title: GS2

status: Public on Jun 01 2023

city: Shanghai

first: Hanqing

last: Yu

state: Shanghai

address: No. 301 Middle Yanchang Road

country: China

institute: Shanghai Tenth People's Hospital

description:
10x Genomics
GS2_barcodes.tsv
GS2_genes.tsv
GS2_matrix.mtx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: advanced

extract_protocol:
2ml peripheral blood from each patient or healthy volunteer in EDTA anticoagulant tube was diluted with 2ml 1×PBS. Equal volume Ficoll lymphocyte separation solution (solarbio, P4350) was added into 50ml centrifuge tube. The diluted blood was slowly spread onto the lymphocyte separation solution. Centrifugation was conducted at 20 ℃ with the horizontal rotor at 2000rpm for 20min, with break set to 0. The intermediate white membrane layer cells (PBMCs) were carefully extracted into 15ml centrifuge tube. The white membrane layer cells were washed with 10ml 1×PBS and were centrifuged with the horizontal rotor at 300g for 10min. The supernatant was discarded, and the cells were suspended with 5ml 1×PBS. The suspension was centrifuged at 300g for 10min and washed twice. The supernatant was discarded again, and the cells were suspended with 1ml RPMI 1640 medium (Conring,Art.10-040-CVR) added with 0.04%BSA. Luna cell counter or Trypan blue staining was used to count single cell suspension concentration and cell viability.
Single-cell RNA sequencing libraries were constructed by using Chromium Single cell 3’ Reagent v2 Kits in accordance with the manufacturer’s protocol. PBMC suspensions were loaded on the Chromium Single Cell Controller Instrument (10×Genomics) with partitioning oil, reverse transcription (RT) reagents, and a collection of gel beads containing 3,500,000 unique 10 × barcodes. Single cell gel beads were generated in emulsions (GEMs). Transcription reactions were performed to generate barcoded full-length cDNA. Emulsions were disrupted by the recovery agent and barcoded-cDNA was purified with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). cDNAs were amplified with appropriate cycles (98°C for 3 minutes; cycled 12 times: 98°C for 15 second, 63°C for 20 second, and 72°C for 1 minute; 72°C for 1 minute; end at 4°C) and cleaned up with the SPRIselect Reagent Kit (Beckman Coulter, USA). The amplified cDNA received fragmentation, end-repair, polyA-tailing, index adaptor ligation. PCR amplification was conducted by sample indexing primers (98°C for 45 sec; 14-16 cycles of 98°C for 20 sec, 54°C for 30 sec, 72°C for 20 sec; 72°C for 1 min; end at 4°C) and double-sided size selected with SPRIselect beads. High-throughput sequencing was performed on the Illumina sequencing platform (Illumina Nova 6000) and 150 bp paired-end reads were generated.

value: blood

value: PBMCs

tag: disease

value: advanced gout remission


title: GR2

type: SRA

description:
10x Genomics
GR2_barcodes.tsv
GR2_genes.tsv
GR2_matrix.mtx

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

source_name: intercritical

tag: tissue

tag: cell type

value: gout remission patient


title: GS3

description:
10x Genomics
GS3_barcodes.tsv
GS3_genes.tsv
GS3_matrix.mtx


title: GS1

description:
10x Genomics
GS1_barcodes.tsv
GS1_genes.tsv
GS1_matrix.mtx


title: GR3

description:
10x Genomics
GR3_barcodes.tsv
GR3_genes.tsv
GR3_matrix.mtx


title: GR1

description:
10x Genomics
GR1_barcodes.tsv
GR1_genes.tsv
GR1_matrix.mtx


title: HUTU80-CTN2P

status: Public on Jul 01 2023

city: Amsterdam

first: Nicolas

last: Léveillé

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description: count.txt

library_source: transcriptomic

data_processing:
library strategy: GRO-seq
GROseq data was analysed by mapping reads to the human genome and quantifying the expression of annotated coding genes and lncR NAs as well as performing de novo detection of enhancer RNAs (eRNAs)
Assembly: hg19
Supplementary files format and content: For RNA-seq data we used Hisat2 (2.0.4) for alignment and Subread (1.6.4) for identifying gene counts (Liao et al., 2014; Pertea et al., 2016). For the GRO-seq datawe used NRSA (Wang et al., 2018)

extract_protocol:
For RNA sequencing, total RNA was isolated using Trizol-Chloroform extraction (see section RNA isolation). RNA integrity was assessed with the Tapestation RNA ScreenTape Assay (Agilent Technologies).
libraries were prepared using the KAPA mRNA Hyperprep with RiboErase (Roche) according to manufacturer’s recommendation from 1 ug total RNA. Barcoded samples were multiplexed sequenced using single-end 50 bp reads on the Illumina HiSeq4000 platform.

tag: strain

tag: treatment

value: β-catenin knockdown


title: HUTU80-CTN1P

description: count.txt


title: Con2

description:
10x Genomics
Con2_barcodes.tsv
Con2_genes.tsv
Con2_matrix.mtx

source_name: healthy control

value: healthy


title: GFP over-expression [Xtuna-4_S16_L001]

status: Public on May 31 2023

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

country: USA

institute: NCSU

data_processing:
Illumina Casava1.7 software used for basecalling.
Data analysis was performed in consultation with Bioinformatics Core at NCSU Center for Human Health and the Environment. An average ~28.5 million paired-end raw RNAseq data were generated for each replicate. The quality of sequenced data was assessed using fastqc application, and 12 poor-quality bases were trimmed from the 5’-end. The remaining good-quality reads were aligned to the Human reference genome (hg38) downloaded from the Ensembl database using STAR aligner. Per-gene counts of uniquely mapped reads were calculated for each replicate using htseq-count script from the HTSeq python package. The count matrix was imported to R statistical computing environment for further analysis. Initially, genes that have no count in most of the replicate samples were discarded. The remaining count data were normalized for sequencing depth and distortion, and dispersion was estimated using the DESeq2 Bioconductor package in the R statistical computing environment. We fitted a linear model using the treatment levels, and differentially expressed genes were identified after applying multiple testing corrections using the Benjamini-Hjockberg procedure. We conducted individual analyses of the paired experiments, comparing Tuna and GFP over-expression as well as 0 micromolar and 5 micromolar CdCl2 treatments.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Jeg-3 human choriocarcinoma cell line

extract_protocol:
RNA from Jeg-3 cells was isolated via NucleoSpin RNA kit (Macherey-Nagel).
cDNA libraries for Illumina sequencing were constructed via the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) according to the manufacturer’s protocol.
NovaSeq S4, utilizing a 150x2 bp paired end S4 sequencing

treatment_protocol: Cells were seeded in 6-well plates for 24 hours at 4x105 cells/well until reaching ~80% confluency. Expression of GFP (control) or Tuna was achieved by transfecting cells with 3.5 μg of pcopGFP or pcopGFP-mTuna using Lipofectamine 3000 according to the manufacturer’s protocol (ThermoFisher). pcopGFP-mTuna was created by inserting the mouse Tuna sequence into the multiple cloning site (MCS) of pCDH-CMV-MCS-EF1α-GreenPuro Cloning and Expression Lentivector (System Biosciences). To remove the Tuna sequence and generate the pcopGFP control vector, the pcopGFP-mTuna construct was cut at the EcoRI and BamHI restriction sites, blunted with T4 DNA polymerase and ligated with T4 DNA ligase (New England Biolabs). Alternatively, cells were seeded in 6-well plates for 24 hours at 4x105 cells/well until reaching ~80% confluency. Cells were starved with serum free media for 24 hours at which point serum free media was aspirated, cells were washed in PBS, and exposed to 0 or 5.0 µM concentrations of CdCl2 in serum free media. Cells were collected after 24 hours of exposure.

tag: cell line

value: human choriocarcinoma cell line

value: Transient transfection with GFP expression construct


title: HT55-GFP2P

description: count.txt


title: GFP over-expression [Xtuna-3_S15_L001]


title: GFP over-expression [Xtuna-2_S14_L001]


title: GFP over-expression [Xtuna-1_S13_L001]


title: Tuna over-expression [Tuna-4_S4_L001]

value: Transient transfection with Tuna expression construct


title: Tuna over-expression [Tuna-3_S3_L001]


title: Tuna over-expression [Tuna-2_S2_L001]


title: Tuna over-expression [Tuna-1_S1_L001]


title: 0 micromolar CdCl2 [Cnt-1_S9_L001]

value: 0 micromolar CdCl2 in media


title: 0 micromolar CdCl2 [Cnt-2_S10_L001]


title: 0 micromolar CdCl2 [Cnt-3_S11_L001]


title: Cd_50 [R50-354_S7_L001]

description: Gene Expression in Placenta

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of sequenced data was assessed usingthe fastqcapplication, and 12 poor-quality bases were trimmed from the 5’-end. The remaining good-quality reads were aligned to the mouse or human reference genome (mm10 version 87 or GRCh38 respectively) databases using the STAR aligner. To validate single nucleotide polymorphisms (SNPs) in the hybrid mouse model, the following WASP options were passed to the STAR aligner (--varVCFfile C57BL_6NJ.mgp.v5.snps.dbSNP142.vcf --waspOutputMode SAMtag). Per-gene counts of uniquely mapped reads for each replicate were calculated usingthe htseq-countscript from the HTSeq Python package. The count matrix was imported to R statistical computing environment for further analysis. Initially, genes that had no count in greater than half of the replicate samples were discarded. The remaining count data were normalized for sequencing depth and distortion, and dispersion was estimated using DESeq2 Bioconductor package. We fitted a linear model using the treatment levels, and differentially expressed genes (DEGs) were identified after applying multiple testing corrections using the Benjamini-Hochberg procedure. The final list of significant genes was generated using an adjusted p-value < 0.05.
Assembly: mm38 version 87 and CAST/EiJ version 1.86
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Mus musculus

source_name: Placenta

extract_protocol:
Placentae were isolated at e18.5, weighed, snap-frozen immediately and stored at −80°C. Frozen tissues were homogenized in lysis buffer and RNA was isolated via AllPrep DNA/RNA/miRNA kit (Qiagen).
cDNA libraries for Illumina sequencing were constructed via the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) according to the manufacturer’s protocol.
NovaSeq S4, utilizing a 150x2 bp paired end S4 sequencing

treatment_protocol: Mothers were exposed to 0ppm or 50ppm CdCl2 in their drinking water prior to and during gestation. Placentas were collected at embryonic day 18.5

value: F1 between C57BL/6 (mother) and  CAST/EiJ (father)

value: Homogenized whole placenta

tag: age

tag: genotype

value: C57BL/6J x CAST/EiJ hybrid

value: 50ppm CdCl2 in mother's H2O


title: 0 micromolar CdCl2 [Cnt-4_S12_L001]


title: Cd_50 [R50-329_S8_L001]

description: Gene Expression in Placenta


title: 5 micromolar CdCl2 [Cd-1_S5_L001]

value: 5 micromolar CdCl2 in media


title: 5 micromolar CdCl2 [Cd-2_S6_L001]


title: Cd_50 [R50-217_S6_L001]

description: Gene Expression in Placenta


title: 5 micromolar CdCl2 [Cd-3_S7_L001]


title: Cd_0 [R0-360_S4_L001]

description: Gene Expression in Placenta

value: 0ppm CdCl2 in mother's H2O


title: Cd_50 [R50-242_S5_L001]

description: Gene Expression in Placenta


title: Cd_0 [R0-231_S3_L001]

description: Gene Expression in Placenta


title: 5 micromolar CdCl2 [Cd-4_S8_L001]


title: Cd_0 [R0-371_S1_L001]

description: Gene Expression in Placenta


title: Con1

description:
10x Genomics
Con1_barcodes.tsv
Con1_genes.tsv
Con1_matrix.mtx


title: Con3

description:
10x Genomics
Con3_barcodes.tsv
Con3_genes.tsv
Con3_matrix.mtx


title: Cd_0 [R0-206_S2_L001]

description: Gene Expression in Placenta


title: demultiplexed data for Bud22 crosslink

status: Public on Apr 30 2023

city: Heidelberg

first: Ed

last: Hurt

address: Im Neuenheimer Feld 328

department: BZH

country: Germany

institute: Biochemie Zentrum Heidelberg

data_processing:
use of pyCRAC software tool
Assembly: Distribution of hit along the yeast genome
Supplementary files format and content: alignment with rRNA and U14 snoRNA

organism: Saccharomyces cerevisiae

source_name: Bud22 crosslink

growth_protocol: Yeast cells Bud22-His-TEV-protA were grown in YPD to OD600 of1.0, then shifted to SDC-URA + 4-thiouracil for 4h

treatment_protocol: 30 min UV treatment at 365nm wavelength


title: demultiplexed data for wildtype control

source_name: WT control

value: W303 wildtype


title: C10_R1 RNA

status: Public on Mar 03 2023

city: Bethesda

first: Jens

last: Lichtenberg

state: MD

address: 49 Convent Dr 3A19

department: National Human Genome Research Institute

institute: National Institutes of Health

data_processing:
Raw sequencing data was processed with RTA (v1.18.54.4).
Alignment was performed using STAR (v2.7.2a)
Transcript expression was estimated using RSEM (v1.3.2) and edgeR (v3.30.3)
Genome_build: mm10
Supplementary_files_format_and_content: TPM counts

source_name: KIT+ CD16/32- CD34dim CD41+ CD9+ CD48bright

extract_protocol:
Total RNA was extracted from primary mouse bone marrow using the Ambion PureLink RNA Mini Kit (Thermo Fisher cat# 9655) with Trizol according to the maufacturer's protocol.
Libraries were constructed from 5 ng total RNA using the Ovation RNA-Seq System V2 (Tecan). RNA-Seq libraries were prepared from 1 ug of cDNA using the TruSeq Stranded RNA Kit. Due to the amplification method, libraries are not stranded. Libraries were sequenced on the NovaSeq 6000.

