title: PBMCs from sample A8-10_Memory_CD8

description: PBMCs from sample A8-10_Memory_CD8


title: Corpus_182

status: Public on Feb 23 2024

type: SRA

city: Marburg

first: Laura

last: Koebbe

address: Baldingerstraße

country: Germany

institute: University of Marburg

library_source: transcriptomic

data_processing:
Quality control of sequencing data was performed with FastQC v0.11.7.
For adaptor trimming bbduk from the BBMap v37.44 was used.
The read alignment against GRCh38 was performed with STAR Aligner 2.5.2b.
FeatureCounts v1.5.1 was used for quantification of gene expression using the Ensembl annotation GRCh38.89 as reference.
Further QC was performed using RSeQC.
Assembly: GRCh38
Supplementary files format and content: gastric_expression_unique_counts.csv: comma-separated file with number of unique counts per gene and sample (columns = samples, rows = genes (Ensembl Ids))

molecule: polyA RNA

organism: Homo sapiens

source_name: Corpus

extract_protocol:
Tissue samples were mechanically homogenized with ceramic beads and a Precellys tissue homogenizer. Total RNA (and genomic DNA) was extracted using the Allprep DNA/RNA Mini Kit from Qiagen.
RNA libraries for RNA-Seq were prepared using Lexogen's QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina following manufacturer's protocol.

tag: tissue

value: Corpus


title: WT_HBSS_647_753_RV

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

country: USA

institute: Tenaya Therapeutics Inc.

description:
TNYA0042_study
647_753_RV

data_processing:
Adapter trimming by FASTP (ver. 0.23.3)
Read alignment by Salmon (ver. 1.8.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl mouse reference genome release 107
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: GRCm39, July 2022
Supplementary files format and content: TXT

organism: Mus musculus

source_name: Right ventricle

extract_protocol:
Total RNA was extracted from cardiac RV and LV tissue using the RNeasy Mini or Universal Mini Kit (Qiagen Sciences, 74106 and 73404), cDNA synthesized (Invitrogen SuperScript III First-Strand Synthesis SuperMix for RT) and analyzed by qPCR using Taqman probes to human PKP2 or mouse Pkp2 gene, heart failure genes (Nppa, Nppb), and fibrosis genes (Col1a1, Col3a1, and Timp1).  Mouse Gapdh served as an internal housekeeping gene control.  Absolute transgene mRNA copy number was determined by RT-qPCR using a WPRE-specific RNA standard (GenScript) across six orders of magnitude.  DSP protein level in both supernatant and pellet was analyzed to ensure a complete evaluation.
From each replicate, 100 ng total RNA was extracted via the polyA-tail-specific protocol according to Illumina Inc.. RNA quality control was performed before library prep using Agilent TapeStation instrument. The RNA libraries were prepared using a Stranded Total RNA Library Prep with Ribo-Zero Plus kit (Illumina), which also removes ribosomal RNA. The libraries were sequenced as 2x50 base pair paired-end reads using Illumina NovaSeq 6000 using V1.5 reagent kit on S1 flow cell with an average of 25.66 million reads per each read file (51.32M reads per sample).

treatment_protocol: TN-401 or AAV9:PKP2 was given as a single dose via retro-orbital injection 1 week before animals were induced with tamoxifen.  HBSS, as vehicle control, was injected to WT or non-AAV treated Pkp2-cKO animals.  Tamoxifen injection activates Cre recombinase in Cre-positive animals and induces homozygous deletion of Pkp2 gene.  Pkp2fl/fl Cre-negative littermates were used as controls.

value: Right ventricle

tag: genotype

value: WT

tag: strain

tag: treatment

value: HBSS


title: Corpus_189


title: PBMCs from sample A8-10_Memory_CD4

city: Stanford

first: Aaron

middle: James

last: Wilk

state: California

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

description: PBMCs from sample A8-10_Memory_CD4

data_processing:
Sequencing reads were aligned against V-, D-, J-, and C- human gene segment library database by MiXCR
Clonotypes were assembled from aligned reads by MiXCR
Assembly: Sequencing reads were aligned against V-, D-, J-, and C- human gene segment library database by MiXCR
Supplementary files format and content: .txt files containing counts of clonotypes in tabular form

molecule: total RNA

source_name: PBMCs

growth_protocol: No growth or treatment performed

extract_protocol:
RNA was purified from each sorted sample using the RNAeasy Plus Micro kit (Qiagen)
Libraries were prepared for TCR sequencing as described by Rubelt, et al.. This was performed at the University of Cape Town. Briefly, purified RNA was reverse transcribed in a Rapid amplification of cDNA ends (RACE) reaction using SMARTScribe Reverse Transcriptase using previously designed oligos (isoC-5′-GTCAGATGTGTATAAGAGACAGnnnnnnnnnnCGATAGrGrGrG -3′-C3_Spacer and for the Poly A tail 5′-GTGTCACGTACAGAGTCATCtttttttttttttttttttttttttttttt -3′ VN) that captures polyadenylated transcripts and introduces a 10bp unique molecular identifier (UMI) at the 5’ end of the product. cDNA was purified with AmpureXP beads (Beckman Coulter) before whole transcriptome amplification using Advantage 2 Polymerase (Clontech) using oligos that introduce Illumina Nextera Multiplex Identifier (MID) P5 Adapter sequences. The libraries were then sent to Stanford University (Department of Microbiology and Immunology, Stanford University) in a blinded fashion, where TCRβ-specific amplification was achieved with Q5 Hot Start Master Mix (NEB) using constant region-specific oligos, simultaneously introducing P7 MID sequences. Final sequencing libraries were purified using SPRISelect beads (Beckman Coulter), quantified using the Agilent TapeStation and pooled for sequencing. Paired-end sequencing was performed on an Illumina NovaSeq SP with 2x250 cycles, performed by the Chan-Zuckerberg Biohub Initiative.

treatment_protocol: No growth or treatment performed

tag: cell type

value: PBMCs


title: Corpus_181


title: Antrum_176

source_name: Antrum

value: Antrum


title: WT_HBSS_647_753_LV

description:
TNYA0042_study
647_753_LV

source_name: Left ventricle

value: Left ventricle


title: PBMCs from sample A7-4_Naive_CD8

description: PBMCs from sample A7-4_Naive_CD8


title: PBMCs from sample A7-4_Naive_CD4

description: PBMCs from sample A7-4_Naive_CD4


title: Pkp2KO_6E13_645_750_RV

description:
TNYA0042_study
645_750_RV

value: CardiacKO


title: Pkp2KO_6E13_645_750_LV

description:
TNYA0042_study
645_750_LV


title: Antrum_170


title: Corpus_179


title: Antrum_169


title: PBMCs from sample A7-4_Memory_CD8

description: PBMCs from sample A7-4_Memory_CD8


title: Corpus_184


title: PBMCs from sample A7-4_Memory_CD4

description: PBMCs from sample A7-4_Memory_CD4


title: WT_HBSS_637_741_LV

description:
TNYA0042_study
637_741_LV


title: PBMCs from sample A7-3_Naive_CD8

description: PBMCs from sample A7-3_Naive_CD8


title: Antrum_167


title: Antrum_165


title: Antrum_168


title: WT_HBSS_637_741_RV

description:
TNYA0042_study
637_741_RV


title: WT_HBSS_636_740_RV

description:
TNYA0042_study
636_740_RV


title: Antrum_164


title: PBMCs from sample A7-3_Naive_CD4

description: PBMCs from sample A7-3_Naive_CD4


title: WT_HBSS_13_LV

extract_protocol:
Total RNA was extracted from cardiac RV and LV tissue using the RNeasy Mini or Universal Mini Kit (Qiagen Sciences, 74106 and 73404), cDNA synthesized (Invitrogen SuperScript III First-Strand Synthesis SuperMix for RT) and analyzed by qPCR using Taqman probes to mouse Pkp2 gene, heart failure genes (Nppa, Nppb), and fibrosis genes (Col1a1, Col3a1, and Timp1).  Mouse Gapdh served as an internal housekeeping gene control.  Absolute transgene mRNA copy number was determined by RT-qPCR using a WPRE-specific RNA standard (GenScript) across six orders of magnitude.  DSP protein level in both supernatant and pellet was analyzed to ensure a complete evaluation.
From each replicate, 100 ng total RNA was extracted via the polyA-tail-specific protocol according to Illumina Inc.. RNA quality control was performed before library prep using Agilent TapeStation instrument.  The RNA libraries were prepared using a Stranded Total RNA Library Prep with Ribo-Zero Plus kit (Illumina), which also removes ribosomal RNA.  The libraries were sequenced as 2x50 base pair paired-end reads using Illumina NovaSeq 6000 using V1.5 reagent kit on S1 flow cell with an average of 25.66 million reads per each read file (51.32M reads per sample).

treatment_protocol: TN-401 or AAV9:mPkp2 was given as a single dose via retro-orbital injection 1 week before (for PKP2-m3e13 and PKP2-m1e14 groups) or after (PKP2-m1e14-2.5wk group) animals were induced with tamoxifen.  HBSS, as vehicle control, was injected to WT or non-AAV treated Pkp2-cKO animals.  Tamoxifen injection activates Cre recombinase in Cre-positive animals and induces homozygous deletion of Pkp2 gene.  Pkp2fl/fl Cre-negative littermates were used as controls.


title: Antrum_166


title: Corpus_177


title: Corpus_176


title: Corpus_175


title: Antrum_171


title: Corpus_180


title: PBMCs from sample A7-3_Memory_CD8

description: PBMCs from sample A7-3_Memory_CD8


title: WT_HBSS_636_740_LV

description:
TNYA0042_study
636_740_LV


title: Corpus_178


title: Antrum_163


title: Pkp2KO_6E13_631_703_RV

description:
TNYA0042_study
631_703_RV


title: Antrum_162


title: PBMCs from sample A7-3_Memory_CD4

description: PBMCs from sample A7-3_Memory_CD4


title: Antrum_160


title: WT_HBSS_626_692_LV

description:
TNYA0042_study
626_692_LV


title: Antrum_161


title: Pkp2KO_6E13_631_703_LV

description:
TNYA0042_study
631_703_LV


title: Antrum_159


title: PBMCs from sample A7-2_Naive_CD8

description: PBMCs from sample A7-2_Naive_CD8


title: PBMCs from sample A7-2_Naive_CD4

description: PBMCs from sample A7-2_Naive_CD4


title: Corpus_174


title: Pkp2KO_HBSS_264_796_RV

description:
TNYA0042_study
264_796_RV


title: Antrum_157


title: PBMCs from sample A7-2_Memory_CD8

description: PBMCs from sample A7-2_Memory_CD8


title: Corpus_173


title: Pkp2KO_HBSS_257_783_RV

description:
TNYA0042_study
257_783_RV


title: Antrum_155


title: Corpus_172


title: Antrum_156


title: Antrum_158


title: Pkp2KO_HBSS_264_796_LV

description:
TNYA0042_study
264_796_LV


title: Pkp2KO_HBSS_257_783_LV

description:
TNYA0042_study
257_783_LV


title: PBMCs from sample A7-1_Naive_CD8

description: PBMCs from sample A7-1_Naive_CD8


title: PBMCs from sample A7-1_Naive_CD4

description: PBMCs from sample A7-1_Naive_CD4


title: Antrum_154


title: Corpus_171


title: Pkp2KO_3E13_253_674_RV

description:
TNYA0042_study
253_674_RV


title: Corpus_170


title: Corpus_169


title: Corpus_168


title: PBMCs from sample A7-1_Memory_CD8

description: PBMCs from sample A7-1_Memory_CD8


title: Pkp2KO_3E13_253_674_LV

description:
TNYA0042_study
253_674_LV


title: Antrum_153


title: PBMCs from sample A7-1_Memory_CD4

description: PBMCs from sample A7-1_Memory_CD4


title: Corpus_166


title: Corpus_167


title: Cisplatin and Oxaliplatin

city: Boston

first: David

last: Chen

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

library_source: transcriptomic single cell

data_processing:
General analysis: scRNA-seq IntegrateData function in Seuratv4 was used to counteract batch effects among human samples. Principal Component Analysis (PCA) was then completed on the integrated object and the quantity of principal components selected for clustering was determined using the integrated object's elbow plot. Cells were then visualized primarily using UMAP non-linear dimensional reduction from which feature and violin plots were generated to demonstrate distribution of gene expression and expression levels of various marker genes and gene signatures throughout the population.
Pre-processing, alignment and gene counts: De-multiplexing, alignment to the transcriptome, and unique molecular identifier (UMI) collapsing were performed using the Cellranger toolkit provided by 10X Genomics.
General Clustering: Standard procedures for QC filtering, data scaling and normalization, detection of highly variable genes, and hashtag oligo (HTO) demultiplexing were followed using Seurat v4 in RStudio. Cells with unique feature counts lower than 500 and greater than 7,500 as well as cells with greater than 15% mitochondrial DNA were excluded. Counts were log-normalized and scaled by a factor of 10,000 according to the default parameters when using the Seurat LogNormalize function. Variable features were identified, and the data were scaled using the default parameters (Ngenes = 2000) of the FindVariableFeatures Extended Data Fig. ScaleData Seurat functions, respectively. HTOs were demultiplexed using the HTODemux function, and cells were identified as containing HTO-1 or HTO-2 based on their maximal HTO-ID signal. The cell population was filtered to contain only HTO-positive, singlet cells for further analysis. Principle component analysis (PCA) was completed on the remaining cells and 10 principle components were selected for clustering, tSNE, and UMAP analyses. Cells were visualized primarily using UMAP non-linear dimensional reduction (dims 1:10, resolution = 0.3), from which feature plots were generated to demonstrate distribution of gene expression and different drugs treatment cells and expression levels of various marker genes throughout the population. Marker genes for each resulting cluster were found using the FindMarkers function with the minimum prevalence set to 25%. Cluster identities were defined using known marker genes enriched in different pathways.
scRNA-seq gene signature analysis: To analyze existing gene signatures on our scRNA-seq data, the Seurat AddModuleScore function in Seurat v4 was used to calculate the average normalized and scaled gene expression of a given gene list in each individual cell. Specific cell types were identified using established marker genes and gene signatures. Gene signature scoring was then visualized with feature and violin plots. To generate novel gene signatures, the Seurat FindMarkers function was used to create lists of genes differentially expressed in one specified subset in comparison to another given subset. Minimum prevalence was set to 25%.
Assembly: Human NCBI Genome Build GRCh38
Supplementary files format and content: 10X Chromium Output of Feature, Barcode, and Read Count Matrix

source_name: Stomach

growth_protocol: NUGC3 was grown in RPMI 1640 (Life Technologies, #11875119) supplemented with 10% FBS and 1% penicillin/streptomycin. Cells lines were maintained in humidified 37°C the incubator with 5% CO2 and routinely tested for mycoplasma contamination (Lonza #LT07-118)

extract_protocol:
The cells were washed with PBS, trypsinized and labeled with cell hashing antibodies, TotalSeqTM-C0251 Hashtag 1 (BioLegend #394661) and TotalSeqTM-C0252 Hashtag 2 (BioLegend #394662). Viable cells were washed and resuspended in PBS with 0.04% BSA at a cell concentration of 1000 cells/µL
About 17,000 viable mouse cells were loaded onto a 10× Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer's recommendations. The scRNAseq libraries were processed using ChromiumTM single cell 5' library & gel bead kit (10× Genomics). Matched cell hashing libraries were prepared using single cell 5' feature barcode library kit. Quality controls for amplified cDNA libraries, cell hashing libraries, and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq and scTCRseq were normalized to 4nM concentration and pooled using a volume ratio of 4:1. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform. The sequencing parameters were: Read 1 of 150bp, Read 2 of 150bp and Index 1 of 8bp. The sequencing data were demultiplexed and aligned to mm10-3.0.0 using cell ranger version 3.1.0 pipeline (10× Genomics).

treatment_protocol: NUGC3 cells were treated with the IC50 concentration of Cisplatin, Oxaliplatin, 5-FU and DMSO for 2 days.

