title: CTX, Cd8-cre+, rep3

data_processing:
Raw data was analyzed using Partek Flow.
Reads were subjected to base trim and STAR alignment to obtain transcript counts, then normalized.
Assembly: mm39
Supplementary files format and content: tab-demilited text file includes raw counts for each sample
Supplementary files format and content: tab-demilited text file includes Partek E/M values for each sample

source_name: CTX

growth_protocol: Mice were infected with WNV-NS5-E218A. Brain tissues were harvested at 30 days post infection.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

treatment_protocol: CTX and HPC were dissected from mouse brains.

value: CTX


title: UV213 Aqueous BCR

status: Public on Jan 02 2025

type: SRA

city: Aurora

first: Christian

last: Concepcion

state: Colorado

country: USA

institute: University of Colorado Denver Anschutz Medical

description: 10x Genomics

library_source: transcriptomic

data_processing:
"We processed the raw FASTQ sequencing files using CellRanger with alignment to the 10x Genomics human reference genome (refdata-gex-GRCh38-2020-A).  We imported the count matrices into Seurat and  used the Immcantation suite of R packages to observe the mutations in BCRs and TCRs.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scBCR-seq

molecule: polyA RNA

organism: Homo sapiens

source_name: Ocular Aqueous fluid

extract_protocol:
We sampled 100-200 ul of the inflamed anterior chamber fluid using a 25- to 30-gauge needle. We pelleted cells by centrifugation (400 x g, 5 min) to remove the aqueous fluid and cryopreserved cells in fetal bovine serum containing 10% DMSO.
We used the 10x Genomics 5'v2 gene expression kit according to the manufacturer's protocol.

tag: tissue

value: Ocular Aqueous fluid

tag: cell type


title: CTX, Cd8-cre+, rep4

city: St. Louis

first: Robyn

last: Klein

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

organism: Mus musculus

tag: genotype

tag: treatment


title: UV213 Blood BCR

description: 10x Genomics

source_name: Peripheral blood

value: Peripheral blood


title: UV196 Blood BCR

description: 10x Genomics


title: SUCSUL

city: Riverside

first: Ye

last: Xu

state: CA

address: 900 University Ave

institute: University of California, Riverside

library_source: genomic

data_processing:
The MethylC-seq raw reads were mapped and converted to every cytosine according to description previously (Li et al., 2016, DOI: 10.1093/nar)
The methylation level of reads mapped to specific genomic loci (SUC:SUL locus, endogenous SUL locus, IR-71 locus and At5g22960 locus) were calculated according to  methods described previously (Li et al., 2016, DOI: 10.1093/nar).
Assembly: TAIR10

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: SUCSUL transgenic line

growth_protocol: 16 hr light and 8 hr dark at 22 ˚C on 1/2 MS medium

extract_protocol:
Genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen) and sonicated as described previously (Li et al., 2016, DOI: 10.1093/nar)
The sonicated DNA fragments were purified and ligated with methylated adapters from the TruSeq DNA Sample Preparation Kit (Illumina) at 16°C overnight. Less than 400 ng ligated product was used for bisulfite conversion using the Methyl- Code Kit (Invitrogen) according to the manufacturer’s guidelines.

tag: ecotype

value: WT

tag: transgene

tag: time

value: 13-d-old seedling


title: CTX, Cd8-cre+, rep2


title: HMEC, IFNy, LPS, ALEKSIN, rep3

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

data_processing:
After quality control, adapter trimming, and quality filtering with fastp (v.0.22.0), fastq files were mapped to the Homo sapiens GRCh38/hg38 genome using STAR version 2.6.1d
Read counts were generated using FeatureCounts v1.6.2 with default parameters
Counts normalization and DEG analysis were performed using the edgeR (v.3.30.3) package in R version 3.6.3
Assembly: GRCh38/hg38 genome build (release-100)
Supplementary files format and content: text file (csv) with raw counts for each sample

molecule: total RNA

source_name: skin

growth_protocol: HMEC cell line (https://pubmed.ncbi.nlm.nih.gov/1361507/) was cultured in MCDB complete medium supplemented with 10% FBS (10500-064, TFS), 1:100 L-glutamine (X0550, BioWest) and 1:100 antibiotic/antimycotic solution (A5955, Sigma-Aldrich), hydrocortisone (H0888, MERCK) and EGF (324831, MERCK) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated with GeneMATRIX Universal RNA Purification Kit (E3598, EURx) following the manufacturer's protocol.
RNA-seq libraries were prepared in three biological replicates from 1ug of total RNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) together with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Multiplex Oligos for Illumina® (NEB) according to manufacturer's protocol

treatment_protocol:
Cells were seeded on the 6-well plates in MCDB complete medium. After around 24-28 h when they reached around 70% confluency, the medium was changed, and cells were kept in 1% FBS MCDB starving medium
After at least 8h of starvation they were pre-treated with ALEKSIN compound (10μM, ZINC9547778, MolPort-004-931-223; supplier: IBS (STOCK6S-36352)) for 24h or STATTIC (10μM, 19983-44-9, Sigma) for 8h. In order to mimic inflammation in the cell culture environment HMECs were stimulated with IFNγ (10 ng/ml, IF002, MERCK) for 8h and LPS (1µg/ml, L4391, Sigma-Aldrich)  for 4h before RNA was isolated.

value: skin

tag: cell line

value: primary endothelial cells

value: IFNgamma (8h, 10 ng/ml), LPS (4h, 1microg/ml ) in the presence of 10microM ALEKSIN (24h)


title: brain, Cd8-cre+, rep2

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Gene couting and aggregation were made using the Cell ranger-7.2.0.
Cell count matrix was analyzed in Partek Flow software v12.0.2 suite with the standard pipeline for scRNA-seq analyses to conduct QA/QC filtering, align and normalize reads, identify cell clusters, generate lists of DEGs and conduct GSEA.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Forebrain

extract_protocol:
Mice were anesthetized and sacrificed by cardiac perfusion with ice-cold dPBS (Gibco). Brains were aseptically dissected, minced and enzymatically digested in HBSS containing 0.05% collagenase D (Sigma), 0.1 μg/mL TLCK trypsin inhibitor (Sigma), 10 μg/mL DNase I (Sigma), and 10 mM HEPES (Gibco) at 37°C for 1h with shaking. Tissues were then pushed through a 70 μm strainer and centrifuged at 500× g for 10 min. Brain cell pellets were resuspended in 37% isotonic Percoll (Cytiva, cat. no. 17089101) and centrifuged at 1200× g for 30 min to remove myelin debris. Cells were washed in PBS. Dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, cat. no. 130-090-101). Live cells were diluted to 1000 cells/µL with ice-cold 0.04% BSA in PBS.
Samples were sent to Genome Access Technology Center at the McDonnell Genome Institute for library preparation using 10x Genomics Chromium Single Cell 5' Reagent Kits and sequencing.

value: Forebrain

value: Immune cells


title: HMEC, IFNy, LPS, ALEKSIN, rep2


title: UV196 Aqueous BCR

description: 10x Genomics


title: UV195 Blood BCR

description: 10x Genomics


title: HMEC, IFNy, LPS, STATTIC, rep1

value: IFNgamma (8h, 10 ng/ml), LPS (4h, 1microg/ml ) in the presence of 10microM STATTIC (8h)


title: HMEC, IFNy, LPS, ALEKSIN, rep1


title: HCC827-Resistant-OC3

city: nanjing

first: Qianfan

last: Hu

state: jiangsu

address: nanjing

country: China

institute: nanjing medical university

description: Library name: Unknown_BW178-001T0006

data_processing:
Sequencing data were quality controlled using "fastqc" software and rRNA sequencing was removed using "SortMeRNA".
Using CIRI (CircRNA Identifier) tools to identification circRNA
Aligning to Genome with STAR-aligner and Summarizing Gene Counts with featureCounts.
Generating analysis report with multiQC.
Assembly: hg19
Supplementary files format and content: Csv files with FPKM data.

source_name: Lung

growth_protocol: HCC827 and PC9 cells were cultured in DMEM with 10% FBS (Corning). Before the experiment, cells were tested for mycoplasma, cross-contamination between species and authenticity. Cell lines in the experiments were used within 20 passages.

extract_protocol:
RNA degradation and contamination, especially DNA contamination, was monitored on 1.5% agarose gels. RNA concentration and purity was measured using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （ 5X）. First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.

value: Lung

value: HCC827 cells

value: Human non-small cell lung cancer

value: cATF6 overexpression


title: HCC827-Resistant-OC2

description: Library name: Unknown_BW178-001T0005


title: HCC827-Resistant-OC1

description: Library name: Unknown_BW178-001T0004


title: UV195 Aqueous BCR

description: 10x Genomics


title: HMEC, IFNy, LPS, rep3

value: IFNgamma (8h, 10 ng/ml), LPS (4h, 1microg/ml )


title: HCC827-Resistant-EV3

description: Library name: Unknown_BW178-001T0003

value: EV


title: CTX, cre-, rep3

value: CTX

value: cre-


title: UV180 Blood BCR

description: 10x Genomics

value: Peripheral blood


title: HCC827-Resistant-EV2

description: Library name: Unknown_BW178-001T0002

value: WT


title: CTX, cre-, rep2


title: HMEC, IFNy, LPS, rep2


title: HCC827-Resistant-EV1

description: Library name: Unknown_BW178-001T0001


title: UV179 Blood BCR

description: 10x Genomics


title: CTX, cre-, rep1


title: UV179 Aqueous BCR

description: 10x Genomics

value: Ocular Aqueous fluid


title: HCC827-DTP-OC3

description: Library name: Unknown_BG988-03T0012


title: HPC, Cd8-cre+, rep4

source_name: HPC

value: HPC


title: HMEC, IFNy, LPS, rep1

value: skin

value: primary endothelial cells


title: HMEC, control, rep3

value: untreated


title: UV176 Blood BCR

description: 10x Genomics


title: CTX, Cd8-cre+, rep1


title: CTX, cre-, rep4


title: HMEC, control, rep2


title: HCC827-DTP-OC2

description: Library name: Unknown_BG988-03T0011


title: UV176 Aqueous BCR

description: 10x Genomics


title: HMEC, control, rep1


title: HPC, Cd8-cre+, rep2


title: UV174 Blood BCR

description: 10x Genomics


title: HCC827-DTP-EV3

description: Library name: Unknown_BG988-03T0009


title: DNMT1 rep3

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

data_processing:
STAR 2.6.1 aligned to HG38
Quantified to Ensembl human genome 92
Normalized via Log2 Counts per million with offset of 1
Log normal shrinkage was used to remove batch effect between runs
Counts with a maximum of less than 2 were filtered out for a normal distribution
Assembly: HG38
Supplementary files format and content: tab-delimited text files, includes RPKM values for each sample

extract_protocol:
Total RNA was extracted from the cells according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the NEB Ultra II Library Preparation Kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs) following the manufacturer’s protocol.