value: Primary bone marrow

value: Wild type

tag: cell population


title: C18_R2 RNA

source_name: KIT+ CD16/32- CD34dim CD41+ CD9+ CD48dim


title: C13_R1 RNA

source_name: KIT+ CD16/32- CD34dim CD41- CD9-

value: KIT+ CD16/32- CD34dim CD41- CD9-


title: C13_R2 RNA


title: C18_R1 RNA

value: KIT+ CD16/32- CD34dim CD41+ CD9+ CD48dim


title: C10_R2 RNA

value: KIT+ CD16/32- CD34dim CD41+ CD9+ CD48bright


title: C2_R1 RNA

source_name: KIT+ CD16/32- CD34bright CD41+ CD9+

value: KIT+ CD16/32- CD34bright CD41+ CD9+


title: C10_R1 ATAC

library_source: genomic

data_processing:
Reads were mapped using Bowtie v1.0.0
Accessible reagions were identified wiht FSeq v1.85
Peaks were called using HOMER v1.0
Genome_build: mm10
Supplementary_files_format_and_content: genomic regions

molecule: genomic DNA

extract_protocol:
40,000 - 50,000 cells were collected from primary mouse bone marrow and resuspended with transposase TDE1 in buffer containing digitonin.
Right-side selection was performed with SPRIselect beads and amplified using the NEBnext PCR master mix and Nextera PCR primers 1 and 2. Libraries were subsequently purified using AMPure XP beads and the Kapa SYBR FAST Universal kit.


title: C18_R2 ATAC


title: C18_R1 ATAC


title: C13_R1 ATAC


title: C2_R2 ATAC


title: C10_R2 ATAC


title: CMP_3K

data_processing:
Raw sequencing data was processed using RTA (v1.18.64) and Casava (v1.8.2)
Sequencing data was demultiplexed and aligned to the the mm10 genome using the 10x Genomics Cell Ranger software (v2.0.0).
Count matrices were constructed using the Read10X function in Seurat (v2.3.0)
Genome_build: mm10
Supplementary_files_format_and_content: UMI counts

source_name: Lin-KIT+SCA1-CD34+CD16/32- bone marrow

extract_protocol:
RNA was isolated and cDNA constructed using the 10x Genomics Single cell 3' Library and Gel Bead Kit according to the manufacturer's protocol.
Libraries were constructed using Chromium Single Cell 3’ library and Gel Bead Kits (10x Genomics) and sequencing performed on a HiSeq 2500 DNA Sequencer (with a 26 base read for cell and molecule barcodes, an 8 base library index read, and a 98 base insert read)

treatment_protocol: Bone marrow was collected from healthy controls and targeted population isolated by FACS.


title: GMP scRNA

source_name: Lin-KIT+SCA1-CD34+CD16/32+ bone marrow


title: LSK scRNA

source_name: Lin-SCA1+KIT+ bone marrow


title: C2_R1 ATAC


title: CMP scRNA


title: S24h-12-o_S39_L006_R1_24h_ODM_TCDD

status: Public on Feb 08 2023

data_processing:
The sequence data quality was assessed using FastQC command line application and 12 poor quality bases were trimmed from the 5’-end. The remaining high-quality reads were aligned to the Human reference genome (hg38) using the STAR (Dobin et al., 2013) aligner. Per-gene counts for each replicate were calculated using the htseq-count script from the HTSEQ python package (version 0.11.1). Count data were imported to R statistical computing environment (R Core Team, 2020). Genes with less than 0.5 counts per million in at least 3 samples within each experimental condition were deemed non-expressors and removed from downstream analyses. A principal component analysis (PCA) was performed on the filtered count matrix using the function prcomp (R Core Team, 2020). One outlier sample within the ODM+TCDD treatment was detected on the PCA and removed from the data set (Data not shown). Data normalization and analysis were conducted using the DESeq2 Bioconductor package (Love et al., 2014). Data were fitted using a linear model with media, treatment and time-points as experimental conditions. Differentially expressed genes were identified after applying Benjamini-Hochberg multiple testing correction (padj<0.05), (Benjamini and Hochberg, 1995; Love et al., 2014).
Assembly: Ensembl hg38 version 87
Supplementary files format and content: csv format  normalized count in log scale

source_name: bone derived mesenchymal stem cells

growth_protocol: hBMSCs used for transcriptomic assessment were obtained from a 25-year-old, non-osteoporotic female, donor at the University of North Carolina-Chapel Hill hospitals (IRB exemption protocol: 10-0201). Bone fragments were washed in phosphate-buffered saline (PBS) containing 100 U/mL penicillin and 100 mg/mL streptomycin (Corning Inc.), minced into approximately 1 mm3 pieces and digested in a 3 mg/ml collagenase XI solution (Sigma-Aldrich) for three hours at 37°C on an orbital shaker. The digest solution was filtered through a 100-μm cell strainer, centrifuged and resuspended in growth media (GM). Cell suspensions were plated and incubated overnight at 37 °C and 5% CO2 in a humidified incubator and non-adherent cells removed by washing with PBS. Adherent cells were to 80% confluency, trypsinized and frozen down. Cells were characterized, via immunohistochemical staining and assessed for multipotency by determining  adipogenic or osteogenic potential.

extract_protocol:
Cells were harvested for total RNA from each treatment (GM-DMSO, ODM-DMSO, or ODM+TCDD) at 3 hours (3H), 24 hours (D1), 3 days (D3), 7 days (D7), and 17 days (D17) post osteoinduction in ODM for a total of n=4 individual samples/treatment/timepoint. Briefly, cells were washed twice in PBS and lysed in TRI Reagent® (Ambion®, Life Technologies) and total RNA was isolated according to the manufacturer’s instructions. Total RNA was quantified using Agilent 2100 Bioanalyzer and 2100 Expert Software package (Agilent Technologies). RNAs with RNA Integrity numbers (RINs) lower than 9 were excluded from subsequent RNA-Seq experiments.
RNA integrity, purity, and concentration were assessed using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies, USA). Purification of messenger RNA (mRNA) was performed using the oligo-dT beads provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA). Complementary DNA (cDNA) libraries for Illumina sequencing were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Mulitplex Oligos for Illumina (NEB) using the manufacturer-specified protocol.

treatment_protocol: For studies with TCDD, passage 2 hBMSCs were seeded into 12-well tissue culture treated plates at a density of 1x104 cells/cm2 in GM. After 24 hours, GM was replaced with osteogenic differentiation media (ODM) consisting of -MEM supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin, 50 μM ascorbic acid (Sigma-Aldrich), 0.1 μM dexamethasone (Sigma-Aldrich), and 10 mM β-glycerophosphate (Sigma-Aldrich) to induce differentiation (day 0). Beginning on day 0, cells were cultured for up to 17 days in ODM containing 0.1% dimethyl sulfoxide (DMSO, vehicle control) (ODM) or 10 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, Cambridge Isotopes Laboratory) (ODM+TCDD). An osteogenic negative control consisted of hBMSCs cultured in GM with 0.1% DMSO (GM) to provide an undifferentiated reference cell population. Media was replaced every three to four days, and cells were cultured under standard culture conditions until the appropriate timepoint for RNA isolation.

tag: source

value: 25-year-old, non-osteoporotic female

value: bone

value: 10nM TCDD

tag: time

value: 24 hours

tag: characteristic

value: media_type:ODM:Osteogenic media


title: S24h-11-o_S38_L006_R1_24h_ODM_TCDD


title: MEP scRNA

source_name: Lin-KIT+SCA1-CD34-CD16/32- bone marrow


title: S24h-10-o_S37_L006_R1_24h_ODM_TCDD


title: S24h-8-o_S35_L006_R1_24h_ODM_DMSO

value: DMSO


title: S24h-7-o_S34_L006_R1_24h_ODM_DMSO


title: aged gastric organoids

status: Public on Mar 22 2023

type: RNA

city: Sendai

first: Naoki

last: Asano

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Division of Gastroenterology

country: Japan

institute: Tohoku University Graduate School of Medicine

description:
gene expression data from aged gastric organoids
210216_38_a08_at_210121

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse Clariom-S chip at 45°C for 16hour. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: Gene chips were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Signal values were computed using the Affymetrix® GeneChip™ Command Console software. The data were summarized and normalized with SST-RMA (Signal Space Transformation-Robust Multichip Analysis) method implemented in Affymetrix® Power Tools (APT).

label: biotin

source_name: aged gastric organoids

label_protocol: The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol  (GeneChip Whole Transcript PLUS reagent Kit). cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Organoids were established from the stomachs of young and aged mice, and cultured in medium which consisted of Advanced DMEM/F-12 medium supplemented with GlutaMAX-I , HEPES, Penicillin-Streptomycin, B-27 and N-2 supplement , N-Acetylcysteine, Valproic acid, Recombinant murine EGF and Noggin, Afamin/Wnt3a CM, Chir99021, Recombinant human FGF10, Y-27632 and SB431542, R-Spondin1 conditioned medium.

extract_protocol: Total RNA was extracted using TRIzol according to manufacturer's protocol

treatment_protocol: Young and aged gastric organoids were washed with PBS, harvested using Organoid harvesting solution, and were subjected to RNA extraction.

