title: V1D11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CGG TGA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: DNMTs-Tg #5

status: Public on Feb 15 2019

type: RNA

city: Setagaya-ku

first: Keisuke

last: Sasaki

state: Tokyo

address: 1-1-1, Sakuragaoka

department: Department of BioScience

country: Japan

institute: Tokyo University of Agriculture

description: Gene expression data from the heart of a DNMTs-Tg mouse at 8-week of age.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 460.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing:
The array data were analyzed in GeneSpring v12.4 (Agilent Technology) to filter out probes with raw value less than 200 in all the samples. Differentially expressed genes between DNMTs-Tg and WT samples were determined by moderated t-test (Benjamini-Hochberg FDR, p < 0.05).
algorithm-name-0 = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
Q_probeset_summarize-Version = V916
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Biotin-labeled cDNA was prepared using GeneChip IVT labeling Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: DNMTs-Tg mice were generated by crossing FVB-Tg(Ddx4-cre)1Dcas/J (006954, The Jackson Laboratory) female mouse with the flox male mouse (Hara et al., 2014 Hum Mol Genet).

extract_protocol: Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer's instructions. The first-strand cDNA was synthesized using the Eukaryotic Poly-A RNA Control Kit (Affymetrix) and One-cycle cDNA synthesis Kit (Affymetrix).Obtained cDNA was purified using Sample Clean Up Module (Affymetrix)

treatment_protocol: Heart tissues were freezed inliquid nitrogen immediately after sampling and homogenized in RLT Buffer containing 2-mercaptoethanol (Qiagen).

tag: genotype/variation

value: DNMTs-Tg

tag: Sex

value: female

tag: age

tag: tissue

value: heart


title: RNA-hNPC-Ctl replicate 2

type: SRA

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (v24) (Harrow et al., 2012).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: raw reads count by HTSEQ

organism: Homo sapiens

source_name: Cell Line

growth_protocol: H9/WA09 cells (WiCell) were grown on Matrigel with reduced growth factors (ThermoFisher Scientific, #354230) in mTeSR1 medium (STEMCELL Technologies, #85850) at 37°C and 5% CO2. To induce neural lineage, cells were plated in PSC neural induction medium (Life Technologies) at 15–25% confluency, with medium changed every other day. On day 7, cells were harvested or expanded for further analyses.

extract_protocol:
RNA was purified with the GeneJET RNA purification kit (ThermoFisher Scientific, K0732). The cDNA was reverse transcribed from 300 ng of RNA, using SuperScript IV reverse transcriptase (ThermoFisher Scientific, #18090050) with random hexamers. RT reactions were performed in triplicate to minimize variability.
total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)

treatment_protocol: Neuronal maturation assay was performed using STEMdiff™ neuron differentiation kit (STEMCELL Technologies, #08500) and STEMdiff™ neuron maturation kit (STEMCELL Technologies, #08510). ES cells were seeded onto AggreWell800 plates (STEMCELL Technologies, #34811) and fed with neural induction medium (STEMCELL Technologies, #05835) to form uni-sized embryoid bodies (EBs). On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation started from day 11 to day 16. On day 17, cells were treated with Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium till days 22–24. RNA samples were collected on days 10, 11, and 22 for deep-sequencing analysis. Cells were also seeded onto multi-chamber slides for immunofluorescence (IF) analysis.

tag: cell type

value: Human Neural Progenitor cells

tag: cell line

value: derived from H9

value: wildtype


title: V1A11

city: New York

first: Nicholas

last: Tatonetti

state: New York

address: 622 W 168th Street

department: Department of Biomedical Informatics

institute: Columbia University

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CAT AGT CTT TTT TTT TTT TTT TTT TTT TTT TT

data_processing:
Base calling was performed by the Illumina HiSeq 4000's built-in control software
Reads were matched to original samples based on primer-linked barcode sequences (indicated on per-sample basis in the "Samples" table) - refer to Bush et al for further details.
Reads were demultiplexed and mapped to the human genome (GRCh38) and spike-ins library (ERCC92, Ambion) using the STAR aligner.
Counts for each gene are computed as the number of uniquely mapped reads associated with that gene.
Genome_build: hg38
Supplementary_files_format_and_content: Each processed data file is a tab-delimited text file where the first column is a gene symbol (or spike-in ID), and the second column is the number of counts of that gene (or spike-in) in the current sample.

source_name: IMR-32 neuroblastoma cells in culture

growth_protocol: IMR-32 cells were grown to confluence in FBS-supplemented EMEM.

extract_protocol: The PLATE-Seq protocol was used, as described by Bush et al (https://doi.org/10.1038/s41467-017-00136-z)

treatment_protocol: Treatments of 25 crude venoms (or water) were applied at the indicated timepoint prior to mRNA isolation in each sample, as described in the "Samples" table.

tag: venom treatment

tag: venom concentration (ug/ul)

tag: time post-treatment


title: V1B11

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CCA AAC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: T404A-0

city: cleveland

first: Yuxin

last: Wang

state: OH

address: 9500 Euclid avenue

department: Cancer Biology

institute: cleveland clinic foundation

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio

label: Standard Illumina Label

source_name: fibrosarcoma cell line

label_protocol: Standard Illumina protocol

growth_protocol: U6A cells were growed in DMEM medium with 5%FBS

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: U6A cells were treated with 100 IU/ml IFN-beta as indicated.


title: T404A-4


title: WT-8 (T404A STAT2 control)


title: WT-24 (T404A STAT2 control)


title: RNA-hESC-Ctl replicate 5

value: Human Embryonic Stem cell


title: V1H10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC ACA TTC CTT TTT TTT TTT TTT TTT TTT TTT TT


title: a1

city: Kyoto

first: Kenji

last: Sakurai

address: 54 Shogoin Kawara-cho, Sakyo

department: Dermatology

institute: Kyoto University

hyb_protocol: 2 ug of labeled DNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA (quantile) using Affymetrix default analysis settings.

source_name: whole ear skin

label_protocol: Amplified sense-strand DNA products were synthesized by the Ambion WT Expression Kit, and were fragmented and labeled by the WT Terminal Labeling and Controls Kit.

growth_protocol: Seven to 9-week-old female mice were used in this study. All animals used were of C57BL/6 genetic background.

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

treatment_protocol: Anisomycin (Wako Pure Chemical Industries, Osaka, Japan) solution was applied on inner and outer sides of a murine ear once daily. The concentration was 2 mg/ml in 99.5% ethanol, and the dose was 10 uL per one side of the ear. For IMQ model, 10 mg of IMQ-containing cream, Aldara (Beselna Cream5%, Mochida Pharmaceuticals), was applied onto inner and outer sides of a murine ear once daily for 5 days.

tag: treatment

value: Anisomycin treatment 1

tag: strain

value: whole ear skin

tag: gender


title: T404A-24


title: V1G10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CAG GCA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: RNA-hESC-Ctl replicate 4


title: V1F10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA GAT GCT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: 201530950051_R07C01: CF_2_RLL

type: genomic

city: Lebanon

first: Youdinghuan

last: Chen

state: NH

address: Hinman Box 7650

department: Epidemiology

institute: Dartmouth College

hyb_protocol: EPIC array hybridization and scanning were performed at the University of Southern California Molecular Genomics Core.

data_processing: The minfi pipeline v.1.21 was used to normalize the data. Polymorphic, non-CpG/technical, and sex-chromosome probes and probes failing to meet detection P ≤ 0.05 in ≥20% samples were excluded.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Bronchoalveolar Lavage (BAL)

label_protocol: Bisulfite conversion of DNA was carried out with the Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA).

extract_protocol: DNA was extracted from bronchoalveolar lavage-derived cells via Qiagen (Germantown, MD) DNeasy Blood and Tissue Kit. DNA was quantitated on a Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA).