value: Stomach

tag: cell line

value: Gastric adenocarcinoma

value: Cisplatin and Oxaliplatin


title: Corpus_165


title: Pkp2KO_6E13_250_668_RV

description:
TNYA0042_study
250_668_RV


title: PBMCs from sample A7-2_Memory_CD4

description: PBMCs from sample A7-2_Memory_CD4


title: Corpus_164


title: Pkp2KO_6E13_250_668_LV

description:
TNYA0042_study
250_668_LV


title: Control and 5-FU

value: Control and 5-FU


title: Corpus_163


title: Antrum_152


title: Corpus_161


title: WT_HBSS_248_770_LV

description:
TNYA0042_study
248_770_LV


title: Pkp2KO_3E13_182_762_LV

description:
TNYA0042_study
182_762_LV


title: Corpus_160


title: Antrum_151


title: Antrum_150


title: Corpus_162


title: Pkp2KO_3E13_181_761_RV

description:
TNYA0042_study
181_761_RV


title: Antrum_149


title: G112-MixedSamples

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

description: IXTCB00192_R:FEMALE; IXTCB01415_R:FEMALE; IXTCB01357_R:FEMALE; IXTCB01402_R:FEMALE

data_processing:
*library strategy: Adaptive Immune Receptor Repertoire(AIRR)-seq
Illumina paired-end reads were demultiplexed and collapsed by 8 base pairs barcode and 10 base pairs UMI tag using the default MIG size threshold set by MiGEC v1.2 software. In order to assemble the full TCR/BCR sequences, the resulting UMI-collapsed fastq files were mapped to the V, D, J and C reference sequences from the International ImMunoGeneTics (IMGT) database using the MiXCR software (v3.0.14) with the clustering parameters turned off. From the two alignment algorithms that are implemented in MiXCR software which were developed for immune repertoire data based on a seed-and-vote strategy, the default Kaligner and its own built-in reference library (repseqio v1.7) were used. Sequences that were out-of-frame or contained stop codons were filtered out from the analysis. The resulting AIRR-seq data contained sequences from the seven chains that cover the receptor sequence spanning from the FR1-IMGT to FR4-IMGT region, as well as the constant region of the receptor.
Assembly: hg19
Supplementary files format and content: AIRR-seq information is provided separately for each lymphoctye receptor chain. For each sample and replicate, a tsv file containing quantitative information at the clone level (e.g., expression counts, fraction, CDR3 sequence, gene segments, etc) is provided.

source_name: Peripheral whole blood

extract_protocol:
Peripheral whole blood from venipuncture was dispensed into PAXgene™ Blood RNA Tubes (Qiagen). Whole blood samples in PAXgene™ Blood RNA Tubes were stored at -80°C until RNA extraction. RNA was extracted from PAXgene™ Blood RNA Tubes via the PreAnalytiX PAXgene™ blood RNA kit (Qiagen) and automated using the QIAcube.
Two independent next generation sequencing libraries covering all TCR (i.e., TRA, TRB, TRD and TRG) and BCR (i.e., IGH, IGL and IGK) chains were generated from each sample using iR-RepSeq+ 7-Chain service (iRepertoire, US). This technology allows the amplification of the seven receptors chains by addressing every known source of errors in AIRR-seq analyses30. In this procedure, the first set of primer pairs for each V-J combination is used, allowing the extension with tags that, in turn, enable a second set of primers to be utilized for global amplification of all seven chains. This essentially bias-free amplification was conducted in a single assay using UMI during the reverse transcription step. The introduction of UMI to distinguish between single RNA molecules during cDNA synthesis was essential to minimize the impact of PCR duplicates and sequencing errors. All necessary reagents for amplification and purification are preloaded into the cassette. Extracted RNA (1,000 ng) with an appropriate volume of RT mix and nuclease-free water were added into the cassette, which was processed by the iR-Processor. The instrument can automatically set up and carry out all amplification and purification. Briefly, RT is performed using Qiagen OneStep RT-PCR mix (Qiagen). First-strand cDNA was selected, and remnant primers were removed by SPRIselect bead selection (Beckman Coulter) followed by the second round of binding and extension with the V-gene primer mix. After binding and extension, SPRIselect beads were used to purify the first and second strand synthesis products. Library amplification was performed with a pair of primers that are specific for communal sites engineered onto the 5’ end of the C- and V- primers used in first and second-strand synthesis. The final constructed library includes Illumina dual index sequencing adapters, a 10-nucleotide UMIs, and an 8-nucleotide internal barcode associated with the C-gene primer. Amplified libraries were multiplexed and pooled for sequencing on the Illumina NovaSeq platform with a 500-cycle kit (250 paired-end reads) at Hudson Alpha Institute for Biotechnology (Huntsville, AL, USA). The output of the immune receptor sequence covers within the first framework region through the beginning of the constant region, including the CDR3 hypervariable region

tag: mixed sample_id

value: Peripheral whole blood

tag: gender

value: pooled male and female

tag: age

tag: imid

value: IXTCB00192_R:CTRL; IXTCB01415_R:RA; IXTCB01357_R:RA; IXTCB01402_R:RA

tag: week

tag: resp

value: IXTCB00192_R:CTRL; IXTCB01415_R:GOOD; IXTCB01357_R:GOOD; IXTCB01402_R:MOD

value: IXTCB00192_R:CTRL; IXTCB01415_R:Certolizumab; IXTCB01357_R:Etanercept; IXTCB01402_R:Etanercept

tag: acpa

value: IXTCB00192_R:CTRL; IXTCB01415_R:Neg; IXTCB01357_R:Pos; IXTCB01402_R:Pos

tag: rf

value: IXTCB00192_R:CTRL; IXTCB01415_R:Pos; IXTCB01357_R:Pos; IXTCB01402_R:Pos

tag: actb

value: IXTCB00192_R:CTRL; IXTCB01415_R:High; IXTCB01357_R:High; IXTCB01402_R:High


title: Pkp2KO_3E13_252_673_LV

description:
TNYA0042_study
252_673_LV


title: Antrum_148


title: Pkp2KO_3E13_181_761_LV

description:
TNYA0042_study
181_761_LV


title: Antrum_147


title: G110-MixedSamples

description: IXTCB00279_R:FEMALE; IXTCB00285_R:FEMALE; IXTCB01442_R:FEMALE; IXTCB01387_R:FEMALE; IXTCB01463_R:FEMALE

value: IXTCB00279_R:CTRL; IXTCB00285_R:CTRL; IXTCB01442_R:RA; IXTCB01387_R:RA; IXTCB01463_R:RA

value: IXTCB00279_R:CTRL; IXTCB00285_R:CTRL; IXTCB01442_R:wk0; IXTCB01387_R:wk0; IXTCB01463_R:wk0

value: IXTCB00279_R:CTRL; IXTCB00285_R:CTRL; IXTCB01442_R:GOOD; IXTCB01387_R:MOD; IXTCB01463_R:GOOD

value: IXTCB00279_R:CTRL; IXTCB00285_R:CTRL; IXTCB01442_R:Certolizumab; IXTCB01387_R:Etanercept; IXTCB01463_R:Certolizumab

value: IXTCB00279_R:CTRL; IXTCB00285_R:CTRL; IXTCB01442_R:Neg; IXTCB01387_R:Pos; IXTCB01463_R:Pos

value: IXTCB00279_R:CTRL; IXTCB00285_R:CTRL; IXTCB01442_R:Neg; IXTCB01387_R:Neg; IXTCB01463_R:Neg

value: IXTCB00279_R:CTRL; IXTCB00285_R:CTRL; IXTCB01442_R:High; IXTCB01387_R:High; IXTCB01463_R:High


title: Corpus_158

value: Corpus


title: Corpus_159


title: Pkp2KO_HBSS_180_760_RV

description:
TNYA0042_study
180_760_RV

value: Right ventricle

value: CardiacKO

value: HBSS


title: Antrum_146

value: Antrum


title: Pkp2KO_HBSS_180_760_LV

description:
TNYA0042_study
180_760_LV

value: Left ventricle


title: Antrum_145


title: G109-MixedSamples

description: IXTCB00279:FEMALE; IXTCB00285:FEMALE; IXTCB01442:FEMALE; IXTCB01387:FEMALE; IXTCB01463:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00279:CTRL; IXTCB00285:CTRL; IXTCB01442:RA; IXTCB01387:RA; IXTCB01463:RA

value: IXTCB00279:CTRL; IXTCB00285:CTRL; IXTCB01442:wk0; IXTCB01387:wk0; IXTCB01463:wk0

value: IXTCB00279:CTRL; IXTCB00285:CTRL; IXTCB01442:GOOD; IXTCB01387:MOD; IXTCB01463:GOOD

value: IXTCB00279:CTRL; IXTCB00285:CTRL; IXTCB01442:Certolizumab; IXTCB01387:Etanercept; IXTCB01463:Certolizumab

value: IXTCB00279:CTRL; IXTCB00285:CTRL; IXTCB01442:Neg; IXTCB01387:Pos; IXTCB01463:Pos

value: IXTCB00279:CTRL; IXTCB00285:CTRL; IXTCB01442:Neg; IXTCB01387:Neg; IXTCB01463:Neg

value: IXTCB00279:CTRL; IXTCB00285:CTRL; IXTCB01442:High; IXTCB01387:High; IXTCB01463:High


title: Corpus_156


title: G108-MixedSamples

description: IXTCB00093_R:MALE; IXTCB00099_R:FEMALE; IXTCB01336_R:FEMALE; IXTCB01392_R:FEMALE; IXTCB01411_R:FEMALE

value: IXTCB00093_R:CTRL; IXTCB00099_R:CTRL; IXTCB01336_R:RA; IXTCB01392_R:RA; IXTCB01411_R:RA

value: IXTCB00093_R:CTRL; IXTCB00099_R:CTRL; IXTCB01336_R:wk0; IXTCB01392_R:wk0; IXTCB01411_R:wk12

value: IXTCB00093_R:CTRL; IXTCB00099_R:CTRL; IXTCB01336_R:MOD; IXTCB01392_R:GOOD; IXTCB01411_R:GOOD

value: IXTCB00093_R:CTRL; IXTCB00099_R:CTRL; IXTCB01336_R:Golimumab; IXTCB01392_R:Etanercept; IXTCB01411_R:Etanercept

value: IXTCB00093_R:CTRL; IXTCB00099_R:CTRL; IXTCB01336_R:Pos; IXTCB01392_R:Neg; IXTCB01411_R:Neg

value: IXTCB00093_R:CTRL; IXTCB00099_R:CTRL; IXTCB01336_R:Neg; IXTCB01392_R:NA; IXTCB01411_R:NA

value: IXTCB00093_R:CTRL; IXTCB00099_R:CTRL; IXTCB01336_R:High; IXTCB01392_R:High; IXTCB01411_R:Low


title: Corpus_157

value: Corpus


title: G111-MixedSamples

description: IXTCB00192:FEMALE; IXTCB01415:FEMALE; IXTCB01357:FEMALE; IXTCB01402:FEMALE

value: Peripheral whole blood

value: IXTCB00192:CTRL; IXTCB01415:RA; IXTCB01357:RA; IXTCB01402:RA

value: IXTCB00192:CTRL; IXTCB01415:GOOD; IXTCB01357:GOOD; IXTCB01402:MOD

value: IXTCB00192:CTRL; IXTCB01415:Certolizumab; IXTCB01357:Etanercept; IXTCB01402:Etanercept

value: IXTCB00192:CTRL; IXTCB01415:Neg; IXTCB01357:Pos; IXTCB01402:Pos

value: IXTCB00192:CTRL; IXTCB01415:Pos; IXTCB01357:Pos; IXTCB01402:Pos

value: IXTCB00192:CTRL; IXTCB01415:High; IXTCB01357:High; IXTCB01402:High


title: Pkp2KO_HBSS_177_759_LV

description:
TNYA0042_study
177_759_LV

value: Left ventricle

value: CardiacKO

value: HBSS


title: Corpus_155


title: Antrum_143

value: Antrum


title: G107-MixedSamples

description: IXTCB00093:MALE; IXTCB00099:FEMALE; IXTCB01336:FEMALE; IXTCB01392:FEMALE; IXTCB01411:FEMALE

value: pooled male and female

value: IXTCB00093:CTRL; IXTCB00099:CTRL; IXTCB01336:RA; IXTCB01392:RA; IXTCB01411:RA

value: IXTCB00093:CTRL; IXTCB00099:CTRL; IXTCB01336:wk0; IXTCB01392:wk0; IXTCB01411:wk12

value: IXTCB00093:CTRL; IXTCB00099:CTRL; IXTCB01336:MOD; IXTCB01392:GOOD; IXTCB01411:GOOD

value: IXTCB00093:CTRL; IXTCB00099:CTRL; IXTCB01336:Golimumab; IXTCB01392:Etanercept; IXTCB01411:Etanercept

value: IXTCB00093:CTRL; IXTCB00099:CTRL; IXTCB01336:Pos; IXTCB01392:Neg; IXTCB01411:Neg

value: IXTCB00093:CTRL; IXTCB00099:CTRL; IXTCB01336:Neg; IXTCB01392:NA; IXTCB01411:NA

value: IXTCB00093:CTRL; IXTCB00099:CTRL; IXTCB01336:High; IXTCB01392:High; IXTCB01411:Low


title: Corpus_153

value: Corpus


title: Corpus_152


title: G106-MixedSamples

description: IXTCB00414_R:MALE; IXTCB00420_R:MALE; IXTCB01493_R:FEMALE; IXTCB01537_R:FEMALE; IXTCB01488_R:FEMALE

value: Peripheral whole blood

value: IXTCB00414_R:CTRL; IXTCB00420_R:CTRL; IXTCB01493_R:RA; IXTCB01537_R:RA; IXTCB01488_R:RA

value: IXTCB00414_R:CTRL; IXTCB00420_R:CTRL; IXTCB01493_R:wk0; IXTCB01537_R:wk12; IXTCB01488_R:wk0

value: IXTCB00414_R:CTRL; IXTCB00420_R:CTRL; IXTCB01493_R:GOOD; IXTCB01537_R:GOOD; IXTCB01488_R:NA

value: IXTCB00414_R:CTRL; IXTCB00420_R:CTRL; IXTCB01493_R:Etanercept; IXTCB01537_R:Golimumab; IXTCB01488_R:Adalimumab

value: IXTCB00414_R:CTRL; IXTCB00420_R:CTRL; IXTCB01493_R:Pos; IXTCB01537_R:Pos; IXTCB01488_R:Pos

value: IXTCB00414_R:CTRL; IXTCB00420_R:CTRL; IXTCB01493_R:Low; IXTCB01537_R:Low; IXTCB01488_R:Low


title: brain tissue, Ch25h-KO and Tau transgenic, rep5 [S20_tcko5]

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined, aligned with STAR v2.5.1a, and quantitated with Subread:featureCount v1.4.6-p5
Assembly: Mouse Ensembl GRCm38.76
Supplementary files format and content: all_16_samples_gene_counts.txt, tab-separated value, contains gene counts of all samples
Supplementary files format and content: per sample genecounts.sf, tab-separated value, contains gene counts with TPM values

source_name: brain

growth_protocol: The PS19 transgenic mouse model overexpresses 1N4R human microtubule-associated protein tau (MAPT) driven by the PrP promoter, containing the P301S mutation that causes a familial form of frontotemporal dementia. The PS19 (T) mice were crossed to the Ch25h knockout (CKO) mice to generate wild type (WT), Ch25h KO (CKO), T and TCKO mice.

