title: respiratory organoids_RSV_B4

first: Kazuo

last: Takayama

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.1. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.10a with the GENCODE (release 36, GRCh38.p13) gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.2 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: respiratory tract

growth_protocol: To start the differentiation, human iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. After centrifugation, cells were seeded onto Matrigel Growth Factor Reduced Basement Membrane (Cat# 354230, Corning)-coated cell culture plates (2.0×105 cells/4 cm2) and cultured for 2 days. The differentiation of the respiratory organoids was performed in serum-free differentiation (SFD) medium, composed of DMEM/F12 (3:1) (Cat# 044-29765, FUJIFILM Wako Pure Chemical and Cat# 11320033, Thermo Fisher Scientific) supplemented with N2 (Cat# 141-08941, FUJIFILM Wako Pure Chemical), B-27 Supplement Minus Vitamin A (Cat# 12587001, Thermo Fisher Scientific), ascorbic acid (50 μg/mL, Cat# ST-72132, STEMCELL Technologies), 1× GlutaMAX (Cat# 35050-061, Thermo Fisher Scientific), 1% monothioglycerol (Cat# 195-15791, FUJIFILM Wako Pure Chemical), 0.05% bovine serum albumin (Cat# 820024, Sigma-Aldrich), and 1× penicillin/streptomycin). During days 0-1 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), and 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems). During days 1–3 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems) and 1% FBS. Between days 3–5 of differentiation, cells were cultured in SFD medium supplemented with 1.5 μM Dorsomorphin dihydrochloride (Cat# 047-33763, FUJIFILM Wako Pure Chemical) and 10 μM SB431542 (Cat# 037-24293, FUJIFILM Wako Pure Chemical) for 24 h, and then SFD medium supplemented with 10 μM SB431542 and 1 μM IWP2 (Cat# 04-0034, Stemolecule) for another 24 h. During days 5–12 of differentiation, cells were cultured with SFD medium supplemented with 3 μM CHIR99021 (Cat# 034-23103, FUJIFILM Wako Pure Chemical), 10 ng/mL human FGF10 (Cat# AF-100-26, PeproTech), 10 ng/mL human FGF7 (Cat# AF-100-19, PeproTech), 10 ng/mL human BMP4 (Cat# 120-05ET, PeproTech), 20 ng/mL human EGF (Cat# AF-100-15, PeproTech), and all-trans retinoic acid (Cat# R2625 ATRA, Sigma-Aldrich). On day 12 of differentiation, cells were dissociated and embedded in the Matrigel Growth Factor Reduced Basement Membrane to generate organoids. During days 12–20 of the differentiation, organoids were cultured in SFD medium containing 3 μM CHIR99021, 10 ng/mL human FGF10, 10 ng/mL human FGF7, 10 ng/mL human BMP4, and 50 nM ATRA. On day 20 of differentiation, organoids were recovered from the Matrigel, and the resulting suspension of organoids (small free-floating clumps) was seeded onto Matrigel-coated cell culture plates. During days 20–30 of differentiation, organoids were cultured in SFD medium containing 50 nM dexamethasone (Cat# S1322, Selleck Chemicals), 0.1 mM 8-bromo-cAMP (Cat# 1140/50, Tocris Bioscience), and 0.1 mM IBMX (3-isobutyl-1-methylxanthine) (Cat# 095-03413, FUJIFILM Wako Pure Chemical).

extract_protocol:
Total RNA was isolated from human respiratory organoids using ISOGENE (NIPPON GENE).
The library preparation was performed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Respiratory organoids were infected with 0.1 MOI isolated RSV-A or RSV-B

value: respiratory tract

value: human iPS cells

value: iPS cell-derived respiratory organoids

value: wild type

value: RSV-B infected


title: C01409

status: Public on Apr 21 2025

type: SRA

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

country: USA

institute: ToxStrategies

description: Library name: Sample 173

library_source: transcriptomic

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software and sample-specific barcodes to give a FASTQ file for each sample
bcl2fastq2 v2.20 for demultiplexing
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
fastq files were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: templated oligo sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Mounted, unstained FFPE liver samples were scraped from the slides and processed according to the TempO-Seq® protocol by BioSpyder Technologies
TempO-Seq® protocol by BioSpyder Technologies

treatment_protocol: This study consisted of four arms based on chemical treatment: HFPO-DA (chemical of interest), GW7647 (prototypical PPARa agonist), rosiglitazone (prototypical PPARg agonist), and APAP (prototypical cytotoxic agent). Male mice from each of the three strains (i.e., J:ARC(S), B6129SF2/J, PPARa KO) were randomly allocated based on body weight to each dose group (vehicle control, low, medium, or high) within each study arm (n = 4/dose/strain/arm). Dosing solutions of HFPO-DA, GW7647, and rosiglitazone were administered via oral gavage at a dose volume of 10 mL/kg body weight once per day for five days. The doses were as follows: 0, 3, 15, or 30 mg/kg-d HFPO-DA; 0, 5, 10, or 20 mg/kg-d GW7647; and 0, 5, 10, or 20 mg/kg-d rosiglitazone. APAP was administered to 12-hour fasted mice as a single intraperitoneal (IP) injection at 0, 150, 300, or 600 mg/kg. Feed was restored immediately after APAP dosing and mice were sacrificed 6 hours post-dose. Following the last treatment, mice were euthanized by CO2 anesthesia and exsanguination. Livers were fixed in 10% neutral-buffered formalin, embedded in paraffin (FFPE), and sections approximately 4 – 6 µm in thickness were mounted to glass slides.

tag: tissue

value: liver

tag: strain

tag: Sex

value: male

tag: genotype

value: WT

tag: exposure route

value: oral

tag: exposure duration

value: 5 days

tag: treatment

value: 600 mg/kg APAP


title: 2032, A.japonica infected, 6hr, biological replicate 3

city: Saint Louis

first: Jennette

last: Codjoe

state: Missouri

address: 1005 N Warson Rd, Suite 305

institute: CoverCress Inc.

description:
Library name: Library 36
Column title in read_counts_raw_all_samples.csv: Aj_I6_2032_3

data_processing:
Reads cleaned with fastp software. Removed adapters and reads with N > 10% or reads containing >50% low quality bases (Qphred ≤ 5).
Cleaned reads aligned to Tarvense_v2 genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 used to count reads mapped to each gene.
Assembly: GenBank assembly GCA_911865555.2
Supplementary files format and content: csv file contains raw read counts for each sample

molecule: polyA RNA

organism: Thlaspi arvense

source_name: rosette leaf

extract_protocol:
Sclerotinia sclerotiorum samples: Total RNA isolated by NucleoSpin Plant RNA Kit (Machery-Nagel). Alternaria japonica samples: Total RNA isolated by E.Z.N.A. Plant RNA Kit (Omega Bio-tek). 1ug total RNA used for library preparation.
Libraries prepared by NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer's instructions for polyA mRNA enrichment.

