title: Progeny1-1007 [a550818-4325018-051918-783_H08]


title: CON_B_1

status: Public on Dec 17 2019

type: SRA

city: London

first: Victor

middle: KM

last: Han

state: Ontario

address: 1151 Richmond St

department: Biochemistry

country: Canada

institute: University of Western Ontario

description:
Control, Litter B
fetal_counts.txt
C3B

library_source: transcriptomic

data_processing:
Hiseq 2500 was used at McGill University and Genome Innovation Centre, D00278.
Fastqc was used to ensure all samples obtained good quality reads, then reads were aligned to the mm9 transcriptome using bowtie2 (default settings).
Sample tables were merged into a master count table in R console.
Transcripts were collapsed to the gene level in the R console using Biomart "ensembl_transcript_id" and "ensembl_gene_id" from the may 2012 mm9 archived version.
Data was normalized and differential expression was determined using DESeq2, ALDex2 and EdgeR tools.
Genome_build: mm9
Supplementary_files_format_and_content: Individual sample raw counts aligned to the transcriptome but not yet collapsed to the gene level; master count table is raw counts for all samples collapsed to the gene level

molecule: polyA RNA

organism: Mus musculus

source_name: Right liver lobe

extract_protocol:
Frozen tissue was pulverized then homogenized. Total RNA was isolated with TRIzol the PureLink Mini RNA kit (Invitrogen, USA) using the manufactuer's on-column DNAseI protocol.
Libraries were created with the NEBNext® UltraTM Directional RNA library Prep Kit for Illumina® at McGill University and Genome Quebec Innovation Center (Quebec, CA) according to the manufacter's protocol

tag: strain

value: CD-1 IGS

tag: stress

value: control

tag: tissue

value: fetal liver

tag: developmental stage

value: Embryonic day 18.5

tag: litter

value: B


title: Progeny1-1385 [a550818-4325018-051918-783_H09]

type: genomic

city: Gainesville

first: Jianping

last: Wang

state: Florida

address: 2033 Mowry Road

department: Agronomy

country: USA

institute: University of Florida

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array

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:
The Affymetrix bioinformatics team processed the raw intensities in cell intensity files (.CEL) to obtain normalized intensities for each probe set. Further, these normalized intensities were converted to genotype calls with the Axiom Genotyping Algorithm version one
primary data description: Genotype Call (SNP call): AA=0, AB=1, BB=2, NoCall="-"; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Saccharum officinarum

source_name: Progeny from cross Green German and IND81-146

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: These plant samples were maintained at the United States Department of Agriculture (USDA), Agricultural Research Service (ARS) Sugarcane Field Station at Canal Point, FL, which were under nature condition.

extract_protocol: Genomic DNA samples were extracted using MagJET Plant Genomic DNA Kit (Thermo Fisher Scientific, MA, USA).

treatment_protocol: Young leaf tissues were collected and stored at -80 °C for DNA extraction.

value: Sugarcane yellow leaf virus free


title: CON_A_2

description:
Control, Litter A
fetal_counts.txt
C2A

value: A


title: Progeny1-1232 [a550818-4325018-051918-783_H05]


title: Progeny1-1026 [a550818-4325018-051918-783_H04]


title: Progeny1-1318 [a550818-4325018-051918-783_H07]


title: Progeny1-1402 [a550818-4325018-051918-783_H06]


title: A549_0-75mg_Pirf_6h_Rep1

type: RNA

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

country: Germany

institute: Research Center Borstel - Leibniz Lung Center

hyb_protocol: Agilent Low Input Quick Amp Labelling Kit One Color according to manufacturers instructions

data_processing: Data has been log-transformed and normalized (percentile shift) within the Agilent GeneSpring V13 software

molecule: total RNA

organism: Homo sapiens

growth_protocol: 24h or 6h at 37°C and 5%CO2

extract_protocol: Qiagen Rneasy according to manufacturers instructions

treatment_protocol: 0.75 mg/ml of Pirfenidone or respective volume of PBS

tag: cell line

tag: treatmnet

value: Pirfenidone

tag: treatment  time


title: Hi-C GO II DMSO 24h rep1

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

country: China

institute: Tsinghua University

description: GOII_DMSO_24h_rep12_allValidPairs.txt.gz

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Cmpartment analysis are done as previously described. (Lieberman et al., 2009)
TAD calling is done with insulation score as previously described ( Crane et al., 2015)
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: Growing oocytes

extract_protocol:
After removing the zona pellucida, oocytes were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using sisHi-C (Du et al., Nature, 2017)

treatment_protocol: Follicles were isolated from 14-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were cultured in KSOM medium at 37° with DMSO for 24h.

value: Growing oocytes


title: Hi-C GVBD rep1

source_name: GVBD oocytes

treatment_protocol: Collection of full grown oocytes from 5IU PMSG injected 8w-old female C57BL/6N mice was performed, followed by hyaluronidase treatment to remove cumulus cells. Then the full grown oocytes are cultured in M2 medium without milrinone. Oocytes were collected when the germinal vesicle break down.

value: GVBD oocytes


title: Hi-C control for GVBD rep1

description: control_for_GVBD_rep12_allValidPairs.txt.gz

source_name: Full-grown oocytes

treatment_protocol: Collection of full grown oocytes from 5IU PMSG injected 8w-old female C57BL/6N mice was performed, followed by hyaluronidase treatment to remove cumulus cells. Then the full grown oocytes are cultured in M2 medium supplemented with 5uM milrinone.

value: Full-grown oocytes


title: Progeny1-1338 [a550818-4325018-051918-783_H03]


title: Progeny1-1080 [a550818-4325018-051918-783_H02]


title: Hi-C FGO rep1

treatment_protocol: Collection of FGOs oocytes from 5IU PMSG injected C57BL/6N mice was performed 44-48h after hCG injection, followed by hyaluronidase treatment to remove cumulus cells.


title: Hi-C GOII rep1

treatment_protocol: Follicles were isolated from 14-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then cross-linked with 1% formaldehyde after removing the zona pellucida by pronase treatment.

value: Growing oocytes II


title: Progeny1-1258 [a550818-4325018-051918-783_G12]


title: Hi-C E13.5 male PGC rep1

description: E13.5_male_PGC_rep12_allValidPairs.txt.gz

source_name: Primordial germ cells (PGCs)

extract_protocol:
PGCs were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using sisHi-C (Du et al., Nature, 2017)

treatment_protocol: Germinal ridges, collected from E13.5 male embryos by mating the PWK/PhJ mice with OG2 strain (with Oct4-GFP reporter), were digested with trypsin-EDTA (0.25%) at 37℃ for 10min. GFP-positive PGCs were sorted and collected by FACS and then cross-linked with 1% formaldehyde.

value: OG2 x PWK/PhJ

value: E13.5 male PGC


title: Progeny1-1193 [a550818-4325018-051918-783_G11]


title: Progeny1-1442 [a550818-4325018-051918-783_G10]


title: Hi-C E13.5 female PGC rep1

description: E13.5_female_PGC_rep12_allValidPairs.txt.gz

treatment_protocol: Germinal ridges, collected from E13.5 female embryos by mating the PWK/PhJ mice with OG2 strain (with Oct4-GFP reporter), were digested with trypsin-EDTA (0.25%) at 37℃ for 10min. GFP-positive PGCs were sorted and collected by FACS and then cross-linked with 1% formaldehyde.

value: E13.5 female PGC


title: Hi-C E11.5 PGC rep1

treatment_protocol: Germinal ridges, collected from E11.5 embryos by mating the PWK/PhJ mice with OG2 strain (with Oct4-GFP reporter), were digested with trypsin-EDTA (0.25%) at 37℃ for 10min. GFP-positive PGCs were sorted and collected by FACS and then cross-linked with 1% formaldehyde.

value: E11.5 PGC


title: Recovery14h2

city: La Jolla

first: Joanne

last: Chory

state: CA

address: 10010 N Torrey Pines Rd

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

data_processing:
BRB Digital Gene Expression (BRB-DGE) tool (https://linus.nci.nih.gov/bdge/) was used to get the raw counts of each gene. Briefly, RNA-seq reads were aligned to Arabidopsis reference genome (TAIR10) using TopHat version 2.1.1 and gene-level raw count data files were generated using HTSeq version 0.6.0. The raw count data was imported into Bioconductor package edgeR in R language to identify the differentially expressed genes and to calculate the RPKM of genes.
Genome_build: Arabidopsis reference genome (TAIR10)
Supplementary_files_format_and_content: tab-delimited text files include raw counts of each gene for each sample

organism: Arabidopsis thaliana

source_name: Recovery14h, 7-day old whole seedlings

extract_protocol:
Total RNA was isolated from pooled (25 individual plants of the each time course) whole seedlings using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) with dsDNase treated.
4 μg total RNA of each sample was used to prepare the RNA-seq libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA). Single-end sequencing was run on Illumina HiSeq 2500 sequencing machine (Illumina).

treatment_protocol: Seedling were grown under 24 h growth light (60 µmol.m-2.s-1) condition at 22 °C  for 7 days, then half plates treated with high light (1200 μmol.m-2.s-1, leaf temperature: 22 oC) for 0.5h, 6h, 12h, 24h, 48h and 72h, rest half plates keep on growht light conditon as controls and collect RNAs at 0.5h, 6h, 12h, 24h, 48h and 72h. The recovery samples were collected after 14 h recovery in growth light condition following the 72 h high light treatment.