value: Bronchoalveolar Lavage (BAL)

value: cystic fibrosis (CF)

tag: lobe

value: RLL

value: M

tag: mutation


title: RNA-hNPC-Ctl replicate 1


title: V1E10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TGG GAC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: RNA-hNPC-Ctl replicate 3


title: WT-4 (T404A STAT2 control)


title: 201530950051_R05C01: CF_1_RLL

scan_protocol: EPIC array hybridization and scanning were performed at the University of Southern California Molecular Genomics Core.


title: 201530950052_R07C01: CF_4_RLL

value: F


title: post-vaccination blood sample from donor 851396 stimulate 15 hours with DMSO

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).

data_processing: Raw probe intensities were preprocessed using the R (version 3.3.2) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.48.0). Log2 transformation was performed for variance stabilization and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.30.7).

source_name: Blood sample from donor 851396

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: RNA was isolated using the Rneasy micro kit (Qiagen) and the quality of the RNA was conﬁrmed using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.

treatment_protocol: Peripheral blood mononuclear cells were stimulated in vitro for 15 hours with short peptides (15-mers) of HIV-1 Env or for 15 hours with the vehicle (DMSO).

tag: donor

tag: scanning note

value: ok

tag: rna extraction protocol

value: Micro kit

tag: stimulation

value: DMSO

tag: stimulation time

tag: stimulation time unit

value: hours

value: VACCINE

tag: hiv infection

value: No


title: post-vaccination blood sample from donor 851396 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV


title: 201530950052_R01C01: CF_3_RLL

tag: tissue

tag: Sex

tag: age


title: RNA-hESC-Ctl replicate 3

tag: cell type

tag: cell line

tag: genotype/variation


title: T404A-8


title: 201530950051_R06C01: CF_1_RUL

value: RUL


title: WT-0 (T404A STAT2 control)


title: 201530950051_R08C01: CF_2_RUL


title: post-vaccination blood sample from donor 849475 stimulate 15 hours with DMSO

source_name: Blood sample from donor 849475

tag: treatment

value: Yes


title: post-vaccination blood sample from donor 852086 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 852086


title: post-vaccination blood sample from donor 852086 stimulate 15 hours with DMSO


title: 201530950051_R03C01: H_2_RLL

value: healthy (H)


title: 201530950052_R08C01: CF_4_RUL


title: post-vaccination blood sample from donor 849655 stimulate 15 hours with DMSO

source_name: Blood sample from donor 849655


title: 201530950052_R06C01: H_4_RUL


title: 201530950051_R01C01: H_1_RLL


title: 201530950052_R02C01: CF_3_RUL


title: V1C10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG AGT TAC TTT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom treatment

tag: venom concentration (ug/ul)

tag: time post-treatment


title: 201530950051_R02C01: H_1_RUL

tag: lobe

tag: mutation


title: hESC_UTX-ab91231 replicate 1

description:
processed data file:
hESC_UTX-AB3-ab84190.merge.broadPeak

library_source: genomic

data_processing:
Basecalls performed using CASAVA
Single-end reads of 50 bp were obtained. BWA (version 0.5.9-r26-dev, default parameter) was used to align reads to human genome hg19. Duplicated reads were marked by Picard (version 1.65(1160)), and uniquely mapped reads were retained by SAMtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). When clear peaks were observed by inspection on Integrated Genomics Viewer (Broad Institute)  and there was high consistency among replicates, peaks for each replicate were called by MACS2 (version 2.0.9 20111102). Peaks within 100 bp were merged by bedtools (version 2.17.0).
Almost every CHIPSEQ sample have 20M unique mapped reads, only few have less but more than 15M unique mapped reads. We confirmed quality control results were good following the ENCODE guideline for CHIPSEQ, reads were then extend to the estimated fragment size and converted to bigwig files.  With clear peaks observed by inspection on Integrated Genomics Viewer (Broad Institute) and there was high consistency among replicates. We further extend reads to the estimated fragment size and counted at each called peaks, pearson correlation coefficients were calculated among replicates suggested high reproducibility.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: broadpeak or txt file with peaks

extract_protocol:
Approximately 2 mg of nuclear extracts was incubated with primary antibody overnight at 4°C. Extract and antibody were added to protein A and protein G Dynabeads™ (ThermoFisher Scientific, #10002D and 10004D) for 4 h at 4°C, washed with PBST, and eluted with 0.1 M glycine (pH 2.3). Eluates were neutralized with 1.5 M Tris buffer (pH 8.8).
Cells were harvested in PBS. Cytoplasmic fractions were extracted using buffer A with 1× protease inhibitors and 1 mM DTT. Nuclear pellets were cross-linked by 1.1% formaldehyde in buffer B with 1× protease inhibitors and 1 mM DTT; washed; and lysed in lysis buffer 3 with 1× protease inhibitors, 1 mM DTT, and 1 mM PMSF. The fixed and lysed nuclear extract was sonicated with Bioruptor® Pico (Diagenode) 10 times for 15 s each , with 45-s intervals. Chromatin was added to Dynabeads™ (Life Technologies) prebound with 4 µg of antibodies. For UTX chromatin immunoprecipitation (ChIP), chromatin and antibodies were incubated overnight, followed by 4 h of recapture with Dynabeads™ the next day. After incubation, beads were washed and immunoprecipitates were eluted.  DNA from eluates was recovered by the GeneJET FFPE DNA purification kit (ThermoFisher Scientific, #K0882). ChIP-qPCR signals were calculated as the percentage of input. DNA libraries were generated using the NEBNext™ Ultra DNA Library Prep kit (NEB, #E7370S) and sequenced at the St. Jude Hartwell Center.

value: Human Embryonic Stem cell H9

value: wildtype

tag: chip antibody


title: INPUT-hNPC

value: Human Neural Progenitor cells

value: derived from H9


title: V1B10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT AGA GAT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1H09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GTC CCC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: hNPC_UTX-ab84190 replicate 1

description:
processed data file:
hNPC_UTX-ab84190-Rep1.broadPeak


title: 201530950052_R04C01: H_3_RUL

value: Bronchoalveolar Lavage (BAL)


title: 201530950052_R05C01: H_4_RLL

value: RLL


title: 201530950052_R03C01: H_3_RLL


title: 201530950051_R04C01: H_2_RUL

value: M


title: V1G09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TGA GAC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: INPUT-hESC


title: post-vaccination blood sample from donor 843994 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 843994

tag: donor

tag: scanning note

tag: rna extraction protocol

tag: stimulation


title: RNA-hESC-Ctl replicate 1

value: Human Embryonic Stem cell


title: V1D10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TTA GCG TTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 844459 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 844459

value: ok

tag: stimulation time

tag: stimulation time unit

tag: hiv infection


title: post-vaccination blood sample from donor 844459 stimulate 15 hours with DMSO

value: Micro kit


title: post-vaccination blood sample from donor 844343 stimulate 15 hours with DMSO

source_name: Blood sample from donor 844343

value: DMSO


title: post-vaccination blood sample from donor 844343 stimulate 15 hours with 92TH023ENV

value: hours


title: post-vaccination blood sample from donor 842921 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV

source_name: Blood sample from donor 842921

value: PLACEBO


title: hESC_UTX-ab84190 replicate 5

tag: cell type


title: V1A10

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GTT TCA TTT TTT TTT TTT TTT TTT TTT TTT TT

tag: cell line


title: post-vaccination blood sample from donor 842921 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO


title: post-vaccination blood sample from donor 849475 stimulate 15 hours with 92TH023ENV

value: VACCINE


title: hESC_UTX-ab84190 replicate 4

tag: genotype/variation


title: V1F09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC AGT TCG GTT TTT TTT TTT TTT TTT TTT TTT TT


title: hESC_UTX-ab84190 replicate 3


title: hESC_UTX-ab84190 replicate 2


title: V1C09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG GTT TCG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1D09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GCA AAA TTT TTT TTT TTT TTT TTT TTT TTT TT


title: RNA-hESC-Ctl replicate 2


title: post-vaccination blood sample from donor 845316 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 845316

tag: treatment

value: No


title: V1E09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TAC TGA CTT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom treatment


