title: WT_16m_9970_1_1

description:
1WT#1
WT_16m_9970_1_1


title: WT_4m_9969_1_3

status: Public on Jul 26 2017

type: RNA

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

country: USA

institute: UCLA

description:
1WT#3
WT_4m_9969_1_3

hyb_protocol: Standard agilent protocol

scan_protocol: Standard agilent protocol

data_processing: Agilent Feature Extraction software with default parameters was used for data processing. Expression levels were extracted from Agilent microarray image files, then normalized and log2-transformed, with software R (version 2.15.3) and Bioconductor (version 2.11) packages.

molecule: total RNA

organism: Mus musculus

source_name: WT_4 month_microglia

label_protocol: Standard agilent protocol

growth_protocol: Animals were generated on C57B/6J background as previously described (Martins et al 2012, PMID 23041626)

extract_protocol: we isolated microglia from 4 and 16 month old Grn+/+ and Grn−/− mice using Percoll gradients and fluorescence-activated cell sorting (FACS) with microglia/macrophage/neutrophil markers, CD11b PE, CD45 APC and anti-Ly6G PE-Cy7

tag: strain background

tag: genotype

value: WT

tag: age

value: 4 month

tag: tissue

value: microglia


title: KO_4m_9969_2_3

description:
2KO#3
KO_4m_9969_2_3

source_name: KO_4 month_microglia

value: KO


title: SU5

city: Braunschweig

first: Daniel

last: Goedbloed

address: Mendelssohnstrasse 4

country: Germany

institute: TUBS

description: gene expression from samples in the field

hyb_protocol: Agilent Low Input Quick Amp Labelling kit for ‘One-Color Microarray-Based Gene Expression Analysis’

scan_protocol: Agilent DNA Microarray Scanner (type C)

data_processing: feature extraction software (Agilent)

organism: Salamandra infraimmaculata

source_name: tail-tip

growth_protocol: field samples

extract_protocol: Trizol total RNA extraction

treatment_protocol: tissue samples taken in the field and stored in RNA-later at -20 degrees C

value: tail-tip

tag: site

value: Sumakh


title: SPC-A-1_rep2

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: lncRNA expression in SPC-A-1 cell line

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: SPC-A-1 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

extract_protocol: RNA was prepared using the TRIzol reagent (Invitrogen, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo, Japan) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SPC-A-1 and SPC-A-1sci cell lines were routinely cultured at 37°C in a humidified air atmosphere containing 5% carbon dioxide in Dulbecco’s Modified Eagle Media supplemented with 10% fetal bovine serum (FBS) (Biowest, South America origin), 100u/ml penicillin (Sigma-Aldrich), and 100ug/ml streptomycin (Sigma-Aldrich).

tag: cell line

tag: cell type

value: non-small cell lung cancer (NSCLC) cell line

tag: cell phenotype

value: weakly metastatic


title: overexpression of the truncated FMRP_rep2

city: Fuzhou

first: Yang

last: wenjing

address: 156 Xierhuan Road

institute: Fuzhou General Hospital

description: overexpression of the truncated FMRP in HEK293T cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000.

data_processing: The data were analyzed using Affymetrix GeneChip Command Console Software.

label: biotin

source_name: overexpression of the new truncated FMRP in HEK293T cells

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

growth_protocol: cell lines were grown at 37C with 5% CO2

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

treatment_protocol: DMEM medium with 10% FBS and 1% penicillin/streptomycin

value: human emborynic kidney 293 cells


title: SPC_A-1sci_rep3

description: lncRNA expression in SPC-A-1sci cell line

source_name: SPC-A-1sci cell line

value: highly metastatic


title: WT_4m_9969_1_2

description:
1WT#2
WT_4m_9969_1_2


title: SU4


title: overexpression of the truncated FMRP_rep1


title: SU2


title: KO_4m_9969_2_1

description:
2KO#1
KO_4m_9969_2_1


title: WT_4m_9969_1_1

description:
1WT#1
WT_4m_9969_1_1


title: KO_4m_9969_2_2

description:
2KO#2
KO_4m_9969_2_2


title: OCIMY5/NS

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

description: NS

hyb_protocol: Samples are then bead purified and 5.5 ug of ss-cDNA was fragmented, and hybridized onto Affymetrix GeneChip™ Human Transcriptome Array 2.0 at 45º C for 16 hours. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: After hybridization, the arrays were scanned in an Affymetrix GeneChip® Scanner 3000 (Thermo Fisher Scientific, Waltham, MA). Images were then acquired using AGCC 4.1.2.

data_processing: Raw data was processed and normalized with Affymetrix Expression Console and the differential analysis was performed with Affymetrix Transcriptome Analysis Console.

label: Biotin

source_name: patient-derived multiple myeloma cell line

label_protocol: RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA). Single-stranded cDNA was generated, using primers with a T7 promoter sequence, from 100 ng of total RNA. The single-stranded cDNA is converted into double-stranded cDNA using DNA polymerase. The products were in vitro transcribed to generate cRNA, and then bead-purified (Thermo Fisher Scientific). Complementary RNA is then reverse transcribed to single-stranded cDNA using 2nd cycle primers and RNase H.

growth_protocol: Cells were maintained in RPMI-1640 media, supplemented with 5% of sterile fetal calf serum and antibiotics.

extract_protocol: Total RNA was prepared using RNeasy plus kit under the protocols of the manufacturer (Qiagen, Valencia, CA).

value: multiple myeloma cell line

tag: grna

value: non-specific


title: DNA6050-056(2)_16ten

city: Gosselies

first: Baharak

last: Hooshiar Kashani

state: Charleroi

address: Rue Adrienne Bolland 8

department: Institute for Medical Immunology

country: Belgium

institute: Université Libre de Bruxelles

description: HCMV infected_16 hours

hyb_protocol: About 10 mg from each experimental sample along with Affymetrix eukaryotic hybridization controls were hybridized for 16 h to Human U 133 Plus 2.0 genome arrays, containing 54 676 transcripts.

scan_protocol: Arrays were scanned with an Affymetrix GeneChips Scanner 3000 at 570nm.

data_processing:
Simpleaffy package was used to pre-process the raw data for background correction, normalization and probe summarization by the RMA method
Differentially expressed genes were defined using a statistical tool called LIMMA package, which is part of the Bioconductor statistical analysis software.

source_name: Adult

label_protocol: Probes were generated using the Affymetrix GeneChip Expression 3’ Amplification Two-cycle Target Labeling and Controls Reagents kit

growth_protocol: Dendritic cells derived from cord or adult blood monocytes

extract_protocol: Total RNA was isolated using TRIzol reagent and RNeasy Micro kit

treatment_protocol: HCMV or Mock infection for 6 and 16 hours

value: Dendritic cells

tag: agent

value: HCMV

tag: time point

value: 16 hours


title: WT_4m_9969_1_4

description:
1WT#4
WT_4m_9969_1_4


title: OCIMY5/FAM46C gRNA #6

description: CRISP #6

value: FAM46C #6


title: SPC_A-1sci_rep1


title: WT_16m_9970_1_2

description:
1WT#2
WT_16m_9970_1_2

source_name: WT_16 month_microglia

value: 16 month


title: SPC-A-1_rep3

description: lncRNA expression in SPC-A-1 cell line


title: OCIMY5/FAM46C gRNA #1

description: CRISP #1

value: FAM46C #1


title: SPC-A-1_rep1

description: lncRNA expression in SPC-A-1 cell line


title: SR8

value: Sarach


title: SR2


title: SR11


title: NG4

value: Nahal Galim


title: SC5

value: Secher


title: HA11

value: tail-tip

value: Harashim


title: KR11

value: Karraman


title: NG2


title: SR14


title: HA5


title: NG12


title: SU13

value: Sumakh


title: HA1


title: TD28

value: Tel Dan


title: KR2


title: DO12

value: Dovev


title: TD4


title: TD27


title: SC13


title: TD26


title: TD29


title: HA3


title: TD24


title: NG5


title: TD25


title: TD30


title: DO6


title: DO3


title: TD23


title: TD12


title: TD15B


title: TD21


title: DO8


title: TD15a


title: 2516 [906]

type: genomic

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

country: Canada

institute: Université Laval

description: White spruce

hyb_protocol: Array CGH hybridizations were performed with the SureTag DNA Labeling Kit (Agilent, protocol version 7.2), following manufacturer’s instructions.

scan_protocol: Arrays were scanned using Tecan scanner station.

data_processing: The fluorescence intensities were analyzed using an in-house pipeline of R (v3.1.3) and Python (v2.7.9) scripts (available in https://bitbucket.org/jprunier/git-CNVgene-discovery) in order to correct for dye bias, take into account the GC content in the intensity variations and finally compare the 'test' genome (a descendant) to the 'reference' genome (a parent).

molecule: genomic DNA

organism: Picea glauca

label_protocol: 250 ng of DNA were labelled using the Agilent consumable and protocol.

growth_protocol: Samples were obtained cutting branches in outdoor sites.

extract_protocol: Total DNA extracted using DNeasy Plant Mini Kit (QIAgen, http://www.qiagen.com/).

treatment_protocol: No treatment.

tag: generation

value: descendant

value: needles

value: parent


title: 2516 [2388]

description: White spruce


title: 2516 [910]

description: White spruce


title: 2516 [930]

description: White spruce


title: 2516 [924]

description: White spruce


title: 2516 [920]

description: White spruce


title: 2516 [850]

description: White spruce


title: 2516 [844]

description: White spruce


title: 2516 [839]

description: White spruce


title: 2516 [799]

description: White spruce


title: 2516 [849]

description: White spruce


title: 2516 [830]

description: White spruce


title: 2516 [766]

description: White spruce


title: 2516 [775]

description: White spruce


title: 2516 [812]

description: White spruce


title: 2516 [843]

description: White spruce


title: 2516 [789]

description: White spruce


title: 2516 [728]

description: White spruce


title: 2516 [787]

description: White spruce


title: 2516 [734]

description: White spruce


title: 2516 [746]

description: White spruce


title: 2516 [891]

description: White spruce


title: 2516 [721]

description: White spruce


title: 2516 [840]

description: White spruce


title: 2516 [848]

description: White spruce


title: 2516 [753]

description: White spruce


title: 2516 [755]

description: White spruce


title: 2516 [856]

description: White spruce


title: 2516 [706]

description: White spruce


title: 2516 [667]

description: White spruce


title: SC9


title: 2516 [690]

description: White spruce


title: 2516 [700]

description: White spruce


title: 2516 [657]

description: White spruce


title: 2516 [661]

description: White spruce


title: 2516 [649]

description: White spruce


title: 2516 [658]

description: White spruce


title: 2516 [576]

description: White spruce


title: 2516 [533]

description: White spruce


title: 2516 [646]

description: White spruce


title: 2516 [618]

description: White spruce


title: 2516 [493]

description: White spruce


title: 2516 [463]

description: White spruce


title: 2516 [495]

description: White spruce


title: 2516 [420]

description: White spruce


title: 2516 [448]

description: White spruce


title: 2516 [635]

description: White spruce


title: 2516 [518]

description: White spruce


title: 2516 [545]

description: White spruce


title: 2516 [422]

description: White spruce


title: 2516 [490]

description: White spruce


title: 2516 [457]

description: White spruce


title: 2516 [508]

description: White spruce


title: 2516 [519]

description: White spruce


title: 2516 [491]

description: White spruce


title: 2516 [444]

description: White spruce


title: 2516 [606]

description: White spruce


title: 2516 [385]

description: White spruce


title: 2516 [405]

description: White spruce


title: 2516 [377]

description: White spruce


title: 2516 [449]

description: White spruce


title: 2516 [411]

description: White spruce


title: 2516 [403]

description: White spruce


title: 2516 [392]

description: White spruce


title: 2516 [336]

description: White spruce


title: 2516 [320]

description: White spruce


title: 2516 [396]

description: White spruce


title: 2516 [277]

description: White spruce


title: 2516 [407]

description: White spruce


title: 2516 [408]

description: White spruce


title: 2516 [346]

description: White spruce


title: 2516 [364]

description: White spruce


title: 2516 [307]

description: White spruce


title: 2516 [302]

description: White spruce


title: 2516 [344]

description: White spruce


title: 2516 [312]

description: White spruce


title: 2516 [329]

description: White spruce


title: 2516 [300]

description: White spruce


title: 2516 [232]

description: White spruce


title: 2516 [410]

description: White spruce


title: 2516 [224]

description: White spruce


title: 2516 [389]

description: White spruce


title: 2516 [238]

description: White spruce


title: 2516 [214]

description: White spruce


title: 2516 [159]

description: White spruce


title: 2516 [538]

description: White spruce


title: 2516 [153]

description: White spruce


title: Ts194 Healthy Cord Whole Blood

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Average Beta or normalized (provide the normalization method) Average Beta

data_processing: Raw intensities extracted using GenomeStudio v2010.1 and exported into R. Lumi colour correction and background subtraction, followed by quantile and SWAN correction.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen) as per manufacturer’s instructions.