value: rosette leaf

tag: time

value: 6 hours

value: Alternaria japonica


title: MN106, A.japonica infected, 6hr, biological replicate 3

description:
Library name: Library 24
Column title in read_counts_raw_all_samples.csv: Aj_I6_MN106_3


title: MN106, mock (for A.japonica infection), 6hr, biological replicate 1

description:
Library name: Library 25
Column title in read_counts_raw_all_samples.csv: Aj_C6_MN106_1

value: mock


title: MN106, mock (for A.japonica infection), 6hr, biological replicate 3

description:
Library name: Library 27
Column title in read_counts_raw_all_samples.csv: Aj_C6_MN106_3


title: respiratory organoids_RSV_B2

city: Kyoto

state: Kyoto

country: Japan

institute: Kyoto University

organism: Homo sapiens

tag: cell line

tag: cell type


title: C01408

description: Library name: Sample 172

value: 300 mg/kg APAP


title: MN106, A.japonica infected, 6hr, biological replicate 2

description:
Library name: Library 23
Column title in read_counts_raw_all_samples.csv: Aj_I6_MN106_2


title: MN106, A.japonica infected, 6hr, biological replicate 1

description:
Library name: Library 22
Column title in read_counts_raw_all_samples.csv: Aj_I6_MN106_1


title: C01407

description: Library name: Sample 171


title: 2032, mock (for Sclerotinia infection), 6hr, biological replicate 3

description:
Library name: Library 21
Column title in read_counts_raw_all_samples.csv: Ss_C6_2032_3


title: 2032, mock (for Sclerotinia infection), 6hr, biological replicate 2

description:
Library name: Library 20
Column title in read_counts_raw_all_samples.csv: Ss_C6_2032_2


title: C01406

description: Library name: Sample 170


title: B1, DGA treated, biol rep1

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Library name: B1_DGA_01

data_processing:
Concatenated base call files (.cbcl) generated from the sequencing run were converted to a FASTQ file for each sample by the DRAGEN BCL Convert pipeline. The .cbcl files were further analyzed by the DRAGEN RNA pipeline to generate transcript quantification results at the gene level (.quant.genes.sf).
Assembly: Human reference genome hg38-alt-aware
Supplementary files format and content: Files in .sf format containing transcript quantification results at the gene level.

growth_protocol: Human iPSCs were maintained as single-cell cultures (no colony formation) on COAT-1 pre-coated 6-well tissue culture plates in the Cellartis DEF-CS Culture System (Takara Bio USA, San Jose, CA) at 37˚C in a humidified incubator supplied with 5% CO2. Hepatocyte differentiation from the iPSC lines were conducted using the Cellartis iPS Cell to Hepatocyte Differentiation System (Takara Bio USA), and instructions from the manufacturer were followed.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.
Sequencing libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit (San Diego, CA) following protocols provided by the manufacturer.

treatment_protocol: Hepatocytes differentiated from iPSCs on day 23 were exposed to 3.0 mM DGA or 10.0 μM UA in duplicate (n = 2) for 24 h.

tag: ethnicity

value: BAA

value: iPSC-derived hepatocytes

value: DGA


title: respiratory organoids_RSV_B1

value: respiratory tract

value: human iPS cells

value: iPS cell-derived respiratory organoids


title: 2032, Sclerotinia infected, 6hr, biological replicate 3

description:
Library name: Library 18
Column title in read_counts_raw_all_samples.csv: Ss_I6_2032_3

value: Sclerotinia sclerotiorum


title: 2032, mock (for Sclerotinia infection), 6hr, biological replicate 1

description:
Library name: Library 19
Column title in read_counts_raw_all_samples.csv: Ss_C6_2032_1


title: respiratory organoids_RSV_A4

value: wild type

value: RSV-A infected


title: C01405

description: Library name: Sample 169

value: liver

value: male

value: WT

value: oral


title: 2032, Sclerotinia infected, 6hr, biological replicate 2

description:
Library name: Library 17
Column title in read_counts_raw_all_samples.csv: Ss_I6_2032_2

value: rosette leaf

value: 6 hours


title: 2032, Sclerotinia infected, 6hr, biological replicate 1

description:
Library name: Library 16
Column title in read_counts_raw_all_samples.csv: Ss_I6_2032_1


title: respiratory organoids_RSV_A3


title: respiratory organoids_RSV_B3

value: RSV-B infected


title: 2032, mock, 3hr, biological replicate 1

description:
Library name: Library 14
Column title in read_counts_raw_all_samples.csv: Ss_C3_2032_1

value: 3 hours

value: mock


title: 2032, Sclerotinia infected, 3hr, biological replicate 3

description:
Library name: Library 13
Column title in read_counts_raw_all_samples.csv: Ss_I3_2032_4


title: 2032, mock, 3hr, biological replicate 2

description:
Library name: Library 15
Column title in read_counts_raw_all_samples.csv: Ss_C3_2032_3


title: respiratory organoids_RSV_A2


title: C01404

description: Library name: Sample 168

value: 5 days

value: 150 mg/kg APAP


title: C01403

description: Library name: Sample 167


title: respiratory organoids_CNT4

value: respiratory tract


title: 2032, Sclerotinia infected, 3hr, biological replicate 2

description:
Library name: Library 12
Column title in read_counts_raw_all_samples.csv: Ss_I3_2032_3


title: C01402

description: Library name: Sample 166


title: C01401

description: Library name: Sample 165


title: respiratory organoids_CNT3

value: human iPS cells


title: respiratory organoids_RSV_A1

value: iPS cell-derived respiratory organoids


title: respiratory organoids_CNT2


title: C01400

description: Library name: Sample 164

value: 0 mg/kg APAP


title: MN106, Sclerotinia infected, 6hr, biological replicate 1

description:
Library name: Library 6
Column title in read_counts_raw_all_samples.csv: Ss_I6_MN106_1

value: Sclerotinia sclerotiorum


title: MN106, mock (for Sclerotinia infection), 6hr, biological replicate 2

description:
Library name: Library 9
Column title in read_counts_raw_all_samples.csv: Ss_C6_MN106_2


title: C01399

description: Library name: Sample 163


title: MN106, mock, 3hr, biological replicate 2

description:
Library name: Library 4
Column title in read_counts_raw_all_samples.csv: Ss_C3_MN106_2


title: MN106, Sclerotinia infected, 6hr, biological replicate 2

description:
Library name: Library 7
Column title in read_counts_raw_all_samples.csv: Ss_I6_MN106_2


title: C01398

description: Library name: Sample 162


title: MN106, mock (for Sclerotinia infection), 6hr, biological replicate 1

description:
Library name: Library 8
Column title in read_counts_raw_all_samples.csv: Ss_C6_MN106_1


title: MN106, mock, 3hr, biological replicate 3

description:
Library name: Library 5
Column title in read_counts_raw_all_samples.csv: Ss_C3_MN106_3


title: 2032, Sclerotinia infected, 3hr, biological replicate 1

description:
Library name: Library 11
Column title in read_counts_raw_all_samples.csv: Ss_I3_2032_1


title: Peripheral blood of SCAN02 14 days after canakinumab

first: Naotomo

last: Kambe

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Dermatology

description:
Library name: SCAN02_Post
10x Genomics

library_source: transcriptomic single cell

data_processing:
The CellRanger pipeline 3.1.0 (10x Genomics) was used to generate count matrices from FASTQ files using default parameters.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data

source_name: Peripheral blood

extract_protocol:
In the 2 cases of SCAN01 and SCAN02, the remaining cell pellet after plasma collection was treated with Ammonium-Chloride-Potassium Lysing Buffer to lyse red blood cells, followed by resuspension in PBS.
Isolated cells were loaded onto a Chromium instrument (10x Genomics, Pleasanton, CA) according to the Chromium Single Cell 3′ Reagent Kit, version 3, according to the user guide. Sample libraries were sequenced at a depth of over 20,000 reads per cell using DNBSEQG400 (MGI Tech, Tokyo).

treatment_protocol: Schnitzler syndrome patients were administered a single subcutaneous injection of 150 mg of canakinumab, and peripheral blood samples were collected 14 days post-injection.

