title: Warm brown adipocyte H3K27ac ChIP rep 1

description: biological replicate

source_name: interscapular BAT


title: Cold beige adipocyte H3K27ac ChIP rep 1

status: Public on Mar 01 2018

type: SRA

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

country: USA

institute: Beth Israel Deconess Medical Center

description: biological replicate

library_source: genomic

data_processing:
ChIP-seq data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than whole cell extract (WCE)) were removed.
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. Low signal peaks (log2 CPM<2) were removed, and differential peaks were defined at log2 FC≥1 and log2 FDR≤0.05 (except H3K4me1 which used FDR≤0.25).
For ChIP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
ChIP-seq peak heatmaps and distribution plots were generated with the normalized BigWig files within 10kb genomic regions surrounding peaks by using deepTools2 (Ramirez et al., 2016).
Overlaps between H3K27ac and H3K4me1 were determined using bedtools. Peaks were assigned to genomic annotations and genes with HOMER (Heinz et al., 2010), and GO pathway analysis was performed by DAVID Bioinformatics Resources 6.8.
Motif enrichment analysis was conducted using FIMO from the MEME package (Grant et al., 2011) with the JASPAR database (Mathelier et al., 2014)
genome build: mm10
processed data files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: inguinal WAT

growth_protocol: Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).

extract_protocol:
Tissues were dounce homogenized, and cross-linked nuclei were isolated and sorted by BD FACS Aria II using mCherry fluorescence. Sorted nuclei were sheared by Covaris E220 and used for ChIP for overnight. Immunoprecipitates were washed and subjected to elution and reverse crosslinking. DNA was then extracted by AMPure XP beads according to the manufacturer’s manual.
Sequencing libraries were constructed using the “on-bead” preparation method as previously described (Roh et al., Cell Rep, 2017). ChIP-isolated DNA was subjected to end repair/phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment and index adaptor ligation using Quick Ligase (NEB). AMPure XP beads were left in all the reactions to allow isolation of DNA using PEG (Polyethylene Glycol 8000)/NaCl solution, thus minimizing loss between reactions. After ligation, DNA was eluted and amplified by PCR for 14-16 cycles using the PfuUltra II Hotstart PCR Master Mix. DNA sized between 250 and 600bp was selected by gel electrophoresis and extraction using E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction kits (Qiagen). Libraries were analyzed using the Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM and sequenced on a HiSeq2500 or NextSeq500 system.

treatment_protocol: Mice were exposed to cold (4°C for 1 week (cold brown/beige adipocyte samples), and subsequently incubated at 30°C for 4 weeks (warm brown/beige adipocyte samples). Mice born and maintained at 30°C at all times used for warm white adipocyte samples.

tag: strain

tag: tissue

value: adipose

tag: chip antibody

value: H3K27ac (Active Motif, 39133)


title: Cold brown adipocyte H3K27ac ChIP rep 1

description: biological replicate


title: BP165_5219_C2_D0_B_D

type: RNA

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: gene expression challenge 2, day 0 , no adjuvant

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Agilent Rhesus (8x60K) oligonucleotide microarrays  were used. Dry slides were scanned on an Agilent Technologies Scanner G2505C US93503719 using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 10.7.3.1) and the GE1-v5_95_Feb07 extraction protocol.

molecule: total RNA

organism: Macaca mulatta

source_name: gene expression challenge 2, day 0

growth_protocol: 22 Indian-orgin Rhesus Macaques were used. 10 vaccinated animals that acquired SIV infection with two challenges (early SIV acquirers) and 12 vaccinated animals that acquired SIV infection after 6 challenges (late SIV acquirers).

extract_protocol: Microarray analysis was performed on whole blood samples on 22 vaccined animals. (10 early acquires and 12 late acquirers).  For both set of animals at multiple days after the 1st DNA vaccine (Wk0), 1st MVA boost (Wk16), 2nd MVA boost (Wk32) and 1st rectal challenge

treatment_protocol: Total RNA was isolated from Paxgene tubes by use of Paxgene Blood RNeasy minikits (Qiagen) following the manufacturer's protocol.

value: whole blood

tag: vaccine treatment

value: no adjuvant

tag: siv acquirers

value: Late acquisition


title: Mim12_28d_L_Midbrain

city: Montpellier

first: Gina

last: DEVAU

address: Place Eugene Bataillon

department: Universite de Montpellier CC105

country: France

institute: Inserm U1198-UM-EPHE

description: Gene expression changes induced by CAV-2 in primate midbrain, 28 days after infection

hyb_protocol: Following fragmentation, 1 à 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent Scanner 3000.

data_processing: he data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Microcebus murinus

source_name: Left midbrain from brain Microcebus murinus 28 days after CAV-2 infection, contralateral side

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were all born in captivity in our breeding colony (CECEMA, University of Montpellier, France). 12 animals were used in this study. All animal  experiments  were conducted in strict accordance with the European Union Directive (2010/63/EU) for the care and the use of laboratory animals (Animal authorization CE-LR-0502, ethical committee of the Languedoc-Roussillon, France).

extract_protocol: Extraction of total RNA  was performed using Rneasy mini Kit (QIAGEN, Santa Clarina, CA) according to the manufacturer's instructions.

tag: gender

value: female

tag: age

value: 2 year old

tag: cav-2 infection helper dependent 109 physical particles

value: Contralateral to CAV-2 infection

tag: brain tissue

value: Midbrain


title: BP165_5418_C1_D0_B_CTRL

description: gene expression challenge 1, day 0 , control group

source_name: gene expression challenge 1, day 0

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

value: control group

value: Early acquisition


title: BP165_5222_C2_D0_B_Dg

description: gene expression challenge 2, day 0 ,GM-CSF adjuvant

value: GM-CSF adjuvant


title: Choroid plexus carcinoma / Malignant peripheral nerve sheeth tumor Sample 2

city: Copenhagen

first: Wiktor

last: Majewski

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital

hyb_protocol: affymetrix manufactures procedure

scan_protocol: affymetrix manufactures procedure

data_processing: CEL file data were processed using quantile normalization, background correction and summarized using RMA algorithm implemented in Bioconductor package 'affy'

label: biotin

organism: Homo sapiens

source_name: tumor biopsy

label_protocol: affymetrix manufactures procedure

extract_protocol: Qiagen manufactures procedure automatized on QiaCube; specifically Rneasy MIniPrep. RNA quality and quantity was controled by BioAnalyzer and Nanodrop.

tag: condition


title: BP165_5237_W1_D7_B_D

description: gene expression week 1, day 7 , no adjuvant

source_name: gene expression week 1, day 7


title: BP165_5418_W17_D7_B_CTRL

description: gene expression week 17, day 7 , control group

source_name: gene expression week 17, day 7


title: BP165_5222_W32_D1_B_Dg

description: gene expression week 32, day 1 ,GM-CSF adjuvant

source_name: gene expression week 32, day 1


title: BP165_5222_W-1_D0_B_Dg

description: gene expression week -1, day 0 ,GM-CSF adjuvant

source_name: gene expression week -1, day 0


title: Mim10_28d_L_Midbrain


title: Mim11_28d_L_Midbrain


title: Atypical meningioma Sample 1

value: Atypical meningioma


title: BP165_5237_W32_D0_B_D

description: gene expression week 32, day 0 , no adjuvant

source_name: gene expression week 32, day 0


title: BP165_5231_W16_D3_B_Dg

description: gene expression week 16, day 3 ,GM-CSF adjuvant

source_name: gene expression week 16, day 3


title: BP165_5222_W16_D0_B_Dg

description: gene expression week 16, day 0 ,GM-CSF adjuvant

source_name: gene expression week 16, day 0


title: BP165_5219_C1_D0_B_D

description: gene expression challenge 1, day 0 , no adjuvant


title: BP165_5231_W0_D3_B_Dg

description: gene expression week 0, day 3 ,GM-CSF adjuvant

source_name: gene expression week 0, day 3


title: Mim11_28d_R_Midbrain

source_name: Right midbrain from brain Microcebus murinus 28 days after CAV-2 infection, ipsilateral side

value: Ipsilateral to CAV-2  infection


title: BP165_5418_C1_D1_B_CTRL

description: gene expression challenge 1, day 1 , control group

source_name: gene expression challenge 1, day 1


title: BP165_5219_W1_D7_B_D


title: BP165_5222_C1_D0_B_Dg

description: gene expression challenge 1, day 0 ,GM-CSF adjuvant


title: Mim9_28d_L_Midbrain


title: BP165_5222_C3_D0_B_Dg

description: gene expression challenge 3, day 0 ,GM-CSF adjuvant

source_name: gene expression challenge 3, day 0


title: BP165_5418_W32_D0_B_CTRL

description: gene expression week 32, day 0 , control group


title: Mim10_28d_R_Midbrain


title: Mim8_24h_L_Midbrain

description: Gene expression changes induced by CAV-2 in primate midbrain, 24h after infection

source_name: Left midbrain from brain Microcebus murinus 24h after CAV-2 infection, contralateral side


title: BP165_5237_C1_D1_B_D

description: gene expression challenge 1, day 1 , no adjuvant


title: BP165_5219_W0_D3_B_D

description: gene expression week 0, day 3 , no adjuvant


title: BP165_5219_C1_D1_B_D


title: BP165_5418_W16_D3_B_CTRL

description: gene expression week 16, day 3 , control group


title: Mim12_28d_R_Midbrain

description: Gene expression changes induced by CAV-2 in primate midbrain, 28 days after infection


title: Mim5_24h_L_Midbrain


title: Mim9_28d_R_Midbrain


title: BP165_5231_W16_D0_B_Dg


title: Mim6_24h_L_Midbrain


title: BP165_5237_W32_D3_B_D

description: gene expression week 32, day 3 , no adjuvant

source_name: gene expression week 32, day 3


title: Mim7_24h_L_Midbrain


title: BP165_5222_C1_D4_B_Dg

description: gene expression challenge 1, day 4 ,GM-CSF adjuvant

source_name: gene expression challenge 1, day 4


title: BP165_5231_C1_D0_B_Dg


title: BP165_5219_C12_D21_B_D

description: gene expression challenge 12, day 21 , no adjuvant

source_name: gene expression challenge 12, day 21


title: Mim8_24h_R_Midbrain

source_name: Right midbrain from brain Microcebus murinus  24h after CAV-2 infection, ipsilateral side


title: BP165_5219_W32_D0_B_D

description: gene expression week 32, day 0 , no adjuvant


title: BP165_5222_W16_D1_B_Dg

description: gene expression week 16, day 1 ,GM-CSF adjuvant

source_name: gene expression week 16, day 1


title: mRNA_ded1-cs(hcDBP1)_ replicate 1_15 deg

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 CENTER DR Room 230, MSC 0609

institute: NICHD

description:
mRNA
Experiment 2
ded1cs_hcDBP1_15deg.csv

library_source: transcriptomic

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with Bowtie2-2.6.0
Transcriptome alignment with TopHat v2.1.0
Read quantitation using custom scripts
Analysis of reads using DESeq2
Genome_build: sacCer2
Supplementary_files_format_and_content: processed  txt (csv) files per experiment show a matrix (with columns: yORF name, gene name, WT ribosome occupancy, mutant ribosome occupancy, WT mRNA occupancy, mutant mRNA occupancy, ribosome occupancy change, mRNA occupancy change, TE change). All numerical columns have log values with base 2

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD600 of ~  0.7 in SC medium (maintaining selection for plasmids as needed) and subjected to temperature shifts as indicated