extract_protocol:
Animals were perfused with PBS. Left hemisphere was fixed in 4% paraformaldehyde for immunostaining. Hippocampus from the right hemisphere was flash frozen and stored at -80˚C until RNA isolation using Zymo Research Quick-RNA MiniPrep Plus kit (Cat. #: R1058).
an oligo-dT based SMARTer Ultra Low RNA kit from the Takara-Clontech was used to prepare the libraries

treatment_protocol: Mice were aged to 9.5 months

value: brain

tag: Sex

value: female

value: 40 weeks

value: TCKO


title: Antrum_142

value: Antrum


title: Pkp2KO_HBSS_177_759_RV

description:
TNYA0042_study
177_759_RV

value: Right ventricle

value: CardiacKO

value: HBSS


title: Antrum_144


title: Antrum_141


title: brain tissue, Ch25h-KO and Tau transgenic, rep3 [S18_tcko3]


title: G104-MixedSamples

description: IXTCB00144_R:FEMALE; IXTCB00174_R:FEMALE; IXTCB01332_R:FEMALE; IXTCB01429_R:FEMALE; IXTCB01393_R:FEMALE

value: pooled male and female

value: IXTCB00144_R:CTRL; IXTCB00174_R:CTRL; IXTCB01332_R:RA; IXTCB01429_R:RA; IXTCB01393_R:RA

value: IXTCB00144_R:CTRL; IXTCB00174_R:CTRL; IXTCB01332_R:wk0; IXTCB01429_R:wk0; IXTCB01393_R:wk0

value: IXTCB00144_R:CTRL; IXTCB00174_R:CTRL; IXTCB01332_R:NON_RESP; IXTCB01429_R:GOOD; IXTCB01393_R:MOD

value: IXTCB00144_R:CTRL; IXTCB00174_R:CTRL; IXTCB01332_R:Golimumab; IXTCB01429_R:Certolizumab; IXTCB01393_R:Etanercept

value: IXTCB00144_R:CTRL; IXTCB00174_R:CTRL; IXTCB01332_R:Neg; IXTCB01429_R:Neg; IXTCB01393_R:Pos

value: IXTCB00144_R:CTRL; IXTCB00174_R:CTRL; IXTCB01332_R:Pos; IXTCB01429_R:Pos; IXTCB01393_R:Pos

value: IXTCB00144_R:CTRL; IXTCB00174_R:CTRL; IXTCB01332_R:High; IXTCB01429_R:Low; IXTCB01393_R:High


title: brain tissue, Ch25h-KO and Tau transgenic, rep2 [S17_tcko2]


title: Antrum_140


title: brain tissue, Tau transgenic, rep5 [S15_tg5]

value: T


title: G102-MixedSamples

description: IXTCB00135_R:FEMALE; IXTCB00036_R:FEMALE; IXTCB01331_R:FEMALE; IXTCB01372_R:FEMALE; IXTCB01404_R:FEMALE

value: Peripheral whole blood

value: IXTCB00135_R:CTRL; IXTCB00036_R:CTRL; IXTCB01331_R:RA; IXTCB01372_R:RA; IXTCB01404_R:RA

value: IXTCB00135_R:CTRL; IXTCB00036_R:CTRL; IXTCB01331_R:wk0; IXTCB01372_R:wk12; IXTCB01404_R:wk0

value: IXTCB00135_R:CTRL; IXTCB00036_R:CTRL; IXTCB01331_R:NON_RESP; IXTCB01372_R:MOD; IXTCB01404_R:GOOD

value: IXTCB00135_R:CTRL; IXTCB00036_R:CTRL; IXTCB01331_R:Golimumab; IXTCB01372_R:Certolizumab; IXTCB01404_R:Etanercept

value: IXTCB00135_R:CTRL; IXTCB00036_R:CTRL; IXTCB01331_R:Pos; IXTCB01372_R:Pos; IXTCB01404_R:Pos

value: IXTCB00135_R:CTRL; IXTCB00036_R:CTRL; IXTCB01331_R:Neg; IXTCB01372_R:Pos; IXTCB01404_R:Pos

value: IXTCB00135_R:CTRL; IXTCB00036_R:CTRL; IXTCB01331_R:High; IXTCB01372_R:Low; IXTCB01404_R:Low


title: G103-MixedSamples

description: IXTCB00144:FEMALE; IXTCB00174:FEMALE; IXTCB01332:FEMALE; IXTCB01429:FEMALE; IXTCB01393:FEMALE

value: pooled male and female

value: IXTCB00144:CTRL; IXTCB00174:CTRL; IXTCB01332:RA; IXTCB01429:RA; IXTCB01393:RA

value: IXTCB00144:CTRL; IXTCB00174:CTRL; IXTCB01332:wk0; IXTCB01429:wk0; IXTCB01393:wk0

value: IXTCB00144:CTRL; IXTCB00174:CTRL; IXTCB01332:NON_RESP; IXTCB01429:GOOD; IXTCB01393:MOD

value: IXTCB00144:CTRL; IXTCB00174:CTRL; IXTCB01332:Golimumab; IXTCB01429:Certolizumab; IXTCB01393:Etanercept

value: IXTCB00144:CTRL; IXTCB00174:CTRL; IXTCB01332:Neg; IXTCB01429:Neg; IXTCB01393:Pos

value: IXTCB00144:CTRL; IXTCB00174:CTRL; IXTCB01332:Pos; IXTCB01429:Pos; IXTCB01393:Pos

value: IXTCB00144:CTRL; IXTCB00174:CTRL; IXTCB01332:High; IXTCB01429:Low; IXTCB01393:High


title: Corpus_151

value: Corpus


title: Corpus_154


title: brain tissue, Ch25h-KO and Tau transgenic, rep4 [S19_tcko4]

value: brain

value: female

value: 40 weeks

value: TCKO


title: Antrum_138

value: Antrum


title: G101-MixedSamples

description: IXTCB00135:FEMALE; IXTCB00036:FEMALE; IXTCB01331:FEMALE; IXTCB01372:FEMALE; IXTCB01404:FEMALE

value: Peripheral whole blood

value: IXTCB00135:CTRL; IXTCB00036:CTRL; IXTCB01331:RA; IXTCB01372:RA; IXTCB01404:RA

value: IXTCB00135:CTRL; IXTCB00036:CTRL; IXTCB01331:wk0; IXTCB01372:wk12; IXTCB01404:wk0

value: IXTCB00135:CTRL; IXTCB00036:CTRL; IXTCB01331:NON_RESP; IXTCB01372:MOD; IXTCB01404:GOOD

value: IXTCB00135:CTRL; IXTCB00036:CTRL; IXTCB01331:Golimumab; IXTCB01372:Certolizumab; IXTCB01404:Etanercept

value: IXTCB00135:CTRL; IXTCB00036:CTRL; IXTCB01331:Pos; IXTCB01372:Pos; IXTCB01404:Pos

value: IXTCB00135:CTRL; IXTCB00036:CTRL; IXTCB01331:Neg; IXTCB01372:Pos; IXTCB01404:Pos

value: IXTCB00135:CTRL; IXTCB00036:CTRL; IXTCB01331:High; IXTCB01372:Low; IXTCB01404:Low


title: G105-MixedSamples

description: IXTCB00414:MALE; IXTCB00420:MALE; IXTCB01493:FEMALE; IXTCB01537:FEMALE; IXTCB01488:FEMALE

value: pooled male and female

value: IXTCB00414:CTRL; IXTCB00420:CTRL; IXTCB01493:RA; IXTCB01537:RA; IXTCB01488:RA

value: IXTCB00414:CTRL; IXTCB00420:CTRL; IXTCB01493:wk0; IXTCB01537:wk12; IXTCB01488:wk0

value: IXTCB00414:CTRL; IXTCB00420:CTRL; IXTCB01493:GOOD; IXTCB01537:GOOD; IXTCB01488:NA

value: IXTCB00414:CTRL; IXTCB00420:CTRL; IXTCB01493:Etanercept; IXTCB01537:Golimumab; IXTCB01488:Adalimumab

value: IXTCB00414:CTRL; IXTCB00420:CTRL; IXTCB01493:Pos; IXTCB01537:Pos; IXTCB01488:Pos

value: IXTCB00414:CTRL; IXTCB00420:CTRL; IXTCB01493:Low; IXTCB01537:Low; IXTCB01488:Low


title: Corpus_150

value: Corpus


title: Antrum_137

value: Antrum


title: brain tissue, Tau transgenic, rep4 [S14_tg4]

value: brain

value: female

value: 40 weeks

value: T


title: Antrum_136


title: brain tissue, Tau transgenic, rep3 [S13_tg3]


title: Antrum_135


title: G99-MixedSamples

description: IXTCB00348:FEMALE; IXTCB00309:FEMALE; IXTCB01451:FEMALE; IXTCB01504:FEMALE

value: Peripheral whole blood

value: IXTCB00348:CTRL; IXTCB00309:CTRL; IXTCB01451:RA; IXTCB01504:RA

value: IXTCB00348:CTRL; IXTCB00309:CTRL; IXTCB01451:wk0; IXTCB01504:wk12

value: IXTCB00348:CTRL; IXTCB00309:CTRL; IXTCB01451:MOD; IXTCB01504:NON_RESP

value: IXTCB00348:CTRL; IXTCB00309:CTRL; IXTCB01451:Certolizumab; IXTCB01504:Adalimumab

value: IXTCB00348:CTRL; IXTCB00309:CTRL; IXTCB01451:Pos; IXTCB01504:Pos

value: IXTCB00348:CTRL; IXTCB00309:CTRL; IXTCB01451:Low; IXTCB01504:High


title: Antrum_139


title: Corpus_149


title: G98-MixedSamples

description: IXTCB00399_R:FEMALE; IXTCB00369_R:FEMALE; IXTCB01416_R:FEMALE; IXTCB01448_R:FEMALE; IXTCB01482_R:FEMALE

value: pooled male and female

value: IXTCB00399_R:CTRL; IXTCB00369_R:CTRL; IXTCB01416_R:RA; IXTCB01448_R:RA; IXTCB01482_R:RA

value: IXTCB00399_R:CTRL; IXTCB00369_R:CTRL; IXTCB01416_R:wk12; IXTCB01448_R:wk0; IXTCB01482_R:wk0

value: IXTCB00399_R:CTRL; IXTCB00369_R:CTRL; IXTCB01416_R:GOOD; IXTCB01448_R:GOOD; IXTCB01482_R:MOD

value: IXTCB00399_R:CTRL; IXTCB00369_R:CTRL; IXTCB01416_R:Etanercept; IXTCB01448_R:Adalimumab; IXTCB01482_R:Etanercept

value: IXTCB00399_R:CTRL; IXTCB00369_R:CTRL; IXTCB01416_R:Pos; IXTCB01448_R:Pos; IXTCB01482_R:Pos

value: IXTCB00399_R:CTRL; IXTCB00369_R:CTRL; IXTCB01416_R:Low; IXTCB01448_R:High; IXTCB01482_R:Low


title: brain tissue, Tau transgenic, rep2 [S12_tg2]

value: brain

value: female


title: brain tissue, Ch25h-knockout, rep5 [S10_cko5]

value: 40 weeks

value: CKO


title: Corpus_147

value: Corpus


title: brain tissue, Ch25h-knockout, rep4 [S09_cko4]


title: Antrum_133

value: Antrum


title: Corpus_148


title: G100-MixedSamples

description: IXTCB00348_R:FEMALE; IXTCB00309_R:FEMALE; IXTCB01451_R:FEMALE; IXTCB01504_R:FEMALE

value: Peripheral whole blood

value: IXTCB00348_R:CTRL; IXTCB00309_R:CTRL; IXTCB01451_R:RA; IXTCB01504_R:RA

value: IXTCB00348_R:CTRL; IXTCB00309_R:CTRL; IXTCB01451_R:wk0; IXTCB01504_R:wk12

value: IXTCB00348_R:CTRL; IXTCB00309_R:CTRL; IXTCB01451_R:MOD; IXTCB01504_R:NON_RESP

value: IXTCB00348_R:CTRL; IXTCB00309_R:CTRL; IXTCB01451_R:Certolizumab; IXTCB01504_R:Adalimumab

value: IXTCB00348_R:CTRL; IXTCB00309_R:CTRL; IXTCB01451_R:Pos; IXTCB01504_R:Pos

value: IXTCB00348_R:CTRL; IXTCB00309_R:CTRL; IXTCB01451_R:Low; IXTCB01504_R:High


title: Corpus_145


title: Corpus_146


title: Antrum_132


title: brain tissue, Ch25h-knockout, rep2 [S07_cko2]


title: G96-MixedSamples

description: IXTCB00222_R:MALE; IXTCB01510_R:FEMALE; IXTCB01423_R:MALE; IXTCB01430_R:FEMALE

value: pooled male and female

value: IXTCB00222_R:CTRL; IXTCB01510_R:RA; IXTCB01423_R:RA; IXTCB01430_R:RA

value: IXTCB00222_R:CTRL; IXTCB01510_R:GOOD; IXTCB01423_R:GOOD; IXTCB01430_R:NON_RESP

value: IXTCB00222_R:CTRL; IXTCB01510_R:Etanercept; IXTCB01423_R:Golimumab; IXTCB01430_R:Etanercept

value: IXTCB00222_R:CTRL; IXTCB01510_R:Pos; IXTCB01423_R:Neg; IXTCB01430_R:Pos

value: IXTCB00222_R:CTRL; IXTCB01510_R:Low; IXTCB01423_R:Low; IXTCB01430_R:Low


title: Corpus_142


title: brain tissue, wild-type, rep5 [S05_wt5]

value: brain

value: female

value: 40 weeks

value: WT


title: Corpus_144

value: Corpus


title: Antrum_134

value: Antrum


title: Corpus_141


title: G95-MixedSamples

description: IXTCB00222:MALE; IXTCB01510:FEMALE; IXTCB01423:MALE; IXTCB01430:FEMALE

value: Peripheral whole blood

value: IXTCB00222:CTRL; IXTCB01510:RA; IXTCB01423:RA; IXTCB01430:RA

value: IXTCB00222:CTRL; IXTCB01510:GOOD; IXTCB01423:GOOD; IXTCB01430:NON_RESP

value: IXTCB00222:CTRL; IXTCB01510:Etanercept; IXTCB01423:Golimumab; IXTCB01430:Etanercept

value: IXTCB00222:CTRL; IXTCB01510:Pos; IXTCB01423:Neg; IXTCB01430:Pos

value: IXTCB00222:CTRL; IXTCB01510:Low; IXTCB01423:Low; IXTCB01430:Low


title: brain tissue, wild-type, rep4 [S04_wt4]


title: Corpus_143


title: Corpus_140


title: G94-MixedSamples

description: IXTCB00435_R:FEMALE; IXTCB00300_R:FEMALE; IXTCB01401_R:FEMALE; IXTCB01513_R:FEMALE; IXTCB01465_R:FEMALE

value: pooled male and female

value: IXTCB00435_R:CTRL; IXTCB00300_R:CTRL; IXTCB01401_R:RA; IXTCB01513_R:RA; IXTCB01465_R:RA

value: IXTCB00435_R:CTRL; IXTCB00300_R:CTRL; IXTCB01401_R:wk0; IXTCB01513_R:wk0; IXTCB01465_R:wk12

value: IXTCB00435_R:CTRL; IXTCB00300_R:CTRL; IXTCB01401_R:GOOD; IXTCB01513_R:MOD; IXTCB01465_R:GOOD

value: IXTCB00435_R:CTRL; IXTCB00300_R:CTRL; IXTCB01401_R:Etanercept; IXTCB01513_R:Adalimumab; IXTCB01465_R:Etanercept

value: IXTCB00435_R:CTRL; IXTCB00300_R:CTRL; IXTCB01401_R:Pos; IXTCB01513_R:Pos; IXTCB01465_R:Pos

value: IXTCB00435_R:CTRL; IXTCB00300_R:CTRL; IXTCB01401_R:Pos; IXTCB01513_R:Neg; IXTCB01465_R:Pos

value: IXTCB00435_R:CTRL; IXTCB00300_R:CTRL; IXTCB01401_R:Low; IXTCB01513_R:High; IXTCB01465_R:Low


title: G97-MixedSamples

description: IXTCB00399:FEMALE; IXTCB00369:FEMALE; IXTCB01416:FEMALE; IXTCB01448:FEMALE; IXTCB01482:FEMALE

value: IXTCB00399:CTRL; IXTCB00369:CTRL; IXTCB01416:RA; IXTCB01448:RA; IXTCB01482:RA

value: IXTCB00399:CTRL; IXTCB00369:CTRL; IXTCB01416:wk12; IXTCB01448:wk0; IXTCB01482:wk0

value: IXTCB00399:CTRL; IXTCB00369:CTRL; IXTCB01416:GOOD; IXTCB01448:GOOD; IXTCB01482:MOD

value: IXTCB00399:CTRL; IXTCB00369:CTRL; IXTCB01416:Etanercept; IXTCB01448:Adalimumab; IXTCB01482:Etanercept

value: IXTCB00399:CTRL; IXTCB00369:CTRL; IXTCB01416:Pos; IXTCB01448:Pos; IXTCB01482:Pos

value: IXTCB00399:CTRL; IXTCB00369:CTRL; IXTCB01416:Low; IXTCB01448:High; IXTCB01482:Low


title: Antrum_131

value: Antrum


title: G92-MixedSamples

description: IXTCB00324_R:FEMALE; IXTCB01459_R:FEMALE; IXTCB01491_R:FEMALE; IXTCB01497_R:FEMALE

value: Peripheral whole blood

value: IXTCB00324_R:CTRL; IXTCB01459_R:RA; IXTCB01491_R:RA; IXTCB01497_R:RA

value: IXTCB00324_R:CTRL; IXTCB01459_R:MOD; IXTCB01491_R:GOOD; IXTCB01497_R:GOOD

value: IXTCB00324_R:CTRL; IXTCB01459_R:Certolizumab; IXTCB01491_R:Etanercept; IXTCB01497_R:Etanercept

value: IXTCB00324_R:CTRL; IXTCB01459_R:Pos; IXTCB01491_R:Pos; IXTCB01497_R:Pos

value: IXTCB00324_R:CTRL; IXTCB01459_R:High; IXTCB01491_R:Low; IXTCB01497_R:High


title: Antrum_130


title: G93-MixedSamples

description: IXTCB00435:FEMALE; IXTCB00300:FEMALE; IXTCB01401:FEMALE; IXTCB01513:FEMALE; IXTCB01465:FEMALE

value: pooled male and female

value: IXTCB00435:CTRL; IXTCB00300:CTRL; IXTCB01401:RA; IXTCB01513:RA; IXTCB01465:RA

value: IXTCB00435:CTRL; IXTCB00300:CTRL; IXTCB01401:wk0; IXTCB01513:wk0; IXTCB01465:wk12

value: IXTCB00435:CTRL; IXTCB00300:CTRL; IXTCB01401:GOOD; IXTCB01513:MOD; IXTCB01465:GOOD

value: IXTCB00435:CTRL; IXTCB00300:CTRL; IXTCB01401:Etanercept; IXTCB01513:Adalimumab; IXTCB01465:Etanercept

value: IXTCB00435:CTRL; IXTCB00300:CTRL; IXTCB01401:Pos; IXTCB01513:Pos; IXTCB01465:Pos

