title: N2a-Scramble siRNA Rep1


title: ProNeut_Neutrophil2

status: Public on Jul 17 2018

type: SRA

city: La Jolla

first: Huy

middle: Q

last: Dinh

state: CA

address: 9420 Athena Circle

department: Division of Inflammation Biology

country: USA

institute: La Jolla Institute

library_source: transcriptomic

data_processing:
Read quality was QC using FastQC 0.11.7
Read mapping was done by Rsubread 1.30.5
CPM counts (log) was calculated using FeatureCount 1.22.2 and edgeR 1.30.5
Genes with at least 2 samples with CPM>1 were kept for downstream analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: NeP_log2_cpm.txt: tab-delimited text files includes log2 CPM for each samples (Column names: Gene ID, Gene Symbol, and 15 samples as described in the SAMPLES section)

molecule: total RNA

organism: Mus musculus

extract_protocol: Universal Plus mRNA-Seq (Nugen)

treatment_protocol: Five Mouse cell subsets were FACS sorted from healthy mice fresh BM.

tag: tissue

value: Bone marrow

tag: cell type


title: Neutrophil_1

description: BM Neuts

source_name: Neutrophil

value: Neutrophil


title: ProNeut_Neutrophil3


title: PreNeut_Neutrophil3


title: Neutrophil_3

description: BM Neuts


title: PFC_WENp2

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description:
Ribo-depleted total RNA
Replicate 2

data_processing:
The raw reads were mapping to mm10 genome using TopHat 2.0.1 followed by Tmap 3.0.1 for unaligned reads
The transcript FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) levels were quantified using the Cufflinks v2.2.1 and GTF from the Ensembl gene database.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Prefrontal cortex

extract_protocol:
RNA was isolated following the manufacturer’s protocol and further purified using the RNeasy Mini Kit (Qiagen Inc.). The total RNA concentration was measured using an ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).
rRNA-depleted RNA was used as the template to prepare the RNA-seq library generated using the Ion  123 Total RNA-seq Kit v2 system, according to the manufacturer’s protocol. The template-positive ion sphere particles (ISPs) were loaded onto an Ion  127 PI Chip v2 and sequenced (single end reads > 100 bp).

value: Prefrontal cortex

tag: treatment

value: venlafaxine


title: PFC_SALIp4

description:
Ribo-depleted total RNA
Replicate 4

value: saline


title: PFC_RISp3

description:
Ribo-depleted total RNA
Replicate 3

value: risperidone


title: PFC_MIAp4

description:
Ribo-depleted total RNA
Replicate 4

value: mianserin


title: PFC_SALIIp3

description:
Ribo-depleted total RNA
Replicate 3


title: PFC_WENp1

description:
Ribo-depleted total RNA
Replicate 1


title: PFC_WENp4

description:
Ribo-depleted total RNA
Replicate 4


title: PFC_SALIp2

description:
Ribo-depleted total RNA
Replicate 2


title: PFC_RISp2

description:
Ribo-depleted total RNA
Replicate 2


title: PFC_RISp4

description:
Ribo-depleted total RNA
Replicate 4


title: PFC_WENp3

description:
Ribo-depleted total RNA
Replicate 3


title: PFC_SALIIp4

description:
Ribo-depleted total RNA
Replicate 4


title: PFC_SALIp3

description:
Ribo-depleted total RNA
Replicate 3


title: PFC_SALIIp2

description:
Ribo-depleted total RNA
Replicate 2


title: PFC_RISp1

description:
Ribo-depleted total RNA
Replicate 1


title: PFC_SALIp1

description:
Ribo-depleted total RNA
Replicate 1


title: PFC_SALIIp1

description:
Ribo-depleted total RNA
Replicate 1


title: CD115plusGMP_3

description: #B


title: PFC_MIAp3

description:
Ribo-depleted total RNA
Replicate 3


title: PFC_MIAp2

description:
Ribo-depleted total RNA
Replicate 2


title: PFC_METp4

description:
Ribo-depleted total RNA
Replicate 4

value: methamphetamine


title: PFC_METp1

description:
Ribo-depleted total RNA
Replicate 1


title: PFC_METp2

description:
Ribo-depleted total RNA
Replicate 2


title: CMP_3

description: #E

source_name: CMP

value: CMP


title: CD115plusGMP_2

description: #B


title: PFC_METp3

description:
Ribo-depleted total RNA
Replicate 3


title: PFC_KETp4

description:
Ribo-depleted total RNA
Replicate 4

value: ketamine


title: CD115plusGMP_1

description: #B


title: NAc_WENp4

description:
Ribo-depleted total RNA
Replicate 4

source_name: Nucleus accumbens

value: Nucleus accumbens


title: PFC_HALp2

description:
Ribo-depleted total RNA
Replicate 2

value: haloperidol


title: PFC_MIAp1

description:
Ribo-depleted total RNA
Replicate 1


title: NAc_WENp3

description:
Ribo-depleted total RNA
Replicate 3


title: PFC_HALp4

description:
Ribo-depleted total RNA
Replicate 4


title: CMP_1

description: #E


title: PFC_KETp3

description:
Ribo-depleted total RNA
Replicate 3


title: PFC_HALp3

description:
Ribo-depleted total RNA
Replicate 3


title: PFC_KETp2

description:
Ribo-depleted total RNA
Replicate 2


title: NAc_WENp2

description:
Ribo-depleted total RNA
Replicate 2


title: PFC_KETp1

description:
Ribo-depleted total RNA
Replicate 1


title: PFC_HALp1

description:
Ribo-depleted total RNA
Replicate 1


title: NAc_SALIp3

description:
Ribo-depleted total RNA
Replicate 3


title: NAc_SALIp2

description:
Ribo-depleted total RNA
Replicate 2


title: Liver_s_039

city: Madison

first: James

last: Thomson

state: WI

address: 330 N. Orchard st.

department: Cellular and regenerative biology

institute: Morgridge institute for discovery

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046679_0042361

data_processing:
Single end reads of 51 bp were sequenced on an Illumina HiSeq 2500 system. Sequencer outputs were processed using Illumina’s CASAVA-1.8.2.DOI:https://doi.org/10.1186/1471-2105-12-323).
The demultiplexed reads were trimmed and filtered to eliminate adapter sequence and low-quality basecalls.
The reads were mapped to an mm10 mRNA transcript reference (extended with ERCC transcripts) using bowtie bowtie-0.12.9 (Langmead B. et al. 2009  DOI:https://doi.org/10.1186/gb-2009-10-3-r25);
expression estimates were generated using RSEM v.1.2.3 (Li B. and Dewey C. N. 2011) and normalized using scNorm (Bacher R. et al 2017)
Samples were then re-ordered using WaveCrest (Chu L-F. et al 2016)
Genome_build: mm10
Supplementary_files_format_and_content: Liver_SCnormEC_ALLcells_WavecrestPoly3.csv contains a table Expected Counts from RSEM, normalized using scNorm, with sample columns ordered via the WaveCrest algorithm (per data processing steps)

source_name: Liver

growth_protocol: The wildtype 8-week-old male C57BL/6 mouse was kept under standard husbandry conditions.

extract_protocol:
Single cell RNA sequencing was performed as previously described (Chu L-F. et al 2016 DOI:https://doi.org/10.1186/s13059-016-1033-x  ) with the following modifications. In this study, we used small (5-10 μm), medium (10-17 μm), and large (17-25 μm) plate sizes. ERCC RNA Spike-In (ThermoFisher Cat. No. 4456740) was diluted in the lysis mix following the manufacturer’s user guide and previous studies (Brennecke P. et al. 2013 DOI:https://doi.org/10.1038/nmeth.2645).
Library construction was performed as previously described (Chu L-F. et al 2016 DOI:https://doi.org/10.1186/s13059-016-1033-x)

treatment_protocol: The mouse was anesthetized using isoflurane before euthanizing by cervical dislocation mouse was pinned to a Styrofoam plate using 20 ga needles to aid in dissection. The abdominal cavity was opened and the portal vein exposed. A piece of 4-0 suture thread (Ethicon vicryl coated) was threaded under the portal vein and used to secure a 26 ga catheter inserted into the portal vein (Butler Schein animal health 26 G IV Catheter, Fisher Scientific). Hepatocytes were isolated using a 2-step perfusion protocol. First, Liver Perfusion Medium (Gibco) warmed to 37 °C was pumped through the catheter for 10 minutes using a peristaltic pump at 7 ml/min flowrate. Then, Liver Digest Medium (Gibco) warmed to 37 °C was pumped through the liver at the same settings for 10 minutes. After perfusion, the liver was excised and transferred to a 10 cm dish containing 20 ml liver digest medium. The liver was dissected allowing the cells to spill into the media. The cells were then filtered through a 40 μm cell strainer into a 50 ml tube and 30 ml media (Williams E media + 2 μg/ml human insulin + 1x glutamax + 10% FBS) were added and placed on ice. The hepatocytes were purified by centrifugation at 50 x G, four times for 3 minutes each, each time discarding the supernatant and adding media.

