title: GMSA_069_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_069 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: tissue

value: A

value: TDF

value: No

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive

tag: rin

tag: inclusion

value: Included

tag: paired

value: Unpaired


title: GMSA_072_Vagina_TDF-OnTreatment

status: Public on Jul 07 2020

type: RNA

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

country: USA

institute: University of Washington

hyb_protocol: Standard as recommended by Illumina, except that the temperature was 48C

scan_protocol: Standard Illumina protocol using Illumina iScan system

data_processing:
The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.
Matrix normalized table: This table contains detection p-values and signal intensity data that were transformed with a variance stabilizing transformation and normalized with a robust spline normalization using the Bioconductor lumi package (version 2.34.0). The normalized data was filtered to only include probes with a detection threshold p value <0.05 in at least 10 samples. Matrix non-normalized table: This table contains raw signal intensity values and detection p-values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Vagina from GMSA_072 treated with TDF-OnTreatment

label_protocol: 50 ng of total RNA was labeled using the Ovation PicoSL WTA System V2 kit and the Encore BiotinIL kit (both NuGEN)

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit

tag: collectiondate

value: Vagina

tag: age

tag: arm

tag: drug

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

value: oral

value: NonDecided

value: Paired


title: sample5_S55

type: SRA

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were mapped to mouse genome GRCm38 using STAR version 2.2.1 with default parameters except --sjdbOverhang 49 --outSAMstrandField intronMotif --outFilterMultimapNmax 1 (The max number of multiple alignments allowed for a read is 1. if exceeded, the read is considered unmapped).
Read counting was performed using HTSeq-Count (version 0.9.1) with parameters --stranded=no -m union, and using the annotations of mouse genome GRCm38 release 94 downloaded from the ENSembl website. In short, our RNA-Seq data has not been made with a strand-specific protocol. When a read was mapped to more than one gene, it was considered as ambiguous and assigned to none of them.
Genome_build: GRCm38 with an additional artificial chromosome for the YFP sequence
Supplementary_files_format_and_content: Text files with tab delimiters including raw gene counts and metadata (including index sorting information) for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: splenic plasmacytoid dendritic cells

extract_protocol:
Single cells were FACS sorted into 96-well PCR plates (Eppendorf), each well containing 10 µl of TCL buffer (Qiagen) supplemented with 1% β-mercaptoethanol. Plates were spun down at 800g for 1 min, flash frozen on dry ice and stored at -80°C until further processing (Villani and Shekhar, 2017).
Single cell RNA-sequencing libraries were generated using an adaptation of Smart-Seq2 (Villani and Shekhar, 2017).
Full-length RNA-sequencing was performed.

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

value: LIFRLow

tag: plate


title: GMSA_068_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_068 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

value: B

value: FTC/TDF

tag: birthcontrollab

value: injectable

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin


title: GMSA_070_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_070 treated with TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: inclusion

tag: paired


title: sample4_S54

tag: mouse genotype

tag: cell type

tag: tissue

tag: infection time

tag: plate


title: GMSA_070_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_070 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

value: Positive


title: GMSA_066_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_066 treated with FTC/TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

value: implant

tag: nugent

value: Negative

value: unknown

tag: rin

value: Included


title: GMSA_066_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_066 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: tissue

value: Vagina

value: prep

value: Yes

tag: inclusion

tag: paired


title: GMSA_067_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_067 treated with TDF-OnTreatment

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: NonDecided

tag: mpa

tag: lng

value: Paired


title: sample3_S53

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

value: LIFRLow

tag: plate


title: GMSA_064_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_064 treated with TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: NoHC

tag: eng

tag: net

value: Unavailable


title: BRBS196

tag: tissue

tag: eyfp status

value: MCMV YFPneg


title: sample2_S52


title: GMSA_064_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_064 treated with TDF-OnTreatment

tag: ptid

tag: visit

value: A

value: TDF

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: nugent

tag: rin

tag: inclusion

tag: paired


title: GMSA_067_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_067 treated with TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

value: No

value: implant

tag: lng


title: GMSA_062_Vagina_Placebo

source_name: Vagina from GMSA_062 treated with Placebo

tag: tissue

value: C

value: Placebo

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: eng

tag: net

value: Positive

value: Unpaired


title: GMSA_063_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_063 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

value: Vagina

value: B

value: FTC/TDF

value: prep

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: Indeterminate

value: unknown

value: Excluded:drug levels


title: GMSA_063_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_063 treated with FTC/TDF-OffTreatment

value: NonDecided

tag: mpa

tag: nugent

tag: rin

tag: inclusion

value: Included

tag: paired


title: GMSA_060_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_060 treated with FTC/TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

value: NoHC

value: Negative

value: Paired


title: GMSA_061_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_061 treated with TDF-OffTreatment

tag: tissue

value: A

value: TDF

tag: tdfngperml

tag: tdfdetected

value: No

value: oral

tag: lng

tag: eng


title: BRBS193

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BRBS194


title: GMSA_055_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_055 treated with TDF-OffTreatment

tag: ptid

tag: visit

value: Vagina

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: net

tag: nugent

value: Positive

tag: rin

tag: inclusion

value: Unpaired


title: sample1_S51

tag: tissue

value: LIFRLow


title: GMSA_061_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_061 treated with TDF-OnTreatment

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

value: implant

tag: lng

tag: eng

tag: paired


title: GMSA_065_Vagina_Placebo

source_name: Vagina from GMSA_065 treated with Placebo

tag: ptid

tag: visit

value: C

value: Placebo

value: placebo

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: birthcontrollab

value: Included


title: BRBS191

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_060_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_060 treated with FTC/TDF-OnTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: mpa

tag: net

tag: nugent

value: Negative

value: unknown

tag: rin

tag: inclusion

value: Paired


title: GMSA_058_Vagina_Placebo

source_name: Vagina from GMSA_058 treated with Placebo

tag: ptid

tag: visit

value: Vagina

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: lng

tag: eng

tag: paired


title: GMSA_056_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_056 treated with FTC/TDF-OnTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: No

tag: birthcontrollab

value: Excluded:drug levels

value: Unpaired


title: GMSA_057_Vagina_Placebo

source_name: Vagina from GMSA_057 treated with Placebo

tag: drug

tag: mpa

tag: net

tag: nugent

value: Positive

tag: rin


title: GMSA_059_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_059 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

tag: prep

tag: tdfngperml

tag: inclusion


title: GMSA_054_Vagina_Placebo

source_name: Vagina from GMSA_054 treated with Placebo

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: eng


title: GMSA_053_Vagina_Placebo

source_name: Vagina from GMSA_053 treated with Placebo

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: implant

tag: paired


title: GMSA_052_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_052 treated with TDF-OnTreatment

value: A

tag: drug

value: TDF

value: prep

tag: birthcontrollab

tag: mpa

tag: net

tag: nugent


title: BRBS192

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BRBS197

value: MCMV YFPpos


title: GMSA_050_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_050 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: rin

tag: inclusion


title: BRBS189

tag: tissue


title: BRBS190


title: GMSA_049_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_049 treated with FTC/TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

value: oral

tag: birthcontrollab

value: NoHC

tag: mpa

tag: eng

tag: net

tag: nugent

value: Negative

value: unknown

value: Included

tag: paired


title: GMSA_048_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_048 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

value: Vagina

tag: prep

tag: tdfngperml

tag: tdfdetected

value: Positive

value: Excluded:drug levels

value: Unpaired


title: GMSA_047_Vagina_Placebo

source_name: Vagina from GMSA_047 treated with Placebo

value: C

value: Placebo

value: placebo

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: rin

tag: inclusion


title: BRBS188

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BRBS107


title: BRBS187


title: GMSA_046_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_046 treated with TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

value: No

tag: birthcontrollab

value: injectable

tag: mpa

tag: eng

tag: net

tag: nugent

tag: paired


title: GMSA_045_Vagina_Placebo

source_name: Vagina from GMSA_045 treated with Placebo

tag: ptid

tag: visit

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: NonDecided

tag: lng

tag: rin

tag: inclusion


title: GMSA_044_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_044 treated with FTC/TDF-OnTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

value: prep

value: Negative

value: unknown


title: BRBS186

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_042_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_042 treated with TDF-OnTreatment

tag: ptid

tag: visit

value: Vagina

tag: prep

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

tag: nugent

value: Excluded:drug levels

tag: paired

value: Unpaired


title: GMSA_043_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_043 treated with TDF-OffTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: lng

value: Positive

tag: rin

tag: inclusion

value: Included


title: BRBS184

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_040_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_040 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: drug

tag: prep

tag: tdfngperml

value: No

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

tag: nugent


title: GMSA_041_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_041 treated with TDF-OnTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: A

value: TDF

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: rin

tag: paired


title: GMSA_033_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_033 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

value: B

tag: drug

tag: prep

value: Yes

tag: inclusion


title: BRBS181

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_037_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_037 treated with FTC/TDF-OnTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: FTC/TDF

value: prep

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

tag: nugent


title: GMSA_036_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_036 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: drug

tag: prep

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: lng

tag: rin

tag: paired


title: GMSA_035_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_035 treated with FTC/TDF-OffTreatment

tag: collectiondate

tag: tissue

value: Vagina

tag: age

tag: arm

tag: inclusion


title: GMSA_034_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_034 treated with FTC/TDF-OnTreatment