value: IXTCB00435:CTRL; IXTCB00300:CTRL; IXTCB01401:Pos; IXTCB01513:Neg; IXTCB01465:Pos

value: IXTCB00435:CTRL; IXTCB00300:CTRL; IXTCB01401:Low; IXTCB01513:High; IXTCB01465:Low


title: Antrum_129


title: brain tissue, Ch25h-knockout, rep1 [S06_cko1]

value: brain

value: female

value: 40 weeks

value: CKO


title: brain tissue, wild-type, rep2 [S02_wt2]

value: WT


title: Antrum_128

value: Antrum


title: brain tissue, wild-type, rep1 [S01_wt1]


title: Corpus_139

value: Corpus


title: Antrum_126


title: Jag1-3  [LN008]

city: New York

first: Utpal

last: Pajvani

state: NY

address: 1150 St. Nicholas Avenue

institute: Columbia University Medical Center

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
Raw counts were pseudoaligned to the mouse transcriptome (GRCm38) by Kallisto and gene count tables generated
Differenrial gene expression analyses were performed with limma, implemented in the BioJupies application
Assembly: mm10, GCRm38
Supplementary files format and content: TetO-Jag1-Raw_count_table.txt
Supplementary files format and content: tetO-Jag1-DEGs.txt

source_name: pancreas

extract_protocol:
Islets were islated from mice after doxyciline supplementatuoon in drinking water for 8 weeks, and RNA was harvested using Trizol reagent. For TruSeq Stranded mRNA LT Sample Prep Kit/TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E. Macrogen. For library construction, RNA is extracted from a sample. After performing quality control(QC), qualified samples proceed to library construction.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5’ and 3’ adapter ligation. Alternatively, “tagmentation” combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

value: pancreas

value: pancreatic islets

value: RIP-Cre+, Rosa26-rtTA+, tetO_Jag1+

value: doxycycline supplementation:8 weeks


title: G88-MixedSamples

description: IXTCB00057_R:FEMALE; IXTCB00015_R:FEMALE; IXTCB01338_R:FEMALE; IXTCB01366_R:FEMALE; IXTCB01361_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00057_R:CTRL; IXTCB00015_R:CTRL; IXTCB01338_R:RA; IXTCB01366_R:RA; IXTCB01361_R:RA

value: IXTCB00057_R:CTRL; IXTCB00015_R:CTRL; IXTCB01338_R:wk0; IXTCB01366_R:wk12; IXTCB01361_R:wk12

value: IXTCB00057_R:CTRL; IXTCB00015_R:CTRL; IXTCB01338_R:NON_RESP; IXTCB01366_R:GOOD; IXTCB01361_R:GOOD

value: IXTCB00057_R:CTRL; IXTCB00015_R:CTRL; IXTCB01338_R:Etanercept; IXTCB01366_R:Etanercept; IXTCB01361_R:Certolizumab

value: IXTCB00057_R:CTRL; IXTCB00015_R:CTRL; IXTCB01338_R:Pos; IXTCB01366_R:Pos; IXTCB01361_R:Pos

value: IXTCB00057_R:CTRL; IXTCB00015_R:CTRL; IXTCB01338_R:Low; IXTCB01366_R:Low; IXTCB01361_R:Low


title: G89-MixedSamples

description: IXTCB00246:FEMALE; IXTCB00228:MALE; IXTCB01444:FEMALE; IXTCB01481:FEMALE; IXTCB01483:FEMALE

value: IXTCB00246:CTRL; IXTCB00228:CTRL; IXTCB01444:RA; IXTCB01481:RA; IXTCB01483:RA

value: IXTCB00246:CTRL; IXTCB00228:CTRL; IXTCB01444:wk12; IXTCB01481:wk12; IXTCB01483:wk0

value: IXTCB00246:CTRL; IXTCB00228:CTRL; IXTCB01444:MOD; IXTCB01481:GOOD; IXTCB01483:NON_RESP

value: IXTCB00246:CTRL; IXTCB00228:CTRL; IXTCB01444:Etanercept; IXTCB01481:Certolizumab; IXTCB01483:Certolizumab

value: IXTCB00246:CTRL; IXTCB00228:CTRL; IXTCB01444:Pos; IXTCB01481:Pos; IXTCB01483:Neg

value: IXTCB00246:CTRL; IXTCB00228:CTRL; IXTCB01444:Neg; IXTCB01481:Neg; IXTCB01483:Neg

value: IXTCB00246:CTRL; IXTCB00228:CTRL; IXTCB01444:High; IXTCB01481:Low; IXTCB01483:High


title: G90-MixedSamples

description: IXTCB00246_R:FEMALE; IXTCB00228_R:MALE; IXTCB01444_R:FEMALE; IXTCB01481_R:FEMALE; IXTCB01483_R:FEMALE

value: IXTCB00246_R:CTRL; IXTCB00228_R:CTRL; IXTCB01444_R:RA; IXTCB01481_R:RA; IXTCB01483_R:RA

value: IXTCB00246_R:CTRL; IXTCB00228_R:CTRL; IXTCB01444_R:wk12; IXTCB01481_R:wk12; IXTCB01483_R:wk0

value: IXTCB00246_R:CTRL; IXTCB00228_R:CTRL; IXTCB01444_R:MOD; IXTCB01481_R:GOOD; IXTCB01483_R:NON_RESP

value: IXTCB00246_R:CTRL; IXTCB00228_R:CTRL; IXTCB01444_R:Etanercept; IXTCB01481_R:Certolizumab; IXTCB01483_R:Certolizumab

value: IXTCB00246_R:CTRL; IXTCB00228_R:CTRL; IXTCB01444_R:Pos; IXTCB01481_R:Pos; IXTCB01483_R:Neg

value: IXTCB00246_R:CTRL; IXTCB00228_R:CTRL; IXTCB01444_R:Neg; IXTCB01481_R:Neg; IXTCB01483_R:Neg

value: IXTCB00246_R:CTRL; IXTCB00228_R:CTRL; IXTCB01444_R:High; IXTCB01481_R:Low; IXTCB01483_R:High


title: Antrum_125

value: Antrum


title: Jag1-2 [LN006]

value: pancreas

value: pancreatic islets

value: RIP-Cre+, Rosa26-rtTA+, tetO_Jag1+

value: doxycycline supplementation:8 weeks


title: Antrum_124


title: Corpus_138

value: Corpus


title: G87-MixedSamples

description: IXTCB00057:FEMALE; IXTCB00015:FEMALE; IXTCB01338:FEMALE; IXTCB01366:FEMALE; IXTCB01361:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00057:CTRL; IXTCB00015:CTRL; IXTCB01338:RA; IXTCB01366:RA; IXTCB01361:RA

value: IXTCB00057:CTRL; IXTCB00015:CTRL; IXTCB01338:wk0; IXTCB01366:wk12; IXTCB01361:wk12

value: IXTCB00057:CTRL; IXTCB00015:CTRL; IXTCB01338:NON_RESP; IXTCB01366:GOOD; IXTCB01361:GOOD

value: IXTCB00057:CTRL; IXTCB00015:CTRL; IXTCB01338:Etanercept; IXTCB01366:Etanercept; IXTCB01361:Certolizumab

value: IXTCB00057:CTRL; IXTCB00015:CTRL; IXTCB01338:Pos; IXTCB01366:Pos; IXTCB01361:Pos

value: IXTCB00057:CTRL; IXTCB00015:CTRL; IXTCB01338:Low; IXTCB01366:Low; IXTCB01361:Low


title: Jag1-1 [LN005]


title: G91-MixedSamples

description: IXTCB00324:FEMALE; IXTCB01459:FEMALE; IXTCB01491:FEMALE; IXTCB01497:FEMALE

value: IXTCB00324:CTRL; IXTCB01459:RA; IXTCB01491:RA; IXTCB01497:RA

value: IXTCB00324:CTRL; IXTCB01459:MOD; IXTCB01491:GOOD; IXTCB01497:GOOD

value: IXTCB00324:CTRL; IXTCB01459:Certolizumab; IXTCB01491:Etanercept; IXTCB01497:Etanercept

value: IXTCB00324:CTRL; IXTCB01459:Pos; IXTCB01491:Pos; IXTCB01497:Pos

value: IXTCB00324:CTRL; IXTCB01459:High; IXTCB01491:Low; IXTCB01497:High


title: Corpus_137


title: Antrum_123

value: Antrum


title: G86-MixedSamples

description: IXTCB00069_R:FEMALE; IXTCB01345_R:FEMALE; IXTCB01405_R:MALE


title: Corpus_136


title: Antrum_127


title: G85-MixedSamples

description: IXTCB00069:FEMALE; IXTCB01345:FEMALE; IXTCB01405:MALE


title: Control-2 [LN003]

value: pancreas

value: pancreatic islets

value: RIP-Cre+, Rosa26-rtTA+, tetO_Jag1-


title: Corpus_135

value: Corpus


title: G84-MixedSamples

description: IXTCB00477_R:FEMALE; IXTCB01454_R:FEMALE; IXTCB01474_R:FEMALE; IXTCB01539_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00477_R:CTRL; IXTCB01454_R:RA; IXTCB01474_R:RA; IXTCB01539_R:RA

value: IXTCB00477_R:CTRL; IXTCB01454_R:GOOD; IXTCB01474_R:GOOD; IXTCB01539_R:NA

value: IXTCB00477_R:CTRL; IXTCB01454_R:Adalimumab; IXTCB01474_R:Golimumab; IXTCB01539_R:Adalimumab

value: IXTCB00477_R:CTRL; IXTCB01454_R:Neg; IXTCB01474_R:Pos; IXTCB01539_R:Pos

value: IXTCB00477_R:CTRL; IXTCB01454_R:Low; IXTCB01474_R:High; IXTCB01539_R:Low


title: Antrum_121


title: Antrum_120


title: G83-MixedSamples

description: IXTCB00477:FEMALE; IXTCB01454:FEMALE; IXTCB01474:FEMALE; IXTCB01539:FEMALE

value: IXTCB00477:CTRL; IXTCB01454:RA; IXTCB01474:RA; IXTCB01539:RA

value: IXTCB00477:CTRL; IXTCB01454:GOOD; IXTCB01474:GOOD; IXTCB01539:NA

value: IXTCB00477:CTRL; IXTCB01454:Adalimumab; IXTCB01474:Golimumab; IXTCB01539:Adalimumab

value: IXTCB00477:CTRL; IXTCB01454:Neg; IXTCB01474:Pos; IXTCB01539:Pos

value: IXTCB00477:CTRL; IXTCB01454:Low; IXTCB01474:High; IXTCB01539:Low


title: Control-1 [LN002]

value: doxycycline supplementation:8 weeks


title: Corpus_134


title: WTPL4

city: Tokyo

first: ANHAO

last: LIU

state: Tokyo

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Periodontology

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Data (26.7M reads/13.3M pairs per sample) was processed using packages based on R.
Low-quality and adapter sequences from the paired-end reads were trimmed using Trimmomatic v0.39
The quality of the trimmed reads was assessed using FastQC v0.11.9.
Trimmed paired-end reads were aligned to the mouse reference genome (GRCm39) using HISAT2 v2.2.1.
Assembly: StringTie v2.1.7 was used to assemble transcripts and estimate abundance based on GRCm39 gene annotations.
Supplementary files format and content: Comma-separated spreadsheet files include raw counts for each sample (concluded by tissue type).

source_name: Peri-root tissue(Approximately periodontal tissue)

extract_protocol:
RNA was harvested from maxillae samples fixed in RNAlater (Sigma) using Direct-zol-96 RNA Kits (ZYMO). 0.2 ug (lowest sample) of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM ll Directional RNA Library Prep Kit following manufacturer's protocols.

value: Ligature placement for 11 days

value: Male


title: Antrum_119

value: Antrum


title: Corpus_133

value: Corpus


title: Corpus_132


title: Corpus_131


title: Control-3 [LN004]

value: pancreas

value: pancreatic islets

value: RIP-Cre+, Rosa26-rtTA+, tetO_Jag1-


title: Antrum_122


title: Corpus_130


title: G82-MixedSamples

description: IXTCB00327_R:FEMALE; IXTCB00288_R:MALE; IXTCB01512_R:FEMALE; IXTCB01484_R:FEMALE; IXTCB01479_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00327_R:CTRL; IXTCB00288_R:CTRL; IXTCB01512_R:RA; IXTCB01484_R:RA; IXTCB01479_R:RA

value: IXTCB00327_R:CTRL; IXTCB00288_R:CTRL; IXTCB01512_R:wk0; IXTCB01484_R:wk12; IXTCB01479_R:wk0

value: IXTCB00327_R:CTRL; IXTCB00288_R:CTRL; IXTCB01512_R:GOOD; IXTCB01484_R:NON_RESP; IXTCB01479_R:NON_RESP

value: IXTCB00327_R:CTRL; IXTCB00288_R:CTRL; IXTCB01512_R:Certolizumab; IXTCB01484_R:Etanercept; IXTCB01479_R:Etanercept

value: IXTCB00327_R:CTRL; IXTCB00288_R:CTRL; IXTCB01512_R:Neg; IXTCB01484_R:Neg; IXTCB01479_R:Pos

value: IXTCB00327_R:CTRL; IXTCB00288_R:CTRL; IXTCB01512_R:Pos; IXTCB01484_R:Neg; IXTCB01479_R:Pos

value: IXTCB00327_R:CTRL; IXTCB00288_R:CTRL; IXTCB01512_R:High; IXTCB01484_R:High; IXTCB01479_R:High


title: WTPL2

value: Peri-root tissue(Approximately periodontal tissue)


title: WTPL1

value: Ligature placement for 11 days


title: G81-MixedSamples

description: IXTCB00327:FEMALE; IXTCB00288:MALE; IXTCB01512:FEMALE; IXTCB01484:FEMALE; IXTCB01479:FEMALE

value: IXTCB00327:CTRL; IXTCB00288:CTRL; IXTCB01512:RA; IXTCB01484:RA; IXTCB01479:RA

value: IXTCB00327:CTRL; IXTCB00288:CTRL; IXTCB01512:wk0; IXTCB01484:wk12; IXTCB01479:wk0

value: IXTCB00327:CTRL; IXTCB00288:CTRL; IXTCB01512:GOOD; IXTCB01484:NON_RESP; IXTCB01479:NON_RESP

value: IXTCB00327:CTRL; IXTCB00288:CTRL; IXTCB01512:Certolizumab; IXTCB01484:Etanercept; IXTCB01479:Etanercept

value: IXTCB00327:CTRL; IXTCB00288:CTRL; IXTCB01512:Neg; IXTCB01484:Neg; IXTCB01479:Pos

value: IXTCB00327:CTRL; IXTCB00288:CTRL; IXTCB01512:Pos; IXTCB01484:Neg; IXTCB01479:Pos

value: IXTCB00327:CTRL; IXTCB00288:CTRL; IXTCB01512:High; IXTCB01484:High; IXTCB01479:High


title: Corpus_129

value: Corpus


title: Corpus_128


title: Antrum_118

value: Antrum


title: G80-MixedSamples

description: IXTCB00294_R:MALE; IXTCB00351_R:FEMALE; IXTCB01431_R:FEMALE; IXTCB01494_R:FEMALE; IXTCB01475_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00294_R:CTRL; IXTCB00351_R:CTRL; IXTCB01431_R:RA; IXTCB01494_R:RA; IXTCB01475_R:RA

value: IXTCB00294_R:CTRL; IXTCB00351_R:CTRL; IXTCB01431_R:NON_RESP; IXTCB01494_R:GOOD; IXTCB01475_R:GOOD

value: IXTCB00294_R:CTRL; IXTCB00351_R:CTRL; IXTCB01431_R:Etanercept; IXTCB01494_R:Golimumab; IXTCB01475_R:Etanercept

value: IXTCB00294_R:CTRL; IXTCB00351_R:CTRL; IXTCB01431_R:Pos; IXTCB01494_R:Pos; IXTCB01475_R:Neg

value: IXTCB00294_R:CTRL; IXTCB00351_R:CTRL; IXTCB01431_R:High; IXTCB01494_R:Low; IXTCB01475_R:Low


title: WTPC4

value: Peri-root tissue(Approximately periodontal tissue)

value: Male


title: Corpus_127


title: WTPC3


title: Antrum_117


title: G79-MixedSamples

description: IXTCB00294:MALE; IXTCB00351:FEMALE; IXTCB01431:FEMALE; IXTCB01494:FEMALE; IXTCB01475:FEMALE

value: IXTCB00294:CTRL; IXTCB00351:CTRL; IXTCB01431:RA; IXTCB01494:RA; IXTCB01475:RA

value: IXTCB00294:CTRL; IXTCB00351:CTRL; IXTCB01431:NON_RESP; IXTCB01494:GOOD; IXTCB01475:GOOD

value: IXTCB00294:CTRL; IXTCB00351:CTRL; IXTCB01431:Etanercept; IXTCB01494:Golimumab; IXTCB01475:Etanercept