tag: Sex

value: F

value: whole cord blood

tag: sentrix id

tag: sentrix position


title: Ts190 Healthy Cord Whole Blood


title: 2516 [122]

description: White spruce


title: 2516 [210]

description: White spruce


title: 2516 [89]

description: White spruce


title: 2516 [131]

description: White spruce


title: 2516 [274]

description: White spruce


title: 2516 [259]

description: White spruce


title: 2516 [167]

description: White spruce


title: 2516 [310]

description: White spruce


title: 2516 [278]

description: White spruce


title: 2516 [83]

description: White spruce


title: 2516 [186]

description: White spruce


title: 2516 [80]

description: White spruce


title: 2516 [163]

description: White spruce


title: 2516 [245]

description: White spruce


title: 2516 [171]

description: White spruce


title: 2516 [26]

description: White spruce


title: 2516 [22]

description: White spruce


title: Ts191 Healthy Cord Whole Blood

value: M


title: Ts192 Healthy Cord Whole Blood


title: 2516 [58]

description: White spruce


title: 2516 [34]

description: White spruce


title: Hybrid_Saccharomyces_cerevisiae_Hyb-8_replicate 2

status: Public on Jul 25 2017

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

country: Japan

institute: Kobe University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Yeast Microarrays for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Region 61x21.6 mm, Scan resolution 5um, R PMT is set to 100% and G PMT is set to 100%, XRD=0.10).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 Apr08) and Grid: 015072_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Saccharomyces cerevisiae

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the One-Color Low-input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer, and its quality checked by Agilent 2100 Bioanalyzer.

growth_protocol: Yeast strains were precultured in 5 mL YPD medium containing 50 μg/mL clonNAT, 200 μg/mL zeocin, and 300 μg/mL G418 at 150 rpm and 30°C for 24 h, followed by aerobic culturing in 500 mL YPD medium with 50 μg/mL clonNAT at 150 rpm and 30°C for 48 h. The cells were then harvested by centrifugation at 3000 ×g for 10 min and washed twice with distilled water. Cells were inoculated in 50 mL YPX medium (10 g/L yeast extract, 20 g/L Bacto-peptone, and 50 g/L xylose) with 20 mM acetic acid and 15 mM formic acid in closed 100-mL bottles equipped with a CO2 outlet at an initial cell concentration of 50 g wet cells/L. Fermentation was initiated by the addition of yeast cells into the bottle. Temperature was controlled using a water bath equipped with a magnetic stirrer. Fermentation temperatures were set to 38°C with stirring at 500 rpm. Samples obtained after 3 h of fermentation were used for RNA preparation to observe levels of gene expression.

extract_protocol: Total RNA was obtained by following the protocol provided for the Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA, USA). RNA concentration and quality were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.

tag: strain

tag: strain info

value: hybrid strain

tag: genotype/variation

value: PHO13 deleted


title: 2516 [36]

description: White spruce


title: 2516 [18]

description: White spruce


title: 2516 [33]

description: White spruce


title: Ts198 Healthy Cord Whole Blood


title: 2516 [15]

description: White spruce


title: 2516 [304]

description: White spruce


title: 2516 [70]

description: White spruce


title: 2516 [49]

description: White spruce


title: 2516 [67]

description: White spruce


title: Hybrid_Saccharomyces_cerevisiae_Hyb-8_replicate 3


title: Ts199 Healthy Cord Whole Blood


title: 2516 [65]

description: White spruce


title: Thermotolerant_Saccharomyces_cerevisiae_Sun049T-Z_replicate 3

value: xylose-utilizing diploid parental strain

value: Control


title: Acid_tolerant_Saccharomyces_cerevisiae_Sun224T-K_replicate 3


title: Acid_tolerant_Saccharomyces_cerevisiae_Sun224T-K_replicate 1


title: Thermotolerant_Saccharomyces_cerevisiae_Sun049T-Z_replicate 1


title: Hybrid_Saccharomyces_cerevisiae_Hyb-8_replicate 1


title: 2516 [73]

description: White spruce


title: Heathy CG 3

city: Shenzhen

first: Dayong

last: Gu

address: 1011, Fuqiang Road, Futian District

department: Central Laboratory of Health quarantine

institute: Shenzhen Entry-exit Inspection and Quarantine Bureau

description: The quality of RNA extraction from plasma samples, the purification quality and the activity of cRNA were assessed by the optical density ratio of OD260/OD280 using spectrometry (Nanodrop-ND 1000) and the ratios of total RNAs all lay between 1.6 and 1.8, indicating a good purity of RNA. The activity of labeled RNA (specific activity) was calculated using the following formula: specific activity = (pmol dyes per μg cRNA) = [(pmol per μL dye) / (μg per μL cRNA)]. Monochromatic labeling was performed using Cy3 dye, the total quantity of labeled RNA was ≥ 1.65μg and the specific activity was ≥ 9.0 pmol Cy3 per μg cRNA for all samples.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: The microarray raw data and images were acquired using Agilent Feature Extraction software (v11.0.1.1). Quantile normalization and data processing of raw data were performed using GeneSpring GX v12.1 software (Agilent Technologies).

label: fluorescent cRNA (Cy3 dye)

source_name: Plasma

label_protocol: The synthesis and the labeling of cRNA were performed with Quick Amp Labeling Kit, One-Color (Agilent). Briefly, the total RNA was amplified and transcribed into fluorescent cRNA with the random priming method. Fluorescence labeling of each sample was performed using 1μg of RNA. The labeled cRNAs were then purified with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

extract_protocol: The total RNA, including lncRNA, was extracted using TRIzol® Reagent (Life Technologies) and RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

tag: status

value: Alive

tag: disease state

value: healthy


title: Heathy CG 2


title: Heathy CG 1


title: Thermotolerant_Saccharomyces_cerevisiae_Sun049T-Z_replicate 2


title: Acid_tolerant_Saccharomyces_cerevisiae_Sun224T-K_replicate 2


title: CPCG_0342_H3K27ac ChIP-seq

type: SRA

city: Toronto

first: Ken

last: Kron

state: ON

address: 101 College Street, TMDT, 11th floor, room 11-601B

institute: University Health Network

description: The raw data cannot be stored with GEO due to patient privacy and has instead been uploaded to the European Genome/Phenome Archive (EGAS00001002496)

library_source: genomic

data_processing:
Bowtie 2 was used to align reads to the reference Hg19 genome.
MACS2 was used to call peaks using a q-value threshold of less than or equal to 0.005
Bedgraph files were generated using HOMER v4.7 with the makeUCSCfile command
Genome_build: hg19
Supplementary_files_format_and_content: Bed files correspond to the called peaks files from MACS2 after aligning to hg19 using Bowtie 2

source_name: primary prostate cancer tissue

extract_protocol:
Genomic DNA was extracted following sonication, clearing of lysates, and immunoprecipitation of protein/DNA complexes.
Libraries were constructed using Rubicon Thruplex FD kit using manufacturer's recommended protocol

tag: tissue

value: primary prostate cancer

tag: antibody

value: H3K27ac (Abcam cat. ab4729)


title: CPCG_0341_H3K27ac ChIP-seq


title: CPCG_0262_H3K27ac ChIP-seq


title: CPCG_0340_H3K27ac ChIP-seq


title: CPCG_0366_H3K27ac ChIP-seq


title: CPCG_0348_H3K27ac ChIP-seq


title: CPCG_0265_H3K27ac ChIP-seq


title: TB positive patient 1

value: TB


title: CPCG_0248_H3K27ac ChIP-seq


title: CPCG_0266_H3K27ac ChIP-seq


title: CPCG_0365_H3K27ac ChIP-seq


title: CAP patient 2

value: CAP


title: CPCG_0259_H3K27ac ChIP-seq


title: CAP patient 1


title: CAP patient 3


title: CPCG_0267_H3K27ac ChIP-seq


title: CPCG_0339_H3K27ac ChIP-seq


title: CPCG_0236_H3K27ac ChIP-seq


title: CPCG_0246_H3K27ac ChIP-seq


title: CPCG_0269_H3K27ac ChIP-seq


title: TB positive patient 2


title: mouse_blood_control

city: shanghai

first: Dean

last: Liu

state: shanghai

address: new ring road 138,minghang area

department: Bioinformatics

institute: OE biotech

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse blood control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: the control line and experiment line includes 3 replicates, the heat-induced ones are pretreatment in waterbath for 1h at 37℃,then moved to 38.5℃ for 1h

value: blood


title: TB positive patient 3


title: mouse_blood_ht

source_name: mouse blood after 1h heat-induced


title: CPCG_0258_H3K27ac ChIP-seq


title: 20986002_IDA_DFM

city: Mitaka

first: Takako

last: Osaki

state: Tokyo

department: Department of Infectious Diseases

institute: Kyorin University School of Medicine

hyb_protocol: not provided

scan_protocol: The arrays were washed, dried, and scanned at 5 µm resolution using a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale CA).

data_processing:
Data were extracted from scanned images using NimbleScanTM software (Roche) . Quantile normalization was performed across replicate arrays, and RMA (Robust Multiple Average) analysis was performed to generate gene expression values. The gene expression values were compared between IDA and control strains using total RNA extracted from bacterial culture in Brucella containing with 7% horse serum(BHS)(Ex 1, 07THKS17-227473).  In addition, total RNA extracted from the culture in BHS with DFM or without DFM were also compared. Actually, the gene expression values of Ex 1 were used as culture without DFM, and the gene expression values of the culture with DFM was newly obtained (08THKS24).
A ≥3.5-fold difference in gene expression values was defined as significant between culture samples of IDA and control isolates, and between those with or without addition of 50 µM DFM. Student’s t –test with Bonferroni correction also were performed and p values < 0.05 were considered significant.

organism: Helicobacter pylori

source_name: bacterial culture+DFM

label_protocol: A total of 10 µg of bacterial RNA was processed and labeled as per the standard NimbleChip protocol. Briefly, RNA was converted into cDNA using the SuperScript II cDNA Conversion Kit (Invitrogen). Double-stranded cDNA was random-prime labeled with Cy3-nonamers and hybridized to the microarray for 16 h at 42ºC.

growth_protocol: The isolates were inoculated under microaerobic conditions (5% O2, 10% CO2, 85% N2) at 37 ºC onto Brucella horse serum agar (BHA), containing Brucella broth (Difco, Detroit MI), 1.5% Bacto agar and 7% horse serum.For liquid cultures, H. pylori cells were inoculated to an OD595 of 0.05-0.10 and cultured in Brucella broth containing 7% horse serum with shaking under microaerobic conditions. Liquid cultures (60mL) of each isolate (OD600 = 0.5-0.9) were treated with Bacterial RNA Protect (Qiagen, Valencia CA), according to the manufacturer’s guideline and stored at -80 ºC until use.

extract_protocol: Total RNA was purified from each culture using ChargeSwitch® Total RNA Cell Kits (Invitrogen Corporation, Carlsbad CA). The integrity of the purified RNA was verified using 1% agarose gel electrophoresis.