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

value: Excluded:drug levels


title: GMSA_031_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_031 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: drug

tag: prep

value: oral

tag: nugent

value: Unpaired


title: GMSA_030_Vagina_Placebo

source_name: Vagina from GMSA_030 treated with Placebo

value: C

value: Placebo

value: placebo

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: lng

value: Positive

tag: rin


title: GMSA_040_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_040 treated with FTC/TDF-OffTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: No

value: Included

tag: paired


title: BRBS183

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_028_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_028 treated with TDF-OnTreatment

tag: ptid

tag: visit

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

value: Negative

value: unknown

tag: inclusion


title: GMSA_032_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_032 treated with FTC/TDF-OnTreatment

tag: collectiondate

tag: tissue

value: Vagina

tag: age

tag: arm

value: B

value: FTC/TDF

value: prep

tag: tdfdetected

value: Maybe

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: lng

tag: nugent

tag: rin

value: Excluded:drug levels


title: BRBS182

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: BRBS180


title: GMSA_025_Vagina_Placebo

source_name: Vagina from GMSA_025 treated with Placebo

tag: ptid

tag: visit

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

value: Positive

tag: paired

value: Unpaired


title: BRBS178

value: pDC

tag: tissue

value: spleen

value: UN


title: BRBS185


title: GMSA_023_Vagina_Placebo

source_name: Vagina from GMSA_023 treated with Placebo

tag: collectiondate

tag: age

tag: arm

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: nugent

tag: rin

tag: inclusion

value: Included


title: GMSA_027_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_027 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: drug

tag: prep

tag: tdfngperml


title: GMSA_022_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_022 treated with FTC/TDF-OnTreatment

value: No

value: implant

tag: birthcontrollab

value: NonDecided

tag: mpa

tag: eng

tag: net

tag: paired


title: GMSA_019_Vagina_Placebo

source_name: Vagina from GMSA_019 treated with Placebo

tag: collectiondate

tag: tissue

value: Vagina

tag: age

tag: arm

tag: tdfdetected


title: GMSA_018_Vagina_Placebo

source_name: Vagina from GMSA_018 treated with Placebo

tag: tdfresultdate

tag: birthcontrolepi

value: oral

value: NoHC

tag: lng

tag: nugent

tag: rin


title: GMSA_026_Vagina_Placebo

source_name: Vagina from GMSA_026 treated with Placebo

tag: ptid

tag: visit

tag: drug

tag: prep

tag: inclusion


title: GMSA_020_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_020 treated with TDF-OnTreatment

value: A

value: TDF

value: prep

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

value: Negative

value: unknown


title: BRBS177

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

tag: tissue

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_021_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_021 treated with TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: nugent

tag: rin

tag: paired


title: BRBS175


title: BRBS174


title: GMSA_024_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_024 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: drug

tag: prep

tag: tdfngperml

value: Yes

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

value: Positive

tag: inclusion


title: BRBS173

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_029_Vagina_Placebo

source_name: Vagina from GMSA_029 treated with Placebo

tag: collectiondate

tag: age

tag: arm

value: C

value: Placebo

value: placebo

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: lng

tag: nugent

tag: rin

tag: paired

value: Unpaired


title: GMSA_016_Vagina_Placebo

source_name: Vagina from GMSA_016 treated with Placebo

tag: ptid

tag: visit

tag: drug

tag: prep

tag: tdfngperml

value: implant

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

tag: inclusion

value: Included


title: GMSA_015_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_015 treated with FTC/TDF-OffTreatment

tag: collectiondate

tag: tissue

value: Vagina

tag: age

tag: arm

value: B

value: FTC/TDF

tag: tdfdetected

value: No

value: NonDecided


title: GMSA_013_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_013 treated with TDF-OnTreatment

value: A

value: TDF

value: prep

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: nugent

tag: rin


title: GMSA_017_Vagina_Placebo

source_name: Vagina from GMSA_017 treated with Placebo

tag: ptid

tag: visit

tag: drug

tag: prep

value: NoHC

value: Positive

tag: paired


title: GMSA_010_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_010 treated with TDF-OffTreatment

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: net

value: Negative


title: GMSA_012_Vagina_Placebo

source_name: Vagina from GMSA_012 treated with Placebo

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: C

value: Placebo

tag: inclusion


title: GMSA_011_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_011 treated with TDF-OffTreatment

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: lng

tag: nugent

value: Paired


title: BRBS179

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_010_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_010 treated with TDF-OnTreatment

tag: ptid

tag: visit

value: Vagina

tag: drug

tag: prep

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: rin

value: Excluded:drug levels

tag: paired

value: Unpaired


title: GMSA_014_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_014 treated with TDF-OnTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

value: oral

tag: lng

tag: net

tag: inclusion

value: Included


title: BRBS171

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: BRBS105


title: GMSA_009_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_009 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

value: B

tag: drug

value: FTC/TDF

tag: prep

tag: tdfngperml

value: No

tag: birthcontrollab

tag: mpa

tag: eng

tag: nugent

tag: rin


title: GMSA_008_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_008 treated with TDF-OffTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: A

value: TDF

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: lng

tag: net

value: Negative

value: Positive

tag: paired


title: GMSA_009_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_009 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: drug

tag: prep

value: prep

value: injectable

tag: inclusion

value: Paired


title: GMSA_011_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_011 treated with TDF-OnTreatment

value: Vagina

tag: tdfngperml

tag: birthcontrollab

value: NonDecided

tag: mpa

tag: eng

tag: nugent


title: BRBS167

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BRBS176


title: BRBS164


title: BRBS166


title: BRBS169


title: GMSA_003_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_003 treated with TDF-OffTreatment

tag: collectiondate

tag: age

tag: arm

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: net

tag: rin

value: Included

tag: paired


title: BRBS168


title: GMSA_007_Vagina_FTC/TDF-OffTreatment

source_name: Vagina from GMSA_007 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

value: B

tag: drug

tag: prep

tag: tdfngperml

value: oral

tag: birthcontrollab

tag: mpa

tag: eng

tag: nugent

tag: inclusion

value: Unpaired


title: BRBS170

tag: mouse genotype

tag: cell type

tag: tissue

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_007_Vagina_FTC/TDF-OnTreatment

source_name: Vagina from GMSA_007 treated with FTC/TDF-OnTreatment

tag: collectiondate

tag: age

tag: arm

value: FTC/TDF

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: net

tag: rin

value: Excluded:drug levels

tag: paired


title: GMSA_008_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_008 treated with TDF-OnTreatment

tag: ptid

tag: visit

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

value: Yes

tag: birthcontrollab

tag: mpa

tag: eng

tag: nugent

value: Negative

tag: inclusion


title: GMSA_005_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_005 treated with TDF-OnTreatment

tag: collectiondate

tag: tissue

tag: age

tag: arm

value: prep

tag: tdfdetected

value: NoHC

value: Indeterminate

value: unknown

value: Paired


title: GMSA_005_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_005 treated with TDF-OffTreatment

value: Vagina

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: net

tag: rin


title: GMSA_004_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_004 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: drug

tag: prep

value: Positive

value: Included

tag: paired


title: GMSA_004_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_004 treated with TDF-OnTreatment

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: nugent


title: EZH2m-p+ zygote H3K27me2_ChIPSeq input

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

library_source: genomic

data_processing:
The raw reads were processed by Trimmomatic (version 0.38) to cut adapters and to trim low quality reads with the minimal length 90bp and minimal quality of bases 20.
Clean reads were mapped to the mouse mm10 genome by Bowtie2 with parameters as described previously and the default parameters in zygote ChIP sequencing data.
High quality unique mapping was performed by Samtools with MAPQ more than 30 and self-coded Perl scripts.
The duplication reads were removed by Picard to obtain the non-redundant reads.
SNP split was utilized to split the maternal and paternal reads alignment with the allele-specific C57BL6 and PWK mm10 genome.
SICER was utilized to call peaks (windows 200, Gap 600, q value 1e-5) with SICER.sh module and the differential peaks were found with SICER-df.sh module
Genome_build: mm10
Supplementary_files_format_and_content: wig files of EZH2m+p+ and EZH2m-p+ zygotes H3K27me2 ChIP-seq. Genome1 represents maternal genome(C57BL/6J), and genome2 represents paternal genome(PWK). Depth.csv shows the result of H3K27me2 reads depth on each chromosome. The last four csv files shows annotated peaks called by SICER. bdg files were used to check the distribution of reads in the genome.

molecule: genomic DNA

source_name: Zygotes

extract_protocol:
Samples were collected in Nuclei Extraction Buffer directly and sheared by micrococcal nuclease (MNase) at 25°C for 5 min. Then the samples were the was incubated with H3K27me2 antibody overnight with rotation under constant rotation on a rotator at 4°C. The next day, 10ul Dyna beads Protein A (Thermo Fisher Scientific) was added to each sample and incubated 2 hours up to overnight at 4 °C. Subsequently, the beads were washed twice with low salt wash buffer, twice high salt wash buffer. For each sample, 100 ul eluiton buffer were added to resuspend beads and incubated at 65℃ for 2h to elute DNA from the beads. The DNA was purified by phenol:chloroform:isoamyl alcohol method.
Then samples were subjected to ULI-NChIP library preparation. ULI-NChIP library was generated using the KAPA Hyper Prep Kit according to the manufacture’s protocol. Paired-end 150-bp sequencing was performed on a Illumina HiSeq 2500.