treatment_protocol: MDA-MB-231 were transduced with KMT2B, KMT2D and DNMT1 shRNA

value: Breast Cancer

value: DNMT1 knockdown


title: HPC, Cd8-cre+, rep1


title: UV174 Aqueous BCR

description: 10x Genomics


title: HCC827-DTP-EV2

description: Library name: Unknown_BG988-03T0008

value: Lung


title: HPC, cre-, rep4


title: DNMT1 rep2


title: HCC827-DTP-EV1

description: Library name: Unknown_BG988-03T0007

value: HCC827 cells


title: UV170 Blood BCR

description: 10x Genomics


title: DNMT1 rep1


title: UV170 Aqueous BCR

description: 10x Genomics


title: HCC827-Parental-OC3

description: Library name: Unknown_BG988-03T0006

value: Human non-small cell lung cancer


title: HPC, cre-, rep3


title: HPC, cre-, rep2


title: HPC, cre-, rep1


title: HPC, Cd8-cre+, rep3


title: KMT2D rep2

value: KMT2D knockdown


title: HCC827-Parental-OC2

description: Library name: Unknown_BG988-03T0005

value: cATF6 overexpression


title: KMT2D rep1


title: UV160 Blood BCR

description: 10x Genomics


title: UV150 Blood BCR

description: 10x Genomics


title: HCC827-Parental-OC1

description: Library name: Unknown_BG988-03T0004


title: KMT2B rep3

value: KMT2B knockdown


title: HFD-Veh_rep3

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

data_processing:
Quality of the raw fastq files were determined using FastQC(v0.11.9). Adapters were trimmed using Cutadapt.  Trimmed and filtered reads were aligned to mouse reference genome (mm39- GENCODE Release M30) using STAR aligner (version 2.7.8a). Transcript levels were quantified to the reference using a modified expectation-maximization (EM) algorithm. Normalization was done using median ratio method. Differential expression analysis was performed using DESeq2 (v3.5). Genes were considered to be differentially expressed based on fold change>1.5 and p-value<0.05. Functional enrichment analysis for the differentially expressed genes was performed using Ingenuity Pathway analysis (IPA, Qiagen). Heatmaps were generated in R (v4.2.3) using pheatmap package (v1.0.12).
Assembly: mm39-Gencode Genes- release M30
Supplementary files format and content: tab-delimited text files include normalized counts for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated using QIAGEN RNeasy Mini kit and quantified using Qubit fluorometer (Thermo Fisher Scientific). Quality of the isolated RNA was checked using Agilent Bioanalyzer 2100. Universal Plus mRNA-Seq Library with NuQuant (TECAN) was used to generate stranded RNA-seq libraries. Briefly, poly(A) RNA was selected followed by RNA fragmentation. Double stranded cDNA was generated thereafter using a mixture of random and oilgo(dT) priming. The library was then constructed by end repairing the cDNA to generate blunt ends, ligation of Unique Dual Index (UDI) adaptors, strand selection and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Quality of the library was checked using Agilent Bioanalyzer 2100. Sequencing was performed on Illumina NovaSeq X Plus with paired-end 50 base pair reads.
Universal Plus mRNA-Seq Library with NuQuant (TECAN)

treatment_protocol: 1-year-old aged male C57BL/6 mice were placed on high-fat diet and administered R159 or vehicle (Veh) twice a week via intraperitoneal injection for 12 weeks

value: Liver

value: HFD, Vehicle


title: HCC827-DTP-OC1

description: Library name: Unknown_BG988-03T0010


title: HCC827-Parental-EV3

description: Library name: Unknown_BG988-03T0003

value: EV


title: KMT2B rep2


title: HFD-Veh_rep2


title: UV129 Blood BCR

description: 10x Genomics

value: Peripheral blood


title: HFD-Veh_rep1


title: KMT2B rep1


title: scramble rep3

value: WT


title: HCC827-Parental-EV1

description: Library name: Unknown_BG988-03T0001


title: UV122 Aqueous BCR

description: 10x Genomics

value: Ocular Aqueous fluid


title: HCC827-Osi3

description: Library name: Unknown_BG988-02L0006

value: Osi for 10 days


title: HFD-R159_rep3

value: HFD, R159


title: UV129 Aqueous BCR

description: 10x Genomics


title: scramble rep2


title: HFD-R159_rep2


title: HFD-R159_rep1


title: HCC827-Osi2

description: Library name: Unknown_BG988-02L0005


title: UV031 Blood BCR

description: 10x Genomics


title: scramble rep1


title: UV031 Aqueous BCR

description: 10x Genomics


title: HCC827-Osi1

description: Library name: Unknown_BG988-02L0004


title: SC5314, Baicalin, rep2

city: Hefei

first: Wenqian

last: Li

address: Longzihu Road

institute: Anhui University of Chinese Medicine

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp(0.19.5) with default parameters.Then clean reads were separately aligned to reference genome with orientation mode using HISAT2(Version 2.1.0) software. The mapped reads of each sample were assembled by StringTie(Version2.1.2) in a reference-based approach.
The expression level of each transcript was  calculated  according  to  the  transcripts per million  reads  (TPM)  method.  RSEM(Version 1.3.3) was used to quantify  gene  abundances.
Assembly: GCF_000182965.3
Supplementary files format and content: table-delimited text file includes read counts for each sample
Supplementary files format and content: table-delimited text file includes tpm for each sample

organism: Candida albicans SC5314

source_name: fungi

growth_protocol: C. albicans strain SC5314 was grown in YPD medium at 37 ℃

extract_protocol:
Total RNA was extracted using MJZol total RNA extraction kit(Shanghai Majorbio Bio-pharm Technology Co.,Ltd) according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150 bp read length).

treatment_protocol: C. albicans strain SC5314 was cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 2.5×10^4 CFU/mL and incubated at 37 ℃ for 24 hours in the presence or absence of baicalin at 500 μg/mL.

value: fungi

tag: strain

value: fungal cell

value: wild type

value: incubated at 37 degreeC for 24 hours in the presence of baicalin at 500 μg/mL


title: SC5314, Baicalin, rep3


title: Budesonide_2D_day 3 rep 3

city: Naples

first: Cristina

last: D'Aniello

address: Via Pietro Castellino, 111

country: Italy

institute: IGB-CNR

data_processing:
Illumina NextSeq
Raw data were aligned to HG38 - Release 37 (GRCh38.p13)
Read count extraction using FeatureCounts. Normalization was performed using DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample.

source_name: pancreatic ductal adenocarcinoma

growth_protocol: Patient-derived PDAC cells (PDAC#253) were plated (15 x 10^3 cells/cm2) at day –1 on gelatin-coated plates in RPMI + 10%FBS.

extract_protocol:
Total RNA was extracted using Trizol (iInvitrogen).
Libraries for RNA-seq were prepared using standard using Illumina platform.
3' prime mRNA-seq

treatment_protocol: At day 0, cells were treated ± budesonide (20 μM; SIGMA) or untreated for three days.

value: pancreatic ductal adenocarcinoma

value: patient-derived PDAC cell line

value: treated with budesonide (20 uM) for 3 days


title: UV286 Blood TCR

description: 10x Genomics

data_processing:
"We processed the raw FASTQ sequencing files using CellRanger with alignment to the 10x Genomics human reference genome (refdata-gex-GRCh38-2020-A).  We imported the count matrices into Seurat and  used the Immcantation suite of R packages to observe the mutations in BCRs and TCRs.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq


title: HCC827-DMSO3

description: Library name: Unknown_BG988-02L0003

value: Lung

value: HCC827 cells

value: Human non-small cell lung cancer

value: DMSO for 10 days


title: UV150 Aqueous BCR

description: 10x Genomics


title: HCC827-DMSO2

description: Library name: Unknown_BG988-02L0002


title: SC5314, Baicalin, rep1


title: UV285 Aqueous TCR

description: 10x Genomics


title: UV284 Blood TCR

description: 10x Genomics


title: Budesonide_2D_day 3 rep 2


title: Control_2D_day 3 rep 3

value: untreated


title: HCC827-Parental-EV2

description: Library name: Unknown_BG988-03T0002

value: EV


title: UV284 Aqueous TCR

description: 10x Genomics


title: SC5314, Control, rep2

value: incubated at 37 degreeC for 24 hours in the absence of baicalin


title: Budesonide_2D_day 3 rep 1


title: HCC827-DMSO1

description: Library name: Unknown_BG988-02L0001

value: WT


title: LNCaP_R1881_DMSO_22h rep10

city: Berlin

first: Andreas

last: Schlicker

address: Muellerstr 178

department: Translational Sciences Oncology Computational Biology

country: Germany

institute: Bayer AG

data_processing:
Illumina bcl2fastq v2.17 was used to convert bcl to fastqs.
RNA-seq reads were aligned to GRCh38 using STAR aligner.
featureCounts from subread package was used to quantify reads in genes
Counts per Million (CPM) were calculated per gene and sample by dividing raw counts by the overall sum of counts for the given sample and multiplying by 1 million
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts per million (cpm) for all genes and samples

source_name: prostate cancer

growth_protocol: Cells were routinely grown in the recommended medium in the presence of 10% (v/v) fetal bovine serum (Life Technologies, Carlsbad, CA) at 37°C and 5% CO2. Authentication was performed by the DSMZ using short tandem repeat DNA typing analysis.

extract_protocol:
Cells were lyzed and RNA was isolated using RNeasy columns with on-column DNA digestion, as described by the manufacturer (Qiagen, Hilden, Germany). RNA integrity was measured and samples with values above 8 were further processed.
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit and sequenced on Illumina HiSeq2500 HTv4 (single-end, dual-indexing, 50 Cycles).

treatment_protocol: Cells were stimulated with the synthetic androgen R1881 at a concentration of 1 nM after two days of starvation in medium supplemented with 10% charcoal-stripped fetal calf serum (cFCS). Darolutamide was added at a final concentration of 2 µM, and the cells were harvested 22 h post-treatment.

value: prostate cancer

value: LNCaP


title: SC5314, Control, rep3

value: fungi


title: Control_2D_day 3 rep 1


title: LNCaP_R1881_Darolutamide_22h rep5

description: 88_1nM_R1881_high_Darolutamide_22h_S63_R1_001

value: R1881 1nM + Darolutamide 2uM


title: SC5314, Control, rep1

value: fungal cell

value: wild type


title: Control_2D_day 3 rep 2

value: pancreatic ductal adenocarcinoma


title: UV229 Aqueous TCR

description: 10x Genomics

value: Ocular Aqueous fluid


title: UV229 Blood TCR

description: 10x Genomics

value: Peripheral blood


title: HUVEC TMP-269 rep2

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

description: HUVEC_TMP269_rep2_Lexogen_12nt_i7_i712_0038_ATGGGCTAGACA_S38

data_processing:
Sequencing reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2; https://nf-co.re/rnaseq) with the hg19 reference genome and Ensembl release 87 transcript definitions.
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing raw counts

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich, St. Louis, MO) in Endothelial Cell Growth medium with endothelial cell growth supplement w/o VEGF-A (Promocell, Heidelberg, Germany, passage <3). Human pulmonary fibroblasts (HPF, passage < 11) were cultured in Fibroblast Growth Medium 2 with SupplementMix (Promocell).