value: Peripheral blood

tag: disease state

value: Schnitzler syndrome

value: canakinumab, anti-IL-1beta


title: 096_sub_int

city: London

first: Holly

last: Philpott

state: Ontario

address: 1151 Richmond St

country: Canada

institute: Western University

description: FFPE spatial profiling

data_processing:
NanoString GeoMX Platform was used for probe QC and Q3 normalization as recommended by NanoString. Then patient samples were grouped based on those with more pain and those with less pain for analysis and adjusted for ID and BMI. All microenvironment ROI subtypes were analyzed separately. For example, all ROIs of synovial intimal lining were included in one analysis, then all sublining ROIs, and then all microvessel ROIs.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files, PKC file, probe QC, Q3 normalization, metadata file
Library strategy: GeoMx Seq

source_name: synovial tissue

extract_protocol:
Synovial tissue samples were processed for FFPE and constructed into a tissue microarray, so that all samples could be analyzed on a single slide. The slide was sent to NanoString for library construction and
https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/
https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/

value: late-stage knee osteoarthritis

value: synovial tissue

value: more pain


title: MN106, mock (for Sclerotinia infection), 6hr, biological replicate 3

description:
Library name: Library 10
Column title in read_counts_raw_all_samples.csv: Ss_C6_MN106_3

value: rosette leaf

value: 6 hours


title: MN106, mock, 3hr, biological replicate 1

description:
Library name: Library 3
Column title in read_counts_raw_all_samples.csv: Ss_C3_MN106_1

value: 3 hours


title: C01397

description: Library name: Sample 161

value: liver

value: male

value: WT

value: oral


title: Peripheral blood of SCAN01 14 days after canakinumab

description:
Library name: SCAN01_Post
10x Genomics


title: 095_vessel

description: FFPE spatial profiling


title: C01396

description: Library name: Sample 160

value: PPARa KO

value: 5 days

value: 600 mg/kg APAP


title: C01395

description: Library name: Sample 159


title: Peripheral blood of SCAN02 before canakinumab

description:
Library name: SCAN02_Pre
10x Genomics


title: respiratory organoids_CNT1

value: respiratory tract

value: human iPS cells

value: iPS cell-derived respiratory organoids

value: wild type

value: mock


title: MN106, Sclerotinia infected, 3hr, biological replicate 2

description:
Library name: Library 2
Column title in read_counts_raw_all_samples.csv: Ss_I3_MN106_3

value: Sclerotinia sclerotiorum


title: MN106, Sclerotinia infected, 3hr, biological replicate 1

description:
Library name: Library 1
Column title in read_counts_raw_all_samples.csv: Ss_I3_MN106_1


title: Peripheral blood of SCAN01 before canakinumab

description:
Library name: SCAN01_Pre
10x Genomics

value: Peripheral blood

value: Schnitzler syndrome


title: 093_sub_int

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

value: synovial tissue

value: more pain


title: C01394

description: Library name: Sample 158

value: liver

value: male


title: RAW 264.7, gCebpb+40esculetin-3

city: Xiamen

first: Binbin

last: Liu

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

country: China

institute: Xiamen University

description: Library name: Sample 12

library_source: genomic

data_processing:
The raw reads generated by ATAC-seq and ChIP-seq were trimmed with Trim-Galore and aligned to the mm10 reference genome using Bowtie2 [40]. PCR duplicates and multiple mapped reads were removed with Sambamba.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: RAW 264.7 cells, a mouse macrophage cell line, and sorted ATMs were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/ml penicillin and 0.1 mg/ml streptomycin at 37°C under 5% CO2.

extract_protocol:
For ATAC-seq, cells (5 x 104) were washed twice in cold PBS and resuspended in 50 μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween, 0.1% NP40, and 0.01% Digitonin).
Lysates were centrifuged (750 x g, 10 min, 4°C), and nuclei were resuspended in 50 μl of transposition reaction mix with 5 μl Tn5 Transposase (TruePrep DNA Library Prep kit V2 for Illumina) and incubated for 30 min at 37°C. Transposed DNA fragments were purified using a QIAGEN Reaction MiniElute Kit, barcoded with Novo NGS Index Kit for Illumina, and amplified to 240 fmol by NEBNext Ultra II Q5 Master Mix. PCR products were purified using a PCR Purification Kit for paired-end sequencing.

treatment_protocol: RAW 264.6 cells were transfected with the LentiCRISPR v2 plasmid containing gRNA against Cebpb or empty vector using the Gene Pulser Xcell Eukaryotic System (165-2661, Bio-Rad, CA, USA). Cells were stimulated with 25 µg/mL DIL-oxLDL and either 0 or 40 µg/mL esculetin for 24 hr

value: mouse  macrophage

value: gCebpb

value: 40 µg/mL esculetin

tag: batch


title: Human Control REP3

city: Beijing

first: Gengshen

last: Song

state: Beijing

address: No. 6, Hongda ZhongLu, Beijing Economic-Technological Development Area

institute: Beijing Youcare Kechuang Pharmaceutical Technology Co., Ltd.

description: Library name: HNC-3

data_processing:
Raw RNAseq reads were trimmed and filtered using Trimmomatic software. Filtered reads were aligned to human or rat genomes using HISAT2 and expression was quantified using StringTie. Differentially expressed genes were analyzed using DESeq.
Assembly: hg38/rn6
Supplementary files format and content: .xls file containing ENSEMBL gene id, Mean TPM, log2FoldChange, p value and q value

source_name: primary hepatocyte

extract_protocol:
Hepatocytes were cultured for 48 h before being harvested with TRIzol (Invitrogen, 15596018CN) according to manufacturer's instructions.
RNA extracted from TRIzol was used for cDNA library preparation using the Hieff mRNA Library Prep Kit (Yeasen, 12309ES08) and sequenced on a HiSeq sequencer (Illumina), according to the manufacturer’s instructions.