value: gastric organoids

value: aged


title: S24h-9-o_S36_L006_R1_24h_ODM_TCDD


title: C2_R2 RNA


title: S24h-6-o_S33_L006_R1_24h_ODM_DMSO


title: young gastric organoids

description:
gene expression data from young gastric organoids
210216_37_y25_at_210121

source_name: young gastric organoids

value: young


title: S24h-5-o_S32_L006_R1_24h_ODM_DMSO


title: S24h-2-g_S29_L006_R1_24h_GM_DMSO

value: media_type:GM:Growth Media


title: S24h-3-g_S30_L006_R1_24h_GM_DMSO


title: S24h-4-g_S31_L006_R1_24h_GM_DMSO


title: C13_R2 ATAC


title: S11_S62_L007_R1_17d_ODM_TCDD

value: Day 17


title: S10_S61_L007_R1_17d_ODM_TCDD


title: S8_S59_L007_R1_17d_ODM_DMSO


title: S6_S57_L007_R1_17d_ODM_DMSO


title: S9_S60_L007_17d_ODM_TCDD


title: S7_S58_L007_R1_17d_ODM_DMSO


title: S5_S56_L007_R1_17d_ODM_DMSO


title: S3_S54_L007_R1_17d_GM_DMSO


title: S1_S52_L007_R1_17d_GM_DMSO


title: S7-14-o_R1_7d_ODM_TCDD

value: Day 7


title: S7-13-o_R1_7d_ODM_TCDD


title: S7-7-o_R1_7d_ODM_DMSO


title: S7-8-o_R1_7d_ODM_DMSO


title: S7-6-o_R1_7d_ODM_DMSO


title: S7-3-g_R1_7d_GM_DMSO


title: S7-4-g_R1_7d_GM_DMSO


title: S7-5-o_R1_7d_ODM_DMSO


title: S7-2-g_R1_7d_GM_DMSO


title: S3h-12-o_S27_L005_R1_3h_ODM_TCDD

value: 3 hours


title: S3h-11-o_S26_L005_R1_3h_ODM_TCDD


title: S3h-9-o_S24_L005_R1_3h_ODM_TCDD


title: S3h-10-o_S25_L005_R1_3h_ODM_TCDD


title: S24h-1-g_S28_L006_R1_24h_GM_DMSO


title: S3h-8-o_S23_L005_R1_3h_ODM_DMSO


title: S3h-7-o_S22_L005_R1_3h_ODM_DMSO


title: S4_S55_L007_R1_17d_GM_DMSO


title: S3h-6-o_S21_L005_R1_3h_ODM_DMSO


title: S3h-4-g_S19_L005_R1_3h_GM_DMSO


title: S7-1-g_R1_7d_GM_DMSO


title: S7-16-o_R1_7d_ODM_TCDD


title: S7-15-o_R1_7d_ODM_TCDD


title: S3h-3-g_S18_L005_R1_3h_GM_DMSO


title: S3h-1-g_S16_L005_R1_3h_GM_DMSO


title: S3h-5-o_S20_L005_R1_3h_ODM_DMSO


title: S12_S63_L007_R1_17d_ODM_TCDD


title: S3-15-o_R1_3d_ODM_TCDD

value: Day 3


title: S2_S53_L007_R1_17d_GM_DMSO


title: S3-16-o_R1_3d_ODM_TCDD


title: S3-14-o_R1_3d_ODM_TCDD


title: S3-13-o_R1_3d_ODM_TCDD


title: S3-8-o_R1_3d_ODM_DMSO


title: S3-7-o_R1_3d_ODM_DMSO


title: S3-6-o_R1_3d_ODM_DMSO


title: S3-3-g_R1_3d_GM_DMSO


title: S3-2-g_R1_3d_GM_DMSO


title: S3-5-o_R1_3d_ODM_DMSO


title: Sen

status: Public on Dec 08 2022

city: Fujisawa

first: Kensuke

last: Sakuma

state: Kanagawa

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

institute: Orizuru Therapeutics, Inc.

description: 10x Genomics

data_processing:
FASTQ files were aligned to the human GRCh38 reference and count UMIs using Cell Ranger v5.0.1 software.
Gene barcode matrices were generated from Cell Ranger software.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Islet-like cells

extract_protocol:
Chromium Single Cell 3′ kits v3.1 (10x Genomics, Pleasanton, CA, USA)
100 to 180 ng of cDNA was subjected to library construction according to the manufacturer’s instructions.

value: Islet-like cells


title: S3-4-g_R1_3d_GM_DMSO


title: ALK5iII

description: 10x Genomics


title: Sen/SB

description: 10x Genomics


title: Cn_D_7

status: Public on Nov 30 2022

city: Klong-luang

first: Pornpimon

last: Angkasekwinai

state: Patumthani

country: Thailand

institute: Thammasat University

data_processing:
All high-quality paired-end reads were aligned to the Mus musculus reference genome GRCm38/mm10 using TopHat2 v2.0.12/Bowtie v2.2.3.
NCBI BLAST v2.2.28 was used to annotate the reads based on known mouse genes with the expected value (e-value) of 1.0 x 10-10.
To estimate the abundance of the gene expression, the read numbers mapped of each gene from each transcript were counted and then normalized by fragment per kilobases per million mapped reads (FPKM) approach using HTSeq v0.6.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Alveolar macrophage

extract_protocol:
The alveolar macrophages isolated from mice (6-10 mice per group) were pooled and extracted for total RNA by using RNeasy® Plus Mini kit (Qiagen). 600 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA library prep kit for Illumina® following the manufacturer's protocols.

treatment_protocol: BALB/c mice were anesthetized and treated with PBS or C. neoformans H99 cell suspension at 5 × 104 cells/mouse by the intranasal route. At indicated time points, mice were euthanized by inhalation of CO2, and lungs were aseptically collected to isolate alveolar macrophage by FACS.

value: BALB/c

value: Alveolar macrophage

tag: agent

value: Cryptococcus neoformans


title: S3h-2-g_S17_L005_R1_3h_GM_DMSO

value: 25-year-old, non-osteoporotic female

value: bone


title: PBS

value: PBS

value: Day 14


title: SECISBP2 KO rep2 RNA

status: Public on Nov 02 2022

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

institute: Universitätsklinikum Bonn

data_processing:
Sequence reads were trimmed with TrimGalore v0.4.3 and cutadapt v1.12 and size selected, reads with N>15 were used for further analysis
Ribosome profiling data was aligned using STAR Aligner v2.6.0a against rRNA and tRNA sequences retrieved from UCSC Table Browser, not matched reads were used for further analysis
Trimmed RNA-Seq and Ribo-seq (after tRNA and rRNA removal) data was aligned with STAR aligner v2.6.0a against UCSC hg38 RefSeq mouse transcriptome, Trimmed RNA-Seq data was aligned agains GRCh38 genome retrieved from Ensembl database
Amount of sequences aligned to transcripts was counted with STAR aligner
Genome_build: hg38
Supplementary_files_format_and_content: table with 2 columns in .txt format, column1: Gene symbols, column2: corresponding counts

source_name: Hap1 Cells

extract_protocol:
Qiazol (Qiagen) according to manufacturer protocol, Poly(A) Purist Mag kit (Ambion) was used to isolate ployA mRNA
Randomly fragmented PolyA enriched total RNA was electrophoresed on a 15% Tris-Borate-EDTA (TBE) Urea gel and RNA fragments between 20 and 40 nts in size were purified prior to the construction of libraries for deep-sequencing. Small RNA sequencing libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), according to the manufacturer's instructions
RNA-seq: Qiazol (Qiagen) according to manufacturer protocol, Poly(A) Purist Mag kit (Ambion) was used to isolate ployA mRNA; Ribo-Seq: lysis buffer (10 mM Tris-Cl (pH 7.5), 300 mM KCl, 10 mM MgCl2,  1 mM DTT, 1% Triton X-100 and 10 U/ml DNAse I), ribosome pellets were resuspended in Qiazol (Quiagen) after centrifugation of RNAse I digested monosomes in 50% sucrose buffer, ribosome protected fragments were isolated using miRNAeasy kit (Quiagen) according to manufacturer protocol with modification to retain small RNAs
RNA/Ribo-seq: RPFs and randomly fragmented PolyA enriched total RNA were electrophoresed on a 15% Tris-Borate-EDTA (TBE) Urea gel and RNA fragments between 15 and 40 nts in size were purified prior to the construction of libraries for deep-sequencing. Small RNA sequencing libraries were constructed using the BGISeq

value: Hap1 Cells

value: SECISBP2 KO


title: SECISBP2 KO rep1 RNA


title: WT rep1 RNA

value: WT


title: SECISBP2 KO rep2 RPF

data_processing:
Library strategy: Ribo-seq
Sequence reads were trimmed with TrimGalore v0.4.3 and cutadapt v1.12 and size selected, reads with N>15 were used for further analysis
Ribosome profiling data was aligned using STAR Aligner v2.6.0a against rRNA and tRNA sequences retrieved from UCSC Table Browser, not matched reads were used for further analysis
Trimmed RNA-Seq and Ribo-seq (after tRNA and rRNA removal) data was aligned with STAR aligner v2.6.0a against UCSC hg38 RefSeq mouse transcriptome, Trimmed RNA-Seq data was aligned agains GRCh38 genome retrieved from Ensembl database
Amount of sequences aligned to transcripts was counted with STAR aligner
Genome_build: hg38
Supplementary_files_format_and_content: table with 2 columns in .txt format, column1: Gene symbols, column2: corresponding counts

extract_protocol:
10 cm dish with confluent grown cells was placed on ice, the media removed and washed once with ice-cold 1x PBS. 400 µl of ice-cold lysis buffer (10 mM Tris-Cl (pH 7.5), 300 mM KCl, 10 mM MgCl2, 1 mM DTT, 1% Triton X-100 and 10 U/ml DNAse I) was used for lysis, ribosome pellets were resuspended in Qiazol (Quiagen) after centrifugation of RNAseI digested monosomes (45 min at RT) in 50% sucrose buffer, ribosome protected fragments were isolated using miRNAeasy kit (Quiagen) according to manufacturer protocol with modification to retain small RNAs
RPFs were electrophoresed on a 15% Tris-Borate-EDTA (TBE) Urea gel and RNA fragments between 15 and 40 nts in size were purified prior to the construction of libraries for deep-sequencing. Small RNA sequencing libraries were constructed by BGISeq with a depth of 30 M reads
RNA-seq: Qiazol (Qiagen) according to manufacturer protocol, Poly(A) Purist Mag kit (Ambion) was used to isolate ployA mRNA; Ribo-Seq: lysis buffer (10 mM Tris-Cl (pH 7.5), 300 mM KCl, 10 mM MgCl2,  1 mM DTT, 1% Triton X-100 and 10 U/ml DNAse I), ribosome pellets were resuspended in Qiazol (Quiagen) after centrifugation of RNAse I digested monosomes in 50% sucrose buffer, ribosome protected fragments were isolated using miRNAeasy kit (Quiagen) according to manufacturer protocol with modification to retain small RNAs
RNA/Ribo-seq: RPFs and randomly fragmented PolyA enriched total RNA were electrophoresed on a 15% Tris-Borate-EDTA (TBE) Urea gel and RNA fragments between 15 and 40 nts in size were purified prior to the construction of libraries for deep-sequencing. Small RNA sequencing libraries were constructed using the BGISeq


title: WT rep2 RNA


title: SECISBP2 KO rep1 RPF


title: S3-1-g_R1_3d_GM_DMSO

value: DMSO


title: WT rep2 RPF


title: SB

description: 10x Genomics


title: WT rep1 RPF


title: S9_PND0_50_M

status: Public on Oct 21 2022

data_processing:
The quality of sequenced data was assessed using fastqc application and 12 poor quality bases were trimmed from the 5’-end. The remaining good quality reads were aligned to the Mouse reference genome (mm38 version 87) downloaded from Ensembl database using STAR aligner with a WASP approach. This option allows mapping of one haplotype and supplies the other haplotype variants as VCF files (C57BL_6NJ version 5 SNPs downloaded from dbSNP142). For each replicate, per-gene counts of uniquely mapped reads were calculated using htseq-count script from the HTSeq python package. The count matrix was imported to R statistical computing environment for further analysis. Initially, genes that have no count in most of the replicate sample were discarded. The remaining count data were normalized for sequencing depth and distortion, and dispersion was estimated using DESeq2 Bioconductor package in the R statistical computing environment. We fitted a leaner model using the treatment levels and a differential expressed genes were identified after applying multiple testing correction using Benjamini-Hjockberg procedure. The final significant genes were generated using padj<0.05.
Assembly: Ensembl mm38 version 87
Supplementary files format and content: csv format  normalized count in log scale

extract_protocol:
Livers were removed and flash frozen. RNA was isolated from liver samples using the NucleoSpin kit (Macherey Nagel) and quantified using a Nanodrop 2000. Dnase I treatment was performed as part of the protocol.
RNA-seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina (NEB).

treatment_protocol: Female C57Bl/6J and male CAST/EiJ mice were obtained from Jackson Laboratory at three and four weeks old, respectively, and were allowed an acclimation period of one week before experimental manipulations. Mice were maintained on a 14-hour/10-hour light/dark cycle at 30-70 % humidity, 22°C ± 4°C and housed in Green Line IVC Sealsafe cage housing systems (Tecniplast) and fed AIN-93G rodent diet (Research Diets, D10012G) ad libitum for the duration of the study. At 4 weeks of age, female mice were provided unrestricted access to filtered drinking water (Millipore RiOs Essential RO water purification system) containing 0, 1, or 50 ppm cadmium chloride (CdCl2) (Sigma-Aldrich, 202908). At 9 weeks of age, female mice were mated with unexposed CAST/EiJ males. CdCl2 exposure ended when offspring reached postnatal day (PND) 10.