tag: fluidigm c1 capture chip size

value: Isolated Primary Hepatocytes

tag: gender

value: Male

tag: age

value: 8 week-old

tag: strain


title: Liver_s_035

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046675_0042393


title: Liver_s_038

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046678_0042360


title: Liver_s_037

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046677_0042359


title: CMP_2

description: #E


title: NAc_SALIp4

description:
Ribo-depleted total RNA
Replicate 4


title: NAc_WENp1

description:
Ribo-depleted total RNA
Replicate 1


title: Liver_s_034

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046674_0042392


title: NAc_SALIIp4

description:
Ribo-depleted total RNA
Replicate 4


title: Liver_s_036

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046676_0042394


title: Liver_s_033

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046673_0042391


title: NAc_SALIp1

description:
Ribo-depleted total RNA
Replicate 1


title: Liver_s_032

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046672_0042390


title: NAc_SALIIp3

description:
Ribo-depleted total RNA
Replicate 3


title: NAc_SALIIp2

description:
Ribo-depleted total RNA
Replicate 2


title: NAc_SALIIp1

description:
Ribo-depleted total RNA
Replicate 1


title: NAc_RISp3

description:
Ribo-depleted total RNA
Replicate 3


title: NAc_RISp2

description:
Ribo-depleted total RNA
Replicate 2


title: Liver_s_031

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046671_0042389


title: NAc_RISp1

description:
Ribo-depleted total RNA
Replicate 1


title: NAc_MIAp4

description:
Ribo-depleted total RNA
Replicate 4


title: NAc_RISp4

description:
Ribo-depleted total RNA
Replicate 4


title: Liver_s_030

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046670_0042358


title: NAc_MIAp3

description:
Ribo-depleted total RNA
Replicate 3


title: Liver_s_028

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046668_0042356


title: Liver_s_027

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046667_0042355


title: NAc_METp4

description:
Ribo-depleted total RNA
Replicate 4


title: NAc_METp2

description:
Ribo-depleted total RNA
Replicate 2


title: NAc_METp3

description:
Ribo-depleted total RNA
Replicate 3


title: NAc_METp1

description:
Ribo-depleted total RNA
Replicate 1


title: NAc_KETp4

description:
Ribo-depleted total RNA
Replicate 4


title: NAc_KETp3

description:
Ribo-depleted total RNA
Replicate 3


title: NAc_KETp2

description:
Ribo-depleted total RNA
Replicate 2


title: Liver_s_024

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046664_0042388


title: Liver_s_023

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046663_0042387


title: Liver_s_025

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046665_0042353


title: NAc_MIAp2

description:
Ribo-depleted total RNA
Replicate 2


title: NAc_MIAp1

description:
Ribo-depleted total RNA
Replicate 1


title: NAc_KETp1

description:
Ribo-depleted total RNA
Replicate 1


title: Liver_s_018

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046658_0042352


title: NAc_HALp3

description:
Ribo-depleted total RNA
Replicate 3


title: Liver_s_029

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046669_0042357


title: Liver_s_021

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046661_0042385


title: NAc_HALp2

description:
Ribo-depleted total RNA
Replicate 2


title: Liver_s_020

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046660_0042384


title: Liver_s_017

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046657_0042351


title: Liver_s_019

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046659_0042383


title: Liver_s_022

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046662_0042386


title: Liver_s_015

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046655_0042349


title: Liver_s_026

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046666_0042354


title: Liver_s_013

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046653_0042347


title: Liver_s_012

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046652_0042382


title: NAc_HALp1

description:
Ribo-depleted total RNA
Replicate 1


title: Liver_s_011

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046651_0042381


title: Liver_s_009

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046649_0042379


title: Liver_s_010

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046650_0042380


title: Liver_s_016

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046656_0042350


title: Liver_s_007

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046647_0042377


title: NAc_HALp4

description:
Ribo-depleted total RNA
Replicate 4


title: Liver_s_006

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046646_0042346


title: Liver_s_003

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046643_0042343


title: Liver_s_014

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046654_0042348


title: Liver_s_002

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046642_0042342


title: Liver_s_004

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046644_0042344


title: Liver_m_028

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046707_0042407


title: Liver_m_026

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046705_0042375


title: Liver_m_025

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046704_0042374


title: Liver_s_001

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046641_0042341


title: Liver_m_030

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046709_0042409


title: Liver_m_029

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046708_0042408


title: Liver_m_019

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046698_0042404


title: Liver_m_021

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046700_0042406


title: Liver_m_022

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046701_0042371


title: Liver_s_008

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046648_0042378


title: Liver_m_018

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046697_0042403


title: Liver_m_016

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046695_0042401


title: Liver_m_017

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046696_0042402


title: Liver_m_027

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046706_0042376


title: Liver_m_014

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046693_0042369


title: Liver_m_023

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046702_0042372


title: Liver_m_024

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046703_0042373


title: Liver_m_015

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046694_0042370


title: 9533774106_R06C01: ependymoma tissue 159

type: genomic

city: Toronto

first: Vijay

last: Ramaswamy

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: ependymoma tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from posterior fossa ependymoma using Qiagen DNeasy Kit according to standard instructions

value: primary posterior fossa ependymoma

tag: tissue type

value: FFPE Tumor

tag: pfs

tag: os

tag: progression (1=progression event)

tag: status (1=dead)

tag: pfb subtype


title: Liver_m_012

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046691_0042367


title: Liver_m_011

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046690_0042366


title: Liver_s_005

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046645_0042345


title: Liver_m_010

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046689_0042365


title: Liver_m_009

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046688_0042400


title: Liver_m_008

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046687_0042399


title: Liver_m_020

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046699_0042405


title: Liver_m_007

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046686_0042398


title: Liver_m_006

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046685_0042397


title: Liver_m_013

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046692_0042368


title: Liver_m_005

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046684_0042396


title: Liver_m_004

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046683_0042395


title: Liver_m_003

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046682_0042364


title: Oxolinic acid Rep 3 +A-IP

city: Seattle

first: Dmitry

last: Sutormin

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description:
Cells treated with oxolinic acid (120 microMolar)
Cell culture
Total DNA (mock DNA)

library_source: genomic

data_processing:
Raw reads were aligned to the E. coli w3110 MuSGS genome (containing a strong gyrase binding site from bacteriophage Mu) with BWA MEM (default settings)
Resulting SAM files were processed with custom script (SAM_to_coverage_and_N5E_N3E.py, github: https://github.com/sutormin94/Gyrase_Topo-seq), giving coverage depth of the genome and N3E values (number of DNA fragments 3'-ends) for every position
Gyrase Cleavage Sites (GCSs) were called using custom script (GCSs_calling.py, github: https://github.com/sutormin94/Gyrase_Topo-seq) that takes 4 files (tetrade) as input: +A+IP, +A-IP, -A+IP, -A-IP
Genome_build: Escherichia coli W3110 MuSGS (on the basis of NC_007779.1). FASTA and GFF are included on series record.
Supplementary_files_format_and_content: tar archives contain the following:
text wig files contain N3E values (number of DNA fragments 3' ends for each position of the genome)
text wig files contain coverage depth data
tab-delimited text files with GCSs coordinates, N3E values ("height of the peak") and GCSs scores (score of the sequence under the GCS obtained after scanning the genome with DNA-gyrase binding motif)

organism: Escherichia coli

growth_protocol:
1 ml of overnight culture was prepared for E. coli DY 330 GyrA-SPA or E. coli DY 330 GyrA-SPA MuSGS by seeding 2YT medium supplemented with antibiotics (kanamycin 50 µg/ml for DY 330 GyrA-SPA and kanamycin 50 µg/ml, chloramphenicol 15 µg/ml for DY 330 GyrA-SPA MuSGS) with cells from one isolate colony.
Starter was cultivated at 32°C with shaking (180 rpm), then was inoculated into 100 ml of 2YT without antibiotics and cultivation was proceeded under the same conditions until culture reaching mid-logphase (OD600=0.6-0.8).

extract_protocol:
DNA was extracted from resulting supernatant with phenol/chlorophorm method followed by ethanol precipitation. Mock controls (-IP) were made both for +A and for -A: 100 μl aliquots of lysates obtained after sonication were deproteinized and DNA was purified as described earlier. The procedure described gives a quartet of samples (+A+IP, +A-IP, -A+IP, -A-IP), where +A-IP, -A+IP, and -A-IP serves as controls for gyrase poison action and immunoprecipitation.
Sequencing libraries were prepared with Accel NGS 1S kit (Swift Bioscience) in accordanse with manufacturer’s protocol.

treatment_protocol:
When reaching  the optical density indicated (OD600=0.6-0.8) the culture was bisected and DNA gyrase poison (ciprofloxacin, oxolinic acid or microcin B17) was added to the first half (+A samples), while second served as a control (-A samples).
Cultures (+A and -A) were incubated at 32°C with shaking for additional 15 min, then cells were pelleted by centrifugation at 10°C (4500xg) and resuspended in 10 ml of TES buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 250 mM NaCl). Washing procedure was repeated twice to remove culture liquid and excess of gyrase poison.
Washed pellets were resuspended in 1 ml of TESS buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 250 mM NaCl, 0.02% SDS, 0.2% Tween-20) with addition of proteases inhibitors cocktail (cOmplete ultra EDTA free, Roche) and RNAse A (Thermo Scientific). Resulting suspensions were sonicated with parameters optimized to obtain DNA fragments between 200 and 700 bp (SONOPULS HD 3100). Lysates were diluted with 1 ml of TES buffer and 100 μl of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich) was added. Immunoprecipitation was performed for 1.5-2 hours at room temperature with moderate mixing, then affinity gel was washed 4 times by repeating steps of centrifugation (1.5 minute, 1000xg at room temperature) and resuspention (x2 with 1 ml of TESS buffer, x1 with 1 ml of TES buffer, x1 with 1 ml of TE buffer).
Lysates were diluted with 1 ml of TES buffer and 100 μl of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich) was added. Immunoprecipitation was performed for 1.5-2 hours at room temperature with moderate mixing, then affinity gel was washed 4 times by repeating steps of centrifugation (1.5 minute, 1000xg at room temperature) and resuspention (x2 with 1 ml of TESS buffer, x1 with 1 ml of TES buffer, x1 with 1 ml of TE buffer).
For proteolysis, affinity gel obtained after the last centrifugation step was diluted with TES buffer up to final volume 200 μl, proteinase K (Sigma-Aldrich) was added (0.5 mg/ml) and samples were incubated at 55°C for at least 3 hours. After this step samples were centrifuged (2 minutes, 2000xg at room temperature) and supernatants were collected for DNA extraction.