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in a freezer mill.
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223

treatment_protocol: All cultures were treated  with cycloheximide (100 ug / ml) for 2 min prior to harvesting

tag: strain (genetic background)

value: ded1-cs_hcDBP1 (NSY56)


title: BP165_5219_W32_D3_B_D


title: BP165_5237_W0_D3_B_D


title: BP165_5418_W16_D0_B_CTRL

description: gene expression week 16, day 0 , control group


title: Mim7_24h_R_Midbrain


title: Mim6_24h_R_Midbrain


title: BP165_5231_W0_D1_B_Dg

description: gene expression week 0, day 1 ,GM-CSF adjuvant

source_name: gene expression week 0, day 1


title: BP165_5231_W1_D7_B_Dg

description: gene expression week 1, day 7 ,GM-CSF adjuvant

source_name: gene expression week 1, day 7


title: Mim3_Ctrl_Midbrain

description: Non-human primate midbrain

source_name: Control, midbrain from brain Microcebus murinus

value: no infection


title: Mim2_Ctrl_Midbrain

description: Non-human primate midbrain


title: BP165_5222_W1_D7_B_Dg


title: BP165_5219_W16_D3_B_D

description: gene expression week 16, day 3 , no adjuvant


title: BP165_4817_C1_D4_B_CTRL_2

description: gene expression challenge 1, day 4 , control group


title: BP165_5237_W32_D1_B_D

description: gene expression week 32, day 1 , no adjuvant

source_name: gene expression week 32, day 1


title: BP165_5219_W32_D1_B_D


title: Mim10_28d_L_FCx

description: Gene expression changes induced by CAV-2 in primate frontal cortex, 28 days after infection

source_name: Left frontal cortex from brain Microcebus murinus 28 days after CAV-2 infection, contralateral side

value: Contralateral infection

value: Frontal Cortex (FC)


title: BP165_5208_W32_D3_B_Dg_2

description: gene expression week 32, day 3 ,GM-CSF adjuvant


title: BP165_5418_W32_D3_B_CTRL

description: gene expression week 32, day 3 , control group


title: BP165_5219_C12_D0_B_D

description: gene expression challenge 12, day 0 , no adjuvant

source_name: gene expression challenge 12, day 0


title: BP165_5219_C12_D43_B_D

description: gene expression challenge 12, day 43 , no adjuvant

source_name: gene expression challenge 12, day 43


title: BP165_5237_W0_D1_B_D

description: gene expression week 0, day 1 , no adjuvant


title: Mim11_28d_L_FCx


title: BP165_5231_W-1_D0_B_Dg

description: gene expression week -1, day 0 ,GM-CSF adjuvant

source_name: gene expression week -1, day 0


title: BP165_5222_W32_D3_B_Dg


title: BP165_5222_C1_D1_B_Dg

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant

source_name: gene expression challenge 1, day 1


title: Mim9_28d_L_FCx


title: BP165_5222_W17_D7_B_Dg

description: gene expression week 17, day 7 ,GM-CSF adjuvant

source_name: gene expression week 17, day 7


title: BP165_5237_W17_D7_B_D

description: gene expression week 17, day 7 , no adjuvant


title: Mim12_28d_L_FCx

source_name: Leftfrontal cortex from brain Microcebus murinus 28 days after CAV-2 infection, contralateral side


title: BP165_5219_W0_D1_B_D


title: Mim12_28d_R_FCx

source_name: Right frontal cortex from brain Microcebus murinus 28 days after CAV-2 infection, ipsilateral side

value: Ipsilateral infection


title: BP165_5219_W17_D7_B_D

value: whole blood


title: Mim1_Ctrl_Midbrain

description: Non-human primate midbrain


title: BP165_5231_W32_D0_B_Dg

description: gene expression week 32, day 0 ,GM-CSF adjuvant

source_name: gene expression week 32, day 0


title: BP165_5233_W32_D0_B_D_2

description: gene expression week 32, day 0 , no adjuvant

value: no adjuvant


title: Mim10_28d_R_FCx


title: BP165_5237_W-1_D0_B_D

description: gene expression week -1, day 0 , no adjuvant


title: AB9_KDM2B. 4835-1

city: New York

first: Nicholas

middle: D.

last: Socci

state: NY

address: 1275 York Ave

department: bioinformatics core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (Bolger et al 2014). RNA-seq reads were then aligned to GRCh37.75(hg19) with STAR (Dobin et. al 2012) and genome-wide transcript counting was performed by HTSeq (Anders et al. 2015) to generate a matrix of raw counts. This matrix was then normalized with DESeq (R/Bioconductor)
Genome_build: hg19
Supplementary_files_format_and_content: TAB delimited TXT file matrix table of normalized counts (DESeq)

source_name: Human Synovial sarcoma cells (HS-SY-II)

growth_protocol: Genome-wide maps of chromatin-binding proteins and state in a human synovial sarcoma cell line in control cells (Ren. 713), and upon knocdown of SS18-SSX1. 1274) or of KDM2B (KDM2B. 4395).

extract_protocol:
Cells were lysed by adding RLT buffer directly to the culture dish. RNA was extracted using Rneasy Qiagen Kit.
RNA samples were used for Hi-Seq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. Samples are barcoded with TruSeq SBS Kit v3 (Illumina).

treatment_protocol: Human sarcoma cells were transduced with lentiviral vectors expressing an shRNA control (Ren.713) and shRNAs against SS18-SSX1 (SS18.273 and SSX.1274) or KDM2B (KDM2B. 4395 and KDM2B.4835). shRNA expression was induced with doxycyclin treatment and cells where collected 12 days later.

tag: hs-sy-ii parental or tagged

value: HS-SY-II parental line untagged

tag: condition/shrna


title: AB8_KDM2B. 4395-2


title: AB7_KDM2B. 4395-1


title: AB6_SSX.1274-2


title: Mim11_28d_R_FCx

value: female


title: BP165_5219_W16_D0_B_D

description: gene expression week 16, day 0 , no adjuvant

source_name: gene expression week 16, day 0

value: Late acquisition


title: AB4_SS18. 273-2


title: BP165_5237_W16_D1_B_D

description: gene expression week 16, day 1 , no adjuvant

source_name: gene expression week 16, day 1


title: BP165_5222_W16_D3_B_Dg

description: gene expression week 16, day 3 ,GM-CSF adjuvant

source_name: gene expression week 16, day 3


title: BP165_5222_W0_D3_B_Dg

description: gene expression week 0, day 3 ,GM-CSF adjuvant

source_name: gene expression week 0, day 3


title: BP165_5231_W32_D1_B_Dg

description: gene expression week 32, day 1 ,GM-CSF adjuvant


title: BP165_5237_W16_D3_B_D

description: gene expression week 16, day 3 , no adjuvant


title: BP165_5219_C1_D4_B_D

description: gene expression challenge 1, day 4 , no adjuvant

source_name: gene expression challenge 1, day 4


title: BP165_5222_W0_D1_B_Dg

description: gene expression week 0, day 1 ,GM-CSF adjuvant

source_name: gene expression week 0, day 1


title: Mim5_24h_R_Midbrain

description: Gene expression changes induced by CAV-2 in primate midbrain, 24h after infection

source_name: Right midbrain from brain Microcebus murinus  24h after CAV-2 infection, ipsilateral side

value: 2 year old


title: Mim7_24h_L_FCx

description: Gene expression changes induced by CAV-2 in primate frontal cortex, 24h after infection

source_name: Left frontal cortex from brain Microcebus murinus 24h after CAV-2 infection, contralateral side


title: BP165_5224_W16_D0_B_D_B

value: Not infected


title: Mim9_28d_R_FCx

description: Gene expression changes induced by CAV-2 in primate frontal cortex, 28 days after infection


title: AB3_SS18. 273-1


title: BP165_5214_C1_D4_B_Dg_B

description: gene expression challenge 1, day 4 ,GM-CSF adjuvant


title: BP165_5231_C1_D4_B_Dg


title: AB5_SSX.1274-1


title: Mim8_24h_L_FCx


title: BP165_5224_W32_D1_B_D_B

description: gene expression week 32, day 1 , no adjuvant

source_name: gene expression week 32, day 1


title: Mim6_24h_L_FCx


title: BP165_5218_W32_D3_B_Dg_B

description: gene expression week 32, day 3 ,GM-CSF adjuvant

source_name: gene expression week 32, day 3


title: Mim6_24h_R_FCx

source_name: Right frontal cortex from brain Microcebus murinus  24h after CAV-2 infection, ipsilateral side


title: BP165_5218_W32_D1_B_Dg_B


title: BP165_5233_C1_D1_B_D_B

description: gene expression challenge 1, day 1 , no adjuvant

source_name: gene expression challenge 1, day 1


title: BP165_5218_C3_D0_B_Dg_B

description: gene expression challenge 3, day 0 ,GM-CSF adjuvant

source_name: gene expression challenge 3, day 0


title: Mim5_24h_L_FCx


title: Mim8_24h_R_FCx


title: Mim7_24h_R_FCx


title: AB2_Ren. 713-2


title: AB10_KDM2B. 4835-2


title: AB3_KDM2B.4395_ATAC-Seq

data_processing:
Raw reads were trimmed for quality and Illumina adapter sequences using ‘trim_galore’ (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Reads were aligned to the human genome assembly hg19 using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2) with the default parameters.
To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using the Picard tool MarkDuplicates (http://broadinstitute.github.io/picard/).
For further analyses, HOMER suit of tools was used (Heinz et al., 2010). Please see STAR methods for more details.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, normalized density tracks

growth_protocol: ATAC-seq profiling of a human synovial sarcoma cell line in control cells (Ren. 713), and upon knocdown of SS18-SSX1 (SSX.1274) or of KDM2B (KDM2B. 4395).

extract_protocol:
ATAC-Seq was performed as previously described (Buenrostro et al., 2013). Fifty thousand GFP positive cells were sorted by fluorescence-activated cell sorting (FACS). Cells were lysed in lysis buffer (10mM Tris, pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% (v/v) IGEPAL) and centrifuged for 10 min (500 x g) to isolate the nuclear fraction. The transposition reaction was performed for 30 minutes at 37oC using the Tn5 Transposase kit from Nextera accordingly to the manufacture’s instructions.
Transposed DNA fragments were amplified by PCR using barcoded primers and the NEBNext High Fidelity 2X master mix (12 PCR cycles). Amplified libraries were purified using Qiagen MinElute. Samples were pooled to have a minimum of 50-60 million reads (3-4 per lane)

treatment_protocol: Human sarcoma cells were transduced with lentiviral vectors expressing an shRNA control (Ren.713) and shRNAs against SS18-SSX1. (SSX.1274) or KDM2B (KDM2B. 4395). shRNA expression was induced with doxycyclin treatment and cells where collected 12 days later.


title: BP165_5224_W16_D1_B_D_B


title: AB1_Ren. 713-1


title: AB2_SSX.1274_ATAC-Seq


title: BP165_5233_W-1_D0_B_D_B

description: gene expression week -1, day 0 , no adjuvant

source_name: gene expression week -1, day 0


title: AB1_Ren. 713_ATAC-Seq


title: BP165_5235_C1_D4_B_CTRL_B

description: gene expression challenge 1, day 4 , control group

value: control group


title: Mim5_24h_R_FCx


title: AB9_REN. 713_BRG1

description:
ChIP-Seq_ AB9
AB9-59-REN-BRG1-IP-TS25-A11_ACTGAT_BH5HNHBCXY_L001_001

data_processing:
Raw reads were trimmed for quality and Illumina adapter sequences using ‘trim_galore’ (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Reads were aligned to the human genome assembly hg19 using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2) with the default parameters.
To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using the Picard tool MarkDuplicates (http://broadinstitute.github.io/picard/).
For further analyses, HOMER suit of tools was used (Heinz et al., 2010). Aligned bam files were subjected to peak calling using findPeaks tools with the default setting, except -style histone was implemented to find for broad regions of H3K27me3 peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, normalized density tracks

source_name: HA tagged HS-SY-II cell line

growth_protocol: Genome-wide maps of chromatin-binding proteins and state (H3K27me3) in a human synovial sarcoma cell line in control cells (Ren. 713), and upon knockdown of SS18-SSX1 (SSX.1274) or of KDM2B (KDM2B. 4395).