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.
Library preparation was carried out using the Lexogen Quantseq 3’mRNA-seq Library Prep Kit-FWD for Illumina (Lexogen, Vienna, Austria) with the unique dual indexing add-on kit according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with A-196 (1 uM), TMP-269 (10 uM) or DMSO (vehicle control) for 72 hours.

value: HUVEC

tag: replicate


title: LNCaP_R1881_DMSO_22h rep9


title: Chimp_4x0529 [SP5E4067]

city: Cambridge

first: wenzhong

last: xiao

state: ma

address: 38 sidney st, suite 161

institute: massachusetts general hospital

data_processing:
Sequencing quality was assessed additionally using FASTQC (v0.11.9). Transcriptome annotations of each species were downloaded from Ensembl (https://www.ensembl.org, v90). For each sample, firstly, reads were aligned to human genome hg38 using STAR in the established bulk-RNA sequencing workflow of Bcbio (v1.2.1).  Secondly, the abundance of the annotated genes of the species was estimated from the RNA-seq reads as Transcripts per Million (TPM) using Sailfish. Thirdly, to compare the gene expression between species, the abundance of the genes in each species was then translated to that of the corresponding human orthologues. Here, only genes in a non-human species that had known orthologous human genes (Ensembl v90) were considered in further analysis. When m genes in a non-human species had n orthologous genes in human (m>=0, n>=1), the abundance of each of the human orthologues is assumed to be the sum of the abundance of the m genes divided by n.
Assembly: hg38 Ensembl v90
Supplementary files format and content: TPM matrix

organism: Pan troglodytes

source_name: blood

extract_protocol:
After incubation, blood in TruCulture tubes was separated according to the manufacturer’s instructions with additional centrifugation at 800 ×g for 10 minutes.  Supernatants were saved and frozen at −80 °C for cytokine analysis.  The cell pellets were lysed using red blood cell lysis solution for 10 min followed by centrifugation at 2,000 ×g for 3 minutes, and remaining white blood cells were lysed in Qiazol and frozen at −80 °C until library construction (Qiagen).
RNA isolated from white blood cells (Qiazol, Qiagen) was quality controlled using A260/A280 ratio, 28S/18S rRNA ratio, and an RNA integrity summary score (Agilent RIN). Total RNA samples (250ngs, RIN>=7.0) were enriched for mRNA, fragmented, and converted into indexed cDNA libraries according to Illumina TruSeq Stranded mRNA protocol and quantity controlled using Agilent TapeStation. Samples were sequenced to at least 25M of 2 x 50bp paired-end reads and assessed using in-house QA/QC metric (Q2Solutions Expression Analysis).

treatment_protocol: Blood was collected into heparin tubes using meticulous pyrogen-free conditions. TruCulture tubes (Myriad RBM) containing either cell culture media only (“control”) or cell culture media plus 10 ng, 100 ng, or 1 μg/mL E. coli0113 US national reference strain LPS were prepared in advance, stored at -20 °C or below, and thawed at room temperature immediately prior to use. 1 mL blood was added to each tube and samples were incubated for 2, 6 and 24 h at 37 °C with 5% CO2.

value: blood

tag: subject

value: NC

tag: timeunit

value: Hour

tag: dose

tag: doseunit

value: ng/mL

tag: group

value: S (sensitive)


title: UV215-004 Blood TCR

description: 10x Genomics


title: HUVEC TMP-269 rep1

description: HUVEC_TMP269_rep1_Lexogen_12nt_i7_i712_0037_TTAGGACGCAAA_S37


title: Chimp_4x0529 [SP2234A0]


title: UV215-004 Aqueous TCR

description: 10x Genomics


title: LNCaP_R1881_DMSO_22h rep8


title: LNCaP_R1881_Darolutamide_22h rep4

description: 89_1nM_R1881_high_Darolutamide_22h_S29_R1_001


title: Chimp_4x0529 [SP528FF2]


title: HUVEC DMSO rep2

description: HUVEC_DMSO_rep2_Lexogen_12nt_i7_i712_0034_AGCAAAGGATGT_S34

value: DMSO


title: UV215-003 Blood TCR

description: 10x Genomics


title: HUVEC DMSO rep1

description: HUVEC_DMSO_rep1_Lexogen_12nt_i7_i712_0033_CACCTTCGGTTG_S33


title: UV215-003 Aqueous TCR

description: 10x Genomics


title: Chimp_4x0529 [SPFBB2EB]

value: LPS


title: Chimp_4x0529 [SPCEDEC7]


title: LNCaP_R1881_Darolutamide_22h rep2

description: 86_1nM_R1881_high_Darolutamide_22h_S47_R1_001

value: prostate cancer


title: HUVEC A-196 rep2

description: HUVEC_A196_rep2_Lexogen_12nt_i7_i712_0036_GCGCGAAGTTGA_S36


title: LNCaP_R1881_DMSO_22h rep7

value: LNCaP


title: UV213 Blood TCR

description: 10x Genomics


title: Chimp_4x0529 [SP67D635]


title: LNCaP_R1881_DMSO_22h rep6


title: UV213 Aqueous TCR

description: 10x Genomics


title: Chimp_4x0529 [SP1041F2]


title: UV196 Blood TCR

description: 10x Genomics


title: Chimp_4x0529 [SP96EC7E]


title: HPF TMP-269 rep1

description: hPF_TMP269_rep1_Lexogen_12nt_i7_i712_0043_CAAGGTCCCCTT_S43

source_name: HPF

value: HPF


title: LNCaP_R1881_DMSO_22h rep4


title: Chimp_4x0529 [SP35442D]


title: UV196 Aqueous TCR

description: 10x Genomics


title: LNCaP_R1881_DMSO_22h rep3


title: UV195 Blood TCR

description: 10x Genomics


title: HPF DMSO rep2

description: hPF_DMSO_rep2_Lexogen_12nt_i7_i712_0040_GAATTCGTATAC_S40


title: LNCaP_R1881_Darolutamide_22h rep3

description: 90_1nM_R1881_high_Darolutamide_22h_S9_R1_001

value: R1881 1nM + Darolutamide 2uM


title: Chimp_4x0529 [SP29CB71]


title: Chimp_4x0529 [SPEBCDC7]


title: HPF DMSO rep1

description: hPF_DMSO_rep1_Lexogen_12nt_i7_i712_0039_TTTGTGGACACG_S39


title: UV195 Aqueous TCR

description: 10x Genomics


title: LNCaP_R1881_DMSO_22h rep2


title: LNCaP_R1881_DMSO_22h rep1


title: HPF A-196 rep1

description: hPF_A196_rep1_Lexogen_12nt_i7_i712_0041_TCGAGTCCCGGA_S41


title: HUVEC A-196 rep1

description: HUVEC_A196_rep1_Lexogen_12nt_i7_i712_0035_AGGCTTAATCGG_S35


title: UV186 Blood TCR

description: 10x Genomics


title: LNCaP_R1881_Darolutamide_22h rep1

description: 87_1nM_R1881_high_Darolutamide_22h_S1_R1_001


title: UV186 Aqueous TCR

description: 10x Genomics


title: Chimp_4x0529 [SP528436]


title: HPF TMP-269 rep2

description: hPF_TMP269_rep2_Lexogen_12nt_i7_i712_0044_TCCTAGCGATTT_S44


title: Human_5 [SP2B4889]


title: LNCaP_R1881_DMSO_22h rep5


title: Chimp_4x0527 [SP3636D3]


title: Human_5 [SP04C27D]


title: Colon fibroblast, healthy, strain, donor H2, rep3

city: Boston

first: Alican

last: Ozkan

state: MA

address: 201 Brookline Ave, Suite 401

department: Wyss Institute

institute: Harvard University

data_processing:
Trimmomatic v.0.36 was used to remove possible adapter sequences and nucleotides with poor quality from sequence reads.
STAR aligner v.2.5.2b was then used to map the trimmed reads to the Homo sapiens GRCh38 with ERCC genes reference genome available on ENSEMBL.
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Before differential expression analysis, genes were filtered to include only genes with at least 3 reads counted in at least 20% of samples in any group. Differential expression analysis was then performed with the DESeq2 R package , which tests for differential expression based on a model using the negative binomial distribution.
Assembly: Homo sapiens GRCh38 with ERCC genes reference genome available on ENSEMBL
Supplementary files format and content: CSV file of raw gene counts

source_name: colon

growth_protocol: Optically clear Organ Chips made of poly-dimethylsiloxane (PDMS) and containing two parallel microchannels (top, 1 x 1 mm; bottom, 1 x 0.2 mm) separated by 50 m thick PDMS porous membrane (7 m pore diameter, 40 m spacing) were purchased from Emulate Inc (Basic Research Kit). Surfaces were activated using 0.5 mg/mL sulfo-SANPAH solution (A35395; Thermo Fisher Scientific) for 20 min and coated with 0.2 mg/mL collagen type I (354236; Corning) and 1% Matrigel (354230, Corning) in Dulbecco’s phosphate-buffered saline (DPBS). During the coating step, colonoids were obtained by dissolving Matrigel using cell recovery solution 354253 (Corning) for 40 min on ice and spun down at 400 xg for 5 min at 4 oC. Colonoids were then fragmented with TrypLE Express Enzyme (12605010; Thermo Fisher Scientific), diluted in DPBS 1:1, and supplemented with 10 mmol/L Y-27632 (2 mL/well of a 24-well plate) for 2 min at 37 oC. After adding the same amount of EM with 10 mmol/L Y-27632, colonoids were spun down at 400 xg for 5 min at 4 oC and resuspended at 6 x 106 cells/mL for seeding. Colonoid fragments were seeded in the apical channel of Colon Chips and incubated overnight at 37 oC under 5% CO2 to promote adhesion. Channels were washed with EM the following day and connected to 60 uL/h flow in both channels for two weeks to establish a mucus layer. After expansion in FM, fibroblasts were seeded with Expansion Medium (EM) in the basal channel one day after epithelial cell seeding and were allowed to adhere to all microchannel surfaces for 2 h. After 3 days of co-culture during which both epithelial and fibroblast monolayers were established, EM perfused through the apical channel was changed to Hank’s balanced salt solution (HBSS) with calcium and magnesium (21-023-cv; Corning) supplemented with 100 mg/mL Primocin (ant-pm-1; InvivoGen) while EM remained flowing through the basal channel (both at 60 uL/h).

extract_protocol:
RNA was extracted from Colon Chips at two weeks of culture, after functional monolayer and mucus layer formation. Cells in apical and basal channels were harvested separately with RLT lysis buffer from RNeasy Mini Kit (74106; Qiagen, Hilden, Germany). Channels were washed with 100 µL PBS three times. Fibroblasts were lysed first by quickly pressing and releasing the micropipette plunger at least four times. Lysates were collected in 1.5 mL tubes and stored immediately at -80 °C for RNA sequencing analysis. Subsequently, epithelial cell lysates were collected and processed in a similar manner. High-grade RNA (RIN > 8) was prepared for transcriptomic analysis (Agilent Nano Kit (Agilent 2100 Bioanalyzer, Agilent Technologies).
Total RNA was isolated from each sample and mRNA was enriched by poly(A) tail selection. Purified mRNA was converted into cDNA libraries and amplified via PCR to increase library concentration.

treatment_protocol: For strain-related experiments, physiologically relevant strain (10% Strain 0.15 Hz) was applied for 2 weeks after monolayer formation in addition to dynamic flow. Other samples were cultured for the same duration of time but only under dynamic flow without physiologically relevant strain.