tag: tagged gyrase subunit

value: GyrA-SPA

tag: musgs presence


title: Liver_L_080

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046789_0042583


title: Liver_m_002

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046681_0042363


title: Liver_m_001

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046680_0042362


title: Liver_L_077

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046786_0042450


title: Liver_L_079

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046788_0042582


title: Liver_L_078

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046787_0042451


title: Oxolinic acid Rep 3 +A+IP

description:
Cells treated with oxolinic acid (120 microMolar)
Cell culture
DNA coimmunoprecipitated with DNA-gyrase


title: Oxolinic acid Rep 2 +A-IP

value: MuSGS


title: Oxolinic acid Rep 2 +A+IP


title: Liver_L_074

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046783_0042447


title: Liver_L_076

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046785_0042449


title: Liver_L_075

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046784_0042448


title: Liver_L_071

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046780_0042580


title: Microcin B17 Rep 3 +A-IP

description:
Cells treated with microcin B17 (50 microMolar)
Cell culture
Total DNA (mock DNA)


title: Oxolinic acid Rep 1 +A-IP


title: Oxolinic acid Rep 1 +A+IP


title: Microcin B17 Rep 3 +A+IP

description:
Cells treated with microcin B17 (50 microMolar)
Cell culture
DNA coimmunoprecipitated with DNA-gyrase


title: Microcin B17 Rep 2 +A-IP

description:
Cells treated with microcin B17 (10 microMolar)
Cell culture
Total DNA (mock DNA)


title: Liver_L_073

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046782_0042446


title: Liver_L_072

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046781_0042581


title: Liver_L_070

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046779_0042579


title: Microcin B17 Rep 2 +A+IP

description:
Cells treated with microcin B17 (10 microMolar)
Cell culture
DNA coimmunoprecipitated with DNA-gyrase


title: Microcin B17 Rep 1 +A+IP


title: Microcin B17 Rep 1 +A-IP


title: Liver_L_069

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046778_0042578


title: Liver_L_067

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046776_0042576


title: Liver_L_068

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046777_0042577


title: Rifampicine Ciprofloxacin Rep 3 +A+IP

description:
Cells treated with rifampicine (122 microMolar) and ciprofloxacin (10 microMolar)
Cell culture
DNA coimmunoprecipitated with DNA-gyrase


title: Rifampicine Ciprofloxacin Rep 2 +A-IP

description:
Cells treated with rifampicine (122 microMolar) and ciprofloxacin (10 microMolar)
Cell culture
Total DNA (mock DNA)


title: Rifampicine Ciprofloxacin Rep 1 +A+IP


title: Liver_L_064

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046773_0042443


title: Liver_L_065

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046774_0042444


title: Liver_L_066

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046775_0042445


title: Liver_L_060

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046769_0042575


title: Ciprofloxacin Rep 1 +A-IP

description:
Cells treated with ciprofloxacin (10 microMolar)
Cell culture
Total DNA (mock DNA)


title: Liver_L_061

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046770_0042440


title: Rifampicine Ciprofloxacin Rep 2 +A+IP


title: Liver_L_059

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046768_0042574


title: Liver_L_062

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046771_0042441


title: Liver_L_063

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046772_0042442


title: Rifampicine Ciprofloxacin Rep 1 +A-IP


title: Liver_L_055

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046764_0042570


title: Liver_L_056

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046765_0042571


title: Liver_L_057

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046766_0042572


title: Ciprofloxacin Rep 3 +A-IP


title: Ciprofloxacin Rep 2 +A+IP

description:
Cells treated with ciprofloxacin (10 microMolar)
Cell culture
DNA coimmunoprecipitated with DNA-gyrase


title: Rifampicine Ciprofloxacin Rep 3 +A-IP


title: Untreated Rep 3 -A-IP

description:
Untreated cells
Cell culture
Total DNA (mock DNA)


title: Rifampicine Ciprofloxacin Rep 1 -A-IP

description:
Cells treated with rifampicine (122 microMolar)
Cell culture
Total DNA (mock DNA)


title: Liver_L_054

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046763_0042439


title: Liver_L_053

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046762_0042438


title: Liver_L_052

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046761_0042437


title: Ciprofloxacin Rep 3 +A+IP


title: Untreated Rep 2 -A-IP


title: Liver_L_058

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046767_0042573


title: Ciprofloxacin Rep 2 +A-IP


title: Untreated Rep 2 -A+IP

description:
Untreated cells
Cell culture
DNA coimmunoprecipitated with DNA-gyrase


title: Ciprofloxacin Rep 1 +A+IP


title: Untreated Rep 1 -A-IP


title: Untreated Rep 1 -A+IP


title: Untreated Rep 3 -A+IP


title: Liver_L_043

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046752_0042564


title: Liver_L_040

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046749_0042431


title: Liver_L_045

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046754_0042566


title: Liver_L_046

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046755_0042567


title: Liver_L_049

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046758_0042434


title: Liver_L_051

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046760_0042436


title: Liver_L_041

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046750_0042432


title: Liver_L_042

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046751_0042433


title: Liver_L_039

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046748_0042430


title: Liver_L_048

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046757_0042569


title: Liver_L_047

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046756_0042568


title: Liver_L_044

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046753_0042565


title: Liver_L_037

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046746_0042428


title: Liver_L_050

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046759_0042435


title: Liver_L_035

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046744_0042562


title: Liver_L_036

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046745_0042563


title: Liver_L_034

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046743_0042561


title: Liver_L_038

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046747_0042429


title: Liver_L_033

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046742_0042560


title: HAEC_HpeV3_t72h_rep3

type: RNA

city: Amsterdam

first: Cosimo

last: Cristella

address: Meibergdreef 9

country: Netherlands

institute: Academic Medical Center

description:
HAEC_HpeV3_3
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV5

hyb_protocol: Hybridization, wash and staining was performed using the GeneTitan™ Hybridization, Wash, and Stain Kit for WT Array Plates (Affyetrix/Termo Fisher)

scan_protocol: Arrays were scanned using the GeneTitan instrument (Affyetrix/Termo Fisher)

data_processing: The BrainArray (version 22) custom Chip Description File (CDF) was used to re-map probesets on the arrays based on the latest genome and transcriptome information (Dai et al., 2005). Probesets normalization was achieved by Robust Multi-array Average (RMA) function implemented in the Affy R package.

label: biotin

source_name: HAEC_HPeV3 infected_72h

label_protocol: Total RNA was used as input for the amplification and labelling of samples using the Affymetrix WT Nano Kit

extract_protocol: Total RNA was extracted by High Pure RNA Isolation Kit (Roche LifeScience, Penzberg, Germany). RNA samples were concentrated to 33ng/μl using Eppendorf Concentrator Plus (Eppendorf, Hamburg, Germany)

value: Nasal MucilAir HAE cell

tag: inoculated with


title: HAEC_HpeV3_t72h_rep4

description:
HAEC_HpeV3_4
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV6


title: HAEC_HpeV3_t72h_rep1

description:
HAEC_HpeV3_1
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV3


title: HAEC_HpeV1_t72h_rep1

description:
HAEC_HpeV1_1
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV1

source_name: HAEC_HPeV1 infected_72h


title: HAEC_HpeV1_t72h_rep4

description:
HAEC_HpeV1_4
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV1


title: Liver_L_032

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046741_0042559


title: HAEC_HpeV3_t72h_rep2

description:
HAEC_HpeV3_2
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV4


title: Liver_L_028

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046737_0042425


title: Liver_L_030

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046739_0042427


title: HAEC_HpeV1_t72h_rep2

description:
HAEC_HpeV1_2
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV1


title: Liver_L_029

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046738_0042426


title: Liver_L_027

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046736_0042424


title: Liver_L_026

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046735_0042423


title: HAEC_HpeV1_t72h_rep5

description:
HAEC_HpeV1_5
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV1


title: Liver_L_025

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046734_0042422


title: HAEC_Mock_t0_rep5

description:
HAEC_Mock_5
Gene expression data from uninfected Nasal HAE cells

value: mock (uninfected)


title: 9_Saliva-IgG_1

type: protein

city: Vienna

first: Peter

last: Hettegger

address: Giefinggasse 4

department: Center for Health and Bioresources

country: Austria

institute: Austrian Institute of Technology

description: IgG

hyb_protocol: Processing of microarrays was done equally for plasma and saliva IgG samples. Arrays were blocked with blocking buffer (PBS pH 7.4, 3% Milk Powder, 0.1% Tween-20) for 30 min with agitation (150rpm on plate shaker) at RT and washed three times with PBST (PBS pH 7.4, 0.1% Tween-20). Slides were spin-dried and incubated with 100µL of 0.02µg/µL sample IgG (2µg total IgG) in blocking buffer with agitation (150rpm) for 1.5 hours at RT. After washing for three times with PBST, slides were incubated with goat anti-human IgG Alexa 647 detection antibody (Invitrogen A21445) diluted 1:10.000 in blocking buffer with agitation for 1 hour at RT in the dark. Slides were washed another three times with PBST, two times with H2O and spin-dried immediately after the final wash step.