tag: treatment

value: High light (1200 μmol.m-2.s-1, leaf temperature:22 oC) treatment, followed by recovery in Growth light (60 μmol.m-2.s-1, 22 oC)

tag: time (treatment)

tag: time (recovery)

tag: ecotype

value: 7 days old whole seedling


title: Recovery14h1


title: Progeny1-1314 [a550818-4325018-051918-783_G08]


title: HL72h2

source_name: HL72h, 7-day old whole seedlings

value: High light (1200 μmol.m-2.s-1, leaf temperature:22 oC)


title: Progeny1-1209 [a550818-4325018-051918-783_G09]


title: HL72h1


title: Progeny1-1305 [a550818-4325018-051918-783_G06]


title: HL48h2

source_name: HL48h, 7-day old whole seedlings


title: Progeny1-1012 [a550818-4325018-051918-783_G05]


title: Progeny1-1279 [a550818-4325018-051918-783_G04]


title: Progeny1-1161 [a550818-4325018-051918-783_G07]


title: HL24h2

source_name: HL24h, 7-day old whole seedlings


title: HL48h1


title: Progeny1-1411 [a550818-4325018-051918-783_G02]


title: Progeny1-1123 [a550818-4325018-051918-783_G01]


title: HL24h1


title: CON_A_1

description:
Control, Litter A
fetal_counts.txt
C1A

value: CD-1 IGS

value: control

value: fetal liver


title: HL12h1

source_name: HL12h, 7-day old whole seedlings


title: Progeny1-1335 [a550818-4325018-051918-783_H01]

value: Sugarcane yellow leaf virus free


title: HL12h2


title: Progeny1-1090 [a550818-4325018-051918-783_F12]


title: HL6h2

source_name: HL6h, 7-day old whole seedlings


title: Progeny1-1349 [a550818-4325018-051918-783_F10]


title: HL6h1


title: HL0.5h2

source_name: HL0.5h, 7-day old whole seedlings


title: Progeny1-1126 [a550818-4325018-051918-783_F09]


title: Progeny1-1218 [a550818-4325018-051918-783_F11]


title: Progeny1-1078 [a550818-4325018-051918-783_F08]


title: Progeny1-1325 [a550818-4325018-051918-783_F07]


title: GL72h2

source_name: GL72h, 7-day old whole seedlings

value: Growth light (60 μmol.m-2.s-1, 22 oC)


title: Progeny1-1205 [a550818-4325018-051918-783_F06]


title: Progeny1-1162 [a550818-4325018-051918-783_G03]


title: GL48h2

source_name: GL48h, 7-day old whole seedlings


title: GL48h1


title: Progeny1-1154 [a550818-4325018-051918-783_F05]


title: Progeny1-1163 [a550818-4325018-051918-783_F04]

value: Sugarcane yellow leaf virus infected


title: Progeny1-1367 [a550818-4325018-051918-783_F03]


title: Progeny1-1194 [a550818-4325018-051918-783_F02]


title: GL24h1

source_name: GL24h, 7-day old whole seedlings


title: GL24h2


title: GL12h1

source_name: GL12h, 7-day old whole seedlings


title: GL12h2


title: Progeny1-1251 [a550818-4325018-051918-783_E11]


title: Progeny1-1103 [a550818-4325018-051918-783_F01]


title: Progeny1-1092 [a550818-4325018-051918-783_E12]


title: GL6h2

source_name: GL6h, 7-day old whole seedlings


title: GL6h1


title: Progeny1-1139 [a550818-4325018-051918-783_E10]

source_name: Progeny from cross Green German and IND81-146


title: HL0.5h1


title: Male-parent-IND81-146-2 [a550818-4325018-051918-783_E09]

value: Sugarcane yellow leaf virus resistant


title: GL0.5h2

source_name: GL0.5h, 7-day old whole seedlings


title: Progeny1-1166 [a550818-4325018-051918-783_E08]


title: MG_glu_2

city: San Diego

first: Anand

last: Sastry

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 MG1655

growth_protocol: glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2.

extract_protocol:
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: media

value: M9 minimal media w/ 0.2% glucose and 10mM glutamate

tag: knock-out


title: GL0.5h1


title: GL72h1


title: Progeny1-1252 [a550818-4325018-051918-783_E06]


title: MG_no_te_2

value: M9 minimal media w/ 0.2% glucose w/o trace elements


title: MG_glu_1


title: MG_no_te_1


title: Progeny1-1216 [a550818-4325018-051918-783_E04]


title: Progeny1-1332 [a550818-4325018-051918-783_E02]


title: Progeny1-1369 [a550818-4325018-051918-783_E03]


title: Progeny1-1147 [a550818-4325018-051918-783_D12]


title: Progeny1-1190 [a550818-4325018-051918-783_E01]


title: P300_ChIP-Seq_ZnSO4 Treatment

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

institute: The Jackson Laboratory

description: P300_ChIP-Seq_ZnSO4 Treatment

data_processing:
Filtering linker sequence in ChIA-PET using in-house script
Mapping ChIA-PET reads to reference genome using BWA MEM (version 0.7.16)
Deduplicating ChIA-PET reads using Picard (MarkDuplicates)
Peak-calling for ChIA-PET using MACS (v.1.4.2)
Producing 2D contact map of ChIA-PET using Juicer tool (version 1.6.1)
Mapping ChIP-Seq reads from ABI SOLiD sequencing platform (csfasta+QV.qual) using SOLiD BioScope (version 1.0.1)
Mapping ChIP-Seq reads from Illumina sequencing platform using BWA-MEM (version 0.7.16), and peak-calling using MACS (version 1.4.2)
Mapping RNA-Seq reads uinsg Bowtie2, and processing using edge R
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt format for peak (bed), loop (bedpe), binary data format for Juicebox (hic)

growth_protocol: Both U937-PR9 and NB4 cells were cultured in RPMI 1640 (ThermoFisher, A10491), supplemented with 10% fetal bovine serum (ThermoFisher, 10082147). These cells were cultured at 37 ℃ , 5% CO2, and ambient oxygen levels.

extract_protocol:
When performing ChIA-PET library, the same precedures were used as those in previous paper. (Li et al., 2012; Tang et al., 2015)
Paired-end sequencing (2 ×150bp) was used for ChIP-Seq libraries  with  Illumina Nextseq 500.

treatment_protocol: The U937-PR9 cells were treated with 100 μM ZnSO4 (Sigma, Z0251) for 4 hours for ChIA-PET and ChIP-Seq experiment. The U937-PR9 cells were treated with 100 μM ZnSO4  and then collected these cells at 4, 6, 12, 24 hours for RNA-Seq experiment. These cells was preincubated with 100 μM ZnSO4 for 4 hours and then treated with ATRA (Sigma, R2625) for 24 and 48 hours used for RNA-Seq experiment. NB4 cells were treated with ATRA for 24 and 48 hours used for RNA-Seq experiment.

tag: cell type

tag: method

value: ChIP-Seq

tag: factor

value: P300 (Abcam, catalog# ab14984)

tag: molecule subtype

value: nuclear chromatin


title: P300_ChIP-Seq_Control


title: Progeny1-1470 [a550818-4325018-051918-783_D10]


title: Progeny1-1005 [a550818-4325018-051918-783_D08]


title: Progeny1-1063 [a550818-4325018-051918-783_D09]


title: Progeny1-1237 [a550818-4325018-051918-783_E05]


title: Progeny1-1467 [a550818-4325018-051918-783_D07]


title: Progeny1-1020 [a550818-4325018-051918-783_D06]


title: B cells Newcastle Early Arthritis Clinic number 868

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

description: Freshly isolated and purified peripheral blood B cells- GEO: NA

hyb_protocol: Illumina HT12 BeadChip.

scan_protocol: Illumina iScan.

data_processing: Samples with mean detection pvalue > 0.05 and probes whose detection p-value was >0.05 in over 25% of samples were excluded prior to background correction and quantile normalization, following which additional probes were removed where they mapped to (i) sex chromosomes, (ii) repeat or intronic/intergenic regions or (iii) unmapped regions.

label: biotin

source_name: Disease control B cells

label_protocol: cRNA generated from 250ng total RNA using Illumina TotalPrep RNA Amplification kit

growth_protocol: Peripheral blood mononuclear cells first isolated by density centrifugation on Lymphoprep (Axis-Shield Diagnostics, Dundee, UK) underwent positive selection using anti-CD19 magnetic microbeads (Miltenyi Biotec, Bergisch, Gladback, Germany); median cell purity was 96.4% by flow cytometry.

extract_protocol: Total B lymphocyte RNA was immediately extracted using the AllPrep DNA/RNA Mini kit (Qiagen GmbH, Germany), then quality controlled using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA). The median RNA integrity number of samples used was 9.4

tag: patient

tag: gender

value: M

tag: age

value: peripheral blood

value: CD19+ B cells

value: Undifferentiated Inflammatory Arthritis

value: Osteoarthritis


title: B cells Newcastle Early Arthritis Clinic number 867

value: F

tag: tissue

value: Reactive Arthritis


title: Progeny1-1203 [a550818-4325018-051918-783_D05]


title: Progeny1-1122 [a550818-4325018-051918-783_D11]


title: Progeny1-1124 [a550818-4325018-051918-783_D04]


title: N/TERT-1 control mimic 1

city: Singapore

first: Prabha

last: Sampath

address: Novena

country: Singapore

institute: Skin Research Institute

description:
Replicate 1
SAMPLE 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was back ground substracted and normalized using  Illumina Inc. GenomeStudio version 1.9.0

source_name: Keratinocytes

label_protocol: Biotinylated cRNA were prepared with the Target Amp-Nano kit for Illumina arrays

growth_protocol: N/TERT cells were grown in Keratinocyte serum free media supplemented with 0.2ng/mL epidermal growth factor (EGF), 25 μg/mL bovine pituitary extract (BPE), 0.4 mM CaCl2and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted two days post transfection using Exiqon miRcury total RNA extraction kit

treatment_protocol: N/TERT cells were transfected with 20nM of Exiqon negative control mimic or miR-335 mimic

tag: sample type

value: Cell culture transfection


title: N/TERT-1 miR-335 mimic 3

description:
Replicate 3
SAMPLE 6


title: N/TERT-1 control mimic 2

description:
Replicate 2
SAMPLE 2


title: N/TERT-1 control mimic 3

description:
Replicate 3
SAMPLE 3


title: N/TERT-1 miR-335 mimic 2

description:
Replicate 2
SAMPLE 5


title: Progeny1-1398 [a550818-4325018-051918-783_D03]


title: Progeny1-1018 [a550818-4325018-051918-783_D02]