title: post-vaccination blood sample from donor 845316 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 839288 stimulate 15 hours with DMSO

source_name: Blood sample from donor 839288

value: Yes


title: post-vaccination blood sample from donor 841530 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 841530


title: post-vaccination blood sample from donor 835280 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 835280


title: post-vaccination blood sample from donor 841530 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 839288 stimulate 15 hours with 92TH023ENV


title: hESC_UTX-ab84190 replicate 1

source_name: Cell Line


title: post-vaccination blood sample from donor 843994 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 827743 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 827743


title: hNPC_53BP1-Novus replicate 1

description:
processed data file:
hNPC_53BP1-Novus-Rep1.broadPeak


title: V1B09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GCG AAT CTT TTT TTT TTT TTT TTT TTT TTT TT

source_name: IMR-32 neuroblastoma cells in culture

tag: venom concentration (ug/ul)


title: post-vaccination blood sample from donor 827158 stimulate 15 hours with DMSO

source_name: Blood sample from donor 827158


title: V1A09

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GCG TTA TTT TTT TTT TTT TTT TTT TTT TTT TT

tag: time post-treatment


title: post-vaccination blood sample from donor 827743 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO


title: hESC_53BP1-Novus replicate 2

description:
processed data file:
hESC_53BP1-Novus.merge.broadPeak


title: post-vaccination blood sample from donor 835280 stimulate 15 hours with DMSO


title: V1G08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GTT ACG TTT TTT TTT TTT TTT TTT TTT TTT TT

value: Untreated


title: V1F08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG AAT TGT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: hNPC_53BP1-Abcam replicate 1

description:
processed data file:
hNPC_53BP1-Abcam-Rep1.broadPeak


title: V1H08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CGT TAA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: hESC_53BP1-Novus replicate 1

value: Human Embryonic Stem cell H9


title: V1E08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TTT CCC TTT TTT TTT TTT TTT TTT TTT TTT TT

value: Water


title: hESC_53BP1-Novus replicate 3

value: wildtype


title: hESC_53BP1-Abcam replicate 3

description:
processed data file:
hESC_53BP1-Abcam.merge.broadPeak


title: hESC_53BP1-Abcam replicate 2


title: post-vaccination blood sample from donor 823668 stimulate 15 hours with DMSO

source_name: Blood sample from donor 823668


title: post-vaccination blood sample from donor 825617 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV

source_name: Blood sample from donor 825617


title: post-vaccination blood sample from donor 825482 stimulate 15 hours with DMSO

source_name: Blood sample from donor 825482


title: post-vaccination blood sample from donor 824374 stimulate 15 hours with DMSO

source_name: Blood sample from donor 824374


title: post-vaccination blood sample from donor 826468 stimulate 15 hours with DMSO

source_name: Blood sample from donor 826468


title: post-vaccination blood sample from donor 825617 stimulate 15 hours with DMSO


title: V1C08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CAA CTA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1B08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA AAG CGA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 816004 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 816004


title: post-vaccination blood sample from donor 816763 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV

source_name: Blood sample from donor 816763


title: post-vaccination blood sample from donor 816004 stimulate 15 hours with DMSO


title: V1D08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TCC CCT TTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 816763 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO


title: post-vaccination blood sample from donor 822158 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 822158


title: post-vaccination blood sample from donor 822158 stimulate 15 hours with DMSO


title: V1A08

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GAG GAC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 811303 stimulate 15 hours with DMSO

source_name: Blood sample from donor 811303


title: V1H07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA AGA GAG GTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 823668 stimulate 15 hours with 92TH023ENV


title: hESC_53BP1-Abcam replicate 1


title: post-vaccination blood sample from donor 809604 stimulate 15 hours with DMSO

source_name: Blood sample from donor 809604


title: post-vaccination blood sample from donor 826468 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 811303 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 809604 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 809408 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 809408


title: V1G07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TGT GCT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V1F07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TAC CCA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1E07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG ACT CCC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V1D07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TCA AGG TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1C07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT AGC TAG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 804495 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO

source_name: Blood sample from donor 804495


title: post-vaccination blood sample from donor 808390 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 808390


title: post-vaccination blood sample from donor 809408 stimulate 15 hours with DMSO


title: V1G06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CTT TGC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1A07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CTC AAG CTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 804495 stimulate 15 hours with 92TH023ENV


title: V1B07

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TCA CAT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 800976 stimulate 15 hours with DMSO

source_name: Blood sample from donor 800976


title: post-vaccination blood sample from donor 803985 stimulate 15 hours with DMSO

source_name: Blood sample from donor 803985


title: V1H06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CCT GTC ATT TTT TTT TTT TTT TTT TTT TTT TT

source_name: IMR-32 neuroblastoma cells in culture


title: post-vaccination blood sample from donor 737450 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV

source_name: Blood sample from donor 737450


title: V1E06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TTC TCC CTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 729489 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV

source_name: Blood sample from donor 729489


title: V1D06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CAC GCC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 736104 stimulate 15 hours with DMSO

source_name: Blood sample from donor 736104


title: post-vaccination blood sample from donor 808390 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 733526 stimulate 15 hours with DMSO

source_name: Blood sample from donor 733526


title: post-vaccination blood sample from donor 726599 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 726599


title: post-vaccination blood sample from donor 726168 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 726168


title: post-vaccination blood sample from donor 737450 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 726599 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 800976 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 729489 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO


title: post-vaccination blood sample from donor 720317 stimulate 15 hours with DMSO

source_name: Blood sample from donor 720317


title: post-vaccination blood sample from donor 723863 stimulate 15 hours with DMSO

source_name: Blood sample from donor 723863


title: post-vaccination blood sample from donor 725838 stimulate 15 hours with DMSO

source_name: Blood sample from donor 725838


title: post-vaccination blood sample from donor 726168 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 733526 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 725896 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 725896


title: post-vaccination blood sample from donor 725896 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 725838 stimulate 15 hours with 92TH023ENV


title: V1F06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CAT TGG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 720317 stimulate 15 hours with 92TH023ENV


title: V1B06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TTC GTC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1A06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GTG CTG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V1H05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TTA GGC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V1F05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TGC GGA TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1G05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CAA GAC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1E05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG GTG ATC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 719498 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 719498


title: V1D05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CGA CCT CTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 713113 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO

source_name: Blood sample from donor 713113


title: V1C05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TCC CGC ATT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 707432 stimulate 15 hours with DMSO

source_name: Blood sample from donor 707432


title: post-vaccination blood sample from donor 718988 stimulate 15 hours with DMSO

source_name: Blood sample from donor 718988


title: post-vaccination blood sample from donor 716238 stimulate 15 hours with DMSO

source_name: Blood sample from donor 716238


title: post-vaccination blood sample from donor 719498 stimulate 15 hours with DMSO


title: shRenilla.713_CD8_RNAseq

first: Craig

last: Thompson

state: NY

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ files were processed with kallisto using an mm10 index file from an ENSEMBL GTF annotation file. Count estimates from kallisto were extracted and aggregated to gene-level counts by summation. Differential expression (DE) analysis was conducted on the entire count matrix using voom and limma with an additive model for the main perturbational effect (i.e. shDnmt1), and the CD4+ effect to control for variability seen in the PCA. DE genes were considered with an FDR<0.05 (Benjamini-Hochberg corrected p-value) and an absolute log2(FC)>1
Genome_build: mm10

source_name: T cells

growth_protocol: Naïve CD8+ T cells were isolated from spleen and lymph nodes of C57BL/6J mice by cell sorting (CD8+CD4-CD62L+CD44-CD25-) and activated with anti-CD3 and anti-CD28 in T cell media (RPMI, 10% FBS, 4mM glutamine, 50uM BME, 20mM HEPES, 100U/mL human IL-2) for 24h followed by transduction with shRNA retrovirus. Cells were then cultured in T cell media for additional 5d prior to cell sorting based on CD8 and CD4 expression.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) followed by DNase I treatment and cleanup with RNeasy MinElute kit (Qiagen). RNA libraries were prepared by HudsonAlpha using the Nugen Ovation Ultralow Library Systems V2 and sequencing was performed on Illumina HiSeq 2500 v4 (pe, 50bp, 50Mreads)

value: CD8+ T cells

tag: strain

tag: cell population

value: shRenilla knock-down


title: post-vaccination blood sample from donor 705306 stimulate 15 hours with DMSO

source_name: Blood sample from donor 705306


title: post-vaccination blood sample from donor 713113 stimulate 15 hours with 92TH023ENV


title: V1B05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CTC AGA ATT TTT TTT TTT TTT TTT TTT TTT TT

source_name: IMR-32 neuroblastoma cells in culture


title: shDnmt1.4462_CD8CD4_RNAseq

value: Dnmt1 knock-down


title: post-vaccination blood sample from donor 716238 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 707432 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 704526 stimulate 15 hours with DMSO

source_name: Blood sample from donor 704526


title: BMDM_KO_mean

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

description: Gene expression

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 27 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the R software (version 2.15). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: BMDM infected with Pruku80[delta]TEEGR (KO), mean of replicate 1,2 and 3