value: IXTCB00294:CTRL; IXTCB00351:CTRL; IXTCB01431:Pos; IXTCB01494:Pos; IXTCB01475:Neg

value: IXTCB00294:CTRL; IXTCB00351:CTRL; IXTCB01431:High; IXTCB01494:Low; IXTCB01475:Low


title: Corpus_125


title: Antrum_116


title: WTPC2


title: Corpus_124


title: G78-MixedSamples

description: IXTCB00042_R:FEMALE; IXTCB01340_R:FEMALE; IXTCB01384_R:FEMALE; IXTCB01375_R:FEMALE

value: IXTCB00042_R:CTRL; IXTCB01340_R:RA; IXTCB01384_R:RA; IXTCB01375_R:RA

value: IXTCB00042_R:CTRL; IXTCB01340_R:GOOD; IXTCB01384_R:MOD; IXTCB01375_R:MOD

value: IXTCB00042_R:CTRL; IXTCB01340_R:Certolizumab; IXTCB01384_R:Certolizumab; IXTCB01375_R:Etanercept

value: IXTCB00042_R:CTRL; IXTCB01340_R:Pos; IXTCB01384_R:Pos; IXTCB01375_R:Pos

value: IXTCB00042_R:CTRL; IXTCB01340_R:Low; IXTCB01384_R:High; IXTCB01375_R:High


title: WTPL3

value: Ligature placement for 11 days


title: Antrum_115

value: Antrum


title: G76-MixedSamples

description: IXTCB00249_R:MALE; IXTCB00255_R:FEMALE; IXTCB01417_R:FEMALE; IXTCB01407_R:FEMALE; IXTCB01505_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00249_R:CTRL; IXTCB00255_R:CTRL; IXTCB01417_R:RA; IXTCB01407_R:RA; IXTCB01505_R:RA

value: IXTCB00249_R:CTRL; IXTCB00255_R:CTRL; IXTCB01417_R:wk12; IXTCB01407_R:wk0; IXTCB01505_R:wk12

value: IXTCB00249_R:CTRL; IXTCB00255_R:CTRL; IXTCB01417_R:GOOD; IXTCB01407_R:GOOD; IXTCB01505_R:NON_RESP

value: IXTCB00249_R:CTRL; IXTCB00255_R:CTRL; IXTCB01417_R:Certolizumab; IXTCB01407_R:Etanercept; IXTCB01505_R:Certolizumab

value: IXTCB00249_R:CTRL; IXTCB00255_R:CTRL; IXTCB01417_R:Neg; IXTCB01407_R:Pos; IXTCB01505_R:Neg

value: IXTCB00249_R:CTRL; IXTCB00255_R:CTRL; IXTCB01417_R:Low; IXTCB01407_R:Low; IXTCB01505_R:High


title: Corpus_123

value: Corpus


title: WTBL3

source_name: Bone tissue

value: Bone tissue

value: Male


title: Antrum_114


title: Corpus_122


title: WTBL4


title: G75-MixedSamples

description: IXTCB00249:MALE; IXTCB00255:FEMALE; IXTCB01417:FEMALE; IXTCB01407:FEMALE; IXTCB01505:FEMALE

value: IXTCB00249:CTRL; IXTCB00255:CTRL; IXTCB01417:RA; IXTCB01407:RA; IXTCB01505:RA

value: IXTCB00249:CTRL; IXTCB00255:CTRL; IXTCB01417:wk12; IXTCB01407:wk0; IXTCB01505:wk12

value: IXTCB00249:CTRL; IXTCB00255:CTRL; IXTCB01417:GOOD; IXTCB01407:GOOD; IXTCB01505:NON_RESP

value: IXTCB00249:CTRL; IXTCB00255:CTRL; IXTCB01417:Certolizumab; IXTCB01407:Etanercept; IXTCB01505:Certolizumab

value: IXTCB00249:CTRL; IXTCB00255:CTRL; IXTCB01417:Neg; IXTCB01407:Pos; IXTCB01505:Neg

value: IXTCB00249:CTRL; IXTCB00255:CTRL; IXTCB01417:Low; IXTCB01407:Low; IXTCB01505:High


title: Antrum_113

value: Antrum


title: Antrum_112


title: Corpus_121


title: Corpus_126


title: WTBL2

value: Ligature placement for 11 days


title: G73-MixedSamples

description: IXTCB00072:MALE; IXTCB00159:FEMALE; IXTCB01335:FEMALE; IXTCB01391:FEMALE; IXTCB01360:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00072:CTRL; IXTCB00159:CTRL; IXTCB01335:RA; IXTCB01391:RA; IXTCB01360:RA

value: IXTCB00072:CTRL; IXTCB00159:CTRL; IXTCB01335:wk12; IXTCB01391:wk0; IXTCB01360:wk0

value: IXTCB00072:CTRL; IXTCB00159:CTRL; IXTCB01335:NON_RESP; IXTCB01391:MOD; IXTCB01360:GOOD

value: IXTCB00072:CTRL; IXTCB00159:CTRL; IXTCB01335:Golimumab; IXTCB01391:Certolizumab; IXTCB01360:Etanercept

value: IXTCB00072:CTRL; IXTCB00159:CTRL; IXTCB01335:Pos; IXTCB01391:Pos; IXTCB01360:Neg

value: IXTCB00072:CTRL; IXTCB00159:CTRL; IXTCB01335:Neg; IXTCB01391:Pos; IXTCB01360:Pos

value: IXTCB00072:CTRL; IXTCB00159:CTRL; IXTCB01335:High; IXTCB01391:Low; IXTCB01360:Low


title: Corpus_120

value: Corpus


title: WTBL1

value: Bone tissue

value: Male


title: Antrum_111


title: WTPC1

value: Peri-root tissue(Approximately periodontal tissue)


title: G77-MixedSamples

description: IXTCB00042:FEMALE; IXTCB01340:FEMALE; IXTCB01384:FEMALE; IXTCB01375:FEMALE

value: IXTCB00042:CTRL; IXTCB01340:RA; IXTCB01384:RA; IXTCB01375:RA

value: IXTCB00042:CTRL; IXTCB01340:GOOD; IXTCB01384:MOD; IXTCB01375:MOD

value: IXTCB00042:CTRL; IXTCB01340:Certolizumab; IXTCB01384:Certolizumab; IXTCB01375:Etanercept

value: IXTCB00042:CTRL; IXTCB01340:Pos; IXTCB01384:Pos; IXTCB01375:Pos

value: IXTCB00042:CTRL; IXTCB01340:Low; IXTCB01384:High; IXTCB01375:High


title: Antrum_110

value: Antrum


title: WTBC4


title: Corpus_119


title: Corpus_118


title: G70-MixedSamples

description: IXTCB00375_R:FEMALE; IXTCB00378_R:FEMALE; IXTCB01508_R:FEMALE; IXTCB01426_R:MALE; IXTCB01514_R:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00375_R:CTRL; IXTCB00378_R:CTRL; IXTCB01508_R:RA; IXTCB01426_R:RA; IXTCB01514_R:RA

value: IXTCB00375_R:CTRL; IXTCB00378_R:CTRL; IXTCB01508_R:wk0; IXTCB01426_R:wk0; IXTCB01514_R:wk12

value: IXTCB00375_R:CTRL; IXTCB00378_R:CTRL; IXTCB01508_R:NON_RESP; IXTCB01426_R:GOOD; IXTCB01514_R:NON_RESP

value: IXTCB00375_R:CTRL; IXTCB00378_R:CTRL; IXTCB01508_R:Etanercept; IXTCB01426_R:Golimumab; IXTCB01514_R:Golimumab

value: IXTCB00375_R:CTRL; IXTCB00378_R:CTRL; IXTCB01508_R:Pos; IXTCB01426_R:Neg; IXTCB01514_R:Pos

value: IXTCB00375_R:CTRL; IXTCB00378_R:CTRL; IXTCB01508_R:High; IXTCB01426_R:Low; IXTCB01514_R:High


title: G71-MixedSamples

description: IXTCB00447:MALE; IXTCB00312:FEMALE; IXTCB01410:FEMALE; IXTCB01457:FEMALE; IXTCB01490:FEMALE

value: IXTCB00447:CTRL; IXTCB00312:CTRL; IXTCB01410:RA; IXTCB01457:RA; IXTCB01490:RA

value: IXTCB00447:CTRL; IXTCB00312:CTRL; IXTCB01410:wk12; IXTCB01457:wk0; IXTCB01490:wk12

value: IXTCB00447:CTRL; IXTCB00312:CTRL; IXTCB01410:MOD; IXTCB01457:MOD; IXTCB01490:MOD

value: IXTCB00447:CTRL; IXTCB00312:CTRL; IXTCB01410:Certolizumab; IXTCB01457:Etanercept; IXTCB01490:Golimumab

value: IXTCB00447:CTRL; IXTCB00312:CTRL; IXTCB01410:Pos; IXTCB01457:Neg; IXTCB01490:Pos

value: IXTCB00447:CTRL; IXTCB00312:CTRL; IXTCB01410:Pos; IXTCB01457:Pos; IXTCB01490:Pos

value: IXTCB00447:CTRL; IXTCB00312:CTRL; IXTCB01410:High; IXTCB01457:High; IXTCB01490:High


title: WTBC3

value: Bone tissue

value: Male


title: G72-MixedSamples

description: IXTCB00447_R:MALE; IXTCB00312_R:FEMALE; IXTCB01410_R:FEMALE; IXTCB01457_R:FEMALE; IXTCB01490_R:FEMALE

value: Peripheral whole blood

value: IXTCB00447_R:CTRL; IXTCB00312_R:CTRL; IXTCB01410_R:RA; IXTCB01457_R:RA; IXTCB01490_R:RA

value: IXTCB00447_R:CTRL; IXTCB00312_R:CTRL; IXTCB01410_R:wk12; IXTCB01457_R:wk0; IXTCB01490_R:wk12

value: IXTCB00447_R:CTRL; IXTCB00312_R:CTRL; IXTCB01410_R:MOD; IXTCB01457_R:MOD; IXTCB01490_R:MOD

value: IXTCB00447_R:CTRL; IXTCB00312_R:CTRL; IXTCB01410_R:Certolizumab; IXTCB01457_R:Etanercept; IXTCB01490_R:Golimumab

value: IXTCB00447_R:CTRL; IXTCB00312_R:CTRL; IXTCB01410_R:Pos; IXTCB01457_R:Neg; IXTCB01490_R:Pos

value: IXTCB00447_R:CTRL; IXTCB00312_R:CTRL; IXTCB01410_R:Pos; IXTCB01457_R:Pos; IXTCB01490_R:Pos

value: IXTCB00447_R:CTRL; IXTCB00312_R:CTRL; IXTCB01410_R:High; IXTCB01457_R:High; IXTCB01490_R:High


title: Corpus_117

value: Corpus


title: G69-MixedSamples

description: IXTCB00375:FEMALE; IXTCB00378:FEMALE; IXTCB01508:FEMALE; IXTCB01426:MALE; IXTCB01514:MALE

value: pooled male and female

value: IXTCB00375:CTRL; IXTCB00378:CTRL; IXTCB01508:RA; IXTCB01426:RA; IXTCB01514:RA

value: IXTCB00375:CTRL; IXTCB00378:CTRL; IXTCB01508:wk0; IXTCB01426:wk0; IXTCB01514:wk12

value: IXTCB00375:CTRL; IXTCB00378:CTRL; IXTCB01508:NON_RESP; IXTCB01426:GOOD; IXTCB01514:NON_RESP

value: IXTCB00375:CTRL; IXTCB00378:CTRL; IXTCB01508:Etanercept; IXTCB01426:Golimumab; IXTCB01514:Golimumab

value: IXTCB00375:CTRL; IXTCB00378:CTRL; IXTCB01508:Pos; IXTCB01426:Neg; IXTCB01514:Pos

value: IXTCB00375:CTRL; IXTCB00378:CTRL; IXTCB01508:High; IXTCB01426:Low; IXTCB01514:High


title: Corpus_116


title: WTBC2

value: Bone tissue

value: Male


title: Corpus_115


title: Corpus_114


title: G74-MixedSamples

description: IXTCB00072_R:MALE; IXTCB00159_R:FEMALE; IXTCB01335_R:FEMALE; IXTCB01391_R:FEMALE; IXTCB01360_R:MALE

value: Peripheral whole blood

value: IXTCB00072_R:CTRL; IXTCB00159_R:CTRL; IXTCB01335_R:RA; IXTCB01391_R:RA; IXTCB01360_R:RA

value: IXTCB00072_R:CTRL; IXTCB00159_R:CTRL; IXTCB01335_R:wk12; IXTCB01391_R:wk0; IXTCB01360_R:wk0

value: IXTCB00072_R:CTRL; IXTCB00159_R:CTRL; IXTCB01335_R:NON_RESP; IXTCB01391_R:MOD; IXTCB01360_R:GOOD

value: IXTCB00072_R:CTRL; IXTCB00159_R:CTRL; IXTCB01335_R:Golimumab; IXTCB01391_R:Certolizumab; IXTCB01360_R:Etanercept

value: IXTCB00072_R:CTRL; IXTCB00159_R:CTRL; IXTCB01335_R:Pos; IXTCB01391_R:Pos; IXTCB01360_R:Neg

value: IXTCB00072_R:CTRL; IXTCB00159_R:CTRL; IXTCB01335_R:Neg; IXTCB01391_R:Pos; IXTCB01360_R:Pos

value: IXTCB00072_R:CTRL; IXTCB00159_R:CTRL; IXTCB01335_R:High; IXTCB01391_R:Low; IXTCB01360_R:Low


title: WTBC1


title: Antrum_109

value: Antrum


title: Antrum_108


title: Corpus_113

value: Corpus


title: G68-MixedSamples

description: IXTCB00012_R:MALE; IXTCB00090_R:MALE; IXTCB01355_R:FEMALE; IXTCB01353_R:FEMALE; IXTCB01403_R:FEMALE

value: pooled male and female

value: IXTCB00012_R:CTRL; IXTCB00090_R:CTRL; IXTCB01355_R:RA; IXTCB01353_R:RA; IXTCB01403_R:RA

value: IXTCB00012_R:CTRL; IXTCB00090_R:CTRL; IXTCB01355_R:wk0; IXTCB01353_R:wk0; IXTCB01403_R:wk12

value: IXTCB00012_R:CTRL; IXTCB00090_R:CTRL; IXTCB01355_R:GOOD; IXTCB01353_R:GOOD; IXTCB01403_R:GOOD

value: IXTCB00012_R:CTRL; IXTCB00090_R:CTRL; IXTCB01355_R:Etanercept; IXTCB01353_R:Certolizumab; IXTCB01403_R:Etanercept

value: IXTCB00012_R:CTRL; IXTCB00090_R:CTRL; IXTCB01355_R:Pos; IXTCB01353_R:Pos; IXTCB01403_R:Pos

value: IXTCB00012_R:CTRL; IXTCB00090_R:CTRL; IXTCB01355_R:High; IXTCB01353_R:Low; IXTCB01403_R:Low


title: KOPL4

value: Peri-root tissue(Approximately periodontal tissue)

value: Ligature placement for 11 days

value: Male


title: G67-MixedSamples

description: IXTCB00012:MALE; IXTCB00090:MALE; IXTCB01355:FEMALE; IXTCB01353:FEMALE; IXTCB01403:FEMALE

value: Peripheral whole blood

value: IXTCB00012:CTRL; IXTCB00090:CTRL; IXTCB01355:RA; IXTCB01353:RA; IXTCB01403:RA

value: IXTCB00012:CTRL; IXTCB00090:CTRL; IXTCB01355:wk0; IXTCB01353:wk0; IXTCB01403:wk12

value: IXTCB00012:CTRL; IXTCB00090:CTRL; IXTCB01355:GOOD; IXTCB01353:GOOD; IXTCB01403:GOOD

value: IXTCB00012:CTRL; IXTCB00090:CTRL; IXTCB01355:Etanercept; IXTCB01353:Certolizumab; IXTCB01403:Etanercept

value: IXTCB00012:CTRL; IXTCB00090:CTRL; IXTCB01355:Pos; IXTCB01353:Pos; IXTCB01403:Pos

value: IXTCB00012:CTRL; IXTCB00090:CTRL; IXTCB01355:High; IXTCB01353:Low; IXTCB01403:Low


title: Antrum_107

value: Antrum


title: KOPL3


title: Antrum_106


title: Corpus_112

value: Corpus


title: KOPL2


title: Corpus_111


title: Antrum_105


title: G66-MixedSamples

description: IXTCB00402_R:FEMALE; IXTCB00396_R:FEMALE; IXTCB01468_R:FEMALE; IXTCB01516_R:FEMALE; IXTCB01538_R:FEMALE

value: pooled male and female

value: IXTCB00402_R:CTRL; IXTCB00396_R:CTRL; IXTCB01468_R:RA; IXTCB01516_R:RA; IXTCB01538_R:RA

value: IXTCB00402_R:CTRL; IXTCB00396_R:CTRL; IXTCB01468_R:wk12; IXTCB01516_R:wk0; IXTCB01538_R:wk12