value: Unknown


title: B cells Newcastle Early Arthritis Clinic number 2090

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690372

source_name: Rheumatoid Arthritis B cells

value: Rheumatoid Arthritis


title: B cells Newcastle Early Arthritis Clinic number 2034

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690353


title: B cells Newcastle Early Arthritis Clinic number 2322

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690435

value: Crystal Arthritis


title: B cells Newcastle Early Arthritis Clinic number 1032

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690317


title: B cells Newcastle Early Arthritis Clinic number 878

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690246

value: Psoriatic Arthritis


title: B cells Newcastle Early Arthritis Clinic number 2222

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690406


title: Progeny1-1448 [a550818-4325018-051918-783_D01]

value: Sugarcane yellow leaf virus free


title: N/TERT-1 miR-335 mimic 1

description:
Replicate 1
SAMPLE 4


title: B cells Newcastle Early Arthritis Clinic number 967

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690288


title: B cells Newcastle Early Arthritis Clinic number 937

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690276


title: B cells Newcastle Early Arthritis Clinic number 978

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690294


title: B cells Newcastle Early Arthritis Clinic number 1058

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690327

value: Non-Inflammatory


title: B cells Newcastle Early Arthritis Clinic number 946

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690281


title: B cells Newcastle Early Arthritis Clinic number 975

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690293


title: B cells Newcastle Early Arthritis Clinic number 912

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690264

value: Other Inflammatory Arthritis


title: B cells Newcastle Early Arthritis Clinic number 1008

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690305


title: Progeny1-1053 [a550818-4325018-051918-783_C12]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array

value: Sugarcane yellow leaf virus infected


title: Progeny1-1142 [a550818-4325018-051918-783_C11]


title: B cells Newcastle Early Arthritis Clinic number 827

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690232


title: Progeny1-1323 [a550818-4325018-051918-783_H11]


title: Progeny1-1047 [a550818-4325018-051918-783_C10]


title: Progeny1-1083 [a550818-4325018-051918-783_C09]


title: Progeny1-1076 [a550818-4325018-051918-783_C08]


title: Progeny1-1259 [a550818-4325018-051918-783_C07]


title: Progeny1-1211 [a550818-4325018-051918-783_C06]


title: Progeny1-1316 [a550818-4325018-051918-783_C05]


title: Progeny1-1309 [a550818-4325018-051918-783_C04]


title: B cells Newcastle Early Arthritis Clinic number 996

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690299


title: B cells Newcastle Early Arthritis Clinic number 893

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690255


title: B cells Newcastle Early Arthritis Clinic number 1019

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690312


title: B cells Newcastle Early Arthritis Clinic number 826

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690231


title: B cells Newcastle Early Arthritis Clinic number 923

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690268


title: B cells Newcastle Early Arthritis Clinic number 884

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690251


title: B cells Newcastle Early Arthritis Clinic number 1005

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690303


title: B cells Newcastle Early Arthritis Clinic number 892

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690254


title: Progeny1-1330 [a550818-4325018-051918-783_C03]


title: B cells Newcastle Early Arthritis Clinic number 944

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690279


title: B cells Newcastle Early Arthritis Clinic number 835

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690234


title: B cells Newcastle Early Arthritis Clinic number 974

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690292


title: B cells Newcastle Early Arthritis Clinic number 1003

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690302


title: B cells Newcastle Early Arthritis Clinic number 1020

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690313


title: B cells Newcastle Early Arthritis Clinic number 915

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690267


title: B cells Newcastle Early Arthritis Clinic number 891

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690253


title: B cells Newcastle Early Arthritis Clinic number 1022

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690314

value: Undifferentiated Spondylo-Arthropathy


title: B cells Newcastle Early Arthritis Clinic number 969

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690290


title: Progeny1-1179 [a550818-4325018-051918-783_C02]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: B cells Newcastle Early Arthritis Clinic number 973

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690291


title: B cells Newcastle Early Arthritis Clinic number 2133

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690380


title: B cells Newcastle Early Arthritis Clinic number 938

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690277

value: M


title: B cells Newcastle Early Arthritis Clinic number 1000

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690301

value: peripheral blood


title: Progeny1-1002 [a550818-4325018-051918-783_C01]


title: B cells Newcastle Early Arthritis Clinic number 2166

description: Freshly isolated and purified peripheral blood B cells- GEO: NA

value: CD19+ B cells


title: B cells Newcastle Early Arthritis Clinic number 2767

value: Undifferentiated Inflammatory Arthritis


title: B cells Newcastle Early Arthritis Clinic number 2197

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690396


title: Progeny1-1050 [a550818-4325018-051918-783_B12]


title: Progeny1-1469 [a550818-4325018-051918-783_B11]


title: B cells Newcastle Early Arthritis Clinic number 2203

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690398


title: Progeny1-1198 [a550818-4325018-051918-783_B09]


title: Progeny1-1141 [a550818-4325018-051918-783_B07]


title: Progeny1-1197 [a550818-4325018-051918-783_B08]


title: Progeny1-1130 [a550818-4325018-051918-783_B06]


title: Progeny1-1327 [a550818-4325018-051918-783_E07]


title: Progeny1-1311 [a550818-4325018-051918-783_B05]


title: B cells Newcastle Early Arthritis Clinic number 2476

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690458


title: B cells Newcastle Early Arthritis Clinic number 2086

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690369


title: B cells Newcastle Early Arthritis Clinic number 930

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690271


title: B cells Newcastle Early Arthritis Clinic number 1037

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690320


title: B cells Newcastle Early Arthritis Clinic number 879

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690247


title: B cells Newcastle Early Arthritis Clinic number 957

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690284


title: B cells Newcastle Early Arthritis Clinic number 954

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690283


title: Progeny1-1157 [a550818-4325018-051918-783_B10]


title: B cells Newcastle Early Arthritis Clinic number 2759

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690470


title: B cells Newcastle Early Arthritis Clinic number 2087

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690370


title: B cells Newcastle Early Arthritis Clinic number 2345

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690440


title: B cells Newcastle Early Arthritis Clinic number 2330

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690438


title: B cells Newcastle Early Arthritis Clinic number 2264

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690415

value: Enteropathic Arthritis


title: B cells Newcastle Early Arthritis Clinic number 2348

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690442


title: B cells Newcastle Early Arthritis Clinic number 2281

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690422

value: F


title: B cells Newcastle Early Arthritis Clinic number 2311

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690430


title: Progeny1-1315 [a550818-4325018-051918-783_B04]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: B cells Newcastle Early Arthritis Clinic number 2510

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690463


title: B cells Newcastle Early Arthritis Clinic number 2549

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690466


title: Progeny1-1177 [a550818-4325018-051918-783_B01]


title: Progeny1-1405 [a550818-4325018-051918-783_B03]


title: Progeny1-1375 [a550818-4325018-051918-783_B02]


title: B cells Newcastle Early Arthritis Clinic number 2506

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690461


title: B cells Newcastle Early Arthritis Clinic number 2507

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690462

value: Reactive Arthritis


title: B cells Newcastle Early Arthritis Clinic number 2511

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690464


title: B cells Newcastle Early Arthritis Clinic number 2305

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690428

value: Lupus/Other CTD-Associated


title: Progeny1-1015 [a550818-4325018-051918-783_A12]


title: B cells Newcastle Early Arthritis Clinic number 2493

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690460


title: B cells Newcastle Early Arthritis Clinic number 932

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690273


title: Progeny1-1049 [a550818-4325018-051918-783_A10]


title: Progeny1-1386 [a550818-4325018-051918-783_A08]


title: Progeny1-1031 [a550818-4325018-051918-783_A07]


title: Progeny1-1082 [a550818-4325018-051918-783_A06]


title: B cells Newcastle Early Arthritis Clinic number 2519

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690465


title: B cells Newcastle Early Arthritis Clinic number 845

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690238


title: B cells Newcastle Early Arthritis Clinic number 1094

description: Freshly isolated and purified peripheral blood B cells- GEO: NA


title: B cells Newcastle Early Arthritis Clinic number 2010

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690345


title: B cells Newcastle Early Arthritis Clinic number 1087

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690341


title: B cells Newcastle Early Arthritis Clinic number 2012

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690346


title: Progeny1-1281 [a550818-4325018-051918-783_A11]


title: B cells Newcastle Early Arthritis Clinic number 1088

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690342


title: B cells Newcastle Early Arthritis Clinic number 965

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690287

value: Osteoarthritis


title: Progeny1-1039 [a550818-4325018-051918-783_A04]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: B cells Newcastle Early Arthritis Clinic number 2062

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690363


title: B cells Newcastle Early Arthritis Clinic number 882

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690249

value: Rheumatoid Arthritis


title: Progeny1-1331 [a550818-4325018-051918-783_A03]


title: B cells Newcastle Early Arthritis Clinic number 962

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690286


title: B cells Newcastle Early Arthritis Clinic number 1085

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690339


title: B cells Newcastle Early Arthritis Clinic number 992

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690297


title: B cells Newcastle Early Arthritis Clinic number 2078

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690368

value: Crystal Arthritis


title: B cells Newcastle Early Arthritis Clinic number 2072

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690366


title: Progeny1-1065 [a550818-4325018-051918-783_A02]


title: B cells Newcastle Early Arthritis Clinic number 2052

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690359


title: B cells Newcastle Early Arthritis Clinic number 2047

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690358

value: Psoriatic Arthritis


title: Progeny1-1417 [a550818-4325018-051918-783_A09]

value: Sugarcane yellow leaf virus free


title: B cells Newcastle Early Arthritis Clinic number 1083

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690337


title: B cells Newcastle Early Arthritis Clinic number 2054

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690361


title: Progeny1-1029 [a550818-4325018-051918-783_A05]


title: Progeny1-1060 [a550818-4325018-051918-783_A01]


title: B cells Newcastle Early Arthritis Clinic number 1076

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690334


title: B cells Newcastle Early Arthritis Clinic number 1080

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690336


title: Cultivar-CP95 [a550818-4325018-051918-782_H12]

description:
processed data file: AxiomGT1.calls.batch2.txt
Hybridized to Axiom Sugarcane100K SNP array

value: Unknown


title: Cultivar-CP88 [a550818-4325018-051918-782_H11]


title: S788 [a550818-4325018-051918-782_H09]

source_name: Accession


title: B cells Newcastle Early Arthritis Clinic number 2044

description: Freshly isolated and purified peripheral blood B cells- GEO: NA


title: S712 [a550818-4325018-051918-782_H08]