tag: strain

value: C57BL/6 X PWK/PHJ

tag: genotype

tag: tissue

value: Zygotes

tag: chip antibody


title: EZH2m-p+ zygote H3K27me2_ChIPSeq

value: H3K27me2 Active Motif; 61435)


title: BRBS165

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_003_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_003 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: net

tag: rin

tag: inclusion


title: GMSA_006_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_006 treated with TDF-OffTreatment

tag: tissue

tag: prep

tag: tdfngperml

value: No

tag: birthcontrollab

value: injectable

tag: mpa

tag: eng

tag: nugent

tag: paired


title: GMSA_075_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_075 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

value: PBMC

tag: age

tag: arm

value: implant

value: Negative

value: Unpaired


title: GMSA_006_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_006 treated with TDF-OnTreatment

value: Vagina

tag: drug

value: prep

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

value: Paired


title: GMSA_070_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_070 treated with TDF-OffTreatment

tag: tissue

tag: prep

value: NonDecided

tag: net

value: Positive

tag: rin

tag: inclusion

value: Included


title: GMSA_069_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_069 treated with TDF-OffTreatment

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: nugent


title: GMSA_002_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_002 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: paired


title: GMSA_001_Vagina_TDF-OffTreatment

source_name: Vagina from GMSA_001 treated with TDF-OffTreatment

tag: arm

tag: drug

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: oral


title: GMSA_002_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_002 treated with TDF-OnTreatment

tag: tissue

tag: prep

value: NoHC

tag: lng

tag: net

tag: rin


title: BRBS160

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BRBS162


title: GMSA_001_Vagina_TDF-OnTreatment

source_name: Vagina from GMSA_001 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

value: A

value: TDF

tag: tdfngperml

tag: birthcontrollab

tag: mpa

tag: eng

tag: nugent

tag: inclusion


title: GMSA_072_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_072 treated with TDF-OffTreatment

tag: tissue

value: PBMC

tag: arm

tag: drug

tag: prep

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: net

tag: paired


title: GMSA_069_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_069 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

value: injectable

tag: rin


title: BRBS163

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: BRBS159

tag: tissue


title: BRBS158


title: GMSA_067_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_067 treated with TDF-OnTreatment

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: implant

tag: birthcontrollab

tag: mpa

tag: eng

tag: nugent

value: Negative

value: unknown

tag: inclusion

value: Unpaired


title: BRBS161


title: EZH2m+p+ zygote H3K27me2_ChIPSeq input

tag: strain

value: C57BL/6 X PWK/PHJ

tag: genotype

value: Zygotes

tag: chip antibody


title: GMSA_064_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_064 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: tdfresultdate

tag: birthcontrolepi

tag: lng

tag: net

value: Unavailable

tag: rin

value: Included

tag: paired


title: EZH2m+p+ zygote H3K27me2_ChIPSeq

tag: tissue

value: H3K27me2 Active Motif; 61435)


title: BRBS104

tag: mouse genotype

tag: cell type

value: pDC

tag: infection time

tag: eyfp status

tag: plate


title: BRBS157

value: spleen


title: BRBS156

value: UN


title: GMSA_066_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_066 treated with FTC/TDF-OnTreatment

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: birthcontrollab

value: NonDecided

tag: mpa

tag: eng

tag: nugent

tag: inclusion


title: GMSA_060_PBMC_FTC/TDF-OffTreatment

source_name: PBMC from GMSA_060 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

value: PBMC

tag: age

value: No

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: lng

tag: net

tag: rin

tag: paired


title: GMSA_063_PBMC_FTC/TDF-OffTreatment

source_name: PBMC from GMSA_063 treated with FTC/TDF-OffTreatment

tag: tissue

tag: arm

tag: drug

tag: prep

tag: tdfngperml

value: implant

value: Indeterminate

value: unknown

value: Unpaired


title: BMDM, polyp_R5

city: Boston

first: Markus

last: Bosmann

state: MA

address: 72 East Concord Street

department: Pulmonary Center, Department of Medicine

institute: Boston University School of Medicine

description: animal 5 - 50 µM L-polyP

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0b)
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (version version 2.8.0, Marini et al., 2016)
Differential expression analysis was performed with DESeq2 (version 1.16.0), setting the False Discovery Rate to 0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts as input matrix to DESeq2

source_name: bone marrow-derived macrophages

growth_protocol:
Bone marrow-derived macrophages (BMDM) were generated by culturing bone marrow cells with L929 cell-conditioned medium for 7 days as described before (Bosmann, M. et al.)
Complement activation product C5a is a selective suppressor of TLR4-induced, but not TLR3-induced, production of IL-27(p28) from macrophages. Journal of immunology 188, 5086-5093, doi:10.4049/jimmunol.1102914 (2012).)

extract_protocol:
Qiagen Rneasy kit with on-column DNA digestion following manufacture's guidelines.
RNA integrity was evaluated with an RNA 6000 Nano total RNA kit (Agilent Genomics, Santa Clara, CA, USA) on a 2100 Bioanalyzer (Agilent Genomics).
Library preparation was performed following manufacturer’s instructions (TruSeq stranded mRNA kit, Illumina, San Diego, CA, USA)

treatment_protocol: 1.5 x 10^6 cells in 1.5 ml medium on a 6 cm petri dish were rested 4 h for seeding. Cells were stimulated for 12 h with LPS/LPS+L-polyP/L-polyP or remained untreated.

tag: cell type

value: bone marrow-derived macrophages

tag: condition

value: 50 µM L-polyP

tag: genotype

value: 8 weeks


title: BMDM, polyp_R4

description: animal 4 - 50 µM L-polyP


title: GMSA_044_PBMC_FTC/TDF-OffTreatment

source_name: PBMC from GMSA_044 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

tag: tdfdetected

tag: birthcontrollab

value: injectable

tag: mpa

tag: eng

tag: nugent

value: Negative

tag: inclusion

value: Included


title: GMSA_061_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_061 treated with TDF-OffTreatment

tag: collectiondate

tag: age

value: A

value: TDF

tag: tdfresultdate

tag: birthcontrolepi

value: oral

tag: lng

tag: net

value: Positive

tag: rin

tag: paired

value: Paired


title: GMSA_043_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_043 treated with TDF-OnTreatment

tag: tissue

value: PBMC

tag: arm

tag: drug

tag: prep

value: prep

tag: tdfngperml

value: Yes


title: GMSA_044_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_044 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

value: B

value: FTC/TDF

tag: tdfdetected

value: No

tag: birthcontrollab

tag: mpa

value: Excluded:drug levels


title: GMSA_041_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_041 treated with TDF-OnTreatment

tag: collectiondate

tag: age

tag: eng

tag: nugent

tag: inclusion

value: Unpaired


title: GMSA_043_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_043 treated with TDF-OffTreatment

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: lng

tag: net

tag: rin


title: GMSA_041_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_041 treated with TDF-OffTreatment

tag: tissue

tag: arm

tag: drug

tag: prep

value: injectable

tag: paired


title: GMSA_042_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_042 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: tdfngperml

tag: tdfdetected

tag: birthcontrollab

value: Negative

value: unknown


title: BMDM, polyp_R3

description: animal 3 - 50 µM L-polyP

tag: cell type

value: bone marrow-derived macrophages

tag: condition

value: 50 µM L-polyP

tag: genotype

tag: age

value: 8 weeks


title: GMSA_042_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_042 treated with TDF-OnTreatment

tag: collectiondate

value: A

value: TDF

tag: tdfresultdate

tag: birthcontrolepi

tag: mpa

tag: lng

tag: eng

tag: nugent

tag: inclusion


title: BRBS155

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BMDM, polyp_R1

description: animal 1 - 50 µM L-polyP

tag: cell type


title: BRBS154


title: BMDM, polyp_R2

description: animal 2 - 50 µM L-polyP

tag: condition


title: BRBS153


title: BMDM, lpspolyp_R5

description: animal 5 - 100 ng/ml LPS + 50 µM L-polyP

value: 100 ng/ml LPS + 50 µM L-polyP

tag: genotype


title: BRBS152


title: GMSA_036_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_036 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

value: PBMC

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: birthcontrollab

tag: net

value: Positive

tag: rin

value: Included

tag: paired


title: BRBS151

tag: mouse genotype

tag: tissue

tag: infection time

tag: eyfp status


title: GMSA_040_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_040 treated with FTC/TDF-OnTreatment

tag: collectiondate

value: No

tag: tdfresultdate

tag: birthcontrolepi

value: NonDecided

tag: mpa

tag: lng

tag: eng

tag: nugent

tag: inclusion

value: Excluded:drug levels

value: Unpaired


title: GMSA_035_PBMC_FTC/TDF-OffTreatment

source_name: PBMC from GMSA_035 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: injectable


title: GMSA_039_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_039 treated with TDF-OnTreatment

tag: tissue

value: A

value: TDF

tag: birthcontrollab

tag: net

tag: rin

tag: paired


title: BRBS172

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_034_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_034 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tdfresultdate

tag: birthcontrolepi

tag: mpa

tag: lng

tag: eng

tag: nugent

tag: inclusion


title: BMDM, lpspolyp_R4

description: animal 4 - 100 ng/ml LPS + 50 µM L-polyP

value: bone marrow-derived macrophages

tag: condition

value: 100 ng/ml LPS + 50 µM L-polyP

tag: genotype

tag: age

value: 8 weeks


title: GMSA_038_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_038 treated with TDF-OnTreatment

tag: tissue

value: PBMC

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: birthcontrollab

tag: net

tag: rin

tag: paired


title: BRBS150

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_033_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_033 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

value: B

value: FTC/TDF

value: prep

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: mpa

tag: lng

tag: eng

tag: nugent

tag: inclusion


title: BMDM, lpspolyp_R3

description: animal 3 - 100 ng/ml LPS + 50 µM L-polyP

source_name: bone marrow-derived macrophages

tag: condition

tag: genotype

tag: age


title: BRBS149

tag: mouse genotype

tag: cell type

tag: tissue


title: GMSA_032_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_032 treated with FTC/TDF-OnTreatment