scan_protocol: Fluorescence intensity in the red channel (excitation 635nm laser, emission filter 676/37nm) was scanned with a Tecan PowerScanner.

data_processing: Fluorescence images of microarrays were processed with GenePix Pro 6.0 (Molecular devices) to quantify median fluorescence intensity (MFI), local background intensity (BG) and to identify low quality or damaged spots. Spots were removed from analyses if either spot was flagged (flag = -100) or spot diameter was lower than 41 or higher than 180. No background correction was performed. Data was median-normalised to log2 MFI of 9 (or MFI = 512).

label: AlexaFluor®647-labelled anti-human secondary antibody

molecule: protein

source_name: Saliva

label_protocol: Goat anti-human IgG Alexa 647 detection antibody (Invitrogen A21445) was labeled by the company.

extract_protocol: Saliva IgG purification: Frozen aliquots of saliva/buffer mixture were thawed at room temperature. 4mL of saliva/buffer mixture was buffer exchanged in 100mM sodium phosphate 150mM NaCl and concentrated to 200µL using an Amicon 30k centrifugal filter device (Merck UFC803024). IgG was purified from this concentrate using a 96-well format Protein G column kit (Thermo 45204) according to the kit manual. In brief, the columns were pre-rinsed with binding buffer (100mM sodium phosphate 150mM NaCl pH 7.2), 200µL of buffer exchanged sample was applied to the columns and incubated for 30min with moderate agitation at RT. Subsequently, columns were washed 4 times with binding buffer, bound IgG was eluted with 400µL of 100mM glycine pH 2.5 and pH was adjusted to 7.2 with 1M sodium phosphate pH 9. The eluate was buffer exchanged with H2O and concentrated to 35µL using a Microcon 10k centrifugal filter device (Merck MRCPRT010) yielding a final concentration of roughly 0.15µg/µL or a total of 5.3µg IgG.  Plasma IgG purification: Plasma IgG was purified using a 96-well format Melon Gel kit (Thermo 45208) according to the kit manual with a slightly modified protocol. In brief, 15µL of plasma was diluted in 95µL of purification buffer, applied to the resin, incubated for 5 min with moderate agitation at RT and centrifuged at 1000xg for 1min to obtain the purified IgG (roughly 1mg/mL in 100µL purification buffer).

tag: individual id

value: Saliva

value: m

tag: smoker

value: n

tag: pmt gain


title: HAEC_HpeV1_t72h_rep3

description:
HAEC_HpeV1_3
Gene expression data from Nasal HAE cells after 72 hrs infection with with HPeV1

tag: cell type


title: 9_Plasma-IgG_2

description:
IgG
sample replicate of 9.Pla

data_processing: Fluorescence images of microarrays were processed with GenePix Pro 6.0 (Molecular devices) to quantify median fluorescence intensity (MFI), local background intensity (BG) and to identify low quality or damaged spots. Spots were removed from analyses if either spot was flagged (flag = -100) or spot diameter was lower than 41 or higher than 150. No background correction was performed. Data was median-normalised to log2 MFI of 9 (or MFI = 512).

source_name: Plasma

tag: tissue

value: Plasma


title: 9_Saliva-IgG_2

description:
IgG
sample replicate of 9.Sal

tag: gender


title: 9_Plasma-IgG_1

description: IgG


title: 8_Saliva-IgG_1

description: IgG

value: f

value: y


title: Liver_L_024

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046733_0042557

tag: fluidigm c1 capture chip size

tag: age


title: HAEC_Mock_t0_rep2

description:
HAEC_Mock_2
Gene expression data from uninfected Nasal HAE cells


title: Liver_L_031

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046740_0042558

tag: strain


title: HAEC_Mock_t0_rep4

description:
HAEC_Mock_4
Gene expression data from uninfected Nasal HAE cells


title: HAEC_Mock_t0_rep1

description:
HAEC_Mock_1
Gene expression data from uninfected Nasal HAE cells


title: HAEC_Mock_t0_rep3

description:
HAEC_Mock_3
Gene expression data from uninfected Nasal HAE cells


title: 8_Plasma-IgG_1

description: IgG


title: Liver_L_023

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046732_0042556


title: 9_Plasma-IgG_1

description: IgG


title: Liver_L_022

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046731_0042555


title: 9_Saliva-IgG_1

description: IgG


title: 8_Saliva-IgG_1

description: IgG


title: 7_Saliva-IgG_1

description: IgG


title: Liver_L_021

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046730_0042554


title: Liver_L_020

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046729_0042553


title: 6_Saliva-IgG_1

description: IgG


title: 8_Plasma-IgG_1

description: IgG


title: 7_Plasma-IgG_1

description: IgG


title: 6_Saliva-IgG_1

description: IgG


title: 6_Plasma-IgG_1

description: IgG


title: 7_Saliva-IgG_1

description: IgG


title: Liver_L_018

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046727_0042421


title: Liver_L_017

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046726_0042420


title: 7_Plasma-IgG_1

description: IgG


title: 5_Saliva-IgG_1

description: IgG


title: 6_Plasma-IgG_1

description: IgG


title: 5_Plasma-IgG_1

description: IgG


title: 4_Saliva-IgG_1

description: IgG


title: Liver_L_016

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046725_0042419


title: 5_Plasma-IgG_1

description: IgG


title: Liver_L_015

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046724_0042418


title: 4_Plasma-IgG_1

description: IgG


title: Liver_L_014

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046723_0042417


title: 3_Saliva-IgG_1

description: IgG


title: Liver_L_019

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046728_0042552


title: Liver_L_013

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046722_0042416


title: 3_Plasma-IgG_1

description: IgG


title: 4_Saliva-IgG_1

description: IgG


title: 4_Plasma-IgG_1

description: IgG


title: Liver_L_012

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046721_0042551


title: Liver_L_011

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046720_0042550


title: 5_Saliva-IgG_1

description: IgG


title: 20_Saliva-IgG_1

description: IgG


title: 20_Plasma-IgG_1

description: IgG


title: 2_Saliva-IgG_1

description: IgG


title: 3_Plasma-IgG_1

description: IgG


title: Liver_L_010

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046719_0042549


title: Liver_L_008

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046717_0042547


title: 20_Saliva-IgG_1

description: IgG


title: 20_Plasma-IgG_1

description: IgG


title: 19_Saliva-IgG_1

description: IgG


title: 2_Saliva-IgG_2

description:
IgG
technical replicate of 2.Sal


title: Liver_L_007

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046716_0042546


title: 19_Plasma-IgG_1

description: IgG


title: 2_Plasma-IgG_2

description:
IgG
sample replicate of 2.Pla


title: 18_Saliva-IgG_1

description: IgG


title: 2_Plasma-IgG_3

description:
IgG
technical replicate pf 2.Pla.3


title: 18_Plasma-IgG_1

description: IgG


title: 3_Saliva-IgG_1

description: IgG


title: 2_Saliva-IgG_1

description: IgG


title: Liver_L_004

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046713_0042413


title: Liver_L_006

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046715_0042415


title: Liver_L_005

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046714_0042414


title: 17_Plasma-IgG_1

description: IgG


title: 17_Saliva-IgG_1

description: IgG


title: Liver_L_009

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046718_0042548


title: Liver_L_002

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046711_0042411


title: Liver_L_003

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046712_0042412


title: 2_Plasma-IgG_1

description: IgG


title: 16_Saliva-IgG_1

description: IgG


title: 16_Plasma-IgG_1

description: IgG


title: 19_Plasma-IgG_2

description:
IgG
sample replicate of 19.Pla


title: 19_Plasma-IgG_1

description: IgG


title: Liver_L_001

description:
Cells were isolated by 2 step perfusion protocol and prurified by 3x 50xg spindowns for 3 min.
jat_046710_0042410


title: 18_Saliva-IgG_1

description: IgG


title: 19_Saliva-IgG_1

description: IgG


title: P5.wt3

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: Sox9.rnaseq.data.cnts.Pgenes.qnorm.floor50.q10.xlsx

data_processing:
Sequenced reads were mapped to the Mus musculus genome (mm10), using TopHat v2.0.10
Genes were identified using a .gtf obtained from Ensembl release 82. Per gene reads were counted using HTSeq.
Expression levels were normalized using quantile normalization, and then a floor level of 50.0 was set.
Genome_build: mm10
Supplementary_files_format_and_content: Excel table with qnorm expression levels

molecule: polyA RNA

source_name: RPE

extract_protocol:
RNA was extracted using the QIAshredder and the RNeasy kits (QIAGEN)
Sequencing libraries were prepared using the INCPM mRNA protocol