tag: donor

value: colon

value: fibroblast

tag: phenotype

value: healthy

tag: ibd subtype

tag: stimulus

value: strain


title: UV180 Aqueous TCR

description: 10x Genomics

tag: tissue

value: Ocular Aqueous fluid

tag: cell type


title: Colon epithelium, healthy, strain, donor H2, rep3

value: epithelial


title: Chimp_4x0527 [SP19DB6E]

value: blood

tag: treatment


title: Human_5 [SP137F04]

value: NC


title: UV179 Blood TCR

description: 10x Genomics

value: Peripheral blood


title: Colon fibroblast, healthy, strain, donor H2, rep2


title: Human_5 [SP035991]

value: Hour

value: ng/mL


title: Chimp_4x0527 [SP3EE6D8]

value: S (sensitive)


title: UV179 Aqueous TCR

description: 10x Genomics


title: Colon epithelium, healthy, strain, donor H2, rep2


title: Chimp_4x0527 [SPDB1277]

value: LPS


title: Human_5 [SPA63523]


title: HPF A-196 rep2

description: hPF_A196_rep2_Lexogen_12nt_i7_i712_0042_CCGTTGAAGGGG_S42


title: Colon fibroblast, healthy, strain, donor H2, rep1


title: Chimp_4x0527 [SPD5DBFA]


title: Chimp_4x0527 [SP7E7309]


title: UV176 Aqueous TCR

description: 10x Genomics


title: Colon epithelium, healthy, strain, donor H2, rep1


title: Human_5 [SP072705]


title: UV180 Blood TCR

description: 10x Genomics


title: UV174 Blood TCR

description: 10x Genomics


title: Chimp_4x0527 [SPA7C281]


title: Chimp_4x0527 [SP5CE8E3]


title: Colon fibroblast, healthy, strain, donor H1, rep3


title: Human_5 [SP1E67F0]


title: Human_5 [SP6F6639]


title: Human_5 [SPEA8D66]


title: Colon epithelium, healthy, strain, donor H1, rep3


title: Chimp_4x0527 [SPE6BA41]


title: UV170 Blood TCR

description: 10x Genomics


title: Chimp_4x0527 [SP63C7B9]


title: UV174 Aqueous TCR

description: 10x Genomics


title: Human_5 [SP138911]


title: Colon epithelium, healthy, strain, donor H1, rep2


title: Human_5 [SP13640D]


title: UV176 Blood TCR

description: 10x Genomics


title: Chimp_4x0527 [SPFE0467]


title: UV165 Blood TCR

description: 10x Genomics


title: Colon fibroblast, healthy, strain, donor H1, rep2


title: Human_5 [SP1388AD]


title: Colon epithelium, healthy, strain, donor H1, rep1


title: Chimp_4x0525 [SPA89BB6]


title: Human_4 [SP590145]


title: UV160 Blood TCR

description: 10x Genomics


title: UV165 Aqueous TCR

description: 10x Genomics


title: Human_4 [SP8B5F06]


title: Chimp_4x0527 [SP134C59]


title: Chimp_4x0525 [SP09D0E0]


title: UV160 Aqueous TCR

description: 10x Genomics


title: Colon epithelium, IBD, crohn's, strain, donor C1, rep3

value: IBD

value: crohn's


title: Human_4 [SP3DAECD]


title: UV150 Blood TCR

description: 10x Genomics


title: Human_4 [SPCF0B5D]


title: Chimp_4x0525 [SPDB2496]


title: Colon fibroblast, healthy, strain, donor H1, rep1


title: Colon epithelium, IBD, crohn's, strain, donor C1, rep2


title: Colon fibroblast, IBD, crohn's, strain, donor C1, rep2


title: UV170 Aqueous TCR

description: 10x Genomics


title: Chimp_4x0525 [SPADC8CD]


title: Colon fibroblast, IBD, crohn's, strain, donor C1, rep1


title: UV143 Blood TCR

description: 10x Genomics


title: Chimp_4x0525 [SP04084B]


title: Human_4 [SP27C3CD]


title: Colon epithelium, IBD, crohn's, strain, donor C1, rep1


title: Chimp_4x0525 [SP5A6D62]


title: UV143 Aqueous TCR

description: 10x Genomics


title: Human_4 [SP576FA4]


title: Colon fibroblast, IBD, crohn's, strain, donor C1, rep3


title: UV132 Blood TCR

description: 10x Genomics


title: Colon fibroblast, healthy, no strain, donor H2, rep2

value: no strain


title: Chimp_4x0525 [SP1B8B3F]


title: Human_4 [SPF5A0AF]


title: Chimp_4x0525 [SP432A29]


title: UV132 Aqueous TCR

description: 10x Genomics


title: Colon epithelium, healthy, no strain, donor H2, rep2


title: UV129 Blood TCR

description: 10x Genomics


title: Chimp_4x0525 [SP9B61B2]


title: UV150 Aqueous TCR

description: 10x Genomics


title: Chimp_4x0525 [SPC91DA3]


title: Colon fibroblast, healthy, no strain, donor H2, rep1


title: Human_4 [SPD73C40]


title: Colon epithelium, healthy, no strain, donor H2, rep1


title: UV129 Aqueous TCR

description: 10x Genomics


title: Human_4 [SPBE2481]


title: Chimp_4x0525 [SP8CC386]


title: UV122 Blood TCR

description: 10x Genomics


title: Human_4 [SP9D809B]


title: Human_3 [SP36F582]


title: Colon fibroblast, healthy, no strain, donor H1, rep2


title: Colon epithelium, healthy, no strain, donor H1, rep2


title: UV122 Aqueous TCR

description: 10x Genomics


title: Chimp_4x0525 [SP4A786D]


title: Chimp_4x0521 [SP526E8E]


title: Human_3 [SP134073]


title: UV031 Blood TCR

description: 10x Genomics


title: Chimp_4x0521 [SP52D824]


title: UV031 Aqueous TCR

description: 10x Genomics


title: Human_3 [SP39CA89]


title: Human_4 [SPDAD3A2]


title: Chimp_4x0521 [SP49060A]


title: Colon epithelium, healthy, no strain, donor H1, rep1


title: Colon fibroblast, healthy, no strain, donor H1, rep1


title: Human_3 [SP682837]


title: Human_3 [SP7E25AD]


title: Chimp_4x0521 [SP526205]


title: Chimp_4x0521 [SP52641E]


title: UV029 Aqueous TCR

description: 10x Genomics


title: Colon fibroblast, IBD, crohn's, no strain, donor C1, rep2


title: Human_3 [SPCA48E6]


title: Chimp_4x0521 [SP526773]


title: UV029 Blood TCR

description: 10x Genomics


title: Colon fibroblast, IBD, crohn's, no strain, donor C1, rep3


title: Human_3 [SPC45346]


title: Colon epithelium, IBD, crohn's, no strain, donor C1, rep2


title: Human_3 [SP71C4F1]


title: UV027 Aqueous TCR

description: 10x Genomics


title: Colon epithelium, IBD, crohn's, no strain, donor C1, rep1


title: Chimp_4x0521 [SP52CE70]


title: Human_3 [SP78D9A9]


title: Chimp_4x0521 [SP52C441]


title: WHR-OUTPUT-rep03-clean

city: Xi'an China

first: Renjie

last: Zhu

state: Shaanxi

address: No.28 Xianning West Road, Xi'an, Shaanxi 710049, P.R. China

department: School of Life Science and Technology

institute: Xi'an Jiaotong University

description: input sequencing library

data_processing:
Each replicated sample paired reads were separated according to 8-bp barcode sequences
Low quality reads (Q-score<30) were removed using fastp 0.20.1
The 120-bp SNP element sequences were extracted and merged reads were aligned to our selected SNP sequences using Bowtie 2.4.1
All 100% matched reads were extracted and each SNP reference/alternative allele was counted according to unique UMI (removing PCR duplicates)
Assembly: h19
Supplementary files format and content: Count.txt with raw reads counts for every SNP sequence and every sample
Library strategy: STARR-Seq

source_name: preadipocyte cells

growth_protocol: Human preadipocytes were cultured in DMEM (HyClone, USA) with 10% fetal bovine serum (Biological Industries, Israel), 100U/mL penicillin and 0.1 mg/mL streptomycin (Solarbio, USA) at 37 °C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using Monarch Total RNA Miniprep Kit (New England Biolabs), and treated with TURBO DNA-free Kit (Thermo Fisher) following the manufacturer’s protocol. We then isolated the poly(A) RNA using NEB Next Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and precipitated each replicate using Monarch RNA Cleanup Kit (New England Biolabs).
The plasmid library was used to construct input sequencing library before cell transfection. In brief, 100ng plasmid library was treated with RT-UMI as following: 98°C for 30s, 63°C for 30s and 72°C for 2 min. Subsequently, two rounds of amplification were applied using Vector-F and Read1-R or barcode primers, respectively. On the other hand, total RNA was extracted and treated with DNase I for output sequencing construction after 24 h post-transfection. The poly(A) RNA was further isolated for cDNA synthesis (NEB, USA). Next, specific reverse transcription was performed using RT-UMI  (NEB, USA), and treated with RNase A (Takara, Japan). Similarly, two rounds of amplification were performed using junction primer  and Read1-R or barcode primers, respectively.

treatment_protocol: The STARR-seq plasmid library was transfected into 1.0×107 cells for 24h according to manufacturer’s instructions. Three biological replicates were performed.

value: preadipocyte cells


title: Colon epithelium, IBD, ulcerative colitis, strain, donor UC3, rep3

value: colon

value: ulcerative colitis


title: Chimp_4x0521 [SP525C83]


title: UV019 Aqueous TCR

description: 10x Genomics


title: UV019 Blood TCR

description: 10x Genomics


title: Human_3 [SP8C8D67]


title: UV027 Blood TCR

description: 10x Genomics


title: Colon fibroblast, IBD, crohn's, no strain, donor C1, rep1

value: fibroblast


title: Colon epithelium, IBD, crohn's, no strain, donor C1, rep3


title: Chimp_4x0521 [SP52B968]


title: Colon epithelium, IBD, ulcerative colitis, strain, donor UC3, rep2

value: strain


title: WHR-OUTPUT-rep02-clean

description: input sequencing library


title: Colon epithelium, IBD, ulcerative colitis, strain, donor UC3, rep1


title: Colon epithelium, IBD, ulcerative colitis, no strain, donor UC3, rep3


title: Chimp_4x0521 [SP525C26]


title: Human_2 [SPA11538]


title: WHR-INPUT-rep03-clean

description: input sequencing library


title: Human_3 [SP6EAA7A]


title: WHR-INPUT-rep02-clean

description: input sequencing library


title: DRG proprioceptor13

city: Salt Lake City

first: Baldomero

last: Olivera

state: UT

address: 201 Presidents' Cir, Salt Lake City

institute: University of Utah

data_processing:
Illumina adapters were trimmed from the paired-end (mate length 125-bp) reads by cutadapt (v1.16). Reads and adapters were required to overlap a minimum of 6 bp for trimming to take place and reads shorter than 20 bp were discarded. Adapter trimming was followed by initial sample quality control metrics were generated with FASTQC (v0.11.5). Trimmed reads were aligned with STAR (v 2.5.4a) using the ENCODE parameterization. Additional alignment metrics were generated with Picard’s ‘CollectRNASeqMetrics’ utility (v2.9.0) and QoRTs’ (v1.3.0). Finally, the QC metrics were collated with multiqc (v1.6).
Star alignment to Mouse genome.  Seurat normalization of raw gene counts
Assembly: mm39
Supplementary files format and content: raw.counts.csv, comma separated raw gene counts for all samples.  Seurat.norm.csv has seurant log normalized values for all genes