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: Maybe

tag: birthcontrollab

tag: net

value: Negative

value: unknown

tag: rin

value: Excluded:drug levels

tag: paired


title: BRBS103

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_031_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_031 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

value: A

value: TDF

tag: tdfresultdate

tag: birthcontrolepi

tag: mpa

tag: lng

tag: eng

tag: nugent

value: Positive

tag: inclusion

value: Included

value: Unpaired


title: BMDM, lpspolyp_R2

description: animal 2 - 100 ng/ml LPS + 50 µM L-polyP

tag: cell type

value: bone marrow-derived macrophages

tag: condition

value: 100 ng/ml LPS + 50 µM L-polyP

tag: genotype

tag: age

value: 8 weeks


title: GMSA_030_PBMC_Placebo

source_name: PBMC from GMSA_030 treated with Placebo

tag: tissue

value: PBMC

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: birthcontrollab

tag: net

tag: rin

tag: paired


title: GMSA_029_PBMC_Placebo

source_name: PBMC from GMSA_029 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: mpa

tag: lng

tag: eng


title: BRBS148

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BMDM, lpspolyp_R1

description: animal 1 - 100 ng/ml LPS + 50 µM L-polyP

tag: condition

tag: genotype

tag: age


title: BMDM, lps_R4

description: animal 4 - 100 ng/ml LPS

value: 100 ng/ml LPS


title: BRBS146


title: BMDM, lps_R3

description: animal 3 - 100 ng/ml LPS


title: GMSA_028_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_028 treated with TDF-OnTreatment

tag: ptid

tag: arm

value: A

tag: drug

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

tag: birthcontrollab

tag: net

tag: nugent

value: Negative

value: unknown

tag: rin

tag: inclusion

value: Excluded:drug levels

tag: paired


title: BMDM, lps_R5

description: animal 5 - 100 ng/ml LPS

tag: cell type

value: bone marrow-derived macrophages


title: GMSA_024_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_024 treated with TDF-OnTreatment

tag: visit

tag: collectiondate

tag: tissue

value: TDF

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: mpa

tag: lng

tag: eng

value: Positive

value: Included

value: Unpaired


title: BMDM, lps_R2

description: animal 2 - 100 ng/ml LPS

tag: condition

tag: genotype

tag: age

value: 8 weeks


title: BRBS145

tag: mouse genotype

value: pDC

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_022_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_022 treated with FTC/TDF-OnTreatment

tag: ptid

value: PBMC

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

value: implant

tag: birthcontrollab

value: NonDecided

tag: net

tag: nugent

tag: rin

tag: inclusion

tag: paired


title: GMSA_023_PBMC_Placebo

source_name: PBMC from GMSA_023 treated with Placebo

tag: visit

tag: collectiondate

tag: tissue

tag: age

value: C

value: Placebo

value: placebo

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: mpa

tag: lng

tag: eng


title: GMSA_026_PBMC_Placebo

source_name: PBMC from GMSA_026 treated with Placebo

tag: ptid

tag: arm

tag: drug

tag: prep

tag: tdfngperml


title: GMSA_025_PBMC_Placebo

source_name: PBMC from GMSA_025 treated with Placebo

tag: tdfdetected

tag: birthcontrollab

tag: net

tag: nugent

tag: rin


title: BMDM, lps_R1

description: animal 1 - 100 ng/ml LPS

tag: cell type

value: bone marrow-derived macrophages

tag: condition

value: 100 ng/ml LPS

tag: genotype


title: BRBS144

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_016_PBMC_Placebo

source_name: PBMC from GMSA_016 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

tag: tdfresultdate

tag: birthcontrolepi

tag: mpa

tag: lng

tag: eng

value: Positive

tag: inclusion

value: Included

tag: paired

value: Unpaired


title: BRBS143

tag: mouse genotype

tag: cell type

value: pDC


title: GMSA_017_PBMC_Placebo

source_name: PBMC from GMSA_017 treated with Placebo

tag: tissue

value: PBMC

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: birthcontrollab

value: NoHC

tag: net

tag: nugent

tag: rin


title: BRBS147

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_027_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_027 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: B

value: FTC/TDF

value: prep

tag: tdfresultdate

tag: birthcontrolepi

tag: mpa

tag: lng

tag: eng

value: Excluded:drug levels


title: GMSA_019_PBMC_Placebo

source_name: PBMC from GMSA_019 treated with Placebo

tag: tissue

value: C

tag: drug

value: Placebo

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: birthcontrollab

value: NonDecided

tag: inclusion

tag: paired


title: BMDM, unst_R3

description: animal 3 - CTRL

tag: cell type

value: bone marrow-derived macrophages

tag: condition

value: CTRL

tag: genotype

value: 8 weeks


title: GMSA_014_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_014 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

value: TDF

value: Yes

value: oral

tag: net

tag: nugent

tag: rin


title: GMSA_021_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_021 treated with TDF-OffTreatment

tag: tissue

tag: drug

tag: prep

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: mpa

tag: lng

tag: eng

value: Negative

value: unknown

value: Included

value: Unpaired


title: BMDM, unst_R2

description: animal 2 - CTRL

source_name: bone marrow-derived macrophages

tag: cell type

tag: condition

tag: genotype


title: GMSA_020_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_020 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

value: PBMC

value: prep

tag: tdfngperml

tag: tdfdetected

value: NoHC

tag: birthcontrollab

tag: inclusion

tag: paired


title: GMSA_018_PBMC_Placebo

source_name: PBMC from GMSA_018 treated with Placebo

tag: tissue

tag: age

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: net

tag: nugent

value: Positive

tag: rin


title: GMSA_012_PBMC_Placebo

source_name: PBMC from GMSA_012 treated with Placebo

tag: tdfresultdate

tag: birthcontrolepi

tag: mpa

tag: lng

tag: eng


title: BMDM, unst_R5

description: animal 5 - CTRL

tag: cell type

value: bone marrow-derived macrophages

tag: condition

value: CTRL

tag: genotype

value: 8 weeks


title: BRBS142

tag: mouse genotype

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BRBS141

tag: tissue


title: BRBS140


title: GMSA_013_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_013 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

value: implant

tag: birthcontrollab

tag: inclusion

tag: paired


title: GMSA_015_PBMC_FTC/TDF-OffTreatment

source_name: PBMC from GMSA_015 treated with FTC/TDF-OffTreatment

value: PBMC

value: B

value: FTC/TDF

value: No

tag: tdfresultdate

tag: birthcontrolepi

value: NonDecided

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

value: unknown

tag: rin

value: Included

value: Unpaired


title: GMSA_008_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_008 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: age

value: NoHC

value: Positive

value: Paired


title: GMSA_010_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_010 treated with TDF-OffTreatment

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: injectable


title: GMSA_011_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_011 treated with TDF-OnTreatment

value: A

value: prep

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: inclusion

tag: paired


title: GMSA_009_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_009 treated with FTC/TDF-OnTreatment

value: Yes

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent


title: BRBS139

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BMDM, unst_R4

description: animal 4 - CTRL

value: bone marrow-derived macrophages

tag: condition

value: CTRL

tag: genotype

tag: age

value: 8 weeks


title: BMDM, unst_R1

description: animal 1 - CTRL


title: BRBS138


title: Female_Sult3a2_Repl3_G146_M34

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: 4C-seq Library

data_processing:
Library strategy: 4C-seq
READ FILTERING: The raw fastq file (with multiple viewpoints) was filtered to select only sequences that contain the known viewpoint-specific primers used.
READ MAPPING: Reads were aligned using Bowtie2 to a custom genome representing all uniquely-mappable DpnII cutsites in the mouse genome +/- the read length to keep only reads mapping to valid ligation junctions in the genome and increase mapping rate. To further improve mapping, unmapped reads were iteratively trimmed from the 3' end and mapping was attempted again.
NORMALIZATION: Reads were normalized to account for differences in sequencing depth (reads per million) and smoothed to represent the median normalized sequencing depth for a sliding window of 11 restriction fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Supplemental bigWig tracks were generated representing a read depth normalized (reads per million) 4C signal for the merged male and female samples per viewpoint

source_name: Liver

growth_protocol: Male and female CD1 mice, 8-9 weeks of age, were purchased from Charles River Laboratories (Crl:CD1(ICR)).

extract_protocol:
Nuclei were isolated by ultracentrifugation in a high sucrose buffer then crosslinked with 0.8% formaldehyde for 9 minutes. 10M Crosslinked nuclei were processed as described previously (van de Werken et al 2012, Splinter et al 2012). DpnII was used as the primary restriction enzyme and Csp6I was used as the secondary. All ligations and disgestions were overnight (minimum 16 hr), and were verified by running a small aliquot in a 1% agarose gel.
Samples were amplified for 25 cycles of inverse PCR using a custom primer pair containing sequence specific to the indicated viewpoint as well as a partial adaptor sequence to facilitate barcoding in a secondary PCR reaction. To reduce the impact of PCR domination, samples represent pools of 6 independent (but otherwise identical) inverse PCR reactions. The reading primer was anchored directly at the DpnII cutsite, while the nonreading primer was positioned ~75bp from the Csp6I site. The samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 5 rounds of additional PCR per the manufacturer's instructions.