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: T. gondii strains were maintained in vitro by serial passage on monolayers of human primary fibroblasts, cultured in DMEM supplemented with 10% heat inactivated FBS (Invitrogen), 10 mM Hepes buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin. Bone marrow-derived macrophages were obtained from 8-10-week old C57BL/6 mice purchased from JANVIER (France). Bone marrow was isolated by flushing hind tibias and femurs using a 25-gauge needle and DMEM media supplemented with 10% heat-inactivated FBS (Invitrogen), 1 mM L-glutamine, 50 µg/mL each of penicillin and streptomycin. ~5 x 10^6 cells were resuspended in DMEM supplemented with 20 ng/mL M-CSF (Invitrogen)and plated in 10-cm nontissue culture-treated dishes (Corning). Cells were incubated at 37°C, with 5% CO2 in humidified air for 6 days. Adherent cells were harvested in cold-PBS(4°C) using a cell scraper, and replated at 8 x 10e6 cells per 10-cm2 plate for the assay.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Host cells were left uninfected or infected for 24 hours with Toxoplasma type II strains.

tag: host cell

value: Bone Marrow Derived Macrophage (BMDM)

tag: infection

value: Pruku80[delta]TEEGR (KO)

tag: tg type strain

value: Type II


title: post-vaccination blood sample from donor 705306 stimulate 15 hours with 92TH023ENV

tag: donor

tag: scanning note

value: ok

tag: rna extraction protocol

value: Micro kit


title: post-vaccination blood sample from donor 710339 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 710339

tag: stimulation

tag: stimulation time

tag: stimulation time unit

value: hours


title: post-vaccination blood sample from donor 718988 stimulate 15 hours with 92TH023ENV

tag: hiv infection


title: post-vaccination blood sample from donor 710339 stimulate 15 hours with DMSO

value: DMSO


title: post-vaccination blood sample from donor 704410 stimulate 15 hours with DMSO

source_name: Blood sample from donor 704410

value: VACCINE


title: post-vaccination blood sample from donor 803985 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 803985

value: No


title: post-vaccination blood sample from donor 703357 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 703357

value: Yes


title: post-vaccination blood sample from donor 704526 stimulate 15 hours with 92TH023ENV


title: BMDM_WT_mean

description: Gene expression

source_name: BMDM infected with Pruku80 (WT), mean of replicate 1,2 and 3

value: Pruku80 (WT)


title: V1H04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TCA GTC CTT TTT TTT TTT TTT TTT TTT TTT TT

value: Untreated

tag: cell line


title: shDnmt1.4462_CD8_RNAseq

tag: cell type

tag: genotype/variation


title: shDnmt1.1137_CD8CD4_RNAseq


title: V1G04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG GAA ATT GTT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom treatment


title: shChaf1a.3118_CD8CD4_RNAseq

value: Chaf1a knock-down


title: shDnmt1.1137_CD8_RNAseq


title: V1F04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG TGT ACA CTT TTT TTT TTT TTT TTT TTT TTT TT

tag: time post-treatment


title: shChaf1a.3118_CD8_RNAseq

tag: strain


title: shChaf1a.576_CD8CD4_RNAseq

tag: cell population


title: V1A05

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC TTA GTT GTT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom concentration (ug/ul)


title: shChaf1a.576_CD8_RNAseq


title: post-vaccination blood sample from donor 704410 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV

tag: treatment


title: V1C04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC ATA ACC CTT TTT TTT TTT TTT TTT TTT TTT TT

value: Water


title: V1D04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA GGA AGA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 644521 stimulate 15 hours with DMSO

source_name: Blood sample from donor 644521


title: post-vaccination blood sample from donor 701472 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO

source_name: Blood sample from donor 701472

value: PLACEBO


title: post-vaccination blood sample from donor 644521 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 645909 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 645909


title: post-vaccination blood sample from donor 641673 stimulate 15 hours with DMSO

source_name: Blood sample from donor 641673


title: post-vaccination blood sample from donor 645909 stimulate 15 hours with DMSO


title: B1r3

city: Berlin

first: Robin

last: Graf

address: Robert Rössle Str. 10

department: Immune Regulation and Cancer

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

data_processing:
Illumina CASAVA (v1.8.2)  software was used for basecalling.
RNAseq reads were mapped to the mRNAs of mm10 using kallisto (kallisto -b 100 -t 2 -l 200 -s 75 --single [reads])
tpms were summed up per gene
Genome_build: mm10
Supplementary_files_format_and_content: tsv file with tpm

molecule: polyA RNA

source_name: B cells

growth_protocol: Cells were isolated from spleens and peritoneal cavities

extract_protocol:
RNA was isolated using the RNEasy MICRO kit (Qiagen)
The libraries were generated using the TruSeq RNA Sample Kit v2-SetA (Illumina) according to the manufacturer’s protocol.

treatment_protocol: The BCR switch in the B2toB1 cells was induced ~30 days prior to isolation

tag: tissue

value: Peritoneal cavity

tag: genetic background

value: C57BL/6 (backcrossed)


title: post-vaccination blood sample from donor 641088 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 641088

tag: donor

tag: scanning note


title: post-vaccination blood sample from donor 641673 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV

tag: rna extraction protocol

tag: stimulation


title: post-vaccination blood sample from donor 639556 stimulate 15 hours with DMSO

source_name: Blood sample from donor 639556

tag: stimulation time

tag: stimulation time unit


title: V1E04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CAG ATA CTT TTT TTT TTT TTT TTT TTT TTT TT

tag: cell line


title: post-vaccination blood sample from donor 641088 stimulate 15 hours with DMSO

tag: hiv infection


title: post-vaccination blood sample from donor 637295 stimulate 15 hours with DMSO

source_name: Blood sample from donor 637295


title: post-vaccination blood sample from donor 637295 stimulate 15 hours with 92TH023ENV


title: V1A04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TCG ACT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 639556 stimulate 15 hours with 92TH023ENV


title: B1r1

tag: cell type


title: post-vaccination blood sample from donor 703357 stimulate 15 hours with DMSO


title: V1B04

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TGC CTC ATT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom treatment


title: post-vaccination blood sample from donor 701472 stimulate 15 hours with 92TH023ENV


title: B2B1r3


title: B2B1r2


title: V1G03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT ACG AGC ATT TTT TTT TTT TTT TTT TTT TTT TT

tag: time post-treatment


title: V1H03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CGC CTT ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V1C06