value: primary hepatocyte


title: 092_vessel

description: FFPE spatial profiling


title: RAW 264.7, gCebpb+40esculetin-2

description: Library name: Sample 11


title: C01393

description: Library name: Sample 157

value: PPARa KO

value: WT

value: oral

value: 5 days

value: 600 mg/kg APAP


title: C01392

description: Library name: Sample 156

value: 300 mg/kg APAP


title: Human Control REP2

description: Library name: HNC-2


title: C01391

description: Library name: Sample 155


title: 091_lining

description: FFPE spatial profiling


title: RAW 264.7, gCebpb+0-3

description: Library name: Sample 9

value: DMSO


title: Human si060-DV25PG5 1 nM REP3

description: Library name: H73-3


title: Human Control REP1

description: Library name: HNC-1


title: 094_lining

description: FFPE spatial profiling


title: RAW 264.7, gCebpb+0-2

description: Library name: Sample 8


title: Human si060-DV25PG5 1 nM REP2

description: Library name: H73-2


title: 088_lining

description: FFPE spatial profiling


title: C01389

description: Library name: Sample 153


title: 087_vessel

description: FFPE spatial profiling

value: less pain


title: RAW 264.7, gEV+40esculetin-3

description: Library name: Sample 6

value: gEV


title: Human si060-DV25PG5 1 nM REP1

description: Library name: H73-1


title: RAW 264.7, gEV+40esculetin-2

description: Library name: Sample 5


title: C01387

description: Library name: Sample 151

value: 150 mg/kg APAP


title: Human si060-DV25PG5 10 nM REP2

description: Library name: H72-2


title: 086_sub_int

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

value: synovial tissue


title: RAW 264.7, gCebpb+0-1

description: Library name: Sample 7


title: Human si060-DV25PG5 10 nM REP3

description: Library name: H72-3


title: RAW 264.7, gCebpb+40esculetin-1

description: Library name: Sample 10


title: 090_vessel

description: FFPE spatial profiling

value: more pain


title: C01386

description: Library name: Sample 150

value: liver

value: male


title: Human si060-DV25PG5 10 nM REP1

description: Library name: H72-1


title: RAW 264.7, gEV+0-3

description: Library name: Sample 3

value: mouse  macrophage


title: Human si060-DV25PG5 100 nM REP3

description: Library name: H71-3

value: primary hepatocyte


title: C01390

description: Library name: Sample 154

value: PPARa KO


title: 084_sub_int

description: FFPE spatial profiling


title: 083_vessel

description: FFPE spatial profiling


title: C01385

description: Library name: Sample 149

value: WT


title: RAW 264.7, gEV+0-2

description: Library name: Sample 2


title: Human si060-DV25PG5 100 nM REP2

description: Library name: H71-2


title: C01384

description: Library name: Sample 148

value: oral

value: 0 mg/kg APAP


title: 089_sub_int

description: FFPE spatial profiling


title: C01383

description: Library name: Sample 147

value: 5 days


title: RAW 264.7, gEV+0-1

description: Library name: Sample 1


title: 082_lining

description: FFPE spatial profiling


title: Liver,E3_180

data_processing:
The sequencing reads were mapped to the reference mouse genome GRCm39 by HISAT 2.2.1
Read counts per gene locus were obtained with featureCounts
Assembly: mm10
Supplementary files format and content: table-delimitted txt files containing raw counts for each smaplws

source_name: livers

growth_protocol: C57BL6/J male mice (8-9 weeks old) were housed in specific pathogen free facilities with 12 h light:12 h dark cycles at 22-23°C in Xiamen University.

extract_protocol:
RNAs were purified from the livers  by Trizol Reagent
A cDNA library was prepared by using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: esculetin (0 or 180mg/kg/d) were daily administered to the mice by oral gavage for 7 days. In the first 4 days, the mice were fed with a control diet (CD) containing 10% kcal from fat. Then the mice were fed with a high- fat diet (HFD) containing 60% kcal from fat for additional 3 days to understand lipid-rich meals-induced postprandial lipid circulation.

value: livers

value: 90mg/kg/d esculetin


title: C01382

description: Library name: Sample 146


title: Human si061-DV27PG5 1 nM REP3

description: Library name: H63-3


title: 085_lining

description: FFPE spatial profiling

value: less pain


title: RAW 264.7, gEV+40esculetin-1

description: Library name: Sample 4

value: gEV

value: 40 µg/mL esculetin


title: 080_vessel

description: FFPE spatial profiling

value: late-stage knee osteoarthritis


title: Liver,E2_180


title: C01381

description: Library name: Sample 145


title: Human si061-DV27PG5 1 nM REP2

description: Library name: H63-2


title: C01388

description: Library name: Sample 152

value: 150 mg/kg APAP


title: Liver,E1_180


title: 1528_144

description: Library name: Sample 144

value: 10 mg/kg/day GW7647


title: Human si061-DV27PG5 1 nM REP1

description: Library name: H63-1


title: 078_sub_int

description: FFPE spatial profiling

value: synovial tissue

value: more pain


title: Liver,C3_0


title: 1528_143

description: Library name: Sample 143

value: liver

value: male

value: 5 mg/kg/day GW7647


title: Human si061-DV27PG5 10 nM REP3

description: Library name: H62-3

value: primary hepatocyte


title: 1528_142

description: Library name: Sample 142

value: WT

value: oral

value: 20 mg/kg/day GW7647


title: Human si061-DV27PG5 10 nM REP2

description: Library name: H62-2


title: Liver,C2_0

value: livers


title: 077_vessel

description: FFPE spatial profiling


title: Human si060-DV25PG5 100 nM REP1

description: Library name: H71-1


title: 076_lining

description: FFPE spatial profiling


title: Liver,C1_0


title: 1528_141

description: Library name: Sample 141

value: 5 days


title: 081_sub_int

description: FFPE spatial profiling

value: less pain


title: Human si061-DV27PG5 10 nM REP1

description: Library name: H62-1


title: 075_sub_int

description: FFPE spatial profiling


title: 1528_140

description: Library name: Sample 140


title: 074_vessel

description: FFPE spatial profiling


title: Human si061-DV27PG5 100 nM REP2

description: Library name: H61-2


title: 1528_139

description: Library name: Sample 139

value: 0 mg/kg/day GW7647


title: 079_lining

description: FFPE spatial profiling


title: 073_lining

description: FFPE spatial profiling


title: Human si061-DV27PG5 100 nM REP1

description: Library name: H61-1


title: 1528_138

description: Library name: Sample 138


title: 072_vessel

description: FFPE spatial profiling


title: 1528_137

description: Library name: Sample 137


title: Human si098-DV29Pd7BG5 1 nM REP3

description: Library name: H53-3


title: Shingrix_04

type: RNA

city: Bethesda

first: Nicolas

last: Cuburu

address: 37 convent drive

department: CCR

institute: NIH/NCI

hyb_protocol: Set up a hybridization reaction at room temperature for each sample with the following components: 3 μL of Reporter CodeSet, 5 μL of hybridization buffer, up to 5 μL (25–100 ng) of sample RNA, and 2 μL of Capture ProbeSet

scan_protocol: nCounter XT CodeSet

data_processing: nSolver

source_name: 48h, fourth injection, TC-1 tumor

growth_protocol: Injected sucutaneously 5x10^5 cells (TC1)

extract_protocol: Frozen tumors were pulverized in 1mL Trizol (Thermo Fisher) using ceramic beads in reinforced tubes and a Precellys24 Homogenizer (Bertin Instruments). A volume of 0.2mL of chloroform was added to the tumor lysate and mixed thoroughly before centrifugation at 12,000rpm for 15min at 4 ̊C. Aqueous phase was further processed using the RNeasy Mini QIAcube Kit (Qiagen). Purified RNA was analyzed and quantified using Nanodrop device (Nanodrop Products). A total of 200ng of RNA was used for gene expression analysis using the mouse nCounter Immune Exhaustion Panel (Nanostring Technologies). Sample preparation and hybridization was done following manufacturer’s instruction. The gene expression data were normalized using the nSolver Analysis Software 4.0 (Nanostring Technologies) before further analysis.

treatment_protocol: Tumor tissues were collected 48hrs after the last of 4 i.t. injections and flash-frozen in liquid nitrogen.