tag: patient diagnosis

value: IDA


title: 20986102_IDA_DFM


title: MCF7 cells treated with TGF-β, biological rep1

city: Xi'an

first: Lei

address: 169 Changle West Road

department: Department of Biochemistry and Molecular Biology

institute: Fourth Military Medical University

description: Gene expression data from MCF7 cells treated with TGF-β for 4 days

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

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

tag: cell type

value: Breast cancer cell line


title: 227473A03_IDA

source_name: bacterial culture


title: 20985902_control_DFM

value: Control (other gastric disorder)


title: 227473A04_IDA


title: MCF7 cells treated with TGF-β, biological rep2

source_name: MCF7 cells treated with TGF-β for 4 days


title: 227439A01_IDA


title: 227473A02_control


title: MCF7 cells not treated with TGF-β, biological rep2

description: Gene expression data from MCF7 cells not treated with TGF-β for 4 days


title: MCF7 cells not treated with TGF-β, biological rep3

source_name: MCF7 cells not treated with TGF-β for 4 days


title: 227439A04_control


title: MCF7 cells not treated with TGF-β, biological rep1


title: 20986202_control_DFM


title: CR6, IEL, day 30, biological rep4

status: Public on Jul 24 2017

city: Philadelphia

first: Vesselin

middle: T

last: Tomov

state: PA

address: 421 Curie Boulevard

department: Medicine/GI

institute: University of Pennsylvania

description: Gene expression data from Tet+ CD8 T cells from IEL at day 30 of MNV-CR6 infection

hyb_protocol: RNA from sorted cells was isolated, processed, amplified, labeled, and hybridized to MoGene 2.0 Micorarrays (Affymetrix, Santa Clara, CA) at the Molecular Profiling Facility at the University of Pennsylvania.

data_processing: The data were analyzed with Affymetrix Expression Console Build 1.4.1.46 using the RMA Algorithm with default settings.

extract_protocol:
MNV-specific (Tet+) CD8 T cells were isolated from spleen and IEL at days 8, 15, and 30, and sorted to >90% purity.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: intraepithelial lymphocytes

tag: day post infection

value: day 30

tag: mnv strain


title: 227473A01_IDA


title: NAIVE, IEL, biological rep3

description: Gene expression data from CD8 T cells from IEL of naïve mouse

scan_protocol: RNA from sorted cells was isolated, processed, amplified, labeled, and hybridized to MoGene 2.0 Micorarrays (Affymetrix, Santa Clara, CA) at the Molecular Profiling Facility at the University of Pennsylvania.

source_name: CD8 T cells from IEL of naïve mouse

value: NAÏVE


title: CPCG_0242_H3K27ac ChIP-seq


title: CR6, IEL, day 30, biological rep3

source_name: Tet+ CD8 T cells from IEL at day 30 of MNV-CR6 infection

label_protocol: RNA from sorted cells was isolated, processed, amplified, labeled, and hybridized to MoGene 2.0 Micorarrays (Affymetrix, Santa Clara, CA) at the Molecular Profiling Facility at the University of Pennsylvania.


title: NAIVE, IEL, biological rep2


title: CR6, IEL, day 30, biological rep2


title: 227439A02_control


title: 227439A03_control


title: CW3, IEL, day 30, biological rep3

description: Gene expression data from Tet+ CD8 T cells from IEL at day 30 of MNV-CW3 infection


title: NAIVE, IEL, biological rep1


title: CW3, IEL, day 30, biological rep2

source_name: Tet+ CD8 T cells from IEL at day 30 of MNV-CW3 infection


title: MCF7 cells treated with TGF-β, biological rep3


title: CR6, IEL, day 30, biological rep1


title: CW3, IEL, day 30, biological rep1


title: CR6, IEL, day 15, biological rep4

description: Gene expression data from Tet+ CD8 T cells from IEL at day 15 of MNV-CR6 infection

value: day 15


title: CW3, IEL, day 8, biological rep3

description: Gene expression data from Tet+ CD8 T cells from IEL at day 8 of MNV-CW3 infection

value: day 8


title: CW3, IEL, day 15, biological rep4

description: Gene expression data from Tet+ CD8 T cells from IEL at day 15 of MNV-CW3 infection


title: CR6, IEL, day 15, biological rep3

source_name: Tet+ CD8 T cells from IEL at day 15 of MNV-CR6 infection


title: CR6, IEL, day 8, biological rep3

description: Gene expression data from Tet+ CD8 T cells from IEL at day 8 of MNV-CR6 infection


title: CW3, IEL, day 8, biological rep2

source_name: Tet+ CD8 T cells from IEL at day 8 of MNV-CW3 infection


title: CW3, IEL, day 15, biological rep3

source_name: Tet+ CD8 T cells from IEL at day 15 of MNV-CW3 infection


title: CR6, IEL, day 8, biological rep2

source_name: Tet+ CD8 T cells from IEL at day 8 of MNV-CR6 infection


title: CR6, IEL, day 15, biological rep1


title: CR6, SPL, day 30, biological rep3

description: Gene expression data from Tet+ CD8 T cells from spleen at day 30 of MNV-CR6 infection

value: spleen


title: CW3, IEL, day 8, biological rep4


title: CPCG_0233_H3K27ac ChIP-seq


title: CR6, SPL, day 30, biological rep2

source_name: Tet+ CD8 T cells from spleen at day 30 of MNV-CR6 infection


title: CW3, IEL, day 15, biological rep2


title: CR6, SPL, day 30, biological rep4


title: CR6, SPL, day 30, biological rep1


title: CR6, IEL, day 8, biological rep1


title: NAIVE, SPL, biological rep1

description: Gene expression data from CD8 T cells from spleen of naïve mouse

source_name: CD8 T cells from spleen of naïve mouse


title: CW3, SPL, day 30, biological rep4

description: Gene expression data from Tet+ CD8 T cells from spleen at day 30 of MNV-CW3 infection


title: CW3, IEL, day 15, biological rep1


title: NAIVE, SPL, biological rep3


title: CW3, IEL, day 8, biological rep1


title: CR6, IEL, day 15, biological rep2


title: CR6, SPL, day 15, biological rep4

description: Gene expression data from Tet+ CD8 T cells from spleen at day 15 of MNV-CR6 infection


title: NAIVE, SPL, biological rep4


title: CW3, SPL, day 30, biological rep3

source_name: Tet+ CD8 T cells from spleen at day 30 of MNV-CW3 infection


title: NAIVE, SPL, biological rep2


title: CW3, SPL, day 15, biological rep4

description: Gene expression data from Tet+ CD8 T cells from spleen at day 15 of MNV-CW3 infection


title: CR6, SPL, day 15, biological rep2

source_name: Tet+ CD8 T cells from spleen at day 15 of MNV-CR6 infection


title: CR6, SPL, day 8, biological rep2

description: Gene expression data from Tet+ CD8 T cells from spleen at day 8 of MNV-CR6 infection


title: CW3, SPL, day 30, biological rep2


title: CW3, SPL, day 30, biological rep1


title: CR6, SPL, day 8, biological rep1

source_name: Tet+ CD8 T cells from spleen at day 8 of MNV-CR6 infection


title: CR6, SPL, day 8, biological rep4


title: CW3, SPL, day 15, biological rep2

source_name: Tet+ CD8 T cells from spleen at day 15 of MNV-CW3 infection


title: CW3, SPL, day 15, biological rep1


title: CD154pos CD4 T cells from BCG2

status: Public on Jul 23 2017

city: Bronx

first: Shajo

last: Kunnath Velayudhan

state: New York

address: 1300 Morris Park Avenue

department: M&I

institute: Albert Einstein College of Medicine

description: expression analysis of activated mycobacteria-specific CD4 T cells

hyb_protocol: as suggested by Affymetrix

scan_protocol: GeneChip Scanner 3000 by Affymetrix

data_processing: Probe summarization and normalization using Robust Multi-array Average (RMA) method was performed using Expression Console software (Affymetrix).

source_name: CD4 T cells from spleen

label_protocol: as suggested by Affymetrix

growth_protocol: Mice were vaccinated with M. bovis BCG 6 weeks prior to experiments.

extract_protocol: Total RNA was isolated with Qiagen RNeasy Micro kit and amplified using Ovation Pico WTA Systems (NuGEN).

treatment_protocol: Splenocytes were isolated and stimulated with M. tuberculosis lysate in the presence of Monensin and CD154-PE antibody.  CD154 positive and negative live cells that are also positive for CD and CD44 were sorted into RNA protect cell reagent.

tag: tissue type

value: FACS sorted CD4 T cells


title: CW3, SPL, day 8, biological rep2

description: Gene expression data from Tet+ CD8 T cells from spleen at day 8 of MNV-CW3 infection


title: CW3, SPL, day 8, biological rep1

source_name: Tet+ CD8 T cells from spleen at day 8 of MNV-CW3 infection


title: CR6, SPL, day 15, biological rep3


title: KANSL lung 1

status: Public on Jul 22 2017

city: Frederick

first: Zane

last: Gray

state: MD

address: 1050 Boyles Street

department: Cancer and Inflammation Program

institute: National Cancer Institute

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: CEL files were analyzed using Partek Genomics Suite 6.6 software. Samples were grouped on basis of mouse background (KAL vs KANSL) and differentially expressed genes were generated in ANOVA format.

source_name: Total mouse lung at 14 weeks

label_protocol: GeneChip microarray (430 2.0) was prepared and performed by Genomics Laboratory and core facility at National Cancer Institute. 3’ IVT Express labeling kit

growth_protocol: Mice matured to 14 weeks of age before euthanization and lung harvesting

treatment_protocol: Mice and samples taken from mice were untreated and without stimulation by agent

value: lung

tag: age

value: 14 weeks

tag: description

value: Mice crossed with NOS2 knockout fail to develop lung SCC

value: KANSL


title: CW3, SPL, day 8, biological rep4


title: CD154neg CD4 T cells from BCG2


title: CD154neg CD4 T cells from BCG1


title: CR6, SPL, day 8, biological rep3


title: KALori lung 2

value: Mouse background recapitulates human lung SCC

value: KALori


title: KANSL lung 2


title: CW3, SPL, day 8, biological rep3


title: CR6, SPL, day 15, biological rep1


title: HN160-Met, rep2

status: Public on Jul 21 2017

city: Singapore

first: Shumei

last: Chia

state: Singapore

country: Singapore

institute: Genome Institute of Singapore

description: Replicate 2

hyb_protocol: Standard Agilent hybridization protocol.

scan_protocol: Standard Agilent scanning protocol.

data_processing: Data was g-process.

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Incubation medium: RPMI

extract_protocol: RNA was extracted with Qiazol reagent, followed by purification using RNeasy Mini Kit in accordance with the prescribed protocol provided with the kit.

tag: patient id

tag: cell line

value: metastatic cancer cells


title: CD154pos CD4 T cells from BCG1


title: KALori lung 1


title: CD154pos CD4 T cells from BCG3


title: CD154neg CD4 T cells from BCG3


title: CW3, SPL, day 15, biological rep3


title: HN137-Met, rep2

description: Replicate 2


title: HN159-Met, rep1

description: Replicate 1


title: HN160-Met, rep1

description: Replicate 1


title: HN148-Met, rep1

description: Replicate 1


title: plate13_beta_H5 [scPCR]

city: Aurora

first: Andrew

middle: P

last: Fontenot

state: Colorado

department: Dept. of Medicine

institute: University of Colorado Denver

description:
TCR specific primers were used on single cells after flow sorting TRAV12-1+ CD4+ cells into 96 well plates (1 cell per well) to amplify only TCRs from single CD4 T cells in each well.
Amplicon sequencing following RT-PCR of a specific gene(s).

library_source: transcriptomic

data_processing:
Library strategy: Amplicon sequencing
All processed files contain the identified TCRs and frequencies for each TCR sequence. The TCR chain and well number are included in the file names.
Paired reads were joined following the reverse complementation of the Read 1 sequences to create a 250bp total length read. Files were then split by barcode for export into individual files for each well.
Sequences were then processed using miTCR to (1) identify the V, J, and CDR3 and (2) compute frequency values for individual TCRs.
Genome_build: IMGT TCR database
Supplementary_files_format_and_content: *.txt: All processed data files contain the identified TCRs and frequencies for each TCR sequence in the well. The primer names and well location are included in the file names.