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA ACA GTT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1F03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GCT TAA CTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 635989 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO

source_name: Blood sample from donor 635989


title: post-vaccination blood sample from donor 635989 stimulate 15 hours with 92TH023ENV


title: B1r2

tag: strain


title: post-vaccination blood sample from donor 633033 stimulate 15 hours with DMSO

source_name: Blood sample from donor 633033


title: B2B1r1


title: B2r3

value: Spleen


title: V1D03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT CTC TAG TTT TTT TTT TTT TTT TTT TTT TTT TT

source_name: IMR-32 neuroblastoma cells in culture


title: post-vaccination blood sample from donor 631103 stimulate 15 hours with DMSO

source_name: Blood sample from donor 631103


title: post-vaccination blood sample from donor 633033 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 631103 stimulate 15 hours with 92TH023ENV


title: V1E03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TAC CGT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 629639 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 629639


title: post-vaccination blood sample from donor 629581 stimulate 15 hours with DMSO

source_name: Blood sample from donor 629581


title: post-vaccination blood sample from donor 629581 stimulate 15 hours with 92TH023ENV


title: V1C03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CTA ACG GTT TTT TTT TTT TTT TTT TTT TTT TT


title: B2r1


title: V1B03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GAC TTG TTT TTT TTT TTT TTT TTT TTT TTT TT


title: B2r2


title: EB_384R_T1_S53: +/+;Cas9/+ treated by gLmna-1

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite using the -fpkm -count exons -noCondensingParts parameters
Genome_build: mm10
Supplementary_files_format_and_content: fpkm normalized table (text file)

source_name: tail tip

growth_protocol: Primary fibroblasts isolated from the tail tips of the mice were cultured at 37oC with 5% CO2 on plastic flasks.  DMEM medium including 10% Fetal Bovine Serum was used as the culture medium. The cells were passaged with Tryple-Express when reached to the sub-confluency level.

extract_protocol: The cultures were at passage #5 when the cells were dissociated with Tryple, washed with 1X PBS, flash-frozen in liquid nitrogen and stored at -80oC until processed for the RNA isolation.  Total RNA was isolated from the frozen samples by Qiashredder spin columns (Qiagen) and processed with RNeasy Mini Kit (Qiagen) without DNase digestion.

treatment_protocol: gRNAs (Lmna target gRNAs or mock) were delivered into the cells by Lentiviral vectors containing mCherry gene as the reporter.  The infection was performed by "Spinfection" (The cells were plated into the flasks at sub-confluent level with the medium containing the viral prep and 4μg/ml Polybrene, and the culture was first incubated at 32-33oC for 30 minutes then spun at 750g at room temperature for 45 minutes).  The culture was incubated at 32-33oC until the next day when the medium containing the virus and polybrene was removed from the culture with a medium change and the culture was placed into the 37oC incubator.  All the samples showed more than 80% mCherry-positive cells under the fluorescent microscope prior to being processed for total RNA isolation.  No selection or cell sorting was performed before RNA isolation.

value: tail tip

tag: genotype

value: Primary fibroblast

tag: age

value: 2 months old

tag: passage number


title: EB_384R_mock_S52: +/+;Cas9/+ treated by gMock

tag: treatment

value: gMock

tag: tissue


title: EB_384R_T2_S54: +/+;Cas9/+ treated by gLmna-2


title: V1A03

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GAA TCA GTT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom concentration (ug/ul)


title: post-vaccination blood sample from donor 628859 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV

source_name: Blood sample from donor 628859

tag: donor

tag: scanning note

value: ok

value: Micro kit

value: hours


title: post-vaccination blood sample from donor 627323 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 627323

tag: rna extraction protocol

tag: stimulation

value: VACCINE

value: No


title: post-vaccination blood sample from donor 628859 stimulate 15 hours with DMSO

value: DMSO

tag: stimulation time

tag: stimulation time unit


title: V1H02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG AGA CCG ATT TTT TTT TTT TTT TTT TTT TTT TT

tag: cell line


title: post-vaccination blood sample from donor 627783 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO

source_name: Blood sample from donor 627783

tag: hiv infection


title: post-vaccination blood sample from donor 629639 stimulate 15 hours with DMSO


title: V1G02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC CTC TTA GTT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom treatment


title: EB_383L_T2: +/+;Cas9/+ treated by gLmna-2

tag: cell type


title: EB_383L_T1: +/+;Cas9/+ treated by gLmna-1


title: post-vaccination blood sample from donor 626077 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 626077


title: post-vaccination blood sample from donor 626077 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 627783 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 627323 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 627156 stimulate 15 hours with DMSO

source_name: Blood sample from donor 627156


title: EB_383L_mock: +/+;Cas9/+ treated by gMock


title: V1F02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC AGG CGT ATT TTT TTT TTT TTT TTT TTT TTT TT

tag: time post-treatment


title: V1E02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GAG TAA ATT TTT TTT TTT TTT TTT TTT TTT TT


title: V1D02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TCA TGT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: EB_374_375_T2_S36: Pro/+; +/+ treated by gLmna-2

tag: genotype


title: V1B02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC AGT ACC TTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1C02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT TTT ACC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 625525 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 625525

value: Yes


title: EB_374_375_mock_S34: Pro/+; +/+ treated by gMock

tag: age


title: post-vaccination blood sample from donor 619127 stimulate 15 hours with DMSO

source_name: Blood sample from donor 619127


title: post-vaccination blood sample from donor 614918 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 614918


title: post-vaccination blood sample from donor 621813 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 621813


title: post-vaccination blood sample from donor 619127 stimulate 15 hours with 92TH023ENV


title: V1H01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCG CCA TTG GTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 610309 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO

source_name: Blood sample from donor 610309


title: post-vaccination blood sample from donor 608822 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 608822


title: post-vaccination blood sample from donor 610309 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 605125 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 605125


title: post-vaccination blood sample from donor 608822 stimulate 15 hours with DMSO


title: V1A02

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC GTT GTC ATT TTT TTT TTT TTT TTT TTT TTT TT

source_name: IMR-32 neuroblastoma cells in culture


title: post-vaccination blood sample from donor 621813 stimulate 15 hours with DMSO


title: EB_382R_T2: Pro/+; +/+ treated by gLmna-2

tag: passage number


title: post-vaccination blood sample from donor 625525 stimulate 15 hours with DMSO

tag: treatment


title: EB_374_375_T1_S35: Pro/+; +/+ treated by gLmna-1

tag: tissue


title: post-vaccination blood sample from donor 605125 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 614918 stimulate 15 hours with DMSO


title: EB_382R_mock: Pro/+; +/+ treated by gMock


title: EB_381L_T2_S45: Pro/Pro;Cas9/+ treated by gLmna-2


title: V1G01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC ATG CCT TTT TTT TTT TTT TTT TTT TTT TTT TT

tag: venom concentration (ug/ul)


title: EB_382R_T1: Pro/+; +/+ treated by gLmna-1


title: V1F01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GCA GCT GTT TTT TTT TTT TTT TTT TTT TTT TT


title: V1E01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA CTG ACT TTT TTT TTT TTT TTT TTT TTT TTT TT


title: EB_381L_T1_S44: Pro/Pro;Cas9/+ treated by gLmna-1


title: EB_381L_mock_S43: Pro/Pro;Cas9/+ treated by gMock


title: V1D01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA TCT AGG ATT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 603880 stimulate 15 hours with DMSO

source_name: Blood sample from donor 603880

tag: donor


title: EB_379L_T2: Pro/Pro;Cas9/+ treated by gLmna-2


title: post-vaccination blood sample from donor 603880 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV

tag: scanning note


title: post-vaccination blood sample from donor 603909 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 603909

tag: rna extraction protocol


title: post-vaccination blood sample from donor 603909 stimulate 15 hours with DMSO

tag: stimulation


title: V1B01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCC AAG GAA GTT TTT TTT TTT TTT TTT TTT TTT TT


title: EB_379L_T1: Pro/Pro;Cas9/+ treated by gLmna-1


title: V1A01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCT GAA CAC GTT TTT TTT TTT TTT TTT TTT TTT TT


title: post-vaccination blood sample from donor 601024 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 601024

tag: stimulation time


title: EB_379L_mock: Pro/Pro;Cas9/+ treated by gMock

source_name: tail tip


title: post-vaccination blood sample from donor 600125 stimulate 15 hours with DMSO

source_name: Blood sample from donor 600125

tag: stimulation time unit


title: post-vaccination blood sample from donor 600125 stimulate 15 hours with 92TH023ENV


title: V1C01

description: barcode sequence: GTT CAG AGT TCT ACA GTC CGA CGA TCA GAC TCG CTT TTT TTT TTT TTT TTT TTT TTT TT

tag: cell line


title: post-vaccination blood sample from donor 526915 stimulate 15 hours with DMSO

source_name: Blood sample from donor 526915

tag: hiv infection


title: FOXM1b rep3

city: Omaha

first: Adam

middle: R.