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: Sult3a2 Enhancer

tag: Sex

value: Female


title: Female_Sult3a2_Repl2_G146_M33

description: 4C-seq Library


title: BRBS102


title: BRBS137


title: GMSA_009_PBMC_FTC/TDF-OffTreatment

source_name: PBMC from GMSA_009 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

value: PBMC

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: rin

tag: inclusion

value: Included

tag: paired


title: Female_Sult3a2_Repl1_G145_M38

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

tag: age


title: BRBS136

tag: mouse genotype

tag: cell type

tag: tissue

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_008_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_008 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: injectable

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

value: Positive

value: Paired


title: Male_Sult3a2_Repl3_G145_M37

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

tag: Sex

value: Male

tag: age


title: BRBS135

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_011_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_011 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: arm

tag: drug

tag: prep

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: rin

tag: inclusion

tag: paired


title: GMSA_061_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_061 treated with TDF-OnTreatment

tag: tissue

tag: age

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

value: oral

value: implant

tag: lng

tag: eng

tag: net

tag: nugent


title: GMSA_007_PBMC_FTC/TDF-OnTreatment

source_name: PBMC from GMSA_007 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

value: PBMC

tag: arm

value: B

tag: drug

value: FTC/TDF

value: NoHC

value: Excluded:drug levels

value: Unpaired


title: Male_Sult3a2_Repl2_G145_M36

description: 4C-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: Sult3a2 Enhancer

tag: Sex

value: 8 weeks


title: GMSA_005_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_005 treated with TDF-OffTreatment

value: A

value: TDF

tag: prep

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

value: Indeterminate

value: unknown

tag: rin

tag: inclusion

value: Included

tag: paired

value: Paired


title: GMSA_006_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_006 treated with TDF-OnTreatment

tag: tissue

tag: age

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

value: injectable

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive


title: GMSA_005_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_005 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

value: PBMC

tag: arm

tag: drug

value: NoHC


title: GMSA_007_PBMC_FTC/TDF-OffTreatment

source_name: PBMC from GMSA_007 treated with FTC/TDF-OffTreatment

value: B

value: FTC/TDF

tag: prep

tag: tdfresultdate

tag: birthcontrolepi

value: oral

tag: birthcontrollab

tag: mpa

value: Unpaired


title: GMSA_006_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_006 treated with TDF-OffTreatment

tag: tissue

tag: age

value: A

tag: rin

tag: inclusion

tag: paired


title: GMSA_003_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_003 treated with TDF-OffTreatment

value: TDF

tag: tdfngperml

tag: tdfdetected

tag: lng

tag: eng

tag: net


title: GMSA_004_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_004 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: arm

value: No

tag: nugent

value: Excluded:drug levels


title: BRBS134

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_003_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_003 treated with TDF-OnTreatment

tag: tissue

tag: age

tag: drug

tag: prep

value: prep

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: rin

tag: inclusion

value: Included

value: Paired


title: Female_Nudt7_Repl3_G169_M2

description: 4C-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: Nudt7 Enhancer

tag: Sex

value: Female

value: 8 weeks


title: BRBS132

tag: mouse genotype

tag: cell type


title: BRBS130

tag: infection time

tag: eyfp status


title: GMSA_001_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_001 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: PBMC

tag: arm

tag: tdfngperml

tag: tdfdetected

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive

tag: paired


title: BRBS131

tag: plate


title: Female_Nudt7_Repl2_G168_M2

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

tag: Sex

tag: age


title: Female_Nudt7_Repl1_G165_M4

description: 4C-seq Library


title: BRBS133

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status


title: Male_Nudt7_Repl3_G169_M1

description: 4C-seq Library

value: Male


title: GMSA_010_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_010 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: arm

value: A

tag: drug

tag: prep

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: NoHC

tag: mpa

value: Negative

tag: rin

tag: inclusion

value: Unpaired


title: Male_Nudt7_Repl1_G165_M3

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

tag: Sex

tag: age


title: GMSA_067_ImputedEndocervix_TDF-OnTreatment

source_name: ImputedEndocervix from GMSA_067 treated with TDF-OnTreatment

tag: ptid

value: ImputedEndocervix

value: TDF

tag: tdfngperml

tag: tdfdetected

value: Yes

value: implant

value: NonDecided

tag: lng

tag: eng

tag: net

tag: nugent

value: unknown

tag: paired


title: GMSA_001_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_001 treated with TDF-OnTreatment

tag: visit

tag: collectiondate

tag: tissue

tag: arm

tag: drug

tag: prep

value: prep

tag: tdfresultdate

tag: birthcontrolepi

value: oral

value: Included

value: Paired


title: GMSA_002_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_002 treated with TDF-OffTreatment

value: PBMC

tag: age

value: No

tag: birthcontrollab

value: injectable

tag: mpa

tag: rin

tag: inclusion


title: GMSA_070_ImputedEndocervix_TDF-OffTreatment

source_name: ImputedEndocervix from GMSA_070 treated with TDF-OffTreatment

tag: ptid

value: A

tag: tdfngperml

tag: tdfdetected

tag: lng

tag: eng

value: Positive


title: GMSA_066_ImputedEndocervix_FTC/TDF-OffTreatment

source_name: ImputedEndocervix from GMSA_066 treated with FTC/TDF-OffTreatment

tag: visit

tag: collectiondate

value: B

value: FTC/TDF

tag: net

tag: nugent

value: Negative

tag: paired


title: GMSA_002_PBMC_TDF-OnTreatment

source_name: PBMC from GMSA_002 treated with TDF-OnTreatment

tag: tissue

tag: arm

tag: drug

value: TDF

tag: prep

tag: tdfresultdate

value: NoHC


title: Male_Sult3a2_Repl1_G146_M35

description: 4C-seq Library

source_name: Liver

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: Sult3a2 Enhancer

tag: Sex

value: Male

tag: age

value: 8 weeks


title: GMSA_067_ImputedEndocervix_TDF-OffTreatment

source_name: ImputedEndocervix from GMSA_067 treated with TDF-OffTreatment

tag: ptid

value: ImputedEndocervix

tag: tdfngperml

tag: tdfdetected

tag: birthcontrolepi

value: implant

tag: birthcontrollab

tag: mpa

value: unknown

tag: rin

tag: inclusion


title: GMSA_004_PBMC_TDF-OffTreatment

source_name: PBMC from GMSA_004 treated with TDF-OffTreatment

tag: visit

tag: collectiondate

tag: tissue

value: PBMC

tag: lng

tag: eng

tag: net

tag: nugent

value: Included

tag: paired

value: Unpaired


title: BRBS129

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_066_ImputedEndocervix_FTC/TDF-OnTreatment

source_name: ImputedEndocervix from GMSA_066 treated with FTC/TDF-OnTreatment

tag: ptid

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: NonDecided

value: Paired


title: Male_Nudt7_Repl2_G168_M1

description: 4C-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: Nudt7 Enhancer

tag: Sex

value: Male


title: GMSA_060_ImputedEndocervix_FTC/TDF-OnTreatment

source_name: ImputedEndocervix from GMSA_060 treated with FTC/TDF-OnTreatment

tag: visit

tag: collectiondate

tag: tissue

value: ImputedEndocervix

value: NoHC

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

tag: rin

tag: inclusion

tag: paired


title: Female_Nox4e2_Repl3_G169_M2

description: 4C-seq Library

value: Nox4 Enhancer 2

value: Female

tag: age

value: 8 weeks


title: Female_Nox4e2_Repl2_G168_M2

description: 4C-seq Library


title: BRBS128

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

tag: plate


title: BRBS126

value: UN


title: BRBS101


title: Female_Nox4e2_Repl1_G165_M4

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

tag: Sex


title: GMSA_051_ImputedEndocervix_TDF-OnTreatment, BiopsyB

source_name: ImputedEndocervix from GMSA_051 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