source_name: Bronchoalveolar lavage

extract_protocol:
Cells were lysed and RNA reverse transcribed using a combination of random hexamers and TCRAC/BC gene specific primers. Superscript was added, and the sealed plates were incubated in an oven for 75 minutes at 55C. For each T cell, TCRA and TCRB gene expression were separately ascertained in a series of three PCR reactions done in 96 well PCR plates.
The initial PCR was a multiplex reaction (40 TRAV and 33 TRBV primers plus constant region primers, each at 0.5 μM) using Advantage 2 polymerase mix in a 50 μl reaction volume for 35 cycles. The first round PCR products were diluted, and 2.5 μl of template was added to a 25 μl second round PCR reaction utilizing nested TCRAC and BC primers on the 3’ end. The 5’ primer for the second round PCR reaction was a common sequence that was added to the 5’ end of each of the V region primers used in PCR round 1 (designated the Illumina “short” primer). After 35 cycles of amplification, the products were diluted and used as template in a third round of PCR. This final amplification of 18-20 cycles incorporated barcodes on both ends of each PCR product to enable identification of sequences run on the Illumina MiSeq platform. Thus, unique pairs of forward and reverse primers were added to each well of a 96 well plate that specified each T cell by its position on the plate.

treatment_protocol: BAL cells were thawed and placed in culture at 2.5 x 10e6 cells/ml at 37C overnight in standard tissue culture medium supplemented with IL-2. Single cell sorting of DAPI-, CD3+, CD4+, TRAV12-1+ stained T cells was performed on a BD FACS Aria (Becton Dickinson, San Jose, CA). Cells were directly sorted as one cell/well into reverse transcription buffer in 96 well polypropylene plates.

tag: disease

value: Lofgren's syndrome sarcoidosis

tag: hla type

tag: illumina barcode r2

value: 5' - CCGTCC - 3'

tag: r2 primer name

tag: illumina barcode r1

value: 5' - TGGTATGT - 3'

tag: r1 primer name

tag: cell type isolated

value: TRAV12-1+, CD4+ T cells


title: plate13_beta_H1 [scPCR]

value: 5' - GGTCTACG - 3'


title: plate13_beta_H2 [scPCR]

value: 5' - TGCTCGTA - 3'


title: plate13_beta_H9 [scPCR]

value: 5' - TGCGTACT - 3'


title: HN159-Met, rep2

description: Replicate 2

tag: tissue


title: plate13_beta_H11 [scPCR]

value: 5' - GTGTACTG - 3'


title: HN148-Met, rep2

description: Replicate 2


title: plate13_beta_H7 [scPCR]

value: 5' - GGTACAGT - 3'


title: plate13_beta_G12 [scPCR]

value: 5' - TGAGTACA - 3'


title: plate13_beta_H12 [scPCR]

value: 5' - TGTGTGTA - 3'


title: plate13_beta_H8 [scPCR]

value: 5' - GTGACGCT - 3'


title: plate13_beta_H10 [scPCR]

value: 5' - GTAGCGTG - 3'


title: plate13_beta_H6 [scPCR]

value: 5' - TGAGTAGT - 3'


title: plate13_beta_H4 [scPCR]

value: 5' - GGCGACGA - 3'


title: plate13_beta_G6 [scPCR]

value: 5' - GTGACACG - 3'


title: plate13_beta_H3 [scPCR]

value: 5' - GTGCTCTA - 3'


title: plate13_beta_G8 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - TGACTATG - 3'


title: plate13_beta_G11 [scPCR]

value: 5' - CCGTCC - 3'

value: 5' - GTGCGTGA - 3'


title: plate13_beta_G3 [scPCR]

value: 5' - TGAGTGCT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_beta_G4 [scPCR]

value: 5' - GGTCTGAT - 3'


title: plate13_beta_G7 [scPCR]

value: 5' - GCGTATCA - 3'


title: plate13_beta_G9 [scPCR]

value: 5' - GTGTCTCG - 3'


title: HN137-Met, rep1

description: Replicate 1

value: metastatic cancer cells


title: HN120-Met, rep1

description: Replicate 1


title: plate13_beta_G5 [scPCR]

value: 5' - TGCGATAT - 3'


title: plate13_beta_G2 [scPCR]

value: 5' - GTGCGTCT - 3'


title: plate13_alpha_G10 [scPCR]

value: 5' - CGTCGTAT - 3'


title: plate13_alpha_G11 [scPCR]

value: 5' - AGCCGTGA - 3'


title: plate13_alpha_H2 [scPCR]

value: 5' - GCCTCGTA - 3'


title: plate13_alpha_H11 [scPCR]

value: 5' - AGCTACTG - 3'


title: plate13_alpha_H4 [scPCR]

value: 5' - CGCGACGA - 3'


title: plate13_alpha_G6 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - AGCACACG - 3'


title: plate13_alpha_G7 [scPCR]

value: 5' - CCGTCC - 3'

value: 5' - CCGTATCA - 3'


title: plate13_alpha_G2 [scPCR]

value: 5' - AGCCGTCT - 3'


title: plate13_alpha_H10 [scPCR]

value: 5' - CTAGCGTG - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_alpha_H5 [scPCR]

value: 5' - GCGTATGT - 3'


title: plate13_alpha_H3 [scPCR]

value: 5' - AGCCTCTA - 3'


title: plate13_alpha_H6 [scPCR]

value: 5' - GCAGTAGT - 3'


title: plate13_alpha_H9 [scPCR]

value: 5' - GCCGTACT - 3'


title: plate13_alpha_H8 [scPCR]

value: 5' - AGCACGCT - 3'


title: plate13_alpha_G8 [scPCR]

value: 5' - GCACTATG - 3'


title: plate13_alpha_G3 [scPCR]

value: 5' - GCAGTGCT - 3'


title: plate13_alpha_H12 [scPCR]

value: 5' - GCTGTGTA - 3'


title: plate13_alpha_G12 [scPCR]

value: 5' - GCAGTACA - 3'


title: plate13_beta_G10 [scPCR]

value: 5' - GGTCGTAT - 3'


title: plate13_alpha_G1 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - CCGAGCGT - 3'


title: plate13_alpha_H7 [scPCR]

value: 5' - CCGTCC - 3'

value: 5' - CGTACAGT - 3'


title: plate13_beta_F4 [scPCR]

value: 5' - ATGTCA - 3'

value: 5' - GGCGACGA - 3'


title: plate13_beta_F12 [scPCR]

value: 5' - TGTGTGTA - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_alpha_H1 [scPCR]

value: 5' - CGTCTACG - 3'


title: plate13_beta_F1 [scPCR]

value: 5' - GGTCTACG - 3'


title: plate13_beta_F2 [scPCR]

value: 5' - TGCTCGTA - 3'


title: plate13_beta_F11 [scPCR]

value: 5' - GTGTACTG - 3'


title: plate13_alpha_G5 [scPCR]

value: 5' - GCCGATAT - 3'


title: plate13_beta_G1 [scPCR]

value: 5' - GCGAGCGT - 3'


title: plate13_beta_E11 [scPCR]

value: 5' - GTGCGTGA - 3'


title: plate13_beta_E8 [scPCR]

value: 5' - TGACTATG - 3'


title: plate13_beta_E5 [scPCR]

value: 5' - TGCGATAT - 3'


title: plate13_beta_E7 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GCGTATCA - 3'


title: plate13_beta_E6 [scPCR]

value: 5' - GTGACACG - 3'


title: plate13_beta_E4 [scPCR]

value: 5' - GGTCTGAT - 3'


title: plate13_alpha_G4 [scPCR]

value: 5' - CCGTCC - 3'

value: 5' - CGTCTGAT - 3'


title: plate13_alpha_G9 [scPCR]

value: 5' - AGCTCTCG - 3'


title: plate13_beta_E3 [scPCR]

value: 5' - ATGTCA - 3'

value: 5' - TGAGTGCT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_alpha_F12 [scPCR]

value: 5' - GCTGTGTA - 3'


title: plate13_alpha_F11 [scPCR]

value: 5' - AGCTACTG - 3'


title: plate13_alpha_F9 [scPCR]

value: 5' - GCCGTACT - 3'


title: plate13_alpha_F7 [scPCR]

value: 5' - CGTACAGT - 3'


title: plate13_beta_F8 [scPCR]

value: 5' - GTGACGCT - 3'


title: plate13_alpha_F10 [scPCR]

value: 5' - CTAGCGTG - 3'


title: plate13_beta_F10 [scPCR]

value: 5' - GTAGCGTG - 3'


title: plate13_beta_F7 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GGTACAGT - 3'


title: plate13_beta_F9 [scPCR]

value: 5' - TGCGTACT - 3'


title: plate13_beta_F6 [scPCR]

value: 5' - TGAGTAGT - 3'


title: plate13_alpha_F5 [scPCR]

value: 5' - GCGTATGT - 3'


title: plate13_beta_F5 [scPCR]

value: 5' - TGGTATGT - 3'


title: plate13_beta_E12 [scPCR]

value: 5' - TGAGTACA - 3'


title: plate13_beta_E2 [scPCR]

value: 5' - ATGTCA - 3'

value: 5' - GTGCGTCT - 3'


title: plate13_alpha_E10 [scPCR]

value: 5' - CGTCGTAT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_alpha_E11 [scPCR]

value: 5' - AGCCGTGA - 3'


title: plate13_alpha_E9 [scPCR]

value: 5' - AGCTCTCG - 3'


title: plate13_beta_E9 [scPCR]

value: 5' - GTGTCTCG - 3'


title: plate13_alpha_E4 [scPCR]

value: 5' - CGTCTGAT - 3'


title: plate13_beta_E10 [scPCR]

value: 5' - GGTCGTAT - 3'


title: plate13_alpha_F8 [scPCR]

value: 5' - AGCACGCT - 3'


title: plate13_alpha_E3 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GCAGTGCT - 3'


title: plate13_alpha_F1 [scPCR]

value: 5' - CGTCTACG - 3'


title: plate13_alpha_F3 [scPCR]

value: 5' - AGCCTCTA - 3'


title: plate13_alpha_F2 [scPCR]

value: 5' - GCCTCGTA - 3'


title: plate13_alpha_E8 [scPCR]

value: 5' - GCACTATG - 3'


title: plate13_alpha_E12 [scPCR]

value: 5' - GCAGTACA - 3'


title: plate13_beta_F3 [scPCR]

value: 5' - ATGTCA - 3'

value: 5' - GTGCTCTA - 3'


title: plate13_alpha_F4 [scPCR]

value: 5' - CGCGACGA - 3'


title: plate13_alpha_E1 [scPCR]

value: 5' - CCGAGCGT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_alpha_E7 [scPCR]

value: 5' - CCGTATCA - 3'


title: plate13_alpha_E5 [scPCR]

value: 5' - GCCGATAT - 3'


title: plate13_alpha_E6 [scPCR]

value: 5' - AGCACACG - 3'


title: plate13_beta_D4 [scPCR]

value: 5' - AGTTCC - 3'

value: 5' - GGCGACGA - 3'


title: plate13_beta_E1 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GCGAGCGT - 3'


title: plate13_beta_D5 [scPCR]

value: 5' - TGGTATGT - 3'


title: plate13_alpha_F6 [scPCR]

value: 5' - GCAGTAGT - 3'


title: plate13_beta_D9 [scPCR]

value: 5' - TGCGTACT - 3'


title: plate13_beta_C12 [scPCR]

value: 5' - TGAGTACA - 3'


title: plate13_beta_C11 [scPCR]

value: 5' - GTGCGTGA - 3'


title: plate13_beta_D11 [scPCR]

value: 5' - GTGTACTG - 3'


title: plate13_beta_D10 [scPCR]

value: 5' - GTAGCGTG - 3'


title: plate13_beta_D12 [scPCR]

value: 5' - TGTGTGTA - 3'


title: plate13_beta_C10 [scPCR]

value: 5' - GGTCGTAT - 3'


title: plate13_alpha_E2 [scPCR]

value: 5' - ATGTCA - 3'

value: 5' - AGCCGTCT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_beta_C9 [scPCR]

value: 5' - GTGTCTCG - 3'


title: plate13_beta_D7 [scPCR]

value: 5' - AGTTCC - 3'

value: 5' - GGTACAGT - 3'


title: plate13_beta_D8 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GTGACGCT - 3'


title: plate13_beta_D1 [scPCR]