source_name: DRG

extract_protocol:
Individual cells were picked at the end of constellation pharmacology experiments, using fire polished glass capillaries (using Sutter P-90 puller) with a diameter of ~3-10 microns. The cells were held at the tip and immediately placed in a microfuge PCR tube containing lysis buffer from Takara Bio Smart-Seq Single Cell kit (Catalog #R400751). The transcriptomic libraries were constructed as per manufacturer protocols and submitted to University of Utah Sequencing core
Takara Bio Smart-Seq Single Cell kit (Catalog #R400751). The transcriptomic libraries were constructed as per manufacturer protocols and submitted to University of Utah Sequencing core

value: DRG

value: Neuron


title: Colon epithelium, IBD, ulcerative colitis, no strain, donor UC3, rep1

value: epithelial


title: Human_2 [SP40EFBA]

value: blood


title: WHR-INPUT-rep01-clean

description: input sequencing library


title: Colon epithelium, IBD, ulcerative colitis, no strain, donor UC3, rep2


title: DRG proprioceptor12


title: DRG proprioceptor11


title: Human_2 [SP0726B0]


title: Human_2 [SP901ADB]


title: A7 isogenic variant biol. rep.4

city: Amsterdam

first: Connie

last: Bezzina

address: Meibergdreef 9

department: Exp. Card.

country: Netherlands

institute: Amsterdam UMC

description:
IM8
PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx

data_processing:
Reads were mapped to hg19 build of the mouse and human transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Assembly: hg19
Supplementary files format and content: PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx: Excel file with normalized (DESeq2) count data per gene & differential expression analysis
Supplementary files format and content: IM1_PGP1_WT.bigwig, IM2_A7_Mut.bigwig, IM3_PGP1_WT.bigwig, IM4_A7_Mut.bigwig, IM5_PGP1_WT.bigwig, IM6_A7_Mut.bigwig, IM7_PGP1_WT.bigwig, IM8_A7_Mut.bigwig

source_name: PGP1-SV1-isogenic clone A7

growth_protocol: The PGP1-SV1 and isogenic A7 hiPSC lines were maintained on growth factor-reduced Matrigel Matrix-coated plates in presence of mTeSR1 medium at 37°C, with 5% CO 2 and 20% O 2. Cells were passaged every 3-4 days using 0.5mM EDTA.

extract_protocol:
Total RNA was isolated using TRIzol Reagent followed by chloroform addition, hydrophilic phase isolation and precipitation in isopropanol.
RNA integrity was tested by Tapestation analysis. 1.25ug of total RNA /sample was used for libraries preparation using the KAPA Total RNA Hyperprep (Riboerase) kit protocol.

treatment_protocol: Cardiomyocytes differentiation started in RPMI 1640 medium containing 2% B27 supplement without insulin (hereafter indicated as RPMI/B27−) and 6 µM CHIR99021.  After 24 hours a volume of RPMI/B27− medium without CHIR99021 equal to 2/3 of the original differentiation medium was added. On day 3 of differentiation 1/3 of the original volume of RPMI/B27− medium was further added. The differentiation protocol continued with 3-days treatment with 2 µM Wnt-C59 in RPMI/B27− medium. The culture was then maintained until day 43 in RPMI/B27− medium alone, with medium change every 3-4 days. On day 44, a 7-8 days metabolic- selection that enriches the culture for cardiomyocytes started by switching the medium to RPMI 1640 without glucose supplemented with 500 µg/mL bovine serum albumin and 8 mM Na-L-lactate with medium change every other day. The culture was switched to RPMI 1640/B27− for 1 day before RNA isolation or electrophysiological analysis.

value: PGP1-SV1-isogenic clone A7

value: hiPSC

tag: genotype

value: cardiomyocytes differentiation from hiPSCs


title: Colon fibroblast, healthy, no strain, donor H3, rep3

value: healthy


title: WHR-OUTPUT-rep01-clean

description: input sequencing library


title: Colon epithelium, healthy, no strain, donor H3, rep3


title: DRG proprioceptor10


title: Chimp_4x0521 [SPC7A9BB]

value: LPS

tag: time

value: Hour

value: ng/mL

value: S (sensitive)


title: Colon fibroblast, healthy, no strain, donor H3, rep2

value: no strain


title: A7 isogenic variant biol. rep.3

description:
IM6
PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx

tag: cell line


title: DRG proprioceptor14


title: Human_2 [SP8EDD16]


title: Human_2 [SP8AEB1A]

value: NC


title: PGP1 control biol. rep.3

description:
IM5
PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx


title: Human_2 [SPE5BB28]


title: DRG proprioceptor8


title: Colon epithelium, healthy, no strain, donor H3, rep2

value: colon


title: DRG proprioceptor9


title: Human_2 [SP817193]


title: Human_2 [SP220673]


title: A7 isogenic variant biol. rep.2

description:
IM4
PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx


title: DRG proprioceptor7


title: Colon fibroblast, healthy, no strain, donor H3, rep1

value: fibroblast


title: PGP1 control biol. rep.2

description:
IM3
PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx


title: Colon epithelium, healthy, no strain, donor H3, rep1


title: Human_2 [SP19826A]


title: DRG proprioceptor6


title: PGP1 control biol. rep.4

description:
IM7
PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx


title: DRG proprioceptor5


title: Human_2 [SP079D95]


title: Human_2 [SP049571]


title: Colon epithelium, healthy, strain, donor H3, rep3

value: strain


title: PGP1 control biol. rep.1

description:
IM1
PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx


title: DRG proprioceptor4

value: DRG


title: A7 isogenic variant biol. rep.1

description:
IM2
PGP1_A7_RNA-seq_DESEQ2_Mengarelli_hg19.xlsx


title: Human_1 [SPE26655]


title: Budesonide_3D_day 3 rep 3

data_processing:
Illumina NovaSeq 6000
Raw data were aligned to HG38 - Release 37 (GRCh38.p13)
Read count extraction was performed using FeatureCounts. Normalization was performed using DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample.

growth_protocol: Patient-derived PDAC cells (PDAC#253) were allowed to aggregate (5 x 10^2 cells/well) in V-shaped ultra low attachment 96 multiwell in RPMI + 10%FBS.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep (Zymo Research).
Libraries for RNA-seq were prepared using standard using Illumina platform.

treatment_protocol: At day 0 cells were treated ± budesonide (1 μM; SIGMA) or untreated for three days.

value: pancreatic ductal adenocarcinoma

value: patient-derived PDAC cell line

value: treated with budesonide (1 uM) for 3 days


title: DRG proprioceptor3

value: Neuron


title: Human_1 [SPB61CE8]

value: blood


title: Colon epithelium, healthy, strain, donor H3, rep2

value: epithelial


title: Human_1 [SPD14AEC]


title: Colon fibroblast, healthy, strain, donor H3, rep1

value: healthy


title: Budesonide_3D_day 3 rep 2


title: DRG proprioceptor1


title: Human_1 [SP780563]

value: LPS


title: Colon epithelium, healthy, strain, donor H3, rep1


title: Control_3D_day 3 rep 3

value: untreated


title: Budesonide_3D_day 3 rep 1


title: Pig_9 [SP82146F]

organism: Sus scrofa

value: Hour

value: ng/mL


title: Human_1 [SPC8F598]

value: S (sensitive)


title: Colon fibroblast, healthy, strain, donor H3, rep3


title: Colon fibroblast, IBD, ulcerative colitis, no strain, donor UC1, rep3

value: IBD

value: ulcerative colitis

value: no strain


title: Pig_9 [SP32AA14]

value: NC


title: Human_1 [SP943DEF]


title: Control_3D_day 3 rep 1


title: Colon epithelium, IBD, ulcerative colitis, no strain, donor UC1, rep3

value: colon


title: Pig_9 [SP4BB89E]


title: Colon fibroblast, healthy, strain, donor H3, rep2

value: fibroblast

value: strain


title: Ishikawa cells, TEFM-2

city: Kaifeng

first: Dengke

last: Bao

state: Henan

address: Jinming Road

department: School of Pharmacy

institute: Henan University

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Assembly: hg19
Supplementary files format and content: Excel spreadsheet file include FPKM values for each Sample.

source_name: Endometrium

growth_protocol: Ishikawa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) .

extract_protocol:
Total RNA from cell lines was extracted using TRIzol reagent (Invitrogen).1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: Endometrium

value: Ishikawa

value: tumor cell

value: TEFM overexpression

value: not have


title: Pig_9 [SP781160]

value: blood

value: LPS


title: Human_1 [SP129750]

value: Hour


title: Ishikawa cells, TEFM-1


title: Human_1 [SPE8841A]

value: ng/mL


title: Colon fibroblast, IBD, ulcerative colitis, no strain, donor UC1, rep1


title: Ishikawa cells, TEFM-3


title: Colon fibroblast, IBD, ulcerative colitis, no strain, donor UC1, rep2


title: Pig_9 [SP151E1A]

value: S (sensitive)


title: Human_1 [SPA94946]


title: Pig_9 [SP6C09E3]


title: Human_1 [SPA5C8DE]


title: Human_1 [SP3008B6]


title: Ishikawa cells, EV-2

value: EV


title: Colon epithelium, IBD, ulcerative colitis, no strain, donor UC1, rep2

value: epithelial

value: IBD

value: ulcerative colitis


title: DRG proprioceptor2

value: DRG

value: Neuron


title: Pig_9 [SP573664]


title: Ishikawa cells, EV-3


title: Pig_9 [SP9491DF]


title: Cow_5 [SPE4EB85]

organism: Bos taurus

value: NC


title: Ishikawa cells, EV-1

value: Endometrium


title: Control_3D_day 3 rep 2

value: pancreatic ductal adenocarcinoma

value: patient-derived PDAC cell line

value: untreated


title: Colon fibroblast, IBD, ulcerative colitis, strain, donor UC1, rep2

value: colon

value: fibroblast

value: strain


title: Colon epithelium, IBD, ulcerative colitis, strain, donor UC1, rep2


title: Colon fibroblast, IBD, ulcerative colitis, strain, donor UC1, rep1


title: Pig_9 [SP80FE63]

value: blood

value: LPS

value: Hour


title: Pig_9 [SPD009CD]

value: ng/mL

value: S (sensitive)


title: MDA-MB-453, suspension, treated Vehicle ,2

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTQ generated with bcl2fastq (version 2.20.0.422) files were processed using the nf-core/rnaseq pipeline (version 3.12, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the human transcriptome (GRCh38, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCh38
Supplementary files format and content: *_quant.sf.gz: Salmon transcript quantification file (tab-sparated text, https://salmon.readthedocs.io/en/latest/file_formats.html); to be used together with salmon_tx2gene.tsv by software accepting Salmon data

growth_protocol: MDA-MB-453 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere incubator with 5% CO2 at 37C

extract_protocol:
Total RNAs were extracted using Rneasy mini Kit (Qiagen, USA) base on the manufacture's instructions.
The RNA library preparation was using SMARTER mRNA preparation kit according to the protocols.