tag: gender

value: female

tag: age

value: 4 months

tag: vaccination

value: Shingrix

tag: injection

value: Intratumoral


title: Shingrix+L1_04

value: Shingrix + HPV16 L1(165-173) peptide


title: 071_sub_int

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

tag: tissue

value: synovial tissue

value: more pain


title: 1528_136

description: Library name: Sample 136

value: liver

tag: strain

value: male


title: Human si098-DV29Pd7BG5 1 nM REP2

description: Library name: H53-2

value: primary hepatocyte


title: Shingrix_03


title: 070_lining

description: FFPE spatial profiling


title: Human si098-DV29Pd7BG5 1 nM REP1

description: Library name: H53-1


title: Human si098-DV29Pd7BG5 10 nM REP3

description: Library name: H52-3


title: AS01B_04


title: 1528_134

description: Library name: Sample 134

tag: Sex

value: WT

value: oral

value: 5 mg/kg/day GW7647


title: 069_sub_int

description: FFPE spatial profiling


title: Human si061-DV27PG5 100 nM REP3

description: Library name: H61-3


title: Saline_04

value: Saline


title: 068_vessel

description: FFPE spatial profiling


title: 1528_133

description: Library name: Sample 133

tag: genotype

value: 5 days


title: Human si098-DV29Pd7BG5 10 nM REP2

description: Library name: H52-2


title: 1528_132

description: Library name: Sample 132

tag: exposure route

value: 0 mg/kg/day GW7647


title: Human si098-DV29Pd7BG5 10 nM REP1

description: Library name: H52-1


title: Shingrix+L1_03

value: female


title: 1528_131

description: Library name: Sample 131

tag: exposure duration


title: Shingrix+L1_02

value: 4 months

tag: treatment


title: Shingrix+L1_01


title: 1528_135

description: Library name: Sample 135


title: Human si098-DV29Pd7BG5 100 nM REP3

description: Library name: H51-3


title: 1528_130

description: Library name: Sample 130

value: 10 mg/kg/day GW7647


title: 065_vessel

description: FFPE spatial profiling


title: Human si098-DV29Pd7BG5 100 nM REP2

description: Library name: H51-2


title: 064_lining

description: FFPE spatial profiling


title: 1528_129

description: Library name: Sample 129


title: 066_sub_int

description: FFPE spatial profiling


title: Human si098-DV29Pd7BG5 100 nM REP1

description: Library name: H51-1


title: 063_sub_int

description: FFPE spatial profiling


title: Human si080-DV25PG5 1 nM REP3

description: Library name: H43-3


title: 062_vessel

description: FFPE spatial profiling


title: 1528_128

description: Library name: Sample 128

value: 20 mg/kg/day GW7647


title: Human si080-DV25PG5 1 nM REP2

description: Library name: H43-2


title: AS01B_03

value: Intratumoral


title: 1528_127

description: Library name: Sample 127


title: 067_lining

description: FFPE spatial profiling

value: late-stage knee osteoarthritis


title: 061_lining

description: FFPE spatial profiling

value: synovial tissue


title: Human si080-DV25PG5 1 nM REP1

description: Library name: H43-1


title: 060_sub_int

description: FFPE spatial profiling

value: less pain


title: Saline_03


title: AS01B_02


title: Shingrix_01

value: Shingrix


title: 1528_126

description: Library name: Sample 126

value: liver

value: male


title: 1528_125

description: Library name: Sample 125

value: WT


title: Human si080-DV25PG5 10 nM REP3

description: Library name: H42-3

value: primary hepatocyte


title: Saline_02


title: Shingrix_02


title: AS01B_01


title: 1528_124

description: Library name: Sample 124

value: oral


title: 059_vessel

description: FFPE spatial profiling


title: Saline_01

value: Saline


title: Human si080-DV25PG5 10 nM REP2

description: Library name: H42-2


title: 058_lining

description: FFPE spatial profiling


title: 1528_123

description: Library name: Sample 123

value: 5 days


title: Human si080-DV25PG5 10 nM REP1

description: Library name: H42-1


title: 057_sub_int

description: FFPE spatial profiling


title: 1528_122

description: Library name: Sample 122


title: 1528_121

description: Library name: Sample 121


title: Human si080-DV25PG5 100 nM REP2

description: Library name: H41-2


title: 056_vessel

description: FFPE spatial profiling


title: 055_lining

description: FFPE spatial profiling


title: 1528_120

description: Library name: Sample 120

value: 5 mg/kg/day GW7647


title: Human si080-DV25PG5 100 nM REP1

description: Library name: H41-1


title: 054_sub_int

description: FFPE spatial profiling


title: Human si080-DV25PG5 100 nM REP3

description: Library name: H41-3


title: Human si097-DV29PG5 1 nM REP3

description: Library name: H33-3


title: 1528_119

description: Library name: Sample 119


title: BRONJ, total

city: Chengdu

first: Yixin

last: Shi

state: Sichuan

address: No.14, Section 3, Renmin South Road, Wuhou District, Chengdu, Sichuan, China

institute: Sichuan University

description: Library name: BRONJ, total, scRNAseq

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
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: murine mandible tissue

extract_protocol:
Nine C57/B6 male mice were used to acquire single-cell suspensions each group. Mandibles were dissected with soft tissues removed. Then, mandible tissue was cut into small pieces and digested with 3 mg/mL collagenase type I (Gibco) and 4 mg/mL dispase II (Sigma) for 60 min at 37°C as previously described (Cui et al., 2020; Yamaza et al., 2011). Red blood cells were lysed with 1 mL Red Cell Lysis Solution (Biosharp). Cells were centrifuged and resuspended in 1% BSA solution. Then, mandible tissue was digested to acquire single cell suspension, which enriched with CD45- cells using Meiteni Mouse CD45 MicroBeads. The final concentration of cells was 1 x 10^6 cells per mL.
Cellular suspensions were loaded into Chromium microfluidic chips and barcoded with a 10x Chromium Controller (10x Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10x Genomics) and sequenced with the NovaSeq system (Illumina).

value: murine mandible tissue

value: B cells, Endothelial cells,Fibroblasts, Macrophages, Neutrophil, T cells, et al.

value: wildtype


title: 052_lining

description: FFPE spatial profiling


title: 1528_118

description: Library name: Sample 118


title: Control, total

description: Library name: Control, total, scRNAseq


title: Human si097-DV29PG5 1 nM REP2

description: Library name: H33-2


title: 051_vessel

description: FFPE spatial profiling


title: Human si097-DV29PG5 1 nM REP1

description: Library name: H33-1


title: 1528_117

description: Library name: Sample 117


title: Human si097-DV29PG5 10 nM REP3

description: Library name: H32-3


title: PM2.5_2

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from Human Aortic Smooth Muscle Cells treated with PM2.5

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on Clariom S Array(mouse, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: Cells exposed to PM2.5 (50 μg/mL) for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Human Aortic Smooth Muscle Cells were cultivated at 37°C with 5% CO2 in DMEM low-glucose medium (Gibco, USA) supplemented with 10% bovine serum (Excell, Australia) and 1% penicillin-streptomycin combination. Cells were grown and congregated to a density of 70–80% in the plate before the treatment.

extract_protocol: Total RNA was extracted from cells using Trizol reagent (Life Technologies, Carlsbad, CA, USA) and purified with a RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Human Aortic Smooth Muscle Cells were treated with PM2.5 (50 μg/mL) containing medium for 24 h.

value: Aortic Smooth Muscle Cells


title: Con_1

description: Gene expression data from Human Aortic Smooth Muscle Cells without treatment

source_name: Control group without PM2.5 treatment


title: Con_3


title: 050_sub_int

description: FFPE spatial profiling


title: Control, CD45-

description: Library name: Control, CD45-, scRNAseq

value: Endothelial cells, Fibroblasts, et al.


title: PM2.5_1


title: Con_2


title: PM2.5_3


title: 1528_114

description: Library name: Sample 114

value: 0 mg/kg/day GW7647


title: Human si097-DV29PG5 10 nM REP2

description: Library name: H32-2


title: 048_vessel

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

value: synovial tissue

value: more pain


title: 053_vessel

description: FFPE spatial profiling

value: less pain


title: 1528_115

description: Library name: Sample 115

value: liver

value: male


title: Human si097-DV29PG5 100 nM REP3

description: Library name: H31-3

value: primary hepatocyte


title: 1528_111

description: Library name: Sample 111

value: PPARa KO

value: WT

value: oral

value: 20 mg/kg/day GW7647


title: BRONJ, CD45-

description: Library name: BRONJ, CD45-, scRNAseq

value: murine mandible tissue


title: Human si097-DV29PG5 100 nM REP2

description: Library name: H31-2


title: Human si097-DV29PG5 10 nM REP1

description: Library name: H32-1


title: 1528_113

description: Library name: Sample 113

value: 5 days


title: Pbrm1 KO, PA502

city: Taipei City

first: Li-Wen

last: Chiou

address: Chung Shan S. Rd.