value: IXTCB00402_R:CTRL; IXTCB00396_R:CTRL; IXTCB01468_R:GOOD; IXTCB01516_R:GOOD; IXTCB01538_R:NA

value: IXTCB00402_R:CTRL; IXTCB00396_R:CTRL; IXTCB01468_R:Etanercept; IXTCB01516_R:Etanercept; IXTCB01538_R:Adalimumab

value: IXTCB00402_R:CTRL; IXTCB00396_R:CTRL; IXTCB01468_R:Pos; IXTCB01516_R:Pos; IXTCB01538_R:Pos

value: IXTCB00402_R:CTRL; IXTCB00396_R:CTRL; IXTCB01468_R:Low; IXTCB01516_R:Low; IXTCB01538_R:Low


title: KOPL1

value: Peri-root tissue(Approximately periodontal tissue)

value: Ligature placement for 11 days

value: Male


title: KOPC4


title: G65-MixedSamples

description: IXTCB00402:FEMALE; IXTCB00396:FEMALE; IXTCB01468:FEMALE; IXTCB01516:FEMALE; IXTCB01538:FEMALE

value: Peripheral whole blood

value: IXTCB00402:CTRL; IXTCB00396:CTRL; IXTCB01468:RA; IXTCB01516:RA; IXTCB01538:RA

value: IXTCB00402:CTRL; IXTCB00396:CTRL; IXTCB01468:wk12; IXTCB01516:wk0; IXTCB01538:wk12

value: IXTCB00402:CTRL; IXTCB00396:CTRL; IXTCB01468:GOOD; IXTCB01516:GOOD; IXTCB01538:NA

value: IXTCB00402:CTRL; IXTCB00396:CTRL; IXTCB01468:Etanercept; IXTCB01516:Etanercept; IXTCB01538:Adalimumab

value: IXTCB00402:CTRL; IXTCB00396:CTRL; IXTCB01468:Pos; IXTCB01516:Pos; IXTCB01538:Pos

value: IXTCB00402:CTRL; IXTCB00396:CTRL; IXTCB01468:Low; IXTCB01516:Low; IXTCB01538:Low


title: Antrum_103

value: Antrum


title: Antrum_102


title: KOPC3


title: Antrum_104


title: G64-MixedSamples

description: IXTCB00297_R:FEMALE; IXTCB00336_R:FEMALE; IXTCB01480_R:FEMALE; IXTCB01500_R:FEMALE; IXTCB01469_R:FEMALE

value: pooled male and female

value: IXTCB00297_R:CTRL; IXTCB00336_R:CTRL; IXTCB01480_R:RA; IXTCB01500_R:RA; IXTCB01469_R:RA

value: IXTCB00297_R:CTRL; IXTCB00336_R:CTRL; IXTCB01480_R:wk0; IXTCB01500_R:wk0; IXTCB01469_R:wk12

value: IXTCB00297_R:CTRL; IXTCB00336_R:CTRL; IXTCB01480_R:MOD; IXTCB01500_R:GOOD; IXTCB01469_R:MOD

value: IXTCB00297_R:CTRL; IXTCB00336_R:CTRL; IXTCB01480_R:Golimumab; IXTCB01500_R:Etanercept; IXTCB01469_R:Etanercept

value: IXTCB00297_R:CTRL; IXTCB00336_R:CTRL; IXTCB01480_R:Pos; IXTCB01500_R:Neg; IXTCB01469_R:Pos

value: IXTCB00297_R:CTRL; IXTCB00336_R:CTRL; IXTCB01480_R:High; IXTCB01500_R:High; IXTCB01469_R:High


title: Corpus_110

value: Corpus


title: Antrum_101


title: KOPC2

value: Peri-root tissue(Approximately periodontal tissue)

value: Male


title: Antrum_99


title: G61-MixedSamples

description: IXTCB00186:MALE; IXTCB00180:FEMALE; IXTCB01346:FEMALE; IXTCB01364:FEMALE; IXTCB01428:MALE

value: Peripheral whole blood

value: IXTCB00186:CTRL; IXTCB00180:CTRL; IXTCB01346:RA; IXTCB01364:RA; IXTCB01428:RA

value: IXTCB00186:CTRL; IXTCB00180:CTRL; IXTCB01346:wk0; IXTCB01364:wk0; IXTCB01428:wk0

value: IXTCB00186:CTRL; IXTCB00180:CTRL; IXTCB01346:MOD; IXTCB01364:NON_RESP; IXTCB01428:GOOD

value: IXTCB00186:CTRL; IXTCB00180:CTRL; IXTCB01346:Golimumab; IXTCB01364:Golimumab; IXTCB01428:Etanercept

value: IXTCB00186:CTRL; IXTCB00180:CTRL; IXTCB01346:Pos; IXTCB01364:Pos; IXTCB01428:Pos

value: IXTCB00186:CTRL; IXTCB00180:CTRL; IXTCB01346:Pos; IXTCB01364:Neg; IXTCB01428:Pos

value: IXTCB00186:CTRL; IXTCB00180:CTRL; IXTCB01346:High; IXTCB01364:High; IXTCB01428:Low


title: G62-MixedSamples

description: IXTCB00186_R:MALE; IXTCB00180_R:FEMALE; IXTCB01346_R:FEMALE; IXTCB01364_R:FEMALE; IXTCB01428_R:MALE

value: pooled male and female

value: IXTCB00186_R:CTRL; IXTCB00180_R:CTRL; IXTCB01346_R:RA; IXTCB01364_R:RA; IXTCB01428_R:RA

value: IXTCB00186_R:CTRL; IXTCB00180_R:CTRL; IXTCB01346_R:wk0; IXTCB01364_R:wk0; IXTCB01428_R:wk0

value: IXTCB00186_R:CTRL; IXTCB00180_R:CTRL; IXTCB01346_R:MOD; IXTCB01364_R:NON_RESP; IXTCB01428_R:GOOD

value: IXTCB00186_R:CTRL; IXTCB00180_R:CTRL; IXTCB01346_R:Golimumab; IXTCB01364_R:Golimumab; IXTCB01428_R:Etanercept

value: IXTCB00186_R:CTRL; IXTCB00180_R:CTRL; IXTCB01346_R:Pos; IXTCB01364_R:Pos; IXTCB01428_R:Pos

value: IXTCB00186_R:CTRL; IXTCB00180_R:CTRL; IXTCB01346_R:Pos; IXTCB01364_R:Neg; IXTCB01428_R:Pos

value: IXTCB00186_R:CTRL; IXTCB00180_R:CTRL; IXTCB01346_R:High; IXTCB01364_R:High; IXTCB01428_R:Low


title: Antrum_100

value: Antrum


title: Antrum_98


title: Antrum_97


title: KOPC1

value: Peri-root tissue(Approximately periodontal tissue)

value: Male


title: Antrum_96


title: KOBL4

value: Bone tissue

value: Ligature placement for 11 days


title: Corpus_109

value: Corpus


title: G60-MixedSamples

description: IXTCB00024_R:FEMALE; IXTCB00123_R:FEMALE; IXTCB01374_R:MALE; IXTCB01369_R:FEMALE; IXTCB01377_R:MALE

value: Peripheral whole blood

value: IXTCB00024_R:CTRL; IXTCB00123_R:CTRL; IXTCB01374_R:RA; IXTCB01369_R:RA; IXTCB01377_R:RA

value: IXTCB00024_R:CTRL; IXTCB00123_R:CTRL; IXTCB01374_R:wk0; IXTCB01369_R:wk0; IXTCB01377_R:wk12

value: IXTCB00024_R:CTRL; IXTCB00123_R:CTRL; IXTCB01374_R:MOD; IXTCB01369_R:MOD; IXTCB01377_R:MOD

value: IXTCB00024_R:CTRL; IXTCB00123_R:CTRL; IXTCB01374_R:Etanercept; IXTCB01369_R:Etanercept; IXTCB01377_R:Etanercept

value: IXTCB00024_R:CTRL; IXTCB00123_R:CTRL; IXTCB01374_R:Neg; IXTCB01369_R:Pos; IXTCB01377_R:Neg

value: IXTCB00024_R:CTRL; IXTCB00123_R:CTRL; IXTCB01374_R:Low; IXTCB01369_R:Low; IXTCB01377_R:High


title: KOBL3


title: G59-MixedSamples

description: IXTCB00024:FEMALE; IXTCB00123:FEMALE; IXTCB01374:MALE; IXTCB01369:FEMALE; IXTCB01377:MALE

value: pooled male and female

value: IXTCB00024:CTRL; IXTCB00123:CTRL; IXTCB01374:RA; IXTCB01369:RA; IXTCB01377:RA

value: IXTCB00024:CTRL; IXTCB00123:CTRL; IXTCB01374:wk0; IXTCB01369:wk0; IXTCB01377:wk12

value: IXTCB00024:CTRL; IXTCB00123:CTRL; IXTCB01374:MOD; IXTCB01369:MOD; IXTCB01377:MOD

value: IXTCB00024:CTRL; IXTCB00123:CTRL; IXTCB01374:Etanercept; IXTCB01369:Etanercept; IXTCB01377:Etanercept

value: IXTCB00024:CTRL; IXTCB00123:CTRL; IXTCB01374:Neg; IXTCB01369:Pos; IXTCB01377:Neg

value: IXTCB00024:CTRL; IXTCB00123:CTRL; IXTCB01374:Low; IXTCB01369:Low; IXTCB01377:High


title: G63-MixedSamples

description: IXTCB00297:FEMALE; IXTCB00336:FEMALE; IXTCB01480:FEMALE; IXTCB01500:FEMALE; IXTCB01469:FEMALE

value: IXTCB00297:CTRL; IXTCB00336:CTRL; IXTCB01480:RA; IXTCB01500:RA; IXTCB01469:RA

value: IXTCB00297:CTRL; IXTCB00336:CTRL; IXTCB01480:wk0; IXTCB01500:wk0; IXTCB01469:wk12

value: IXTCB00297:CTRL; IXTCB00336:CTRL; IXTCB01480:MOD; IXTCB01500:GOOD; IXTCB01469:MOD

value: IXTCB00297:CTRL; IXTCB00336:CTRL; IXTCB01480:Golimumab; IXTCB01500:Etanercept; IXTCB01469:Etanercept

value: IXTCB00297:CTRL; IXTCB00336:CTRL; IXTCB01480:Pos; IXTCB01500:Neg; IXTCB01469:Pos

value: IXTCB00297:CTRL; IXTCB00336:CTRL; IXTCB01480:High; IXTCB01500:High; IXTCB01469:High


title: Antrum_95

value: Antrum


title: Corpus_108

value: Corpus


title: Antrum_94


title: Antrum_93


title: Corpus_107


title: G58-MixedSamples

description: IXTCB00048_R:FEMALE; IXTCB00147_R:FEMALE; IXTCB01367_R:FEMALE; IXTCB01427_R:FEMALE; IXTCB01388_R:FEMALE

value: Peripheral whole blood

value: IXTCB00048_R:CTRL; IXTCB00147_R:CTRL; IXTCB01367_R:RA; IXTCB01427_R:RA; IXTCB01388_R:RA

value: IXTCB00048_R:CTRL; IXTCB00147_R:CTRL; IXTCB01367_R:wk0; IXTCB01427_R:wk0; IXTCB01388_R:wk12

value: IXTCB00048_R:CTRL; IXTCB00147_R:CTRL; IXTCB01367_R:GOOD; IXTCB01427_R:GOOD; IXTCB01388_R:GOOD

value: IXTCB00048_R:CTRL; IXTCB00147_R:CTRL; IXTCB01367_R:Etanercept; IXTCB01427_R:Etanercept; IXTCB01388_R:Etanercept

value: IXTCB00048_R:CTRL; IXTCB00147_R:CTRL; IXTCB01367_R:Pos; IXTCB01427_R:Neg; IXTCB01388_R:Pos

value: IXTCB00048_R:CTRL; IXTCB00147_R:CTRL; IXTCB01367_R:Pos; IXTCB01427_R:Neg; IXTCB01388_R:Neg

value: IXTCB00048_R:CTRL; IXTCB00147_R:CTRL; IXTCB01367_R:Low; IXTCB01427_R:Low; IXTCB01388_R:Low


title: Corpus_106


title: Corpus_105


title: G57-MixedSamples

description: IXTCB00048:FEMALE; IXTCB00147:FEMALE; IXTCB01367:FEMALE; IXTCB01427:FEMALE; IXTCB01388:FEMALE

value: pooled male and female

value: IXTCB00048:CTRL; IXTCB00147:CTRL; IXTCB01367:RA; IXTCB01427:RA; IXTCB01388:RA

value: IXTCB00048:CTRL; IXTCB00147:CTRL; IXTCB01367:wk0; IXTCB01427:wk0; IXTCB01388:wk12

value: IXTCB00048:CTRL; IXTCB00147:CTRL; IXTCB01367:GOOD; IXTCB01427:GOOD; IXTCB01388:GOOD

value: IXTCB00048:CTRL; IXTCB00147:CTRL; IXTCB01367:Etanercept; IXTCB01427:Etanercept; IXTCB01388:Etanercept

value: IXTCB00048:CTRL; IXTCB00147:CTRL; IXTCB01367:Pos; IXTCB01427:Neg; IXTCB01388:Pos

value: IXTCB00048:CTRL; IXTCB00147:CTRL; IXTCB01367:Pos; IXTCB01427:Neg; IXTCB01388:Neg

value: IXTCB00048:CTRL; IXTCB00147:CTRL; IXTCB01367:Low; IXTCB01427:Low; IXTCB01388:Low


title: G56-MixedSamples

description: IXTCB00363_R:FEMALE; IXTCB00330_R:FEMALE; IXTCB01511_R:FEMALE; IXTCB01445_R:MALE; IXTCB01376_R:MALE

value: IXTCB00363_R:CTRL; IXTCB00330_R:CTRL; IXTCB01511_R:RA; IXTCB01445_R:RA; IXTCB01376_R:RA

value: IXTCB00363_R:CTRL; IXTCB00330_R:CTRL; IXTCB01511_R:wk0; IXTCB01445_R:wk0; IXTCB01376_R:wk12

value: IXTCB00363_R:CTRL; IXTCB00330_R:CTRL; IXTCB01511_R:NON_RESP; IXTCB01445_R:MOD; IXTCB01376_R:GOOD

value: IXTCB00363_R:CTRL; IXTCB00330_R:CTRL; IXTCB01511_R:Etanercept; IXTCB01445_R:Adalimumab; IXTCB01376_R:Etanercept

value: IXTCB00363_R:CTRL; IXTCB00330_R:CTRL; IXTCB01511_R:Neg; IXTCB01445_R:Pos; IXTCB01376_R:Neg

value: IXTCB00363_R:CTRL; IXTCB00330_R:CTRL; IXTCB01511_R:Pos; IXTCB01445_R:Pos; IXTCB01376_R:Pos

value: IXTCB00363_R:CTRL; IXTCB00330_R:CTRL; IXTCB01511_R:Low; IXTCB01445_R:High; IXTCB01376_R:Low


title: Corpus_104

value: Corpus


title: KOBC4

value: Bone tissue

value: Male


title: G55-MixedSamples

description: IXTCB00363:FEMALE; IXTCB00330:FEMALE; IXTCB01511:FEMALE; IXTCB01445:MALE; IXTCB01376:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00363:CTRL; IXTCB00330:CTRL; IXTCB01511:RA; IXTCB01445:RA; IXTCB01376:RA

value: IXTCB00363:CTRL; IXTCB00330:CTRL; IXTCB01511:wk0; IXTCB01445:wk0; IXTCB01376:wk12

value: IXTCB00363:CTRL; IXTCB00330:CTRL; IXTCB01511:NON_RESP; IXTCB01445:MOD; IXTCB01376:GOOD

value: IXTCB00363:CTRL; IXTCB00330:CTRL; IXTCB01511:Etanercept; IXTCB01445:Adalimumab; IXTCB01376:Etanercept

value: IXTCB00363:CTRL; IXTCB00330:CTRL; IXTCB01511:Neg; IXTCB01445:Pos; IXTCB01376:Neg

value: IXTCB00363:CTRL; IXTCB00330:CTRL; IXTCB01511:Pos; IXTCB01445:Pos; IXTCB01376:Pos

value: IXTCB00363:CTRL; IXTCB00330:CTRL; IXTCB01511:Low; IXTCB01445:High; IXTCB01376:Low


title: KOBC3


title: Antrum_92

value: Antrum


title: Corpus_103


title: KOBL2

value: Ligature placement for 11 days


title: KOBC2


title: Antrum_91


title: G53-MixedSamples

description: IXTCB00006:MALE; IXTCB00039:FEMALE; IXTCB01333:FEMALE; IXTCB01365:FEMALE; IXTCB01363:FEMALE

value: IXTCB00006:CTRL; IXTCB00039:CTRL; IXTCB01333:RA; IXTCB01365:RA; IXTCB01363:RA

value: IXTCB00006:CTRL; IXTCB00039:CTRL; IXTCB01333:wk0; IXTCB01365:wk12; IXTCB01363:wk0