title: S487 [a550818-4325018-051918-782_H07]


title: S381 [a550818-4325018-051918-782_H06]


title: B cells Newcastle Early Arthritis Clinic number 905

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690260


title: B cells Newcastle Early Arthritis Clinic number 1054

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690325


title: B cells Newcastle Early Arthritis Clinic number 1072

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690333


title: B cells Newcastle Early Arthritis Clinic number 2257

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690414


title: B cells Newcastle Early Arthritis Clinic number 1070

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690331


title: B cells Newcastle Early Arthritis Clinic number 2261


title: B cells Newcastle Early Arthritis Clinic number 2231

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690408


title: B cells Newcastle Early Arthritis Clinic number 2029

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690350


title: B cells Newcastle Early Arthritis Clinic number 2233

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690409

value: Other Inflammatory Arthritis


title: B cells Newcastle Early Arthritis Clinic number 2030

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690351


title: B cells Newcastle Early Arthritis Clinic number 2045

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690357


title: Progeny1-1333 [a550818-4325018-051918-782_H04]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: S801 [a550818-4325018-051918-782_H10]


title: B cells Newcastle Early Arthritis Clinic number 2040

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690355


title: B cells Newcastle Early Arthritis Clinic number 2145

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690384


title: B cells Newcastle Early Arthritis Clinic number 2036

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690354


title: B cells Newcastle Early Arthritis Clinic number 898

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690258


title: B cells Newcastle Early Arthritis Clinic number 980

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690295


title: B cells Newcastle Early Arthritis Clinic number 926

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690270


title: B cells Newcastle Early Arthritis Clinic number 948

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690282


title: B cells Newcastle Early Arthritis Clinic number 841

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690236


title: B cells Newcastle Early Arthritis Clinic number 1010

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690306


title: Progeny1-1395 [a550818-4325018-051918-782_H03]


title: B cells Newcastle Early Arthritis Clinic number 2379

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690452


title: Progeny1-1321 [a550818-4325018-051918-782_H02]


title: B cells Newcastle Early Arthritis Clinic number 2439

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690455


title: Progeny1-1077 [a550818-4325018-051918-782_H05]


title: Progeny1-1174 [a550818-4325018-051918-782_H01]


title: Progeny1-1235 [a550818-4325018-051918-782_G12]


title: Progeny1-1300 [a550818-4325018-051918-782_G11]


title: B cells Newcastle Early Arthritis Clinic number 2437

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690454


title: Progeny1-1420 [a550818-4325018-051918-782_G10]


title: Progeny1-1308 [a550818-4325018-051918-782_G09]

value: Sugarcane yellow leaf virus infected


title: Progeny1-1133 [a550818-4325018-051918-782_G08]


title: B cells Newcastle Early Arthritis Clinic number 2368

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690450


title: Progeny1-1351 [a550818-4325018-051918-782_G06]


title: B cells Newcastle Early Arthritis Clinic number 2367

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690449

value: Undifferentiated Spondylo-Arthropathy


title: Progeny1-1222 [a550818-4325018-051918-782_G07]


title: Progeny1-1381 [a550818-4325018-051918-782_G05]


title: B cells Newcastle Early Arthritis Clinic number 995

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690298


title: Progeny1-1037 [a550818-4325018-051918-782_G03]


title: T cells Newcastle Early Arthritis Clinic number 975

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129026

source_name: Rheumatoid Arthritis T cells

label_protocol: 50ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).

growth_protocol: Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA).

extract_protocol: RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.

value: CD4+ T cells


title: T cells Newcastle Early Arthritis Clinic number 980

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128977

source_name: Disease control T cells

value: peripheral blood


title: T cells Newcastle Early Arthritis Clinic number 978

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129028


title: T cells Newcastle Early Arthritis Clinic number 967

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128985


title: T cells Newcastle Early Arthritis Clinic number 992

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128982


title: B cells Newcastle Early Arthritis Clinic number 2390

description: Freshly isolated and purified peripheral blood B cells- GEO: GSM2690453

value: M

value: CD19+ B cells


title: T cells Newcastle Early Arthritis Clinic number 973

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129022

value: Undifferentiated Inflammatory Arthritis


title: T cells Newcastle Early Arthritis Clinic number 929

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128965

value: F


title: T cells Newcastle Early Arthritis Clinic number 937

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128975


title: T cells Newcastle Early Arthritis Clinic number 934

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128971


title: T cells Newcastle Early Arthritis Clinic number 935

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128973


title: T cells Newcastle Early Arthritis Clinic number 926

description: Freshly isolated and purified peripheral blood T cells- GEO: NA


title: T cells Newcastle Early Arthritis Clinic number 946

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129016


title: Progeny1-1380 [a550818-4325018-051918-782_G04]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: T cells Newcastle Early Arthritis Clinic number 974

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129024


title: T cells Newcastle Early Arthritis Clinic number 930

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128967


title: Progeny1-1347 [a550818-4325018-051918-782_G01]


title: Progeny1-1286 [a550818-4325018-051918-782_G02]


title: T cells Newcastle Early Arthritis Clinic number 912

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129120


title: T cells Newcastle Early Arthritis Clinic number 945

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129014


title: T cells Newcastle Early Arthritis Clinic number 882

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128961


title: T cells Newcastle Early Arthritis Clinic number 854

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128958


title: T cells Newcastle Early Arthritis Clinic number 891

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129002


title: T cells Newcastle Early Arthritis Clinic number 898

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128966

value: Reactive Arthritis


title: T cells Newcastle Early Arthritis Clinic number 905

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128970


title: T cells Newcastle Early Arthritis Clinic number 896

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129007


title: T cells Newcastle Early Arthritis Clinic number 845

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128955


title: Progeny1-1392 [a550818-4325018-051918-782_F12]


title: T cells Newcastle Early Arthritis Clinic number 1000

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129021


title: Progeny1-1096 [a550818-4325018-051918-782_F10]


title: T cells Newcastle Early Arthritis Clinic number 996

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128986


title: Progeny1-1215 [a550818-4325018-051918-782_F09]


title: T cells Newcastle Early Arthritis Clinic number 1022

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129075


title: T cells Newcastle Early Arthritis Clinic number 995

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128984


title: Progeny1-1348 [a550818-4325018-051918-782_F08]


title: T cells Newcastle Early Arthritis Clinic number 965

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128983


title: Progeny1-1370 [a550818-4325018-051918-782_F07]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: T cells Newcastle Early Arthritis Clinic number 954

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128976


title: Progeny1-1271 [a550818-4325018-051918-782_F05]


title: Progeny1-1249 [a550818-4325018-051918-782_F06]


title: T cells Newcastle Early Arthritis Clinic number 1042

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129039


title: Progeny1-1181 [a550818-4325018-051918-782_F11]


title: T cells Newcastle Early Arthritis Clinic number 938

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129009


title: T cells Newcastle Early Arthritis Clinic number 810

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128950


title: T cells Newcastle Early Arthritis Clinic number 962

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128981


title: Progeny1-1278 [a550818-4325018-051918-782_F03]


title: T cells Newcastle Early Arthritis Clinic number 969

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129020


title: T cells Newcastle Early Arthritis Clinic number 829

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128996


title: Progeny1-1195 [a550818-4325018-051918-782_F02]


title: T cells Newcastle Early Arthritis Clinic number 809

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128948


title: T cells Newcastle Early Arthritis Clinic number 878

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128956


title: T cells Newcastle Early Arthritis Clinic number 2257

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129117


title: T cells Newcastle Early Arthritis Clinic number 842

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128995

value: Enteropathic Arthritis


title: T cells Newcastle Early Arthritis Clinic number 2261

description: Freshly isolated and purified peripheral blood T cells- GEO: NA


title: T cells Newcastle Early Arthritis Clinic number 2264


title: T cells Newcastle Early Arthritis Clinic number 841

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128993


title: Progeny1-1317 [a550818-4325018-051918-782_F04]


title: T cells Newcastle Early Arthritis Clinic number 1032

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129081


title: Progeny1-1151 [a550818-4325018-051918-782_E12]


title: T cells Newcastle Early Arthritis Clinic number 844


title: Progeny1-1464 [a550818-4325018-051918-782_E11]


title: T cells Newcastle Early Arthritis Clinic number 1010

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129030


title: T cells Newcastle Early Arthritis Clinic number 838

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128988


title: T cells Newcastle Early Arthritis Clinic number 840

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128991


title: Progeny1-1189 [a550818-4325018-051918-782_E10]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: Progeny1-1387 [a550818-4325018-051918-782_E09]


title: Progeny1-1433 [a550818-4325018-051918-782_E08]


title: T cells Newcastle Early Arthritis Clinic number 932

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128969


title: Progeny1-1106 [a550818-4325018-051918-782_E07]


title: T cells Newcastle Early Arthritis Clinic number 1005

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129025


title: T cells Newcastle Early Arthritis Clinic number 826

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128990

value: Osteoarthritis


title: Progeny1-1098 [a550818-4325018-051918-782_E06]


title: T cells Newcastle Early Arthritis Clinic number 1037

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129035


title: Progeny1-1233 [a550818-4325018-051918-782_E04]


title: T cells Newcastle Early Arthritis Clinic number 915

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129010

value: Rheumatoid Arthritis


title: Progeny1-1462 [a550818-4325018-051918-782_E03]


title: Progeny1-1014 [a550818-4325018-051918-782_E05]


title: T cells Newcastle Early Arthritis Clinic number 2148

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129108


title: T cells Newcastle Early Arthritis Clinic number 815

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128989


title: T cells Newcastle Early Arthritis Clinic number 813

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128954


title: T cells Newcastle Early Arthritis Clinic number 827

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128992


title: T cells Newcastle Early Arthritis Clinic number 814

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2128987

value: Crystal Arthritis


title: T cells Newcastle Early Arthritis Clinic number 2222

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129113


title: T cells Newcastle Early Arthritis Clinic number 2233

description: Freshly isolated and purified peripheral blood T cells- GEO: NA


title: Progeny1-1416 [a550818-4325018-051918-782_E02]