extract_protocol:
For HA-tag, BRG1 and KDM2B ChIP 60-100 million cells were collected, pre-fixed with ethylene glycol bis(succinimidyl succinate) (EGS) for 30 min, and crosllinked with 1% formaldehyde for 15 min. For H3K27me3 ChIP about 10-20 million cells were crosslinkined with 1% formaldehyde for 15 min.
Libraries were constructed using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina accordingly with manufactor instructions.  6-10 samples were pooled per sequencing lane in order to generate 20-40 million reads per sample

treatment_protocol: Human sarcoma cells were transduced with lentiviral vectors expressing a control shRNA (Ren.713) and shRNAs against SS18-SSX1 (SSX.1274) or KDM2B (KDM2B. 4395). shRNA expression was induced with doxycyclin treatment and cells where collected 12 days later.

tag: cell line/type

value: Human Synovial sarcoma cells (HS-SY-II)

tag: genotype/variation

value: HA tagged HS-SY-II cell line

value: BRG1 (Abcam, Ab110641)


title: Mim3_Ctrl_FCx

description: Non-human primate frontal cortex

source_name: Control, frontal cortex from brain Microcebus murinus


title: BP165_5214_C1_D0_B_Dg_B

description: gene expression challenge 1, day 0 ,GM-CSF adjuvant

source_name: gene expression challenge 1, day 0

value: GM-CSF adjuvant

value: Early acquisition


title: BP165_5224_W32_D3_B_D_B

description: gene expression week 32, day 3 , no adjuvant


title: BP165_5224_C12_D0_B_D_B

description: gene expression challenge 12, day 0 , no adjuvant

source_name: gene expression challenge 12, day 0


title: BP165_5214_W16_D1_B_Dg_B

description: gene expression week 16, day 1 ,GM-CSF adjuvant

source_name: gene expression week 16, day 1


title: BP165_5214_W32_D3_B_Dg_B


title: BP165_5218_C1_D1_B_Dg_B

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant


title: Mim2_Ctrl_FCx

description: Non-human primate frontal cortex

value: no infection


title: BP165_5233_W1_D7_B_D_B

description: gene expression week 1, day 7 , no adjuvant

source_name: gene expression week 1, day 7


title: BP165_5218_C12_D0_B_Dg_B

description: gene expression challenge 12, day 0 ,GM-CSF adjuvant


title: BP165_5233_W16_D3_B_D_B

description: gene expression week 16, day 3 , no adjuvant

source_name: gene expression week 16, day 3


title: Mim4_Ctrl_FCx

description: Non-human primate frontal cortex


title: AB8_KDM2B. 4395_INPUT

description:
ChIP-Seq_ AB8
AB8-594395INPUT-TS8-A10_ACTTGA_AH5J35BCXY_L001_001

value: INPUT for HA ChIP


title: AB7_SSX. 1274_HA-INPUT

description:
ChIP-Seq_ AB7
AB7-591274INPUT-TS7-A10_CAGATC_AH5J35BCXY_L001_001


title: Mim1_Ctrl_FCx

description: Non-human primate frontal cortex

value: Frontal Cortex (FC)


title: AB6_REN. 713_INPUT

description:
ChIP-Seq_ AB6
AB6-59RENINPUT-TS6-A10_GCCAAT_AH5J35BCXY_L001_001


title: BP165_5233_W16_D0_B_D_B

description: gene expression week 16, day 0 , no adjuvant

source_name: gene expression week 16, day 0


title: BP165_5214_W-1_D0_B_Dg_B

description: gene expression week -1, day 0 ,GM-CSF adjuvant


title: BP165_5218_W0_D3_B_Dg_B

description: gene expression week 0, day 3 ,GM-CSF adjuvant

source_name: gene expression week 0, day 3


title: Mim12_28d_L_Str

description: Gene expression changes induced by CAV-2 in primate striatum, 28 days after infection

source_name: Left striatum from brain Microcebus murinus 28 days after CAV-2 infection, contralateral side

value: Contralateral infection

value: Striatum


title: AB4_KDM2B. 4395_HA-tag (SS18-SSX)

description:
ChIP-Seq_ AB4
AB4-594395HAIP-TS4-A10_TGACCA_AH5J35BCXY_L001_001

value: HA-tag (Abcam, ab9110)


title: AB3_SSX. 1274_HA-tag (SS18-SSX)

description:
ChIP-Seq_ AB3
AB3-591274HAIP-TS3-A10_TTAGGC_AH5J35BCXY_L001_001


title: Mim10_28d_L_Str


title: BP165_5224_W32_D0_B_D_B

description: gene expression week 32, day 0 , no adjuvant

source_name: gene expression week 32, day 0

value: whole blood

value: no adjuvant


title: BP165_5224_C3_D0_B_D_B

description: gene expression challenge 3, day 0 , no adjuvant


title: BP165_5224_C12_D15_B_D_B

description: gene expression challenge 12, day 15 , no adjuvant

source_name: gene expression challenge 12, day 15


title: Mim11_28d_L_Str

value: female


title: BP165_5214_W0_D3_B_Dg_B


title: AB5_HS-SY-II parental line untagged_INPUT

description:
ChIP-Seq_ AB5
AB5-HSSINPUT-TS5-A10_ACAGTG_AH5J35BCXY_L001_001

source_name: HS-SY-II parental line untagged

value: HS-SY-II parental line untagged

value: no shRNA


title: Mim11_28d_R_Str

source_name: Right striatum from brain Microcebus murinus 28 days after CAV-2 infection, ipsilateral side

value: 2 year old

value: Ipsilateral infection


title: AB27_KDM2B. 4395_INPUT for BRG1 and KDM2B

description:
ChIP-Seq_ AB27
AB27_4395INPUT-TS14-A10_AGTTCC_AH5J35BCXY_L002_001

value: Human Synovial sarcoma cells (HS-SY-II)

value: INPUT for BRG1 and KDM2B ChIP


title: BP165_5224_C2_D0_B_D_B

description: gene expression challenge 2, day 0 , no adjuvant

source_name: gene expression challenge 2, day 0

value: Not infected


title: BP165_5218_W32_D0_B_Dg_B

description: gene expression week 32, day 0 ,GM-CSF adjuvant

value: GM-CSF adjuvant

value: Late acquisition


title: BP165_5224_W0_D1_B_D_B

description: gene expression week 0, day 1 , no adjuvant

source_name: gene expression week 0, day 1


title: BP165_5235_C1_D0_B_CTRL_B

description: gene expression challenge 1, day 0 , control group

value: control group

value: Early acquisition


title: BP165_5233_W32_D1_B_D_B

description: gene expression week 32, day 1 , no adjuvant

source_name: gene expression week 32, day 1


title: BP165_5224_C1_D0_B_D_B

description: gene expression challenge 1, day 0 , no adjuvant


title: BP165_5235_W32_D3_B_CTRL_B

description: gene expression week 32, day 3 , control group

source_name: gene expression week 32, day 3


title: Mim8_24h_L_Str

description: Gene expression changes induced by CAV-2 in primate striatum, 24h after infection

source_name: Left striatum from brain Microcebus murinus 24h after CAV-2 infection, contralateral side

value: Contralateral infection


title: Mim9_28d_R_Str

value: Striatum


title: AB26_SSX. 1274_HA-INPUT for BRG1 and KDM2B

description:
ChIP-Seq_ AB26
AB26_HSS1274INPUT-TS13-A10_AGTCAA_AH5J35BCXY_L002_001


title: AB25_REN. 713_INPUT for BRG1 and KDM2B

description:
ChIP-Seq_ AB25
AB25_HSSRENINPUT-TS12-A10_CTTGTA_AH5J35BCXY_L002_001


title: BP165_5224_W17_D7_B_D_B

description: gene expression week 17, day 7 , no adjuvant

source_name: gene expression week 17, day 7


title: Mim12_28d_R_Str

description: Gene expression changes induced by CAV-2 in primate striatum, 28 days after infection


title: Mim10_28d_R_Str


title: BP165_5233_W17_D7_B_D_B


title: BP165_5218_W0_D1_B_Dg_B

description: gene expression week 0, day 1 ,GM-CSF adjuvant


title: AB24_KDM2B. 4395_BRG1

description:
ChIP-Seq_ AB24
AB24-_HSS_4395_KDM2B-TS8-A12_IGO_08030_6_S1

value: KDM2B (Millipore_09-864)


title: AB23_SSX. 1274_BRG1

description:
ChIP-Seq_ AB23
AB23-_HSS_1274_KDM2B-TS7-A12_IGO_08030_5_S9


title: Mim9_28d_L_Str


title: AB22_REN. 713_BRG1

description:
ChIP-Seq_ AB22
AB22-_HSS_REN_KDM2B-TS13-A12_IGO_08030_4_S3


title: Mim7_24h_L_Str


title: BP165_5235_W16_D3_B_CTRL_B

description: gene expression week 16, day 3 , control group

value: whole blood


title: BP165_5214_W32_D1_B_Dg_B

description: gene expression week 32, day 1 ,GM-CSF adjuvant


title: Mim5_24h_L_Str


title: AB21_KDM2B. 4395_BRG1

description:
ChIP-Seq_ AB21
AB21-_HSS_4395_BRG1-TS5-A12_IGO_08030_3_S8

value: BRG1 (Abcam, Ab110641)


title: Mim6_24h_L_Str

value: female


title: BP165_5235_C1_D1_B_CTRL_B

description: gene expression challenge 1, day 1 , control group

source_name: gene expression challenge 1, day 1


title: BP165_5214_W16_D3_B_Dg_B

description: gene expression week 16, day 3 ,GM-CSF adjuvant


title: Mim8_24h_R_Str

source_name: Right striatum from brain Microcebus murinus  24h after CAV-2 infection, ipsilateral side


title: BP165_5214_C1_D1_B_Dg_B

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant


title: BP165_5218_W16_D0_B_Dg_B

description: gene expression week 16, day 0 ,GM-CSF adjuvant


title: BP165_5218_C12_D20_B_Dg_B

description: gene expression challenge 12, day 20 ,GM-CSF adjuvant

source_name: gene expression challenge 12, day 20


title: BP165_5233_C1_D4_B_D_B

description: gene expression challenge 1, day 4 , no adjuvant

source_name: gene expression challenge 1, day 4

value: no adjuvant


title: AB2_REN. 713_HA-tag (SS18-SSX)

description:
ChIP-Seq_ AB2
AB2-59RENHAIP-TS2-A10_CGATGT_AH5J35BCXY_L001_001

source_name: HA tagged HS-SY-II cell line

value: HA tagged HS-SY-II cell line

value: HA-tag (Abcam, ab9110)


title: Mim7_24h_R_Str

description: Gene expression changes induced by CAV-2 in primate striatum, 24h after infection

value: 2 year old

value: Ipsilateral infection


title: BP165_5218_W1_D7_B_Dg_B

description: gene expression week 1, day 7 ,GM-CSF adjuvant

source_name: gene expression week 1, day 7


title: BP165_5214_W0_D1_B_Dg_B


title: BP165_5224_C1_D4_B_D_B


title: BP165_5224_C1_D1_B_D_B

description: gene expression challenge 1, day 1 , no adjuvant


title: Mim6_24h_R_Str


title: Mim5_24h_R_Str


title: BP165_5214_W32_D0_B_Dg_B

description: gene expression week 32, day 0 ,GM-CSF adjuvant


title: AB20_SSX. 1274_BRG1

description:
ChIP-Seq_ AB20
AB20-_HSS_1274_BRG1-TS3-A12_IGO_08030_2_S7

value: Human Synovial sarcoma cells (HS-SY-II)