value: IXTCB00006:CTRL; IXTCB00039:CTRL; IXTCB01333:GOOD; IXTCB01365:GOOD; IXTCB01363:MOD

value: IXTCB00006:CTRL; IXTCB00039:CTRL; IXTCB01333:Certolizumab; IXTCB01365:Etanercept; IXTCB01363:Certolizumab

value: IXTCB00006:CTRL; IXTCB00039:CTRL; IXTCB01333:Pos; IXTCB01365:Neg; IXTCB01363:Pos

value: IXTCB00006:CTRL; IXTCB00039:CTRL; IXTCB01333:Pos; IXTCB01365:Pos; IXTCB01363:Pos

value: IXTCB00006:CTRL; IXTCB00039:CTRL; IXTCB01333:Low; IXTCB01365:Low; IXTCB01363:High


title: Antrum_90


title: G52-MixedSamples

description: IXTCB00441_R:FEMALE; IXTCB01440_R:MALE; IXTCB01458_R:FEMALE; IXTCB01540_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00441_R:CTRL; IXTCB01440_R:RA; IXTCB01458_R:RA; IXTCB01540_R:RA

value: IXTCB00441_R:CTRL; IXTCB01440_R:MOD; IXTCB01458_R:GOOD; IXTCB01540_R:NA

value: IXTCB00441_R:CTRL; IXTCB01440_R:Etanercept; IXTCB01458_R:Etanercept; IXTCB01540_R:Adalimumab

value: IXTCB00441_R:CTRL; IXTCB01440_R:Pos; IXTCB01458_R:Pos; IXTCB01540_R:Pos

value: IXTCB00441_R:CTRL; IXTCB01440_R:High; IXTCB01458_R:High; IXTCB01540_R:Low


title: KOBC1

value: Bone tissue

value: Male


title: MIN6 cells, high glucose and TMAO3

city: Beijing

first: lijuan

last: kong

state: 北京

address: 1 Xian Nong Tan Street

country: China

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts to obtain clean reads
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis  was performed using the DESeq2 R package (1.16.1).
Assembly: mm10
Supplementary files format and content: Microsoft Excel file includes FPKM values for each sample
Supplementary files format and content: Microsoft Excel file includes raw counts for each sample

extract_protocol:
Total RNA was extracted by Trizol according to the manufacturer's instructions. RNA degradation and contamination, RNA purity, and RNA integrity was assessed according to the manufacturer's instructions.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: mouse-derived insulin-secreting Beta-cell line

value: WT

value: high glucose and TMAO


title: Corpus_101

value: Corpus


title: G51-MixedSamples

description: IXTCB00441:FEMALE; IXTCB01440:MALE; IXTCB01458:FEMALE; IXTCB01540:FEMALE

value: IXTCB00441:CTRL; IXTCB01440:RA; IXTCB01458:RA; IXTCB01540:RA

value: IXTCB00441:CTRL; IXTCB01440:MOD; IXTCB01458:GOOD; IXTCB01540:NA

value: IXTCB00441:CTRL; IXTCB01440:Etanercept; IXTCB01458:Etanercept; IXTCB01540:Adalimumab

value: IXTCB00441:CTRL; IXTCB01440:Pos; IXTCB01458:Pos; IXTCB01540:Pos

value: IXTCB00441:CTRL; IXTCB01440:High; IXTCB01458:High; IXTCB01540:Low


title: KOBL1

value: Ligature placement for 11 days


title: Antrum_89

value: Antrum


title: Corpus_100


title: MIN6 cells, high glucose and TMAO2


title: G49-MixedSamples

description: IXTCB00339:FEMALE; IXTCB01446:MALE; IXTCB01499:FEMALE; IXTCB01462:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00339:CTRL; IXTCB01446:RA; IXTCB01499:RA; IXTCB01462:RA

value: IXTCB00339:CTRL; IXTCB01446:MOD; IXTCB01499:GOOD; IXTCB01462:GOOD

value: IXTCB00339:CTRL; IXTCB01446:Adalimumab; IXTCB01499:Golimumab; IXTCB01462:Certolizumab

value: IXTCB00339:CTRL; IXTCB01446:Pos; IXTCB01499:Pos; IXTCB01462:Neg

value: IXTCB00339:CTRL; IXTCB01446:Pos; IXTCB01499:Pos; IXTCB01462:Pos

value: IXTCB00339:CTRL; IXTCB01446:High; IXTCB01499:Low; IXTCB01462:Low


title: MIN6 cells, high glucose and TMAO1

value: mouse-derived insulin-secreting Beta-cell line

value: WT

value: high glucose and TMAO


title: Antrum_86


title: MIN6 cells, high glucose and vehicle3

value: high glucose and vehicle


title: Corpus_97

value: Corpus


title: Corpus_98


title: G54-MixedSamples

description: IXTCB00006_R:MALE; IXTCB00039_R:FEMALE; IXTCB01333_R:FEMALE; IXTCB01365_R:FEMALE; IXTCB01363_R:FEMALE

value: IXTCB00006_R:CTRL; IXTCB00039_R:CTRL; IXTCB01333_R:RA; IXTCB01365_R:RA; IXTCB01363_R:RA

value: IXTCB00006_R:CTRL; IXTCB00039_R:CTRL; IXTCB01333_R:wk0; IXTCB01365_R:wk12; IXTCB01363_R:wk0

value: IXTCB00006_R:CTRL; IXTCB00039_R:CTRL; IXTCB01333_R:GOOD; IXTCB01365_R:GOOD; IXTCB01363_R:MOD

value: IXTCB00006_R:CTRL; IXTCB00039_R:CTRL; IXTCB01333_R:Certolizumab; IXTCB01365_R:Etanercept; IXTCB01363_R:Certolizumab

value: IXTCB00006_R:CTRL; IXTCB00039_R:CTRL; IXTCB01333_R:Pos; IXTCB01365_R:Neg; IXTCB01363_R:Pos

value: IXTCB00006_R:CTRL; IXTCB00039_R:CTRL; IXTCB01333_R:Pos; IXTCB01365_R:Pos; IXTCB01363_R:Pos

value: IXTCB00006_R:CTRL; IXTCB00039_R:CTRL; IXTCB01333_R:Low; IXTCB01365_R:Low; IXTCB01363_R:High


title: Corpus_102


title: Corpus_96


title: MIN6 cells, high glucose and vehicle2


title: Corpus_95


title: G46-MixedSamples

description: IXTCB00252_R:MALE; IXTCB00291_R:MALE; IXTCB01452_R:FEMALE; IXTCB01396_R:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00252_R:CTRL; IXTCB00291_R:CTRL; IXTCB01452_R:RA; IXTCB01396_R:RA

value: IXTCB00252_R:CTRL; IXTCB00291_R:CTRL; IXTCB01452_R:wk12; IXTCB01396_R:wk0

value: IXTCB00252_R:CTRL; IXTCB00291_R:CTRL; IXTCB01452_R:NON_RESP; IXTCB01396_R:GOOD

value: IXTCB00252_R:CTRL; IXTCB00291_R:CTRL; IXTCB01452_R:Etanercept; IXTCB01396_R:Certolizumab

value: IXTCB00252_R:CTRL; IXTCB00291_R:CTRL; IXTCB01452_R:Neg; IXTCB01396_R:Pos

value: IXTCB00252_R:CTRL; IXTCB00291_R:CTRL; IXTCB01452_R:Pos; IXTCB01396_R:Pos

value: IXTCB00252_R:CTRL; IXTCB00291_R:CTRL; IXTCB01452_R:High; IXTCB01396_R:High


title: MIN6 cells, high glucose and vehicle1

value: mouse-derived insulin-secreting Beta-cell line

value: WT

value: high glucose and vehicle


title: Antrum_88

value: Antrum


title: Corpus_93

value: Corpus


title: G47-MixedSamples

description: IXTCB00081:MALE; IXTCB00102:MALE; IXTCB01425:FEMALE; IXTCB01343:FEMALE; IXTCB01406:FEMALE

value: IXTCB00081:CTRL; IXTCB00102:CTRL; IXTCB01425:RA; IXTCB01343:RA; IXTCB01406:RA

value: IXTCB00081:CTRL; IXTCB00102:CTRL; IXTCB01425:wk0; IXTCB01343:wk12; IXTCB01406:wk12

value: IXTCB00081:CTRL; IXTCB00102:CTRL; IXTCB01425:NON_RESP; IXTCB01343:GOOD; IXTCB01406:MOD

value: IXTCB00081:CTRL; IXTCB00102:CTRL; IXTCB01425:Etanercept; IXTCB01343:Etanercept; IXTCB01406:Etanercept

value: IXTCB00081:CTRL; IXTCB00102:CTRL; IXTCB01425:Neg; IXTCB01343:Neg; IXTCB01406:Pos

value: IXTCB00081:CTRL; IXTCB00102:CTRL; IXTCB01425:High; IXTCB01343:Low; IXTCB01406:Low


title: Corpus_94


title: MIN6 cells, low glucose and TMAO3

value: low glucose and TMAO


title: G48-MixedSamples

description: IXTCB00081_R:MALE; IXTCB00102_R:MALE; IXTCB01425_R:FEMALE; IXTCB01343_R:FEMALE; IXTCB01406_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00081_R:CTRL; IXTCB00102_R:CTRL; IXTCB01425_R:RA; IXTCB01343_R:RA; IXTCB01406_R:RA

value: IXTCB00081_R:CTRL; IXTCB00102_R:CTRL; IXTCB01425_R:wk0; IXTCB01343_R:wk12; IXTCB01406_R:wk12

value: IXTCB00081_R:CTRL; IXTCB00102_R:CTRL; IXTCB01425_R:NON_RESP; IXTCB01343_R:GOOD; IXTCB01406_R:MOD

value: IXTCB00081_R:CTRL; IXTCB00102_R:CTRL; IXTCB01425_R:Etanercept; IXTCB01343_R:Etanercept; IXTCB01406_R:Etanercept

value: IXTCB00081_R:CTRL; IXTCB00102_R:CTRL; IXTCB01425_R:Neg; IXTCB01343_R:Neg; IXTCB01406_R:Pos

value: IXTCB00081_R:CTRL; IXTCB00102_R:CTRL; IXTCB01425_R:High; IXTCB01343_R:Low; IXTCB01406_R:Low


title: Corpus_92


title: Corpus_99


title: Antrum_85

value: Antrum


title: G50-MixedSamples

description: IXTCB00339_R:FEMALE; IXTCB01446_R:MALE; IXTCB01499_R:FEMALE; IXTCB01462_R:FEMALE

value: IXTCB00339_R:CTRL; IXTCB01446_R:RA; IXTCB01499_R:RA; IXTCB01462_R:RA

value: IXTCB00339_R:CTRL; IXTCB01446_R:MOD; IXTCB01499_R:GOOD; IXTCB01462_R:GOOD

value: IXTCB00339_R:CTRL; IXTCB01446_R:Adalimumab; IXTCB01499_R:Golimumab; IXTCB01462_R:Certolizumab

value: IXTCB00339_R:CTRL; IXTCB01446_R:Pos; IXTCB01499_R:Pos; IXTCB01462_R:Neg

value: IXTCB00339_R:CTRL; IXTCB01446_R:Pos; IXTCB01499_R:Pos; IXTCB01462_R:Pos

value: IXTCB00339_R:CTRL; IXTCB01446_R:High; IXTCB01499_R:Low; IXTCB01462_R:Low


title: Corpus_91

value: Corpus


title: MIN6 cells, low glucose and TMAO2

value: mouse-derived insulin-secreting Beta-cell line

value: WT

value: low glucose and TMAO


title: G45-MixedSamples

description: IXTCB00252:MALE; IXTCB00291:MALE; IXTCB01452:FEMALE; IXTCB01396:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00252:CTRL; IXTCB00291:CTRL; IXTCB01452:RA; IXTCB01396:RA

value: IXTCB00252:CTRL; IXTCB00291:CTRL; IXTCB01452:wk12; IXTCB01396:wk0

value: IXTCB00252:CTRL; IXTCB00291:CTRL; IXTCB01452:NON_RESP; IXTCB01396:GOOD

value: IXTCB00252:CTRL; IXTCB00291:CTRL; IXTCB01452:Etanercept; IXTCB01396:Certolizumab

value: IXTCB00252:CTRL; IXTCB00291:CTRL; IXTCB01452:Neg; IXTCB01396:Pos

value: IXTCB00252:CTRL; IXTCB00291:CTRL; IXTCB01452:Pos; IXTCB01396:Pos

value: IXTCB00252:CTRL; IXTCB00291:CTRL; IXTCB01452:High; IXTCB01396:High


title: Antrum_87

value: Antrum


title: MIN6 cells, low glucose and TMAO1


title: Corpus_90


title: Antrum_84


title: Corpus_89


title: G44-MixedSamples

description: IXTCB00267_R:FEMALE; IXTCB00273_R:FEMALE; IXTCB01435_R:FEMALE; IXTCB01409_R:FEMALE; IXTCB01515_R:FEMALE

value: IXTCB00267_R:CTRL; IXTCB00273_R:CTRL; IXTCB01435_R:RA; IXTCB01409_R:RA; IXTCB01515_R:RA

value: IXTCB00267_R:CTRL; IXTCB00273_R:CTRL; IXTCB01435_R:wk0; IXTCB01409_R:wk0; IXTCB01515_R:wk12

value: IXTCB00267_R:CTRL; IXTCB00273_R:CTRL; IXTCB01435_R:NON_RESP; IXTCB01409_R:MOD; IXTCB01515_R:GOOD

value: IXTCB00267_R:CTRL; IXTCB00273_R:CTRL; IXTCB01435_R:Certolizumab; IXTCB01409_R:Certolizumab; IXTCB01515_R:Adalimumab

value: IXTCB00267_R:CTRL; IXTCB00273_R:CTRL; IXTCB01435_R:Pos; IXTCB01409_R:Neg; IXTCB01515_R:NA

value: IXTCB00267_R:CTRL; IXTCB00273_R:CTRL; IXTCB01435_R:Pos; IXTCB01409_R:Pos; IXTCB01515_R:Neg

value: IXTCB00267_R:CTRL; IXTCB00273_R:CTRL; IXTCB01435_R:Low; IXTCB01409_R:High; IXTCB01515_R:Low


title: Corpus_88

value: Corpus


title: Antrum_82


title: Antrum_83


title: G42-MixedSamples

description: IXTCB00462_R:FEMALE; IXTCB00429_R:FEMALE; IXTCB01449_R:FEMALE; IXTCB01522_R:FEMALE; IXTCB01506_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00462_R:CTRL; IXTCB00429_R:CTRL; IXTCB01449_R:RA; IXTCB01522_R:RA; IXTCB01506_R:RA

value: IXTCB00462_R:CTRL; IXTCB00429_R:CTRL; IXTCB01449_R:wk0; IXTCB01522_R:wk0; IXTCB01506_R:wk0

value: IXTCB00462_R:CTRL; IXTCB00429_R:CTRL; IXTCB01449_R:GOOD; IXTCB01522_R:MOD; IXTCB01506_R:GOOD

value: IXTCB00462_R:CTRL; IXTCB00429_R:CTRL; IXTCB01449_R:Adalimumab; IXTCB01522_R:Adalimumab; IXTCB01506_R:Adalimumab

value: IXTCB00462_R:CTRL; IXTCB00429_R:CTRL; IXTCB01449_R:Neg; IXTCB01522_R:Pos; IXTCB01506_R:Pos

value: IXTCB00462_R:CTRL; IXTCB00429_R:CTRL; IXTCB01449_R:High; IXTCB01522_R:Low; IXTCB01506_R:High


title: MIN6 cells, low glucose and vehicle1

value: mouse-derived insulin-secreting Beta-cell line

value: WT

value: low glucose and vehicle


title: MIN6 cells, low glucose and vehicle2


title: G41-MixedSamples

description: IXTCB00462:FEMALE; IXTCB00429:FEMALE; IXTCB01449:FEMALE; IXTCB01522:FEMALE; IXTCB01506:FEMALE

value: IXTCB00462:CTRL; IXTCB00429:CTRL; IXTCB01449:RA; IXTCB01522:RA; IXTCB01506:RA

value: IXTCB00462:CTRL; IXTCB00429:CTRL; IXTCB01449:wk0; IXTCB01522:wk0; IXTCB01506:wk0

value: IXTCB00462:CTRL; IXTCB00429:CTRL; IXTCB01449:GOOD; IXTCB01522:MOD; IXTCB01506:GOOD

value: IXTCB00462:CTRL; IXTCB00429:CTRL; IXTCB01449:Adalimumab; IXTCB01522:Adalimumab; IXTCB01506:Adalimumab