tag: genotype

value: WT


title: 2_Plasma-IgG_1

description: IgG


title: 17_Saliva-IgG_1

description: IgG


title: 14_Saliva-IgG_1

description: IgG


title: P5.wt2


title: 18_Plasma-IgG_1

description: IgG


title: P5.wt1


title: P5.kd3


title: P5.kd2


title: 14_Plasma-IgG_1

description: IgG


title: 13_Saliva-IgG_1

description: IgG


title: 17_Plasma-IgG_2

description:
IgG
technical replicate of 17.Pla


title: 13_Plasma-IgG_1

description: IgG


title: 16_Saliva-IgG_2

description:
IgG
sample replicate of 16.Sal


title: E15.wt3


title: 15_Saliva-IgG_1

description: IgG


title: P5.kd1


title: 12_Plasma-IgG_1

description: IgG


title: 17_Plasma-IgG_1

description: IgG


title: 16_Plasma-IgG_1

description: IgG


title: 16_Saliva-IgG_1

description: IgG


title: 15_Plasma-IgG_1

description: IgG


title: 11_Saliva-IgG_1

description: IgG


title: E15.wt2


title: E15.wt1


title: 11_Plasma-IgG_1

description: IgG


title: E15.kd3


title: 15_Plasma-IgG_1

description: IgG


title: 15_Saliva-IgG_1

description: IgG


title: 12_Saliva-IgG_1

description: IgG


title: E15.kd2


title: 10_Saliva-IgG_1

description: IgG


title: 14_Saliva-IgG_5

description:
IgG
sample replicate of 14.Sal


title: E15.kd1


title: 1_Saliva-IgG_1

description: IgG


title: 14_Saliva-IgG_3

description:
IgG
sample replicate of 14.Sal


title: 14_Saliva-IgG_4

description:
IgG
technical replicate of 14.Sal.3


title: 1_Plasma-IgG_1

description: IgG


title: 14_Saliva-IgG_1

description: IgG


title: 14_Plasma-IgG_3

description:
IgG
sample replicate of 14.Pla


title: n2_unc73prp8fx_sy008

city: Santa Cruz

first: Alan

middle: M

last: Zahler

address: Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

description:
SZ197-2
n2_unc73prp8fx_sy008

data_processing:
10bp were trimmed from the 5' end of read1 and read2 (including 8bp of molecular index). 11bp (length 101 reads) or 10bp (length 100 reads) were trimmed from the 3' end of read1 and read2 leaving 80bp for read1 and 80bp for read2 for each sample.
Trimmed reads were mapped with Bowtie2 to the RepeatMasker library of C.elegans repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining trimmed reads were mapped to the indicated genome assembly using STAR.
Potential PCR duplicates within each set of reads having a common molecular index were removed with samtools rmdup.
Splice junctions were extracted from the bam files by examining the CIGAR string, resulting in a non-redundant set of introns spanned by these splice junctions.
Alternative splicing events were identified from the splice junctions.
A5SS events: A custom script was employed to identify junctions that define alternative 5' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
A3SS events: A custom script was employed to identify junctions that define alternative 3' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
SE events: AltEventFinder (Zhou A et al. 2012) was used to identify alternative cassette exons in the wormBase genes for each genome assembly.
MISO was run on each sample to determine PSI (percent spliced in) for A5SS, A3SS, and SE events from the indicated genome assembly.
The MISO results for a sample were merged into a gtf with the scores for the 2 transcripts of an event representing its PSI value.
Genome_build: May 2008 (WS190/ce6) for samples *_mrNNN. Oct. 2010 (WS220/ce10) for samples *_syNNN.
Supplementary_files_format_and_content: For each sample, a gtf file, including a UCSC genome browser track line, of A5SS, A3SS, SE events, where the score field for a transcript represents PSI for that event in this sample.

organism: Caenorhabditis elegans

growth_protocol: Indicated strains were grown at 20C on NGM agar plates fed OP50 E. coli

extract_protocol:
Worms were lysed in Trizol and total RNA recovered according to manufacturers protocol.
mRNA libraries for high throughput sequencing were prepared from polyA selected mRNAs extracted from 5µg of total RNA using the NEXTflex Rapid Directional qRNA-Seq Kit (BioO Scientific). 8bp at the 5' ends of both read1 and read2 constitute a molecular index. Paired directional 101nt or 100nt reads, 8 libraries per lane, were obtained from an Illumina HiSeq 4000 operated by the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.

treatment_protocol: Worms were harvested from the plates by washing them off with M9 media

tag: strain background

tag: genotype/variation

tag: developmental stage

value: mixed stage

value: whole worm


title: 10_Plasma-IgG_1

description: IgG


title: 14_Plasma-IgG_2

description:
IgG
sample replicate of 14.Pla


title: 12_Saliva-IgG_1

description: IgG


title: n2_unc73prp8fx_sy007

description:
SZ197-1
n2_unc73prp8fx_sy007


title: n2_unc73prp8eo_sy006

description:
SZ195-2
n2_unc73prp8eo_sy006


title: n2_unc73prp8eo_sy005

description:
SZ195-1
n2_unc73prp8eo_sy005


title: 14_Plasma-IgG_1

description: IgG


title: 13_Plasma-IgG_1

description: IgG


title: n2_unc73prp8ex_sy014

description:
SZ179-2
n2_unc73prp8ex_sy014


title: 14_Saliva-IgG_2

description:
IgG
technical replicate of 14.Sal


title: 11_Saliva-IgG_2

description:
IgG
sample replicate of 11.Sal


title: n2_unc73prp8ex_sy013

description:
SZ179-1
n2_unc73prp8ex_sy013


title: n2_unc73out2xx_sy016

description:
SZ181-2
n2_unc73out2xx_sy016


title: T_SLE_S25 [Human circRNA Array v2.0]

city: Hefei

first: Lian-Ju

last: Li

state: Anhui

address: 81 Meishan Road

department: Department of Epidemiology and Biostatistics, School of Public Health

country: China

institute: Anhui Medical University

description: circRNA expression in T cells from patient S25

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

scan_protocol: The Agilent Scanner G2505C was used to scan the slides

data_processing: Agilent Feature Extraction software was applied to asses the array images. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).After quantile normalization of the raw data, circRNAs that at least 6 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.Differentially expressed circRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: T cell, SLE

label_protocol: Rnase R (Epicentre, Madison, WI) was used to remove linear RNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA by using a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from T cells by using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacture’s protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: CD3+ T cell was positively labeled with anti-human CD3 magnetic Particles-DM (BD IMag™, San Jose, USA) and selected by IMag magnetic cell separation system (BD IMagnet™, San Jose, USA).

value: Peripheral Blood Mononuclear Cells

value: female


title: T_HC_C1 [Human circRNA Array v2.0]

description: circRNA expression in T cells from healthy volunteer C1

source_name: T cell, HC


title: T_HC_C3 [Human circRNA Array v2.0]

description: circRNA expression in T cells from healthy volunteer C3


title: T_HC_C2 [Human circRNA Array v2.0]

description: circRNA expression in T cells from healthy volunteer C2


title: 11_Plasma-IgG_2

description:
IgG
sample replicate of 11.Pla


title: T_SLE_S18 [Human circRNA Array v2.0]

description: circRNA expression in T cells from patient S18


title: T_SLE_S11 [Human circRNA Array v2.0]

description: circRNA expression in T cells from patient S11


title: 12_Plasma-IgG_1

description: IgG


title: 11_Saliva-IgG_1

description: IgG


title: 13_Saliva-IgG_1

description: IgG


title: n2_wildtypexxx_sy002

description:
N2-4
n2_wildtypexxx_sy002

source_name: Bristol N2

value: Bristol N2


title: n2_unc73out2xx_sy015

description:
SZ181-1
n2_unc73out2xx_sy015


title: 11_Plasma-IgG_1

description: IgG


title: T_SLE_S9 [Human circRNA Array v2.0]

description: circRNA expression in T cells from patient S9


title: ChIP-exo, in vitro, ATF4_CEBPb_plus_ATF4 [human]

city: Philadelphia

first: David

middle: J

last: Steger

state: PA

address: 12-193 SCTR 3400 Civic Center Blvd

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

description: hMSC_ATF4_CEBPb_1ul_ATF4_1ul_DS415.plus.bw; hMSC_ATF4_CEBPb_1ul_ATF4_1ul_DS415.minus.bw

data_processing:
Reads were mapped to the hg19 or mm9 genomes using Bowtie. Reads mapping to ambiguous contigs were excluded.
Redundant reads were preserved for the ChIP-exo samples.
genome build: hg19; mm9
processed data files format and content: 1) ChIP seq peaks and motif mapping results are in BED format 2) ChIP-exo processed data are in bigwig format with 5' tag density reported as reads per million.

source_name: hMSC

growth_protocol: hMSCs were cultured in low glucose DMEM supplemented with 1% glutamine, and 10% FBS.

extract_protocol:
Cultured cells and liver tissue were crosslinked in 1 % formaldehyde for 15 minutes. A 5 minute quench was performed with 125mM glycine. To prepare ChIP extracts, nuclei were prepared by hypotonic lysis followed by Dounce homogenization. Nuclei were resuspended in SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: For hMSCs, confluent cells were treated with DMI adipogenic induction medium for 24 hours. For mouse experiments, 8-10 week old C57B/6 WT mice treated with AAV_Null or AAV_Cebpa as described in Bauer et al. J Clin Invest 2015 PMID 26348894.