department: Pathology

country: Taiwan

institute: National Taiwan University

description: Library name: sample 7

data_processing:
The prepared library was sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.
ATAC-seq reads were trimmed using Cutadapt (v3.5). The trimmed reads were then aligned to the human genome (GRCh38) with BWA-mem (v0.7.17).
For downstream analysis, only reads on autosomes, excluding ENCODE human blacklisted regions and PCR duplicates identified by GATK-Picard (v4.1.9.0), were retained.
Aligned reads were adjusted by shifting +4 and -5 bp for positive and negative strands using deepTools' alignmentSieve (v3.5.0).
Assembly: GRCh38
Supplementary files format and content: excel file includes information and fold change of each ATAC peak and over-representation analysis of genes located near the differentially accessible ATAC peaks

extract_protocol:
After euthanasia, liver tissues were snap-frozen and used for nuclei isolation. Nuclei isolated from 50,000 cells underwent transposition using a Nextera DNA Library Prep Kit.
Nuclei isolated from 50,000 cells underwent transposition using a Nextera DNA Library Prep Kit. DNA was amplified in 50-μL reactions using NEBNext High-Fidelity 2× PCR Master Mix and barcoded primers (Illumina ATACseq Tn5).

value: Pbrm1 KO

value: normal diet


title: Pbrm1 KO, PA352

description: Library name: sample 5


title: WT, P353

description: Library name: sample 6


title: 1528_116

description: Library name: Sample 116


title: 046_lining

description: FFPE spatial profiling


title: Human si097-DV29PG5 100 nM REP1

description: Library name: H31-1


title: 047_sub_int

description: FFPE spatial profiling


title: 1528_112

description: Library name: Sample 112


title: WT, P503

description: Library name: sample 8


title: 045_sub_int

description: FFPE spatial profiling


title: 049_lining

description: FFPE spatial profiling


title: Pbrm1 KO, PA316

description: Library name: sample 4


title: 1528_110

description: Library name: Sample 110

value: 5 mg/kg/day GW7647


title: Human si060-DV25Pd7BG5 1 nM REP3

description: Library name: H23-3


title: 1528_109

description: Library name: Sample 109


title: Pbrm1 KO, PA315

description: Library name: sample 3


title: 043_lining

description: FFPE spatial profiling


title: WT, P313

description: Library name: sample 1


title: 1528_107

description: Library name: Sample 107

value: 10 mg/kg/day GW7647


title: 042_vessel

description: FFPE spatial profiling

value: late-stage knee osteoarthritis


title: Human si060-DV25Pd7BG5 1 nM REP1

description: Library name: H23-1


title: 1528_108

description: Library name: Sample 108


title: Human si060-DV25Pd7BG5 10 nM REP3

description: Library name: H22-3


title: Human si060-DV25Pd7BG5 10 nM REP2

description: Library name: H22-2


title: w/o DDC, Pbrm1 KO, PA352

description: Library name: Sample 23

data_processing:
The obtained library was sequenced on an Illumina NovaSeq 6000 sequencer. The adaptor sequences were trimmed using Cutadapt (v3.5).
The trimmed reads were aligned to the human reference genome (GRCh38) using STAR (v 2.7.8a) with two-pass mode, and then gene counts were generated (--quantMode GeneCounts) based on the annotation of Gencode (v35).
Normalization was performed using the Trimmed Mean of M values (TMM) method to ensure comparable distributions across samples, and Transcript Per Million (TPM) values were calculated for subsequent analyses.
Differential expression analysis was performed using the limma R package.
Over-representation analysis of genes with differentially accessible ATAC peaks and differential expression was performed using the clusterProfiler R package with gene sets from MSigDB (v7.4).
Assembly: GRCm38.p6
Supplementary files format and content: tab-separated matrix file includes TPM values and scale expression for each sample and GSEA results

extract_protocol:
Total RNA was extracted from liver tissue using Trizol reagent.
RNA was ligated to adapters for further amplification using a TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: 0.1% DDC diet for 2 weeks or normal chew diet