value: IXTCB00462:CTRL; IXTCB00429:CTRL; IXTCB01449:Neg; IXTCB01522:Pos; IXTCB01506:Pos

value: IXTCB00462:CTRL; IXTCB00429:CTRL; IXTCB01449:High; IXTCB01522:Low; IXTCB01506:High


title: Antrum_81

value: Antrum


title: G40-MixedSamples

description: IXTCB00282_R:MALE; IXTCB00213_R:FEMALE; IXTCB01422_R:FEMALE; IXTCB01472_R:MALE; IXTCB01477_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00282_R:CTRL; IXTCB00213_R:CTRL; IXTCB01422_R:RA; IXTCB01472_R:RA; IXTCB01477_R:RA

value: IXTCB00282_R:CTRL; IXTCB00213_R:CTRL; IXTCB01422_R:NON_RESP; IXTCB01472_R:MOD; IXTCB01477_R:MOD

value: IXTCB00282_R:CTRL; IXTCB00213_R:CTRL; IXTCB01422_R:Certolizumab; IXTCB01472_R:Etanercept; IXTCB01477_R:Etanercept

value: IXTCB00282_R:CTRL; IXTCB00213_R:CTRL; IXTCB01422_R:Pos; IXTCB01472_R:Pos; IXTCB01477_R:Pos

value: IXTCB00282_R:CTRL; IXTCB00213_R:CTRL; IXTCB01422_R:High; IXTCB01472_R:High; IXTCB01477_R:High


title: Corpus_87

value: Corpus


title: Antrum_80


title: DKO, female, 7w (rep 6)

city: New Haven

first: Stefan

last: Somlo

state: CT

address: 333 Cedar Street

institute: Yale University

description:
3257FM6
ribosomal pulldown mRNA

data_processing:
Raw TRAPSeq fastq files were processed using fastp tool (version 0.20.0)
Cleaned reads were aligned using STAR (version 2.7.9)
Expression quantification for aligned reads was performed using featureCounts (version 2.0.0)
an expression threshold of >6 read counts in at least 20% of samples for each sex; genes not meeting this expression threshold were eliminated from downstream analyses
The filtered read counts matrix was normalized by the transcripts per million (TPM) method
Assembly: mouse reference genome gencode version GRCm38.p6 with vM25 gene annotation
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: TRAPseq, DKO, female, 7w (P49)

extract_protocol:
TRAP was performed largely by the method described by PMID: 24810037 with a few mondifications
The sequencing library was prepared using the ribosomal depletion method (KAPA RNA HyperPrep Kit with RiboErase, Roche)
sequencing was run on Illumina’s NovaSeq 6000 platform using 150 bp paired end reads with read depth 100 million reads per sample

value: Kidney

value: DKO, Pkd1fl/fl; Kif3afl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Corpus_86


title: Antrum_78


title: DKO, female, 7w (rep 5)

description:
3116FM6
ribosomal pulldown mRNA


title: Corpus_85


title: G39-MixedSamples

description: IXTCB00282:MALE; IXTCB00213:FEMALE; IXTCB01422:FEMALE; IXTCB01472:MALE; IXTCB01477:FEMALE

value: IXTCB00282:CTRL; IXTCB00213:CTRL; IXTCB01422:RA; IXTCB01472:RA; IXTCB01477:RA

value: IXTCB00282:CTRL; IXTCB00213:CTRL; IXTCB01422:NON_RESP; IXTCB01472:MOD; IXTCB01477:MOD

value: IXTCB00282:CTRL; IXTCB00213:CTRL; IXTCB01422:Certolizumab; IXTCB01472:Etanercept; IXTCB01477:Etanercept

value: IXTCB00282:CTRL; IXTCB00213:CTRL; IXTCB01422:Pos; IXTCB01472:Pos; IXTCB01477:Pos

value: IXTCB00282:CTRL; IXTCB00213:CTRL; IXTCB01422:High; IXTCB01472:High; IXTCB01477:High


title: Antrum_77


title: DKO, female, 7w (rep 4)

description:
3010FM6
ribosomal pulldown mRNA


title: G37-MixedSamples

description: IXTCB00018:MALE; IXTCB00087:MALE; IXTCB01371:FEMALE; IXTCB01349:FEMALE; IXTCB01414:MALE

value: IXTCB00018:CTRL; IXTCB00087:CTRL; IXTCB01371:RA; IXTCB01349:RA; IXTCB01414:RA

value: IXTCB00018:CTRL; IXTCB00087:CTRL; IXTCB01371:wk12; IXTCB01349:wk0; IXTCB01414:wk0

value: IXTCB00018:CTRL; IXTCB00087:CTRL; IXTCB01371:NON_RESP; IXTCB01349:NON_RESP; IXTCB01414:GOOD

value: IXTCB00018:CTRL; IXTCB00087:CTRL; IXTCB01371:Etanercept; IXTCB01349:Etanercept; IXTCB01414:Adalimumab

value: IXTCB00018:CTRL; IXTCB00087:CTRL; IXTCB01371:Pos; IXTCB01349:Pos; IXTCB01414:Pos

value: IXTCB00018:CTRL; IXTCB00087:CTRL; IXTCB01371:Pos; IXTCB01349:Neg; IXTCB01414:Pos

value: IXTCB00018:CTRL; IXTCB00087:CTRL; IXTCB01371:High; IXTCB01349:High; IXTCB01414:Low


title: G38-MixedSamples

description: IXTCB00018_R:MALE; IXTCB00087_R:MALE; IXTCB01371_R:FEMALE; IXTCB01349_R:FEMALE; IXTCB01414_R:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00018_R:CTRL; IXTCB00087_R:CTRL; IXTCB01371_R:RA; IXTCB01349_R:RA; IXTCB01414_R:RA

value: IXTCB00018_R:CTRL; IXTCB00087_R:CTRL; IXTCB01371_R:wk12; IXTCB01349_R:wk0; IXTCB01414_R:wk0

value: IXTCB00018_R:CTRL; IXTCB00087_R:CTRL; IXTCB01371_R:NON_RESP; IXTCB01349_R:NON_RESP; IXTCB01414_R:GOOD

value: IXTCB00018_R:CTRL; IXTCB00087_R:CTRL; IXTCB01371_R:Etanercept; IXTCB01349_R:Etanercept; IXTCB01414_R:Adalimumab

value: IXTCB00018_R:CTRL; IXTCB00087_R:CTRL; IXTCB01371_R:Pos; IXTCB01349_R:Pos; IXTCB01414_R:Pos

value: IXTCB00018_R:CTRL; IXTCB00087_R:CTRL; IXTCB01371_R:Pos; IXTCB01349_R:Neg; IXTCB01414_R:Pos

value: IXTCB00018_R:CTRL; IXTCB00087_R:CTRL; IXTCB01371_R:High; IXTCB01349_R:High; IXTCB01414_R:Low


title: DKO, female, 7w (rep 3)

description:
3009FM6
ribosomal pulldown mRNA

value: Kidney

value: DKO, Pkd1fl/fl; Kif3afl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Corpus_83

value: Corpus


title: G43-MixedSamples

description: IXTCB00267:FEMALE; IXTCB00273:FEMALE; IXTCB01435:FEMALE; IXTCB01409:FEMALE; IXTCB01515:FEMALE

value: IXTCB00267:CTRL; IXTCB00273:CTRL; IXTCB01435:RA; IXTCB01409:RA; IXTCB01515:RA

value: IXTCB00267:CTRL; IXTCB00273:CTRL; IXTCB01435:wk0; IXTCB01409:wk0; IXTCB01515:wk12

value: IXTCB00267:CTRL; IXTCB00273:CTRL; IXTCB01435:NON_RESP; IXTCB01409:MOD; IXTCB01515:GOOD

value: IXTCB00267:CTRL; IXTCB00273:CTRL; IXTCB01435:Certolizumab; IXTCB01409:Certolizumab; IXTCB01515:Adalimumab

value: IXTCB00267:CTRL; IXTCB00273:CTRL; IXTCB01435:Pos; IXTCB01409:Neg; IXTCB01515:NA

value: IXTCB00267:CTRL; IXTCB00273:CTRL; IXTCB01435:Pos; IXTCB01409:Pos; IXTCB01515:Neg

value: IXTCB00267:CTRL; IXTCB00273:CTRL; IXTCB01435:Low; IXTCB01409:High; IXTCB01515:Low


title: Corpus_81


title: Corpus_82


title: Corpus_84


title: Antrum_79

value: Antrum


title: G36-MixedSamples

description: IXTCB00054_R:FEMALE; IXTCB00009_R:MALE; IXTCB01383_R:FEMALE; IXTCB01424_R:FEMALE; IXTCB01386_R:MALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00054_R:CTRL; IXTCB00009_R:CTRL; IXTCB01383_R:RA; IXTCB01424_R:RA; IXTCB01386_R:RA

value: IXTCB00054_R:CTRL; IXTCB00009_R:CTRL; IXTCB01383_R:wk12; IXTCB01424_R:wk0; IXTCB01386_R:wk12

value: IXTCB00054_R:CTRL; IXTCB00009_R:CTRL; IXTCB01383_R:NON_RESP; IXTCB01424_R:GOOD; IXTCB01386_R:GOOD

value: IXTCB00054_R:CTRL; IXTCB00009_R:CTRL; IXTCB01383_R:Etanercept; IXTCB01424_R:Etanercept; IXTCB01386_R:Adalimumab

value: IXTCB00054_R:CTRL; IXTCB00009_R:CTRL; IXTCB01383_R:Pos; IXTCB01424_R:Pos; IXTCB01386_R:Pos

value: IXTCB00054_R:CTRL; IXTCB00009_R:CTRL; IXTCB01383_R:Neg; IXTCB01424_R:Pos; IXTCB01386_R:Pos

value: IXTCB00054_R:CTRL; IXTCB00009_R:CTRL; IXTCB01383_R:High; IXTCB01424_R:High; IXTCB01386_R:Low


title: G35-MixedSamples

description: IXTCB00054:FEMALE; IXTCB00009:MALE; IXTCB01383:FEMALE; IXTCB01424:FEMALE; IXTCB01386:MALE

value: IXTCB00054:CTRL; IXTCB00009:CTRL; IXTCB01383:RA; IXTCB01424:RA; IXTCB01386:RA

value: IXTCB00054:CTRL; IXTCB00009:CTRL; IXTCB01383:wk12; IXTCB01424:wk0; IXTCB01386:wk12

value: IXTCB00054:CTRL; IXTCB00009:CTRL; IXTCB01383:NON_RESP; IXTCB01424:GOOD; IXTCB01386:GOOD

value: IXTCB00054:CTRL; IXTCB00009:CTRL; IXTCB01383:Etanercept; IXTCB01424:Etanercept; IXTCB01386:Adalimumab

value: IXTCB00054:CTRL; IXTCB00009:CTRL; IXTCB01383:Pos; IXTCB01424:Pos; IXTCB01386:Pos

value: IXTCB00054:CTRL; IXTCB00009:CTRL; IXTCB01383:Neg; IXTCB01424:Pos; IXTCB01386:Pos

value: IXTCB00054:CTRL; IXTCB00009:CTRL; IXTCB01383:High; IXTCB01424:High; IXTCB01386:Low


title: Antrum_75

value: Antrum


title: DKO, female, 7w (rep 1)

description:
2717FM6
ribosomal pulldown mRNA

value: Kidney

value: DKO, Pkd1fl/fl; Kif3afl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Corpus_80

value: Corpus


title: SKO, female, 7w (rep 8)

description:
2460FM3
ribosomal pulldown mRNA

source_name: TRAPseq, SKO, female, 7w (P49)

value: SKO, Pkd1fl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: G34-MixedSamples

description: IXTCB00084_R:FEMALE; IXTCB00183_R:MALE; IXTCB01381_R:FEMALE; IXTCB01421_R:FEMALE; IXTCB01420_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00084_R:CTRL; IXTCB00183_R:CTRL; IXTCB01381_R:RA; IXTCB01421_R:RA; IXTCB01420_R:RA

value: IXTCB00084_R:CTRL; IXTCB00183_R:CTRL; IXTCB01381_R:wk12; IXTCB01421_R:wk0; IXTCB01420_R:wk0

value: IXTCB00084_R:CTRL; IXTCB00183_R:CTRL; IXTCB01381_R:GOOD; IXTCB01421_R:GOOD; IXTCB01420_R:MOD

value: IXTCB00084_R:CTRL; IXTCB00183_R:CTRL; IXTCB01381_R:Etanercept; IXTCB01421_R:Etanercept; IXTCB01420_R:Etanercept

value: IXTCB00084_R:CTRL; IXTCB00183_R:CTRL; IXTCB01381_R:Pos; IXTCB01421_R:Pos; IXTCB01420_R:Pos

value: IXTCB00084_R:CTRL; IXTCB00183_R:CTRL; IXTCB01381_R:Pos; IXTCB01421_R:Neg; IXTCB01420_R:Pos

value: IXTCB00084_R:CTRL; IXTCB00183_R:CTRL; IXTCB01381_R:Low; IXTCB01421_R:High; IXTCB01420_R:Low


title: Corpus_79


title: Corpus_78


title: Antrum_73


title: SKO, female, 7w (rep 7)

description:
2974FM3
ribosomal pulldown mRNA


title: Antrum_74


title: G33-MixedSamples

description: IXTCB00084:FEMALE; IXTCB00183:MALE; IXTCB01381:FEMALE; IXTCB01421:FEMALE; IXTCB01420:FEMALE

value: IXTCB00084:CTRL; IXTCB00183:CTRL; IXTCB01381:RA; IXTCB01421:RA; IXTCB01420:RA

value: IXTCB00084:CTRL; IXTCB00183:CTRL; IXTCB01381:wk12; IXTCB01421:wk0; IXTCB01420:wk0

value: IXTCB00084:CTRL; IXTCB00183:CTRL; IXTCB01381:GOOD; IXTCB01421:GOOD; IXTCB01420:MOD

value: IXTCB00084:CTRL; IXTCB00183:CTRL; IXTCB01381:Etanercept; IXTCB01421:Etanercept; IXTCB01420:Etanercept

value: IXTCB00084:CTRL; IXTCB00183:CTRL; IXTCB01381:Pos; IXTCB01421:Pos; IXTCB01420:Pos

value: IXTCB00084:CTRL; IXTCB00183:CTRL; IXTCB01381:Pos; IXTCB01421:Neg; IXTCB01420:Pos

value: IXTCB00084:CTRL; IXTCB00183:CTRL; IXTCB01381:Low; IXTCB01421:High; IXTCB01420:Low


title: Corpus_77

value: Corpus


title: SKO, female, 7w (rep 6)

description:
2775FM3
ribosomal pulldown mRNA

value: Kidney

value: SKO, Pkd1fl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Antrum_72

value: Antrum


title: G32-MixedSamples

description: IXTCB00105_R:FEMALE; IXTCB00195_R:FEMALE; IXTCB01337_R:FEMALE; IXTCB01347_R:FEMALE; IXTCB01432_R:FEMALE

value: Peripheral whole blood

value: pooled male and female

value: IXTCB00105_R:CTRL; IXTCB00195_R:CTRL; IXTCB01337_R:RA; IXTCB01347_R:RA; IXTCB01432_R:RA

value: IXTCB00105_R:CTRL; IXTCB00195_R:CTRL; IXTCB01337_R:wk12; IXTCB01347_R:wk12; IXTCB01432_R:wk0

value: IXTCB00105_R:CTRL; IXTCB00195_R:CTRL; IXTCB01337_R:NON_RESP; IXTCB01347_R:MOD; IXTCB01432_R:MOD

value: IXTCB00105_R:CTRL; IXTCB00195_R:CTRL; IXTCB01337_R:Golimumab; IXTCB01347_R:Golimumab; IXTCB01432_R:Certolizumab

value: IXTCB00105_R:CTRL; IXTCB00195_R:CTRL; IXTCB01337_R:Neg; IXTCB01347_R:Pos; IXTCB01432_R:Pos

value: IXTCB00105_R:CTRL; IXTCB00195_R:CTRL; IXTCB01337_R:Pos; IXTCB01347_R:Pos; IXTCB01432_R:Pos

value: IXTCB00105_R:CTRL; IXTCB00195_R:CTRL; IXTCB01337_R:High; IXTCB01347_R:High; IXTCB01432_R:High


title: DKO, female, 7w (rep 2)

description:
3167FM6
ribosomal pulldown mRNA

value: DKO, Pkd1fl/fl; Kif3afl/fl; RosaEGFP-Rpl10a; Pax8rtTA; TetOCre


title: Antrum_76


title: Antrum_71


title: Corpus_76


title: MIN6 cells, low glucose and vehicle3

value: mouse-derived insulin-secreting Beta-cell line

value: WT

value: low glucose and vehicle


title: SKO, female, 7w (rep 5)

description:
2516FM3
ribosomal pulldown mRNA


title: SKO, female, 7w (rep 4)

description:
2513FM3
ribosomal pulldown mRNA


title: Corpus_75

value: Corpus