value: C57Bl/6J x CAST/EiJ hybrid

value: liver

value: postnatal day 0

value: 50 CdCl2


title: S7_PND0_0_M

value: 0 CdCl2


title: S6_PND0_50_M


title: S8_PND0_50_M


title: S4_PND0_0_M


title: S48_PND21_50_F

value: postnatal day 21


title: S5_PND0_50_M


title: Splenocytes_TCL1_3

status: Public on Nov 14 2022

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

hyb_protocol: Mouse Gene 1.0 ST Arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al.

source_name: Splenocytes from mice transplanted with HPCs expressing TCL1A

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen. RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 50ng total RNA.

treatment_protocol: No treatment. Freshly isolated splenocytes from C57BL/6 (CD45.2) recipient mice of transduced HSCs/HPCs were collected for RNA isolation.

value: Splenocytes

value: Endpoint

tag: transplant

value: TCL1A-transgenic HSC/HSP cells


title: Splenocytes_nlsTCL1_2

source_name: Splenocytes from mice transplanted with HPCs expressing TCL1A with a nuclear localization signal

growth_protocol: Freshly isolated splenocytes from C57BL/6 (CD45.2) recipient mice of transduced HSCs/HPCs were collected for RNA isolation.

value: nls-TCL1A-transgenic HSC/HSP cells


title: Splenocytes_nlsTCL1_3


title: Splenocytes_TCL1_1


title: Splenocytes_TCL1_2


title: Splenocytes_myrTCL1_2

source_name: Splenocytes from mice transplanted with HPCs expressing myristoylated TCL1A

value: myristoylated TCL1A-transgenic HSC/HSP cells


title: Splenocytes_nlsTCL1_1


title: Splenocytes_myrTCL1_3


title: S47_PND21_50_F


title: S45_PND21_0_F


title: S46_PND21_50_F


title: S44_PND21_0_F


title: Splenocytes_myrTCL1_1


title: S43_PND21_0_F


title: S42_PND21_50_F


title: S41_PND21_50_F


title: S40_PND21_0_F


title: S3_PND0_0_M


title: S39_PND21_50_F


title: S38_PND21_0_F


title: S35_PND21_50_M


title: S36_PND21_50_M


title: S32_PND21_0_M


title: S31_PND21_50_M


title: S34_PND21_0_M


title: S33_PND21_0_M


title: S30_PND21_50_M


title: S2_PND0_0_M


title: S28_PND21_0_M


title: S29_PND21_50_M


title: S22_PND0_50_F


title: S25_PND21_0_M


title: S24_PND0_0_F


title: S21_PND0_0_F


title: S20_PND0_50_F


title: S27_PND21_0_M


title: S1_PND0_50_M


title: S19_PND0_0_F


title: S17_PND0_0_F


title: S16_PND0_50_F


title: S14_PND0_0_F


title: S13_PND0_50_F


title: S12_PND0_50_M


title: S37_PND21_0_F


title: S10_PND0_0_M


title: S11_PND0_0_M


title: HS_S15

status: Public on Sep 23 2022

data_processing:
Quality control of read data was briefly evaluated with FastQC, and alignment trimming was performed using sickle (version 1.33, https://github.com/ucdavis-bioinformatics/sickle). Alignment was performed using hisat2 short read aligner to Teff  (https://genomevolution.org/coge/GenomeInfo.pl?gid=50954 ) reference genome. The number of reads mapped to genome features was determined using the htseq-count command-line script, and count data was imported to R statistical computing environment for further analysis. Initially, genes that have no count in at least 4 of the replicate samples were excluded from the study. Data normalization based on dispersion and differential analysis were conducted using the DESeq2 package.
Assembly: teff_r46 https://genomevolution.org/coge/GenomeInfo.pl?gid=50954
Supplementary files format and content: csv format  read count

organism: Eragrostis tef

source_name: Control shoots

growth_protocol: Plants were grown in hydroponic solution with low calcium and optimum calcium

extract_protocol:
RNA was extracted and sequenced
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: In this study, tef plants were grown in hydroponic solution containing optimum (1 mM) or low (0.01 mM) Ca2+. 4 replicates  for each treatment

value: shoots

value: Control


title: S26_PND21_50_M


title: HS_S16


title: S23_PND0_0_F


title: HR_S11

source_name: Control roots

value: roots


title: HR_S10


title: HR_S9


title: LR_S4

source_name: Low calcium roots

value: Low calcium


title: S18_PND0_50_F


title: HS_S14


title: LR_S3


title: S15_PND0_50_F


title: LR_S1


title: HR_S12


title: HS_S13


title: LS_S8

source_name: Low calcium shoots


title: LS_S6


title: MSCCR_reGRID_496, CD participants

status: Public on Sep 16 2022

city: new york city

first: Carmen

last: argmann

state: NY

address: 1425 Madison Avenue

institute: MSSM

data_processing:
Genomic alignment to GRCh37 of single-end RNA-seq reads was performed using 2-pass STAR. Default parameters for STAR were used, as were those for the quantification of aligned reads to GRCh37.75 gene features via featureCounts. Multimapping reads were flagged and discarded
Raw count data was pre-filtered to keep genes with CPM>0.5 for at least 3% of the samples
After filtering, count data was normalized via the weighted trimmed mean of M-values
Gene expression matrices were generated using the voom transformation and adjusted for technical variables (e.g. RIN, processing batch, rRNA rate and exonic rate) using the limma framework
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Blood

extract_protocol:
RNA from whole blood collected in PAXgene tubes was isolated using QIAsymphony Blood PAXgene RNA kit (cat.# 762635).
Globin RNA along with ribosomal RNA was depleted from total blood RNA using Globin zero gold rRNA removal kit (Illumina cat.#  GZG1224) to enrich poly-adenylated coding RNA as well as non-coding RNA. Preparation of the sequencing libraries used the RNA Tru Seq Kit (Illumina (Cat # RS-122-2001-48). The ribozero and globin zero RNA-Seq libraries were sequenced on the Illumina HiSeq 2500 platform using 100 bp paired end protocol following manufacturer’s procedure.