treatment_protocol: The cells under regular attached culture or forced suspension culture (poly-hema coated plate) were treated with 10μM of AT0174 or vehicle control (DMSO)for 48 hours

value: Human Triple-Negative Breast Cancer

value: WT

value: Suspension culture treated Vehicle


title: Colon epithelium, IBD, ulcerative colitis, no strain, donor UC1, rep1

value: epithelial

value: IBD

value: ulcerative colitis

value: no strain


title: MDA-MB-453, suspension, treated Vehicle ,3


title: Cow_5 [SP98D576]

value: NC


title: Pig_9 [SPF056E6]


title: Colon epithelium, IBD, ulcerative colitis, strain, donor UC1, rep1


title: Cow_5 [SPAB96D3]


title: MDA-MB-453, suspension, treated Vehicle ,1


title: Cow_5 [SP662803]


title: Human_1 [SP57A389]


title: Colon fibroblast, IBD, ulcerative colitis, strain, donor UC3, rep1


title: MDA-MB-453, suspension, treated AT0174 ,3

value: Suspension culture treated AT0174


title: Colon fibroblast, IBD, ulcerative colitis, no strain, donor UC3, rep3

value: colon


title: Pig_8 [SPAC8921]


title: Cow_5 [SP1AA43D]


title: Colon fibroblast, IBD, ulcerative colitis, strain, donor UC3, rep3

value: fibroblast


title: MDA-MB-453, suspension, treated AT0174 ,2


title: Pig_8 [SP47F745]


title: Cow_5 [SPBC44B0]


title: Pig_8 [SPBCC231]


title: Colon fibroblast, IBD, ulcerative colitis, strain, donor UC3, rep2

value: strain


title: Cow_5 [SP369B92]

value: blood


title: Colon fibroblast, IBD, ulcerative colitis, no strain, donor UC3, rep2


title: Pig_8 [SP006C18]

value: LPS


title: Colon fibroblast, IBD, ulcerative colitis, no strain, donor UC3, rep1


title: Cow_5 [SPE56C72]

value: Hour


title: MDA-MB-453, attached, treated Vehicle ,2

value: Attached culture treated Vehicle


title: MDA-MB-453, attached, treated Vehicle ,3


title: Pig_8 [SP1F3E0A]

value: ng/mL

value: S (sensitive)


title: Pig_8 [SPD8E0C8]


title: Cow_5 [SP875B3F]


title: Pig_9 [SPA040CA]


title: AD_APOE4_2

city: Chicago

first: Amira

last: Affaneh

state: IL

address: 303 E. Chicago, Ward 10-233

institute: Northwestern University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.36
Trimmed sequence reads were mapped to GrCM38/ STAR 2.7.2a
Read count extraction and normalization were performed using featureCounts v1.5.3 in Subread package
with gene annotation included in GENCODE release 31
Normalized gene expression were obtained through TMM normalization with library size correction
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: AD line

growth_protocol: Cells were grown according to previously established virally induced NGN2 protocol and grown for 35 days

extract_protocol:
RNA was harvested using RNAqueous Micro total RNA isolation kit (Thermo Fisher AM1931). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: AD line

value: neuronal lineage differentiation

value: 35 days post differentiation


title: Cow_5 [SP6D91BF]


title: AD_APOE4_3


title: Cow_5 [SP40E700]


title: SUM159PT, suspension, treated Vehicle, 3

growth_protocol: BT549 cells were cultured in RPMI supplemented with 10% fetal bovine serum (FBS), 1% NEAA, 10μg/ml insulin ; SUM159PT cells were cultured in Ham’s F12 media with 5% FBS, 1% HEPES, 10µg/ml insulin, and 0.3% hydrocortisone. All cells were maintained in humidified atmosphere incubator with 5% CO2 at 37C

treatment_protocol: For BT549 TDO2 shRNA knockdown or overexpression cells, RNAs were colleted after 48hours of cell seeding. For TDO2/IDO dual inhibitor AT0174 treatment, cells at forced suspension culture were treated AT0174 for 48 hours and RNAs were collected.

value: Human Triple-negative breast cancer

value: WT

value: Suspension clulture treated vehicle


title: Pig_8 [SP37DF30]


title: MDA-MB-453, attached, treated Vehicle ,1

value: Human Triple-Negative Breast Cancer


title: Pig_8 [SPAB42CF]


title: Pig_8 [SP815C5F]


title: SUM159PT, suspension, treated Vehicle, 1


title: Cow_5 [SP9F4A4F]


title: AD_APOE4_1


title: AD_APOE3_4

source_name: Crispr Corrected IPSC of 5810

value: Crispr Corrected IPSC of 5810

value: neuron


title: SUM159PT, suspension, treated Vehicle, 2


title: MDA-MB-453, suspension, treated AT0174 ,1

value: Suspension culture treated AT0174


title: SUM159PT, suspension, treated AT0174, 3


title: AD_APOE3_3

source_name: Crispr Corrected IPSC of 11414

value: Crispr Corrected IPSC of 11414


title: Cow_4 [SPB6F52F]

value: blood

value: NC


title: SUM159PT, suspension, treated AT0174, 2


title: Pig_8 [SP385605]

value: LPS

value: Hour


title: Cow_4 [SP2D95EC]

value: ng/mL


title: AD_APOE3_2


title: AD_APOE3_1


title: SUM159PT, suspension, treated AT0174, 1


title: Cow_4 [SP1D4CE9]

value: S (sensitive)


title: Pig_8 [SP1FCD8C]


title: FACS sorted Neurons from FAT4 mutant [NeuN-F1]

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

data_processing:
sequencing reads were aligned to the mouse reference genome (version GRCh38.100) and  gene read counts were calculated with STAR (version 2.7.3a).
Assembly: GRCh38, Ensembl annotation version 100
Supplementary files format and content: count_matrix.txt

molecule: nuclear RNA

source_name: cerebral organois

growth_protocol: hCOs were kept in neural differentiation medium in 10-cm dishes on an orbital shaker at 37°C, 5% CO2 and ambient oxygen level.

extract_protocol:
To isolate nuclei, hCOs were dissociated by Dounce homogenization and filtered with BD Falcon tubes with a cell strainer cap (Corning, 352235) to get single cells. RNase inhibitor (NEB, M0314) (0.4 U/ µl) and DNase I (NEB, M0303) (1 U/ µl) were added to the homogenization buffer. RNase inhibitor (0.2 U/ µl) was added to the blocking solution. Primary antibodies against Pax6 (Biolegend, PRB-278p) and NeuN (Millipore, MAB377) were used at 1:2,500 dilution and 1:1,000, respectively. FACS analysis was performed with a FACS Melody TM cell sorter (BD) in BD FACS Flow TM medium, with a nozzle diameter of 100 lm. Debris and aggregated cells were gated out by forward scatter, sideward scatter; single cells were gated out by FSC-W/FSC-A. RNA was extracted using RNA Clean & Concentrator Kit (Zymo Research, R1015)  according to the manufacturer’s protocol.
The integrity of the extracted RNA was analyzed at the Bioanalyzer by using the RNA 6000 pico kit (Agilent) following the manufacturer’s protocol. First-Strand cDNA synthesis and cDNA amplification were done with the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA) following the manufacturer´s protocol. For the cDNA amplification, we performed a range of PCR cycles. The amplified cDNA was purified with AMPure XP beads (Beckman Coulter) following the manufacturer's protocol. The purified sample was collected and its concentration was measured with the Qubit DNA HS kit following the manufacturer´s protocol. The concentration was ranging between 0.5-2 ng/μl. The cDNA shearing was performed using the S220 Covaris with AFA technology (Covaris) .
The library was prepared with Microplex Library preparation kit v2 (Diagenode) following the manufacturer’s protocol. After the Covaris treatment, the resulting cDNA was in 200–500 bp size range. The concentration, measured with the Qubit DNA HS kit, was 0,5-2 ng/ul (10-20 ng in total). After the library amplification steps with the Microplex Library preparation kit v2 (Diagenode) the DNA concentration was measured again with the Qubit DNA HS Kit. The concentration of the DNA was between 5-6 ng/μl. The library was purified using the AMPure XP beads (Beckman Coulter) and the concentration was checked with Qubit HS DNA kit again, revealing a final concentration between 2-6 ng. Finally, the quality and molarity of the library were also analyzed with the DNA 1000 kit (Agilent).

value: cerebral organois

value: Neurons

value: FAT4 mutant


title: BT549, TDO2 Overexpression (OE), 3

value: Human Triple-negative breast cancer

value: Overexpression TDO2

value: TDO2 Overexpression


title: Cow_4 [SPF0E58F]


title: Pig_7 [SPBC134A]


title: FACS sorted Neurons from DACHSOS mutant [NeuN-D2]

value: DCHS mutant


title: BT549, TDO2 Overexpression (OE), 2


title: Cow_4 [SPA9563F]


title: Pig_7 [SPEE1720]


title: BT549, TDO2 Overexpression (OE), 1


title: Cow_4 [SPD1E902]


title: FACS sorted Neurons from CTRL 1 [NeuN-CTRL]


title: Pig_7 [SP759BE0]


title: BT549, suspension, treated vehicle , 3

value: WT

value: Suspension clulture treated vehicle


title: Pig_8 [SPBEC902]


title: BT549, suspension, treated vehicle , 2


title: Cow_4 [SP7B803C]


title: Wildtype_7

city: LONDON

first: Mariya

last: Moosajee

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Raw reads were quality and adapter trimmed using trimgalore (version 0.6.7) (14) before alignment.
Reads were mapped and subsequent gene-level counted using RSEM 1.3.3 (15) and STAR 2.7.10a (16) against the zebrafish genome GRCz11, both from Ensembl.
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.38.3)within the R programming environment (version 4.2.2).
Assembly: GRCz11
Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.