title: 040_lining

description: FFPE spatial profiling

value: synovial tissue


title: 1528_104

description: Library name: Sample 104

value: 0 mg/kg/day GW7647


title: Human si060-DV25Pd7BG5 100 nM REP3

description: Library name: H21-3


title: Human si060-DV25Pd7BG5 10 nM REP1

description: Library name: H22-1


title: 1528_105

description: Library name: Sample 105


title: w/o DDC, Pbrm1 KO, PA288

description: Library name: Sample 19


title: 041_sub_int

description: FFPE spatial profiling

value: less pain


title: 039_vessel

description: FFPE spatial profiling


title: w/o DDC, WT, P353

description: Library name: Sample 17

value: liver


title: 038_sub_int

description: FFPE spatial profiling


title: 044_vessel

description: FFPE spatial profiling


title: 1528_103

description: Library name: Sample 103

value: male


title: Human si060-DV25Pd7BG5 100 nM REP2

description: Library name: H21-2

value: primary hepatocyte


title: 037_lining

description: FFPE spatial profiling


title: Human si060-DV25Pd7BG5 1 nM REP2

description: Library name: H23-2


title: w/o DDC, WT, P295

description: Library name: Sample 15


title: 1528_102

description: Library name: Sample 102

value: PPARa KO


title: WT, P314

description: Library name: sample 2

value: WT


title: 036_sub_int

description: FFPE spatial profiling

value: more pain


title: 1528_106

description: Library name: Sample 106

value: oral


title: 1528_101

description: Library name: Sample 101


title: w/o DDC, Pbrm1 KO, PA290

description: Library name: Sample 21


title: w/o DDC, WT, P294

description: Library name: Sample 13


title: Human Zilebesiran 1 nM REP3

description: Library name: H13-3


title: 1528_100

description: Library name: Sample 100


title: 035_vessel

description: FFPE spatial profiling


title: 034_lining

description: FFPE spatial profiling


title: w/ DDC, Pbrm1 KO, PA202

description: Library name: Sample 11

value: DDC for 2 weeks


title: w/ DDC, Pbrm1 KO, PA200

description: Library name: Sample 9


title: 033_vessel

description: FFPE spatial profiling


title: Human Zilebesiran 1 nM REP2

description: Library name: H13-2


title: 1528_98

description: Library name: Sample 98

value: 5 days


title: Human Zilebesiran 10 nM REP3

description: Library name: H12-3


title: w/ DDC, Pbrm1 KO, PA198

description: Library name: Sample 7

value: Pbrm1 KO


title: 032_sub_int

description: FFPE spatial profiling


title: w/ DDC, WT, P205

description: Library name: Sample 5


title: w/ DDC, WT, P204

description: Library name: Sample 3


title: Human Zilebesiran 10 nM REP2

description: Library name: H12-2


title: 1528_96

description: Library name: Sample 96

value: 30 mg/kg/day HFPO-DA


title: 031_lining

description: FFPE spatial profiling


title: Human si060-DV25Pd7BG5 100 nM REP1

description: Library name: H21-1


title: Human Zilebesiran 10 nM REP1

description: Library name: H12-1


title: 030_vessel

description: FFPE spatial profiling


title: 1528_97

description: Library name: Sample 97


title: 1528_95

description: Library name: Sample 95


title: 029_sub_int

description: FFPE spatial profiling


title: w/ DDC, WT, P195

description: Library name: Sample 1


title: TBI_Normothermia_rep3

city: Miami

first: Nadine

last: Kerr

state: Florida

address: 1095 NW 14th Terrace

department: The Miami Project to Cure Paralysis

institute: University of Miami

description:
Library name: TBI_Normothermia_rep3
10x Genomics

data_processing:
Assembly: Mouse mm10
Base call files generated by the NovaSeq 6000 were demultiplexed into sample-specific FASTQ files using the 10x Genomics Cell Ranger mkfastq pipeline.
FASTQ files were aligned to the mouse mm10 (GENCODE vM23/Ensembl 98) reference genome using Cell Ranger v4.0.0.. The cellranger count command was run with default parameters to generate raw feature-barcode matrices.
The emptyDrops function (DropletUtils R package) was applied to the unfiltered Cell Ranger raw_feature_bc_matrix to distinguish cell-containing droplets from ambient RNA. Low-quality cells were removed if they had extremely low total UMI, low unique gene counts, or >25% mitochondrial gene content.
Doublets were identified using Scrublet (default parameters) per sample. Remaining high-quality cells were integrated and clustered using Seurat.
Supplementary files format and content: barcodes.tsv.gz (all samples)
Supplementary files format and content: features.tsv.gz (all samples)
Supplementary files format and content: matrix.mtx.gz (all samples)

source_name: Cerebral cortex

growth_protocol: Mice were housed in a temperature-controlled room (22°C) on a 12-hour light/dark cycle with ad libitum access to food and water. They were acclimated for 7 days prior to any surgical or experimental manipulation.

extract_protocol:
1. At 24 hours post-injury (or sham), mice were deeply anesthetized (ketamine 100 mg/kg + xylazine 10 mg/kg).  2. Mice were transcardially perfused with ice-cold oxygenated artificial cerebrospinal fluid (aCSF) to remove blood.  3. The ipsilateral cortex was dissected, avoiding white matter tracts.  4. Cortical tissue was enzymatically and mechanically dissociated using the Miltenyi Neural Tissue Dissociation Kit-P, with modifications:  • 30-minute incubation in Enzyme P/Buffer X at 37°C, triturating every 5 minutes.  • Sequential trituration with decreasing bore pipettes to generate single-cell suspensions.  • Filtration through a 70µm strainer.  • Myelin removal using Myelin Removal Beads II and LS Magnetic Bead Columns (Miltenyi).  5. Cells were resuspended in MACS buffer, counted, and viability assessed (>75% required).  6. Approximately 10,000 cells per sample were loaded into the 10x Chromium platform.
Single-cell 3’ libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Cat# PN-1000121) following the manufacturer’s protocol.Libraries were sequenced on an Illumina NovaSeq 6000 with paired-end 150 bp reads.

treatment_protocol:
Surgical Anesthesia & CCI Procedure  • Mice were anesthetized via intraperitoneal injections of ketamine (100 mg/kg) and xylazine (10 mg/kg).  • A craniotomy (4 mm diameter) was performed between lambda and bregma, 0.5 mm from midline.  • Controlled cortical impact: 4 m/sec velocity, 0.8 mm depth, 150 msec dwell time.  • Incision was closed with staples, and mice received buprenorphine (0.1 mg/kg, SC) post-operatively.  • Sham animals underwent the same surgical preparation without craniotomy or cortical impact.
Temperature Management  • Hypothermia groups: Selective brain hypothermia was initiated 30 minutes post-TBI (or sham) to achieve 33°C for 2 hours.  • Normothermia groups: Temperature was maintained at 37°C for 2 hours.  • Core temperatures were monitored via rectal probes; mice were placed on heating pads post-treatment for recovery.

value: Mixed primary cortical cells

value: Cerebral cortex

value: C57BL/6 (wild-type)

value: TBI

value: 2–3 months old


title: Human Zilebesiran 1 nM REP1

description: Library name: H13-1


title: 028_lining

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

value: synovial tissue

value: less pain


title: 1528_94

description: Library name: Sample 94

value: liver

value: male


title: 1528_93

description: Library name: Sample 93

value: WT


title: TBI_Normothermia_rep2

description:
Library name: TBI_Normothermia_rep2
10x Genomics


title: Human Zilebesiran 100 nM REP1

description: Library name: H11-1

value: primary hepatocyte


title: 1528_92

description: Library name: Sample 92

value: oral

value: 15 mg/kg/day HFPO-DA


title: Human Zilebesiran 100 nM REP2

description: Library name: H11-2


title: 026_vessel

description: FFPE spatial profiling


title: TBI_Hypothermia_rep3

description:
Library name: TBI_Hypothermia_rep3
10x Genomics


title: 1528_91

description: Library name: Sample 91

value: 5 days


title: 025_lining

description: FFPE spatial profiling


title: 1528_90

description: Library name: Sample 90


title: Sham_Normothermia_rep3

description:
Library name: Sham_Normothermia_rep3
10x Genomics

value: Sham


title: cancer cells with C1 CAF

city: Kalyani

first: Sandeep

last: Singh

state: West Bengal

address: NSS TB Hospital, Block A

department: Biomedical Genomics

country: India

institute: BRIC-National Institute of Biomedical Genomics

description: Library name: S2

data_processing:
Agilent high sensitivity chips in TapeStation were used to examine the quality of the libraries and the quantification was done using QuantStudio-7 real time PCR. All the libraries were pooled and sequenced as a paired-end manner in Illumina NovaSeq-6000.
Sequence depth was kept at an average of 50,000 raw reads per cell and per sample 200 million paired-end reads were kept as a standard measure.
Base call files were converted into FASTQ and GRCh38 reference transcriptome was utilized for the read alignment using CellRanger 4.0.0 (10X Genomics).
R package Seurat 4.3.0 was used for the quality control (QC) and the subsequent analysis from the generated gene-barcode matrix from CellRanger.
Assembly: GRCh38
Supplementary files format and content: .tsv and .mtx files, cell ranger output files for genes,barcodes, and counts

source_name: Oral tumor derived cell

growth_protocol: KV07 CAF is cultured in DMEM:F12 (1:1) Media supplimented with  1X Antibiotic-antimycotic, 1% fetal bovine serum, 0.1% ITS, and 3% Sodium bicarbonate during treatment. GBC02 cells were cultured over KV07 CAFs in same media in a 37°C humidified chamber with 5% C02.

extract_protocol:
Co-cultured cells were harvested and made a single cell suspension by incubating with accutase in 37°C for 3-4 minutes followed by filtering through a 70 μm cell strainer. After a brief centrifugation at 300g for 3 minutes, cell pellets were resuspended in the cultured low serum media. Using trypan blue, the cells were counted and checked for viability. The suspension having more than 80% cell viability was diluted to a concentration of approximately 1000 cells/µL.
Chromium controller (10X Genomics), chromium 3ʹ library, Gel bead kit and finally the chromium Single cell 3ʹ chip kit (10X Genomics) were used according to the manufacturer’s instruction to make Single cell gel bead-in emulsion and for sequencing library construction.

treatment_protocol: KV07 CAF is treated with 10 ng/mL TGF-beta, and followed by treatment with Tie2 small molecule inhibitor treatment.

