT12-v4 - standard protocol


title: G0087_2

description: Human HT12-v4 - standard protocol


title: E0622_1

description: Human HT12-v4 - standard protocol


title: 12b_CD4T

description: CD4+ T-cell DNA from pedigree 12 twin b

source_name: Twin 12b CD4+ T-cells


title: G0128_2

description: Human HT12-v4 - standard protocol


title: E0635_2

description: Human HT12-v4 - standard protocol


title: E0604_1

description: Human HT12-v4 - standard protocol


title: E0635_1

description: Human HT12-v4 - standard protocol


title: 8a_CD4T

description: CD4+ T-cell DNA from pedigree 8 twin a

source_name: Twin 8a CD4+ T-cells


title: 15a_CD19B

description: B-cell DNA from pedigree 15 twin a

source_name: Twin 15a B-cells

value: B-cells


title: 15b_CD19B

description: B-cell DNA from pedigree 15 twin b

source_name: Twin 15b B-cells

value: Male


title: G0131_2

description: Human HT12-v4 - standard protocol


title: 3a_CD4T

description: CD4+ T-cell DNA from pedigree 3 twin a

source_name: Twin 3a CD4+ T-cells


title: G0179_1

description: Human HT12-v4 - standard protocol

source_name: PBMC


title: E0593_2

description: Human HT12-v4 - standard protocol


title: E0593_1

description: Human HT12-v4 - standard protocol


title: E0627_1

description: Human HT12-v4 - standard protocol


title: G0179_2

description: Human HT12-v4 - standard protocol


title: 14a_CD19B

description: B-cell DNA from pedigree 14 twin a

source_name: Twin 14a B-cells


title: 1a_CD4T

description: CD4+ T-cell DNA from pedigree 1 twin a

source_name: Twin 1a CD4+ T-cells


title: G0131_1

description: Human HT12-v4 - standard protocol


title: 3b_CD4T

description: CD4+ T-cell DNA from pedigree 3 twin b

source_name: Twin 3b CD4+ T-cells


title: 13b_CD19B

description: B-cell DNA from pedigree 13 twin b

source_name: Twin 13b B-cells


title: 11b_CD19B

description: B-cell DNA from pedigree 11 twin b

source_name: Twin 11b B-cells


title: G0091_2

description: Human HT12-v4 - standard protocol


title: 13a_CD19B

description: B-cell DNA from pedigree 13 twin a

source_name: Twin 13a B-cells


title: 14b_CD19B

description: B-cell DNA from pedigree 14 twin b

source_name: Twin 14b B-cells


title: 11a_CD19B

description: B-cell DNA from pedigree 11 twin a

source_name: Twin 11a B-cells


title: 12b_CD19B

description: B-cell DNA from pedigree 12 twin b

source_name: Twin 12b B-cells


title: 12a_CD19B

description: B-cell DNA from pedigree 12 twin a

source_name: Twin 12a B-cells


title: G0012_2

description: Human HT12-v4 - standard protocol


title: E0627_2

description: Human HT12-v4 - standard protocol


title: 10b_CD19B

description: B-cell DNA from pedigree 10 twin b

source_name: Twin 10b B-cells


title: 10a_CD19B

description: B-cell DNA from pedigree 10 twin a

source_name: Twin 10a B-cells


title: G0051_1

description: Human HT12-v4 - standard protocol


title: E0672_1

description: Human HT12-v4 - standard protocol


title: 8b_CD19B

description: B-cell DNA from pedigree 8 twin b

source_name: Twin 8b B-cells


title: 9b_CD19B

description: B-cell DNA from pedigree 9 twin b

source_name: Twin 9b B-cells


title: 7a_CD19B

description: B-cell DNA from pedigree 7 twin a

source_name: Twin 7a B-cells


title: G0083_2

description: Human HT12-v4 - standard protocol


title: G0091_1

description: Human HT12-v4 - standard protocol


title: G0051_2

description: Human HT12-v4 - standard protocol


title: E0594_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12


title: G0083_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: 7b_CD19B

description: B-cell DNA from pedigree 7 twin b

source_name: Twin 7b B-cells

tag: status

tag: cell type

tag: gender

tag: zygosity