last: Karpf

state: Nebraska

address: 985950 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

data_processing:
Adaptor sequences and low quality (Phred score: 20) 3 base 5' ends were trimmed from sequences using Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Resulting fastq files were aligned to the human genome (NCBI37/hg19) using the software TopHat (v2.0.8) http://ccb.jhu.edu/software/tophat/index.shtml
Cufflinks (v2.1.1) http://cole-trapnell-lab.github.io/cufflinks/ was be used to estimate the gene based expression values.
Cuffdiff (v2.1.1) was used to determine differential gene based expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: HEK293T cells

growth_protocol: HEK293T were grown with Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (heat inactivated) and 2mM L-glutamine.

extract_protocol:
Total RNA was purified from HEK293T cells using TRIzol (Invitrogen) and the Direct-zol RNA Purification Kit (Zymo Research) with in-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEK293T cells were transfected in triplicate with pCMV6 plasmid using Lipofectamine 2000 (Life Technologies). The pCMV6 plasmid expressed empty, FOXM1a, FOXM1c or FOXM1b.

value: HEK293T cells

tag: genotype/variation

value: FOXM1 knockout / reconstituted with FOXM1b

tag: timepoint

value: 48 hours


title: post-vaccination blood sample from donor 601024 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 604004 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 604004


title: post-vaccination blood sample from donor 526526 stimulate 15 hours with DMSO

source_name: Blood sample from donor 526526


title: post-vaccination blood sample from donor 604004 stimulate 15 hours with DMSO


title: FOXM1b rep1


title: post-vaccination blood sample from donor 526452 stimulate 15 hours with DMSO

source_name: Blood sample from donor 526452


title: post-vaccination blood sample from donor 526076 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 526076


title: FOXM1b rep2


title: post-vaccination blood sample from donor 526526 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 526452 stimulate 15 hours with 92TH023ENV


title: FOXM1c rep3

value: FOXM1 knockout / reconstituted with FOXM1c


title: post-vaccination blood sample from donor 526076 stimulate 15 hours with DMSO


title: FOXM1c rep1


title: FOXM1c rep2


title: FOXM1a rep3

value: FOXM1 knockout / reconstituted with FOXM1a


title: post-vaccination blood sample from donor 524834 stimulate 15 hours with DMSO

source_name: Blood sample from donor 524834


title: post-vaccination blood sample from donor 521571 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 521571


title: post-vaccination blood sample from donor 521571 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 526915 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 524834 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 517997 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 517997


title: post-vaccination blood sample from donor 520270 stimulate 15 hours with DMSO

source_name: Blood sample from donor 520270


title: FOXM1a rep2


title: post-vaccination blood sample from donor 520270 stimulate 15 hours with 92TH023ENV


title: FOXM1a rep1


title: Vector control rep2

value: FOXM1 knockout / vector control


title: post-vaccination blood sample from donor 517106 stimulate 15 hours with DMSO

source_name: Blood sample from donor 517106


title: post-vaccination blood sample from donor 517106 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 517997 stimulate 15 hours with DMSO


title: Vector control rep1


title: post-vaccination blood sample from donor 513999 stimulate 15 hours with DMSO

source_name: Blood sample from donor 513999


title: post-vaccination blood sample from donor 513494 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 513494


title: post-vaccination blood sample from donor 515964 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 515964


title: post-vaccination blood sample from donor 515964 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 513494 stimulate 15 hours with DMSO


title: Vector control rep3


title: post-vaccination blood sample from donor 512209 stimulate 15 hours with DMSO

source_name: Blood sample from donor 512209


title: post-vaccination blood sample from donor 511908 stimulate 15 hours with DMSO

source_name: Blood sample from donor 511908


title: post-vaccination blood sample from donor 509119 stimulate 15 hours with DMSO

source_name: Blood sample from donor 509119


title: post-vaccination blood sample from donor 509119 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 511159 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 511159


title: post-vaccination blood sample from donor 511159 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 512209 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 508696 stimulate 15 hours with DMSO

source_name: Blood sample from donor 508696


title: post-vaccination blood sample from donor 508696 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 505690 stimulate 15 hours with DMSO

source_name: Blood sample from donor 505690


title: post-vaccination blood sample from donor 508522 stimulate 15 hours with DMSO

source_name: Blood sample from donor 508522


title: post-vaccination blood sample from donor 508522 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 505018 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 505018


title: post-vaccination blood sample from donor 500375 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 500375


title: post-vaccination blood sample from donor 507430 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 507430


title: post-vaccination blood sample from donor 507430 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 444725 stimulate 15 hours with DMSO

source_name: Blood sample from donor 444725


title: post-vaccination blood sample from donor 444217 stimulate 15 hours with DMSO

source_name: Blood sample from donor 444217


title: post-vaccination blood sample from donor 500375 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 500256 stimulate 15 hours with DMSO

source_name: Blood sample from donor 500256


title: post-vaccination blood sample from donor 449394 stimulate 15 hours with DMSO

source_name: Blood sample from donor 449394


title: post-vaccination blood sample from donor 505018 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 438697 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO

source_name: Blood sample from donor 438697

value: PLACEBO


title: post-vaccination blood sample from donor 444725 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 449394 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 438697 stimulate 15 hours with 92TH023ENV

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 444217 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 500256 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 434239 stimulate 15 hours with DMSO

source_name: Blood sample from donor 434239


title: post-vaccination blood sample from donor 505690 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 603208 stimulate 15 hours with DMSO

source_name: Blood sample from donor 603208


title: post-vaccination blood sample from donor 424589 stimulate 15 hours with DMSO

source_name: Blood sample from donor 424589


title: post-vaccination blood sample from donor 511908 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 511908


title: post-vaccination blood sample from donor 432132 stimulate 15 hours with DMSO

source_name: Blood sample from donor 432132


title: post-vaccination blood sample from donor 431442 stimulate 15 hours with DMSO

source_name: Blood sample from donor 431442


title: post-vaccination blood sample from donor 432132 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 425938 stimulate 15 hours with DMSO

source_name: Blood sample from donor 425938


title: post-vaccination blood sample from donor 434239 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 419318 stimulate 15 hours with DMSO

source_name: Blood sample from donor 419318


title: post-vaccination blood sample from donor 420459 stimulate 15 hours with DMSO

source_name: Blood sample from donor 420459


title: post-vaccination blood sample from donor 417372 stimulate 15 hours with DMSO

source_name: Blood sample from donor 417372


title: post-vaccination blood sample from donor 419202 stimulate 15 hours with DMSO

source_name: Blood sample from donor 419202


title: post-vaccination blood sample from donor 419318 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 417372 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 405017 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 405017


title: post-vaccination blood sample from donor 411547 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 411547


title: post-vaccination blood sample from donor 405464 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 405464


title: post-vaccination blood sample from donor 412134 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 412134


title: post-vaccination blood sample from donor 405686 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 405686


title: post-vaccination blood sample from donor 404343 stimulate 15 hours with DMSO

source_name: Blood sample from donor 404343


title: post-vaccination blood sample from donor 405017 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 405686 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 419202 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 412134 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 424589 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 413107 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 413107


title: post-vaccination blood sample from donor 411547 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 420459 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 413107 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 425938 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 403068 stimulate 15 hours with DMSO

source_name: Blood sample from donor 403068


title: post-vaccination blood sample from donor 403068 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 404343 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 402558 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 402558