value: Positive

value: Excluded:drug levels

value: Unpaired


title: BRBS125

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: Male_Nox4e2_Repl3_G169_M1

description: 4C-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

tag: Sex

tag: age


title: BRBS124

tag: tissue


title: GMSA_047_ImputedEndocervix_Placebo

source_name: ImputedEndocervix from GMSA_047 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin

tag: inclusion

value: Included

tag: paired


title: Male_Nox4e2_Repl2_G168_M1

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

value: Male


title: GMSA_010_ImputedEndocervix_TDF-OnTreatment

source_name: ImputedEndocervix from GMSA_010 treated with TDF-OnTreatment

value: ImputedEndocervix

tag: age

value: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: NoHC

tag: mpa

value: Negative


title: GMSA_051_ImputedEndocervix_TDF-OnTreatment, BiopsyA

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: arm

tag: drug

tag: prep


title: BRBS123

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: BRBS122


title: GMSA_019_ImputedEndocervix_Placebo

source_name: ImputedEndocervix from GMSA_019 treated with Placebo

tag: age

tag: tdfngperml

tag: tdfdetected

value: NonDecided

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive

tag: rin

tag: inclusion

tag: paired


title: BRBS127

tag: tissue


title: Male_Nox4e2_Repl1_G165_M3

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

value: Nox4 Enhancer 2

tag: Sex

value: 8 weeks


title: Female_Nox4e1_Repl3_G169_M2

description: 4C-seq Library

value: Crl:CD1(ICR) (Charles River, strain code #022)

value: Nox4 Enhancer 1

value: Female


title: GMSA_072_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_072 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

value: Ectocervix

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfresultdate

tag: birthcontrolepi

value: oral

tag: birthcontrollab

tag: mpa

value: Included

value: Paired


title: GMSA_068_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_068 treated with FTC/TDF-OffTreatment

tag: age

value: B

value: FTC/TDF

tag: tdfngperml

tag: tdfdetected

value: No

value: injectable

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin

value: Unpaired


title: Female_Nox4e1_Repl2_G168_M2

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

tag: Sex


title: BRBS121

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_065_Ectocervix_Placebo

source_name: Ectocervix from GMSA_065 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: birthcontrollab

tag: mpa

value: Positive

tag: inclusion

tag: paired


title: GMSA_073_Ectocervix_Placebo

source_name: Ectocervix from GMSA_073 treated with Placebo

tag: tissue

value: Ectocervix

tag: tdfngperml

tag: tdfdetected

value: NonDecided

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin


title: GMSA_072_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_072 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

value: TDF

value: prep

value: Yes

value: oral

value: Included


title: GMSA_064_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_064 treated with TDF-OnTreatment

tag: drug

tag: prep

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: Unavailable

value: unknown

value: Paired


title: BRBS120

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_070_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_070 treated with TDF-OnTreatment

tag: tdfngperml

tag: tdfdetected

value: injectable

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin

tag: inclusion

tag: paired

value: Unpaired


title: GMSA_071_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_071 treated with FTC/TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

value: No

tag: tdfresultdate

tag: birthcontrolepi

value: implant

tag: birthcontrollab

value: Negative


title: GMSA_069_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_069 treated with TDF-OffTreatment

tag: tissue

value: Ectocervix

value: A

value: TDF

tag: tdfngperml

tag: tdfdetected

tag: mpa

tag: lng

value: Positive


title: GMSA_063_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_063 treated with FTC/TDF-OffTreatment

value: NonDecided

tag: eng

tag: net

tag: nugent

value: Indeterminate

tag: rin

tag: inclusion

value: Included


title: Female_Nox4e1_Repl1_G165_M4

description: 4C-seq Library

source_name: Liver

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: Nox4 Enhancer 1

tag: Sex

value: Female

tag: age

value: 8 weeks


title: GMSA_069_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_069 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: arm

tag: drug

tag: prep

value: prep

value: Yes

tag: tdfresultdate

value: injectable

tag: paired

value: Paired


title: BRBS119

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: GMSA_074_Ectocervix_Placebo

source_name: Ectocervix from GMSA_074 treated with Placebo

value: Ectocervix

value: C

value: Placebo

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: birthcontrolepi

tag: birthcontrollab

value: NoHC

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin

tag: inclusion

value: Unpaired


title: GMSA_064_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_064 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

value: No

tag: tdfresultdate

value: Unavailable

value: unknown

value: Included

tag: paired


title: BRBS118

tag: mouse genotype

tag: cell type

tag: tissue

tag: infection time

tag: eyfp status

tag: plate


title: Male_Nox4e1_Repl3_G169_M1

description: 4C-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: Nox4 Enhancer 1

tag: Sex

value: Male

value: 8 weeks


title: GMSA_063_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_063 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

value: B

value: FTC/TDF

value: prep

tag: tdfngperml

tag: tdfdetected

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Indeterminate

tag: rin

tag: inclusion

value: Excluded:drug levels


title: GMSA_062_Ectocervix_Placebo

source_name: Ectocervix from GMSA_062 treated with Placebo

tag: collectiondate

tag: tissue

value: Ectocervix

tag: age

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: tdfresultdate

value: NoHC

value: Positive

tag: paired


title: Male_Nox4e1_Repl2_G168_M1

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

tag: Sex


title: BRBS100

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: UN

tag: plate


title: Male_Nox4e1_Repl1_G165_M3

description: 4C-seq Library

value: Crl:CD1(ICR) (Charles River, strain code #022)

value: Nox4 Enhancer 1


title: GMSA_061_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_061 treated with TDF-OnTreatment

tag: ptid

tag: visit

value: A

value: TDF

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: birthcontrolepi

value: oral

tag: birthcontrollab

value: implant

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

tag: rin

tag: inclusion

value: Included

value: Unpaired


title: Female_C9_Repl3_G169_M2

description: 4C-seq Library

tag: strain

tag: 4c viewpoint

value: C9 Promoter

tag: Sex

value: Female

tag: age

value: 8 weeks


title: Female_C9_Repl2_G168_M2

description: 4C-seq Library


title: GMSA_059_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_059 treated with FTC/TDF-OffTreatment

tag: ptid

tag: collectiondate

tag: tissue

value: Ectocervix

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

value: No

tag: tdfresultdate

value: NoHC

value: Positive

tag: paired


title: BRBS290

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPpos

tag: plate


title: BRBS291

value: MCMV YFPneg


title: GMSA_058_Ectocervix_Placebo

source_name: Ectocervix from GMSA_058 treated with Placebo

tag: visit

value: C

value: Placebo

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: birthcontrolepi

tag: birthcontrollab

value: injectable

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: unknown

tag: rin

tag: inclusion


title: GMSA_060_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_060 treated with FTC/TDF-OffTreatment

tag: ptid

tag: collectiondate

tag: tissue

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfresultdate

value: Negative

value: Included

tag: paired

value: Unpaired


title: GMSA_057_Ectocervix_Placebo

source_name: Ectocervix from GMSA_057 treated with Placebo

tag: visit

value: Ectocervix

tag: tdfngperml

tag: tdfdetected

tag: birthcontrolepi

tag: birthcontrollab


title: GMSA_056_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_056 treated with FTC/TDF-OnTreatment

value: B

value: FTC/TDF

value: prep

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Excluded:drug levels


title: GMSA_053_Ectocervix_Placebo

source_name: Ectocervix from GMSA_053 treated with Placebo

tag: ptid

tag: collectiondate

tag: tissue

value: implant

value: Positive

tag: rin

tag: inclusion


title: BRBS289

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

tag: plate


title: BRBS288

value: MCMV YFPneg


title: GMSA_055_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_055 treated with TDF-OffTreatment

tag: visit

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

value: NoHC

tag: paired


title: GMSA_054_Ectocervix_Placebo

source_name: Ectocervix from GMSA_054 treated with Placebo

tag: ptid

tag: collectiondate

tag: tissue

value: C

value: Placebo

value: placebo

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

value: unknown

tag: rin


title: Female_C9_Repl1_G165_M4

description: 4C-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: C9 Promoter

tag: Sex

value: Female

tag: age

value: 8 weeks


title: Male_C9_Repl3_G169_M1

description: 4C-seq Library

value: Male


title: Male_C9_Repl2_G168_M1

description: 4C-seq Library


title: GMSA_052_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_052 treated with TDF-OnTreatment

tag: visit

value: Ectocervix

tag: arm

tag: drug

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

value: Positive

tag: inclusion

value: Excluded:drug levels

value: Unpaired


title: BRBS287

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: GMSA_049_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_049 treated with FTC/TDF-OffTreatment

tag: ptid

tag: collectiondate

value: B

value: FTC/TDF

value: No

tag: birthcontrolepi

value: oral

tag: birthcontrollab

value: NoHC

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin

value: Included

tag: paired


title: GMSA_050_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_050 treated with TDF-OffTreatment

tag: visit

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: tdfresultdate

value: injectable

tag: inclusion


title: Male_C9_Repl1_G165_M3

description: 4C-seq Library

source_name: Liver

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: C9 Promoter

tag: Sex

value: Male

value: 8 weeks


title: GMSA_048_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_048 treated with FTC/TDF-OnTreatment