title: T cells Newcastle Early Arthritis Clinic number 2144

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129105


title: T cells Newcastle Early Arthritis Clinic number 2054

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129057


title: T cells Newcastle Early Arthritis Clinic number 2231

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129114


title: T cells Newcastle Early Arthritis Clinic number 2052

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129054

value: Non-Inflammatory


title: T cells Newcastle Early Arthritis Clinic number 2140

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129070


title: Progeny1-1115 [a550818-4325018-051918-782_E01]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array

value: Sugarcane yellow leaf virus free


title: T cells Newcastle Early Arthritis Clinic number 2030

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129058


title: T cells Newcastle Early Arthritis Clinic number 2145

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129107


title: Progeny1-1253 [a550818-4325018-051918-782_D12]


title: T cells Newcastle Early Arthritis Clinic number 1008

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129029

value: Psoriatic Arthritis


title: T cells Newcastle Early Arthritis Clinic number 2044

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129100


title: T cells Newcastle Early Arthritis Clinic number 2034

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129093


title: T cells Newcastle Early Arthritis Clinic number 2040

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129096


title: T cells Newcastle Early Arthritis Clinic number 2047

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129052


title: T cells Newcastle Early Arthritis Clinic number 1020

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129073


title: T cells Newcastle Early Arthritis Clinic number 2042

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129098


title: T cells Newcastle Early Arthritis Clinic number 1003

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129023


title: Progeny1-1073 [a550818-4325018-051918-782_D10]


title: Progeny1-1239 [a550818-4325018-051918-782_F01]


title: Progeny1-1028 [a550818-4325018-051918-782_D09]


title: Progeny1-1135 [a550818-4325018-051918-782_D07]

value: Unknown


title: T cells Newcastle Early Arthritis Clinic number 2067

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129095


title: T cells Newcastle Early Arthritis Clinic number 2087

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129061


title: T cells Newcastle Early Arthritis Clinic number 2086

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129103


title: Progeny1-1310 [a550818-4325018-051918-782_D06]


title: T cells Newcastle Early Arthritis Clinic number 2072

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129097


title: Progeny1-1088 [a550818-4325018-051918-782_D05]


title: T cells Newcastle Early Arthritis Clinic number 2075

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129099


title: T cells Newcastle Early Arthritis Clinic number 2029

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129056


title: T cells Newcastle Early Arthritis Clinic number 2062

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129060


title: Progeny1-1199 [a550818-4325018-051918-782_D04]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array


title: T cells Newcastle Early Arthritis Clinic number 2090

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129065


title: T cells Newcastle Early Arthritis Clinic number 1019

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129071


title: T cells Newcastle Early Arthritis Clinic number 2012

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129086


title: T cells Newcastle Early Arthritis Clinic number 2078

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129101


title: T cells Newcastle Early Arthritis Clinic number 2010

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129084


title: Progeny1-1372 [a550818-4325018-051918-782_D08]


title: Progeny1-1268 [a550818-4325018-051918-782_D02]


title: Progeny1-1171 [a550818-4325018-051918-782_D03]


title: Progeny1-1383 [a550818-4325018-051918-782_D01]


title: T cells Newcastle Early Arthritis Clinic number 1070

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129047


title: Progeny1-1071 [a550818-4325018-051918-782_C12]


title: T cells Newcastle Early Arthritis Clinic number 1051

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129074


title: Progeny1-1432 [a550818-4325018-051918-782_C11]


title: T cells Newcastle Early Arthritis Clinic number 1050

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129072


title: Progeny1-1224 [a550818-4325018-051918-782_C10]


title: T cells Newcastle Early Arthritis Clinic number 1088

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129044


title: Ctrl sup 3

city: Ann Arbor

first: Martin

last: Myers

state: MI

address: 1000 Wall Street 6317 Brehm Tower

institute: University of Michigan

data_processing:
Filtered using fastq_quality_filter 0.0.14 with -q = 20
Aligned to custom genome using STAR 2.5.3a_modified with default parameters
Genome_build: mm10 with additional chromosomes containing Cre and Gfp_L10a transgenes
Supplementary_files_format_and_content: Raw gene counts from STAR –quantMode GeneCounts

source_name: Brain

growth_protocol: All procedures performed on animals were approved by the University of Michigan Insitutional Committee on the Care and Use of Animals and in accordance with AAALAC and NIH guidelines.  All mice were bred in our colony in the Unit for Laboratory Animal Management at the University of Michigan.  All mice were provided with water ad libitum and housed in temperature-controlled rooms on a 12-hour light-dark cycle.

extract_protocol:
At the midpoint of the light cycle, adult mice were anesthetized with isofluorane, after which their brains were removed and placed onto a mouse coronal brain matrix (1mm sections). For whole hypothalamic dissections, a 3x3x3mm block was dissected from the ventral diencephalon immediately caudal to the optic chiasm and immediately homogenized and processed for TRAP-seq analysis. Hypothalami from 5-8 mice were pooled at the time of collection to produce sufficient mRNA for a single RNA-seq replicate.  Messenger RNA isolated from eGFP-tagged ribosomes and from the eGFP-depleted was assessed for quality using TapeStation (Agilent, Santa Clara, CA)
Samples with RNA Integrity Numbers (RINs) of 8 or greater were prepared usin the Illumina TruSeq mRNA Sample Prep v2 kit (RS-122-2001, RS-122-2002, Illumina), where 0.1-3 ug of RNA was converted to mRNA using a polyA purification. The mRNA was chemically fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3’ ends of the cDNA were adenylated and the 6-nucleotide-barcoded adapters ligated. These products were then purified and enriched by PCR to create the cDNA library, which were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog #KK4835) (Kapa Biosystems, Wilmington MA). They were clustered on cBot (Illumina) and sequenced 4 samples per lane on a 50 cycle single end run on a HiSeq 2000 (Illumina) using version 2 reagents according to manufacturer’s protocols.

value: Hypothalamus

tag: developmental stage

value: Adult

tag: genotype

value: LepRb-Cre/Cre; R26-GFP:L10a/GFP:L10a

tag: fraction

value: supernatant


title: Ctrl bead 3

value: bead bound


title: T cells Newcastle Early Arthritis Clinic number 1067

description: Freshly isolated and purified peripheral blood T cells- GEO: NA

value: M

value: peripheral blood

value: CD4+ T cells


title: T cells Newcastle Early Arthritis Clinic number 1094

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129046

value: Reactive Arthritis


title: Ctrl bead 2


title: T cells Newcastle Early Arthritis Clinic number 1083

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129088

value: F


title: Ctrl sup 2


title: T cells Newcastle Early Arthritis Clinic number 1058

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129080


title: Ctrl sup 1


title: Progeny1-1362 [a550818-4325018-051918-782_C09]


title: T cells Newcastle Early Arthritis Clinic number 1054

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129076

value: Undifferentiated Inflammatory Arthritis

value: Osteoarthritis


title: T cells Newcastle Early Arthritis Clinic number 1087

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129042

value: Crystal Arthritis


title: T cells Newcastle Early Arthritis Clinic number 1080

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129087


title: Ctrl bead 1


title: T cells Newcastle Early Arthritis Clinic number 1072

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129050

value: Rheumatoid Arthritis


title: T cells Newcastle Early Arthritis Clinic number 1085

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129123


title: Stat3KO sup 3


title: Progeny1-1040 [a550818-4325018-051918-782_C08]

description:
processed data file: AxiomGT1.calls.batch1.txt
Hybridized to Axiom Sugarcane100K SNP array

value: Sugarcane yellow leaf virus free


title: T cells Newcastle Early Arthritis Clinic number 1076

description: Freshly isolated and purified peripheral blood T cells- GEO: GSM2129083


title: Stat3KO bead 3


title: Progeny1-1038 [a550818-4325018-051918-782_C07]


title: Progeny1-1107 [a550818-4325018-051918-782_C06]


title: Stat3KO sup 2


title: Stat3KO bead 2


title: Stat3KO sup 1


title: Stat3KO bead 1


title: Progeny1-1435 [a550818-4325018-051918-782_C05]


title: Progeny1-1240 [a550818-4325018-051918-782_C03]


title: EA2767: Newcastle Early Arthritis Clinic patient 2767

description: Freshly isolated and purified peripheral blood B cells

hyb_protocol: 400ng of DNA was bisulphite-converted and hybridised to the Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

data_processing:
Failed probes whose detection p-values were >0.01 in >10% samples were excluded prior to functional normalisation as implemented in the minfi R package, following which additional probes were removed due to; (i) cross-hybridization, (ii) mapping to sex chromosomes, or (iii) presence of a SNP (MAF>0.05) at the interrogated CpG, probe sequence or single base extension site.
matrix processed value definition: Normalized average Beta values (Functional normalisation)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol.