tag: chip antibody

value: ATF4, sc-200, Santa Cruz


title: ChIP-exo, in vitro, CEBPb_CEBPb_only [human]

description: hMSC_CEBPb_CEBPb_1ul_DS412.plus.bw; hMSC_CEBPb_CEBPb_1ul_DS412.minus.bw

value: CEBPb, sc-150, Santa Cruz


title: T_SLE_S5 [Human circRNA Array v2.0]

description: circRNA expression in T cells from patient S5


title: ChIP-exo, CEBPb, replicate 3 [human]

description: hMSC_CEBPb_HD_D1_exo_pool.plus.bw; hMSC_CEBPb_HD_D1_exo_pool.minus.bw; motif.scan.cebpb.hd.d1.bed

source_name: hMSC, DMI-treated


title: 10_Saliva-IgG_1

description: IgG


title: ChIP-exo, CEBPb, replicate 2 [human]


title: n2_unc73prp8bx_mr008

description:
SZ155-2
n2_unc73prp8bx_mr008

value: young adult enriched


title: 10_Plasma-IgG_1

description: IgG


title: ChIP-exo, CEBPb, replicate 1 [human]


title: n2_unc73prp8ax_mr006

description:
SZ116-2
n2_unc73prp8ax_mr006


title: T_SLE_S15 [Human circRNA Array v2.0]

description: circRNA expression in T cells from patient S15


title: n2_unc73prp8ax_mr005

description:
SZ116-1
n2_unc73prp8ax_mr005


title: 1_Saliva-IgG_6

description:
IgG
sample replicate of 1.Sal


title: n2_prp8bonlyxx_mr001

description:
SZ151-1
n2_prp8bonlyxx_mr001


title: n2_prp8bonlyxx_mr002

description:
SZ151-2
n2_prp8bonlyxx_mr002


title: 1_Saliva-IgG_3

description:
IgG
sample replicate of 1.Sal


title: 1_Saliva-IgG_4

description:
IgG
sample replicate of 1.Sal


title: 1_Saliva-IgG_5

description:
IgG
sample replicate of 1.Sal


title: n2_wildtypexxx_sy001

description:
N2-3
n2_wildtypexxx_sy001


title: n2_unc73snrp27_mr011

description:
SZ118-1
n2_unc73snrp27_mr011


title: n2_unc73onlyxx_mr004

description:
CB936-2
n2_unc73onlyxx_mr004


title: n2_unc73prp8bx_mr007

description:
SZ155-1
n2_unc73prp8bx_mr007


title: 1_Plasma-IgG_4

description:
IgG
technical replicate of 1.Pla.3


title: 1_Saliva-IgG_1

description: IgG


title: 1_Plasma-IgG_5

description:
IgG
sample replicate of 1.Pla


title: n2_unc73onlyxx_mr003

description:
CB936-1
n2_unc73onlyxx_mr003


title: n2_wildtypexxx_mr016

description:
N2-2
n2_wildtypexxx_mr016


title: n2_wildtypexxx_mr015

description:
N2-1
n2_wildtypexxx_mr015


title: 1_Plasma-IgG_1

description: IgG


title: 1_Saliva-IgG_2

description:
IgG
technical replicate of 1.Sal


title: n2_unc73snrp27_mr012

description:
SZ118-2
n2_unc73snrp27_mr012


title: 1_Plasma-IgG_2

description:
IgG
sample replicate of 1.Pla


title: brain_irradiated

city: Busan

first: Beomseok

last: Son

address: 322 Biology Building, 2 Busandaehakro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan National University

description: Gene expression data from EMT marker-overexpressing mice (which was confirmed by western blotting and IHC)

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Human Gene 2.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: Xenografted U-87 MG cells, irradiated

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: The mice were maintained in animal care facilities in a temperature-regulated room (23±1°C) with a 12 h light/dark cycle. All animals were fed water and standard mouse chow ad libitum.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The brains of the mice were irradiated with 2 Gy daily for 5 days at a dose rate of 0.4 Gy/min employing an X-ray generator M-150WE (Softex, Tokyo, Japan).

tag: Sex

value: male

tag: cell line

value: U-87 MG


title: c-Fos expressing vector transduced, Replicate 1

city: London

first: Ander

last: Abarrategi

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: The Francis Crick Institute

hyb_protocol: The labeled, fragmented ssDNA was hybridized to the GeneChip Human Gene 2.0ST Array (Affymetrix, Santa Clara, CA) in a GeneChip Hybridization Oven 640 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Genechip Expression Console Software

source_name: Human Bone Marrow_c-Fos expressing

label_protocol: Ambion WT Expression kit was used to prepare the cDNA, which was then labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, High Wycombe, UK).

growth_protocol: Cells were cultured in DMEM complemented with 10% FBS, Antibiotics and L-glutamine during 10 days after transduction and  before RNA extraction.

extract_protocol: RNA was extracted using Qiagen Rneasy kit.

treatment_protocol: c-DNA of c-fos was cloned into pOTB7 plasmid, which carries Tomato gene as reporter fluorescent protein. Lentiviral particles were produced by transient calcium phosphate transfection of HEK-293 cells. hMPCs were transduced with those lentiviral particles. Tomato expression was assessed by flow cytometry and c-fos expression was confirmed via qPCR, western blot and immunofluorescence. Cells transduced with lentivirus coding only for fluorescent proteins were used as controls. Three independent replicas are provided from each treatment: 3H1, 3H2, 3H3 correspond to hMPCs transduced with control lentiviral particles. 3HF1, 3HF2 and 3HF3 correspond to hMPCs tranduced with lentiviral particles designed for c-fos expression

value: Mesenchymal progenitor cells (MPCs)


title: c-Fos expressing vector transduced, Replicate 3


title: c-Fos expressing vector transduced, Replicate 2


title: Empty control tranduced,l Replicate 3

source_name: Human Bone Marrow_empty


title: Fruit_RNAseq

city: Xi'an

first: Bo

last: Cao

state: Shaanxi

address: 620 West Chang'an Road, Changan District

institute: Shaanxi Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cornus officinalis Sieb. et Zucc. whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, et al., Nat Biotech, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Trinity.fasta.gz
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

organism: Cornus officinalis

source_name: fruit

extract_protocol:
Total RNA was extracted from each collected tissues using CTAB RNA isolation method (Chang et al. 1993). Three replicates were sampled and mixed for RNA preparation. RNA samples were treated with RNase-free DNase (TaKaRa, Dalian, China) to eliminate genomic DNA contamination. Degradation of RNA was monitored on 1% agarose gels. Purity of RNA was checked using Nano Photometer spectrophotometer (Implen, CA, USA). The concentration of RNA was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). The integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total of 16.5 μg RNA was equally pooled from the collected tissues for cDNA library preparation. Library quality assessment, assembling, clustering and sequencing were performed following the method of Chen et al. (Chen et al. 2014).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cellection date

value: in June

value: fruit


title: 1_Plasma-IgG_3

description:
IgG
sample replicate of 1.Pla

value: Plasma

value: m

value: n


title: Empty control tranduced,l Replicate 1


title: brain_nonirradiated

description: Gene expression data from negative control mice

source_name: Xenografted U-87 MG cells, nonirradiated


title: NKT from healthy control(HC013)

status: Public on Jul 16 2018

city: Fujisawa

first: Shinya

last: Tasaki

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45℃ on Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with the frozen robust multiarray analysis (fRMA) using Biocunductor with default settings and absence/presence calls were estimated by Microarray Suite version 5.0 (MAS 5.0).

source_name: NKT from healthy control(HC013)

label_protocol: Biotinylated cDNA were prepared using NuGEN Encore Biotin Module from 5ug of amplified cDNA.

growth_protocol: Purifined immune cells from RA patients and human healthy volunteers

extract_protocol: Total RNA was isolated with miRCURY RNA Isolation kit (EXIQON), and then concentrated with RNeasy MinElute Cleanup.

treatment_protocol: Peripheral CD8 T-cell magnetically were purified with CD8 T-cell isolation kit (Myltenyi Biotech.).  After staining with CD45RO APC-Cy7 (Clone UCHL1, BioLegend) and CCR7 Alexa647 (Clone TG8, BioLegend), each subset was isolated with FACS Aria III (BD Biosciences)

tag: disease

value: healthy control

value: F

tag: rin

value: NKT


title: NKT from rheumatoid arthritis(R071)

source_name: NKT from rheumatoid arthritis(R071)

value: rheumatoid arthritis


title: NK from rheumatoid arthritis(R076)

source_name: NK from rheumatoid arthritis(R076)

value: NK


title: NKT from rheumatoid arthritis(R076)

source_name: NKT from rheumatoid arthritis(R076)


title: Empty control tranduced,l Replicate 2


title: NKT from rheumatoid arthritis(R062)

source_name: NKT from rheumatoid arthritis(R062)


title: NKT from rheumatoid arthritis(R061)

source_name: NKT from rheumatoid arthritis(R061)

value: M


title: NKT from rheumatoid arthritis(R056)

source_name: NKT from rheumatoid arthritis(R056)


title: NK from rheumatoid arthritis(R059)

source_name: NK from rheumatoid arthritis(R059)


title: NKT from healthy control(HC008)

source_name: NKT from healthy control(HC008)


title: NK from rheumatoid arthritis(R071)

source_name: NK from rheumatoid arthritis(R071)


title: NKT from healthy control(HC031)

source_name: NKT from healthy control(HC031)


title: NKT from healthy control(HC033)

source_name: NKT from healthy control(HC033)


title: NKT from healthy control(HCM)

source_name: NKT from healthy control(HCM)


title: NKT from healthy control(HC026)

source_name: NKT from healthy control(HC026)


title: NKT from rheumatoid arthritis(R060)