tag: ptid

tag: collectiondate

tag: tissue

value: Ectocervix

value: prep

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

value: Positive

value: Excluded:drug levels

value: Unpaired


title: Female_A1bg_Repl3_G169_M2

description: 4C-seq Library

value: A1bg Enh

value: Female

tag: age


title: GMSA_046_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_046 treated with TDF-OffTreatment

tag: visit

tag: arm

tag: drug

tag: prep

value: No

value: NoHC

tag: net

tag: nugent

tag: rin

tag: paired


title: GMSA_045_Ectocervix_Placebo

source_name: Ectocervix from GMSA_045 treated with Placebo

tag: ptid

value: C

value: Placebo

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

value: NonDecided

tag: inclusion

value: Included


title: GMSA_042_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_042 treated with TDF-OnTreatment

tag: collectiondate

tag: tissue

value: A

value: TDF

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

value: Negative

value: unknown


title: GMSA_044_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_044 treated with FTC/TDF-OnTreatment

tag: visit

value: Ectocervix

tag: age

tag: arm

value: B

value: FTC/TDF

value: prep

tag: lng

tag: eng


title: GMSA_043_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_043 treated with TDF-OffTreatment

tag: drug

tag: prep

value: injectable

tag: net

tag: nugent

value: Positive

tag: rin

value: Unpaired


title: BRBS285

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: GMSA_041_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_041 treated with TDF-OnTreatment

tag: ptid

tag: collectiondate

tag: tissue

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: inclusion

value: Excluded:drug levels

tag: paired


title: Female_A1bg_Repl2_G168_M2

description: 4C-seq Library

tag: strain

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: 4c viewpoint

value: A1bg Enh

tag: Sex

value: Female

tag: age

value: 8 weeks


title: Female_A1bg_Repl1_G165_M4

description: 4C-seq Library


title: BRBS283

tag: mouse genotype

tag: cell type

tag: infection time


title: Male_A1bg_Repl3_G169_M1

description: 4C-seq Library

value: Male


title: BRBS284

tag: eyfp status

value: MCMV YFPpos

tag: plate


title: BRBS117

tag: tissue

value: UN


title: BRBS286


title: BRBS282


title: Male_A1bg_Repl1_G165_M3

description: 4C-seq Library


title: BRBS280


title: Male_A1bg_Repl2_G168_M1

description: 4C-seq Library


title: BRBS281


title: GMSA_036_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_036 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

value: Ectocervix

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

tag: tdfngperml

value: Yes

value: NoHC

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin

value: Included


title: GMSA_040_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_040 treated with FTC/TDF-OnTreatment

tag: age

value: prep

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: NonDecided

value: Positive

tag: inclusion

tag: paired

value: Unpaired


title: BRBS279

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: BRBS116


title: GMSA_030_Ectocervix_Placebo

source_name: Ectocervix from GMSA_030 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: tdfngperml

tag: mpa

tag: lng

tag: eng


title: GMSA_035_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_035 treated with FTC/TDF-OffTreatment

tag: age

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: injectable

tag: net

tag: nugent

tag: rin

tag: inclusion

tag: paired


title: GMSA_034_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_034 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: Ectocervix

tag: arm

value: B

value: Excluded:drug levels


title: GMSA_033_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_033 treated with FTC/TDF-OnTreatment

tag: drug

value: FTC/TDF

tag: prep

tag: tdfngperml

value: Yes

value: NoHC

tag: mpa

tag: lng


title: GMSA_029_Ectocervix_Placebo

source_name: Ectocervix from GMSA_029 treated with Placebo

tag: age

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: eng

value: Included


title: GMSA_028_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_028 treated with TDF-OnTreatment

value: A

value: TDF

value: prep

tag: birthcontrollab

tag: net

tag: nugent

value: Negative

value: unknown

tag: rin

tag: inclusion


title: GMSA_026_Ectocervix_Placebo

source_name: Ectocervix from GMSA_026 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: C

value: Positive

tag: paired

value: Unpaired


title: GMSA_031_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_031 treated with TDF-OffTreatment

tag: arm

tag: drug

tag: prep

tag: tdfngperml

value: No

value: oral

tag: mpa


title: BRBS277

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: GMSA_032_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_032 treated with FTC/TDF-OnTreatment

value: Ectocervix

tag: age

value: B

value: FTC/TDF

tag: tdfdetected

value: Maybe

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: injectable

tag: lng

tag: eng

tag: net

tag: nugent

tag: rin

value: Excluded:drug levels


title: GMSA_027_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_027 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: arm

tag: drug

tag: prep

value: prep

tag: tdfngperml

tag: inclusion

tag: paired


title: GMSA_025_Ectocervix_Placebo

source_name: Ectocervix from GMSA_025 treated with Placebo

tag: age

value: Placebo

value: placebo

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: mpa

value: Included


title: GMSA_024_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_024 treated with TDF-OnTreatment

value: A

value: TDF

value: Yes

tag: birthcontrollab

value: NoHC

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive


title: BRBS275

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

tag: plate


title: BRBS276

value: MCMV YFPpos


title: BRBS278


title: BRBS274


title: GMSA_021_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_021 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

value: Ectocervix

tag: arm

tag: drug

tag: prep

tag: tdfngperml

value: No

value: Negative

value: unknown

tag: rin

tag: inclusion

tag: paired

value: Unpaired


title: GMSA_020_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_020 treated with TDF-OnTreatment

tag: age

value: prep

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

value: NonDecided

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Excluded:drug levels


title: GMSA_023_Ectocervix_Placebo

source_name: Ectocervix from GMSA_023 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: arm

value: C

value: Placebo

value: placebo

value: injectable

value: Included


title: GMSA_016_Ectocervix_Placebo

source_name: Ectocervix from GMSA_016 treated with Placebo

tag: drug

tag: prep

tag: tdfngperml

value: implant

value: Positive

tag: rin

tag: inclusion


title: BRBS273

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: BRBS272


title: BRBS271


title: GMSA_022_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_022 treated with FTC/TDF-OnTreatment

value: Ectocervix

tag: age

value: B

value: FTC/TDF

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: paired


title: GMSA_017_Ectocervix_Placebo

source_name: Ectocervix from GMSA_017 treated with Placebo

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: arm

tag: drug

tag: prep

tag: tdfngperml

value: NoHC

tag: nugent

tag: rin

value: Unpaired


title: GMSA_012_Ectocervix_Placebo

source_name: Ectocervix from GMSA_012 treated with Placebo

tag: age

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: inclusion


title: BRBS270

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

value: MCMV YFPpos

tag: plate


title: GMSA_014_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_014 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: A

value: TDF

value: prep

value: Yes

value: oral

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: paired


title: GMSA_018_Ectocervix_Placebo

source_name: Ectocervix from GMSA_018 treated with Placebo

tag: age

tag: arm

value: C

tag: drug

value: Placebo

tag: prep

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: nugent

tag: rin

value: Included


title: BRBS269

tag: mouse genotype

tag: cell type

value: pDC

tag: tissue

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: GMSA_009_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_009 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

value: Ectocervix

value: B

value: FTC/TDF

tag: birthcontrollab

value: injectable

tag: mpa

tag: lng

tag: eng

tag: net

value: Positive

tag: inclusion

tag: paired

value: Paired


title: GMSA_010_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_010 treated with TDF-OffTreatment

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: nugent

value: Negative

tag: rin

value: Unpaired


title: GMSA_011_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_011 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: prep

value: Yes

tag: birthcontrollab

value: NonDecided


title: GMSA_013_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_013 treated with TDF-OnTreatment

value: implant

tag: mpa

tag: lng

tag: eng

tag: net

tag: inclusion

value: Included


title: GMSA_011_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_011 treated with TDF-OffTreatment

tag: age

tag: arm

tag: drug

tag: prep

value: Excluded:Low probes detected

tag: paired


title: GMSA_008_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_008 treated with TDF-OnTreatment

value: Ectocervix

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: nugent


title: GMSA_008_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_008 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: NoHC

tag: rin


title: GMSA_007_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_007 treated with FTC/TDF-OffTreatment

value: B

value: FTC/TDF

value: oral

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net


title: GMSA_009_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_009 treated with FTC/TDF-OffTreatment

tag: age

tag: arm

tag: drug

tag: prep

value: injectable

value: Positive

tag: inclusion

value: Paired


title: BRBS268

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: GMSA_006_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_006 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: A

value: TDF

value: prep

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: nugent

tag: paired


title: BRBS267


title: BRBS115

value: UN


title: BRBS266


title: BRBS265

value: MCMV YFPpos


title: GMSA_005_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_005 treated with TDF-OnTreatment

tag: age

tag: arm

tag: drug

tag: prep

value: Yes

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

value: Indeterminate

value: unknown

tag: rin

value: Included


title: GMSA_002_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_002 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: Ectocervix

value: No

tag: inclusion


title: GMSA_006_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_006 treated with TDF-OffTreatment