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen, UK).

value: Female

value: CD19+ B cells


title: EA2507: Newcastle Early Arthritis Clinic patient 2507

source_name: Disease control, B cells


title: EA2510: Newcastle Early Arthritis Clinic patient 2510


title: EA2549: Newcastle Early Arthritis Clinic patient 2549


title: Progeny1-1440 [a550818-4325018-051918-782_C04]


title: EA2519: Newcastle Early Arthritis Clinic patient 2519


title: EA2476: Newcastle Early Arthritis Clinic patient 2476


title: EA2506: Newcastle Early Arthritis Clinic patient 2506

value: Male


title: EA2511: Newcastle Early Arthritis Clinic patient 2511


title: EA2493: Newcastle Early Arthritis Clinic patient 2493


title: Progeny1-1068 [a550818-4325018-051918-782_C02]


title: Progeny1-1389 [a550818-4325018-051918-782_C01]

value: Sugarcane yellow leaf virus infected


title: Progeny1-1075 [a550818-4325018-051918-782_B10]


title: EA2439: Newcastle Early Arthritis Clinic patient 2439


title: EA2390: Newcastle Early Arthritis Clinic patient 2390

value: Other Inflammatory Arthritis


title: Progeny1-1084 [a550818-4325018-051918-782_B12]


title: EA2437: Newcastle Early Arthritis Clinic patient 2437


title: Progeny1-1466 [a550818-4325018-051918-782_B11]


title: EA2367: Newcastle Early Arthritis Clinic patient 2367

value: Undifferentiated Spondylo-Arthropathy


title: Progeny1-1401 [a550818-4325018-051918-782_B09]


title: EA2368: Newcastle Early Arthritis Clinic patient 2368


title: EA2348: Newcastle Early Arthritis Clinic patient 2348


title: EA2345: Newcastle Early Arthritis Clinic patient 2345


title: Progeny1-1328 [a550818-4325018-051918-782_B08]


title: EA2759: Newcastle Early Arthritis Clinic patient 2759


title: EA2322: Newcastle Early Arthritis Clinic patient 2322


title: EA2330: Newcastle Early Arthritis Clinic patient 2330

value: Non-Inflammatory


title: Progeny1-1219 [a550818-4325018-051918-782_B07]


title: EA2379: Newcastle Early Arthritis Clinic patient 2379


title: EA2264: Newcastle Early Arthritis Clinic patient 2264

value: Enteropathic Arthritis


title: EA2305: Newcastle Early Arthritis Clinic patient 2305

value: peripheral blood

value: Lupus/Other CTD-Associated


title: EA2231: Newcastle Early Arthritis Clinic patient 2231


title: EA2311: Newcastle Early Arthritis Clinic patient 2311


title: Progeny1-1382 [a550818-4325018-051918-782_B05]


title: EA2261: Newcastle Early Arthritis Clinic patient 2261


title: Progeny1-1275 [a550818-4325018-051918-782_B02]


title: EA2281: Newcastle Early Arthritis Clinic patient 2281


title: EA2233: Newcastle Early Arthritis Clinic patient 2233


title: EA2257: Newcastle Early Arthritis Clinic patient 2257

value: Reactive Arthritis


title: Progeny1-1110 [a550818-4325018-051918-782_B04]


title: Progeny1-1185 [a550818-4325018-051918-782_B01]


title: Progeny1-1091 [a550818-4325018-051918-782_B06]


title: Progeny1-1204 [a550818-4325018-051918-782_B03]


title: Progeny1-1191 [a550818-4325018-051918-782_A12]


title: EA2203: Newcastle Early Arthritis Clinic patient 2203


title: EA2090: Newcastle Early Arthritis Clinic patient 2090


title: EA2133: Newcastle Early Arthritis Clinic patient 2133


title: EA2197: Newcastle Early Arthritis Clinic patient 2197


title: Progeny1-1354 [a550818-4325018-051918-782_A11]

value: Unknown


title: EA2166: Newcastle Early Arthritis Clinic patient 2166


title: EA2087: Newcastle Early Arthritis Clinic patient 2087

value: Psoriatic Arthritis


title: Progeny1-1136 [a550818-4325018-051918-782_A10]


title: EA2086: Newcastle Early Arthritis Clinic patient 2086


title: EA2265: Newcastle Early Arthritis Clinic patient 2265


title: EA2222: Newcastle Early Arthritis Clinic patient 2222


title: EA2078: Newcastle Early Arthritis Clinic patient 2078


title: Progeny1-1229 [a550818-4325018-051918-782_A08]


title: EA2062: Newcastle Early Arthritis Clinic patient 2062


title: Progeny1-1283 [a550818-4325018-051918-782_A07]


title: EA2052: Newcastle Early Arthritis Clinic patient 2052

value: Undifferentiated Inflammatory Arthritis


title: Progeny1-1131 [a550818-4325018-051918-782_A09]


title: EA2072: Newcastle Early Arthritis Clinic patient 2072


title: EA2040: Newcastle Early Arthritis Clinic patient 2040

value: Osteoarthritis


title: EA2044: Newcastle Early Arthritis Clinic patient 2044


title: EA2034: Newcastle Early Arthritis Clinic patient 2034


title: EA2145: Newcastle Early Arthritis Clinic patient 2145


title: EA2045: Newcastle Early Arthritis Clinic patient 2045

value: Rheumatoid Arthritis


title: Progeny1-1173 [a550818-4325018-051918-782_A06]

value: Sugarcane yellow leaf virus free


title: EA2036: Newcastle Early Arthritis Clinic patient 2036


title: EA2030: Newcastle Early Arthritis Clinic patient 2030


title: EA2029: Newcastle Early Arthritis Clinic patient 2029


title: Progeny1-1290 [a550818-4325018-051918-782_A04]


title: EA2012: Newcastle Early Arthritis Clinic patient 2012

value: Female


title: EA1094: Newcastle Early Arthritis Clinic patient 1094

value: CD19+ B cells


title: EA2010: Newcastle Early Arthritis Clinic patient 2010


title: Progeny1-1017 [a550818-4325018-051918-782_A02]


title: Progeny1-1376 [a550818-4325018-051918-782_A03]


title: EA1088: Newcastle Early Arthritis Clinic patient 1088


title: EA1087: Newcastle Early Arthritis Clinic patient 1087

value: Male

value: Crystal Arthritis


title: Progeny1-1414 [a550818-4325018-051918-782_A01]


title: EA2054: Newcastle Early Arthritis Clinic patient 2054


title: EA1085: Newcastle Early Arthritis Clinic patient 1085


title: EA2047: Newcastle Early Arthritis Clinic patient 2047


title: EA1083: Newcastle Early Arthritis Clinic patient 1083


title: Progeny1-1087 [a550818-4325018-051918-781_H12]


title: Progeny1-1074 [a550818-4325018-051918-782_A05]


title: EA1080: Newcastle Early Arthritis Clinic patient 1080


title: Progeny1-1243 [a550818-4325018-051918-781_H11]


title: EA1076: Newcastle Early Arthritis Clinic patient 1076


title: Progeny1-1100 [a550818-4325018-051918-781_H10]


title: Progeny1-1429 [a550818-4325018-051918-781_H09]


title: Progeny1-1210 [a550818-4325018-051918-781_H07]


title: EA1037: Newcastle Early Arthritis Clinic patient 1037


title: EA1070: Newcastle Early Arthritis Clinic patient 1070


title: EA1019: Newcastle Early Arthritis Clinic patient 1019


title: EA1020: Newcastle Early Arthritis Clinic patient 1020


title: EA1010: Newcastle Early Arthritis Clinic patient 1010


title: EA1072: Newcastle Early Arthritis Clinic patient 1072


title: EA1032: Newcastle Early Arthritis Clinic patient 1032


title: EA1054: Newcastle Early Arthritis Clinic patient 1054


title: Progeny1-1196 [a550818-4325018-051918-782_D11]


title: EA1008: Newcastle Early Arthritis Clinic patient 1008


title: Progeny1-1446 [a550818-4325018-051918-781_H05]


title: EA1003: Newcastle Early Arthritis Clinic patient 1003


title: EA1005: Newcastle Early Arthritis Clinic patient 1005


title: EA1000: Newcastle Early Arthritis Clinic patient 1000


title: EA0995: Newcastle Early Arthritis Clinic patient 995


title: Progeny1-1160 [a550818-4325018-051918-781_H03]


title: EA0996: Newcastle Early Arthritis Clinic patient 996


title: EA1058: Newcastle Early Arthritis Clinic patient 1058


title: Progeny1-1346 [a550818-4325018-051918-781_H08]


title: Progeny1-1456 [a550818-4325018-051918-781_H02]


title: EA0975: Newcastle Early Arthritis Clinic patient 975


title: EA0978: Newcastle Early Arthritis Clinic patient 978


title: EA0980: Newcastle Early Arthritis Clinic patient 980


title: Progeny1-1117 [a550818-4325018-051918-781_H01]


title: EA1022: Newcastle Early Arthritis Clinic patient 1022


title: EA0973: Newcastle Early Arthritis Clinic patient 973


title: Progeny1-1109 [a550818-4325018-051918-781_H06]


title: EA0974: Newcastle Early Arthritis Clinic patient 974


title: Progeny1-1390 [a550818-4325018-051918-781_G11]


title: Progeny1-1242 [a550818-4325018-051918-781_G12]


title: EA0967: Newcastle Early Arthritis Clinic patient 967


title: Progeny1-1023 [a550818-4325018-051918-781_G10]


title: EA0965: Newcastle Early Arthritis Clinic patient 965


title: EA0969: Newcastle Early Arthritis Clinic patient 969


title: EA0957: Newcastle Early Arthritis Clinic patient 957


title: EA0946: Newcastle Early Arthritis Clinic patient 946


title: Progeny1-1148 [a550818-4325018-051918-781_G09]


title: Progeny1-1158 [a550818-4325018-051918-781_G08]


title: EA0944: Newcastle Early Arthritis Clinic patient 944


title: Progeny1-1016 [a550818-4325018-051918-781_G07]


title: EA0938: Newcastle Early Arthritis Clinic patient 938


title: EA0992: Newcastle Early Arthritis Clinic patient 992


title: EA0937: Newcastle Early Arthritis Clinic patient 937


title: EA0932: Newcastle Early Arthritis Clinic patient 932


title: Progeny1-1355 [a550818-4325018-051918-781_G06]


title: EA0926: Newcastle Early Arthritis Clinic patient 926


title: Progeny1-1422 [a550818-4325018-051918-781_G05]


title: EA0923: Newcastle Early Arthritis Clinic patient 923


title: EA0929: Newcastle Early Arthritis Clinic patient 929


title: EA0930: Newcastle Early Arthritis Clinic patient 930


title: EA0915: Newcastle Early Arthritis Clinic patient 915


title: Progeny1-1008 [a550818-4325018-051918-781_G04]


title: EA0948: Newcastle Early Arthritis Clinic patient 948


title: EA0962: Newcastle Early Arthritis Clinic patient 962


title: Progeny1-1206 [a550818-4325018-051918-781_G03]


title: EA0898: Newcastle Early Arthritis Clinic patient 898


title: EA0912: Newcastle Early Arthritis Clinic patient 912

value: Other Inflammatory Arthritis


title: EA0954: Newcastle Early Arthritis Clinic patient 954


title: EA0905: Newcastle Early Arthritis Clinic patient 905

value: Undifferentiated Spondylo-Arthropathy


title: EA0893: Newcastle Early Arthritis Clinic patient 893


title: EA0891: Newcastle Early Arthritis Clinic patient 891


title: EA0884: Newcastle Early Arthritis Clinic patient 884


title: Progeny1-1119 [a550818-4325018-051918-781_F12]