value: 5' - GGTCTACG - 3'


title: plate13_beta_D3 [scPCR]

value: 5' - GTGCTCTA - 3'


title: plate13_beta_D2 [scPCR]

value: 5' - TGCTCGTA - 3'


title: plate13_beta_C1 [scPCR]

value: 5' - GCGAGCGT - 3'


title: plate13_beta_C4 [scPCR]

value: 5' - GGTCTGAT - 3'


title: plate13_beta_C3 [scPCR]

value: 5' - TGAGTGCT - 3'


title: plate13_beta_C8 [scPCR]

value: 5' - TGACTATG - 3'


title: plate13_beta_C5 [scPCR]

value: 5' - TGCGATAT - 3'


title: plate13_beta_C2 [scPCR]

value: 5' - GTGCGTCT - 3'


title: plate13_beta_C7 [scPCR]

value: 5' - GCGTATCA - 3'


title: plate13_alpha_D8 [scPCR]

value: 5' - AGCACGCT - 3'


title: plate13_alpha_D12 [scPCR]

value: 5' - GCTGTGTA - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_beta_D6 [scPCR]

value: 5' - AGTTCC - 3'

value: 5' - TGAGTAGT - 3'


title: plate13_alpha_D9 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GCCGTACT - 3'


title: plate13_alpha_D10 [scPCR]

value: 5' - CTAGCGTG - 3'


title: plate13_alpha_D11 [scPCR]

value: 5' - AGCTACTG - 3'


title: plate13_alpha_D6 [scPCR]

value: 5' - GCAGTAGT - 3'


title: plate13_alpha_D7 [scPCR]

value: 5' - CGTACAGT - 3'


title: plate13_alpha_D4 [scPCR]

value: 5' - CGCGACGA - 3'


title: plate13_alpha_D5 [scPCR]

value: 5' - GCGTATGT - 3'


title: plate13_alpha_C12 [scPCR]

value: 5' - GCAGTACA - 3'


title: plate13_beta_C6 [scPCR]

value: 5' - GTGACACG - 3'


title: plate13_alpha_D3 [scPCR]

value: 5' - AGCCTCTA - 3'


title: plate13_alpha_D1 [scPCR]

value: 5' - CGTCTACG - 3'


title: plate13_alpha_C11 [scPCR]

value: 5' - AGCCGTGA - 3'


title: plate13_alpha_C10 [scPCR]

value: 5' - CGTCGTAT - 3'


title: plate13_alpha_C8 [scPCR]

value: 5' - GCACTATG - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_alpha_C9 [scPCR]

value: 5' - AGTTCC - 3'

value: 5' - AGCTCTCG - 3'


title: plate13_alpha_C7 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - CCGTATCA - 3'


title: plate13_alpha_C6 [scPCR]

value: 5' - AGCACACG - 3'


title: plate13_alpha_C4 [scPCR]

value: 5' - CGTCTGAT - 3'


title: plate13_alpha_C5 [scPCR]

value: 5' - GCCGATAT - 3'


title: plate13_alpha_C2 [scPCR]

value: 5' - AGCCGTCT - 3'


title: plate13_alpha_C3 [scPCR]

value: 5' - GCAGTGCT - 3'


title: plate13_beta_B12 [scPCR]

value: 5' - AGTCAA - 3'

value: 5' - TGTGTGTA - 3'


title: plate13_beta_B11 [scPCR]

value: 5' - GTGTACTG - 3'


title: plate13_alpha_C1 [scPCR]

value: 5' - CCGAGCGT - 3'


title: plate13_beta_B10 [scPCR]

value: 5' - GTAGCGTG - 3'


title: plate13_alpha_D2 [scPCR]

value: 5' - GCCTCGTA - 3'


title: plate13_beta_B4 [scPCR]

value: 5' - GGCGACGA - 3'


title: plate13_beta_B9 [scPCR]

value: 5' - TGCGTACT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_beta_B5 [scPCR]

value: 5' - TGGTATGT - 3'


title: plate13_beta_B8 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GTGACGCT - 3'


title: plate13_beta_B3 [scPCR]

value: 5' - GTGCTCTA - 3'


title: plate13_beta_B7 [scPCR]

value: 5' - GGTACAGT - 3'


title: plate13_beta_B6 [scPCR]

value: 5' - TGAGTAGT - 3'


title: plate13_beta_A8 [scPCR]

value: 5' - TGACTATG - 3'


title: plate13_beta_A9 [scPCR]

value: 5' - GTGTCTCG - 3'


title: plate13_beta_A12 [scPCR]

value: 5' - AGTCAA - 3'

value: 5' - TGAGTACA - 3'


title: plate13_beta_B1 [scPCR]

value: 5' - GGTCTACG - 3'


title: plate13_beta_B2 [scPCR]

value: 5' - TGCTCGTA - 3'


title: plate13_beta_A11 [scPCR]

value: 5' - GTGCGTGA - 3'


title: plate13_beta_A10 [scPCR]

value: 5' - GGTCGTAT - 3'


title: plate13_beta_A5 [scPCR]

value: 5' - TGCGATAT - 3'


title: plate13_beta_A6 [scPCR]

value: 5' - GTGACACG - 3'


title: plate13_beta_A7 [scPCR]

value: 5' - GCGTATCA - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_beta_A1 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GCGAGCGT - 3'


title: plate13_beta_A2 [scPCR]

value: 5' - GTGCGTCT - 3'


title: plate13_alpha_B12 [scPCR]

value: 5' - GCTGTGTA - 3'


title: plate13_alpha_B11 [scPCR]

value: 5' - AGCTACTG - 3'


title: plate13_alpha_B8 [scPCR]

value: 5' - AGCACGCT - 3'


title: plate13_alpha_B9 [scPCR]

value: 5' - GCCGTACT - 3'


title: plate13_beta_A3 [scPCR]

value: 5' - AGTCAA - 3'

value: 5' - TGAGTGCT - 3'


title: plate13_alpha_B10 [scPCR]

value: 5' - CTAGCGTG - 3'


title: plate13_alpha_B6 [scPCR]

value: 5' - GCAGTAGT - 3'


title: plate13_alpha_B7 [scPCR]

value: 5' - CGTACAGT - 3'


title: plate13_alpha_B5 [scPCR]

value: 5' - GCGTATGT - 3'


title: plate13_alpha_B3 [scPCR]

value: 5' - AGCCTCTA - 3'


title: plate13_alpha_B2 [scPCR]

value: 5' - GCCTCGTA - 3'


title: plate13_alpha_A12 [scPCR]

value: 5' - GCAGTACA - 3'


title: plate13_alpha_B4 [scPCR]

value: 5' - CGCGACGA - 3'

value: TRAV12-1+, CD4+ T cells


title: plate13_alpha_B1 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - CGTCTACG - 3'


title: plate13_alpha_A10 [scPCR]

value: 5' - CGTCGTAT - 3'


title: plate13_alpha_A7 [scPCR]

value: 5' - CCGTATCA - 3'


title: plate13_alpha_A4 [scPCR]

value: 5' - CGTCTGAT - 3'


title: plate13_alpha_A5 [scPCR]

value: 5' - GCCGATAT - 3'


title: plate13_alpha_A8 [scPCR]

value: 5' - AGTCAA - 3'

value: 5' - GCACTATG - 3'


title: plate13_alpha_A6 [scPCR]

value: 5' - AGCACACG - 3'


title: plate13_alpha_A2 [scPCR]

value: 5' - AGCCGTCT - 3'


title: plate13_alpha_A11 [scPCR]

value: 5' - AGCCGTGA - 3'


title: plate12_beta_H12 [scPCR]

value: 5' - CTTGTA - 3'

value: 5' - TGTGTGTA - 3'


title: plate13_alpha_A9 [scPCR]

value: 5' - AGCTCTCG - 3'


title: plate13_alpha_A1 [scPCR]

value: 5' - CCGAGCGT - 3'


title: plate13_beta_A4 [scPCR]

value: 5' - GGTCTGAT - 3'


title: plate12_beta_H8 [scPCR]

value: 5' - GTGACGCT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_beta_H7 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GGTACAGT - 3'


title: plate12_beta_H10 [scPCR]

value: 5' - GTAGCGTG - 3'


title: plate12_beta_H4 [scPCR]

value: 5' - GGCGACGA - 3'


title: plate12_beta_H5 [scPCR]

value: 5' - TGGTATGT - 3'


title: plate12_beta_H3 [scPCR]

value: 5' - GTGCTCTA - 3'


title: plate12_beta_H2 [scPCR]

value: 5' - TGCTCGTA - 3'


title: plate13_alpha_A3 [scPCR]

value: 5' - AGTCAA - 3'

value: 5' - GCAGTGCT - 3'


title: plate12_beta_G7 [scPCR]

value: 5' - GCGTATCA - 3'


title: plate12_beta_H1 [scPCR]

value: 5' - CTTGTA - 3'

value: 5' - GGTCTACG - 3'


title: plate12_beta_G9 [scPCR]

value: 5' - GTGTCTCG - 3'


title: plate12_beta_G12 [scPCR]

value: 5' - TGAGTACA - 3'


title: plate12_alpha_H12 [scPCR]

value: 5' - GCTGTGTA - 3'


title: plate12_beta_H11 [scPCR]

value: 5' - GTGTACTG - 3'


title: plate12_beta_G8 [scPCR]

value: 5' - TGACTATG - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_beta_G10 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GGTCGTAT - 3'


title: plate12_beta_G5 [scPCR]

value: 5' - TGCGATAT - 3'


title: plate12_beta_H9 [scPCR]

value: 5' - TGCGTACT - 3'


title: plate12_beta_G4 [scPCR]

value: 5' - GGTCTGAT - 3'


title: plate12_beta_G1 [scPCR]

value: 5' - GCGAGCGT - 3'


title: plate12_beta_G2 [scPCR]

value: 5' - GTGCGTCT - 3'


title: plate12_beta_G3 [scPCR]

value: 5' - TGAGTGCT - 3'


title: plate12_beta_G6 [scPCR]

value: 5' - GTGACACG - 3'


title: plate12_beta_H6 [scPCR]

value: 5' - CTTGTA - 3'

value: 5' - TGAGTAGT - 3'


title: plate12_alpha_H10 [scPCR]

value: 5' - CTAGCGTG - 3'


title: plate12_alpha_H6 [scPCR]

value: 5' - GCAGTAGT - 3'


title: plate12_alpha_H9 [scPCR]

value: 5' - GCCGTACT - 3'


title: plate12_alpha_H4 [scPCR]

value: 5' - CGCGACGA - 3'


title: plate12_beta_G11 [scPCR]

value: 5' - GTGCGTGA - 3'


title: plate12_alpha_H1 [scPCR]

value: 5' - CGTCTACG - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_alpha_G6 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - AGCACACG - 3'


title: plate12_alpha_G9 [scPCR]

value: 5' - AGCTCTCG - 3'


title: plate12_alpha_G3 [scPCR]

value: 5' - GCAGTGCT - 3'


title: plate12_alpha_H5 [scPCR]

value: 5' - GCGTATGT - 3'


title: plate12_alpha_G1 [scPCR]

value: 5' - CCGAGCGT - 3'


title: plate12_beta_F10 [scPCR]

value: 5' - GGCTAC - 3'

value: 5' - GTAGCGTG - 3'


title: plate12_alpha_H7 [scPCR]

value: 5' - CTTGTA - 3'

value: 5' - CGTACAGT - 3'


title: plate12_alpha_H11 [scPCR]

value: 5' - AGCTACTG - 3'


title: plate12_alpha_G12 [scPCR]

value: 5' - GCAGTACA - 3'


title: plate12_alpha_H8 [scPCR]

value: 5' - AGCACGCT - 3'


title: plate12_alpha_G11 [scPCR]

value: 5' - AGCCGTGA - 3'


title: plate12_alpha_G5 [scPCR]

value: 5' - GCCGATAT - 3'


title: plate12_alpha_H2 [scPCR]

value: 5' - GCCTCGTA - 3'


title: plate12_alpha_H3 [scPCR]

value: 5' - AGCCTCTA - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_beta_F7 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GGTACAGT - 3'


title: plate12_beta_F6 [scPCR]