value: Female

value: CD

tag: diseasebi

value: IBD

value: Moderate

tag: endoremiss

tag: historemiss


title: LS_S7


title: MSCCR_reGRID_490, UC participants

value: UC

value: Active

value: Inactive


title: MSCCR_reGRID_492, CD participants

value: Male


title: MSCCR_reGRID_500, Control participants


title: MSCCR_reGRID_491, UC participants


title: MSCCR_reGRID_498, CD participants


title: MSCCR_reGRID_493, UC participants


title: MSCCR_reGRID_489, Control participants


title: MSCCR_reGRID_486, UC participants


title: MSCCR_reGRID_485, UC participants

value: Mild


title: MSCCR_reGRID_481, CD participants


title: MSCCR_reGRID_478, UC participants


title: MSCCR_reGRID_484, UC participants


title: LS_S5


title: LR_S2


title: MSCCR_reGRID_477, Control participants


title: MSCCR_reGRID_497, UC participants


title: MSCCR_reGRID_476, UC participants


title: MSCCR_reGRID_472, UC participants


title: MSCCR_reGRID_469, CD participants


title: MSCCR_reGRID_470, CD participants


title: MSCCR_reGRID_474, UC participants


title: MSCCR_reGRID_467, UC participants


title: MSCCR_reGRID_464, CD participants


title: MSCCR_reGRID_463, UC participants


title: MSCCR_reGRID_459, CD participants


title: MSCCR_reGRID_460, CD participants

value: Severe


title: MSCCR_reGRID_487, UC participants


title: MSCCR_reGRID_454, UC participants


title: MSCCR_reGRID_456, UC participants


title: MSCCR_reGRID_450, UC participants


title: MSCCR_reGRID_447, UC participants


title: MSCCR_reGRID_453, UC participants


title: MSCCR_reGRID_446, CD participants


title: MSCCR_reGRID_445, CD participants


title: MSCCR_reGRID_443, CD participants


title: MSCCR_reGRID_444, CD participants


title: MSCCR_reGRID_440, UC participants


title: MSCCR_reGRID_438, UC participants


title: MSCCR_reGRID_437, UC participants


title: MSCCR_reGRID_442, CD participants


title: MSCCR_reGRID_471, CD participants


title: MSCCR_reGRID_436, UC participants


title: MSCCR_reGRID_439, UC participants


title: MSCCR_reGRID_475, UC participants


title: MSCCR_reGRID_433, UC participants


title: MSCCR_reGRID_430, CD participants


title: MSCCR_reGRID_432, UC participants


title: MSCCR_reGRID_429, UC participants


title: MSCCR_reGRID_427, UC participants


title: MSCCR_reGRID_457, UC participants


title: MSCCR_reGRID_434, UC participants


title: MSCCR_reGRID_455, UC participants


title: MSCCR_reGRID_431, UC participants


title: MSCCR_reGRID_426, CD participants


title: MSCCR_reGRID_425, UC participants


title: MSCCR_reGRID_420, CD participants


title: MSCCR_reGRID_418, CD participants


title: MSCCR_reGRID_416, UC participants


title: MSCCR_reGRID_424, UC participants


title: MSCCR_reGRID_419, CD participants


title: MSCCR_reGRID_414, UC participants


title: MSCCR_reGRID_413, CD participants


title: MSCCR_reGRID_412, UC participants


title: MSCCR_reGRID_410, CD participants


title: MSCCR_reGRID_407, UC participants


title: MSCCR_reGRID_408, CD participants


title: MSCCR_reGRID_411, UC participants


title: MSCCR_reGRID_404, UC participants


title: MSCCR_reGRID_406, UC participants


title: MSCCR_reGRID_402, UC participants


title: MSCCR_reGRID_428, UC participants


title: MSCCR_reGRID_401, CD participants


title: MSCCR_reGRID_399, UC participants


title: MSCCR_reGRID_398, CD participants


title: MSCCR_reGRID_397, CD participants


title: MSCCR_reGRID_395, UC participants


title: MSCCR_reGRID_393, CD participants


title: MSCCR_reGRID_392, CD participants


title: MSCCR_reGRID_391, UC participants


title: MSCCR_reGRID_390, UC participants


title: MSCCR_reGRID_417, UC participants


title: MSCCR_reGRID_388, UC participants


title: MSCCR_reGRID_389, UC participants


title: MSCCR_reGRID_387, CD participants


title: MSCCR_reGRID_385, CD participants


title: MSCCR_reGRID_386, CD participants


title: MSCCR_reGRID_384, CD participants


title: MSCCR_reGRID_381, CD participants


title: MSCCR_reGRID_383, UC participants


title: MSCCR_reGRID_380, CD participants


title: MSCCR_reGRID_382, UC participants


title: MSCCR_reGRID_377, CD participants


title: MSCCR_reGRID_376, CD participants


title: MSCCR_reGRID_375, CD participants


title: MSCCR_reGRID_373, CD participants


title: MSCCR_reGRID_374, UC participants


title: MSCCR_reGRID_379, CD participants


title: MSCCR_reGRID_369, CD participants


title: MSCCR_reGRID_378, CD participants


title: MSCCR_reGRID_368, CD participants


title: MSCCR_reGRID_371, UC participants


title: MSCCR_reGRID_367, CD participants


title: MSCCR_reGRID_366, CD participants


title: MSCCR_reGRID_370, UC participants


title: MSCCR_reGRID_362, CD participants


title: MSCCR_reGRID_361, CD participants


title: MSCCR_reGRID_358, CD participants


title: MSCCR_reGRID_355, CD participants


title: MSCCR_reGRID_359, UC participants


title: MSCCR_reGRID_348, CD participants


title: MSCCR_reGRID_352, CD participants


title: MSCCR_reGRID_346, UC participants


title: MSCCR_reGRID_354, CD participants


title: MSCCR_reGRID_351, UC participants


title: MSCCR_reGRID_343, CD participants


title: MSCCR_reGRID_345, CD participants


title: MSCCR_reGRID_372, UC participants


title: MSCCR_reGRID_347, Control participants


title: MSCCR_reGRID_342, UC participants


title: MSCCR_reGRID_337, CD participants


title: MSCCR_reGRID_338, CD participants


title: MSCCR_reGRID_339, UC participants


title: MSCCR_reGRID_333, CD participants


title: MSCCR_reGRID_364, CD participants


title: MSCCR_reGRID_327, CD participants


title: MSCCR_reGRID_324, CD participants


title: MSCCR_reGRID_365, CD participants


title: MSCCR_reGRID_329, UC participants


title: MSCCR_reGRID_322, UC participants


title: MSCCR_reGRID_321, CD participants


title: MSCCR_reGRID_323, UC participants


title: MSCCR_reGRID_320, UC participants


title: MSCCR_reGRID_318, UC participants


title: MSCCR_reGRID_317, CD participants


title: MSCCR_reGRID_316, CD participants


title: MSCCR_reGRID_315, UC participants


title: MSCCR_reGRID_312, CD participants


title: MSCCR_reGRID_311, UC participants


title: MSCCR_reGRID_340, CD participants


title: MSCCR_reGRID_306, CD participants


title: MSCCR_reGRID_307, UC participants


title: MSCCR_reGRID_304, CD participants


title: MSCCR_reGRID_305, UC participants


title: MSCCR_reGRID_303, CD participants


title: MSCCR_reGRID_341, UC participants


title: MSCCR_reGRID_302, UC participants


title: MSCCR_reGRID_301, UC participants


title: MSCCR_reGRID_295, UC participants


title: MSCCR_reGRID_298, CD participants


title: MSCCR_reGRID_293, CD participants


title: MSCCR_reGRID_299, CD participants


title: MSCCR_reGRID_291, CD participants


title: MSCCR_reGRID_297, UC participants


title: MSCCR_reGRID_287, CD participants


title: MSCCR_reGRID_292, UC participants


title: MSCCR_reGRID_289, CD participants


title: MSCCR_reGRID_290, CD participants


title: MSCCR_reGRID_285, UC participants


title: MSCCR_reGRID_280, CD participants


title: MSCCR_reGRID_284, CD participants


title: MSCCR_reGRID_283, UC participants


title: MSCCR_reGRID_278, CD participants


title: MSCCR_reGRID_310, UC participants


title: MSCCR_reGRID_279, UC participants


title: MSCCR_reGRID_277, CD participants


title: MSCCR_reGRID_276, CD participants


title: MSCCR_reGRID_275, UC participants


title: MSCCR_reGRID_273, UC participants


title: MSCCR_reGRID_270, CD participants


title: MSCCR_reGRID_269, CD participants


title: MSCCR_reGRID_268, CD participants


title: MSCCR_reGRID_265, CD participants


title: MSCCR_reGRID_274, CD participants


title: MSCCR_reGRID_266, CD participants


title: MSCCR_reGRID_259, UC participants


title: MSCCR_reGRID_286, CD participants


title: MSCCR_reGRID_256, UC participants


title: MSCCR_reGRID_255, UC participants


title: MSCCR_reGRID_254, UC participants


title: MSCCR_reGRID_251, CD participants


title: MSCCR_reGRID_248, CD participants


title: MSCCR_reGRID_247, CD participants


title: MSCCR_reGRID_252, UC participants


title: MSCCR_reGRID_245, CD participants


title: MSCCR_reGRID_243, CD participants


title: MSCCR_reGRID_242, CD participants


title: MSCCR_reGRID_250, CD participants


title: MSCCR_reGRID_240, UC participants


title: MSCCR_reGRID_239, UC participants


title: MSCCR_reGRID_235, CD participants


title: MSCCR_reGRID_238, UC participants


title: MSCCR_reGRID_234, UC participants


title: MSCCR_reGRID_228, UC participants


title: MSCCR_reGRID_241, UC participants


title: MSCCR_reGRID_224, UC participants


title: MSCCR_reGRID_220, CD participants


title: MSCCR_reGRID_223, CD participants


title: MSCCR_reGRID_257, CD participants


title: MSCCR_reGRID_226, CD participants


title: MSCCR_reGRID_219, UC participants


title: MSCCR_reGRID_217, CD participants


title: MSCCR_reGRID_214, CD participants


title: MSCCR_reGRID_213, CD participants


title: MSCCR_reGRID_212, CD participants


title: MSCCR_reGRID_211, UC participants


title: MSCCR_reGRID_209, UC participants


title: MSCCR_reGRID_210, CD participants


title: MSCCR_reGRID_205, CD participants


title: MSCCR_reGRID_207, UC participants


title: MSCCR_reGRID_202, CD participants


title: MSCCR_reGRID_203, CD participants


title: MSCCR_reGRID_229, CD participants


title: MSCCR_reGRID_199, CD participants


title: MSCCR_reGRID_246, CD participants


title: MSCCR_reGRID_194, CD participants


title: MSCCR_reGRID_196, CD participants


title: MSCCR_reGRID_193, CD participants


title: MSCCR_reGRID_198, UC participants


title: MSCCR_reGRID_197, UC participants


title: MSCCR_reGRID_206, CD participants


title: MSCCR_reGRID_216, CD participants


title: MSCCR_reGRID_191, CD participants


title: MSCCR_reGRID_190, UC participants


title: MSCCR_reGRID_184, CD participants


title: MSCCR_reGRID_185, CD participants


title: MSCCR_reGRID_187, CD participants


title: MSCCR_reGRID_183, UC participants


title: MSCCR_reGRID_201, CD participants


title: MSCCR_reGRID_179, CD participants


title: MSCCR_reGRID_182, CD participants


title: MSCCR_reGRID_178, UC participants


title: MSCCR_reGRID_177, CD participants


title: MSCCR_reGRID_175, CD participants


title: MSCCR_reGRID_170, CD participants


title: MSCCR_reGRID_174, CD participants


title: MSCCR_reGRID_172, CD participants


title: MSCCR_reGRID_192, CD participants


title: MSCCR_reGRID_167, UC participants


title: MSCCR_reGRID_181, CD participants


title: MSCCR_reGRID_166, CD participants


title: MSCCR_reGRID_165, CD participants


title: MSCCR_reGRID_158, CD participants


title: MSCCR_reGRID_160, UC participants


title: MSCCR_reGRID_159, UC participants


title: MSCCR_reGRID_163, Control participants


title: MSCCR_reGRID_157, CD participants


title: MSCCR_reGRID_189, CD participants


title: MSCCR_reGRID_188, UC participants


title: MSCCR_reGRID_154, UC participants


title: MSCCR_reGRID_153, CD participants


title: MSCCR_reGRID_147, CD participants


title: MSCCR_reGRID_151, CD participants


title: MSCCR_reGRID_146, UC participants


title: MSCCR_reGRID_143, UC participants


title: MSCCR_reGRID_145, UC participants


title: MSCCR_reGRID_141, CD participants


title: MSCCR_reGRID_176, UC participants


title: MSCCR_reGRID_138, CD participants


title: MSCCR_reGRID_139, CD participants


title: MSCCR_reGRID_134, CD participants


title: MSCCR_reGRID_136, UC participants


title: MSCCR_reGRID_131, UC participants


title: MSCCR_reGRID_132, CD participants


title: MSCCR_reGRID_125, UC participants


title: MSCCR_reGRID_126, UC participants


title: MSCCR_reGRID_127, CD participants


title: MSCCR_reGRID_129, CD participants


title: MSCCR_reGRID_128, CD participants


title: MSCCR_reGRID_122, CD participants


title: MSCCR_reGRID_117, UC participants


title: MSCCR_reGRID_115, UC participants


title: MSCCR_reGRID_113, CD participants


title: MSCCR_reGRID_118, CD participants


title: MSCCR_reGRID_119, UC participants


title: MSCCR_reGRID_110, CD participants


title: MSCCR_reGRID_107, CD participants


title: MSCCR_reGRID_105, CD participants


title: MSCCR_reGRID_112, CD participants


title: MSCCR_reGRID_109, CD participants


title: MSCCR_reGRID_103, CD participants


title: MSCCR_reGRID_102, CD participants


title: MSCCR_reGRID_101, CD participants


title: MSCCR_reGRID_104, UC participants


title: MSCCR_reGRID_100, CD participants


title: MSCCR_reGRID_97, UC participants


title: MSCCR_reGRID_98, CD participants


title: MSCCR_reGRID_94, UC participants


title: MSCCR_reGRID_93, CD participants


title: MSCCR_reGRID_91, UC participants


title: MSCCR_reGRID_88, CD participants


title: MSCCR_reGRID_90, CD participants


title: MSCCR_reGRID_86, CD participants


title: MSCCR_reGRID_85, CD participants


title: MSCCR_reGRID_84, CD participants


title: MSCCR_reGRID_106, UC participants


title: MSCCR_reGRID_80, CD participants


title: MSCCR_reGRID_81, CD participants


title: MSCCR_reGRID_79, CD participants


title: MSCCR_reGRID_78, CD participants


title: MSCCR_reGRID_75, UC participants


title: MSCCR_reGRID_72, CD participants


title: MSCCR_reGRID_124, UC participants


title: MSCCR_reGRID_70, CD participants


title: MSCCR_reGRID_66, UC participants


title: MSCCR_reGRID_68, CD participants


title: MSCCR_reGRID_95, CD participants


title: MSCCR_reGRID_65, UC participants


title: MSCCR_reGRID_89, UC participants


title: MSCCR_reGRID_55, UC participants


title: MSCCR_reGRID_92, CD participants


title: MSCCR_reGRID_71, UC participants


title: MSCCR_reGRID_56, UC participants


title: MSCCR_reGRID_64, UC participants


title: MSCCR_reGRID_59, CD participants


title: MSCCR_reGRID_53, UC participants


title: MSCCR_reGRID_63, UC participants


title: MSCCR_reGRID_47, CD participants


title: MSCCR_reGRID_41, CD participants


title: MSCCR_reGRID_43, UC participants


title: MSCCR_reGRID_54, CD participants


title: MSCCR_reGRID_82, CD participants


title: MSCCR_reGRID_52, CD participants


title: MSCCR_reGRID_57, CD participants


title: MSCCR_reGRID_38, UC participants


title: MSCCR_reGRID_37, CD participants


title: MSCCR_reGRID_39, UC participants


title: MSCCR_reGRID_33, UC participants


title: MSCCR_reGRID_31, CD participants


title: MSCCR_reGRID_29, CD participants


title: MSCCR_reGRID_36, UC participants


title: MSCCR_reGRID_25, CD participants


title: MSCCR_reGRID_24, UC participants


title: MSCCR_reGRID_27, CD participants


title: MSCCR_reGRID_23, UC participants


title: MSCCR_reGRID_28, CD participants


title: MSCCR_reGRID_18, CD participants


title: MSCCR_reGRID_19, CD participants


title: MSCCR_reGRID_50, UC participants


title: MSCCR_reGRID_17, CD participants


title: MSCCR_reGRID_15, CD participants


title: MSCCR_reGRID_14, UC participants


title: MSCCR_reGRID_12, UC participants


title: MSCCR_reGRID_10, CD participants


title: MSCCR_reGRID_32, CD participants


title: MSCCR_reGRID_6, UC participants


title: MSCCR_reGRID_7, CD participants


title: MSCCR_reGRID_5, UC participants


title: MSCCR_reGRID_4, CD participants


title: MSCCR_reGRID_1, UC participants


title: MSCCR_reGRID_999_Biopsy_1731, Control participants,Rectum NonI tissue

source_name: Biopsy

extract_protocol:
RNA was isolated from frozen tissue using Qiagen QIAsymphony RNA Kit (cat.# 931636) on the QIAsymphony.
Preparation of the sequencing libraries used the RNA Tru Seq Kit (Illumina (Cat # RS-122-2001-48)

tag: regionre

value: Rectum

tag: diseasetypere

tag: typere

value: NonI

tag: nancyindex


title: MSCCR_reGRID_3, CD participants


title: MSCCR_reGRID_999_Biopsy_1730, Control participants,Ileum NonI tissue

value: Ileum


title: MSCCR_reGRID_111, CD participants


title: MSCCR_reGRID_994_Biopsy_1728, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_22, CD participants


title: MSCCR_reGRID_994_Biopsy_1729, Control participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_992_Biopsy_1727, Control participants,Rectum NonI tissue

value: Control


title: MSCCR_reGRID_992_Biopsy_1726, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_991_Biopsy_1725, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_991_Biopsy_1724, CD participants,Ileum I tissue

value: I


title: MSCCR_reGRID_99_Biopsy_200, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_13, CD participants


title: MSCCR_reGRID_984_Biopsy_1719, CD participants,RightColon NonI tissue

value: RightColon


title: MSCCR_reGRID_989_Biopsy_1723, UC participants,Rectum NonI tissue

value: Female


title: MSCCR_reGRID_988_Biopsy_1722, CD participants,Rectum I tissue

value: CD


title: MSCCR_reGRID_983_Biopsy_1718, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_9, CD participants

value: IBD


title: MSCCR_reGRID_984_Biopsy_1720, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_983_Biopsy_1717, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_988_Biopsy_1721, CD participants,Ileum I tissue

value: Moderate


title: MSCCR_reGRID_982_Biopsy_1716, UC participants,Ileum NonI tissue

value: UC


title: MSCCR_reGRID_98_Biopsy_198, CD participants,Rectum I tissue


title: MSCCR_reGRID_98_Biopsy_197, CD participants,RightColon NonI tissue


title: MSCCR_reGRID_971_Biopsy_1715, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_98_Biopsy_196, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_971_Biopsy_1714, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_97_Biopsy_195, UC participants,RightColon NonI tissue


title: MSCCR_reGRID_97_Biopsy_193, UC participants,Rectum I tissue


title: MSCCR_reGRID_967_Biopsy_1713, UC participants,Cecum NonI tissue


title: MSCCR_reGRID_966_Biopsy_1709, CD participants,Rectum I tissue


title: MSCCR_reGRID_966_Biopsy_1710, CD participants,RightColon NonI tissue


title: MSCCR_reGRID_966_Biopsy_1711, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_11, UC participants


title: MSCCR_reGRID_967_Biopsy_1712, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_99_Biopsy_199, CD participants,Sigmoid I tissue

value: Sigmoid


title: MSCCR_reGRID_963_Biopsy_1705, CD participants,Rectum NonI tissue

value: Inactive


title: MSCCR_reGRID_964_Biopsy_1708, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_961_Biopsy_1702, Control participants,Rectum NonI tissue

value: Male


title: MSCCR_reGRID_964_Biopsy_1707, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_961_Biopsy_1703, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_96_Biopsy_191, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_962_Biopsy_1704, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_96_Biopsy_190, CD participants,Transverse NonI tissue

value: Transverse


title: MSCCR_reGRID_956_Biopsy_1699, CD participants,Cecum NonI tissue

value: Mild


title: MSCCR_reGRID_956_Biopsy_1698, CD participants,Ileum I tissue


title: MSCCR_reGRID_959_Biopsy_1701, CD participants,Rectum NonI tissue

value: Rectum


title: MSCCR_reGRID_963_Biopsy_1706, CD participants,Ileum I tissue


title: MSCCR_reGRID_955_Biopsy_1697, Control participants,RightColon NonI tissue

value: NonI


title: MSCCR_reGRID_956_Biopsy_1700, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_951_Biopsy_1696, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_951_Biopsy_1695, UC participants,Ileum NonI tissue

value: Ileum


title: MSCCR_reGRID_950_Biopsy_1694, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_97_Biopsy_194, UC participants,LeftColon NonI tissue

value: LeftColon


title: MSCCR_reGRID_95_Biopsy_189, CD participants,LeftColon NonI tissue


title: MSCCR_reGRID_95_Biopsy_188, CD participants,RightColon NonI tissue


title: MSCCR_reGRID_949_Biopsy_1692, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_950_Biopsy_1693, Control participants,Ileum NonI tissue

value: Control


title: MSCCR_reGRID_948_Biopsy_1690, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_949_Biopsy_1691, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_96_Biopsy_192, CD participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_948_Biopsy_1689, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_946_Biopsy_1686, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_947_Biopsy_1687, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_946_Biopsy_1685, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_947_Biopsy_1688, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_945_Biopsy_1683, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_943_Biopsy_1680, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_945_Biopsy_1684, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_944_Biopsy_1682, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_944_Biopsy_1681, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_942_Biopsy_1678, UC participants,Rectum I tissue

value: I

value: Active


title: MSCCR_reGRID_942_Biopsy_1679, UC participants,Ileum NonI tissue

value: Female


title: MSCCR_reGRID_941_Biopsy_1675, CD participants,Ileum I tissue

value: CD

value: IBD


title: MSCCR_reGRID_941_Biopsy_1676, CD participants,Cecum NonI tissue


title: MSCCR_reGRID_941_Biopsy_1677, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_940_Biopsy_1674, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_939_Biopsy_1673, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_94_Biopsy_187, UC participants,Rectum I tissue

value: UC


title: MSCCR_reGRID_936_Biopsy_1669, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_937_Biopsy_1670, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_936_Biopsy_1668, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_937_Biopsy_1671, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_934_Biopsy_1667, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_934_Biopsy_1666, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_931_Biopsy_1660, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_933_Biopsy_1664, CD participants,Rectum I tissue


title: MSCCR_reGRID_933_Biopsy_1665, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_931_Biopsy_1661, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_93_Biopsy_186, CD participants,Cecum I tissue


title: MSCCR_reGRID_932_Biopsy_1663, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_93_Biopsy_185, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_928_Biopsy_1658, UC participants,Rectum I tissue

value: Severe


title: MSCCR_reGRID_932_Biopsy_1662, CD participants,Ileum NonI tissue

value: Inactive


title: MSCCR_reGRID_926_Biopsy_1657, Control participants,Rectum NonI tissue

value: Male


title: MSCCR_reGRID_93_Biopsy_184, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_926_Biopsy_1656, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_922_Biopsy_1654, UC participants,Rectum I tissue


title: MSCCR_reGRID_939_Biopsy_1672, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_922_Biopsy_1653, UC participants,LeftColon NonI tissue


title: MSCCR_reGRID_92_Biopsy_182, CD participants,LeftColon NonI tissue


title: MSCCR_reGRID_92_Biopsy_181, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_92_Biopsy_183, CD participants,Cecum I tissue


title: MSCCR_reGRID_919_Biopsy_1651, UC participants,LeftColon I tissue


title: MSCCR_reGRID_922_Biopsy_1652, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_919_Biopsy_1650, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_914_Biopsy_1647, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_914_Biopsy_1648, CD participants,Ileum I tissue


title: MSCCR_reGRID_911_Biopsy_1646, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_928_Biopsy_1659, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_910_Biopsy_1644, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_910_Biopsy_1645, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_908_Biopsy_1641, CD participants,Cecum I tissue

value: Moderate


title: MSCCR_reGRID_908_Biopsy_1640, CD participants,Cecum NonI tissue


title: MSCCR_reGRID_907_Biopsy_1638, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_907_Biopsy_1639, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_91_Biopsy_178, UC participants,RightColon NonI tissue

value: RightColon

value: Mild


title: MSCCR_reGRID_906_Biopsy_1636, UC participants,Rectum NonI tissue

value: Rectum

value: NonI


title: MSCCR_reGRID_906_Biopsy_1637, UC participants,Ileum NonI tissue

value: Ileum


title: MSCCR_reGRID_905_Biopsy_1635, UC participants,Rectum I tissue


title: MSCCR_reGRID_904_Biopsy_1633, Control participants,Ileum NonI tissue

value: Control


title: MSCCR_reGRID_919_Biopsy_1649, UC participants,Rectum I tissue


title: MSCCR_reGRID_923_Biopsy_1655, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_905_Biopsy_1634, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_908_Biopsy_1642, CD participants,Rectum I tissue


title: MSCCR_reGRID_91_Biopsy_179, UC participants,Sigmoid I tissue

value: Sigmoid


title: MSCCR_reGRID_91_Biopsy_180, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_909_Biopsy_1643, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_898_Biopsy_1623, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_90_Biopsy_177, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_904_Biopsy_1632, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_902_Biopsy_1629, CD participants,Rectum I tissue

value: I


title: MSCCR_reGRID_901_Biopsy_1626, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_90_Biopsy_176, CD participants,Sigmoid NonI tissue


title: MSCCR_reGRID_903_Biopsy_1631, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_902_Biopsy_1628, CD participants,Ileum I tissue


title: MSCCR_reGRID_903_Biopsy_1630, UC participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_9_Biopsy_17, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_901_Biopsy_1627, CD participants,Rectum NonI tissue

value: Female


title: MSCCR_reGRID_899_Biopsy_1624, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_898_Biopsy_1622, CD participants,Rectum I tissue

value: CD


title: MSCCR_reGRID_899_Biopsy_1625, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_897_Biopsy_1621, CD participants,Rectum I tissue

value: IBD


title: MSCCR_reGRID_897_Biopsy_1620, CD participants,Ileum I tissue


title: MSCCR_reGRID_895_Biopsy_1617, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_896_Biopsy_1618, UC participants,Rectum I tissue

value: UC


title: MSCCR_reGRID_892_Biopsy_1614, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_896_Biopsy_1619, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_892_Biopsy_1615, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_895_Biopsy_1616, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_891_Biopsy_1613, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_890_Biopsy_1611, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_891_Biopsy_1612, CD participants,Ileum I tissue


title: MSCCR_reGRID_890_Biopsy_1609, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_89_Biopsy_175, UC participants,LeftColon NonI tissue

value: LeftColon


title: MSCCR_reGRID_889_Biopsy_1608, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_889_Biopsy_1607, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_888_Biopsy_1605, UC participants,Rectum I tissue

value: Active

value: Severe


title: MSCCR_reGRID_888_Biopsy_1606, UC participants,Cecum I tissue

value: Male


title: MSCCR_reGRID_887_Biopsy_1603, CD participants,Rectum NonI tissue

value: Inactive


title: MSCCR_reGRID_884_Biopsy_1600, CD participants,Cecum I tissue


title: MSCCR_reGRID_884_Biopsy_1599, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_880_Biopsy_1598, CD participants,Rectum I tissue

value: Moderate


title: MSCCR_reGRID_876_Biopsy_1596, Control participants,Rectum NonI tissue

value: Rectum


title: MSCCR_reGRID_879_Biopsy_1597, CD participants,Ileum I tissue

value: Mild


title: MSCCR_reGRID_886_Biopsy_1601, CD participants,Ileum I tissue

value: Ileum


title: MSCCR_reGRID_88_Biopsy_174, CD participants,Rectum NonI tissue

value: NonI


title: MSCCR_reGRID_887_Biopsy_1604, CD participants,Cecum NonI tissue


title: MSCCR_reGRID_876_Biopsy_1595, Control participants,Ileum NonI tissue

value: Control


title: MSCCR_reGRID_88_Biopsy_173, CD participants,RightColon NonI tissue

value: RightColon


title: MSCCR_reGRID_886_Biopsy_1602, CD participants,Rectum I tissue

value: I


title: MSCCR_reGRID_88_Biopsy_172, CD participants,Ileum I tissue


title: MSCCR_reGRID_873_Biopsy_1592, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_873_Biopsy_1591, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_872_Biopsy_1590, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_871_Biopsy_1588, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_890_Biopsy_1610, CD participants,Sigmoid I tissue

value: Female

value: Sigmoid


title: MSCCR_reGRID_871_Biopsy_1587, UC participants,Ileum NonI tissue

value: IBD


title: MSCCR_reGRID_870_Biopsy_1586, UC participants,Ileum NonI tissue

value: UC


title: MSCCR_reGRID_870_Biopsy_1585, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_87_Biopsy_170, UC participants,Rectum I tissue


title: MSCCR_reGRID_87_Biopsy_171, UC participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_869_Biopsy_1584, CD participants,RightColon NonI tissue

value: CD


title: MSCCR_reGRID_875_Biopsy_1594, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_875_Biopsy_1593, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_869_Biopsy_1583, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_872_Biopsy_1589, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_860_Biopsy_1576, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_865_Biopsy_1578, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_868_Biopsy_1581, CD participants,Ileum I tissue


title: MSCCR_reGRID_860_Biopsy_1577, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_86_Biopsy_169, CD participants,Cecum I tissue


title: MSCCR_reGRID_859_Biopsy_1575, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_858_Biopsy_1572, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_857_Biopsy_1571, Control participants,RightColon NonI tissue


title: MSCCR_reGRID_856_Biopsy_1570, CD participants,Ileum I tissue


title: MSCCR_reGRID_858_Biopsy_1573, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_86_Biopsy_168, CD participants,Rectum I tissue


title: MSCCR_reGRID_867_Biopsy_1579, CD participants,Rectum NonI tissue

value: Active


title: MSCCR_reGRID_855_Biopsy_1567, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_856_Biopsy_1569, CD participants,Rectum NonI tissue

value: Male


title: MSCCR_reGRID_859_Biopsy_1574, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_854_Biopsy_1566, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_868_Biopsy_1582, CD participants,Rectum NonI tissue

value: Inactive


title: MSCCR_reGRID_854_Biopsy_1565, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_853_Biopsy_1564, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_852_Biopsy_1562, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_853_Biopsy_1563, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_852_Biopsy_1561, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_867_Biopsy_1580, CD participants,Ileum I tissue


title: MSCCR_reGRID_86_Biopsy_167, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_855_Biopsy_1568, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_851_Biopsy_1559, CD participants,Ileum I tissue


title: MSCCR_reGRID_85_Biopsy_166, CD participants,Rectum I tissue

value: Moderate


title: MSCCR_reGRID_850_Biopsy_1558, UC participants,Rectum I tissue

value: Rectum

value: Severe


title: MSCCR_reGRID_850_Biopsy_1557, UC participants,RightColon I tissue


title: MSCCR_reGRID_849_Biopsy_1556, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_851_Biopsy_1560, CD participants,Rectum NonI tissue

value: Mild


title: MSCCR_reGRID_85_Biopsy_164, CD participants,Ileum NonI tissue

value: Ileum

value: NonI


title: MSCCR_reGRID_85_Biopsy_165, CD participants,Sigmoid I tissue


title: MSCCR_reGRID_848_Biopsy_1553, Control participants,Cecum NonI tissue

value: Control


title: MSCCR_reGRID_848_Biopsy_1554, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_846_Biopsy_1551, CD participants,Rectum I tissue

value: I


title: MSCCR_reGRID_845_Biopsy_1549, Control participants,Rectum NonI tissue

value: Female


title: MSCCR_reGRID_845_Biopsy_1548, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_847_Biopsy_1552, CD participants,Rectum I tissue


title: MSCCR_reGRID_844_Biopsy_1547, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_846_Biopsy_1550, CD participants,RightColon I tissue

value: RightColon


title: MSCCR_reGRID_84_Biopsy_162, CD participants,Ileum NonI tissue

value: IBD


title: MSCCR_reGRID_84_Biopsy_163, CD participants,Sigmoid I tissue

value: Sigmoid


title: MSCCR_reGRID_836_Biopsy_1544, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_841_Biopsy_1545, CD participants,Ileum I tissue


title: MSCCR_reGRID_841_Biopsy_1546, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_836_Biopsy_1543, Control participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_834_Biopsy_1542, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_832_Biopsy_1540, UC participants,Rectum I tissue

value: UC


title: MSCCR_reGRID_834_Biopsy_1541, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_832_Biopsy_1538, UC participants,Sigmoid NonI tissue


title: MSCCR_reGRID_832_Biopsy_1539, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_831_Biopsy_1537, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_849_Biopsy_1555, CD participants,Ileum NonI tissue

value: CD


title: MSCCR_reGRID_829_Biopsy_1536, UC participants,Rectum I tissue

value: Male

value: Active


title: MSCCR_reGRID_827_Biopsy_1532, UC participants,Ileum NonI tissue

value: Inactive

value: Moderate


title: MSCCR_reGRID_828_Biopsy_1534, UC participants,Sigmoid I tissue

value: Severe


title: MSCCR_reGRID_824_Biopsy_1527, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_827_Biopsy_1533, UC participants,Rectum NonI tissue

value: Rectum


title: MSCCR_reGRID_826_Biopsy_1530, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_825_Biopsy_1528, CD participants,Ileum I tissue

value: Ileum


title: MSCCR_reGRID_823_Biopsy_1525, Control participants,Rectum NonI tissue

value: NonI


title: MSCCR_reGRID_823_Biopsy_1524, Control participants,Ileum NonI tissue

value: Control


title: MSCCR_reGRID_822_Biopsy_1523, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_824_Biopsy_1526, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_826_Biopsy_1531, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_821_Biopsy_1521, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_822_Biopsy_1522, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_821_Biopsy_1520, Control participants,Transverse NonI tissue

value: Transverse


title: MSCCR_reGRID_828_Biopsy_1535, UC participants,Rectum I tissue

value: I


title: MSCCR_reGRID_825_Biopsy_1529, CD participants,Rectum NonI tissue

value: Female


title: MSCCR_reGRID_819_Biopsy_1517, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_820_Biopsy_1518, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_82_Biopsy_160, CD participants,RightColon NonI tissue

value: RightColon

value: IBD


title: MSCCR_reGRID_818_Biopsy_1515, CD participants,Ileum I tissue

value: Mild


title: MSCCR_reGRID_820_Biopsy_1519, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_817_Biopsy_1514, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_815_Biopsy_1511, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_816_Biopsy_1512, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_813_Biopsy_1510, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_817_Biopsy_1513, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_813_Biopsy_1509, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_812_Biopsy_1508, Control participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_82_Biopsy_161, CD participants,Rectum I tissue

value: CD


title: MSCCR_reGRID_811_Biopsy_1506, Control participants,Rectum NonI tissue

value: Male


title: MSCCR_reGRID_810_Biopsy_1503, CD participants,RightColon I tissue


title: MSCCR_reGRID_81_Biopsy_159, CD participants,LeftColon NonI tissue

value: LeftColon


title: MSCCR_reGRID_81_Biopsy_157, CD participants,RightColon NonI tissue

value: Inactive


title: MSCCR_reGRID_81_Biopsy_158, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_810_Biopsy_1504, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_805_Biopsy_1496, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_812_Biopsy_1507, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_811_Biopsy_1505, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_806_Biopsy_1497, CD participants,Transverse I tissue

value: Moderate


title: MSCCR_reGRID_819_Biopsy_1516, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_804_Biopsy_1494, UC participants,RightColon I tissue

value: UC

value: Active


title: MSCCR_reGRID_805_Biopsy_1495, Control participants,Ileum NonI tissue

value: Ileum


title: MSCCR_reGRID_809_Biopsy_1501, UC participants,Ileum NonI tissue

value: NonI


title: MSCCR_reGRID_803_Biopsy_1492, Control participants,Rectum NonI tissue

value: Rectum

value: Control


title: MSCCR_reGRID_803_Biopsy_1491, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_801_Biopsy_1490, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_801_Biopsy_1489, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_800_Biopsy_1488, CD participants,Rectum I tissue

value: I


title: MSCCR_reGRID_80_Biopsy_156, CD participants,Transverse I tissue

value: Female

value: Transverse

value: Severe


title: MSCCR_reGRID_80_Biopsy_155, CD participants,Rectum I tissue

value: IBD


title: MSCCR_reGRID_800_Biopsy_1487, CD participants,Ileum NonI tissue

value: Mild


title: MSCCR_reGRID_80_Biopsy_154, CD participants,Sigmoid I tissue

value: Sigmoid

value: CD


title: MSCCR_reGRID_809_Biopsy_1502, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_798_Biopsy_1486, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_807_Biopsy_1499, Control participants,Ileum NonI tissue

value: Male


title: MSCCR_reGRID_806_Biopsy_1498, CD participants,Rectum NonI tissue

value: Inactive


title: MSCCR_reGRID_807_Biopsy_1500, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_797_Biopsy_1484, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_798_Biopsy_1485, CD participants,Ileum I tissue


title: MSCCR_reGRID_796_Biopsy_1481, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_795_Biopsy_1479, Control participants,RightColon NonI tissue

value: RightColon


title: MSCCR_reGRID_804_Biopsy_1493, UC participants,Rectum I tissue

value: UC


title: MSCCR_reGRID_797_Biopsy_1483, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_796_Biopsy_1482, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_793_Biopsy_1478, CD participants,Rectum I tissue


title: MSCCR_reGRID_793_Biopsy_1477, CD participants,Cecum I tissue

value: Cecum


title: MSCCR_reGRID_791_Biopsy_1476, UC participants,Cecum NonI tissue


title: MSCCR_reGRID_790_Biopsy_1474, CD participants,Ileum NonI tissue

value: Ileum


title: MSCCR_reGRID_791_Biopsy_1475, UC participants,Rectum NonI tissue

value: NonI


title: MSCCR_reGRID_795_Biopsy_1480, Control participants,Rectum NonI tissue

value: Rectum


title: MSCCR_reGRID_788_Biopsy_1472, CD participants,Cecum NonI tissue

value: Moderate


title: MSCCR_reGRID_788_Biopsy_1471, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_787_Biopsy_1470, UC participants,Rectum I tissue

value: I

value: Active


title: MSCCR_reGRID_785_Biopsy_1468, Control participants,Ileum NonI tissue

value: Control


title: MSCCR_reGRID_785_Biopsy_1469, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_783_Biopsy_1464, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_784_Biopsy_1467, UC participants,Sigmoid I tissue


title: MSCCR_reGRID_783_Biopsy_1465, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_782_Biopsy_1463, CD participants,Ileum NonI tissue

value: Female


title: MSCCR_reGRID_782_Biopsy_1462, CD participants,Rectum NonI tissue

value: IBD


title: MSCCR_reGRID_781_Biopsy_1461, CD participants,Rectum I tissue

value: Mild


title: MSCCR_reGRID_780_Biopsy_1459, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_781_Biopsy_1460, CD participants,Ileum I tissue


title: MSCCR_reGRID_78_Biopsy_151, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_780_Biopsy_1458, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_79_Biopsy_153, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_775_Biopsy_1454, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_776_Biopsy_1455, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_79_Biopsy_152, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_779_Biopsy_1456, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_775_Biopsy_1453, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_789_Biopsy_1473, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_779_Biopsy_1457, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_773_Biopsy_1452, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_773_Biopsy_1451, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_770_Biopsy_1448, UC participants,Rectum I tissue


title: MSCCR_reGRID_771_Biopsy_1450, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_784_Biopsy_1466, UC participants,Rectum I tissue


title: MSCCR_reGRID_77_Biopsy_149, CD participants,LeftColon NonI tissue

value: LeftColon


title: MSCCR_reGRID_77_Biopsy_148, CD participants,RightColon NonI tissue

value: CD


title: MSCCR_reGRID_769_Biopsy_1446, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_767_Biopsy_1445, CD participants,Rectum I tissue

value: Severe


title: MSCCR_reGRID_766_Biopsy_1443, CD participants,Rectum I tissue


title: MSCCR_reGRID_765_Biopsy_1441, CD participants,Rectum NonI tissue

value: Inactive


title: MSCCR_reGRID_78_Biopsy_150, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_765_Biopsy_1440, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_764_Biopsy_1439, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_766_Biopsy_1442, CD participants,Ileum I tissue


title: MSCCR_reGRID_771_Biopsy_1449, CD participants,Ileum I tissue

value: Male


title: MSCCR_reGRID_764_Biopsy_1438, UC participants,Cecum I tissue

value: UC


title: MSCCR_reGRID_764_Biopsy_1437, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_763_Biopsy_1435, Control participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_761_Biopsy_1432, CD participants,Rectum I tissue


title: MSCCR_reGRID_763_Biopsy_1436, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_762_Biopsy_1434, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_761_Biopsy_1431, CD participants,Ileum NonI tissue

value: Ileum


title: MSCCR_reGRID_760_Biopsy_1430, CD participants,Rectum NonI tissue

value: NonI


title: MSCCR_reGRID_758_Biopsy_1428, UC participants,Rectum NonI tissue

value: Rectum


title: MSCCR_reGRID_755_Biopsy_1426, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_760_Biopsy_1429, CD participants,Ileum I tissue


title: MSCCR_reGRID_755_Biopsy_1425, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_770_Biopsy_1447, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_758_Biopsy_1427, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_754_Biopsy_1424, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_751_Biopsy_1423, CD participants,Rectum I tissue


title: MSCCR_reGRID_751_Biopsy_1422, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_750_Biopsy_1421, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_750_Biopsy_1420, CD participants,Ileum I tissue


title: MSCCR_reGRID_75_Biopsy_147, UC participants,Rectum I tissue


title: MSCCR_reGRID_75_Biopsy_146, UC participants,LeftColon NonI tissue


title: MSCCR_reGRID_748_Biopsy_1418, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_742_Biopsy_1414, CD participants,Rectum NonI tissue

value: Moderate


title: MSCCR_reGRID_745_Biopsy_1415, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_745_Biopsy_1416, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_762_Biopsy_1433, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_742_Biopsy_1413, CD participants,Ileum I tissue

value: I


title: MSCCR_reGRID_739_Biopsy_1410, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_741_Biopsy_1411, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_738_Biopsy_1408, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_741_Biopsy_1412, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_739_Biopsy_1409, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_738_Biopsy_1407, UC participants,Cecum NonI tissue


title: MSCCR_reGRID_736_Biopsy_1406, UC participants,Cecum NonI tissue


title: MSCCR_reGRID_734_Biopsy_1402, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_733_Biopsy_1400, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_733_Biopsy_1399, CD participants,RightColon NonI tissue

value: RightColon


title: MSCCR_reGRID_735_Biopsy_1403, UC participants,Rectum I tissue


title: MSCCR_reGRID_736_Biopsy_1405, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_734_Biopsy_1401, Control participants,Ileum NonI tissue

value: Control


title: MSCCR_reGRID_732_Biopsy_1397, UC participants,Rectum I tissue

value: Female

value: Active


title: MSCCR_reGRID_735_Biopsy_1404, UC participants,Cecum NonI tissue

value: IBD

value: Mild


title: MSCCR_reGRID_732_Biopsy_1398, UC participants,Cecum NonI tissue


title: MSCCR_reGRID_731_Biopsy_1395, CD participants,Ileum NonI tissue

value: CD


title: MSCCR_reGRID_731_Biopsy_1396, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_750_Biopsy_1419, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_730_Biopsy_1394, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_730_Biopsy_1393, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_73_Biopsy_145, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_73_Biopsy_144, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_728_Biopsy_1392, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_728_Biopsy_1391, CD participants,Ileum I tissue


title: MSCCR_reGRID_727_Biopsy_1390, UC participants,Rectum I tissue


title: MSCCR_reGRID_726_Biopsy_1388, CD participants,Rectum I tissue


title: MSCCR_reGRID_727_Biopsy_1389, UC participants,Cecum NonI tissue


title: MSCCR_reGRID_726_Biopsy_1387, CD participants,Cecum I tissue


title: MSCCR_reGRID_725_Biopsy_1386, CD participants,Rectum I tissue

value: Severe


title: MSCCR_reGRID_748_Biopsy_1417, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_724_Biopsy_1384, UC participants,Rectum NonI tissue

value: Inactive


title: MSCCR_reGRID_724_Biopsy_1383, UC participants,Ileum NonI tissue

value: Male


title: MSCCR_reGRID_722_Biopsy_1380, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_723_Biopsy_1382, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_720_Biopsy_1376, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_721_Biopsy_1377, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_721_Biopsy_1378, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_72_Biopsy_142, CD participants,RightColon NonI tissue


title: MSCCR_reGRID_723_Biopsy_1381, Control participants,Transverse NonI tissue

value: Transverse


title: MSCCR_reGRID_72_Biopsy_143, CD participants,Sigmoid I tissue

value: Sigmoid


title: MSCCR_reGRID_719_Biopsy_1373, Control participants,Ileum NonI tissue

value: Ileum


title: MSCCR_reGRID_718_Biopsy_1371, Control participants,Ileum NonI tissue

value: NonI


title: MSCCR_reGRID_767_Biopsy_1444, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_718_Biopsy_1372, Control participants,Rectum NonI tissue

value: Rectum


title: MSCCR_reGRID_722_Biopsy_1379, CD participants,Ileum I tissue


title: MSCCR_reGRID_725_Biopsy_1385, CD participants,Ileum I tissue


title: MSCCR_reGRID_716_Biopsy_1369, UC participants,Ileum NonI tissue

value: UC


title: MSCCR_reGRID_715_Biopsy_1368, Control participants,Sigmoid NonI tissue


title: MSCCR_reGRID_715_Biopsy_1367, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_714_Biopsy_1366, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_713_Biopsy_1365, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_713_Biopsy_1364, Control participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_712_Biopsy_1363, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_712_Biopsy_1362, CD participants,Ileum I tissue

value: I


title: MSCCR_reGRID_711_Biopsy_1361, UC participants,Rectum NonI tissue


title: MSCCR_reGRID_711_Biopsy_1360, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_711_Biopsy_1359, UC participants,Rectum I tissue


title: MSCCR_reGRID_720_Biopsy_1375, Control participants,Rectum NonI tissue

value: Control


title: MSCCR_reGRID_72_Biopsy_141, CD participants,Ileum NonI tissue

value: Moderate


title: MSCCR_reGRID_710_Biopsy_1357, Control participants,Ileum NonI tissue

value: Female


title: MSCCR_reGRID_71_Biopsy_139, UC participants,Rectum NonI tissue

value: IBD


title: MSCCR_reGRID_709_Biopsy_1355, CD participants,Ileum I tissue

value: Mild


title: MSCCR_reGRID_709_Biopsy_1356, CD participants,Rectum NonI tissue

value: CD


title: MSCCR_reGRID_719_Biopsy_1374, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_71_Biopsy_140, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_708_Biopsy_1354, UC participants,Ileum NonI tissue


title: MSCCR_reGRID_716_Biopsy_1370, UC participants,Rectum I tissue


title: MSCCR_reGRID_708_Biopsy_1353, UC participants,Rectum I tissue


title: MSCCR_reGRID_707_Biopsy_1351, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_707_Biopsy_1352, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_706_Biopsy_1350, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_706_Biopsy_1349, CD participants,Sigmoid I tissue


title: MSCCR_reGRID_705_Biopsy_1347, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_705_Biopsy_1346, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_706_Biopsy_1348, CD participants,Ileum I tissue


title: MSCCR_reGRID_704_Biopsy_1345, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_704_Biopsy_1344, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_710_Biopsy_1358, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_702_Biopsy_1342, CD participants,Ileum I tissue

value: Active

value: Severe


title: MSCCR_reGRID_703_Biopsy_1343, CD participants,Rectum NonI tissue

value: Male

value: Inactive


title: MSCCR_reGRID_700_Biopsy_1338, CD participants,RightColon I tissue

value: RightColon


title: MSCCR_reGRID_701_Biopsy_1340, UC participants,Ileum NonI tissue

value: Ileum


title: MSCCR_reGRID_702_Biopsy_1341, CD participants,Rectum I tissue


title: MSCCR_reGRID_701_Biopsy_1339, UC participants,Rectum I tissue


title: MSCCR_reGRID_70_Biopsy_137, CD participants,RightColon NonI tissue

value: NonI


title: MSCCR_reGRID_7_Biopsy_16, CD participants,RightColon I tissue


title: MSCCR_reGRID_698_Biopsy_1337, UC participants,Cecum I tissue


title: MSCCR_reGRID_71_Biopsy_138, UC participants,RightColon NonI tissue


title: MSCCR_reGRID_697_Biopsy_1334, UC participants,Sigmoid I tissue

value: Sigmoid


title: MSCCR_reGRID_698_Biopsy_1336, UC participants,Rectum I tissue

value: Rectum

value: UC


title: MSCCR_reGRID_696_Biopsy_1332, Control participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_7_Biopsy_15, CD participants,LeftColon I tissue

value: LeftColon

value: I


title: MSCCR_reGRID_695_Biopsy_1330, CD participants,Rectum I tissue


title: MSCCR_reGRID_697_Biopsy_1335, UC participants,Rectum I tissue

value: Female


title: MSCCR_reGRID_694_Biopsy_1329, UC participants,Rectum NonI tissue

value: IBD


title: MSCCR_reGRID_694_Biopsy_1328, UC participants,Ileum NonI tissue

value: Mild


title: MSCCR_reGRID_696_Biopsy_1333, Control participants,Rectum NonI tissue

value: Control


title: MSCCR_reGRID_695_Biopsy_1331, CD participants,Cecum I tissue

value: CD


title: MSCCR_reGRID_693_Biopsy_1325, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_692_Biopsy_1324, UC participants,Rectum I tissue

value: Active


title: MSCCR_reGRID_693_Biopsy_1326, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_691_Biopsy_1321, CD participants,Rectum NonI tissue

value: Male

value: Moderate


title: MSCCR_reGRID_692_Biopsy_1323, UC participants,RightColon NonI tissue

value: RightColon


title: MSCCR_reGRID_691_Biopsy_1322, CD participants,Ileum I tissue

value: Ileum


title: MSCCR_reGRID_69_Biopsy_136, CD participants,LeftColon NonI tissue

value: NonI

value: Inactive


title: MSCCR_reGRID_69_Biopsy_134, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_69_Biopsy_135, CD participants,RightColon NonI tissue


title: MSCCR_reGRID_689_Biopsy_1320, Control participants,Rectum NonI tissue

value: Rectum


title: MSCCR_reGRID_689_Biopsy_1319, Control participants,Cecum NonI tissue


title: MSCCR_reGRID_688_Biopsy_1318, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_686_Biopsy_1316, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_684_Biopsy_1314, CD participants,Rectum I tissue


title: MSCCR_reGRID_682_Biopsy_1312, CD participants,Rectum NonI tissue


title: MSCCR_reGRID_684_Biopsy_1313, CD participants,Cecum NonI tissue


title: MSCCR_reGRID_688_Biopsy_1317, Control participants,Ileum NonI tissue


title: MSCCR_reGRID_682_Biopsy_1311, CD participants,Ileum NonI tissue


title: MSCCR_reGRID_680_Biopsy_1307, UC participants,Rectum NonI tissue

value: UC


title: MSCCR_reGRID_694_Biopsy_1327, UC participants,Rectum I tissue


title: MSCCR_reGRID_681_Biopsy_1310, CD participants,Rectum I tissue

value: Severe


title: MSCCR_reGRID_680_Biopsy_1306, UC participants,Sigmoid I tissue

value: Sigmoid


title: MSCCR_reGRID_68_Biopsy_132, CD participants,Cecum NonI tissue

value: Cecum


title: MSCCR_reGRID_68_Biopsy_131, CD participants,Ileum NonI tissue

value: Female


title: MSCCR_reGRID_680_Biopsy_1308, UC participants,Ileum NonI tissue

value: IBD


title: MSCCR_reGRID_68_Biopsy_133, CD participants,LeftColon NonI tissue

value: LeftColon


title: MSCCR_reGRID_678_Biopsy_1304, CD participants,RightColon NonI tissue


title: MSCCR_reGRID_678_Biopsy_1303, CD participants,Sigmoid NonI tissue


title: MSCCR_reGRID_676_Biopsy_1302, UC participants,Rectum I tissue

value: I


title: MSCCR_reGRID_676_Biopsy_1301, UC participants,Cecum NonI tissue


title: MSCCR_reGRID_675_Biopsy_1299, Control participants,Ileum NonI tissue

value: Control


title: MSCCR_reGRID_674_Biopsy_1297, Control participants,LeftColon NonI tissue


title: MSCCR_reGRID_686_Biopsy_1315, CD participants,Ileum I tissue

value: CD

value: Mild


title: MSCCR_reGRID_675_Biopsy_1300, Control participants,Rectum NonI tissue


title: MSCCR_reGRID_673_Biopsy_1296, Control participants,Rectum NonI tissue

value: Male


title: MSCCR_reGRID_671_Biopsy_1292, CD participants,Ileum I tissue

value: Active


title: MSCCR_reGRID_672_Biopsy_1293, Control participants,RightColon NonI tissue

value: RightColon


title: MSCCR_reGRID_681_Biopsy_1309, CD participants,Ileum I tissue

value: Ileum


title: MSCCR_reGRID_670_Biopsy_1289, Control participants,RightColon NonI tissue

value: NonI