source_name: NKT from rheumatoid arthritis(R060)


title: NK from rheumatoid arthritis(R056)

source_name: NK from rheumatoid arthritis(R056)


title: NKT from rheumatoid arthritis(R047)

source_name: NKT from rheumatoid arthritis(R047)


title: NK from rheumatoid arthritis(R060)

source_name: NK from rheumatoid arthritis(R060)


title: NK from healthy control(HC013)

source_name: NK from healthy control(HC013)


title: NK from rheumatoid arthritis(R062)

source_name: NK from rheumatoid arthritis(R062)


title: NK from rheumatoid arthritis(R047)

source_name: NK from rheumatoid arthritis(R047)


title: NK from healthy control(HCM)

source_name: NK from healthy control(HCM)


title: Neutrophils from rheumatoid arthritis(R030)

value: Neutrophils


title: NK from healthy control(HC008)

source_name: NK from healthy control(HC008)


title: NK from healthy control(HC026)

source_name: NK from healthy control(HC026)


title: NK from healthy control(HC033)

source_name: NK from healthy control(HC033)


title: Neutrophils from rheumatoid arthritis(R060)


title: Monocyte_CD14+.CD16+ from rheumatoid arthritis(R076)


title: Neutrophils from rheumatoid arthritis(R026)


title: Neutrophils from rheumatoid arthritis(R022)


title: Neutrophils from rheumatoid arthritis(R059)


title: NK from healthy control(HC031)

source_name: NK from healthy control(HC031)


title: Monocyte_CD14+.CD16+ from rheumatoid arthritis(R059)


title: Neutrophils from rheumatoid arthritis(R029)


title: Monocyte_CD14dim.CD16+ from rheumatoid arthritis(R076)


title: Neutrophils from rheumatoid arthritis(R020)


title: Neutrophils from healthy control(HC031)

source_name: Neutrophils from healthy control(HC031)


title: Monocyte_CD14dim.CD16+ from rheumatoid arthritis(R061)


title: Monocyte_CD14+.CD16- from rheumatoid arthritis(R076)


title: Neutrophils from rheumatoid arthritis(R056)


title: Neutrophils from healthy control(HC035)

source_name: Neutrophils from healthy control(HC035)


title: Neutrophils from healthy control(HCM)

source_name: Neutrophils from healthy control(HCM)


title: Monocyte_CD14+.CD16- from rheumatoid arthritis(R056)


title: Neutrophils from healthy control(HC036)

source_name: Neutrophils from healthy control(HC036)


title: Neutrophils from healthy control(HC026)

source_name: Neutrophils from healthy control(HC026)


title: Monocyte_CD14+.CD16- from rheumatoid arthritis(R059)


title: Monocyte_CD14+.CD16- from rheumatoid arthritis(R061)


title: Monocyte_CD14dim.CD16+ from rheumatoid arthritis(R060)


title: Monocyte_CD14+.CD16- from rheumatoid arthritis(R047)


title: Monocyte_CD14dim.CD16+ from rheumatoid arthritis(R059)


title: Monocyte_CD14+.CD16- from rheumatoid arthritis(R060)


title: Neutrophils from rheumatoid arthritis(R047)


title: Monocyte_CD14+.CD16+ from rheumatoid arthritis(R047)


title: Monocyte_CD14+.CD16- from healthy control(HCN)


title: Neutrophils from healthy control(HC033)

source_name: Neutrophils from healthy control(HC033)


title: Monocyte_CD14+.CD16+ from rheumatoid arthritis(R060)


title: Monocyte_CD14+.CD16+ from healthy control(HCM)


title: Monocyte_CD14dim.CD16+ from healthy control(HCM)


title: Monocyte_CD14+.CD16+ from healthy control(HCN)


title: Monocyte_CD14dim.CD16+ from healthy control(HCN)


title: Monocyte_CD14+.CD16+ from rheumatoid arthritis(R061)


title: Monocyte_CD14+.CD16+ from healthy control(HC013)


title: Monocyte_CD14dim.CD16+ from healthy control(HC013)


title: Monocyte_CD14dim.CD16+ from rheumatoid arthritis(R047)


title: Monocyte_CD14+.CD16+ from rheumatoid arthritis(R056)


title: Monocyte_CD14dim.CD16+ from rheumatoid arthritis(R056)


title: Monocyte_CD14+.CD16- from healthy control(HCM)


title: Monocyte_CD14+.CD16- from healthy control(HC013)


title: Monocyte_CD14+.CD16+ from healthy control(HC008)


title: Monocyte_CD14+.CD16+ from healthy control(HC036)


title: CD8T_naive from rheumatoid arthritis(R077)


title: Monocyte_CD14dim.CD16+ from healthy control(HC008)


title: Monocyte_CD14+.CD16- from healthy control(HC026)


title: CD8T_CD45RO.memory from rheumatoid arthritis(R076)


title: CD8T_naive from rheumatoid arthritis(R076)


title: Monocyte_CD14+.CD16+ from healthy control(HC026)


title: Monocyte_CD14dim.CD16+ from healthy control(HC026)


title: Monocyte_CD14+.CD16- from healthy control(HC036)


title: Monocyte_CD14dim.CD16+ from healthy control(HC036)


title: CD8T_effector.memory from rheumatoid arthritis(R077)


title: CD8T_central.memory from rheumatoid arthritis(R076)


title: CD8T_effector.memory from rheumatoid arthritis(R062)


title: CD8T_naive from rheumatoid arthritis(R062)


title: CD8T_CD45RO.memory from rheumatoid arthritis(R062)


title: CD8T_central.memory from rheumatoid arthritis(R062)


title: CD8T_effector.memory from rheumatoid arthritis(R076)


title: Monocyte_CD14+.CD16- from healthy control(HC008)


title: CD8T_central.memory from rheumatoid arthritis(R059)


title: CD8T_central.memory from rheumatoid arthritis(R077)


title: CD8T_CD45RO.memory from rheumatoid arthritis(R059)


title: CD8T_effector.memory from rheumatoid arthritis(R060)


title: CD8T_naive from rheumatoid arthritis(R059)


title: CD8T_effector.memory from rheumatoid arthritis(R059)


title: CD8T_naive from rheumatoid arthritis(R060)


title: CD8T_effector.memory from rheumatoid arthritis(R047)


title: CD8T_CD45RO.memory from rheumatoid arthritis(R047)


title: CD8T_central.memory from rheumatoid arthritis(R060)


title: CD8T_CD45RO.memory from rheumatoid arthritis(R060)


title: CD8T_effector.memory from healthy control(HCM)


title: CD8T_central.memory from rheumatoid arthritis(R047)


title: CD8T_CD45RO.memory from healthy control(HC008)


title: CD8T_effector.memory from healthy control(HC008)


title: CD8T_central.memory from healthy control(HC013)


title: CD8T_CD45RO.memory from healthy control(HC013)


title: CD8T_central.memory from healthy control(HCM)


title: CD8T_naive from healthy control(HCM)

source_name: CD8T_naive from healthy control(HCM)


title: CD8T_naive from healthy control(HC033)

source_name: CD8T_naive from healthy control(HC033)


title: CD8T_central.memory from healthy control(HC033)


title: CD8T_central.memory from healthy control(HC008)


title: CD8T_CD45RO.memory from healthy control(HC033)


title: CD8T_naive from rheumatoid arthritis(R047)


title: CD8T_effector.memory from healthy control(HC033)


title: CD8T_effector.memory from healthy control(HC031)


title: CD8T_CD45RO.memory from healthy control(HC031)


title: CD8T_naive from healthy control(HC013)

source_name: CD8T_naive from healthy control(HC013)


title: CD8T_naive from healthy control(HC008)

source_name: CD8T_naive from healthy control(HC008)


title: CD8T_effector.memory from healthy control(HC013)


title: CD8T_CD45RO.memory from healthy control(HC026)


title: CD8T_central.memory from healthy control(HC026)


title: CD4T_central.memory from rheumatoid arthritis(R077)


title: CD4T_effector.memory from rheumatoid arthritis(R077)


title: CD8T_naive from healthy control(HC031)

source_name: CD8T_naive from healthy control(HC031)


title: CD8T_central.memory from healthy control(HC031)


title: CD8T_naive from healthy control(HC026)

source_name: CD8T_naive from healthy control(HC026)


title: CD8T_CD45RO.memory from healthy control(HCM)


title: CD4T_naive from rheumatoid arthritis(R077)


title: CD4T_central.memory from rheumatoid arthritis(R076)


title: CD8T_CD45RO.memory from rheumatoid arthritis(R077)


title: CD4T_naive from rheumatoid arthritis(R061)


title: CD4T_naive from rheumatoid arthritis(R076)


title: CD4T_naive from rheumatoid arthritis(R062)


title: CD4T_effector.memory from rheumatoid arthritis(R061)


title: CD4T_effector.memory from rheumatoid arthritis(R062)


title: CD4T_effector.memory from rheumatoid arthritis(R060)


title: CD4T_central.memory from healthy control(HCN)


title: CD4T_central.memory from rheumatoid arthritis(R060)


title: CD4T_effector.memory from healthy control(HCN)


title: CD4T_central.memory from healthy control(HC008)


title: CD4T_central.memory from healthy control(HCM)


title: CD4T_central.memory from rheumatoid arthritis(R062)


title: CD4T_central.memory from rheumatoid arthritis(R061)


title: CD4T_naive from healthy control(HCN)

source_name: CD4T_naive from healthy control(HCN)