value: 5' - TGAGTAGT - 3'


title: plate12_beta_F1 [scPCR]

value: 5' - GGTCTACG - 3'


title: plate12_beta_F8 [scPCR]

value: 5' - GTGACGCT - 3'


title: plate12_beta_F9 [scPCR]

value: 5' - GGCTAC - 3'

value: 5' - TGCGTACT - 3'


title: plate12_beta_F12 [scPCR]

value: 5' - TGTGTGTA - 3'


title: plate12_beta_E7 [scPCR]

value: 5' - GCGTATCA - 3'


title: plate12_beta_E6 [scPCR]

value: 5' - GTGACACG - 3'


title: plate12_beta_F11 [scPCR]

value: 5' - GTGTACTG - 3'


title: plate12_alpha_G2 [scPCR]

value: 5' - CTTGTA - 3'

value: 5' - AGCCGTCT - 3'


title: plate12_alpha_G8 [scPCR]

value: 5' - GCACTATG - 3'


title: plate12_alpha_F12 [scPCR]

value: 5' - GCTGTGTA - 3'


title: plate12_alpha_F11 [scPCR]

value: 5' - AGCTACTG - 3'


title: plate12_alpha_F10 [scPCR]

value: 5' - CTAGCGTG - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_beta_F2 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - TGCTCGTA - 3'


title: plate12_alpha_G7 [scPCR]

value: 5' - CCGTATCA - 3'


title: plate12_alpha_F6 [scPCR]

value: 5' - GCAGTAGT - 3'


title: plate12_alpha_F7 [scPCR]

value: 5' - GGCTAC - 3'

value: 5' - CGTACAGT - 3'


title: plate12_alpha_F3 [scPCR]

value: 5' - AGCCTCTA - 3'


title: plate12_beta_E10 [scPCR]

value: 5' - GGTCGTAT - 3'


title: plate12_alpha_F2 [scPCR]

value: 5' - GCCTCGTA - 3'


title: plate12_beta_F3 [scPCR]

value: 5' - GTGCTCTA - 3'


title: plate12_alpha_F5 [scPCR]

value: 5' - GCGTATGT - 3'


title: plate12_alpha_G4 [scPCR]

value: 5' - CTTGTA - 3'

value: 5' - CGTCTGAT - 3'


title: plate12_beta_E12 [scPCR]

value: 5' - TGAGTACA - 3'


title: plate12_beta_E9 [scPCR]

value: 5' - GTGTCTCG - 3'


title: plate12_beta_E4 [scPCR]

value: 5' - GGTCTGAT - 3'


title: plate12_beta_F4 [scPCR]

value: 5' - GGCGACGA - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_beta_E11 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GTGCGTGA - 3'


title: plate12_beta_E2 [scPCR]

value: 5' - GTGCGTCT - 3'


title: plate12_beta_F5 [scPCR]

value: 5' - GGCTAC - 3'

value: 5' - TGGTATGT - 3'


title: plate12_beta_E8 [scPCR]

value: 5' - TGACTATG - 3'


title: plate12_beta_E1 [scPCR]

value: 5' - GCGAGCGT - 3'


title: plate12_alpha_F4 [scPCR]

value: 5' - CGCGACGA - 3'


title: plate12_alpha_E5 [scPCR]

value: 5' - GCCGATAT - 3'


title: plate12_alpha_F9 [scPCR]

value: 5' - GCCGTACT - 3'


title: plate12_beta_E5 [scPCR]

value: 5' - TGCGATAT - 3'


title: plate12_beta_E3 [scPCR]

value: 5' - TGAGTGCT - 3'


title: plate12_alpha_F8 [scPCR]

value: 5' - AGCACGCT - 3'


title: plate12_beta_D11 [scPCR]

value: 5' - TAGCTT - 3'

value: 5' - GTGTACTG - 3'


title: plate12_beta_D10 [scPCR]

value: 5' - GTAGCGTG - 3'


title: plate12_alpha_F1 [scPCR]

value: 5' - CGTCTACG - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_alpha_E12 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GCAGTACA - 3'


title: plate12_alpha_E10 [scPCR]

value: 5' - GGCTAC - 3'

value: 5' - CGTCGTAT - 3'


title: plate12_beta_D7 [scPCR]

value: 5' - GGTACAGT - 3'


title: plate12_beta_D6 [scPCR]

value: 5' - TGAGTAGT - 3'


title: plate12_alpha_E6 [scPCR]

value: 5' - AGCACACG - 3'


title: plate12_beta_D12 [scPCR]

value: 5' - TGTGTGTA - 3'


title: plate12_alpha_E11 [scPCR]

value: 5' - AGCCGTGA - 3'


title: plate12_alpha_E9 [scPCR]

value: 5' - AGCTCTCG - 3'


title: plate12_beta_D4 [scPCR]

value: 5' - GGCGACGA - 3'


title: plate12_alpha_E7 [scPCR]

value: 5' - CCGTATCA - 3'


title: plate12_alpha_E2 [scPCR]

value: 5' - AGCCGTCT - 3'


title: plate12_alpha_E4 [scPCR]

value: 5' - CGTCTGAT - 3'


title: plate12_alpha_E8 [scPCR]

value: 5' - GCACTATG - 3'


title: plate12_alpha_E3 [scPCR]

value: 5' - GCAGTGCT - 3'


title: plate12_beta_D9 [scPCR]

value: 5' - TAGCTT - 3'

value: 5' - TGCGTACT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_alpha_E1 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GGCTAC - 3'

value: 5' - CCGAGCGT - 3'


title: plate12_beta_D1 [scPCR]

value: 5' - GGTCTACG - 3'


title: plate12_beta_C12 [scPCR]

value: 5' - TGAGTACA - 3'


title: plate12_beta_D5 [scPCR]

value: 5' - TGGTATGT - 3'


title: plate12_beta_D2 [scPCR]

value: 5' - TGCTCGTA - 3'


title: plate12_beta_D3 [scPCR]

value: 5' - GTGCTCTA - 3'


title: plate12_beta_C10 [scPCR]

value: 5' - GGTCGTAT - 3'


title: plate12_beta_C7 [scPCR]

value: 5' - GCGTATCA - 3'


title: plate12_beta_C8 [scPCR]

value: 5' - TGACTATG - 3'


title: plate12_beta_D8 [scPCR]

value: 5' - GTGACGCT - 3'


title: plate12_beta_C5 [scPCR]

value: 5' - TGCGATAT - 3'


title: plate12_beta_C9 [scPCR]

value: 5' - GTGTCTCG - 3'


title: plate12_beta_C4 [scPCR]

value: 5' - TAGCTT - 3'

value: 5' - GGTCTGAT - 3'


title: plate12_beta_C2 [scPCR]

value: 5' - GTGCGTCT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_beta_C6 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GTGACACG - 3'


title: plate12_beta_C11 [scPCR]

value: 5' - GTGCGTGA - 3'


title: plate12_beta_C1 [scPCR]

value: 5' - GCGAGCGT - 3'


title: plate12_alpha_D12 [scPCR]

value: 5' - GCTGTGTA - 3'


title: plate12_beta_C3 [scPCR]

value: 5' - TGAGTGCT - 3'


title: plate12_alpha_D9 [scPCR]

value: 5' - GCCGTACT - 3'


title: plate12_alpha_D4 [scPCR]

value: 5' - CGCGACGA - 3'


title: plate12_alpha_D5 [scPCR]

value: 5' - GCGTATGT - 3'


title: plate12_alpha_D11 [scPCR]

value: 5' - AGCTACTG - 3'


title: plate12_alpha_D2 [scPCR]

value: 5' - GCCTCGTA - 3'


title: plate12_alpha_D3 [scPCR]

value: 5' - AGCCTCTA - 3'


title: plate12_alpha_C10 [scPCR]

value: 5' - CGTCGTAT - 3'


title: plate12_alpha_D7 [scPCR]

value: 5' - TAGCTT - 3'

value: 5' - CGTACAGT - 3'


title: plate12_alpha_C5 [scPCR]

value: 5' - GCCGATAT - 3'


title: plate12_alpha_C6 [scPCR]

value: 5' - AGCACACG - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_alpha_C7 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - CCGTATCA - 3'


title: plate12_alpha_C1 [scPCR]

value: 5' - CCGAGCGT - 3'


title: plate12_alpha_C2 [scPCR]

value: 5' - AGCCGTCT - 3'


title: plate12_alpha_D6 [scPCR]

value: 5' - GCAGTAGT - 3'


title: plate12_beta_B12 [scPCR]

value: 5' - GATCAG - 3'

value: 5' - TGTGTGTA - 3'


title: plate12_beta_B11 [scPCR]

value: 5' - GTGTACTG - 3'


title: plate12_alpha_G10 [scPCR]

value: 5' - CTTGTA - 3'


title: plate12_beta_B6 [scPCR]

value: 5' - TGAGTAGT - 3'


title: plate12_alpha_D1 [scPCR]

value: 5' - CGTCTACG - 3'


title: plate12_beta_A12 [scPCR]

value: 5' - TGAGTACA - 3'


title: plate12_alpha_D8 [scPCR]

value: 5' - TAGCTT - 3'

value: 5' - AGCACGCT - 3'


title: plate12_beta_A10 [scPCR]

value: 5' - GGTCGTAT - 3'


title: plate12_beta_A7 [scPCR]

value: 5' - GCGTATCA - 3'


title: plate12_beta_B9 [scPCR]

value: 5' - TGCGTACT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_alpha_C11 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - AGCCGTGA - 3'


title: plate12_beta_A1 [scPCR]

value: 5' - GCGAGCGT - 3'


title: plate12_alpha_D10 [scPCR]

value: 5' - CTAGCGTG - 3'


title: plate12_beta_B1 [scPCR]

value: 5' - GATCAG - 3'

value: 5' - GGTCTACG - 3'


title: plate12_beta_A2 [scPCR]

value: 5' - GTGCGTCT - 3'


title: plate12_alpha_C12 [scPCR]

value: 5' - GCAGTACA - 3'


title: plate12_beta_B5 [scPCR]

value: 5' - TGGTATGT - 3'


title: plate12_beta_B10 [scPCR]

value: 5' - GTAGCGTG - 3'


title: plate12_beta_B4 [scPCR]

value: 5' - GGCGACGA - 3'


title: plate12_alpha_C8 [scPCR]

value: 5' - TAGCTT - 3'

value: 5' - GCACTATG - 3'


title: plate12_alpha_C3 [scPCR]

value: 5' - GCAGTGCT - 3'


title: plate12_alpha_C9 [scPCR]

value: 5' - AGCTCTCG - 3'


title: plate12_alpha_B10 [scPCR]


title: plate12_beta_B8 [scPCR]

value: 5' - GTGACGCT - 3'


title: plate12_beta_A3 [scPCR]

value: 5' - TGAGTGCT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_beta_B7 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - GGTACAGT - 3'


title: plate12_alpha_C4 [scPCR]

value: 5' - CGTCTGAT - 3'


title: plate12_beta_A8 [scPCR]

value: 5' - GATCAG - 3'

value: 5' - TGACTATG - 3'


title: plate12_alpha_B6 [scPCR]

value: 5' - GCAGTAGT - 3'


title: plate12_alpha_B5 [scPCR]

value: 5' - GCGTATGT - 3'


title: plate12_alpha_B2 [scPCR]

value: 5' - GCCTCGTA - 3'


title: plate12_alpha_B1 [scPCR]

value: 5' - CGTCTACG - 3'


title: plate12_alpha_B9 [scPCR]

value: 5' - GCCGTACT - 3'


title: plate12_beta_A6 [scPCR]

value: 5' - GTGACACG - 3'


title: plate12_alpha_A10 [scPCR]

value: 5' - CGTCGTAT - 3'


title: plate12_alpha_B11 [scPCR]

value: 5' - AGCTACTG - 3'


title: plate12_beta_A9 [scPCR]

value: 5' - GTGTCTCG - 3'


title: plate12_beta_A4 [scPCR]

value: 5' - GGTCTGAT - 3'


title: plate12_alpha_B12 [scPCR]

value: 5' - GCTGTGTA - 3'


title: plate12_beta_B2 [scPCR]