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: nugent


title: GMSA_015_Ectocervix_FTC/TDF-OffTreatment

source_name: Ectocervix from GMSA_015 treated with FTC/TDF-OffTreatment

tag: age

tag: arm

value: B

tag: drug

value: FTC/TDF

tag: prep

value: implant

value: NonDecided

value: Negative

tag: paired

value: Unpaired


title: GMSA_005_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_005 treated with TDF-OffTreatment

value: A

value: TDF

tag: birthcontrollab

value: NoHC

tag: mpa

tag: lng

tag: eng

tag: net

value: Paired


title: GMSA_003_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_003 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: prep

value: Yes

value: Positive

tag: rin


title: BRBS264

source_name: splenic plasmacytoid dendritic cells

tag: mouse genotype

tag: cell type

value: pDC

value: spleen

tag: infection time

tag: eyfp status

value: MCMV YFPneg

tag: plate


title: BRBS262

value: MCMV YFPpos


title: BRBS263


title: GMSA_004_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_004 treated with TDF-OnTreatment

value: Ectocervix

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

tag: nugent

tag: inclusion

value: Excluded:drug levels


title: GMSA_004_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_004 treated with TDF-OffTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

value: Included

tag: paired


title: GMSA_001_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_001 treated with TDF-OnTreatment

tag: age

tag: arm

tag: drug

tag: prep

value: oral

tag: rin


title: GMSA_001_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_001 treated with TDF-OffTreatment

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: nugent


title: GMSA_002_Ectocervix_TDF-OnTreatment

source_name: Ectocervix from GMSA_002 treated with TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

tag: inclusion


title: BRBS260

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: GMSA_003_Ectocervix_TDF-OffTreatment

source_name: Ectocervix from GMSA_003 treated with TDF-OffTreatment

tag: age

tag: arm

tag: drug

tag: prep

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: paired


title: GMSA_007_Ectocervix_FTC/TDF-OnTreatment

source_name: Ectocervix from GMSA_007 treated with FTC/TDF-OnTreatment

tag: ptid

tag: visit

tag: collectiondate

tag: tissue

value: B

value: FTC/TDF

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: nugent

tag: rin

value: Unpaired


title: BRBS259

tag: mouse genotype

tag: cell type

tag: infection time

tag: eyfp status

tag: plate


title: BRBS258


title: PTID8_Enrollment_Rectal

hyb_protocol: standard as recommended by illumina

scan_protocol: standard Illumina protocol using Illumina iScan system

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 7 samples were included in the analysis.

source_name: Rectal from PTID8 at Enrollment

label_protocol: Labeling was performed using 275 ng total RNA and the Life Technologies/Ambion Illumina TotalPrep RNA Amplification kit

extract_protocol: Total RNA was extracted using the Qiagen Fibrous Tissue RNeasy mini kit

value: Enrollment

value: Rectal


title: BRBS261


title: BRBS257


title: PTID4_Visit2_Rectal

source_name: Rectal from PTID4 at Visit2


title: PTID5_Visit2_Rectal

source_name: Rectal from PTID5 at Visit2


title: PTID7_Enrollment_Rectal

source_name: Rectal from PTID7 at Enrollment


title: BRBS256


title: PTID8_Visit2_Rectal

source_name: Rectal from PTID8 at Visit2


title: BRBS255


title: PTID4_Enrollment_Rectal

source_name: Rectal from PTID4 at Enrollment


title: PTID6_Enrollment_Rectal

source_name: Rectal from PTID6 at Enrollment


title: PTID5_Enrollment_Rectal

source_name: Rectal from PTID5 at Enrollment


title: PTID6_Visit2_Rectal

source_name: Rectal from PTID6 at Visit2


title: PTID7_Visit2_Rectal

source_name: Rectal from PTID7 at Visit2


title: PTID1_Visit2_Rectal

source_name: Rectal from PTID1 at Visit2


title: PTID7_Enrollment_PBMC

source_name: PBMC from PTID7 at Enrollment

value: PBMC


title: PTID8_Visit2_PBMC

source_name: PBMC from PTID8 at Visit2


title: PTID3_Enrollment_Rectal

source_name: Rectal from PTID3 at Enrollment


title: PTID2_Visit2_Rectal

source_name: Rectal from PTID2 at Visit2


title: PTID8_Enrollment_PBMC

source_name: PBMC from PTID8 at Enrollment


title: PTID2_Enrollment_Rectal

source_name: Rectal from PTID2 at Enrollment


title: PTID3_Visit2_Rectal

source_name: Rectal from PTID3 at Visit2


title: BRBS254

source_name: splenic plasmacytoid dendritic cells


title: PTID1_Enrollment_Rectal

source_name: Rectal from PTID1 at Enrollment


title: BRBS253


title: BRBS252


title: PTID6_Visit2_PBMC

source_name: PBMC from PTID6 at Visit2


title: PTID6_Enrollment_PBMC

source_name: PBMC from PTID6 at Enrollment


title: PTID7_Visit2_PBMC

source_name: PBMC from PTID7 at Visit2


title: BRBS249


title: BRBS250


title: PTID4_Enrollment_PBMC

source_name: PBMC from PTID4 at Enrollment


title: PTID5_Enrollment_PBMC

source_name: PBMC from PTID5 at Enrollment


title: PTID5_Visit2_PBMC

source_name: PBMC from PTID5 at Visit2


title: PTID3_Enrollment_PBMC

source_name: PBMC from PTID3 at Enrollment


title: PTID1_Visit2_PBMC

source_name: PBMC from PTID1 at Visit2


title: PTID8_Visit2_Duodenal

source_name: Duodenal from PTID8 at Visit2

value: Duodenal


title: Invitro-E3

city: Pittsburgh

first: Samira

last: Kiani

state: Pennsylvania

address: A809-B Scaife Hall 3550 Terrace Street Pittsburgh

department: Division of Experimental Pathology

institute: University of Pittsburgh

description:
tpm_invitro.txt
Invitro-E3_S15
24476 protein-coding and 16648 non-coding RNA genes

data_processing:
FASTQ files for samples were aligned to genome GRCm38 (Ensembl 96) respectively, by STAR (ver 2.6.0.a) with paraters of --outSAMmultNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 6 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.2 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000'
TPM (Transcripts Per Kilobase Million) values were calculated based on the formula  〖RPK〗_i=  (Reads mapped to 〖gene〗_i  ×10^3)/(Longest 〖gene〗_i  transcript in bp)  〖TPM〗_i=〖RPK〗_i×  1/(∑_i▒〖RPK〗_i )×10^6
Longest gene transcripts in bp were obtained from GRCm38 (Ensembl 96).  Customized GRCm38 (Ensembl 96), where gene sequence was added into the reference genome, and been annotated as ‘ENSG0000’ in gene id.
Genome_build: GRCm38
Supplementary_files_format_and_content: A text file with abundance measurement matrix in TPM

source_name: Neuro-2A cells

growth_protocol: For the invitro data, Neuro-2a cell lines (purchased from ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM - Life Technologies) with 10% fetal bovine serum (FBS - Life Technologies), 2mM glutamine, 1.0 mM sodium pyruvate (Life Technologies) and 1% streptomycin– penicillin mix (Gibco) in incubators at 37 °C and 5% CO2.

extract_protocol:
For the invitro data, Cells were lysed, and RNA was extracted using RNeasy Plus mini kit (Qiagen) 72 hrs post transfection and sent to UCLA TCGB core on dry ice. For the invivo data, RNA was extracted from mice bone marrow samples using RNeasy Plus Mini Kit (Qiagen) followed by globin mRNA depletion using GLOBINclear™ Kit, mouse/rat kit (Thermofisher).
For the invitro data,, Ribosomal RNA depletion and paired end read library preparation were performed at UCLA core followed by RNA sequencing using NextSeq500.  Coverage was 20 million reads per sample.  FASTQ files with pair-ended 75bp reads were then aligned to the mouse GRCm38 reference genome sequence (Ensembl release 90) with STAR, and uniquely-mapped read counts (an average of 14.8  million reads per sample) were obtained with Cufflink.  The read counts for each sample were then normalized for the library size to CPM (counts per million reads) with edgeR .  Custom R scripts were then used to generate plots. For the invivo data, None-directional library preparation was performed at Novogene Corporation Inc. followed by RNA sequencing using Illumina Nova Platform with paired-end 150 run (2×150 bases). Coverage was minimum 25 million reads per sample. FASTQ files were then aligned to mouse genome sequence using STAR software and uniquely mapped read counts were visualized with Integrative Genomics Viewer (IGV). Gene expression level was calculated by the number of mapped reads. According to all gene expression level (RPKM or FPKM) of each sample, correlation coefficient of sample between groups was calculated. Read counts obtained from Gene Expression Analysis were used for differential expression analysis and differential expression analysis of different groups was performed using the DESeq2 R package51. Hierarchical clustering analysis was carried out of log10 (FPKM+1) of union differential expression genes, within all comparison groups. ClusterProfiler52 software was used for enrichment analysis, including GO Enrichment, DO Enrichment, KEGG Enrichment and Reactome Enrichment.

treatment_protocol: For the invitro data, Neuro-2a cells were co-transfected with 10ng gRNA targeting Myd88 loci, respectively. 200ng dCas9 constructs, 100ng MS2-HP1aKRAB, 50ng puromycin resistant gene, and 25ng transfection control. Cells were treated with 0.5ug/ml puromycin (Gibco-life tech) at 24 hours post-transfection.

tag: cell line

value: Neuro 2A

tag: treatment

value: Transfected with Cas9, full length gRNA targeting Myd88 locus and repressor domains