title: CD4T_naive from rheumatoid arthritis(R060)


title: CD4T_effector.memory from healthy control(HCM)


title: CD4T_central.memory from rheumatoid arthritis(R059)


title: CD4T_effector.memory from rheumatoid arthritis(R059)


title: CD4T_naive from healthy control(HC008)

source_name: CD4T_naive from healthy control(HC008)


title: CD4T_naive from rheumatoid arthritis(R059)


title: CD4T_effector.memory from healthy control(HC008)


title: CD4T_central.memory from healthy control(HC007)


title: CD4T_central.memory from healthy control(HC031)


title: CD4T_effector.memory from healthy control(HC031)


title: CD4T_naive from healthy control(HC031)

source_name: CD4T_naive from healthy control(HC031)


title: B.memory from healthy control(HC025)

source_name: B.memory from healthy control(HC025)


title: B.naive from healthy control(HC025)

source_name: B.naive from healthy control(HC025)


title: CD4T_effector.memory from healthy control(HC026)


title: CD4T_central.memory from healthy control(HC026)


title: CD8T_effector.memory from healthy control(HC026)


title: CD4T_naive from healthy control(HCM)

source_name: CD4T_naive from healthy control(HCM)


title: CD4T_effector.memory from rheumatoid arthritis(R076)


title: CD4T_effector.memory from healthy control(HC007)


title: B.memory from healthy control(HCAE)

source_name: B.memory from healthy control(HCAE)


title: CD4T_naive from healthy control(HC026)

source_name: CD4T_naive from healthy control(HC026)


title: Whole blood from rheumatoid arthritis(K9969_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9969_2)

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45C on Human Genome U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with the frozen robust multiarray analysis (fRMA) using Bioconductor with default settings and absence/presence calls were estimated by Microarray Suite version 5.0 (MAS 5.0).

source_name: Whole blood from rheumatoid arthritis

extract_protocol: Total  RNA was isolated with  the  PAXgeneTM  Blood  RNA Kit  (Qiagen,  Valencia,   CA,  USA) after  freezing and  storage. The  Ambion  GLOBINclearTM  (Ambion,  Austin  TX, USA) was applied to  total  RNA samples to remove globin transcripts.

treatment_protocol: Blood  samples were collected from healthy  and  RA  human  donors in  PAXGene tubes.

tag: individual id

tag: disease state

value: RA

value: whole blood

tag: batch

tag: cdai

tag: kowabari

tag: haq

tag: crp

tag: esr

tag: acr

tag: sdai

tag: rf

tag: ccp

tag: ana


title: B.memory from healthy control(HCAC)

source_name: B.memory from healthy control(HCAC)

tag: gender

tag: age

tag: cell type


title: Whole blood from rheumatoid arthritis(K9679_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9679_2)

tag: tissue

tag: rin


title: Whole blood from rheumatoid arthritis(K9657_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9657_2)

tag: individual id

tag: disease state


title: Whole blood from rheumatoid arthritis(K9704_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9704_2)

tag: batch

tag: cdai


title: B.naive from healthy control(HCAC)

source_name: B.naive from healthy control(HCAC)

tag: disease


title: B.memory from healthy control(HC038)

source_name: B.memory from healthy control(HC038)


title: B.naive from healthy control(HC038)

source_name: B.naive from healthy control(HC038)


title: B.naive from healthy control(HCAE)

source_name: B.naive from healthy control(HCAE)


title: Whole blood from rheumatoid arthritis(K9968_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9968_2)

tag: kowabari

tag: haq

tag: crp


title: Whole blood from rheumatoid arthritis(K9967_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9967_2)

tag: esr

tag: acr

tag: sdai


title: CD4T_naive from healthy control(HC007)

source_name: CD4T_naive from healthy control(HC007)


title: Whole blood from rheumatoid arthritis(K9765_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9765_2)

tag: rf

tag: ccp

tag: ana


title: B.naive from healthy control(HC006)

source_name: B.naive from healthy control(HC006)

tag: gender

tag: age

tag: cell type


title: Whole blood from rheumatoid arthritis(K9623_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9623_2)

tag: individual id

tag: tissue

tag: rin


title: B.naive from healthy control(HCAA)

source_name: B.naive from healthy control(HCAA)


title: Whole blood from rheumatoid arthritis(K9851_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9851_2)

tag: disease state

tag: batch

tag: cdai


title: B.memory from healthy control(HCAA)

source_name: B.memory from healthy control(HCAA)

tag: disease


title: Whole blood from rheumatoid arthritis(K9617_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9617_2)

tag: kowabari

tag: haq

tag: crp


title: Whole blood from rheumatoid arthritis(K9545_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9545_2)

tag: esr

tag: acr

tag: sdai


title: Whole blood from rheumatoid arthritis(K9867_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9867_2)

tag: rf

tag: ccp

tag: ana


title: Whole blood from rheumatoid arthritis(K9919_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9919_2)

tag: age

tag: gender


title: B.memory from healthy control(HC006)

source_name: B.memory from healthy control(HC006)

tag: cell type


title: Whole blood from rheumatoid arthritis(K9543_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9543_2)

tag: individual id

tag: tissue

tag: rin


title: Whole blood from rheumatoid arthritis(K9472_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9472_2)

tag: disease state

tag: batch

tag: cdai


title: Whole blood from rheumatoid arthritis(K9470_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9470_2)

tag: kowabari

tag: haq


title: Whole blood from rheumatoid arthritis(K9454_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9454_2)

tag: crp

tag: esr


title: Whole blood from rheumatoid arthritis(K9408_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9408_2)

tag: acr

tag: sdai


title: Whole blood from rheumatoid arthritis(K9319_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9319_2)

tag: rf

tag: ccp


title: Whole blood from rheumatoid arthritis(K9043_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9043_2)

tag: age

tag: ana


title: Whole blood from rheumatoid arthritis(K9338_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9338_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K9013_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9013_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K9382_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9382_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K9336_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9336_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K9407_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9407_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K9168_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9168_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K9290_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9290_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K8894_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8894_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K9057_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9057_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K8753_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8753_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K9250_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9250_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K9251_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9251_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K9455_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9455_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K8752_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8752_2)

tag: rf


title: Whole blood from rheumatoid arthritis(K9355_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9355_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K9239_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9239_2)

tag: age


title: Whole blood from rheumatoid arthritis(K8815_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8815_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K8725_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8725_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K8350_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8350_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K9215_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9215_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K9151_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9151_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K8710_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8710_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K8893_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8893_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K8373_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8373_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K9252_2)

description: Whole blood transcriptome from rheumatoid arthritis(K9252_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K8892_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8892_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K7938_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7938_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K8123_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8123_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K8115_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8115_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K7898_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7898_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K8110_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8110_2)

tag: rf


title: Whole blood from rheumatoid arthritis(K7831_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7831_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K8112_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8112_2)

tag: age


title: Whole blood from rheumatoid arthritis(K7901_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7901_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K8113_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8113_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K7819_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7819_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K7696_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7696_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K7733_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7733_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K8276_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8276_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K7718_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7718_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K7785_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7785_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K7879_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7879_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K7818_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7818_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K7200_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7200_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K7203_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7203_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K7598_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7598_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K7158_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7158_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K7830_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7830_2)

tag: rf


title: Whole blood from rheumatoid arthritis(K7202_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7202_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K7683_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7683_2)

tag: age


title: Whole blood from rheumatoid arthritis(K7391_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7391_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K7625_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7625_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K7136_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7136_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K8135_2)

description: Whole blood transcriptome from rheumatoid arthritis(K8135_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K7135_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7135_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K7558_2)

description: Whole blood transcriptome from rheumatoid arthritis(K7558_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K6998_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6998_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K6918_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6918_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K6887_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6887_2)

tag: kowabari


title: Whole blood from rheumatoid arthritis(K6950_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6950_2)

tag: haq


title: Whole blood from rheumatoid arthritis(K6917_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6917_2)

tag: crp


title: Whole blood from rheumatoid arthritis(K6596_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6596_2)

tag: esr


title: Whole blood from rheumatoid arthritis(K6750_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6750_2)

tag: acr


title: Whole blood from rheumatoid arthritis(K6889_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6889_2)

tag: sdai


title: Whole blood from rheumatoid arthritis(K6566_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6566_2)

tag: rf


title: Whole blood from rheumatoid arthritis(K6465_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6465_2)

tag: ccp


title: Whole blood from rheumatoid arthritis(K6222_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6222_2)

tag: age


title: Whole blood from rheumatoid arthritis(K6464_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6464_2)

tag: ana


title: Whole blood from rheumatoid arthritis(K6462_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6462_2)

tag: gender


title: Whole blood from rheumatoid arthritis(K6003_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6003_2)

tag: individual id


title: Whole blood from rheumatoid arthritis(K6255_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6255_2)

tag: tissue


title: Whole blood from rheumatoid arthritis(K6004_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6004_2)

tag: rin


title: Whole blood from rheumatoid arthritis(K6248_2)

description: Whole blood transcriptome from rheumatoid arthritis(K6248_2)

tag: disease state


title: Whole blood from rheumatoid arthritis(K5816_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5816_2)

tag: batch


title: Whole blood from rheumatoid arthritis(K5971_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5971_2)

tag: cdai


title: Whole blood from rheumatoid arthritis(K5955_2)

description: Whole blood transcriptome from rheumatoid arthritis(K5955_2)

tag: kowabari