value: HS-SY-II parental line untagged


title: AB17_SSX. 1274_HA-INPUT for K27me3

description:
ChIP-Seq_ AB17
AB17_Input-ab3-TS9-A13_GATCAG_AC7PEUANXX_L001_001

value: INPUT for H3K27me3 ChIP


title: BP165_5235_W32_D0_B_CTRL_B

description: gene expression week 32, day 0 , control group


title: BP165_5218_C1_D4_B_Dg_B

description: gene expression challenge 1, day 4 ,GM-CSF adjuvant

value: GM-CSF adjuvant

value: Late acquisition


title: AB18_KDM2B. 4395_INPUT for K27me3

description:
ChIP-Seq_ AB18
AB18_Input-ab4-TS10-A13_TAGCTT_AC7PEUANXX_L001_001


title: BP165_5214_W1_D7_B_Dg_B

value: Early acquisition


title: AB19_REN. 713_BRG1

description:
ChIP-Seq_ AB19
AB19-_HSS_REN_BRG1_-TS2-A12_IGO_08030_1_S6


title: AB16_REN. 713_INPUT for K27me3

description:
ChIP-Seq_ AB16
AB16_Input-ab1-TS8-A13_ACTTGA_AC7PEUANXX_L001_001


title: Mim4_Ctrl_Str

description: Non-human primate striatum

source_name: Control, striatum from brain Microcebus murinus

value: no infection


title: Mim3_Ctrl_Str

description: Non-human primate striatum

value: Striatum


title: BP165_5233_W16_D1_B_D_B

description: gene expression week 16, day 1 , no adjuvant

source_name: gene expression week 16, day 1


title: AB15_KDM2B. 4395_H3K27me3

description:
ChIP-Seq_ AB15
AB15_K27me3-ab4-TS4-A13_TGACCA_AC7PEUANXX_L004_001

value: H3K27me3 (Cell Signaling, 9733)


title: BP165_5235_W16_D0_B_CTRL_B

description: gene expression week 16, day 0 , control group

source_name: gene expression week 16, day 0

value: whole blood

value: control group


title: BP165_5214_W16_D0_B_Dg_B

description: gene expression week 16, day 0 ,GM-CSF adjuvant


title: Mim1_Ctrl_Str

description: Non-human primate striatum

value: female


title: AB14_SSX. 1274_H3K27me3

description:
ChIP-Seq_ AB14
AB14_K27me3-ab3-TS3-A13_TTAGGC_AC7PEUANXX_L004_001

source_name: HS-SY-II parental line untagged


title: BP165_5224_W16_D3_B_D_B

description: gene expression week 16, day 3 , no adjuvant

source_name: gene expression week 16, day 3

value: no adjuvant

value: Not infected


title: BP165_5218_W-1_D0_B_Dg_B

description: gene expression week -1, day 0 ,GM-CSF adjuvant

source_name: gene expression week -1, day 0


title: BP165_5235_W17_D7_B_CTRL_B

description: gene expression week 17, day 7 , control group


title: AB12_REN. 713_INPUT for KDM2B

description:
ChIP-Seq_ AB12
AB12-59RENINPUT-TS16-A10_CCGTCC_AH5J35BCXY_L002_001

value: HA tagged HS-SY-II cell line

value: INPUT for KDM2B ChIP


title: AB13_REN. 713_H3K27me3

description:
ChIP-Seq_ AB13
AB13_K27me3-ab1-TS2-A13_CGATGT_AC7PEUANXX_L004_001


title: BP165_5233_W0_D3_B_D_B

description: gene expression week 0, day 3 , no adjuvant

source_name: gene expression week 0, day 3


title: Mim2_Ctrl_Str

description: Non-human primate striatum

value: 2 year old


title: BP165_5235_W16_D1_B_CTRL_B

description: gene expression week 16, day 1 , control group


title: Huh75a

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8) of cRNA hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

source_name: hepatoma cell line

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

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

tag: cell line

value: not transfected


title: BP165_5214_W17_D7_B_Dg_B

description: gene expression week 17, day 7 ,GM-CSF adjuvant


title: BP165_5218_W16_D3_B_Dg_B

description: gene expression week 16, day 3 ,GM-CSF adjuvant


title: BP165_5224_W-1_D0_B_D_B

description: gene expression week -1, day 0 , no adjuvant


title: BP165_5224_W1_D7_B_D_2

description: gene expression week 1, day 7 , no adjuvant


title: AB11_REN. 713_KDM2B

description:
ChIP-Seq_ AB11
AB11-59RENKDM2BIP-TS15-A10_ATGTCA_AH5J35BCXY_L002_001

value: Human Synovial sarcoma cells (HS-SY-II)

value: KDM2B (Millipore_09-864)


title: Huh75b


title: AB10_REN. 713_INPUT for BRG1

description:
ChIP-Seq_ AB10
AB10-59-REN-INPUT-TS27-A11_ATTCCT_BH5HNHBCXY_L001_001

value: INPUT for BRG1 ChIP


title: HepG2b


title: BP165_5222_W32_D0_B_Dg_B

description: gene expression week 32, day 0 ,GM-CSF adjuvant

source_name: gene expression week 32, day 0

value: GM-CSF adjuvant

value: Late acquisition


title: AB1_HS-SY-II parental line untagged_HA-Tag

description:
ChIP-Seq_ AB1
AB1-HSSHAIP-TS1-A10_ATCACG_AH5J35BCXY_L001_001

value: HS-SY-II parental line untagged

value: no shRNA

value: HA-tag (Abcam, ab9110)