value: 5' - TGCTCGTA - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_alpha_B4 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - CGCGACGA - 3'


title: plate12_alpha_B3 [scPCR]

value: 5' - GATCAG - 3'

value: 5' - AGCCTCTA - 3'


title: plate12_alpha_B8 [scPCR]

value: 5' - AGCACGCT - 3'


title: plate12_beta_A5 [scPCR]

value: 5' - TGCGATAT - 3'


title: plate12_alpha_A11 [scPCR]

value: 5' - AGCCGTGA - 3'


title: plate12_alpha_A7 [scPCR]

value: 5' - CCGTATCA - 3'


title: plate12_alpha_A8 [scPCR]

value: 5' - GCACTATG - 3'


title: plate12_alpha_A4 [scPCR]

value: 5' - CGTCTGAT - 3'


title: plate12_beta_B3 [scPCR]

value: 5' - GTGCTCTA - 3'


title: plate12_alpha_B7 [scPCR]

value: 5' - CGTACAGT - 3'


title: plate12_alpha_A12 [scPCR]

value: 5' - GCAGTACA - 3'


title: plate12_alpha_A5 [scPCR]

value: 5' - GCCGATAT - 3'


title: plate12_beta_A11 [scPCR]

value: 5' - GTGCGTGA - 3'


title: plate12_alpha_A6 [scPCR]

value: 5' - AGCACACG - 3'


title: plate12_alpha_A2 [scPCR]

value: 5' - AGCCGTCT - 3'

value: TRAV12-1+, CD4+ T cells


title: plate12_alpha_A9 [scPCR]

value: Lofgren's syndrome sarcoidosis

value: 5' - AGCTCTCG - 3'


title: plate12_alpha_A3 [scPCR]

value: 5' - GATCAG - 3'

value: 5' - GCAGTGCT - 3'


title: Pt. 1215 BAL [ePCR]

description:
TCR specific primers were used in single cell emulsion droplets to amplify only TCRs from single CD4 T cells lysed within the droplets.
Amplicon sequencing following RT-PCR of a specific gene(s).
Total RNA via single cell analysis.

data_processing:
Library strategy: Amplicon sequencing
Paired reads were joined following the reverse complementation of the Read 1 sequences to create a 550bp total length read with the C regions on the ends and the V regions in the center.
Paired reads were then clipped from either end using the overlap sequence used to joined the alpha and beta TCR molecules within the emulsion droplet during PCR amplification and overlap extension, generating an alpha and beta file with shared cluster IDs.
Sequences were then processed using miTCR and miTCRCombine to (1) identify the V, J, and CDR3, (2) to pair the reads using the cluster IDs, and (3) compute frequency values for individual read pairs.
Genome_build: IMGT TCR database
Supplementary_files_format_and_content: *txt: All processed data files contain the identified TCR pairs and frequencies for each pair. The sample source as well as the patient ID are included in the file names.

extract_protocol:
No extraction of RNA was performed. Single cells were lysed within an emulsion droplet, and RT-PCR was performed using TCR specific primers within the emulsion droplet. Two subsequent PCRs were performed after the emulsion was broken to amplify products and add Illumina barcodes to the products.
PCR amplicons were generated using primers containing the Read1, Read2, and Bridge priming sites as well as Illumina indices (Read 2 side) and custom indices on the Read 1 side.

treatment_protocol: Bronchoalveolar lavage (BAL) cells were incubated in 6 or 12 well plates for 20 minutes at 37°C to remove alveolar macrophages. CD4+ T cells were obtained after positive selection cell sorting from BAL or blood and incubated overnight in media supplemented with 30 U/ml IL-2.

value: Lofgren's syndrome (LS) sarcoidosis

tag: illumina read 2 barcode

value: 5' - GATCGC -3'

tag: custom read 1 barcode

value: 5' - CATGNNNNNNNN - 3'

value: CD4+ T cells

tag: patient


title: plate12_alpha_A1 [scPCR]

value: 5' - CCGAGCGT - 3'


title: Pt. 1229 BAL [ePCR]

value: None (healthy control)

value: 5' - CGTGAT - 3'

value: 5' - TGCANNNNNN - 3'


title: Pt. 1177 BAL [ePCR]

value: 5' - ACGTNNNN - 3'


title: Pt. 1162 BAL [ePCR]

value: 5' - ATCATC - 3'


title: Pt. 1162 Blood [ePCR]

source_name: Peripheral blood lymphocytes


title: Pt. 1127 Blood [ePCR]

value: Non-LS sarcoidosis

value: 5' - ACATGT - 3'


title: Pt. 1124 Blood [ePCR]

value: 5' - GCCTAA - 3'


title: Pt. 1124 BAL [ePCR]


title: Pt. 1103 Blood [ePCR]

value: Fibrosis (non-sarcoidosis)

value: Other (DR3-/DRB3-)


title: Pt. 1103 BAL [ePCR]


title: Pt. 1146 BAL [ePCR]


title: Pt. 1147 BAL [ePCR]

value: 5' - TGGTCA - 3'


title: Pt. 1127 BAL [ePCR]


title: Pt. 1102 BAL [ePCR]


title: Pt. 989 Blood [ePCR]


title: Pt. 1000 Blood [ePCR]


title: Pt. 1088 BAL [ePCR]


title: Pt. 1025 BAL [ePCR]


title: Pt. 1000 BAL [ePCR]


title: Pt. 989 BAL [ePCR]


title: Pt. 1180 BAL [ePCR]


title: Beak deformity bird 17

city: Beijing

first: Hao

last: Bai

address: Yuanmingyuan West Road No. 2, Haidian District

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

description: Hybridized to 600K

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
gDNA samples were genotyped using 600K Affymetrix Axiom HD genotyping arrays containing 580,954 SNPs based on the Affymetrix GeneChip platform. The genotypes were identified using Affymetrix Genotyping Console (Version 4.2, Affymetrix Inc., Santa Clara, CA, USA). The RM test was performed for the single SNP association analysis in ROADTRIPS (Version 1.2). A SRT program (Version 3, https://sourceforge.net/projects/snpratiotest/) was employed for the pathway-based analysis. PennCNV, downloaded from http://penncnv.openbioinformatics.org/en/latest/user-guide/download/, was used to detect CNVs on autosomes.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

organism: Gallus gallus

source_name: Beak deformity bird blood 17

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: All of the animal procedures were conducted in strict accordance with the guidelines proposed by the China Council on Animal Care and the Ministry of Agriculture of the People’s Republic of China. Animal experiments were approved by the Science Research Department of the IAS, CAAS (Beijing, China).

extract_protocol: Genomic DNA (gDNA) was isolated from blood samples using the phenol-chloroform method. The purity and concentration of the gDNA samples was measured using a Nanodrop ND-2000 spectrophotometer (Thermo Scientific, USA). The final concentration was adjusted to 50 ng/μL. gDNA samples with an A260/280 ratio of 1.8-2.0 were submitted for genotyping.

tag: breed

value: Beijing-You

tag: gender

value: male

value: blood


title: Beak deformity bird 15

description: Hybridized to 600K

source_name: Beak deformity bird blood 15

value: female


title: Beak deformity bird 16

description: Hybridized to 600K

source_name: Beak deformity bird blood 16


title: Beak deformity bird 13

description: Hybridized to 600K

source_name: Beak deformity bird blood 13


title: Beak deformity bird 14

description: Hybridized to 600K

source_name: Beak deformity bird blood 14


title: Beak deformity bird 12

description: Hybridized to 600K

source_name: Beak deformity bird blood 12


title: Beak deformity bird 11

description: Hybridized to 600K

source_name: Beak deformity bird blood 11


title: Beak deformity bird 7

description: Hybridized to 600K

source_name: Beak deformity bird blood 7


title: Pt. 1102 Blood [ePCR]

value: Lofgren's syndrome (LS) sarcoidosis

value: CD4+ T cells


title: Beak deformity bird 9

description: Hybridized to 600K

source_name: Beak deformity bird blood 9


title: Beak deformity bird 10

description: Hybridized to 600K

source_name: Beak deformity bird blood 10


title: Beak deformity bird 6

description: Hybridized to 600K

source_name: Beak deformity bird blood 6


title: Beak deformity bird 3

description: Hybridized to 600K

source_name: Beak deformity bird blood 3


title: Beak deformity bird 4

description: Hybridized to 600K

source_name: Beak deformity bird blood 4


title: Beak deformity bird 2

description: Hybridized to 600K

source_name: Beak deformity bird blood 2


title: Normal bird 45

description: Hybridized to 600K

source_name: Normal bird blood 45


title: Normal bird 47

description: Hybridized to 600K

source_name: Normal bird blood 47


title: Normal bird 48

description: Hybridized to 600K

source_name: Normal bird blood 48


title: Beak deformity bird 1

description: Hybridized to 600K

source_name: Beak deformity bird blood 1


title: Beak deformity bird 8

description: Hybridized to 600K

source_name: Beak deformity bird blood 8


title: Normal bird 44

description: Hybridized to 600K

source_name: Normal bird blood 44


title: Normal bird 41

description: Hybridized to 600K

source_name: Normal bird blood 41


title: Normal bird 40

description: Hybridized to 600K

source_name: Normal bird blood 40


title: Normal bird 46

description: Hybridized to 600K

source_name: Normal bird blood 46


title: Normal bird 42

description: Hybridized to 600K

source_name: Normal bird blood 42


title: Normal bird 37

description: Hybridized to 600K

source_name: Normal bird blood 37


title: Normal bird 38

description: Hybridized to 600K

source_name: Normal bird blood 38


title: Normal bird 29

description: Hybridized to 600K

source_name: Normal bird blood 29


title: Normal bird 43

description: Hybridized to 600K

source_name: Normal bird blood 43


title: Normal bird 30

description: Hybridized to 600K

source_name: Normal bird blood 30


title: Normal bird 39

description: Hybridized to 600K

source_name: Normal bird blood 39


title: Normal bird 33

description: Hybridized to 600K

source_name: Normal bird blood 33


title: Normal bird 36

description: Hybridized to 600K

source_name: Normal bird blood 36


title: Beak deformity bird 5

description: Hybridized to 600K

source_name: Beak deformity bird blood 5


title: Normal bird 28

description: Hybridized to 600K

source_name: Normal bird blood 28


title: Normal bird 34

description: Hybridized to 600K

source_name: Normal bird blood 34


title: Normal bird 31

description: Hybridized to 600K

source_name: Normal bird blood 31


title: Normal bird 19

description: Hybridized to 600K

source_name: Normal bird blood 19


title: Normal bird 35

description: Hybridized to 600K

source_name: Normal bird blood 35


title: Normal bird 14

description: Hybridized to 600K

source_name: Normal bird blood 14


title: Normal bird 16

description: Hybridized to 600K

source_name: Normal bird blood 16


title: Normal bird 27

description: Hybridized to 600K

source_name: Normal bird blood 27


title: Normal bird 25

description: Hybridized to 600K

source_name: Normal bird blood 25


title: Normal bird 26

description: Hybridized to 600K

source_name: Normal bird blood 26


title: Normal bird 23

description: Hybridized to 600K

source_name: Normal bird blood 23


title: Normal bird 22

description: Hybridized to 600K

source_name: Normal bird blood 22


title: Normal bird 20

description: Hybridized to 600K

source_name: Normal bird blood 20


title: Normal bird 21

description: Hybridized to 600K

source_name: Normal bird blood 21


title: Normal bird 18

description: Hybridized to 600K

source_name: Normal bird blood 18


title: Normal bird 8

description: Hybridized to 600K

source_name: Normal bird blood 8


title: Normal bird 15

description: Hybridized to 600K

source_name: Normal bird blood 15


title: Normal bird 24

description: Hybridized to 600K

source_name: Normal bird blood 24

value: unknown


title: Normal bird 17

description: Hybridized to 600K

source_name: Normal bird blood 17


title: Normal bird 12

description: Hybridized to 600K

source_name: Normal bird blood 12


title: Normal bird 32

description: Hybridized to 600K

source_name: Normal bird blood 32


title: Normal bird 1

description: Hybridized to 600K

source_name: Normal bird blood 1


title: Normal bird 13

description: Hybridized to 600K

source_name: Normal bird blood 13


title: Normal bird 11

description: Hybridized to 600K

source_name: Normal bird blood 11


title: Normal bird 10

description: Hybridized to 600K

source_name: Normal bird blood 10


title: CD271+SSEA-4+DPMSC_31M

city: Hirakata

first: Ryusuke

last: Nakatsuka

state: Osaka

address: 2-5-1 Shin-machi

department: Stem Cell Biology

institute: Kansai medical University

description: Young

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) （the Agilent DNA Microarray Scanner (G2565CA)）using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1（10.10.1.1） (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Femoral neck bone derived cells, treated with collagenase and dispase