title: post-vaccination blood sample from donor 357229 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 357229


title: post-vaccination blood sample from donor 402558 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 357229 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 355894 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 355894


title: post-vaccination blood sample from donor 355698 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 355698


title: post-vaccination blood sample from donor 348298 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 348298


title: post-vaccination blood sample from donor 345102 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 345102


title: post-vaccination blood sample from donor 354609 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 354609


title: post-vaccination blood sample from donor 349290 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 349290


title: post-vaccination blood sample from donor 355698 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 355894 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 348298 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 354609 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 349290 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 345102 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 337366 stimulate 15 hours with DMSO

source_name: Blood sample from donor 337366


title: post-vaccination blood sample from donor 343793 stimulate 15 hours with DMSO

source_name: Blood sample from donor 343793


title: post-vaccination blood sample from donor 343793 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 345025 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 345025


title: post-vaccination blood sample from donor 338098 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 338098


title: post-vaccination blood sample from donor 338098 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 343047 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 343047


title: post-vaccination blood sample from donor 334122 stimulate 15 hours with DMSO

source_name: Blood sample from donor 334122


title: post-vaccination blood sample from donor 343047 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 333162 stimulate 15 hours with DMSO

source_name: Blood sample from donor 333162


title: post-vaccination blood sample from donor 339360 stimulate 15 hours with DMSO

source_name: Blood sample from donor 339360


title: post-vaccination blood sample from donor 335179 stimulate 15 hours with DMSO

source_name: Blood sample from donor 335179


title: post-vaccination blood sample from donor 334122 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 335179 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 339360 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 345025 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 337366 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 333162 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 322089 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 322089


title: post-vaccination blood sample from donor 324610 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 324610


title: post-vaccination blood sample from donor 324610 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 322089 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 317175 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 317175


title: post-vaccination blood sample from donor 331692 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 331692


title: post-vaccination blood sample from donor 331692 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 332469 stimulate 15 hours with DMSO

source_name: Blood sample from donor 332469


title: post-vaccination blood sample from donor 318225 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 318225


title: post-vaccination blood sample from donor 313212 stimulate 15 hours with DMSO

source_name: Blood sample from donor 313212


title: post-vaccination blood sample from donor 332469 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 320249 stimulate 15 hours with DMSO

source_name: Blood sample from donor 320249


title: post-vaccination blood sample from donor 320355 stimulate 15 hours with DMSO

source_name: Blood sample from donor 320355


title: post-vaccination blood sample from donor 320249 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 316340 stimulate 15 hours with DMSO

source_name: Blood sample from donor 316340


title: post-vaccination blood sample from donor 318225 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 308845 stimulate 15 hours with DMSO

source_name: Blood sample from donor 308845


title: post-vaccination blood sample from donor 316340 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 308250 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 308250


title: post-vaccination blood sample from donor 308845 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 313212 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 313180 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 313180


title: post-vaccination blood sample from donor 313180 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 317175 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 307100 stimulate 15 hours with DMSO

source_name: Blood sample from donor 307100


title: post-vaccination blood sample from donor 308250 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 405464 stimulate 15 hours with DMSO

source_name: Blood sample from donor 405464


title: post-vaccination blood sample from donor 304085 stimulate 15 hours with DMSO

source_name: Blood sample from donor 304085


title: post-vaccination blood sample from donor 307100 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 304085 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 236961 stimulate 15 hours with DMSO

source_name: Blood sample from donor 236961


title: post-vaccination blood sample from donor 244363 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 244363


title: post-vaccination blood sample from donor 247912 stimulate 15 hours with DMSO

source_name: Blood sample from donor 247912


title: post-vaccination blood sample from donor 305968 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 305968


title: post-vaccination blood sample from donor 300003 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 300003


title: post-vaccination blood sample from donor 247912 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 243046 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 243046


title: post-vaccination blood sample from donor 300003 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 243046 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 243615 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 243615


title: post-vaccination blood sample from donor 237169 stimulate 15 hours with DMSO

source_name: Blood sample from donor 237169


title: post-vaccination blood sample from donor 241248 stimulate 15 hours with DMSO

source_name: Blood sample from donor 241248


title: post-vaccination blood sample from donor 241248 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 244363 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 243615 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 238682 stimulate 15 hours with DMSO

source_name: Blood sample from donor 238682


title: post-vaccination blood sample from donor 235525 stimulate 15 hours with DMSO

source_name: Blood sample from donor 235525


title: post-vaccination blood sample from donor 242385 stimulate 15 hours with DMSO

source_name: Blood sample from donor 242385


title: post-vaccination blood sample from donor 235525 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 240503 stimulate 15 hours with DMSO

source_name: Blood sample from donor 240503


title: post-vaccination blood sample from donor 236961 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 237169 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 240503 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 238682 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 234549 stimulate 15 hours with DMSO

source_name: Blood sample from donor 234549


title: post-vaccination blood sample from donor 320355 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 320355


title: post-vaccination blood sample from donor 233994 stimulate 15 hours with DMSO

source_name: Blood sample from donor 233994


title: post-vaccination blood sample from donor 233042 stimulate 15 hours with DMSO

source_name: Blood sample from donor 233042


title: post-vaccination blood sample from donor 226150 stimulate 15 hours with DMSO

source_name: Blood sample from donor 226150


title: post-vaccination blood sample from donor 233042 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 229455 stimulate 15 hours with DMSO

source_name: Blood sample from donor 229455


title: post-vaccination blood sample from donor 232709 stimulate 15 hours with DMSO

source_name: Blood sample from donor 232709


title: post-vaccination blood sample from donor 225769 stimulate 15 hours with DMSO

source_name: Blood sample from donor 225769


title: post-vaccination blood sample from donor 226150 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 232709 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 233994 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 225473 stimulate 15 hours with DMSO

source_name: Blood sample from donor 225473


title: post-vaccination blood sample from donor 226385 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 226385


title: post-vaccination blood sample from donor 229455 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 232545 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 232545


title: post-vaccination blood sample from donor 234549 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 224172 stimulate 15 hours with DMSO

source_name: Blood sample from donor 224172


title: post-vaccination blood sample from donor 224574 stimulate 15 hours with DMSO

source_name: Blood sample from donor 224574


title: post-vaccination blood sample from donor 224172 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 222570 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 222570


title: post-vaccination blood sample from donor 222570 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 223884 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 223884


title: post-vaccination blood sample from donor 232545 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 225769 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 225473 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 222271 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 222271


title: post-vaccination blood sample from donor 222271 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 223884 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 226385 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 224574 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 221716 stimulate 15 hours with DMSO

source_name: Blood sample from donor 221716


title: post-vaccination blood sample from donor 221716 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 220293 stimulate 15 hours with DMSO

source_name: Blood sample from donor 220293


title: post-vaccination blood sample from donor 220187 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 220187


title: post-vaccination blood sample from donor 211365 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 211365


title: post-vaccination blood sample from donor 214329 stimulate 15 hours with DMSO

source_name: Blood sample from donor 214329


title: post-vaccination blood sample from donor 203143 stimulate 15 hours with DMSO

source_name: Blood sample from donor 203143


title: post-vaccination blood sample from donor 220187 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 212341 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 212341


title: post-vaccination blood sample from donor 132689 stimulate 15 hours with DMSO

source_name: Blood sample from donor 132689


title: post-vaccination blood sample from donor 220293 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 209743 stimulate 15 hours with DMSO

source_name: Blood sample from donor 209743


title: post-vaccination blood sample from donor 209743 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 209055 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 209055


title: post-vaccination blood sample from donor 206284 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 206284


title: post-vaccination blood sample from donor 211484 stimulate 15 hours with DMSO

source_name: Blood sample from donor 211484


title: post-vaccination blood sample from donor 132689 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 135177 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 135177


title: post-vaccination blood sample from donor 137319 stimulate 15 hours with DMSO

source_name: Blood sample from donor 137319


title: post-vaccination blood sample from donor 135177 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 215765 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 215765