title: BP165_5218_W17_D7_B_Dg_B

value: whole blood


title: BP165_5237_W16_D0_B_D_B

description: gene expression week 16, day 0 , no adjuvant

value: Early acquisition


title: BP165_5233_W32_D3_B_D_B

description: gene expression week 32, day 3 , no adjuvant

source_name: gene expression week 32, day 3


title: BP165_5224_W0_D3_B_D_B


title: BP165_5218_C2_D0_B_Dg_B

description: gene expression challenge 2, day 0 ,GM-CSF adjuvant

source_name: gene expression challenge 2, day 0


title: HepG2a


title: BP165_5233_C1_D0_B_D_B

description: gene expression challenge 1, day 0 , no adjuvant

source_name: gene expression challenge 1, day 0


title: BP165_5233_W0_D1_B_D_B

description: gene expression week 0, day 1 , no adjuvant

source_name: gene expression week 0, day 1


title: patient 233 with HCV-associated HCC: 103-HCC-C-zE

source_name: OLT or partial hepatectomy for HCV-associated HCC

growth_protocol: not applicable

treatment_protocol: not applicable

tag: case

tag: Sex

value: M

value: non tumor

tag: liver area

value: E


title: patient 233 with HCV-associated HCC: 101-HCC-C-zE

tag: tissue


title: patient 233 with HCV-associated HCC: 100-HCC-C-zE


title: patient 233 with HCV-associated HCC: 102-HCC-C-zE


title: BP165_5218_C1_D0_B_Dg_B

description: gene expression challenge 1, day 0 ,GM-CSF adjuvant

tag: vaccine treatment


title: patient 233 with HCV-associated HCC: 99-HCC-C-zD

value: D


title: BP165_5202_W16_D1_B_D_2

description: gene expression week 16, day 1 , no adjuvant

value: no adjuvant

tag: siv acquirers


title: patient 233 with HCV-associated HCC: 98-HCC-C-zD


title: BP165_4808_W32_D1_B_Dg_2

description: gene expression week 32, day 1 ,GM-CSF adjuvant

source_name: gene expression week 32, day 1


title: BP165_5216_W16_D1_B_Dg_2

description: gene expression week 16, day 1 ,GM-CSF adjuvant


title: BP165_5208_W16_D1_B_Dg_2


title: BP165_5215_W16_D1_B_D_2


title: BP165_5235_W32_D1_B_CTRL_2

description: gene expression week 32, day 1 , control group

value: control group


title: BP165_5218_W16_D1_B_Dg_2


title: BP165_5222_W16_D1_B_Dg_2


title: BP165_5237_W16_D1_B_D_2


title: BP165_5214_W32_D1_B_Dg_2


title: patient 233 with HCV-associated HCC: 95-HCC-C-zC

value: C


title: patient 233 with HCV-associated HCC: 97-HCC-C-zD


title: BP165_5237_W16_D0_B_D_2


title: BP165_5231_W16_D1_B_Dg_2


title: BP165_5219_W0_D3_B_D_2

description: gene expression week 0, day 3 , no adjuvant


title: BP165_5231_W32_D1_B_Dg_2


title: BP165_5219_W-1_D0_B_D_2

description: gene expression week -1, day 0 , no adjuvant


title: patient 233 with HCV-associated HCC: 92-HCC-C-zC


title: patient 233 with HCV-associated HCC: 96-HCC-C-zD


title: patient 233 with HCV-associated HCC: 93-HCC-C-zC


title: patient 233 with HCV-associated HCC: 91-HCC-C-zB

value: tumor

value: B


title: patient 233 with HCV-associated HCC: 90-HCC-C-zB


title: patient 233 with HCV-associated HCC: 94-HCC-C-zC


title: patient 233 with HCV-associated HCC: 88-HCC-C-zB


title: BP165_5239_C12_D15_B_Dg_B

description: gene expression challenge 12, day 15 ,GM-CSF adjuvant

source_name: gene expression challenge 12, day 15

value: Not infected


title: BP165_5230_W17_D7_B_D

description: gene expression week 17, day 7 , no adjuvant

source_name: gene expression week 17, day 7


title: BP165_5201_W16_D0_B_D


title: BP165_5220_W32_D1_B_Dg_B

value: GM-CSF adjuvant


title: BP165_5239_C2_D0_B_Dg_B


title: BP165_5202_W16_D0_B_D_B

value: Late acquisition


title: BP165_5198_C1_D4_B_D

description: gene expression challenge 1, day 4 , no adjuvant

source_name: gene expression challenge 1, day 4


title: patient 233 with HCV-associated HCC: 89-HCC-C-zB


title: BP165_5198_W16_D0_B_D


title: BP165_4808_W1_D7_B_Dg

description: gene expression week 1, day 7 ,GM-CSF adjuvant

source_name: gene expression week 1, day 7


title: patient 233 with HCV-associated HCC: 87-HCC-C-zA

value: A


title: BP165_4549_W16_D0_B_CTRL

description: gene expression week 16, day 0 , control group

source_name: gene expression week 16, day 0


title: BP165_5230_C3_D0_B_D

description: gene expression challenge 3, day 0 , no adjuvant

source_name: gene expression challenge 3, day 0


title: BP165_4808_C1_D1_B_Dg

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant

source_name: gene expression challenge 1, day 1


title: BP165_5230_C12_D28_B_D

description: gene expression challenge 12, day 28 , no adjuvant

source_name: gene expression challenge 12, day 28


title: BP165_5230_W-1_D0_B_D

source_name: gene expression week -1, day 0


title: BP165_4808_W16_D0_B_Dg

description: gene expression week 16, day 0 ,GM-CSF adjuvant


title: BP165_4808_W32_D3_B_Dg

description: gene expression week 32, day 3 ,GM-CSF adjuvant


title: patient 173 with HCV-associated HCC: 85-HCC-C-zD


title: patient 173 with HCV-associated HCC: 86-HCC-C-zD


title: BP165_4549_C1_D0_B_CTRL

description: gene expression challenge 1, day 0 , control group


title: BP165_5216_C1_D1_B_Dg


title: BP165_5230_W16_D3_B_D

description: gene expression week 16, day 3 , no adjuvant

source_name: gene expression week 16, day 3


title: BP165_5230_W16_D0_B_D

description: gene expression week 16, day 0 , no adjuvant


title: patient 173 with HCV-associated HCC: 83-HCC-C-zC


title: patient 173 with HCV-associated HCC: 82-HCC-C-zC


title: BP165_5198_C1_D0_B_D

description: gene expression challenge 1, day 0 , no adjuvant


title: BP165_5198_W16_D3_B_D


title: patient 173 with HCV-associated HCC: 80-HCC-C-zB


title: BP165_5201_W-1_D0_B_D


title: BP165_5216_C2_D0_B_Dg

description: gene expression challenge 2, day 0 ,GM-CSF adjuvant


title: patient 173 with HCV-associated HCC: 84-HCC-C-zD


title: BP165_5216_W16_D1_B_Dg

description: gene expression week 16, day 1 ,GM-CSF adjuvant

source_name: gene expression week 16, day 1


title: BP165_5201_W0_D3_B_D

description: gene expression week 0, day 3 , no adjuvant

source_name: gene expression week 0, day 3


title: BP165_4549_W16_D1_B_CTRL

description: gene expression week 16, day 1 , control group


title: patient 127 with HCV-associated HCC: 75-HCC-C-zE


title: BP165_5230_C1_D0_B_D


title: patient 173 with HCV-associated HCC: 81-HCC-C-zC


title: BP165_4808_W0_D3_B_Dg

description: gene expression week 0, day 3 ,GM-CSF adjuvant


title: patient 173 with HCV-associated HCC: 77-HCC-C-zB


title: BP165_5216_W0_D3_B_Dg


title: patient 127 with HCV-associated HCC: 74-HCC-C-zE


title: BP165_5216_W17_D7_B_Dg

description: gene expression week 17, day 7 ,GM-CSF adjuvant


title: patient 173 with HCV-associated HCC: 79-HCC-C-zB


title: patient 173 with HCV-associated HCC: 78-HCC-C-zB


title: BP165_4808_W17_D7_B_Dg


title: BP165_5198_W1_D7_B_D

description: gene expression week 1, day 7 , no adjuvant


title: patient 173 with HCV-associated HCC: 76-HCC-C-zA


title: BP165_5198_W32_D0_B_D

description: gene expression week 32, day 0 , no adjuvant

source_name: gene expression week 32, day 0


title: BP165_5216_W32_D1_B_Dg

description: gene expression week 32, day 1 ,GM-CSF adjuvant


title: BP165_4549_C1_D1_B_CTRL

description: gene expression challenge 1, day 1 , control group


title: BP165_5198_W-1_D0_B_D

description: gene expression week -1, day 0 , no adjuvant


title: patient 127 with HCV-associated HCC: 73-HCC-C-zE


title: BP165_4549_W32_D1_B_CTRL

description: gene expression week 32, day 1 , control group


title: BP165_5230_C12_D0_B_D

description: gene expression challenge 12, day 0 , no adjuvant

source_name: gene expression challenge 12, day 0


title: BP165_5198_W16_D1_B_D

description: gene expression week 16, day 1 , no adjuvant


title: BP165_5216_W16_D3_B_Dg

description: gene expression week 16, day 3 ,GM-CSF adjuvant


title: patient 127 with HCV-associated HCC: 72-HCC-C-zD


title: patient 127 with HCV-associated HCC: 65-HCC-C-zB


title: BP165_4808_W16_D1_B_Dg


title: BP165_5201_W32_D0_B_D


title: patient 127 with HCV-associated HCC: 68-HCC-C-zC


title: patient 127 with HCV-associated HCC: 70-HCC-C-zD


title: BP165_5230_W0_D3_B_D


title: BP165_4549_W17_D7_B_CTRL

description: gene expression week 17, day 7 , control group


title: BP165_5198_W17_D7_B_D

description: gene expression week 17, day 7 , no adjuvant


title: BP165_5216_W-1_D0_B_Dg

description: gene expression week -1, day 0 ,GM-CSF adjuvant


title: patient 127 with HCV-associated HCC: 69-HCC-C-zC


title: patient 127 with HCV-associated HCC: 71-HCC-C-zD


title: BP165_5201_C1_D0_B_D

description: gene expression challenge 1, day 0 , no adjuvant

source_name: gene expression challenge 1, day 0


title: BP165_5201_C1_D4_B_D

description: gene expression challenge 1, day 4 , no adjuvant


title: BP165_5230_C1_D1_B_D

description: gene expression challenge 1, day 1 , no adjuvant


title: BP165_5230_W0_D1_B_D

description: gene expression week 0, day 1 , no adjuvant

source_name: gene expression week 0, day 1


title: patient 127 with HCV-associated HCC: 66-HCC-C-zB

source_name: OLT or partial hepatectomy for HCV-associated HCC


title: BP165_5198_W0_D1_B_D


title: BP165_5201_W32_D1_B_D

description: gene expression week 32, day 1 , no adjuvant

source_name: gene expression week 32, day 1


title: BP165_5216_W0_D1_B_Dg

description: gene expression week 0, day 1 ,GM-CSF adjuvant


title: patient 127 with HCV-associated HCC: 64-HCC-C-zB


title: patient 127 with HCV-associated HCC: 63-HCC-C-zB


title: BP165_5216_W1_D7_B_Dg

description: gene expression week 1, day 7 ,GM-CSF adjuvant


title: patient 127 with HCV-associated HCC: 62-HCC-C-zA


title: BP165_4808_W0_D1_B_Dg


title: BP165_5198_C1_D1_B_D


title: BP165_4808_W-1_D0_B_Dg


title: BP165_5216_C1_D4_B_Dg

description: gene expression challenge 1, day 4 ,GM-CSF adjuvant


title: patient 127 with HCV-associated HCC: 67-HCC-C-zC


title: BP165_4549_W32_D3_B_CTRL

description: gene expression week 32, day 3 , control group

source_name: gene expression week 32, day 3


title: patient 75 with HCV-associated HCC: 61-HCC-C-zE


title: BP165_4549_W32_D0_B_CTRL

description: gene expression week 32, day 0 , control group


title: BP165_5216_C3_D0_B_Dg

description: gene expression challenge 3, day 0 ,GM-CSF adjuvant


title: BP165_5230_W16_D1_B_D


title: BP165_5230_C12_D9_B_D

description: gene expression challenge 12, day 9 , no adjuvant

source_name: gene expression challenge 12, day 9


title: BP165_5216_W32_D3_B_Dg

description: gene expression week 32, day 3 ,GM-CSF adjuvant


title: patient 75 with HCV-associated HCC: 59-HCC-C-zD


title: patient 75 with HCV-associated HCC: 57-HCC-C-zC


title: patient 75 with HCV-associated HCC: 58-HCC-C-zD


title: BP165_5201_W16_D1_B_D

description: gene expression week 16, day 1 , no adjuvant


title: BP165_5216_W32_D0_B_Dg

description: gene expression week 32, day 0 ,GM-CSF adjuvant


title: BP165_4808_C1_D4_B_Dg

source_name: gene expression challenge 1, day 4


title: BP165_5198_W32_D3_B_D

description: gene expression week 32, day 3 , no adjuvant


title: BP165_4808_W16_D3_B_Dg

description: gene expression week 16, day 3 ,GM-CSF adjuvant


title: patient 75 with HCV-associated HCC: 55-HCC-C-zC


title: BP165_5201_C1_D1_B_D


title: BP165_5201_W0_D1_B_D


title: patient 75 with HCV-associated HCC: 54-HCC-C-zC


title: BP165_5230_C2_D0_B_D

description: gene expression challenge 2, day 0 , no adjuvant

source_name: gene expression challenge 2, day 0


title: BP165_5198_W32_D1_B_D


title: BP165_4808_C1_D0_B_Dg

description: gene expression challenge 1, day 0 ,GM-CSF adjuvant


title: BP165_4808_W32_D1_B_Dg

description: gene expression week 32, day 1 ,GM-CSF adjuvant


title: BP165_5201_W17_D7_B_D

description: gene expression week 17, day 7 , no adjuvant

source_name: gene expression week 17, day 7


title: BP165_5201_C2_D0_B_D


title: patient 70 with HCV-associated HCC: 53-HCC-C-zE

value: F


title: patient 75 with HCV-associated HCC: 56-HCC-C-zC


title: patient 70 with HCV-associated HCC: 52-HCC-C-zE


title: BP165_5216_W16_D0_B_Dg

description: gene expression week 16, day 0 ,GM-CSF adjuvant

source_name: gene expression week 16, day 0