title: Progeny1-1365 [a550818-4325018-051918-781_G01]


title: EA0882: Newcastle Early Arthritis Clinic patient 882


title: EA0879: Newcastle Early Arthritis Clinic patient 879


title: Progeny1-1413 [a550818-4325018-051918-781_F11]


title: EA0878: Newcastle Early Arthritis Clinic patient 878


title: EA0868: Newcastle Early Arthritis Clinic patient 868


title: Progeny1-1391 [a550818-4325018-051918-781_F10]


title: Progeny1-1032 [a550818-4325018-051918-781_H04]


title: EA0854: Newcastle Early Arthritis Clinic patient 854


title: EA0867: Newcastle Early Arthritis Clinic patient 867


title: EA0845: Newcastle Early Arthritis Clinic patient 845


title: Progeny1-1361 [a550818-4325018-051918-781_F09]


title: EA0842: Newcastle Early Arthritis Clinic patient 842


title: Progeny1-1263 [a550818-4325018-051918-781_G02]


title: EA0841: Newcastle Early Arthritis Clinic patient 841


title: Progeny1-1036 [a550818-4325018-051918-781_F08]


title: EA0838: Newcastle Early Arthritis Clinic patient 838


title: EA0835: Newcastle Early Arthritis Clinic patient 835


title: EA0892: Newcastle Early Arthritis Clinic patient 892


title: Progeny1-1342 [a550818-4325018-051918-781_F07]


title: Progeny1-1296 [a550818-4325018-051918-781_F06]


title: EA0826: Newcastle Early Arthritis Clinic patient 826


title: EA0827: Newcastle Early Arthritis Clinic patient 827


title: EA2257: Newcastle Early Arthritis Clinic number 2257

description: Freshly isolated and purified peripheral blood T cells

source_name: Disease control, T cells

growth_protocol: Whole peripheral blood was stored at room temperature for ≤4 hours before processing. After monocyte depletion by immuno-rosetting, an automated magnetic bead-based positive selection protocol was used to isolate CD4+ cells (Stemcell Technologies, Vancouver, Canada) yielding a median cell purity of 98.9%.

value: CD4+ T cells


title: Progeny1-1444 [a550818-4325018-051918-781_F05]


title: EA2264: Newcastle Early Arthritis Clinic number 2264

value: Enteropathic Arthritis


title: Progeny1-1451 [a550818-4325018-051918-781_F04]


title: EA2261: Newcastle Early Arthritis Clinic number 2261

value: peripheral blood


title: EA2233: Newcastle Early Arthritis Clinic number 2233


title: EA2231: Newcastle Early Arthritis Clinic number 2231


title: Progeny1-1458 [a550818-4325018-051918-781_F03]


title: EA2222: Newcastle Early Arthritis Clinic number 2222


title: EA2148: Newcastle Early Arthritis Clinic number 2148


title: EA2144: Newcastle Early Arthritis Clinic number 2144


title: Progeny1-1102 [a550818-4325018-051918-781_E12]


title: Progeny1-1011 [a550818-4325018-051918-781_F01]


title: EA2133: Newcastle Early Arthritis Clinic number 2133


title: EA2145: Newcastle Early Arthritis Clinic number 2145


title: Progeny1-1184 [a550818-4325018-051918-781_F02]


title: EA2140: Newcastle Early Arthritis Clinic number 2140


title: EA2090: Newcastle Early Arthritis Clinic number 2090


title: EA2086: Newcastle Early Arthritis Clinic number 2086

value: Non-Inflammatory


title: EA2087: Newcastle Early Arthritis Clinic number 2087


title: Progeny1-1274 [a550818-4325018-051918-781_E11]


title: EA2067: Newcastle Early Arthritis Clinic number 2067


title: EA2078: Newcastle Early Arthritis Clinic number 2078


title: Progeny1-1052 [a550818-4325018-051918-781_E09]

value: Sugarcane yellow leaf virus infected


title: Progeny1-1244 [a550818-4325018-051918-781_E10]


title: Progeny1-1025 [a550818-4325018-051918-781_E07]


title: EA2052: Newcastle Early Arthritis Clinic number 2052


title: EA2044: Newcastle Early Arthritis Clinic number 2044


title: EA2072: Newcastle Early Arthritis Clinic number 2072


title: Progeny1-1208 [a550818-4325018-051918-781_E05]


title: EA2054: Newcastle Early Arthritis Clinic number 2054


title: EA2062: Newcastle Early Arthritis Clinic number 2062


title: EA2047: Newcastle Early Arthritis Clinic number 2047


title: Progeny1-1358 [a550818-4325018-051918-781_E06]


title: EA2042: Newcastle Early Arthritis Clinic number 2042


title: EA2034: Newcastle Early Arthritis Clinic number 2034


title: EA2040: Newcastle Early Arthritis Clinic number 2040


title: EA2029: Newcastle Early Arthritis Clinic number 2029


title: EA2075: Newcastle Early Arthritis Clinic number 2075

value: Reactive Arthritis


title: EA2030: Newcastle Early Arthritis Clinic number 2030


title: EA2012: Newcastle Early Arthritis Clinic number 2012


title: Progeny1-1129 [a550818-4325018-051918-781_E03]


title: Progeny1-1062 [a550818-4325018-051918-781_E04]


title: EA2010: Newcastle Early Arthritis Clinic number 2010


title: EA1088: Newcastle Early Arthritis Clinic number 1088


title: Progeny1-1059 [a550818-4325018-051918-781_E01]


title: Progeny1-1236 [a550818-4325018-051918-781_E08]


title: Progeny1-1341 [a550818-4325018-051918-781_E02]


title: EA1085: Newcastle Early Arthritis Clinic number 1085

value: Psoriatic Arthritis


title: EA1094: Newcastle Early Arthritis Clinic number 1094


title: EA1080: Newcastle Early Arthritis Clinic number 1080


title: EA1076: Newcastle Early Arthritis Clinic number 1076


title: EA1083: Newcastle Early Arthritis Clinic number 1083


title: EA1058: Newcastle Early Arthritis Clinic number 1058


title: EA2036: Newcastle Early Arthritis Clinic number 2036


title: Progeny1-1368 [a550818-4325018-051918-781_D09]


title: EA1072: Newcastle Early Arthritis Clinic number 1072


title: EA1067: Newcastle Early Arthritis Clinic number 1067


title: Progeny1-1247 [a550818-4325018-051918-781_D11]


title: Progeny1-1430 [a550818-4325018-051918-781_D12]


title: EA1070: Newcastle Early Arthritis Clinic number 1070


title: EA1051: Newcastle Early Arthritis Clinic number 1051


title: EA1050: Newcastle Early Arthritis Clinic number 1050


title: EA1042: Newcastle Early Arthritis Clinic number 1042


title: EA1037: Newcastle Early Arthritis Clinic number 1037


title: Progeny1-1035 [a550818-4325018-051918-781_D07]


title: Female-parent -Green German2 [a550818-4325018-051918-781_D06]

source_name: Female-parent -Green German

value: Sugarcane yellow leaf virus susceptible


title: EA1087: Newcastle Early Arthritis Clinic number 1087


title: EA1022: Newcastle Early Arthritis Clinic number 1022


title: EA1032: Newcastle Early Arthritis Clinic number 1032


title: Progeny1-1403 [a550818-4325018-051918-781_D04]


title: EA1020: Newcastle Early Arthritis Clinic number 1020

value: Undifferentiated Inflammatory Arthritis


title: EA1010: Newcastle Early Arthritis Clinic number 1010

value: Rheumatoid Arthritis


title: EA1008: Newcastle Early Arthritis Clinic number 1008


title: EA1019: Newcastle Early Arthritis Clinic number 1019

value: Osteoarthritis


title: Progeny1-1319 [a550818-4325018-051918-781_D01]

value: Sugarcane yellow leaf virus free


title: EA1003: Newcastle Early Arthritis Clinic number 1003


title: Progeny1-1303 [a550818-4325018-051918-781_D02]


title: EA1054: Newcastle Early Arthritis Clinic number 1054

value: Female


title: EA1000: Newcastle Early Arthritis Clinic number 1000


title: EA0992: Newcastle Early Arthritis Clinic number 992


title: Progeny1-1255 [a550818-4325018-051918-781_C12]


title: EA0996: Newcastle Early Arthritis Clinic number 996


title: Progeny1-1153 [a550818-4325018-051918-781_D08]


title: EA0980: Newcastle Early Arthritis Clinic number 980


title: EA0978: Newcastle Early Arthritis Clinic number 978


title: Progeny1-1138 [a550818-4325018-051918-781_C11]


title: Progeny1-1397 [a550818-4325018-051918-781_D05]


title: EA0975: Newcastle Early Arthritis Clinic number 975


title: EA0974: Newcastle Early Arthritis Clinic number 974


title: EA0973: Newcastle Early Arthritis Clinic number 973


title: EA0969: Newcastle Early Arthritis Clinic number 969


title: Progeny1-1120 [a550818-4325018-051918-781_C10]


title: EA0965: Newcastle Early Arthritis Clinic number 965

value: Male


title: Progeny1-1230 [a550818-4325018-051918-781_C08]


title: Progeny1-1055 [a550818-4325018-051918-781_C09]


title: EA0967: Newcastle Early Arthritis Clinic number 967


title: EA1005: Newcastle Early Arthritis Clinic number 1005


title: Progeny1-1167 [a550818-4325018-051918-781_D03]


title: EA0962: Newcastle Early Arthritis Clinic number 962


title: Progeny1-1182 [a550818-4325018-051918-781_C07]


title: EA0954: Newcastle Early Arthritis Clinic number 954


title: EA0995: Newcastle Early Arthritis Clinic number 995


title: EA0946: Newcastle Early Arthritis Clinic number 946


title: EA0937: Newcastle Early Arthritis Clinic number 937

value: Crystal Arthritis


title: EA0938: Newcastle Early Arthritis Clinic number 938


title: EA0935: Newcastle Early Arthritis Clinic number 935


title: Progeny1-1228 [a550818-4325018-051918-781_C05]