title: post-vaccination blood sample from donor 211365 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 212341 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 211484 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 206284 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 209055 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 215765 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 214329 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 129364 stimulate 15 hours with DMSO

source_name: Blood sample from donor 129364


title: post-vaccination blood sample from donor 132483 stimulate 15 hours with DMSO

source_name: Blood sample from donor 132483


title: post-vaccination blood sample from donor 129898 stimulate 15 hours with DMSO

source_name: Blood sample from donor 129898


title: post-vaccination blood sample from donor 132483 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 129898 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 129364 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 129872 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 129872


title: post-vaccination blood sample from donor 129872 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 127241 stimulate 15 hours with DMSO

source_name: Blood sample from donor 127241


title: post-vaccination blood sample from donor 127241 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 124155 stimulate 15 hours with DMSO

source_name: Blood sample from donor 124155


title: post-vaccination blood sample from donor 124155 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 110256 stimulate 15 hours with DMSO

source_name: Blood sample from donor 110256


title: post-vaccination blood sample from donor 110780 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 110780


title: post-vaccination blood sample from donor 116229 stimulate 15 hours with DMSO

source_name: Blood sample from donor 116229


title: post-vaccination blood sample from donor 119450 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 119450


title: post-vaccination blood sample from donor 109816 stimulate 15 hours with DMSO

source_name: Blood sample from donor 109816


title: post-vaccination blood sample from donor 112906 stimulate 15 hours with DMSO

source_name: Blood sample from donor 112906


title: post-vaccination blood sample from donor 109816 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 117102 stimulate 15 hours with DMSO

source_name: Blood sample from donor 117102


title: post-vaccination blood sample from donor 112906 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 119450 stimulate 15 hours with DMSO


title: post-vaccination blood sample from donor 107034 stimulate 15 hours with DMSO

source_name: Blood sample from donor 107034


title: post-vaccination blood sample from donor 116229 stimulate 15 hours with 92TH023ENV


title: post-vaccination blood sample from donor 110256 stimulate 15 hours with 92TH023ENV


title: RNA-hNeuronD22-Ctl replicate 2

source_name: Cell Line

tag: cell type

value: Human Neuron Cell

value: derived from H9 (day 22)

value: wildtype


title: RNA-hNeuronD22-53BP1KO1 replicate 2


title: RNA-hNeuronD22-53BP1KO2 replicate 1


title: RNA-hNeuronD22-Ctl replicate 1


title: RNA-hNeuronD22-53BP1KO1 replicate 1


title: RNA-hESC-UTXKD3

value: Human Embryonic Stem cell

value: UTX KD


title: RNA-hESC-UTXKD2


title: post-vaccination blood sample from donor 107034 stimulate 15 hours with 92TH023ENV

value: ok

value: Micro kit

value: hours


title: post-vaccination blood sample from donor 137319 stimulate 15 hours with 92TH023ENV

source_name: Blood sample from donor 137319

value: VACCINE

value: No


title: post-vaccination blood sample from donor 110780 stimulate 15 hours with DMSO

value: DMSO


title: pre-vaccination blood sample from donor 834635 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d834635_pre_92TH023ENV_15h

source_name: Blood sample from donor 834635

tag: post-thraw resting

value: no

tag: visit

value: pre


title: post-vaccination blood sample from donor 834275 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d834275_post_DMSO_15h

source_name: Blood sample from donor 834275

value: post

value: RV144 vaccine


title: post-vaccination blood sample from donor 834635 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d834635_post_DMSO_15h


title: pre-vaccination blood sample from donor 834275 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d834275_pre_DMSO_15h


title: RNA-hESC-53BP1KO3 replicate 1


title: post-vaccination blood sample from donor 834275 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d834275_post_92TH023ENV_15h


title: RNA-hESC-53BP1KO2 replicate 1


title: pre-vaccination blood sample from donor 834275 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d834275_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 834635 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with 92TH023ENV
RV144_d834635_post_92TH023ENV_15h


title: RNA-hESC-UTXKD1


title: RNA-hESC-53BP1KO1 replicate 1


title: pre-vaccination blood sample from donor 826381 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d826381_pre_92TH023ENV_15h

source_name: Blood sample from donor 826381


title: post-vaccination blood sample from donor 826381 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d826381_post_DMSO_15h

value: RV144 placebo


title: H3K27me3-53BP1KOneuronD17 replicate 2

description:
processed data file:
H3K27me3-53BP1KOneuronD17.common.peak.txt

value: Human Neuron Cell D17

value: derived from H9 (day 17)

value: 53BP1 KO

tag: chip antibody


title: post-vaccination blood sample from donor 824464 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d824464_post_DMSO_15h

source_name: Blood sample from donor 824464

tag: treatment


title: post-vaccination blood sample from donor 826381 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV
RV144_d826381_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 824464 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d824464_pre_DMSO_15h


title: pre-vaccination blood sample from donor 823015 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d823015_pre_DMSO_15h

source_name: Blood sample from donor 823015


title: H3K27ac-53BP1KOneuronD17 replicate 2

description:
processed data file:
H3K27ac-53BP1KOneuronD17.common.peak.txt


title: H3K27me3-53BP1KOneuronD17 replicate 1


title: post-vaccination blood sample from donor 823015 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV
RV144_d823015_post_92TH023ENV_15h


title: post-vaccination blood sample from donor 824464 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with 92TH023ENV
RV144_d824464_post_92TH023ENV_15h


title: pre-vaccination blood sample from donor 834635 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d834635_pre_DMSO_15h


title: H3K27ac-53BP1KOneuronD17 replicate 1


title: pre-vaccination blood sample from donor 822653 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d822653_pre_DMSO_15h

source_name: Blood sample from donor 822653


title: post-vaccination blood sample from donor 127852 stimulate 15 hours with DMSO

description: transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO

source_name: Blood sample from donor 127852


title: pre-vaccination blood sample from donor 826381 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d826381_pre_DMSO_15h


title: pre-vaccination blood sample from donor 823015 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d823015_pre_92TH023ENV_15h


title: H3K27me3-CtrlneuronD17 replicate 1

description:
processed data file:
H3K27me3-CtrlneuronD17.peak.txt

value: wildtype


title: post-vaccination blood sample from donor 822653 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 vaccine and stimulated 15 hours with DMSO
RV144_d822653_post_DMSO_15h


title: pre-vaccination blood sample from donor 824464 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d824464_pre_92TH023ENV_15h


title: post-vaccination blood sample from donor 823015 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken 2 weeks after vaccination with the RV144 placebo and stimulated 15 hours with DMSO
RV144_d823015_post_DMSO_15h


title: H3K27ac-CtrlneuronD17 replicate 1

description:
processed data file:
H3K27ac-CtrlneuronD17.peak.txt


title: pre-vaccination blood sample from donor 818754 stimulated 15 hours with DMSO

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with DMSO
RV144_d818754_pre_DMSO_15h

source_name: Blood sample from donor 818754


title: pre-vaccination blood sample from donor 818754 stimulated 15 hours with 92TH023ENV

description:
transcriptional profilling of blood taken pre-vaccination and stimulated 15 hours with 92TH023ENV
RV144_d818754_pre_92TH023ENV_15h


title: KPC tumor #3

city: La Jolla

first: Michael

last: Hamilton

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

description: cell barcodes for this sample end in "-3"

data_processing:
Cellranger 2.1.1 – for alignment, filtering, barcode counting, and UMI counting
Seurat 3.0 – for secondary analysis of feature-barcode matrices
Genome_build: Mus38
Supplementary_files_format_and_content: .csv, .tsv, .mtx, differential gene expression between clusters, UMI counts

source_name: KPC tumor cells

extract_protocol:
10x genomics manufacturer's protocol
10x genomics 3' expression gene profiling v2

treatment_protocol: Sorted and sequenced KPC cells that were CD45-, CD31- and PDGFRa-

tag: strain

value: KPf/fC

value: KPC tumor cells