title: BP165_5201_C3_D0_B_D

description: gene expression challenge 3, day 0 , no adjuvant

source_name: gene expression challenge 3, day 0


title: BP165_5201_W1_D7_B_D

description: gene expression week 1, day 7 , no adjuvant

source_name: gene expression week 1, day 7


title: patient 70 with HCV-associated HCC: 51-HCC-C-zD


title: BP165_5216_C1_D0_B_Dg


title: BP165_4549_W16_D3_B_CTRL

description: gene expression week 16, day 3 , control group

source_name: gene expression week 16, day 3


title: patient 70 with HCV-associated HCC: 49-HCC-C-zC


title: patient 70 with HCV-associated HCC: 48-HCC-C-zC


title: patient 70 with HCV-associated HCC: 50-HCC-C-zD


title: BP165_5230_C1_D4_B_D

description: gene expression challenge 1, day 4 , no adjuvant


title: patient 70 with HCV-associated HCC: 46-HCC-C-zA


title: BP165_4549_C1_D4_B_CTRL

description: gene expression challenge 1, day 4 , control group


title: BP165_5230_W32_D0_B_D

description: gene expression week 32, day 0 , no adjuvant


title: BP165_5201_W32_D3_B_D


title: BP165_5230_W32_D1_B_D

description: gene expression week 32, day 1 , no adjuvant


title: BP165_4808_W32_D0_B_Dg


title: BP165_5199_W16_D0_B_Dg


title: patient 67 with HCV-associated HCC: 45-HCC-C-zE


title: BP165_5230_W1_D7_B_D


title: BP165_4815_W16_D1_B_CTRL

description: gene expression week 16, day 1 , control group

source_name: gene expression week 16, day 1


title: BP165_5198_W0_D3_B_D_B

description: gene expression week 0, day 3 , no adjuvant

source_name: gene expression week 0, day 3


title: BP165_5202_W0_D3_B_D


title: patient 70 with HCV-associated HCC: 47-HCC-C-zB


title: BP165_5215_W17_D7_B_D


title: patient 67 with HCV-associated HCC: 44-HCC-C-zE


title: patient 67 with HCV-associated HCC: 42-HCC-C-zD


title: BP165_5220_W0_D3_B_Dg

description: gene expression week 0, day 3 ,GM-CSF adjuvant


title: BP165_5199_W32_D0_B_Dg

description: gene expression week 32, day 0 ,GM-CSF adjuvant

source_name: gene expression week 32, day 0


title: BP165_5220_W17_D7_B_Dg

description: gene expression week 17, day 7 ,GM-CSF adjuvant


title: patient 67 with HCV-associated HCC: 43-HCC-C-zE


title: patient 67 with HCV-associated HCC: 41-HCC-C-zD


title: BP165_5215_W16_D0_B_D

description: gene expression week 16, day 0 , no adjuvant


title: BP165_5220_W16_D0_B_Dg


title: BP165_5239_W16_D1_B_Dg

description: gene expression week 16, day 1 ,GM-CSF adjuvant


title: BP165_5202_C1_D0_B_D

description: gene expression challenge 1, day 0 , no adjuvant


title: patient 67 with HCV-associated HCC: 39-HCC-C-zD


title: patient 75 with HCV-associated HCC: 60-HCC-C-zE


title: BP165_5199_W17_D7_B_Dg


title: BP165_5199_W0_D3_B_Dg


title: patient 67 with HCV-associated HCC: 36-HCC-C-zC


title: BP165_5199_W32_D1_B_Dg

description: gene expression week 32, day 1 ,GM-CSF adjuvant


title: patient 67 with HCV-associated HCC: 35-HCC-C-zC


title: patient 67 with HCV-associated HCC: 40-HCC-C-zD


title: BP165_5239_W1_D7_B_Dg

description: gene expression week 1, day 7 ,GM-CSF adjuvant


title: patient 67 with HCV-associated HCC: 38-HCC-C-zC


title: BP165_4815_W32_D1_B_CTRL

description: gene expression week 32, day 1 , control group


title: BP165_5215_C1_D0_B_D


title: patient 67 with HCV-associated HCC: 37-HCC-C-zC


title: BP165_5239_W32_D1_B_Dg


title: BP165_5220_C1_D0_B_Dg

description: gene expression challenge 1, day 0 ,GM-CSF adjuvant


title: BP165_5202_C1_D1_B_D

description: gene expression challenge 1, day 1 , no adjuvant

source_name: gene expression challenge 1, day 1


title: BP165_5199_W-1_D0_B_Dg

description: gene expression week -1, day 0 ,GM-CSF adjuvant

source_name: gene expression week -1, day 0


title: BP165_5215_W0_D1_B_D

description: gene expression week 0, day 1 , no adjuvant

source_name: gene expression week 0, day 1


title: patient 67 with HCV-associated HCC: 34-HCC-C-zB

source_name: OLT or partial hepatectomy for HCV-associated HCC


title: BP165_5220_W1_D7_B_Dg


title: BP165_5230_W32_D3_B_D_B

description: gene expression week 32, day 3 , no adjuvant


title: BP165_4815_W32_D0_B_CTRL

description: gene expression week 32, day 0 , control group


title: BP165_4815_W16_D0_B_CTRL

description: gene expression week 16, day 0 , control group


title: BP165_5220_C2_D0_B_Dg

description: gene expression challenge 2, day 0 ,GM-CSF adjuvant


title: BP165_5202_W32_D1_B_D

description: gene expression week 32, day 1 , no adjuvant

source_name: gene expression week 32, day 1


title: BP165_5239_W-1_D0_B_Dg


title: patient 67 with HCV-associated HCC: 33-HCC-C-zB


title: BP165_5199_C1_D0_B_Dg

source_name: gene expression challenge 1, day 0


title: BP165_5199_W16_D1_B_Dg


title: BP165_5202_W17_D7_B_D

description: gene expression week 17, day 7 , no adjuvant


title: BP165_5215_C1_D1_B_D


title: BP165_5239_W32_D0_B_Dg

description: gene expression week 32, day 0 ,GM-CSF adjuvant


title: BP165_5199_W16_D3_B_Dg

description: gene expression week 16, day 3 ,GM-CSF adjuvant


title: patient 67 with HCV-associated HCC: 32-HCC-C-zB


title: patient 43 with HCV-associated HCC: 28-HCC-C-zB


title: BP165_5239_C1_D1_B_Dg

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant


title: BP165_5220_W32_D0_B_Dg


title: BP165_5202_W0_D1_B_D


title: patient 67 with HCV-associated HCC: 31-HCC-C-zB


title: BP165_5215_W-1_D0_B_D

description: gene expression week -1, day 0 , no adjuvant


title: BP165_5239_C12_D0_B_Dg

description: gene expression challenge 12, day 0 ,GM-CSF adjuvant

source_name: gene expression challenge 12, day 0


title: patient 67 with HCV-associated HCC: 30-HCC-C-zA


title: BP165_5199_W0_D1_B_Dg

description: gene expression week 0, day 1 ,GM-CSF adjuvant


title: BP165_5202_W32_D3_B_D

source_name: gene expression week 32, day 3


title: BP165_4815_C1_D4_B_CTRL

description: gene expression challenge 1, day 4 , control group

source_name: gene expression challenge 1, day 4


title: patient 43 with HCV-associated HCC: 29-HCC-C-zE


title: patient 43 with HCV-associated HCC: 26-HCC-C-zB


title: patient 43 with HCV-associated HCC: 25-HCC-C-zB


title: BP165_5215_W16_D3_B_D

description: gene expression week 16, day 3 , no adjuvant


title: patient 40 with HCV-associated HCC: 23-HCC-C-zE


title: patient 43 with HCV-associated HCC: 27-HCC-C-zB


title: BP165_4815_W32_D3_B_CTRL

description: gene expression week 32, day 3 , control group


title: BP165_5202_W32_D0_B_D

description: gene expression week 32, day 0 , no adjuvant


title: BP165_5202_C1_D4_B_D

description: gene expression challenge 1, day 4 , no adjuvant


title: BP165_5239_W16_D3_B_Dg


title: patient 43 with HCV-associated HCC: 24-HCC-C-zA


title: patient 40 with HCV-associated HCC: 22-HCC-C-zE


title: BP165_5220_W16_D3_B_Dg


title: patient 40 with HCV-associated HCC: 20-HCC-C-zE


title: BP165_4815_C1_D1_B_CTRL

description: gene expression challenge 1, day 1 , control group


title: patient 40 with HCV-associated HCC: 18-HCC-C-zE


title: BP165_5239_W16_D0_B_Dg

description: gene expression week 16, day 0 ,GM-CSF adjuvant


title: BP165_5215_W32_D0_B_D


title: patient 40 with HCV-associated HCC: 21-HCC-C-zE


title: BP165_5239_W17_D7_B_Dg

description: gene expression week 17, day 7 ,GM-CSF adjuvant

source_name: gene expression week 17, day 7


title: BP165_5220_W32_D3_B_Dg

description: gene expression week 32, day 3 ,GM-CSF adjuvant


title: BP165_5215_W16_D1_B_D

description: gene expression week 16, day 1 , no adjuvant


title: BP165_5202_W1_D7_B_D

description: gene expression week 1, day 7 , no adjuvant


title: BP165_5239_C1_D0_B_Dg

description: gene expression challenge 1, day 0 ,GM-CSF adjuvant


title: BP165_5220_W0_D1_B_Dg


title: BP165_5202_W-1_D0_B_D


title: patient 40 with HCV-associated HCC: 16-HCC-C-zE


title: BP165_5202_W16_D3_B_D


title: patient 40 with HCV-associated HCC: 17-HCC-C-zE


title: patient 40 with HCV-associated HCC: 19-HCC-C-zE


title: BP165_5202_W16_D1_B_D


title: BP165_5239_C1_D4_B_Dg

description: gene expression challenge 1, day 4 ,GM-CSF adjuvant


title: patient 40 with HCV-associated HCC: 15-HCC-C-zD


title: patient 40 with HCV-associated HCC: 14-HCC-C-zD


title: BP165_5220_W-1_D0_B_Dg

description: gene expression week -1, day 0 ,GM-CSF adjuvant


title: BP165_5220_W16_D1_B_Dg

description: gene expression week 16, day 1 ,GM-CSF adjuvant


title: patient 40 with HCV-associated HCC: 11-HCC-C-zC


title: BP165_5220_C1_D1_B_Dg

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant


title: BP165_5202_C2_D0_B_D

description: gene expression challenge 2, day 0 , no adjuvant

source_name: gene expression challenge 2, day 0


title: BP165_5202_C3_D0_B_D

description: gene expression challenge 3, day 0 , no adjuvant

source_name: gene expression challenge 3, day 0


title: patient 40 with HCV-associated HCC: 8-HCC-C-zB


title: BP165_5239_W0_D3_B_Dg

description: gene expression week 0, day 3 ,GM-CSF adjuvant


title: BP165_4815_W16_D3_B_CTRL

description: gene expression week 16, day 3 , control group


title: BP165_5220_C3_D0_B_Dg

description: gene expression challenge 3, day 0 ,GM-CSF adjuvant


title: BP165_5199_W1_D7_B_Dg

description: gene expression week 1, day 7 ,GM-CSF adjuvant

source_name: gene expression week 1, day 7


title: BP165_5215_W0_D3_B_D

description: gene expression week 0, day 3 , no adjuvant


title: patient 40 with HCV-associated HCC: 12-HCC-C-zD


title: BP165_5215_W1_D7_B_D


title: BP165_5215_C1_D4_B_D

description: gene expression challenge 1, day 4 , no adjuvant


title: BP165_5199_W32_D3_B_Dg


title: patient 40 with HCV-associated HCC: 7-HCC-C-zB


title: patient 40 with HCV-associated HCC: 10-HCC-C-zB


title: Library 2 Control [E. coli]

city: Würzburg

first: Thorsten

last: Bischler

address: Josef-Schneider-Straße 2 / D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

description: Campy Data.xlsx

data_processing:
Library strategy: DNA amplicon sequencing
Reads were processed by requiring an exact match 10nt upstream, and 30nt downstream, of the PAM region. If those were correct, the PAM was isolated and placed into a list.
Supplementary_files_format_and_content: Processed data forms are counts of each PAM isolated from the sequencing reads

organism: Escherichia coli K-12

source_name: Replicate 2

growth_protocol: Cells were grown in LB medium prior to, and after, cell sorting.

extract_protocol:
After sorting, cells were lysed with the Zymo (CN# D4036) and plasmid DNA containing PAMs was isolated
Library was constructed by amplifying the diverse PAM library with conserved oligos, followed by a seconnd indexing step adding the necessary Illumina adapters.

treatment_protocol: Treatment was performed by sorting cells based on GFP fluorescence.

tag: strain


title: BP165_5220_C1_D4_B_Dg


title: patient 40 with HCV-associated HCC: 13-HCC-C-zD

tag: age


title: Library 2 Sorted Cells [E. coli]

description: Campy Data.xlsx


title: Library 1 Sorted Cells [E. coli]

description: Campy Data.xlsx

source_name: Replicate 1


title: BP165_5239_W0_D1_B_Dg

description: gene expression week 0, day 1 ,GM-CSF adjuvant


title: BP165_4815_C1_D0_B_CTRL

description: gene expression challenge 1, day 0 , control group


title: BP165_5215_W32_D1_B_D

description: gene expression week 32, day 1 , no adjuvant


title: patient 40 with HCV-associated HCC: 9-HCC-C-zB


title: BP165_5239_W32_D3_B_Dg

description: gene expression week 32, day 3 ,GM-CSF adjuvant


title: patient 40 with HCV-associated HCC: 6-HCC-C-zB


title: KLRG1- Reporter+ OT-I cells (exp2)

city: Vienna

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

department: Institute of Cancer Research

country: Austria

institute: Medical University of Vienna

description:
S06615
processed data file: Matrix_table.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38/mm10 whole genome using TopHat2 version 2.0.8.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks version 2.1.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table.txt: Tab-delimited text file includes FPKM values of all six samples.