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Young and elderly patients’ bone-derived 11Lin-CD45-CD271+SSEA-4+ mesenchymal stem/stromal cells at passage 4 were plated onto 6-well culture plate and cultured in aMEM with 10 % FCS.

extract_protocol: Cultured young and elderly patients’ bone-derived 11Lin-CD45-CD271+SSEA-4+ mesenchymal stem/stromal cells reached confluent, total RNA were extracted using an RNeasy Plus Micro kit (QIAGEN).

treatment_protocol: Not applicable.

tag: age

value: Male

tag: cell type


title: Beak deformity bird 44

description: Hybridized to 600K

source_name: Beak deformity bird blood 44


title: Normal bird 9

description: Hybridized to 600K

source_name: Normal bird blood 9


title: Beak deformity bird 40

description: Hybridized to 600K

source_name: Beak deformity bird blood 40


title: Normal bird 6

description: Hybridized to 600K

source_name: Normal bird blood 6


title: Beak deformity bird 39

description: Hybridized to 600K

source_name: Beak deformity bird blood 39


title: Normal bird 5

description: Hybridized to 600K

source_name: Normal bird blood 5


title: Beak deformity bird 48

description: Hybridized to 600K

source_name: Beak deformity bird blood 48


title: Normal bird 3

description: Hybridized to 600K

source_name: Normal bird blood 3


title: Normal bird 2

description: Hybridized to 600K

source_name: Normal bird blood 2


title: Normal bird 7

description: Hybridized to 600K

source_name: Normal bird blood 7


title: Beak deformity bird 47

description: Hybridized to 600K

source_name: Beak deformity bird blood 47


title: Beak deformity bird 45

description: Hybridized to 600K

source_name: Beak deformity bird blood 45


title: Beak deformity bird 36

description: Hybridized to 600K

source_name: Beak deformity bird blood 36


title: Beak deformity bird 43

description: Hybridized to 600K

source_name: Beak deformity bird blood 43


title: Normal bird 4

description: Hybridized to 600K

source_name: Normal bird blood 4


title: Beak deformity bird 41

description: Hybridized to 600K

source_name: Beak deformity bird blood 41


title: CD271+SSEA-4+DPMSC_91F

description: Elderly

source_name: Femoral neck bone derived cells, treated with collagenase and dispase

value: Female


title: Beak deformity bird 42

description: Hybridized to 600K

source_name: Beak deformity bird blood 42


title: CD271+SSEA-4+DPMSC_31F

description: Young


title: Beak deformity bird 33

description: Hybridized to 600K

source_name: Beak deformity bird blood 33


title: CD271+SSEA-4+DPMSC_80F

description: Elderly


title: CD271+SSEA-4+DPMSC_84F

description: Elderly


title: Beak deformity bird 38

description: Hybridized to 600K

source_name: Beak deformity bird blood 38


title: Beak deformity bird 27

description: Hybridized to 600K

source_name: Beak deformity bird blood 27


title: Beak deformity bird 34

description: Hybridized to 600K

source_name: Beak deformity bird blood 34


title: Beak deformity bird 31

description: Hybridized to 600K

source_name: Beak deformity bird blood 31


title: Beak deformity bird 35

description: Hybridized to 600K

source_name: Beak deformity bird blood 35


title: Beak deformity bird 37

description: Hybridized to 600K

source_name: Beak deformity bird blood 37


title: Beak deformity bird 46

description: Hybridized to 600K

source_name: Beak deformity bird blood 46


title: Beak deformity bird 23

description: Hybridized to 600K

source_name: Beak deformity bird blood 23


title: Beak deformity bird 32

description: Hybridized to 600K

source_name: Beak deformity bird blood 32


title: Beak deformity bird 21

description: Hybridized to 600K

source_name: Beak deformity bird blood 21


title: Beak deformity bird 20

description: Hybridized to 600K

source_name: Beak deformity bird blood 20


title: Beak deformity bird 19

description: Hybridized to 600K

source_name: Beak deformity bird blood 19


title: CD271+SSEA-4+DPMSC_28F

description: Young


title: Beak deformity bird 28

description: Hybridized to 600K

source_name: Beak deformity bird blood 28


title: Beak deformity bird 29

description: Hybridized to 600K

source_name: Beak deformity bird blood 29


title: Beak deformity bird 26

description: Hybridized to 600K

source_name: Beak deformity bird blood 26


title: Beak deformity bird 25

description: Hybridized to 600K

source_name: Beak deformity bird blood 25


title: Beak deformity bird 22

description: Hybridized to 600K

source_name: Beak deformity bird blood 22


title: Beak deformity bird 24

description: Hybridized to 600K

source_name: Beak deformity bird blood 24


title: Beak deformity bird 30

description: Hybridized to 600K

source_name: Beak deformity bird blood 30


title: Beak deformity bird 18

description: Hybridized to 600K

source_name: Beak deformity bird blood 18


title: cancer tissue from patient 5

status: Public on Jul 19 2017

city: Nanjing

first: Mantang

last: Qiu

state: Jiangsu

address: 42 Baiziting

department: Thoracic Surgery

institute: Cancer Institute of Jiangsu Province

hyb_protocol: The labeled circRNAs were hybridized onto an Arraystar Human circRNA Array (8×15K, Arraystar)and incubated for 17 hours at 65C in an Agilent Hybridization Oven.

scan_protocol: After the slides were washed, the arrays were scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package. Statistical differences in circRNA expression between the two groups were determined with Volcano Plot filtering. Differentially expressed circRNAs between the two sample sets were identified through Fold Change filtering. Hierarchical Clustering was performed to show distinguishable circRNAs expression patterns among samples.

source_name: lung adenocarcinoma

label_protocol: Total RNA was digested with RNase R (Epicentre, Inc.) to remove linear RNAs and to enrich for circRNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA from lung cancer tissues and lung tissues was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The RNA extractions were stored at -80C. Total RNA from each sample was quantified using a NanoDrop ND-1000. Sample preparation and microarray hybridization were performed based on Arraystar's standard protocols.

treatment_protocol: Five pairs of lung cancer tissues and lung tissues were collected from the Department of Thoracic Surgery, Cancer Hospital of Jiangsu Province. All tissue samples were stored in liquid nitrogen till RNA extraction, and pathologists from the Department of Pathology in the Cancer Hospital of Jiangsu Province performed pathologic diagnosis.

tag: Histology type

value: lung adenocarcinoma


title: lung tissue from patient 4

source_name: lung

value: normal lung tissue


title: lung tissue from patient 3


title: cancer tissue from patient 2


title: cancer tissue from patient 3


title: cancer tissue from patient 4


title: lung tissue from patient 5


title: lung tissue from patient 1


title: cancer tissue from patient 1


title: lung tissue from patient 2


title: sorted human ILCreg cells

status: Public on Jul 20 2017

first: Shuo

last: Wang

state: Beijing

address: 15 DaTun Road,Chaoyang District,Beijing

department: Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

hyb_protocol: At room temperature, prepare the Hybridization Master Mix in a nuclease-free tube. Combine the appropriate amount of components in the sequence shown in the table below. Prepare the master mix for all the fragmented and biotin-labeled ss-cDNA samples in the experiment. Include ~10% overage to correct for pipetting losses. At room temperature, add the appropriate amount of Hybridization Master Mix to each fragmented and biotin-labeled ss-cDNA sample to prepare Hybridization Cocktail. Incubate the hybridization cocktail reaction for 5 min at 99°C (tubes) or 95°C (plates), and then for 5 min at 45°C in a thermal cycler using the Hybridization Cocktail program. After the incubation, centrifuge briefly to collect contents of the tube. Insert a pipet tip into the upper right septum to allow for venting. Remove the pipet tip from the upper right septum of the array. Cover both septa with 1/2” Tough-Spots to minimize evaporation and/or prevent leaks. Place the arrays into hybridization oven trays. Load the trays into the hybridization oven. Incubate with rotation at 60 rpm for 16 hr at 45°C.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label_protocol: The purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of single-stranded cDNA is required for fragmentation and labeling, according to reference of GeneChip® WT Pico Reagent Kit, Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays UserGuide, 2015, Affymetrix.

growth_protocol: Human normal intestinal tissues from resected small intestines

extract_protocol: Sorted cells were subjected to total RNA extraction with TRIZOL reagent, followed by DNase incubation to remove nuclear DNA.

treatment_protocol: For human ILCregs, lymphocytes were isolated from human normal intestinal tissues from resected small intestines and Lin-CD45+ cells were then enriched by MACS (Lin=CD2, CD3, CD14, CD16, CD19, CD56, CD235a). Enriched cells were stained with Lineage cocktail, anti-CD45, and anti-CD127 antibodies followed by intracellular staining of IL-10. Lin-CD45+CD127+IL-10+ cells were isolated and subjected to RNA extraction.

value: ILCreg cell


title: mouse ILCreg_2

source_name: IL-10-GFP knockin mice

growth_protocol: IL-10-GFP knockin mice were maintained in SPF conditions.

treatment_protocol: 8 week-old mice were anesthetized and small intestine cells were collected, followed by ILCreg cell sorting through a BD AriaIII sorter.

tag: strain

tag: genotype/variation

value: IL-10-GFP knockin


title: mouse ILCreg_1


title: TC-RCC#2

city: Oxford

first: charles

last: lawrie

address: John Radcliffe Hospital

department: NDCLS

country: United Kingdom

institute: University of Oxford

description: Tubulocystic Renal Cell Carcinoma (TC-RCC) case

hyb_protocol: Following fragmentation, 2 ug of cRNA were hybridized for 24 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA normalized using miRNAQC software from Affymetrix

source_name: FFPE biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using the Rocoverall kit from Ambion according to manufacturers protocol

treatment_protocol: Samples were extracted from macrodisected from FFPE slides and purified using the Recoverall kit from Ambion

tag: disease state

value: TC-RCC


title: TC-RCC#9


title: TC-RCC#6


title: TC-RCC#11


title: TC-RCC#12


title: TC-RCC#7


title: TC-RCC#5


title: TC-RCC#8


title: TC-RCC#3


title: TC-RCC#10


title: control 5050568003_E

city: Delhi

first: Mohammed

last: Faruq

address: Mall Road

department: Genomics and Molecular Medicine

country: India

institute: CSIR-IGIB

description: control

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensity data was extracted without background correction and normalization using GenomeStudio Software Illumina Inc. We have only retained probes with detection p-value less than equal to 0.05 in atleast 3 samples out of 6 in a given array. Background correction and quantile normalization was performed using limma package in R. Additionally, we have also checked for any batch effect using various methods such as SNM (supervised normalization method) and ComBat (sva package).

source_name: control

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Peripheral whole blood

value: healthy spouse of the SCA12 patients


title: control 5050568003_B

description: control


title: control 5356575043_F

description: control


title: control 5356575043_A

description: control


title: control 5356575043_B

description: control


title: control 5050568003_A

description: control


title: case 5356575043_C

description: case

source_name: case

value: SCA12 symptomatic individual


title: case 5356575005_D

description: case


title: control 5356575043_D

description: control


title: control 5356575005_F

description: control


title: case 5356575043_E

description: case


title: control 5050568019_A

description: control


title: case 5356575005_C

description: case


title: case 5356575005_B

description: case


title: case 5050568019_B

description: case


title: case 5050568019_D

description: case


title: case 5050568019_F

description: case


title: TC-RCC#4


title: case 5356575005_E

description: case


title: case 5050568019_E

description: case


title: case 5050568003_D

description: case


title: case 5356575005_A

description: case


title: case 5050568003_F

description: case


title: case 5050568019_C

description: case