organism: Danio rerio

source_name: Retina

extract_protocol:
Bulk RNA was extracted with RNAeasy Micro Plus kit (Qiagen) from chmru848 and wt control retinas (n=7 per group) and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A
cDNA libraries were subsequently constructed from total RNA (RIN ≥ 8) using the Clontech SMART-Seq v4 Ultra Low Input RNA Kit

value: Retina

value: Wildtype


title: Cow_4 [SP7B198D]

value: blood


title: Cow_4 [SPCE15B7]


title: Pig_7 [SP3261D9]


title: BT549, suspension, treated vehicle , 1


title: Pig_7 [SP2E0306]


title: Wildtype_6


title: Cow_4 [SP6EC5B2]


title: Wildtype_4


title: BT549, suspension, treated AT0174, 3

value: Suspension culture treated AT0174


title: Cow_4 [SP5E1B08]

value: LPS


title: Pig_7 [SPEE1B9D]

value: Hour


title: BT549, suspension, treated AT0174, 2


title: Cow_4 [SPD69506]

value: ng/mL


title: Wildtype_3


title: BT549, suspension, treated AT0174, 1


title: Wildtype_2


title: Pig_7 [SPA674A4]

value: S (sensitive)


title: Pig_7 [SP8D8832]

value: NC


title: Cow_3 [SPB5EDB4]


title: Pig_7 [SP8A817A]


title: Pig_7 [SPE2744E]


title: Choroideremia_7

value: Choroideremia


title: Cow_3 [SPB77D79]


title: Cow_3 [SP2AD049]


title: BT549, shTDO2-098, 2

value: knockdown TDO2 shRNA construct-098

value: knockdown TDO2 construct 2


title: Pig_7 [SPB8DC4A]


title: BT549, shTDO2-098, 1

value: Human Triple-negative breast cancer


title: Wildtype_5


title: Cow_3 [SPDFE6C6]


title: Choroideremia_6


title: Choroideremia_5


title: BT549, shTDO2-082, 3

value: knockdown TDO2 shRNA construct-082

value: knockdown TDO2 construct 1


title: Pig_7 [SP88BDFE]


title: BT549, shTDO2-082, 2


title: Choroideremia_4


title: Pig_6 [SP4BBE77]


title: Pig_6 [SP9B6885]


title: Cow_3 [SPFA9C2A]


title: Choroideremia_3


title: BT549, shTDO2-082, 1


title: Cow_3 [SP0A430D]


title: Pig_6 [SP711678]


title: BT549, shTDO2-098, 3


title: Wildtype_1


title: Choroideremia_2


title: Cow_3 [SP43864E]


title: Pig_6 [SP4DC559]


title: Choroideremia_1


title: BT549, shNegative  control, 2

value: knockdown negative control shNeg

value: Knockdown control


title: Cow_3 [SPAC9F39]


title: Pig_6 [SP3B1B9F]


title: BT549, shNegative  control, 1


title: Sham3, input

city: WuHan

first: zhijun

last: xiang

address: Wuhan

institute: Emergency Center, Zhongnan Hospital of Wuhan University

description:
Methylated_RNA_sites.LncRNA
Methylated_RNA_sites.circRNA
Methylated_RNA_sites.mRNA

data_processing:
Preprocessing - Database Creation
Off-machine data accusation
Matching genomes
Modification site identification
Differential site identification
Translation enrichment analysis
Assembly: RN6
Supplementary files format and content: This table contains information on RNA modification sites identified for each sample
Library strategy: meRIP-seq

organism: Rattus norvegicus

source_name: brain

extract_protocol:
RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.
The m5C-IP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was subjected to immunoprecipitation with the GenSeq® m5C-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m5C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).

value: brain

value: Sham


title: Cow_3 [SP0BE00E]

value: blood


title: Sham2, input


title: Cow_3 [SPC84018]


title: Pig_6 [SP7D985F]


title: Pig_6 [SP90BD4E]


title: Pig_6 [SP705E2E]


title: Cow_3 [SP022FE2]


title: TBI3, input

value: TBI


title: Pig_6 [SP8F0BA9]

value: LPS


title: BT549, Empty Vector, 3

value: Overexpression control, Empty vector

value: Empty Vector control


title: BT549, shNegative  control, 3


title: Pig_6 [SPC84D0C]

value: Hour

value: ng/mL

value: S (sensitive)


title: TBI2, input


title: BT549, Empty Vector, 1


title: Cow_2 [SP65A78E]

value: NC


title: ATCC_uncoated_n1

first: Tanner

last: Shull

address: 1735 W Harrison St

department: Microbial Pathogens and Immunity

institute: Rush University Medical Center

data_processing:
n brief, RNA underwent poly (A) selection, enzymatic fragmentation, and generation of double-stranded cDNA using a mixture of oligo (dT) and random priming. The cDNA underwent end repair, ligation of dual-index adaptors, strand selection, and 14 cycles of PCR amplification. The number of cycles was determined by qPCR on a small aliquot of the unamplified libraries. All intermediate purification steps and final library purification were carried out using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA; #A63881).
Final amplified libraries were measured with the Qubit 1 double-stranded DNA (dsDNA) HS assay kit (Invitrogen; #Q33231), and fragment size distribution was confirmed to be approximately 470 bp using the D5000 ScreenTape assay (Agilent; #5067-5588 and #5067-5589).
The pool was purified with the Agencourt AMPure XP beads (Beckman Coulter; #A63881), quantified by qPCR using KAPA library quantification kit, and sequenced on a NovaSeq 6000 S4 flow cell, 2 150 bp, approximately 30 M clusters per sample, at the University of Illinois Roy J. Carver Biotechnology Center High-Throughput Sequencing and Genotyping Unit (Chicago, IL, USA).
K-means clustering was performed with 10 random initializations on a range of cluster numbers k (2 to 20). For each k, the reproducibility of the repeated clustering runs was computed by comparing the pairwise distance between clustering results as the number of co-clustered feature pairs shared between results divided by the number of co-clustered feature pairs within each result individually.
This difference was averaged across all result pairs for each value of k, and the largest k with an average distance less than 1 × 10−5was selected as the optimal k with highly reproducible clusters. Enrichment clusters for features that were significant (q, 0.05) were generated using Cytoscape. Venn diagrams were also generated using an open-source Venn diagram viewer.
Assembly: hg18
Supplementary files format and content: processed files (genes.results)

source_name: induced pluripotent stem cell

extract_protocol:
miRNeasy extraction kit, Qiagen
NuGen protocol; M01485 v5

value: induced pluripotent stem cell

value: astrocyte

value: uncoated


title: TBI1, input


title: ATCC_coated_n1

value: coated


title: Cow_3 [SP682A13]


title: Cow_2 [SPD3C1D8]


title: Sham3


title: RUCDR_uncoated_n2


title: Pig_6 [SPA94FF9]


title: Pig_6 [SPE004FC]


title: Cow_2 [SPA54CEB]


title: RUCDR_coated_n2


title: Sham2


title: BT549, Empty Vector, 2

value: Human Triple-negative breast cancer


title: Sham1, input


title: Cow_2 [SP2957A2]


title: RUCDR_uncoated_n1


title: Sham1


title: diaphragm, mechanically ventilated, S7

city: Changzhi City

first: Dong

last: Zhang

address: 110 South Yan'an Road, Luzhou District

institute: Department of Critical Care Medicine, Heping Hospital Affiliated to Changzhi Medical College

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.  In barcodes.tsv, format is barcode-sample#, where # is 1- 4.

organism: Oryctolagus cuniculus

source_name: The diaphragm tissue of Japanese white rabbits with large ears

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: anesthetized and mechanically ventilated for 24 hours


title: RUCDR_coated_n1


title: Cow_2 [SP78BDDC]


title: Cow_2 [SP178829]


title: diaphragm, spontaneously breathing, S1

value: The diaphragm tissue of Japanese white rabbits with large ears

value: anesthetized and spontaneously breathing for 24 hours


title: Cow_2 [SPDC8BFC]

value: blood


title: TBI3

value: brain

value: TBI


title: TBI2


title: Cow_2 [SP96C33A]

value: LPS


title: TBI1


title: ApoE,normal diet, rep8

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

institute: Adam Mickiewicz University

data_processing:
After quality control, adapter trimming, and quality filtering with fastp (v.0.22.0), fastq files were mapped to the Mus musculus GRCm38/mm10 genome using STAR version 2.6.1d
Read counts were generated using STAR (--quantMode GeneCounts)
Counts normalization was performed using log2cpm and DEG analysis was performed using the limma (v.3.52.4) package in R version 4.2.2
Assembly: GRCm38/mm10 genome build (release-102)
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: ascending aorta (including aortic arch)

growth_protocol: After a week of acclimatization and handling, 8-week-old mice were subjected to the experiment

extract_protocol:
The tissues were frozen in liquid nitrogen, transferred into Trizol, and then homogenized using a manual Omni tissue homogenizer (TH2, 2308) and dedicated hard tips. All the following steps of RNA isolation were carried out according to Total RNA Zol-Out (A&A Biotechnology) protocol for the rapid purification of ultra-pure total RNA from samples prepared in TRIzol (A&A Biotechnology)
RNA-seq libraries were prepared from 1ug of total RNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) together with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Multiplex Oligos for Illumina® (NEB) according to manufacturer's protocol

treatment_protocol: ApoEKO mice were fed with either normal or high-fat diet. After 12 weeks the mice were euthanized by an overdose of isoflurane, after which the organs were isolated (weighed, frozen in liquid nitrogen and subjected to further histological, protein and RNA analyzes)

value: ascending aorta (including aortic arch)

tag: strain

tag: age

value: 20 weeks old

tag: Sex

value: male

value: ApoEKO

tag: diet

value: normal diet


title: Oligodendroglioma A3

city: Los Angeles

first: David

last: Craig

address: 1450 Biggy St, 2nd Floor

department: Department of Translational Genomics

institute: University of Southern California

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Data was processed using the 10X Genomics spaceranger pipeline (v1.1.0) with the GRCh38 reference. Briefly, this process includes image detection and fiducial alignment, barcode and unique molecular identifier correction, alignment to a genome reference, gene count calculation, principal component analysis, and clustering (graph and k-means). The data represented here are processed output files from this pipeline.
Assembly: GRCh38
Supplementary files format and content: .cloupe:  Loupe Browser file for visualization of spatial transcriptomics data.
Supplementary files format and content: filtered_barcodes.tsv.gz: File contains barcodes within tissue regions in the spatial grid.
Supplementary files format and content: filtered_feature_bc_matrix.h5: File contains gene expression data for only barcodes that are within tissue regions in the spatial grid.
Supplementary files format and content: filtered_features.tsv.gz: File contains gene IDs and names.
Supplementary files format and content: filtered_matrix.mtx.gz: File contains number of UMIs associated with a feature (row) and barcode (column), referenced in filtered_barcodes.tsv.gz and filtered_features.tsv.gz. The only data represented is from barcodes within tissue regions in the spatial grid.
Supplementary files format and content: graphclusters.csv Graph cluster data for each barcode.
Supplementary files format and content: metrics_summary.csv: Spatial run sequencing and barcode metrics.
Supplementary files format and content: scale_factors_json.json: File contains scale factor and pixel information for visualizing the spatial sample.
Supplementary files format and content: tissue_hires_image.png: Downsampled full resolution image of sample.
Supplementary files format and content: tissue_positions_list.csv: File contains position information for spatial barcodes. The first column contains the sequence of the barcode associated to the spot. Column 2 indicates whether the spot is in a tissue area. Columns 3-6 refer to the array in the full resolution image. Column 3 is the row coordinate. Column 4 is the column coordinate. Column 5 is the row pixel coordinate. Column 6 is the column pixel coordinate.
Supplementary files format and content: kmeans3clusters.csv: K means cluster data for each barcode, where k=3 determined clusters.
Supplementary files format and content: integrated_glioma_samples_cohortA.rds: Sequencing data for the 11 samples in cohort A were initially analyzed using the 10X Genomics spaceranger pipeline. Output data files for all cohort A samples were imported in R to individual Seurat objects, normalized with SCTransform, and integrated using the Seurat reciprocal PCA integration method.
Supplementary files format and content: integrated_glioblastoma_samples_cohortB.rds: Sequencing data for the six samples in cohort B were initially analyzed using the 10X Genomics spaceranger pipeline. Output data files for all cohort B samples were imported in R to individual Seurat objects, normalized with SCTransform, and integrated using the Harmony method.