source_name: OT-I cell subset purified from spleen

extract_protocol:
OT-I cell subsets were isolated from spleen, purified by FACS and RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: wild type

value: Spleen

tag: cell type

value: KLRG1- Reporter+ OT-I cells

tag: treatment

value: Infection with ovalbumin-expressing Listeria monocytogenes (LM-OVA)

tag: day post-infection


title: KLRG1+ Reporter+ OT-I cells (exp2)

description:
S06614
processed data file: Matrix_table.txt

value: KLRG1+ Reporter+ OT-I cells


title: patient 40 with HCV-associated HCC: 4-HCC-C-zB

value: M


title: Library 1 Control [E. coli]

description: Campy Data.xlsx


title: BP165_5199_C1_D4_B_Dg

description: gene expression challenge 1, day 4 ,GM-CSF adjuvant

value: whole blood

value: Early acquisition


title: KLRG1- Reporter- OT-I cells (exp2)

description:
S06613
processed data file: Matrix_table.txt

value: KLRG1- Reporter- OT-I cells


title: patient 40 with HCV-associated HCC: 2-HCC-C-zA


title: BP165_5199_C1_D1_B_Dg

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant


title: patient 40 with HCV-associated HCC: 5-HCC-C-zB


title: 344057_D39SMCy5vsD39Cy3

city: Groningen

first: Tomas

last: Kloosterman

address: Nijenborgh 7

department: Natural Sciences

country: Netherlands

institute: University of Groningen

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman TG et al., 2006b

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix Pro software. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain and the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae

source_name: medium without uracil

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: Cells were grown to MID-log phase in CDM without uracil

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from Four replicate cultures.

tag: medium

value: without uracil


title: BP165_4815_W17_D7_B_CTRL

description: gene expression week 17, day 7 , control group

value: control group


title: BP165_5215_W32_D3_B_D

description: gene expression week 32, day 3 , no adjuvant

value: no adjuvant


title: BP165_5206_W32_D3_B_Dg


title: patient 40 with HCV-associated HCC: 3-HCC-C-zB

value: tumor

value: B


title: 344056_D39SMCy3vsD39Cy5

description: Sample 1


title: 344054_D39SMCy5vsD39Cy3

description: Sample 1

source_name: medium with uracil

growth_protocol: Cells were grown to MID-log phase in CDM with uracil

value: with uracil


title: 345432_D39Cy5vsD39PcpsT=>CCy3

description: Sample 2


title: KLRG1+ Reporter+ OT-I cells (exp1)

description:
S06611
processed data file: Matrix_table.txt


title: KLRG1- Reporter- OT-I cells (exp1)

description:
S06610
processed data file: Matrix_table.txt


title: KLRG1- Reporter+ OT-I cells (exp1)

description:
S06612
processed data file: Matrix_table.txt


title: 344055_D39SMCy3vsD39Cy5

description: Sample 2


title: WT-red2h

city: Shanghai

first: Zhenfei

last: Sun

address: Dongchuan Road 500

country: China

institute: Shanghai Jiaotong University

data_processing:
base-calling performed using HCS,RTA and OLB 1.9.4
Data were filtered by the following steps:   1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table)   2) Getting rid of reads with 5' primer contaminants   3) Getting rid of reads without 3' primer   4) Getting rid of reads without the insert tag   5) Getting rid of reads with poly A   6) Getting rid of reads shorter than 18nt
Map the small RNA tags to genome by SOAP2.20 to analyze their expression and distribution on the genome.   Program and Parameters:   soap -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap
Alignments to mirbase, Genbank, Rfam performed by blastn:  blastall -p blastn -F F -e 0.01
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: plants were grown in MS

extract_protocol:
Small RNAs were isolated using mirVana™miRNA Isolation Kit (Ambion, AM1561)
Small RNA libraries were prepared and sequenced by Illumina high-throughput sequencing
The small RNA reads were trimmed for adaptor sequence using Perl scripts and mapped to miRNA hairpin sequences downloaded from mirRBase version 15.0 using the Bowtie program

treatment_protocol: red light treatment for 2h and 8h

value: red light 2hr


title: Ath-TINFdeg

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

country: Spain

institute: Centro de Edafología y Biología Aplicada del Segura

description: 5' end signatures

data_processing:
Basecalls performed using CASAVA version 1.4
Adapters were trimmed using AdapterRemoval and small RNAs were filtered by length (16 to 21 nts) using in-house Perl scripts
Sequence signatures were collapsed using in-house Perl scripts
Supplementary_files_format_and_content: tab delimited files containing sequence signatures and counts per each sequence

source_name: Inflorescences

growth_protocol: Arabidopsis plants were grown in chambers at 22-24 ºC and with a 16h photoperiod

extract_protocol:
Total RNA was extracted using Trizol according to manufacturer’s instructions
Parallel analysis of RNA ends (PARE) libraries were done as described by German et al. , 2009.

treatment_protocol: Rossette leaves were rub inoculated with buffer or with a TRV-infected N. benthamiana extract

tag: ecotype

tag: agent

value: Tobacco rattle virus

value: 8 dpi


title: 345434_D39Cy3vsD39PcpsT=>CCy5

description: Sample 2

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences)


title: WT-red8h

value: red light 8h


title: WT-dark


title: 345429_D39PcpsT=>CCy3vsD39Cy5

description: Sample 1


title: BP165_5208_W32_D0_B_Dg

description: gene expression week 32, day 0 ,GM-CSF adjuvant

source_name: gene expression week 32, day 0

value: GM-CSF adjuvant


title: BP165_5229_W1_D7_B_D

description: gene expression week 1, day 7 , no adjuvant


title: BP165_5206_W-1_D0_B_Dg

description: gene expression week -1, day 0 ,GM-CSF adjuvant

source_name: gene expression week -1, day 0

value: Late acquisition


title: BP165_5206_W16_D0_B_Dg

description: gene expression week 16, day 0 ,GM-CSF adjuvant

source_name: gene expression week 16, day 0


title: BP165_5229_W32_D3_B_D


title: patient 40 with HCV-associated HCC: 1-HCC-C-zA

source_name: OLT or partial hepatectomy for HCV-associated HCC

value: A


title: Ath-TLEAFdeg

description: 5' end signatures

source_name: Leaves


title: BP165_5208_W0_D3_B_Dg

description: gene expression week 0, day 3 ,GM-CSF adjuvant

source_name: gene expression week 0, day 3


title: BP165_4817_W16_D0_B_CTRL

description: gene expression week 16, day 0 , control group


title: BP165_5206_C3_D0_B_Dg

description: gene expression challenge 3, day 0 ,GM-CSF adjuvant


title: BP165_5206_C1_D0_B_Dg

description: gene expression challenge 1, day 0 ,GM-CSF adjuvant

source_name: gene expression challenge 1, day 0


title: Ath-MLEAFdeg

description: 5' end signatures

value: Healthy, none


title: BP165_5228_W16_D3_B_D

description: gene expression week 16, day 3 , no adjuvant

source_name: gene expression week 16, day 3

value: whole blood


title: BP165_4817_W32_D0_B_CTRL

description: gene expression week 32, day 0 , control group

value: Early acquisition


title: BP165_5229_W-1_D0_B_D

description: gene expression week -1, day 0 , no adjuvant


title: 345431_D39PcpsT=>CCy5vsD39Cy3

description: Sample 1


title: BP165_5228_W0_D3_B_D

description: gene expression week 0, day 3 , no adjuvant


title: BP165_5208_W16_D1_B_Dg

description: gene expression week 16, day 1 ,GM-CSF adjuvant

source_name: gene expression week 16, day 1


title: BP165_5229_W32_D1_B_D

description: gene expression week 32, day 1 , no adjuvant

source_name: gene expression week 32, day 1


title: BP165_5228_W16_D0_B_D

description: gene expression week 16, day 0 , no adjuvant


title: BP165_5208_C1_D1_B_Dg

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant

source_name: gene expression challenge 1, day 1


title: BP165_4817_C1_D0_B_CTRL

description: gene expression challenge 1, day 0 , control group


title: U87MG cells with NeuroD2, biological rep2

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

description:
Gene Expression Data from U87MG cells transfected with NeuroD2 expression vector
NeuroD2_2

hyb_protocol: Hybridization was done for 16 hours at 45°C and 60 rpm using Affymetrix Hybridization Oven

scan_protocol: The gene chips were scanned using Affymetrix Gene chip scanner 3000 7G.

data_processing: The data was analyzed using GeneSpring software

source_name: Human U87MG cells transfected with NeuroD2 expression vector

label_protocol: Biotinlyated RNAs were prepared according to genechip 3' IVT  Express kit.

growth_protocol: U87MG cells were maintained in DMEM supplemented with 10% FBS, 5000 U/ml Penicillin and 5000μg/ml Streptomycin at 37°C with 5% carbon-dioxide and 0.2% oxygen.

extract_protocol: Total RNA was isolated using Qiagen RNeasy purification kit as per the manufacturer's instructions.

treatment_protocol: U87MG cells were transfected with NeuroD2-overexpression and control vector and total RNA was harvested post 48 hours transfection.

value: U87MG GBM cell line

tag: genotype/variation


title: HuCCT1-pCASC15-1

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

description: HuCCT1 cells transfected with pCASC15 - Replicate 1

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (V2) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 039494_D_F_20120411). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Features flagged in Feature Extraction as 'Feature not positive and significant' and 'Feature not above background' were excluded. Normalization was based on the 75th percentile shift.

source_name: HuCCT1 cells transfected with pCASC15

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions.

growth_protocol: HuCCT1 (RCB-1960) cholangiocarcinoma cell line was purchased at the RIKEN BioResource Center (Tsukuba-shi, Japan). Cells were grown in RPMI-1640 medium supplemented with 100U/ml penicillin, 100μg/ml streptomycin and 10% fetal bovine serum. Cells were cultured at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: DNA constructs (plasmids pCASC15-L and pControl) were kindly provided by Dr Kristina A. Cole (Children’s Hospital of Philadelphia, USA) and Dr Sumio Sugano (University of Tokyo, Japan). All constructs  were amplified by transformation of One Shot® TOP10 E. coli (Invitrogen) and validated by DNA sequencing after DNA purification (Nucleobond Xtra plasmid maxiprep kit, Macherey Nagel, Hoerdt, France). DNA transfection (2.5 µg of plasmid) was performed for 24hrs by using Lipofectamine 2000 according to manufacturer's instructions (Invitrogen).

tag: cell line

tag: transfection

value: CASC15 plasmid


title: HuCCT1-pCTRL-3

description: HuCCT1 cells transfected with pControl - Replicate 3

source_name: HuCCT1 cells transfected with pControl

value: Control plasmid


title: HuCCT1-pCASC15-3

description: HuCCT1 cells transfected with pCASC15 - Replicate 3


title: U87MG cells with NeuroD2, biological rep1

description:
Gene Expression Data from U87MG cells transfected with NeuroD2 expression vector
NeuroD2_1


title: BP165_5206_C12_D0_B_Dg

description: gene expression challenge 12, day 0 ,GM-CSF adjuvant

source_name: gene expression challenge 12, day 0


title: BP165_5208_W16_D3_B_Dg

description: gene expression week 16, day 3 ,GM-CSF adjuvant


title: BP165_5206_W17_D7_B_Dg

description: gene expression week 17, day 7 ,GM-CSF adjuvant

source_name: gene expression week 17, day 7


title: U87MG cells control, biological rep2

description:
Gene Expression Data from U87MG cells transfected with PCMV control vector
PCMV_2

source_name: Human U87MG cells transfected with PCMV control vector

value: control


title: HuCCT1-pCASC15-2

description: HuCCT1 cells transfected with pCASC15 - Replicate 2


title: BP165_4817_W32_D1_B_CTRL

description: gene expression week 32, day 1 , control group

value: control group


title: BP165_5229_W32_D0_B_D

description: gene expression week 32, day 0 , no adjuvant

source_name: gene expression week 32, day 0

value: no adjuvant


title: BP165_4817_W16_D3_B_CTRL

description: gene expression week 16, day 3 , control group


title: HuCCT1-pCTRL-1

description: HuCCT1 cells transfected with pControl - Replicate 1


title: U87MG cells control, biological rep1

description:
Gene Expression Data from U87MG cells transfected with PCMV control vector
PCMV_1


title: BP165_5228_W-1_D0_B_D

description: gene expression week -1, day 0 , no adjuvant

source_name: gene expression week -1, day 0


title: BP165_5208_W32_D1_B_Dg

description: gene expression week 32, day 1 ,GM-CSF adjuvant


title: BP165_5228_W1_D7_B_D

description: gene expression week 1, day 7 , no adjuvant

source_name: gene expression week 1, day 7


title: BP165_5229_W0_D3_B_D

description: gene expression week 0, day 3 , no adjuvant


title: BP165_5206_C2_D0_B_Dg

description: gene expression challenge 2, day 0 ,GM-CSF adjuvant

source_name: gene expression challenge 2, day 0


title: BP165_4817_W16_D1_B_CTRL

description: gene expression week 16, day 1 , control group


title: HuCCT1-pCTRL-2

description: HuCCT1 cells transfected with pControl - Replicate 2


title: BP165_5229_C1_D4_B_D

description: gene expression challenge 1, day 4 , no adjuvant

source_name: gene expression challenge 1, day 4


title: BP165_5229_W16_D1_B_D

description: gene expression week 16, day 1 , no adjuvant


title: BP165_5208_W-1_D0_B_Dg

description: gene expression week -1, day 0 ,GM-CSF adjuvant


title: CKCS_Saliva_Unaffected_95

type: genomic

city: Montreal

first: Philippe

last: Lemay

state: Quebec

address: 3175 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: Université de Montréal