title: EA0948: Newcastle Early Arthritis Clinic number 948


title: Progeny1-1186 [a550818-4325018-051918-781_D10]


title: EA0934: Newcastle Early Arthritis Clinic number 934


title: Progeny1-1178 [a550818-4325018-051918-781_C04]


title: EA0945: Newcastle Early Arthritis Clinic number 945

value: Unknown


title: Progeny1-1175 [a550818-4325018-051918-781_C03]


title: EA0930: Newcastle Early Arthritis Clinic number 930


title: Progeny1-1301 [a550818-4325018-051918-781_C02]


title: EA0929: Newcastle Early Arthritis Clinic number 929


title: EA0926: Newcastle Early Arthritis Clinic number 926


title: Progeny1-1313 [a550818-4325018-051918-781_C01]


title: EA0912: Newcastle Early Arthritis Clinic number 912

value: Other Inflammatory Arthritis


title: EA0915: Newcastle Early Arthritis Clinic number 915

value: CD4+ T cells


title: Progeny1-1137 [a550818-4325018-051918-781_B12]


title: Progeny1-1024 [a550818-4325018-051918-781_B11]


title: EA0896: Newcastle Early Arthritis Clinic number 896


title: EA0905: Newcastle Early Arthritis Clinic number 905

value: Undifferentiated Spondylo-Arthropathy


title: EA0898: Newcastle Early Arthritis Clinic number 898

value: peripheral blood


title: EA0891: Newcastle Early Arthritis Clinic number 891


title: EA0878: Newcastle Early Arthritis Clinic number 878


title: EA0882: Newcastle Early Arthritis Clinic number 882


title: Progeny1-1445 [a550818-4325018-051918-781_C06]


title: EA0854: Newcastle Early Arthritis Clinic number 854


title: Progeny1-1426 [a550818-4325018-051918-781_B10]


title: EA0932: Newcastle Early Arthritis Clinic number 932


title: EA0841: Newcastle Early Arthritis Clinic number 841


title: Progeny1-1121 [a550818-4325018-051918-781_B08]


title: EA0845: Newcastle Early Arthritis Clinic number 845


title: Progeny1-1285 [a550818-4325018-051918-781_B09]


title: EA0842: Newcastle Early Arthritis Clinic number 842

value: Enteropathic Arthritis


title: EA0844: Newcastle Early Arthritis Clinic number 844


title: Progeny1-1250 [a550818-4325018-051918-781_B06]


title: EA0840: Newcastle Early Arthritis Clinic number 840


title: EA0829: Newcastle Early Arthritis Clinic number 829


title: Progeny1-1408 [a550818-4325018-051918-781_B07]


title: EA0827: Newcastle Early Arthritis Clinic number 827


title: EA0838: Newcastle Early Arthritis Clinic number 838


title: EA0826: Newcastle Early Arthritis Clinic number 826


title: Progeny1-1003 [a550818-4325018-051918-781_B04]


title: EA0815: Newcastle Early Arthritis Clinic number 815


title: EA0814: Newcastle Early Arthritis Clinic number 814


title: EA0809: Newcastle Early Arthritis Clinic number 809


title: Progeny1-1170 [a550818-4325018-051918-781_B03]


title: EA0810: Newcastle Early Arthritis Clinic number 810


title: EA0813: Newcastle Early Arthritis Clinic number 813


title: Progeny1-1410 [a550818-4325018-051918-781_B02]


title: Progeny1-1428 [a550818-4325018-051918-781_B01]


title: Progeny1-1396 [a550818-4325018-051918-781_A11]


title: Progeny1-1415 [a550818-4325018-051918-781_A12]


title: Progeny1-1447 [a550818-4325018-051918-781_A10]


title: Progeny1-1288 [a550818-4325018-051918-781_A09]


title: Progeny1-1061 [a550818-4325018-051918-781_B05]


title: Progeny1-1200 [a550818-4325018-051918-781_A08]


title: Healthy control #5

type: protein

city: Chongqing

first: Jun

last: Rao

address: No 183, Xinqiao street, Shapingba

department: Medical center of hematology

institute: Xinqiao hospital

description:
Secreted proteins
SAMPLE 14

hyb_protocol: Place each membrane printed side up into a Plastic Incubation Tray. Add 8 ml of Blocking Buffer to each membrane and cover with the lid. Incubate at room temperature with gentle shaking for 1 hour. Aspirate Blocking Buffer from each tray. Add 8 ml of diluted or undiluted sample onto each membrane and cover with the lid. Incubate at room temperature with gentle shaking for 2 hours. Dilute 20X Wash Buffer 1 with deionized or distilled water to prepare the 1X Wash Buffer 1. Aspirate the samples from each tray and then wash by adding 20 ml of 1X Wash Buffer I at room temperature with gentle shaking (5 min per wash). Repeat the wash 2 more times for a total of 3 washes. Aspirate the 1X Wash Buffer 1 from each tray. Dilute 20X Wash Buffer 2 with deionized or distilled water to prepare the 1X Wash Buffer 2. Wash 3 times with 20 ml of 1X Wash Buffer 2 at room temperature with gentle shaking. Aspirate the 1X Wash Buffer 2 from each tray. Dilute the 500X HRP-Conjugated Streptavidin with Blocking Buffer to prepare the 1X HRP-Conjugated Streptavidin. Add 8 ml of 1X HRPConjugated Streptavidin to each membrane. Incubate at room temperature with gentle shaking for 2 hours. Wash as previously directed.

scan_protocol: The signal can be detected directly from the membrane using a chemiluminescence imaging system or by exposing the array to x-ray film (we recommend using Kodak X-Omat™ AR film) with subsequent development. Expose the membranes for 40 seconds. Then re-expose the film according to the intensity of signals. If the signals are too strong (background too high), reduce the exposure time (e.g., 5–30 seconds). If the signals are too weak, increase the exposure time (e.g., 5–20 min or overnight) or re-incubate membranes overnight with 1X HRPConjugated Streptavidin, and repeat detection on the second day.

data_processing: The manufac Individual array spots were background subtracted locally by subtracting the median background across spot replicated in each sample, and then normalized using two positive controls.

molecule: protein

source_name: Bone marrow Serum

label_protocol: Immediately before use, prepare 1X Labeling Reagent by briefly centrifuging down the Labeling Reagent vial and add 100 ul 1X PBS (pH=8.0) into the vial. Pipette up and down or vortex briefly to dissolve the powder. Add an appropriate amount of 1X Labeling Reagent into the tube containing the sample and immediately mix the reaction solution. Incubate the reaction solution at room temperature for 30 minutes with gentle shaking. Gently tap the tube to mix the reaction solution every 5 minutes. Add 5 ul Stop Solution (Item D) into the reaction solution and then use the Spin Column to remove any unbound biotin. a). Twist off the bottom closure of the Spin Column and loosen the cap (but keep the cap on). Place the Spin Column into a 50 ml conical collection tube. b). Centrifuge the Spin Column at 1,000 g for 3 minutes to remove storage solution. c). Add 5 ml 1X PBS (pH=8.0) into the Spin Column and centrifuge at 1,000 x g for 3 minutes to remove the 1X PBS. Repeat an additional 2 times to wash the Spin Column. d). Place the Spin Column in a new 50 ml conical collection tube and slowly load 3.5 ml of sample to the center of the compact resin bed. e). Centrifuge the Spin Column at 1,000 x g for 3 minutes. The sample should filter through the resin and deposit into the 50 ml conical collection tube. Store at -80 oC until needed. Discard the Spin Column after use.

extract_protocol: 5-fold diluted culture supernatant from whole blood

treatment_protocol: Whole blood was collected in vacutainer serum tubes, incubated undisturbed at room temperature for 30 min, then centrifuged at 2000 rpm for 15 min at 4 oC . The supernatant was collected and frozen at -80 oC for storage.

tag: disease state

value: healthy control

value: Bone marrow serum

value: male


title: Progeny1-1223 [a550818-4325018-051918-781_A07]


title: Healthy control #3

description:
Secreted proteins
SAMPLE 12


title: patients #4

description:
Secreted proteins
SAMPLE 4

value: acute myeloid leukemia

value: female


title: Healthy control #1

description:
Secreted proteins
SAMPLE 10


title: Healthy control #4

description:
Secreted proteins
SAMPLE 13


title: Healthy control #2

description:
Secreted proteins
SAMPLE 11


title: Progeny1-1081 [a550818-4325018-051918-781_A06]


title: patients #6

description:
Secreted proteins
SAMPLE 6


title: patients #9

description:
Secreted proteins
SAMPLE 9


title: patients #8

description:
Secreted proteins
SAMPLE 8


title: patients #7

description:
Secreted proteins
SAMPLE 7


title: patients #5

description:
Secreted proteins
SAMPLE 5


title: GmMM_GLYMA.08G357600-B-ChIP_br2.2

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads from technical replicates were combined and peaks were identified for each biological replicates using MACS2,  --nomodel --extsize 220 and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

organism: Glycine max

source_name: embryos

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3ug of an an antibody raised against the peptide QQNPDPGLGGTVGEC, corresponding to the amino acids 118-132 of GLYMA.08G35760.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Mid-maturation stage embryos were dissected from seeds weighing between 200 and 250 mg .  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

tag: Stage

value: mid-maturation stage

tag: antibody

value: anti-peptide GLYMA.08G357600


title: GmMM_GLYMA.08G357600-B-ChIP_br2.1


title: Progeny1-1150 [a550818-4325018-051918-781_A05]

value: Sugarcane yellow leaf virus free


title: GmEM-Input_br1 (GLYMA.06G314400  control)

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3 ug of an antibody raised against the peptide SDTRRPGRKRGTSED corresponding to the amino acids 224-238 of GLYMA.06G314400.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Early maturation stage embryos were dissected from 6 to 7 mm seeds.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

value: early maturation stage


title: patients #1

description:
Secreted proteins
SAMPLE 1


title: GmMM_GLYMA.08G357600-B-ChIP_br1.2


title: Progeny1-1345 [a550818-4325018-051918-781_A04]


title: GmMM_GLYMA.08G357600-B-ChIP_br1.1