source_name: glioma

extract_protocol:
Fresh frozen tissues were prepared using the 10X Visium Spatial Tissue Preparation Guide. Tissues were OCT embedded, followed by cryostat sectioning to 10 µm sections.
Sequencing libraries were prepared using the 10X Genomics Visium Spatial Gene Expression protocol.
Other: Spatial Transcriptomics

value: glioma


title: DRG proprioceptor23

value: DRG

value: Neuron


title: Glioblastoma A5


title: Glioblastoma A4


title: Cow_2 [SP246910]

source_name: blood

tag: subject

tag: timeunit

value: Hour

tag: dose

value: ng/mL

value: S (sensitive)


title: DRG proprioceptor22


title: ApoE,normal diet, rep7

value: female


title: ApoE,normal diet, rep6


title: Cow_2 [SP9F4767]

tag: doseunit

tag: group


title: Oligodendroglioma A2


title: ApoE,normal diet, rep5


title: diaphragm, mechanically ventilated, S9

value: The diaphragm tissue of Japanese white rabbits with large ears

value: anesthetized and mechanically ventilated for 24 hours


title: DRG proprioceptor21


title: Cow_2 [SP25BBE0]

value: blood


title: DRG proprioceptor20


title: Diffuse Midline Glioma A1


title: Astrocytoma A2


title: ApoE,normal diet, rep4


title: DRG proprioceptor18


title: diaphragm, spontaneously breathing, S3

value: anesthetized and spontaneously breathing for 24 hours


title: DRG proprioceptor17


title: ApoE,normal diet, rep2


title: Cow_1 [SP03F2D5]

value: NC


title: Cow_1 [SPB96823]


title: Glioblastoma A2


title: Cow_2 [SP254073]

value: LPS


title: ApoE,normal diet, rep3

value: ascending aorta (including aortic arch)

value: 20 weeks old


title: DRG proprioceptor19


title: Cow_1 [SPA2EC49]


title: Astrocytoma A1


title: DRG proprioceptor15


title: ApoE,high fat diet, rep7

value: male

value: ApoEKO

value: High Fat, high Cholesterol Experimental diet, Ssniff Spezialdiäten GmbH Germany


title: ApoE,high fat diet, rep8


title: ApoE,normal diet, rep1

value: normal diet


title: Oligodendroglioma A1

value: glioma


title: Cow_1 [SP48406B]

value: Hour


title: Cow_1 [SP2ACB40]

value: ng/mL


title: RKO cells, OETBX21 rep3

city: Jining

first: Wenzhi

last: Shen

address: No. 133 Hehua Road

institute: Jining Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: mm10
Supplementary files format and content: TXT files include FPKM values for each Sample
Supplementary files format and content: TXT files include count values for each Sample

source_name: RKO cells

growth_protocol: RKO cells were cultured in DMEM medium (HyClone) supplemented with 10% FBS, 1% sodium pyruvate (Gibco), 1.5g/L NaHCO3 (Gibco) and 1% NEAA (Gibco).

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample..

treatment_protocol: N/A.

value: RKO cells

value: Cancer cells


title: sclera.NC.3

city: Shanghai

first: Jibo

last: Zhou

address: Quxi road NO.500, Huangpu district

institute: NINTH PEOPLE'S HOSPITAL SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE

description: Library name: Sample6

data_processing:
Trimmomatic software were used to remove adapter and low quality reads. [Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.]
STAR is used to align clean reads to reference genome. STAR outperforms other aligners by a factor of >50 in mapping speed, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. [Dobin A1, Davis CA, Schlesinger F, Drenkow J, et.al. STAR: ultrafast universal RNA-seq aligner.Bioinformatics. 2013 Jan;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.]
Read counts for individual transcripts of each sample were produced with HTSeq-count. [Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–169.]
After perfoming the PCA on the expression of genes from all samples, plotPCA will sort the principal components according to the amount of variability of the data that they explain. Based on this, you will obtain a plot which is the eigenvalues of the top two principal components
Assembly: mCavPor4.1
Supplementary files format and content: All.HTSeq.counts xlsx includes raw counts for each sample

organism: Cavia porcellus

source_name: sclera

extract_protocol:
Samples were subjected to RNA extraction with Trizol (Thermo Fisher Scientific, 15596018 ).
Library construction was performed with the NEBNext UltraTM RNA Library Prep Kit (NEB #E7490) and libraries were purified with beads (AMPure XP system).

value: sclera


title: sclera.NC.2

description: Library name: Sample5


title: Glioblastoma A1


title: ApoE,high fat diet, rep5

value: female


title: Cow_1 [SP2F448B]

first: wenzhong

last: xiao

address: 38 sidney st, suite 161

institute: massachusetts general hospital

data_processing:
Sequencing quality was assessed additionally using FASTQC (v0.11.9). Transcriptome annotations of each species were downloaded from Ensembl (https://www.ensembl.org, v90). For each sample, firstly, reads were aligned to human genome hg38 using STAR in the established bulk-RNA sequencing workflow of Bcbio (v1.2.1).  Secondly, the abundance of the annotated genes of the species was estimated from the RNA-seq reads as Transcripts per Million (TPM) using Sailfish. Thirdly, to compare the gene expression between species, the abundance of the genes in each species was then translated to that of the corresponding human orthologues. Here, only genes in a non-human species that had known orthologous human genes (Ensembl v90) were considered in further analysis. When m genes in a non-human species had n orthologous genes in human (m>=0, n>=1), the abundance of each of the human orthologues is assumed to be the sum of the abundance of the m genes divided by n.
Assembly: hg38 Ensembl v90
Supplementary files format and content: TPM matrix

extract_protocol:
After incubation, blood in TruCulture tubes was separated according to the manufacturer’s instructions with additional centrifugation at 800 ×g for 10 minutes.  Supernatants were saved and frozen at −80 °C for cytokine analysis.  The cell pellets were lysed using red blood cell lysis solution for 10 min followed by centrifugation at 2,000 ×g for 3 minutes, and remaining white blood cells were lysed in Qiazol and frozen at −80 °C until library construction (Qiagen).
RNA isolated from white blood cells (Qiazol, Qiagen) was quality controlled using A260/A280 ratio, 28S/18S rRNA ratio, and an RNA integrity summary score (Agilent RIN). Total RNA samples (250ngs, RIN>=7.0) were enriched for mRNA, fragmented, and converted into indexed cDNA libraries according to Illumina TruSeq Stranded mRNA protocol and quantity controlled using Agilent TapeStation. Samples were sequenced to at least 25M of 2 x 50bp paired-end reads and assessed using in-house QA/QC metric (Q2Solutions Expression Analysis).

value: blood

value: S (sensitive)


title: ApoE,high fat diet, rep6


title: Glioblastoma A3


title: DRG proprioceptor16

value: DRG

value: Neuron


title: Cow_1 [SP0D9ECB]

value: LPS


title: RKO cells, OETBX21 rep1


title: RKO cells, OECtrl (MCS) rep3

value: OECtrl


title: sclera.NC.1

description: Library name: Sample4

value: NC


title: Cow_1 [SP7EE019]


title: Cow_1 [SP8E6742]


title: ApoE,high fat diet, rep4

value: ascending aorta (including aortic arch)

value: 20 weeks old

value: ApoEKO


title: RKO cells, OECtrl (MCS) rep2


title: ApoE,high fat diet, rep2

value: High Fat, high Cholesterol Experimental diet, Ssniff Spezialdiäten GmbH Germany


title: RKO cells, OETBX21 rep2


title: Cow_1 [SPD6FA9F]

value: Hour


title: ApoE,high fat diet, rep1


title: Cow_1 [SP8EF932]

value: ng/mL


title: (ATF3-3)cells after transfection with treatment plasmid

status: Public on Jan 01 2025

city: Columbia

first: Davis

last: Noblitt

state: SC

address: 631 Sumpter Street

department: IBS

institute: University of South Carolina

description:
Library name: Jurkat-ATF3-3
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample

data_processing:
FASTQ files containing raw paired-end sequencing reads were processed using the CLC Genomics Workbench 24.0.2. The ATF group was renamed from "ATF2" to "ATF3" after sequencing to ensure clarity with unrelated ATF datasets, all raw file names still contain ATF2 nomenclature, but should be taken as ATF3. Quality trimming steps included the removal of adapter sequences detected in reads. Reads with more than two ambiguous nucleotides were trimmed, and sequences shorter than six nucleotides were discarded. Trimming also addressed low-quality sequences with a quality limit of 0.05. As a result of this, the trimmed reads maintained an average length between 144.83 and 147.29 bases across samples. Approximately 13.9% of read pairs were trimmed due to adapter contamination. The final number of genes seen in the expression profile of all samples was 24,493.
Differential expression analysis was performed using the DESeq2 package.
Assembly: hg19 Ensembl v110
Supplementary files format and content: The RawExpresionData file contains counts, TCM, TPM, and RPKM data in a CSV format.
Supplementary files format and content: The Deseq2Results file contains the differential analysis results in CSV format. It specifically include the basemean, Log2FoldChange, Wald "stat", SE, P, and Padj values.

source_name: Lymphocyte

growth_protocol: Human Jurkat cells (ATCC, TIB-152) were cultured in Roswell Park Memorial Institute Medium (RPMI) containing GlutaMax supplemented with 10% v/v fetal bovine serum (FBS, Gibco) and penicillin/streptomycin (Cytiva) at 37 °C in 5% v/v CO2 (g).

extract_protocol:
The total RNA was harvested using an Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using PolyA selection for mRNA species (eukaryotic). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA)

treatment_protocol: Cells suspensions in RPMI (10% FBS + Pen/Strep) were transfected with plasmids using a Bio-Rad Gene Pulser Xcell Electroporator. To a 2 mm MicroPulser cuvette (Bio-Rad, cat. no. 1652086) was added 1x10^6 Jurkat cells and 100 µg of plasmid in RPMI media at a total volume of 200 µL. The transfection was performed using an exponential decay pulse; capacitance = 1000 µF and voltage = 140 V. After equilibrating the cells for 2 h, the media was supplemented with zinc chloride, PMA/Ionomycin, and Brefeldin A.

value: Lymphocyte

value: Jurkat

value: T Lymphocyte

value: WT

tag: batch


title: (ATF3-2)cells after transfection with treatment plasmid

description:
Library name: Jurkat-ATF3-2
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample


title: sclera.FDM.2

description: Library name: Sample2

value: sclera

value: form-deprived


title: (ATF3-1)cells after transfection with treatment plasmid

description:
Library name: Jurkat-ATF3-1
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample


title: (Aart6-1)cells after transfection with ctrl plasmid

description:
Library name: Jurkat-Aart6-1
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample


title: (Aart6-2)cells after transfection with ctrl plasmid

description:
Library name: Jurkat-Aart6-2
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample


title: (Aart6-3)cells after transfection with ctrl plasmid

description:
Library name: Jurkat-Aart6-3
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample


title: (ctlr-3)cells after transfection with buffer

description:
Library name: Jurkat-ctrl-3
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample

value: Shock


title: (ctlr-2)cells after transfection with buffer

description:
Library name: Jurkat-ctrl-2
RNA sequencing of RNA samples (not derived from blood) from Homo Sapiens using 2x150 bp, 30 million paired-end reads per sample


title: ApoE,high fat diet, rep3

value: male