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan Autoloader 2X (Illumina).

data_processing:
Genomic DNA extracted from saliva was genotyped using Infinium CanineHD Genotyping BeadChips (Illumina).
GenomeStudio 2.0 was used to generate processed data using the final report function.

label: CY3 and CY5

organism: Canis lupus familiaris

source_name: Saliva

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MA1, WG-MA2) and primer/neutralization mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted from blood or saliva using the ORAGENE Animal kit (DNAgenotek)

tag: breed

value: Cavalier King Charles Spaniel

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: BP165_5228_W32_D0_B_D

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: BP165_5206_W0_D3_B_Dg

description: gene expression week 0, day 3 ,GM-CSF adjuvant

source_name: gene expression week 0, day 3


title: BP165_5206_C12_D28_B_Dg

description: gene expression challenge 12, day 28 ,GM-CSF adjuvant

source_name: gene expression challenge 12, day 28


title: CKCS_Saliva_Unaffected_96

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj


title: CKCS_Saliva_Affected_94

value: case

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: BP165_5228_W16_D1_B_D

source_name: gene expression week 16, day 1

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: CKCS_Saliva_Affected_91

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj


title: BP165_5206_W0_D1_B_Dg

description: gene expression week 0, day 1 ,GM-CSF adjuvant

source_name: gene expression week 0, day 1

tag: tissue

tag: vaccine treatment


title: BP165_5228_W17_D7_B_D

description: gene expression week 17, day 7 , no adjuvant

tag: siv acquirers


title: BP165_4817_W32_D3_B_CTRL

description: gene expression week 32, day 3 , control group

source_name: gene expression week 32, day 3


title: CKCS_Saliva_Unaffected_92

tag: breed

tag: disease state

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: BP165_5206_C1_D4_B_Dg

description: gene expression challenge 1, day 4 ,GM-CSF adjuvant

tag: tissue

tag: vaccine treatment


title: CKCS_Saliva_Affected_90

tag: breed

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj


title: CKCS_Saliva_Unaffected_93

tag: disease state

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: CKCS_Saliva_Unaffected_87

tag: breed

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac


title: BP165_5229_C1_D1_B_D

description: gene expression challenge 1, day 1 , no adjuvant

source_name: gene expression challenge 1, day 1

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: CKCS_Saliva_Unaffected_85

tag: disease state

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: BP165_5206_C12_D9_B_Dg

description: gene expression challenge 12, day 9 ,GM-CSF adjuvant

source_name: gene expression challenge 12, day 9

tag: tissue

tag: vaccine treatment


title: CKCS_Saliva_Unaffected_86

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: f-d/bc


title: BP165_5208_W1_D7_B_Dg

description: gene expression week 1, day 7 ,GM-CSF adjuvant

tag: siv acquirers


title: BP165_4817_W17_D7_B_CTRL

description: gene expression week 17, day 7 , control group

tag: tissue


title: BP165_5228_W32_D3_B_D

description: gene expression week 32, day 3 , no adjuvant

tag: vaccine treatment


title: BP165_5228_W0_D1_B_D

description: gene expression week 0, day 1 , no adjuvant


title: CKCS_Saliva_Affected_89

tag: breed

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: CKCS_Saliva_Unaffected_84

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: f-d/bc


title: CKCS_Saliva_Affected_82

tag: breed

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)


title: CKCS_Saliva_Unaffected_88

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: BP165_5228_C2_D0_B_D

description: gene expression challenge 2, day 0 , no adjuvant

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: CKCS_Saliva_Unaffected_78

tag: breed

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: f-d/bc


title: CKCS_Saliva_Unaffected_83

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: CKCS_Saliva_Unaffected_77

tag: breed

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)


title: BP165_5228_W32_D1_B_D

description: gene expression week 32, day 1 , no adjuvant

source_name: gene expression week 32, day 1

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: CKCS_Saliva_Unaffected_81

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/bc


title: BP165_4817_C1_D1_B_CTRL

description: gene expression challenge 1, day 1 , control group

tag: tissue

tag: vaccine treatment


title: BP165_5229_W17_D7_B_D

tag: siv acquirers


title: BP165_5206_W32_D1_B_Dg

description: gene expression week 32, day 1 ,GM-CSF adjuvant


title: BP165_5206_W1_D7_B_Dg


title: BP165_5208_W17_D7_B_Dg

description: gene expression week 17, day 7 ,GM-CSF adjuvant


title: BP165_5206_W32_D0_B_Dg

description: gene expression week 32, day 0 ,GM-CSF adjuvant


title: CKCS_Saliva_Unaffected_79

tag: breed

tag: disease state

tag: sm

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: f-d/cd


title: CKCS_Saliva_Unaffected_80

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/bc


title: CKCS_Saliva_Unaffected_76

tag: breed

tag: disease state

tag: sm

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)


title: BP165_5228_C3_D0_B_D

description: gene expression challenge 3, day 0 , no adjuvant

source_name: gene expression challenge 3, day 0

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: CKCS_Saliva_Affected_74

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: BP165_5208_W0_D1_B_Dg

description: gene expression week 0, day 1 ,GM-CSF adjuvant

tag: tissue

tag: vaccine treatment


title: CKCS_Saliva_Affected_67

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: f-d/bc


title: BP165_5208_C1_D4_B_Dg

tag: siv acquirers


title: CKCS_Saliva_Unaffected_70

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: BP165_5206_W16_D3_B_Dg

description: gene expression week 16, day 3 ,GM-CSF adjuvant

source_name: gene expression week 16, day 3

tag: tissue

tag: vaccine treatment


title: BP165_5228_C1_D0_B_D

description: gene expression challenge 1, day 0 , no adjuvant

source_name: gene expression challenge 1, day 0

tag: siv acquirers


title: CKCS_Saliva_Unaffected_73

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: f-d/bc


title: BP165_5229_W16_D3_B_D

description: gene expression week 16, day 3 , no adjuvant

tag: tissue

tag: vaccine treatment


title: CKCS_Saliva_Affected_66

tag: breed

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: BP165_5208_W16_D0_B_Dg

description: gene expression week 16, day 0 ,GM-CSF adjuvant

source_name: gene expression week 16, day 0

tag: siv acquirers


title: BP165_5228_C1_D1_B_D

description: gene expression challenge 1, day 1 , no adjuvant

tag: tissue


title: BP165_5229_W0_D1_B_D

tag: vaccine treatment


title: CKCS_Saliva_Affected_69

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: f-d/bc


title: BP165_5206_W16_D1_B_Dg

description: gene expression week 16, day 1 ,GM-CSF adjuvant

tag: tissue

tag: siv acquirers


title: CKCS_Saliva_Unaffected_75

tag: breed

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: BP165_5206_C1_D1_B_Dg

description: gene expression challenge 1, day 1 ,GM-CSF adjuvant

tag: vaccine treatment


title: CKCS_Saliva_Unaffected_71

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: f-d/bc


title: CKCS_Saliva_Affected_65

tag: breed

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: CKCS_Saliva_Unaffected_72

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: f-d/cd


title: CKCS_Saliva_Unaffected_68

tag: breed

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/bc


title: CKCS_Saliva_Unaffected_64

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: CKCS_Saliva_Unaffected_62

tag: breed

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: f-d/cd


title: CKCS_Saliva_Unaffected_60

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/bc


title: CKCS_Saliva_Unaffected_63

tag: breed

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: BP165_5228_C1_D4_B_D

description: gene expression challenge 1, day 4 , no adjuvant

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: BP165_5220_W32_D1_B_Dg


title: BP165_5201_W16_D3_B_D_2


title: BP165_5229_W16_D0_B_D

description: gene expression week 16, day 0 , no adjuvant


title: CKCS_Saliva_Unaffected_58

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd


title: CKCS_Saliva_Affected_59

tag: breed

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/bc


title: BP165_5231_W16_D1_B_Dg

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: BP165_5202_W16_D0_B_D


title: CKCS_Saliva_Affected_61

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd


title: BP165_5239_C3_D0_B_Dg_B

description: gene expression challenge 3, day 0 ,GM-CSF adjuvant

tag: tissue

tag: vaccine treatment

value: Not infected


title: CKCS_Saliva_Affected_52

tag: breed

tag: disease state

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/bc


title: BP165_5231_W17_D7_B_Dg

source_name: gene expression week 17, day 7

tag: siv acquirers


title: BP165_5418_C1_D4_B_CTRL

description: gene expression challenge 1, day 4 , control group

tag: tissue


title: BP165_5219_C3_D0_B_D

tag: vaccine treatment


title: BP165_5229_C1_D0_B_D


title: BP165_5237_C1_D4_B_D


title: CKCS_Saliva_Unaffected_56

tag: breed

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd


title: BP165_5208_C1_D0_B_Dg

description: gene expression challenge 1, day 0 ,GM-CSF adjuvant

tag: tissue

tag: siv acquirers


title: CKCS_Saliva_Unaffected_54

tag: breed

tag: disease state

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/bc


title: BP165_5219_W-1_D0_B_D

description: gene expression week -1, day 0 , no adjuvant

source_name: gene expression week -1, day 0

tag: vaccine treatment


title: CKCS_Saliva_Unaffected_55

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd


title: CKCS_Saliva_Unaffected_57

tag: breed

tag: disease state

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: BP165_5237_C1_D0_B_D

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: BP165_5231_C1_D1_B_Dg


title: CKCS_Saliva_Affected_48

tag: sm

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd

tag: f-d/bc


title: BP165_5418_W32_D1_B_CTRL

description: gene expression week 32, day 1 , control group

tag: tissue

tag: vaccine treatment


title: CKCS_Saliva_Affected_53

tag: breed

tag: disease state

tag: sm

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: CKCS_Saliva_Affected_47

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd

tag: f-d/bc


title: CKCS_Saliva_Affected_50

tag: breed

tag: disease state

tag: sm

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)

tag: l8 (ebd)


title: BP165_5219_W16_D1_B_D

description: gene expression week 16, day 1 , no adjuvant

tag: tissue

tag: vaccine treatment

tag: siv acquirers


title: CKCS_Saliva_Affected_43

tag: ccd size

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd


title: BP165_5231_W32_D3_B_Dg

description: gene expression week 32, day 3 ,GM-CSF adjuvant

tag: tissue

tag: vaccine treatment


title: CKCS_Saliva_Affected_45

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)

tag: l8 (ebd)

tag: f-d/bc


title: CKCS_Saliva_Affected_46

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd