title: UCC2003PK1 invivo versus UCC2003 invitro

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: sample 1

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). Data processing  DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 potato galactan/ribose ratios from a single array experiment.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003PK1

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 or UCC2003delta nagA1 nagA2 wasrecovered from the large intestine of co associated mice. For invitro grown cultures B. breve UCC2003 was  grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of  Ribose as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) untill OD600 was 0.5  Growth protocol  Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

value: Bifidobacterium breve UCC2003 invivo

source_name: Bifidobacterium breve UCC2003 grown on ribose


title: UCC2003deltanagA1 nagA2 invivo versus UCC2003 invitro

status: Public on Jul 19 2018

type: RNA

molecule: total RNA

source_name: Bifidobacterium breve UCC2003delta nagA1nagA2

tag: tissue

value: Bifidobacterium breve nagA1nagA2 invivo

value: Bifidobacterium breve UCC2003 grown on ribose


title: Middle cerebral artery occlusion (MCAO)_24h_repicate_1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Heart tissue from C57BL/6J animals, 24h after ischemic stroke of the brain

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. Additional analysis was performed with R and HOMER (transcription factor binding motif finder)

label: biotin

organism: Mus musculus

source_name: Middle cerebral artery occlusion (MCAO) 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The study was performed with 8 weeks old C57BL/6J animals, exposed to either sham operation or occlusion of the medial cerebral artery. All mice had free access to food and water. Hearts were isolated 24h and 72h after occlusion of the medial cerebral artery.  As control, age matched sham operated C57BL/6J mice were used.

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

treatment_protocol: For the microarray study hearts were isolated from four study groups and their respective controls: 1) hearts from C57BL/6J animals 24h after occlusion of the middle cerebral artery, 2) hearts from C57BL/6J animals 72h after occlusion of the middle cerebral artery, 3) hearts from C57BL/6J animals, 24h after sham operation and 4) hearts from C57BL/6J 72h after sham operation.

tag: treatment

value: MCAO

tag: time


title: Middle cerebral artery occlusion (MCAO)_24h_repicate_3


title: Middle cerebral artery occlusion (MCAO)_24h_repicate_2


title: donor304pl4cell153

type: SRA

city: Heidelberg

first: Natalie

last: Romanov

address: Meyerhofstr. 1

department: Structural and Computational Biology

institute: EMBL

description:
single-cell RNA
1 out of 192 cells per donor

library_source: transcriptomic

data_processing:
Alignments to Homo sapiens genome (hg38) was performed with Salmon v0.9.1 (Patro et al., 2017)
tximport used to produce gene count table (Soneson et al., 2015)
remove cells with less than 1000 genes at a minimum of 10 reads per gene, python 2.7.14
remove genes with less than 10 reads in at least 5 cells, python 2.7.14
processing with SimpleSingleCell version1.2.0 (Lun et al., 2016) for further filtering and normalization
Genome_build: hg38
Supplementary_files_format_and_content: HTMGNBGX3_Donor_302_GENE_LEVEL_COUNTS_withGeneNames.txt.gz: Salmon count table
Supplementary_files_format_and_content: HTMGNBGX3_Donor_304_GENE_LEVEL_COUNTS_withGeneNames.txt.gz: Salmon count table
Supplementary_files_format_and_content: HTMGNBGX3_Donor_305_GENE_LEVEL_COUNTS_withGeneNames.txt.gz: Salmon count table
Supplementary_files_format_and_content: HTMGNBGX3_Donor_309_GENE_LEVEL_COUNTS_withGeneNames.txt.gz: Salmon count table
Supplementary_files_format_and_content: donor302_geneNum1000_normalizedValues_notScaled.tsv.gz: normalized abundance table
Supplementary_files_format_and_content: donor304_geneNum1000_normalizedValues_notScaled.tsv.gz: normalized abundance table
Supplementary_files_format_and_content: donor305_geneNum1000_normalizedValues_notScaled.tsv.gz: normalized abundance table
Supplementary_files_format_and_content: donor309_geneNum1000_normalizedValues_notScaled.tsv.gz: normalized abundance table

organism: Homo sapiens

source_name: Haematopoietic progenitor cells

growth_protocol: Bone marrow (BM) samples were harvested through puncture at the posterior iliac crest using a Yamshidi needle

extract_protocol:
Sequencing libraries from 192 single CD34+ cells per donor were produced based on the smart-seq2 protocol of Picelli et al. 2014 and the tagmentation procedure of Henning et al. 2018 with slight modifications as described in the publication.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BM aspirates were processed by FICOLL density fractionation for isolation of MNCs; stained with CD34-APC, CD45-FITC and CD14-PE; FACS-sorted and stored at -80°C

tag: donor

tag: donor age

value: 30.6 years

tag: gender

value: female

value: bone marrow


title: SLG9

city: Shanghai

first: Yilun

last: Wang

address: No.12 Wulumuqi Zhong Road

country: China

institute: Fudan University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer's instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software.

data_processing: gProcessedSignal

source_name: moDCs from SLE patient

label_protocol: Labeled cRNA were purified by RNeasy mini kit.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated and CD14+ monocytes were sorted by positive selection using magnetic beads (Miltenyi Biotec, Germany). The cells were then cultured for 5-7 days in RPMI 1640 supplemented with 1000 U/ml GM-CSF and 1000U/ml IL-4 (PeproTech, Rocky Hill).

extract_protocol: Total RNA was extracted from moDCs using the miRNeasy mini kit (Qiagen, Germany).

treatment_protocol: 1μg/ml LPS (Escherichia coli type 055:B6; Sigma) was added to the medium at day 6.

tag: cell type

value: monocyte-derived dendritic cell (moDC)

tag: disease status

value: systemic lupus erythematosus (SLE)


title: Middle cerebral artery occlusion (MCAO)_24h_repicate_4


title: donor304pl4cell152


title: donor304pl4cell150


title: SLG7


title: SLG3


title: donor304pl4cell151


title: donor304pl4cell149


title: donor304pl4cell148


title: SLG5


title: donor304pl4cell147


title: SLG6


title: DC3

source_name: moDCs from healthy control

value: healthy


title: donor304pl4cell146


title: donor304pl4cell145


title: donor304pl3cell144


title: DC4


title: DC6


title: donor304pl3cell143


title: donor304pl3cell141


title: DC2


title: donor304pl3cell140


title: DC7


title: donor304pl3cell139


title: donor304pl3cell137


title: donor304pl3cell142


title: donor304pl3cell136


title: donor304pl3cell138


title: juvenile, SIV-infected, SIVE [CW02-245]

city: Pittsburgh

first: Stephanie

last: Bissel

state: PA

address: 3550 Terrace Street, S758 Scaife Hall

country: USA

institute: University of Pittsburgh

description:
CW02-245
miRNA and total RNA
Gene expression data from midfrontal cortex of juvenile SIVmac251-infected macaque with histological hallmarks of SIV encephalitis.

hyb_protocol: Purified biotin-labeled cRNA was fragmented then resuspended in hybridization buffer. 10 ug cRNA was hybridized for 18 hr at 45C on Affymetrix GeneChip Rhesus Macaque Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were analyzed with the Microarray Suite version 5.0 (MAS 5.0) using the RMA (Robust Multichip Average) algorithm.

organism: Macaca mulatta

source_name: juvenile SIVE

label_protocol: NuGen Ovation FFPE WPA System with Encore Biotin Module according to manufacturer's protocol.

growth_protocol: At the conclusion of the study, animals were euthanized and perfused with phosphate buffered saline.

extract_protocol: Total RNA and microRNA was extracted with the Qiagen miRNeasy kit according to the manufacturer's protocol. The concentration and quality of each sample was evaluated using a NanoDrop Spectrophotometer and an Agilent Bioanalyzer 2100.

treatment_protocol: The right hemisphere from perfused brains was placed on ice. Midfrontal cortex tissue was microdissected in ~100 mg pieces and snap frozen. Tissue was stored at -80 C until extraction.

value: midfrontal cortex


title: age 15.9, SIVmac251, no treatment [CW13-221]

description:
CW13-221
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque. No treatment.

source_name: aged SIV

tag: strain

value: Chinese-origin

tag: age (yrs)


title: age 18.7, SIVmac251, ART [CW13-215]

description:
CW13-215
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque. Treated with reverse transcriptase inhibitors TDF and FTC.

source_name: aged SIV with ART


title: age 19.8, SIVmac251, ART [CW13-207]

description:
CW13-207
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque. Treated with reverse transcriptase inhibitors TDF and FTC.


title: age 18.1, SIVmac251, ART [CW13-224]

description:
CW13-224
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque. Treated with reverse transcriptase inhibitors TDF and FTC.


title: juvenile, SIV-infected, SIVE [CW03-250]

description:
CW03-250
miRNA and total RNA
Gene expression data from midfrontal cortex of juvenile SIVmac251-infected macaque with histological hallmarks of SIV encephalitis.


title: age 18.8, no infection, ART  [CW13-217]

description:
CW13-217
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. Treated with reverse transcriptase inhibitors TDF and FTC.

source_name: aged control with ART


title: age 22.3, SIVmac251, no treatment [CW13-209]

description:
CW13-209
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque. No treatment.


title: age 22.8, SIVmac251, no treatment [CW13-205]

description:
CW13-205
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque. No treatment.


title: age 18.7, no infection, ART  [CW13-219]

description:
CW13-219
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. Treated with reverse transcriptase inhibitors TDF and FTC.


title: age 19.8, no infection, ART  [CW13-210]

description:
CW13-210
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. Treated with reverse transcriptase inhibitors TDF and FTC.


title: age 20.5, SIVmac251, no treatment [CW13-220]

description:
CW13-220
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque. No treatment.


title: age 26, no infection, ART  [CW13-213]

description:
CW13-213
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. Treated with reverse transcriptase inhibitors TDF and FTC.


title: age 18.5, no infection, no treatment [CW13-216]

description:
CW13-216
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. No treatment.

source_name: aged control


title: age 17, no infection, no treatment [CW13-222]

description:
CW13-222
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. No treatment.


title: donor304pl3cell135


title: donor304pl3cell131


title: donor304pl3cell133


title: age 21.8, no infection, ART  [CW13-200]

description:
CW13-200
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. Treated with reverse transcriptase inhibitors TDF and FTC.


title: age 22, no infection, no treatment [CW13-204]

description:
CW13-204
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. No treatment.


title: donor304pl3cell127

description:
single-cell RNA
1 out of 192 cells per donor


title: age 25, no infection, no treatment [CW13-203]

description:
CW13-203
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. No treatment.


title: donor304pl4cell154


title: donor304pl3cell128


title: donor304pl3cell134


title: juvenile, no infection [CW16-208]

description:
CW16-208
miRNA and total RNA
Gene expression data from midfrontal cortex of juvenile macaque. No infection. No treatment. No evidence of neuropathological changes.

source_name: juvenile control


title: donor304pl3cell129


title: donor304pl3cell130


title: donor304pl3cell132


title: juvenile, no infection [CW16-204]

description:
CW16-204
miRNA and total RNA
Gene expression data from midfrontal cortex of juvenile macaque. No infection. No treatment. No evidence of neuropathological changes.


title: age 21.7, no infection, no treatment [CW13-212]

description:
CW13-212
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. No treatment.


title: donor304pl3cell125


title: juvenile, no infection [CW16-209]

description:
CW16-209
miRNA and total RNA
Gene expression data from midfrontal cortex of juvenile macaque. No infection. No treatment. No evidence of neuropathological changes.


title: age 18.1, no infection, no treatment [CW13-218]

description:
CW13-218
miRNA and total RNA
Gene expression data from midfrontal cortex of aged  macaque. No infection. No treatment.


title: juvenile, no infection [CW16-206]

description:
CW16-206
miRNA and total RNA
Gene expression data from midfrontal cortex of juvenile macaque. No infection. No treatment. No evidence of neuropathological changes.


title: donor304pl3cell124


title: donor304pl3cell123


title: donor304pl3cell122


title: donor304pl3cell120


title: donor304pl3cell118


title: donor304pl3cell116


title: donor304pl3cell117


title: donor304pl3cell115


title: donor304pl3cell114


title: juvenile, no infection [CW16-205]

description:
CW16-205
miRNA and total RNA
Gene expression data from midfrontal cortex of juvenile macaque. No infection. No treatment. No evidence of neuropathological changes.


title: age 23.2, SIVmac251, rhesus CMV menigoencephalitis [CW13-214]

description:
CW13-214
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque  with histological hallmarks of rhesus cytomegalovirus meningoencephalitis.

source_name: aged SIV, rhCMV menigoencephalitis


title: age 19.7, SIVmac251, bacterial meningitis [CW13-208]

description:
CW13-208
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque  with histological hallmarks of bacterial meningitis.

source_name: aged SIV, bacterial meningitis


title: UPN727, Recent Onset T1D RO3621 plasma

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data fUPN727 cells stimulated with Recent Onset T1D plasma

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed with Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN727 cells stimulated with Recent Onset T1D RO3621 plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of longitudinal CTLA4 treated patients (n=54) and placebo patients (n=20) plasma at baseline, 3 month, 12 month and 24 month, or recent onset (RO) T1D plasma (n=26).  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: cell line

tag: plasma source

value: Recent Onset T1D patient


title: donor304pl3cell121


title: age 20.9, SIVmac251, SIVE [CW13-211]

description:
CW13-211
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque  with histological hallmarks of SIV encephalitis.

source_name: aged SIVE


title: donor304pl3cell126


title: donor304pl3cell112


title: donor304pl3cell119


title: donor304pl3cell110


title: donor304pl3cell109


title: UPN727, Recent Onset T1D RO3585 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3585 plasma


title: donor304pl3cell108


title: donor304pl3cell113


title: UPN727, Recent Onset T1D RO3572 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3572 plasma


title: UPN727, Recent Onset T1D RO3521 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3521 plasma


title: UPN727, Recent Onset T1D RO3555 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3555 plasma


title: donor304pl3cell107

source_name: Haematopoietic progenitor cells


title: age 18.6, SIVmac251, SIVE [CW13-201]

description:
CW13-201
miRNA and total RNA
Gene expression data from midfrontal cortex of aged SIVmac251-infected macaque  with histological hallmarks of SIV encephalitis.


title: donor304pl3cell111


title: donor304pl3cell106


title: untreated LNCaP cells (mRNA)

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description: Gene expression data from untreated LNCaP cells

hyb_protocol: Labelled samples were hybridized to the Affymetrix GeneChip arrays as recommended by the manufacturer

scan_protocol: Arrays were scanned in a GeneChip scanner 3000 with G7 update

data_processing: HG-133Plus_2.0 CEL files were summarized using the MAS5.0 algorithm (Affymetrix GCOS v1.4)). The experimental samples was compared to the untreated sample using the comparison analysis algorithm (MAS5.0). miRNA_3.0 CEL files were summarized using  the Expression Console (Affymetrix) using the rma-dabg algorithm.

label: Biotin

source_name: prostate carcinoma cell line LNCaP

label_protocol:
mRNA expression: total RNA samples (200 ng) were amplified and labeled with the Affymetrix ExpressKit protocol
miRNA expression: total RNA samples (600 ng) were labelled with the Flashtag Labeling Kit  (Affymetrix) as recommended by the manufacturer

growth_protocol: LNCaP cells were cultivated for 2 weeks in RPMI 1640 medium without phenol red indicator supplemented with 10% heat-inactivated FCS, L-Glutamin (1mM final concentration), Penicillin (100 U/ml) and Streptomycin (100 µg/ml).

extract_protocol: Extraction of total RNA was performed using miRNeasy Kit (Qiagen, Hilden, Germany) with a subsequent DNase digestion according to the manufacturer's instructions.

treatment_protocol: untreated

value: LNCaP

value: control


title: UPN727, Recent Onset T1D RO3367 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3367 plasma


title: UPN727, Recent Onset T1D RO3052 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3052 plasma


title: LNCaP cells cultivated in charcoal-stripped FCS (mRNA)

description: Gene expression data from NE-like LNCaP cells

treatment_protocol: FCS was replaced by charcoal-stripped FCS (Sigma Aldrich, Hamburg, Germany) and LNCaP cells were cultivated for 14 days in androgen-free medium where medium was replaced every 72 h.

value: charcoal-stripped FCS


title: UPN727, Recent Onset T1D RO2936 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2936 plasma


title: donor304pl3cell105


title: UPN727, Recent Onset T1D RO2953 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2953 plasma


title: UPN727, Recent Onset T1D RO3139 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3139 plasma


title: donor304pl3cell104


title: UPN727, Recent Onset T1D RO3309 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3309 plasma


title: UPN727, Recent Onset T1D RO3527 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO3527 plasma


title: donor304pl3cell102


title: donor304pl3cell100


title: donor304pl3cell103


title: donor304pl3cell101


title: donor304pl3cell099


title: donor304pl3cell098


title: donor304pl3cell097


title: donor304pl2cell096


title: donor304pl2cell095


title: donor304pl2cell094


title: UPN727, Recent Onset T1D RO2808 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2808 plasma


title: UPN727, Recent Onset T1D RO2944 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2944 plasma


title: UPN727, Recent Onset T1D RO2348 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2348 plasma


title: UPN727, Recent Onset T1D RO1997 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO1997 plasma


title: donor304pl2cell092


title: donor304pl2cell091


title: donor304pl2cell090


title: donor304pl2cell089


title: donor304pl2cell087


title: donor304pl2cell088


title: UPN727, Recent Onset T1D RO2359 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2359 plasma


title: UPN727, Recent Onset T1D RO1123 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO1123 plasma


title: UPN727, Recent Onset T1D RO972 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO972 plasma


title: UPN727, Recent Onset T1D RO253 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO253 plasma


title: donor304pl2cell086

source_name: Haematopoietic progenitor cells


title: UPN727, Recent Onset T1D RO2034 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2034 plasma


title: UPN727, Recent Onset T1D RO2130 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2130 plasma


title: donor304pl2cell093


title: UPN727, Recent Onset T1D RO1964 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO1964 plasma


title: UPN727, Recent Onset T1D RO2559 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO2559 plasma


title: UPN727, Recent Onset T1D RO946 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO946 plasma


title: UPN727, CTLA4 placebo Pt9096907 plasma @M24

description: Gene expression data from UPN727 cells stimulated with CTLA4 placebo patient plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9096907 plasma @M24

tag: time point

value: placebo treated patient


title: UPN727, Recent Onset T1D RO949 plasma

source_name: UPN727 cells stimulated with Recent Onset T1D RO949 plasma


title: UPN727, CTLA4 placebo Pt9098761 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9098761 plasma @M24


title: UPN727, CTLA4 placebo Pt9098761 plasma @BL

description: Gene expression data from UPN727 cells stimulated with CTLA4 placebo patient plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9098761 plasma @BL

value: BL


title: donor304pl2cell084

description:
single-cell RNA
1 out of 192 cells per donor


title: UPN727, CTLA4 placebo Pt9096907 plasma @M03

description: Gene expression data from UPN727 cells stimulated with CTLA4 placebo patient plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9096907 plasma @M03


title: UPN727, CTLA4 placebo Pt9098761 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9098761 plasma @M03


title: UPN727, CTLA4 placebo Pt9096907 plasma @M12

description: Gene expression data from UPN727 cells stimulated with CTLA4 placebo patient plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9096907 plasma @M12


title: UPN727, CTLA4 placebo Pt9096907 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9096907 plasma @BL


title: UPN727, CTLA4 placebo Pt9098761 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9098761 plasma @M12


title: donor304pl2cell083


title: donor304pl2cell082


title: donor304pl2cell085


title: donor304pl2cell079


title: donor304pl2cell077


title: donor304pl2cell080


title: donor304pl2cell078


title: donor304pl2cell075


title: donor304pl2cell081


title: donor304pl2cell076


title: donor304pl2cell074


title: donor304pl2cell073


title: donor304pl2cell072


title: donor304pl2cell071


title: juvenile, no infection [CW16-202]

description:
CW16-202
miRNA and total RNA
Gene expression data from midfrontal cortex of juvenile macaque. No infection. No treatment. No evidence of neuropathological changes.

source_name: juvenile control


title: donor304pl2cell070


title: donor304pl2cell066


title: donor304pl2cell069


title: donor304pl2cell068


title: donor304pl2cell067


title: donor304pl2cell065


title: donor304pl2cell064


title: donor304pl2cell063


title: UPN727, CTLA4 placebo Pt9092781 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9092781 plasma @M03


title: donor304pl2cell062

source_name: Haematopoietic progenitor cells


title: donor304pl2cell061


title: donor304pl2cell060


title: donor304pl2cell059


title: donor304pl2cell058


title: donor304pl2cell057


title: UPN727, CTLA4 placebo Pt9092781 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9092781 plasma @M24


title: UPN727, CTLA4 placebo Pt9093522 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9093522 plasma @M24


title: UPN727, CTLA4 placebo Pt9092781 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9092781 plasma @M12


title: UPN727, CTLA4 placebo Pt9080548 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9080548 plasma @M03


title: UPN727, CTLA4 placebo Pt9093522 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9093522 plasma @M03


title: UPN727, CTLA4 placebo Pt9057818 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9057818 plasma @M24


title: UPN727, CTLA4 placebo Pt9057818 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9057818 plasma @BL


title: UPN727, CTLA4 placebo Pt9093522 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9093522 plasma @BL


title: UPN727, CTLA4 placebo Pt9062776 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9062776 plasma @M12


title: UPN727, CTLA4 placebo Pt9093522 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9093522 plasma @M12


title: UPN727, CTLA4 placebo Pt9080548 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9080548 plasma @M12


title: UPN727, CTLA4 placebo Pt9092781 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9092781 plasma @BL


title: UPN727, CTLA4 placebo Pt9080548 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9080548 plasma @M24


title: UPN727, CTLA4 placebo Pt9047617 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9047617 plasma @M12


title: UPN727, CTLA4 placebo Pt9062776 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9062776 plasma @M03


title: UPN727, CTLA4 placebo Pt9047617 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9047617 plasma @M24


title: UPN727, CTLA4 placebo Pt9062776 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9062776 plasma @BL


title: UPN727, CTLA4 placebo Pt9057818 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9057818 plasma @M03


title: UPN727, CTLA4 placebo Pt9062776 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9062776 plasma @M24


title: UPN727, CTLA4 placebo Pt9057818 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9057818 plasma @M12


title: donor304pl2cell055

source_name: Haematopoietic progenitor cells


title: donor304pl2cell053


title: UPN727, CTLA4 placebo Pt9080548 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9080548 plasma @BL


title: donor304pl2cell052


title: UPN727, CTLA4 placebo Pt9047617 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9047617 plasma @M03


title: donor304pl2cell051


title: donor304pl2cell050


title: donor304pl2cell054


title: donor304pl2cell049


title: donor304pl2cell056


title: donor304pl1cell048


title: donor304pl1cell047


title: donor304pl1cell044


title: donor304pl1cell046


title: donor304pl1cell045


title: donor304pl1cell042


title: donor304pl1cell043


title: donor304pl1cell039


title: UPN727, CTLA4 placebo Pt9034808 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9034808 plasma @M24


title: UPN727, CTLA4 placebo Pt9037347 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9037347 plasma @M24


title: UPN727, CTLA4 placebo Pt9034808 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9034808 plasma @BL


title: UPN727, CTLA4 placebo Pt9037347 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9037347 plasma @M12


title: UPN727, CTLA4 placebo Pt9034582 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9034582 plasma @BL


title: UPN727, CTLA4 placebo Pt9034808 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9034808 plasma @M03


title: UPN727, CTLA4 placebo Pt9037347 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9037347 plasma @BL


title: UPN727, CTLA4 placebo Pt9022509 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9022509 plasma @M12


title: UPN727, CTLA4 placebo Pt9020619 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9020619 plasma @M24


title: UPN727, CTLA4 placebo Pt9034808 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9034808 plasma @M12


title: donor304pl1cell041


title: UPN727, CTLA4 placebo Pt9031867 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9031867 plasma @M24


title: donor304pl1cell040


title: UPN727, CTLA4 placebo Pt9022509 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9022509 plasma @M03


title: UPN727, CTLA4 placebo Pt9020619 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9020619 plasma @M12


title: UPN727, CTLA4 placebo Pt9047617 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9047617 plasma @BL


title: UPN727, CTLA4 placebo Pt9034582 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9034582 plasma @M12


title: UPN727, CTLA4 placebo Pt9031867 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9031867 plasma @BL


title: UPN727, CTLA4 placebo Pt9022509 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9022509 plasma @BL


title: UPN727, CTLA4 placebo Pt9022509 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9022509 plasma @M24


title: UPN727, CTLA4 placebo Pt9034582 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9034582 plasma @M24


title: donor304pl1cell037

source_name: Haematopoietic progenitor cells


title: UPN727, CTLA4 placebo Pt9031867 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9031867 plasma @M12


title: UPN727, CTLA4 placebo Pt9020619 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9020619 plasma @BL


title: UPN727, CTLA4 placebo Pt9020619 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9020619 plasma @M03


title: donor304pl1cell034


title: donor304pl1cell035


title: donor304pl1cell031


title: donor304pl1cell032


title: donor304pl1cell033


title: UPN727, CTLA4 placebo Pt9012575 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9012575 plasma @M03


title: donor304pl1cell030


title: UPN727, CTLA4 placebo Pt9012575 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9012575 plasma @M12


title: donor304pl1cell028


title: donor304pl1cell027


title: donor304pl1cell026


title: donor304pl1cell025


title: donor304pl1cell029


title: UPN727, CTLA4 placebo Pt9009476 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9009476 plasma @M24


title: donor304pl1cell024


title: donor304pl1cell022


title: UPN727, CTLA4 placebo Pt9009476 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9009476 plasma @M12


title: donor304pl1cell023


title: UPN727, CTLA4 placebo Pt9009476 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9009476 plasma @BL


title: UPN727, CTLA4 placebo Pt9003652 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003652 plasma @M03


title: UPN727, CTLA4 placebo Pt9003276 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003276 plasma @M12


title: UPN727, CTLA4 placebo Pt9003276 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003276 plasma @M24


title: UPN727, CTLA4 placebo Pt9012575 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9012575 plasma @BL


title: UPN727, CTLA4 placebo Pt9009476 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9009476 plasma @M03


title: donor304pl1cell021


title: donor304pl1cell018


title: UPN727, CTLA4 placebo Pt9031867 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9031867 plasma @M03


title: UPN727, CTLA4 placebo Pt9003276 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003276 plasma @M03


title: UPN727, CTLA4 placebo Pt9003652 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003652 plasma @BL


title: UPN727, CTLA4 placebo Pt9003652 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003652 plasma @M24


title: donor304pl1cell020

source_name: Haematopoietic progenitor cells


title: UPN727, CTLA4 placebo Pt9003652 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003652 plasma @M12


title: UPN727, CTLA4 placebo Pt9003177 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003177 plasma @M03


title: UPN727, CTLA4 placebo Pt9003276 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003276 plasma @BL


title: donor304pl1cell017


title: donor304pl1cell016


title: donor304pl1cell019


title: UPN727, CTLA4 placebo Pt9012575 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9012575 plasma @M24


title: UPN727, CTLA4 placebo Pt9003177 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003177 plasma @M24


title: UPN727, CTLA4 placebo Pt9001411 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9001411 plasma @M12


title: UPN727, CTLA4 placebo Pt9003177 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003177 plasma @M12


title: donor304pl1cell013


title: donor304pl1cell015


title: donor304pl1cell014


title: donor304pl1cell012


title: UPN727, CTLA4 treated Pt9098085 plasma @M24

description: Gene expression data from UPN727 cells stimulated with CTLA4 treated patient plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9098085 plasma @M24

value: CTLA4 treated patient


title: UPN727, CTLA4 placebo Pt9001411 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9001411 plasma @BL


title: UPN727, CTLA4 placebo Pt9003177 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9003177 plasma @BL


title: donor304pl1cell009


title: donor304pl1cell008


title: donor304pl1cell011


title: donor304pl1cell007


title: donor304pl1cell010


title: donor304pl1cell006


title: UPN727, CTLA4 placebo Pt9001411 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9001411 plasma @M03


title: UPN727, CTLA4 placebo Pt9001411 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 placebo Pt9001411 plasma @M24


title: donor304pl1cell005


title: donor304pl1cell004


title: donor304pl1cell003


title: donor302pl4cell192

value: 59.2 years

value: male


title: UPN727, CTLA4 treated Pt9095979 plasma @M12

description: Gene expression data from UPN727 cells stimulated with CTLA4 treated patient plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9095979 plasma @M12


title: UPN727, CTLA4 treated Pt9097442 plasma @M03

description: Gene expression data from UPN727 cells stimulated with CTLA4 treated patient plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9097442 plasma @M03


title: UPN727, CTLA4 treated Pt9097442 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9097442 plasma @M12


title: UPN727, CTLA4 treated Pt9098085 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9098085 plasma @M12


title: donor304pl1cell002

source_name: Haematopoietic progenitor cells

value: 30.6 years


title: donor302pl4cell191


title: UPN727, CTLA4 treated Pt9097442 plasma @BL

description: Gene expression data from UPN727 cells stimulated with CTLA4 treated patient plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9097442 plasma @BL


title: UPN727, CTLA4 treated Pt9097442 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9097442 plasma @M24


title: UPN727, CTLA4 treated Pt9095979 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9095979 plasma @M03


title: donor304pl1cell001

value: female


title: UPN727, CTLA4 treated Pt9098085 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9098085 plasma @M03


title: UPN727, CTLA4 treated Pt9095979 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9095979 plasma @M24


title: UPN727, CTLA4 treated Pt9093838 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9093838 plasma @M12


title: UPN727, CTLA4 treated Pt9093838 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9093838 plasma @M03


title: UPN727, CTLA4 treated Pt9093838 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9093838 plasma @M24


title: donor302pl4cell188

value: bone marrow


title: donor302pl4cell190


title: donor302pl4cell189


title: donor302pl4cell187


title: donor302pl4cell186


title: UPN727, CTLA4 treated Pt9092765 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092765 plasma @M24


title: donor302pl4cell184


title: donor302pl4cell185


title: donor302pl4cell183


title: donor304pl1cell036


title: donor302pl4cell180


title: donor302pl4cell179


title: UPN727, CTLA4 treated Pt9092765 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092765 plasma @BL


title: UPN727, CTLA4 treated Pt9092765 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092765 plasma @M12


title: UPN727, CTLA4 treated Pt9093838 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9093838 plasma @BL


title: UPN727, CTLA4 treated Pt9095979 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9095979 plasma @BL


title: UPN727, CTLA4 treated Pt9092765 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092765 plasma @M03


title: donor302pl4cell178


title: UPN727, CTLA4 treated Pt9092037 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092037 plasma @M12


title: donor302pl4cell182


title: donor302pl4cell181


title: donor302pl4cell177


title: donor304pl1cell038


title: donor302pl4cell176


title: UPN727, CTLA4 treated Pt9092037 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092037 plasma @M24


title: donor302pl4cell175

source_name: Haematopoietic progenitor cells


title: UPN727, CTLA4 treated Pt9092010 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092010 plasma @M24


title: UPN727, CTLA4 treated Pt9092037 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092037 plasma @M03


title: donor302pl4cell172


title: UPN727, CTLA4 treated Pt9098085 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9098085 plasma @BL


title: UPN727, CTLA4 treated Pt9092010 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092010 plasma @M03


title: donor302pl4cell173


title: donor302pl4cell168


title: UPN727, CTLA4 treated Pt9092037 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092037 plasma @BL


title: UPN727, CTLA4 treated Pt9091454 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9091454 plasma @M03


title: UPN727, CTLA4 treated Pt9091454 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9091454 plasma @M12


title: UPN727, CTLA4 treated Pt9090498 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9090498 plasma @M24


title: donor302pl4cell171


title: UPN727, CTLA4 treated Pt9092010 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092010 plasma @BL


title: UPN727, CTLA4 treated Pt9090498 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9090498 plasma @BL


title: donor302pl4cell174


title: donor302pl4cell169


title: UPN727, CTLA4 treated Pt9092010 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9092010 plasma @M12


title: UPN727, CTLA4 treated Pt9088997 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088997 plasma @M24


title: donor302pl4cell165


title: donor302pl4cell167


title: donor302pl4cell170


title: donor302pl4cell166


title: UPN727, CTLA4 treated Pt9091454 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9091454 plasma @BL


title: UPN727, CTLA4 treated Pt9090498 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9090498 plasma @M03


title: UPN727, CTLA4 treated Pt9090498 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9090498 plasma @M12


title: UPN727, CTLA4 treated Pt9091454 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9091454 plasma @M24


title: donor302pl4cell164

source_name: Haematopoietic progenitor cells


title: donor302pl4cell163


title: donor302pl4cell162


title: UPN727, CTLA4 treated Pt9088997 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088997 plasma @BL


title: donor302pl4cell160


title: UPN727, CTLA4 treated Pt9088950 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088950 plasma @M03


title: donor302pl4cell159


title: donor302pl4cell158


title: donor302pl4cell157


title: UPN727, CTLA4 treated Pt9088997 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088997 plasma @M12


title: donor302pl4cell155


title: UPN727, CTLA4 treated Pt9088950 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088950 plasma @M24


title: donor302pl4cell154


title: donor302pl4cell161


title: donor302pl4cell153


title: donor302pl4cell152


title: donor302pl4cell151


title: UPN727, CTLA4 treated Pt9088950 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088950 plasma @M12


title: UPN727, CTLA4 treated Pt9088623 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088623 plasma @M24


title: donor302pl4cell150


title: donor302pl4cell156


title: UPN727, CTLA4 treated Pt9088623 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088623 plasma @M03


title: UPN727, CTLA4 treated Pt9088950 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088950 plasma @BL


title: UPN727, CTLA4 treated Pt9087810 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9087810 plasma @M12


title: UPN727, CTLA4 treated Pt9088997 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088997 plasma @M03


title: donor302pl4cell149


title: UPN727, CTLA4 treated Pt9088623 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088623 plasma @BL


title: UPN727, CTLA4 treated Pt9087810 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9087810 plasma @M03


title: UPN727, CTLA4 treated Pt9088623 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9088623 plasma @M12


title: UPN727, CTLA4 treated Pt9087810 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9087810 plasma @M24


title: UPN727, CTLA4 treated Pt9086296 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9086296 plasma @M12


title: donor302pl4cell148


title: donor302pl4cell147


title: donor302pl4cell146


title: donor302pl4cell145


title: donor302pl3cell144


title: UPN727, CTLA4 treated Pt9087810 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9087810 plasma @BL


title: UPN727, CTLA4 treated Pt9086296 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9086296 plasma @M03


title: UPN727, CTLA4 treated Pt9084986 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9084986 plasma @M12


title: donor302pl3cell142

source_name: Haematopoietic progenitor cells


title: donor302pl3cell141


title: donor302pl3cell140


title: donor302pl3cell143


title: UPN727, CTLA4 treated Pt9086296 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9086296 plasma @M24


title: UPN727, CTLA4 treated Pt9086296 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9086296 plasma @BL


title: donor302pl3cell138


title: donor302pl3cell139


title: donor302pl3cell137


title: donor302pl3cell136


title: UPN727, CTLA4 treated Pt9084986 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9084986 plasma @M24


title: UPN727, CTLA4 treated Pt9084986 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9084986 plasma @BL


title: UPN727, CTLA4 treated Pt9084843 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9084843 plasma @M24


title: UPN727, CTLA4 treated Pt9083384 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9083384 plasma @M24


title: UPN727, CTLA4 treated Pt9084986 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9084986 plasma @M03


title: UPN727, CTLA4 treated Pt9084843 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9084843 plasma @M03


title: donor302pl3cell134


title: donor302pl3cell133


title: donor302pl3cell131


title: donor302pl3cell132


title: UPN727, CTLA4 treated Pt9083384 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9083384 plasma @M12


title: donor302pl3cell130


title: UPN727, CTLA4 treated Pt9083384 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9083384 plasma @M03


title: UPN727, CTLA4 treated Pt9084843 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9084843 plasma @BL


title: donor302pl3cell135


title: UPN727, CTLA4 treated Pt9082597 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9082597 plasma @M12


title: UPN727, CTLA4 treated Pt9084843 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9084843 plasma @M12


title: UPN727, CTLA4 treated Pt9083384 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9083384 plasma @BL


title: UPN727, CTLA4 treated Pt9074578 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9074578 plasma @M24


title: UPN727, CTLA4 treated Pt9082597 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9082597 plasma @M03


title: donor302pl3cell129

source_name: Haematopoietic progenitor cells


title: donor302pl3cell128


title: UPN727, CTLA4 treated Pt9082597 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9082597 plasma @M24


title: donor302pl3cell124


title: donor302pl3cell122


title: donor302pl3cell121


title: UPN727, CTLA4 treated Pt9074578 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9074578 plasma @M03


title: UPN727, CTLA4 treated Pt9082597 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9082597 plasma @BL


title: UPN727, CTLA4 treated Pt9074578 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9074578 plasma @BL


title: UPN727, CTLA4 treated Pt9072101 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9072101 plasma @M03


title: UPN727, CTLA4 treated Pt9072101 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9072101 plasma @M24


title: donor302pl3cell126


title: donor302pl3cell127


title: donor302pl3cell125


title: UPN727, CTLA4 treated Pt9074578 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9074578 plasma @M12


title: donor302pl3cell117


title: donor302pl3cell115


title: donor302pl3cell123


title: UPN727, CTLA4 treated Pt9072101 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9072101 plasma @BL


title: donor302pl3cell120


title: UPN727, CTLA4 treated Pt9072101 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9072101 plasma @M12


title: UPN727, CTLA4 treated Pt9068424 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9068424 plasma @M24


title: UPN727, CTLA4 treated Pt9068424 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9068424 plasma @BL


title: donor302pl3cell113


title: UPN727, CTLA4 treated Pt9068024 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9068024 plasma @M12


title: donor302pl3cell119


title: UPN727, CTLA4 treated Pt9068024 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9068024 plasma @M03


title: UPN727, CTLA4 treated Pt9068024 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9068024 plasma @M24


title: donor302pl3cell118


title: UPN727, CTLA4 treated Pt9068424 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9068424 plasma @M12


title: donor302pl3cell114


title: donor302pl3cell110


title: donor302pl3cell116


title: donor302pl3cell111


title: donor302pl3cell108


title: donor302pl3cell109


title: UPN727, CTLA4 treated Pt9066427 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9066427 plasma @M12


title: UPN727, CTLA4 treated Pt9068424 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9068424 plasma @M03


title: UPN727, CTLA4 treated Pt9064499 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9064499 plasma @M12


title: donor302pl3cell107

source_name: Haematopoietic progenitor cells


title: donor302pl3cell106


title: donor302pl3cell112


title: donor302pl3cell104


title: UPN727, CTLA4 treated Pt9064499 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9064499 plasma @M03


title: donor302pl3cell105


title: UPN727, CTLA4 treated Pt9066427 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9066427 plasma @M03


title: UPN727, CTLA4 treated Pt9064499 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9064499 plasma @M24


title: UPN727, CTLA4 treated Pt9066427 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9066427 plasma @BL


title: UPN727, CTLA4 treated Pt9066427 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9066427 plasma @M24


title: UPN727, CTLA4 treated Pt9060824 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9060824 plasma @M24


title: donor302pl3cell102


title: UPN727, CTLA4 treated Pt9068024 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9068024 plasma @BL


title: UPN727, CTLA4 treated Pt9060824 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9060824 plasma @M03


title: UPN727, CTLA4 treated Pt9064499 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9064499 plasma @BL


title: UPN727, CTLA4 treated Pt9060824 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9060824 plasma @BL


title: donor302pl3cell103


title: donor302pl3cell101


title: donor302pl3cell099


title: UPN727, CTLA4 treated Pt9060824 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9060824 plasma @M12


title: UPN727, CTLA4 treated Pt9060795 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9060795 plasma @M03


title: donor302pl3cell097


title: donor302pl2cell096


title: donor302pl2cell095


title: donor302pl2cell094


title: donor302pl2cell093


title: donor302pl3cell100


title: donor302pl2cell092


title: donor302pl2cell091


title: UPN727, CTLA4 treated Pt9059514 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9059514 plasma @M12


title: UPN727, CTLA4 treated Pt9059514 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9059514 plasma @M24


title: UPN727, CTLA4 treated Pt9060795 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9060795 plasma @M12


title: donor302pl3cell098


title: UPN727, CTLA4 treated Pt9055573 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9055573 plasma @M24


title: donor302pl2cell089

source_name: Haematopoietic progenitor cells


title: UPN727, CTLA4 treated Pt9060795 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9060795 plasma @BL


title: UPN727, CTLA4 treated Pt9059514 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9059514 plasma @BL


title: donor302pl2cell088


title: UPN727, CTLA4 treated Pt9055573 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9055573 plasma @M03


title: UPN727, CTLA4 treated Pt9055573 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9055573 plasma @BL


title: UPN727, CTLA4 treated Pt9053269 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9053269 plasma @M24


title: UPN727, CTLA4 treated Pt9055573 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9055573 plasma @M12


title: donor302pl2cell087


title: UPN727, CTLA4 treated Pt9060795 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9060795 plasma @M24


title: donor302pl2cell086


title: UPN727, CTLA4 treated Pt9059514 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9059514 plasma @M03


title: donor302pl2cell090


title: donor302pl2cell084


title: UPN727, CTLA4 treated Pt9053269 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9053269 plasma @M12


title: UPN727, CTLA4 treated Pt9052289 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9052289 plasma @M24


title: donor302pl2cell082


title: donor302pl2cell083


title: UPN727, CTLA4 treated Pt9053269 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9053269 plasma @M03


title: donor302pl2cell081


title: donor302pl2cell085


title: UPN727, CTLA4 treated Pt9053269 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9053269 plasma @BL


title: donor302pl2cell079


title: UPN727, CTLA4 treated Pt9052289 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9052289 plasma @M03


title: donor302pl2cell077


title: UPN727, CTLA4 treated Pt9051989 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9051989 plasma @M12


title: donor302pl2cell076


title: UPN727, CTLA4 treated Pt9051989 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9051989 plasma @M03


title: UPN727, CTLA4 treated Pt9048858 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9048858 plasma @M12


title: UPN727, CTLA4 treated Pt9052289 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9052289 plasma @BL


title: UPN727, CTLA4 treated Pt9052289 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9052289 plasma @M12


title: donor302pl2cell075

source_name: Haematopoietic progenitor cells


title: donor302pl2cell074


title: donor302pl2cell080


title: donor302pl2cell073


title: donor302pl2cell078


title: donor302pl2cell071


title: UPN727, CTLA4 treated Pt9051989 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9051989 plasma @M24


title: UPN727, CTLA4 treated Pt9048858 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9048858 plasma @BL


title: donor302pl2cell070


title: UPN727, CTLA4 treated Pt9051989 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9051989 plasma @BL


title: UPN727, CTLA4 treated Pt9048858 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9048858 plasma @M24


title: UPN727, CTLA4 treated Pt9045146 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9045146 plasma @M03


title: donor302pl2cell069


title: UPN727, CTLA4 treated Pt9048858 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9048858 plasma @M03


title: donor302pl2cell068


title: UPN727, CTLA4 treated Pt9045146 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9045146 plasma @M12


title: donor302pl2cell067


title: donor302pl2cell072


title: UPN727, CTLA4 treated Pt9045146 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9045146 plasma @M24


title: UPN727, CTLA4 treated Pt9043824 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9043824 plasma @M24


title: UPN727, CTLA4 treated Pt9045146 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9045146 plasma @BL


title: donor302pl2cell066


title: UPN727, CTLA4 treated Pt9043824 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9043824 plasma @BL


title: UPN727, CTLA4 treated Pt9042186 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9042186 plasma @M24


title: UPN727, CTLA4 treated Pt9043824 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9043824 plasma @M12


title: donor302pl2cell065


title: donor302pl2cell064


title: donor302pl2cell062


title: donor302pl2cell063


title: UPN727, CTLA4 treated Pt9043824 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9043824 plasma @M03


title: UPN727, CTLA4 treated Pt9042186 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9042186 plasma @M12


title: donor302pl2cell061


title: donor302pl2cell059


title: donor302pl2cell060


title: UPN727, CTLA4 treated Pt9042186 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9042186 plasma @M03


title: donor302pl2cell058

source_name: Haematopoietic progenitor cells


title: donor302pl2cell056


title: donor302pl2cell057


title: UPN727, CTLA4 treated Pt9042186 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9042186 plasma @BL


title: UPN727, CTLA4 treated Pt9041256 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9041256 plasma @M03


title: donor302pl2cell055


title: donor302pl2cell054


title: UPN727, CTLA4 treated Pt9041256 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9041256 plasma @M12


title: UPN727, CTLA4 treated Pt9041256 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9041256 plasma @M24


title: donor302pl2cell053


title: UPN727, CTLA4 treated Pt9041256 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9041256 plasma @BL


title: UPN727, CTLA4 treated Pt9040109 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9040109 plasma @M03


title: UPN727, CTLA4 treated Pt9039251 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9039251 plasma @M24


title: UPN727, CTLA4 treated Pt9040109 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9040109 plasma @M24


title: UPN727, CTLA4 treated Pt9040109 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9040109 plasma @BL


title: UPN727, CTLA4 treated Pt9039251 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9039251 plasma @M12


title: donor302pl2cell052


title: UPN727, CTLA4 treated Pt9040109 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9040109 plasma @M12


title: donor302pl1cell048


title: donor302pl2cell049


title: donor302pl2cell050


title: donor302pl1cell047


title: donor302pl2cell051


title: donor302pl1cell044


title: donor302pl1cell045


title: UPN727, CTLA4 treated Pt9035621 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9035621 plasma @M03


title: UPN727, CTLA4 treated Pt9039251 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9039251 plasma @BL


title: donor302pl1cell042


title: donor302pl1cell043


title: UPN727, CTLA4 treated Pt9035621 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9035621 plasma @M12


title: UPN727, CTLA4 treated Pt9039251 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9039251 plasma @M03


title: donor302pl1cell041


title: UPN727, CTLA4 treated Pt9034944 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9034944 plasma @M24


title: UPN727, CTLA4 treated Pt9034944 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9034944 plasma @BL


title: UPN727, CTLA4 treated Pt9035621 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9035621 plasma @M24


title: UPN727, CTLA4 treated Pt9034944 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9034944 plasma @M03


title: UPN727, CTLA4 treated Pt9035621 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9035621 plasma @BL


title: donor302pl1cell040

source_name: Haematopoietic progenitor cells


title: donor302pl1cell046


title: donor302pl1cell039


title: UPN727, CTLA4 treated Pt9034909 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9034909 plasma @M24


title: UPN727, CTLA4 treated Pt9034944 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9034944 plasma @M12


title: UPN727, CTLA4 treated Pt9034909 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9034909 plasma @M12


title: donor302pl1cell037


title: UPN727, CTLA4 treated Pt9034909 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9034909 plasma @M03


title: UPN727, CTLA4 treated Pt9033311 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9033311 plasma @M24


title: UPN727, CTLA4 treated Pt9033311 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9033311 plasma @M03


title: donor302pl1cell036


title: UPN727, CTLA4 treated Pt9034909 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9034909 plasma @BL


title: UPN727, CTLA4 treated Pt9033311 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9033311 plasma @M12


title: UPN727, CTLA4 treated Pt9033311 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9033311 plasma @BL


title: UPN727, CTLA4 treated Pt9031301 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9031301 plasma @M12


title: UPN727, CTLA4 treated Pt9031301 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9031301 plasma @M24


title: donor302pl1cell035


title: donor302pl1cell034


title: UPN727, CTLA4 treated Pt9031301 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9031301 plasma @M03


title: donor302pl1cell032


title: donor302pl1cell031


title: donor302pl1cell029


title: donor302pl1cell033


title: donor302pl1cell038


title: donor302pl1cell028


title: donor302pl1cell030


title: donor302pl1cell027


title: donor302pl1cell026


title: donor302pl1cell024


title: donor302pl1cell025


title: donor302pl1cell023


title: UPN727, CTLA4 treated Pt9031301 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9031301 plasma @BL


title: donor302pl1cell022


title: donor302pl1cell021


title: UPN727, CTLA4 treated Pt9027000 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9027000 plasma @BL


title: UPN727, CTLA4 treated Pt9019970 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9019970 plasma @M03


title: UPN727, CTLA4 treated Pt9019970 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9019970 plasma @BL


title: UPN727, CTLA4 treated Pt9019970 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9019970 plasma @M24


title: UPN727, CTLA4 treated Pt9027000 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9027000 plasma @M12


title: donor302pl1cell020

source_name: Haematopoietic progenitor cells


title: UPN727, CTLA4 treated Pt9019970 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9019970 plasma @M12


title: UPN727, CTLA4 treated Pt9027000 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9027000 plasma @M03


title: UPN727, CTLA4 treated Pt9027000 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9027000 plasma @M24


title: donor302pl1cell017


title: donor302pl1cell018


title: UPN727, CTLA4 treated Pt9019691 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9019691 plasma @M24


title: UPN727, CTLA4 treated Pt9018458 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9018458 plasma @M03


title: UPN727, CTLA4 treated Pt9019691 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9019691 plasma @M12


title: UPN727, CTLA4 treated Pt9018458 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9018458 plasma @M24


title: donor302pl1cell016


title: donor302pl1cell015


title: donor302pl1cell014


title: UPN727, CTLA4 treated Pt9019691 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9019691 plasma @M03


title: UPN727, CTLA4 treated Pt9018458 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9018458 plasma @M12


title: donor302pl1cell011


title: donor302pl1cell012


title: donor302pl1cell013


title: donor302pl1cell010


title: donor302pl1cell008


title: donor302pl1cell009


title: donor302pl1cell007


title: UPN727, CTLA4 treated Pt9018458 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9018458 plasma @BL


title: UPN727, CTLA4 treated Pt9019691 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9019691 plasma @BL


title: UPN727, CTLA4 treated Pt9016746 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9016746 plasma @M03


title: donor302pl1cell006


title: UPN727, CTLA4 treated Pt9016746 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9016746 plasma @M12


title: UPN727, CTLA4 treated Pt9015071 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9015071 plasma @M24


title: UPN727, CTLA4 treated Pt9016746 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9016746 plasma @BL


title: UPN727, CTLA4 treated Pt9016746 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9016746 plasma @M24


title: UPN727, CTLA4 treated Pt9011880 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9011880 plasma @M12


title: donor302pl1cell005

source_name: Haematopoietic progenitor cells


title: UPN727, CTLA4 treated Pt9015071 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9015071 plasma @M03


title: UPN727, CTLA4 treated Pt9015071 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9015071 plasma @M12


title: donor302pl1cell004


title: donor302pl1cell002


title: donor302pl1cell003


title: UPN727, CTLA4 treated Pt9011880 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9011880 plasma @M24


title: UPN727, CTLA4 treated Pt9015071 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9015071 plasma @BL


title: donor302pl1cell001


title: UPN727, CTLA4 treated Pt9011880 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9011880 plasma @M03


title: donor302pl1cell019


title: UPN727, CTLA4 treated Pt9010058 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9010058 plasma @M24


title: UPN727, CTLA4 treated Pt9010058 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9010058 plasma @M12


title: P1130: Control

city: Valencia

first: Joaquin

last: Panadero

state: Valencia

address: Avenida Fernando Abril Martorell, 106 Torre A

department: Genomics

country: Spain

institute: Instituto Investigación Sanitaria La Fe

description: miRNAs serum  RNAseq

data_processing:
Quality check with FastQC version 0.11.4
Trimming and quality filtering with Cutadapt version 1.13
Alignment against ncRNA (GRCh38)
Normalization and statistics using edgeR/Limma Bioconductor R packages
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV format with counts for all samples and differential expression results when comparing saf2.vs.saf1

source_name: serum sample patient N55

extract_protocol:
Total RNA was extracted from 300microL of human serum using Trizol LS reagent (Invitrogen) followed  by miRNeasy min iKit (Qiagen) prior to serum RNA purification with added 20microgr of RNAase-free glycogen (Roche) as a carrier. Purified RNA was reverse transcribed in two steps: polyadenylation with 1U Poly(A) polymerase from E.coli and reverse transcription with an universal anchor primer and 200U M-MLV reverse transcriptase (Invitrogen)
RNA cDNA libraries were prepared from serum total RNA from 8 patients of the cohort using NEBNext® Multiplex Small RNA Library Prep Set (#E7300 y #7580; New England BioLabs®, Inc., Ipswich, MA, USA) and miRNA were eluted using Pippin Prep System (Sage Science, Inc., Beverly, MA, USA) selecting a range size of 120-200 pb. These libraries were sequenced in a NextSeq 500 System using a 150 cycles Kit (Illumina, Inc., San Diego, CA, USA). The serum samples had a median of 0.9 million miRNA reads (68364 to 512508)

tag: patient

value: serum

tag: classification


title: P1129: Control

description: miRNAs serum  RNAseq

source_name: serum sample patient N37


title: P1127: Case

description: miRNAs serum  RNAseq

source_name: serum sample patient N23


title: P1128: Case

description: miRNAs serum  RNAseq

source_name: serum sample patient N29


title: UPN727, CTLA4 treated Pt9010058 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9010058 plasma @M03


title: P1126: Case

description: miRNAs serum  RNAseq

source_name: serum sample patient N22


title: P1125: Case

description: miRNAs serum  RNAseq

source_name: serum sample patient N12


title: UPN727, CTLA4 treated Pt9009315 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9009315 plasma @M24


title: UPN727, CTLA4 treated Pt9011880 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9011880 plasma @BL


title: UPN727, CTLA4 treated Pt9010058 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9010058 plasma @BL


title: P1124: Control

description: miRNAs serum  RNAseq

source_name: serum sample patient N2


title: P1131: Control

description: miRNAs serum  RNAseq

source_name: serum sample patient N56


title: MDA-MB-231 shPPFIA1 44

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Department of Biomedicine

country: Finland

institute: University of Helsinki

description:
cell line from breast cancer transduced with shPPFIA1 44 shRNA
Mira_RNA _DESeq_results_comparison.xlsx
KD44_S5

data_processing:
Base-calling was done with Real-Time Analysis (RTA), RTA v2, (Illumina NextSeq 500).
Read quality was checked with FASTQC v0.11.3. Trimmomatic v0.36 was used in trimming the data, and qualimap v2.2 platform was used in analyzing the data.
MultiQC v0.8 tool was used in the data analysis. High quality reads were imported into STAR v2.5 for alignment into BAM files.
Genome_build: GRCh38
Supplementary_files_format_and_content: Differential expression analysis was performed by DESeq2 package R v3.2.3 and results underwent logarithmic transformation. Statistical test used was Wald. Processed data files in Excel (.xlsx) format contain log2 fold changes and p-values. Significantly differentially expressed genes were considered those with padj < 0,05 (Benjamini-Hochberg). Comparison between the two conditions shPPFIA1 and shScr has been evaluated with three different biological replicates per cell line (UT-SCC-42A, UT-SCC-42B, MDA-MB-231).

source_name: breast carcinoma cell line

growth_protocol: UT-SCC-42A, UT-SCC-42B and MDA-MB-231 cell lines were grown on DMEM (Lonza) medium, and supplements 10% fetal bovine serum (FBS, Gibco), (100 U/ml) penicillin/streptomycin (Lonza), 2mM L-glutamin (Lonza) and 0,1 mM non essential amino acids (NEAA, Lonza) were added to the medium.

extract_protocol:
Cells (300 000 cells/ml) were suspended in collagen I matrix (500µl) and plated in low adhesion plates (24-well plates from Corning for MDA-MB-231 cell line,poly-HEMA coated 24-well plates for HNSCC cell lines), and grown inside collagen I for five days. To extract the RNA, media was removed from the well and Trizol (Ambion, Life Technologies) was added on top of the collagen I and homogenised by precellys ceramic beads and homogenizator (Precellys). Briefly, RNA was isolated and purified using chloroform/isopropanol based method and purified with Qiagen RNeasy Mini kit, according to manufacturer's instructions (Qiagen).
1µg of total RNA was subjected to library synthesis. Libraries were prepared according to Illumina's instructions accompanied with RiboZero Complete Gold Human and NEBNext Directional RNA library kit. Library quality was checked by Bioanalyzer analysis (Agilent 2100). Library denaturation and dilution was made according to NextSeq500 system guide.

treatment_protocol: Briefly, cells were first transduced with different constructs to silence PPFIA1 (shPPFIA1 14,44,69, from Sigma-Aldrich), and three shScr transductions were used as a controls. Cells were selected with puromycin (1µM/µl). After selection cells were embedded into three dimensional collagen I and were grown for five days at +37˚C, 5%CO2. RNA was extracted from three-dimensional cell cultures.

value: metastasis

tag: shRNA construct

value: shPPFIA1 44 (plKO.1)


title: MDA-MB-231 shPPFIA1 69

description:
cell line from breast cancer transduced with shPPFIA1 69 shRNA
Mira_RNA _DESeq_results_comparison.xlsx
KD69_S6

value: shPPFIA1 69 (plKO.1)


title: UPN727, CTLA4 treated Pt9009315 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9009315 plasma @M12


title: UPN727, CTLA4 treated Pt9003388 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9003388 plasma @M24


title: UPN727, CTLA4 treated Pt9009315 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9009315 plasma @BL


title: MDA-MB-231 shScr 1

description:
cell line from breast cancer transduced with scramble shRNA
Mira_RNA _DESeq_results_comparison.xlsx
ShScr1_S1

value: ctrl/shScramble (plKO.1)


title: UPN727, CTLA4 treated Pt9003388 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9003388 plasma @M03


title: UT-SCC-42B shPPFIA1 69

description:
cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 69 shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
12_UT-SCC-42B_shPPFIA1_69_S12

source_name: head and neck squamous cell carcinoma cell line

value: neck metastasis


title: UT-SCC-42B shPPFIA1 14

description:
cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 14 shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
10_UT-SCC-42B_shPPFIA1_14_S10

value: shPPFIA1 14 (plKO.1)


title: UT-SCC-42B shScr 3

description:
cell line from head and neck squamous cell carcinoma transduced with scramble shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
9_UT-SCC-42B_shScr_3_S9


title: UPN727, CTLA4 treated Pt9003388 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9003388 plasma @M12


title: UT-SCC-42B shPPFIA1 44

description:
cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 44 shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
11_UT-SCC-42B_shPPFIA1_44_S11


title: MDA-MB-231 shScr 3

description:
cell line from breast cancer transduced with scramble shRNA
Mira_RNA _DESeq_results_comparison.xlsx
ShScr3_S3


title: UPN727, CTLA4 treated Pt9003388 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9003388 plasma @BL


title: UPN727, CTLA4 treated Pt9002922 plasma @M12

source_name: UPN727 cells stimulated with CTLA4 treated Pt9002922 plasma @M12


title: MDA-MB-231 shScr 2

description:
cell line from breast cancer transduced with scramble shRNA
Mira_RNA _DESeq_results_comparison.xlsx
ShScr2_S2


title: UPN727, CTLA4 treated Pt9002922 plasma @BL

source_name: UPN727 cells stimulated with CTLA4 treated Pt9002922 plasma @BL


title: UPN727, CTLA4 treated Pt9009315 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9009315 plasma @M03


title: MDA-MB-231 shPPFIA1 14

description:
cell line from breast cancer transduced with shPPFIA1 14 shRNA
Mira_RNA _DESeq_results_comparison.xlsx
KD14_S4


title: UPN727, CTLA4 treated Pt9002922 plasma @M03

source_name: UPN727 cells stimulated with CTLA4 treated Pt9002922 plasma @M03


title: UPN727, CTLA4 treated Pt9002922 plasma @M24

source_name: UPN727 cells stimulated with CTLA4 treated Pt9002922 plasma @M24


title: UT-SCC-42B shScr 2

description:
cell line from head and neck squamous cell carcinoma transduced with scramble shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
8_UT-SCC-42B_shScr_2_S8


title: UT-SCC-42A shPPFIA1 69

description:
cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 69 shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
6_UT-SCC-42A_shPPFIA1_69_S6

value: larynx primary tumor


title: UT-SCC-42A shPPFIA1 14

description:
cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 14 shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
4_UT-SCC-42A_shPPFIA1_14_S4


title: 21 days differentiated Caco-2 cells incubated with Frutafit HD (HD) for 6 hours, biol rep 3

city: Wageningen

first: Nicole

last: de Wit

address: Bornse Weilanden 9

department: Food & Biobased Research

country: Netherlands

institute: Wageningen UR

description: 21 days differentiated Caco-2 cells incubated with Frutafit HD (HD) for 6 hours, biological replicate 3

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm using the Affymetrix® Expression Console™ Software.

source_name: 21 days differentiated Caco-2 cells

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: ATCC derived Caco-2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco-Invitrogen, Bleiswijk, The Netherlands) with 4.5 g/L glucose, 0.58 g/L glutamine, no pyruvate, supplemented with 10% heat inactivated FBS (Hyclone Perbio, Etten-Leur, The Netherlands) and used with passage numbers between 30 and 60. For transwell assays, 0.33x105 cells were grown on ThinCert transwells with 33.6 mm2 membranes and 0.4 μm pores in 24-well suspension culture plates. Cells were grown for 21 days at 5% CO2 and 37°C and apical (150 μl) and basolateral (700 μl) medium were replaced three times per week.

extract_protocol: Total RNA was prepared from the Caco-2 cells using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Glycerol stocks of Lactobacillus acidophilus W37 (W37), Lactobacillus brevis W63 (W63), and Lactobacillus casei W56 (W56) (Winclove, Amsterdam, The Netherlands) were produced from bacteria grown anaerobically overnight in MRS medium. Upon use, glycerol stocks were washed with PBS and resuspended in cells culture medium, brought to 37°C, to reach 10^7 CFU/mL. Inulin-type fructans and oligofructose were solubilized at 0.5 mg/mL in medium and filtered (0.2 m) to eliminate possible contaminations. The cell medium was replaced the day before the exposure experiments. Medium was removed from the apical and basal compartments and diluted samples were added in to the apical compartment while fresh DMEM+10%FBS medium was added to the basal compartment. In each experiment, the compound- and control samples were exposed to Caco-2 cells in triplicate and two or three independent exposure experiments were performed (= independent biological replicates). After 6h incubation, the Caco-2 cells were lysed with 300 μL TRIzol and the triplicates in each experiment were pooled for RNA isolation.

tag: Sex

tag: subjectid

value: HD

tag: cell line origin

value: Caucasian colon adenocarcinoma

tag: passage nr

tag: days of differentiation on transwells


title: 21 days differentiated Caco-2 cells incubated with Frutalose OFP (OFP) for 6 hours, biol rep 3

description: 21 days differentiated Caco-2 cells incubated with Frutalose OFP (OFP) for 6 hours, biological replicate 3

value: OFP

tag: treatment


title: 21 days differentiated Caco-2 cells incubated with DMEM control medium fibers (ctrl Fiber) for 6 hours, biol rep 3

description: 21 days differentiated Caco-2 cells incubated with DMEM control medium fibers (ctrl Fiber) for 6 hours, biological replicate 3

value: Ctrl Fiber


title: 21 days differentiated Caco-2 cells incubated with Frutafit CLR (CLR) for 6 hours, biol rep 3

description: 21 days differentiated Caco-2 cells incubated with Frutafit CLR (CLR) for 6 hours, biological replicate 3

value: CRL


title: UT-SCC-42A shScr 2

description:
cell line from head and neck squamous cell carcinoma transduced with scramble shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
2_UT-SCC-42A_shScr_2_S2


title: UT-SCC-42A shScr 1

description:
cell line from head and neck squamous cell carcinoma transduced with scramble shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
1_UT-SCC-42A_shScr_1_S1


title: 21 days differentiated Caco-2 cells incubated with Frutalose OFP (OFP) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with Frutalose OFP (OFP) for 6 hours, biological replicate 2

value: male


title: 21 days differentiated Caco-2 cells incubated with Frutafit CLR (CLR) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with Frutafit CLR (CLR) for 6 hours, biological replicate 2


title: 21 days differentiated Caco-2 cells incubated with Frutafit TEX! (TEX) for 6 hours, biol rep 3

description: 21 days differentiated Caco-2 cells incubated with Frutafit TEX! (TEX) for 6 hours, biological replicate 3

value: TEX


title: 21 days differentiated Caco-2 cells incubated with Frutafit HD (HD) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with Frutafit HD (HD) for 6 hours, biological replicate 2


title: UT-SCC-42A shPPFIA1 44

description:
cell line from head and neck squamous cell carcinoma transduced with shPPFIA1 44 shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
5_UT-SCC-42A_shPPFIA1_44_S5


title: 7dSS_10-2

city: Los Angeles

first: Hilary

last: Coller

state: CA

address: 610 Charles E Young Drive E

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
Reads from polyadenylation site-enriched cDNA libraries were aligned to the human genome (hg19) using STAR aligner.
Reads were assigned to a polyadenylation site based on annotations in the PolyA_DB version (active on Sept 25, 2014).
Reads matching to polyadenylation sites were then used as input into the DEXSeq differential exon expression-testing algorithm. The different polyadenylation sites for each gene were treated as different exons for DEXSeq analysis.
Significant differences in polyadenylation site use were determined across three biological replicates of the proliferating, 7dSS, and 7dCI cells. Genes with significant differences in polyadenylation site use (q < 0.1) were reported.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated values (CSV) file containing counts for the polyadenylation sites for all the samples.

source_name: 7-day serum-starved_fibroblasts

growth_protocol: Proliferating fibroblasts were grown in a complete medium (DMEM and 10% FBS) and harvested at 60-70% confluency. For 7-day contact inhibited (7dCI) fibroblasts, the cells were plated at a density of 5 x 105 cells per 10 cm dish on day 1. Fresh medium was added every 48 hours and the contact-inhibited cells were harvested on day 7. For serum-starved cells, the cells were plated in complete medium at density of 5 x 105 cells per 10 cm dish. Next day (day 1), the complete medium was replaced with low serum medium (DMEM with 0.1% FBS). The medium was replaced with fresh medium (low-serum) every 48 hours. The serum-starved cells were harvested on day 7.

extract_protocol:
Proliferating, 7dCI, and 7dSS fibroblasts were lysed using 1 mL of Trizol reagent (Life Technologies, Carlsbad, CA) per 10 cm plate for 5 minutes.  RNA was isolated from Trizol lysates following manufacturer instructions. RNA concentrations were determined using a Nanodrop Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA). RNA quality was verified on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) using reagents from the RNA Nano 6000 kit (Agilent Technologies).
cDNA libraries containing fragments enriched for 3´ ends of transcripts were created with the Gnomegen RNA-Seq Library Preparation Kit for RNA profiling (Gnomegen, San Diego, CA). Libraries with a uniform size distribution between 200 and 1000 bp were subjected to gel size selection to enrich for 200 – 300 bp sized fragments. Single-end 140 bp reads were generated on an Illumina HiSeq 2000 Instrument. The sequencing reaction was run for 147 cycles.

treatment_protocol: No treatment.

value: human dermal fibroblasts (foreskin)

tag: cell growth conditions

value: 7 day serum starved cells (quiescent)


title: 7dSS_12-2

tag: cell type


title: UT-SCC-42A shScr 3

description:
cell line from head and neck squamous cell carcinoma transduced with scramble shRNA
Henna_RNA_results_annotated_shPPFIA1_vs_shScr.xlsx
3_UT-SCC-42A_shScr_3_S3


title: 7dSS_12-1


title: 1dayCarb_3: 1 day Carbenicillin-treated plants replica 3

city: Madrid

first: Federico

last: Navarro-García

state: Madrid

address: Plaza de Ramón y Cajal

department: Microbiología y Parasitología

institute: Universidad Complutense de Madrid

data_processing:
Sequenced in an Illumina sequencing system HiSeq 2000 with a depth of 1.5 Gbp.
Quality analysis of libraries was performed with FastQC (Andrews, 2010). Prior to mapping reads to the reference database, all sequences were filtered to remove the first 10 bp of each read, the adaptor sequences, low quality sequences and reads with less than 30 bp using Cutadapt (Martin,2011).
Differentially expressed genes were determined with edgeR (Robinson et al. 2010) using as criteria fold change ≥2 and p-value<0.01. The heatmaps were done using Matrix2png interface platform (Pavlidis and Noble 2003).

organism: Arabidopsis thaliana

growth_protocol: Seeds were stratified for 3-5 days at 4°C and grown in growth chambers under long day conditions (16-h light/8-h dark photoperiod, 100 μmol·m-2·s-1) at 24°C.

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini Kit (Qiagen) according to manufacturer´s instructions and then was frozen at -80°C until analyzed. The RNA concentration and integrity (RIN) were measured in a RNA nanochip (Bioanalyzer, Agilent Technologies 2100).
RNA-Seq libraries were generated using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) .

treatment_protocol: Three types of samples were harvested: seedlings grown on ½ MS plates for 6 days under long day conditions before being transferred to (i) ½ MS (mock) or (ii) ½ MS supplemented with 10 µg·mL-1 of carbenicillin for 1 day (1 day Carbenicillin-treated plants); and (iii) seedlings grown on ½ MS plates supplemented with 10 µg·mL-1 of carbenicillin for 6 days under long day conditions before being transferred to  ½ MS supplemented with 10 µg·mL-1 of carbenicillin for 1 additional day (7 day Carbenicillin-treated plants).

tag: ecotype

tag: tissue

value: root


title: 21 days differentiated Caco-2 cells incubated with DMEM control medium fibers (ctrl Fiber) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with DMEM control medium fibers (ctrl Fiber) for 6 hours, biological replicate 2


title: 21 days differentiated Caco-2 cells incubated with Frutafit TEX! (TEX) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with Frutafit TEX! (TEX) for 6 hours, biological replicate 2


title: BO.027.SM_M

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

institute: IZBI

description:
DESeq2_normalized_counts.txt
BO-027-SM_M

data_processing:
Sequencing was performed according to the paired-end RNA sequencing protocols from Illumina on a HighSeq2000 with paired-end module (Illumina Inc). Seventy-six bps were sequenced, from each side of a fragment about 95-125 bp long and an average number 140 million reads per sample.
Paired-end reads were aligned to the human reference genome (hg19) using gsnap (version 2012-07-20) with default parameters. For each sample all reads overlapping a gene were assigned to the gene. Normalization was done based on the raw counts by library size using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: text file with DESeq2 normalized counts

source_name: skin

extract_protocol:
Biopsies of primary melanomas samples (n=57) and benign melanocytic nevi (n=23). Melanoma and nevus samples were snap frozen using liquid nitrogen and stored at -80oC until further processing. Laser-capture microdissection was performed as described earlier (Jäger et al., 2007). Total RNA was extracted from microdissected nevus and melanoma tissues using commercially available systems (RNeasy kit, Qiagen, Hilden, Germany). RNA quality was analyzed using an Agilent 2100 Bioanalyser (Agilent Technologies, Böblingen, Germany).
High-Throughput paired-end RNA sequencing library construction followed the standard Illumina mRNA library preparation protocol (www.illumina.com; Illumina Inc, San Diego, CA, U.S.A.), including poly-A mRNA isolation, fragmentation, and gel-based size selection.

value: primary melanoma

tag: group

tag: melanoma on nevus

value: no

tag: braf mutation

value: wt

tag: nras mutation

value: mut


title: LE.073.HK_M

description:
DESeq2_normalized_counts.txt
LE-073-HK_M


title: 1dayCarb_2: 1 day Carbenicillin-treated plants replica 2


title: P_10-2

source_name: proliferating fibroblasts

tag: strain

value: proliferating cells


title: 7dCI_12-1

source_name: 7-day contact inhibited_fibroblasts

value: 7 day contact inhibited cells (quiescent)


title: P_12-2


title: 7dCI_12-2


title: 7dCI_10-2


title: P_12-1


title: 21 days differentiated Caco-2 cells incubated with L. casei (W56) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with L. casei (W56) for 6 hours, biological replicate 2

tag: cell line


title: 21 days differentiated Caco-2 cells incubated with DMEM control medium probiotics (ctrl Pro) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with DMEM control medium probiotics (ctrl Pro) for 6 hours, biological replicate 2

value: Ctrl Pro


title: 7dayCarb_3: 7 day Carbenicillin-treated plants replica 3


title: RS_M

description:
DESeq2_normalized_counts.txt
RS_M


title: 1dayCarb_1: 1 day Carbenicillin-treated plants replica 1


title: 7dayCarb_2: 7 day Carbenicillin-treated plants replica 2


title: 21 days differentiated Caco-2 cells incubated with Frutalose OFP (OFP) for 6 hours, biol rep 1

description: 21 days differentiated Caco-2 cells incubated with Frutalose OFP (OFP) for 6 hours, biological replicate 1


title: 21 days differentiated Caco-2 cells incubated with Frutafit CLR (CLR) for 6 hours, biol rep 1

description: 21 days differentiated Caco-2 cells incubated with Frutafit CLR (CLR) for 6 hours, biological replicate 1


title: 21 days differentiated Caco-2 cells incubated with DMEM control medium fibers (ctrl Fiber) for 6 hours, biol rep 1

description: 21 days differentiated Caco-2 cells incubated with DMEM control medium fibers (ctrl Fiber) for 6 hours, biological replicate 1


title: 7dayCarb_1: 7 day Carbenicillin-treated plants replica 1


title: 21 days differentiated Caco-2 cells incubated with L. acidophilus (W37) for 6 hours, biol rep 1

description: 21 days differentiated Caco-2 cells incubated with L. acidophilus (W37) for 6 hours, biological replicate 1


title: 21 days differentiated Caco-2 cells incubated with L. acidophilus (W37) for 6 hours, biol rep 2

description: 21 days differentiated Caco-2 cells incubated with L. acidophilus (W37) for 6 hours, biological replicate 2


title: 21 days differentiated Caco-2 cells incubated with Frutafit HD (HD) for 6 hours, biol rep 1

description: 21 days differentiated Caco-2 cells incubated with Frutafit HD (HD) for 6 hours, biological replicate 1

value: HD