value: Oral tumor derived cell

value: GBC02 and KV07

value: Epithelial and fibroblast

value: untreated KV07


title: cancer cells with Tie2 inhibited C2 CAF

description: Library name: S4

value: TGFβ treated followed by Tie2 inhibition in KV07


title: Human Zilebesiran 100 nM REP3

description: Library name: H11-3


title: 024_sub_int

description: FFPE spatial profiling


title: cancer cells with C2 CAF

description: Library name: S3

value: TGFβ treated KV07


title: 023_vessel

description: FFPE spatial profiling

value: late-stage knee osteoarthritis


title: Sham_Normothermia_rep2

description:
Library name: Sham_Normothermia_rep2
10x Genomics

value: Mixed primary cortical cells

value: Cerebral cortex

value: C57BL/6 (wild-type)

value: 2–3 months old


title: 1528_89

description: Library name: Sample 89

value: liver

value: male

value: WT


title: 027_sub_int

description: FFPE spatial profiling

value: synovial tissue

value: less pain


title: Sham_Normothermia_rep1

description:
Library name: Sham_Normothermia_rep1
10x Genomics

value: Sham


title: 1528_88

description: Library name: Sample 88

value: oral

value: 5 days

value: 0 mg/kg/day HFPO-DA


title: Sham_Hypothermia_rep3

description:
Library name: Sham_Hypothermia_rep3
10x Genomics


title: 1528_87

description: Library name: Sample 87

value: 3 mg/kg/day HFPO-DA


title: 022_lining

description: FFPE spatial profiling


title: 021_vessel

description: FFPE spatial profiling


title: sam-UTD-181030DHB-2L4-2

city: Richardson

first: Theodore

last: Price

state: Texas

address: 800 W. Campbell Road

department: Neuroscience

institute: The University of Texas at Dallas

description:
Library name: sam-UTD-181030DHB-2L4-2
Human DRGs were collected from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme.

data_processing:
Raw data were processed with the 10X SpaceRanger pipeline
Assembly: GRCh38.p10 and GRCh38.p13
Supplementary files format and content: raw and filtered gene counts matrices, cloupe files for !0x loupe browser, barcode positions/coordinates, csv file of annotated barcodes
Library strategy: Spatial Transcriptomics

source_name: dorsal root ganglia

extract_protocol:
Human DRGs were collected from neurologically dead organ donors through a collaboration with the Southwest Transplant Alliance or from AnaBios
Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain.

value: dorsal root ganglia


title: sam-UTD-181030DHB-1L4-7

description:
Library name: sam-UTD-181030DHB-1L4-7
Human DRGs were collected from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme.


title: Sham_Hypothermia_rep2

description:
Library name: Sham_Hypothermia_rep2
10x Genomics


title: sam-UTD-181030DHB-1L4-3

description:
Library name: sam-UTD-181030DHB-1L4-3
Human DRGs were collected from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme.


title: TBI_Hypothermia_rep2

description:
Library name: TBI_Hypothermia_rep2
10x Genomics

value: TBI


title: Sham_Hypothermia_rep1

description:
Library name: Sham_Hypothermia_rep1
10x Genomics


title: 1528_85

description: Library name: Sample 85


title: 019_lining

description: FFPE spatial profiling

value: late-stage knee osteoarthritis


title: sam-UTD-181030DHB-2L4-6

description:
Library name: sam-UTD-181030DHB-2L4-6
Human DRGs were collected from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme.


title: sam-UTD-180714DHB-DRGL4-5

description:
Library name: sam-UTD-180714DHB-DRGL4-5
Human DRGs were collected from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme.


title: TBI_Normothermia_rep1

description:
Library name: TBI_Normothermia_rep1
10x Genomics

value: Mixed primary cortical cells


title: 1528_99

description: Library name: Sample 99

value: PPARa KO

value: 0 mg/kg/day GW7647


title: 1528_84

description: Library name: Sample 84


title: 1528_83

description: Library name: Sample 83


title: sam-UTD-180714DHB-DRGL4-1

description:
Library name: sam-UTD-180714DHB-DRGL4-1
Human DRGs were collected from neurologically dead organ donors, and immediately fresh frozen in dry ice. DRGs were cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each donor and each 10µm section was 200µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme.


title: 018_sub_int

description: FFPE spatial profiling

value: more pain


title: TBI_Hypothermia_rep1

description:
Library name: TBI_Hypothermia_rep1
10x Genomics

value: Cerebral cortex

value: C57BL/6 (wild-type)

value: 2–3 months old


title: Leiomyoma cell culture transfected with FKBP5 siRNA for 48 h then treated with 10-7M Dexamethasone for 24h

city: Tampa

first: Umit

middle: Ali

last: Kayisli

address: 560 Channelside Dr,

department: Ob/Gyn

institute: USF Morsani College of Medicine

description: Library name: E9 (FKBP5 siRNA + Dex)

data_processing:
Sequence reads were trimmed. Indexes of the reference genome was built using STAR and paired end clean reads were aligned to the reference genome using STAR (v2.5)
Assembly: hg38
Supplementary files format and content: each row in excell file includes readcount for each sample

source_name: Primary leiomyoma cell cultures

growth_protocol: Primary leiomyoma cells were grown in basal media including DMEM/F12 media suplemented with 10%FBS and 1% antibiotic and antimycotics.

extract_protocol:
Total RNA was isolated using Qiagen miRNeasy Mini kit
RNA libraies were prepared by Novogene

treatment_protocol: Leiomyoma cells plated into 6-well culture plates were transfected with control or FKBP5 specific siRNA. 48 hours and post-transfection cells were treated with either control media or 10-7 M dexamethasone (Dex) for 24 h.

value: Uterine Leiomyoma

value: leiomyoma smooth muscle cells

value: FKBP5 siRNA

value: Dexamethasone for 24 h


title: 017_vessel

description: FFPE spatial profiling

value: synovial tissue


title: RAW-MCB-2 (RNA-seq)

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

description: RAW 264.7 cells were collected for total RNA extraction with MCB treatment for 12 hours.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to mouse mm10 genome using subread, which produced the BAM type file directly.
The featureCounts and TEtranscripts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The DESeq2 software was used to identify the differantially expressed genes (DEGs).
Assembly: UCSC mm10 genome was used as reference genome.
Supplementary files format and content: CSV file includes the FPKM value for each sample.

growth_protocol: RAW 264.7 were cultured in DMEM medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2..

extract_protocol:
Total RNA was extracted using Trizol reagent (TIANGEN). 1.5 ug of total RNA was used for the construction of sequencing libraries.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: RAW 264.7 were treated with by DMSO, LPS, LPS-MCB and MCB for 12 hours.

value: macrophages

value: wt

value: MCB


title: 1528_82

description: Library name: Sample 82

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software and sample-specific barcodes to give a FASTQ file for each sample
bcl2fastq2 v2.20 for demultiplexing
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
fastq files were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: templated oligo sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

extract_protocol:
Mounted, unstained FFPE liver samples were scraped from the slides and processed according to the TempO-Seq® protocol by BioSpyder Technologies
TempO-Seq® protocol by BioSpyder Technologies

value: liver

value: male

value: WT

value: oral

value: 5 days

value: 0 mg/kg/day HFPO-DA


title: Leiomyoma cell culture transfected with FKBP5 siRNA for 48 h then treated with vehicle  for 24h

description: Library name: E6 (FKBP5 siRNA)

value: Vehicle for 24 h


title: RAW-MCB-1 (RNA-seq)


title: 1528_86

description: Library name: Sample 86

value: 3 mg/kg/day HFPO-DA


title: 1528_81

description: Library name: Sample 81


title: Leiomyoma cell culture transfected with control siRNA for 48 h then treated with 10-7M Dexamethasone for 24h

description: Library name: E4 (Cont siRNA + Dex)

value: Cont siRNA


title: 015_vessel

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

value: less pain


title: RAW-LPS-MCB-2 (RNA-seq)

description: RAW 264.7 cells were collected for total RNA extraction with LPS-MCB treatment for 12 hours.

value: LPS-MCB


title: 1528_80

description: Library name: Sample 80

value: 15 mg/kg/day HFPO-DA


title: 020_sub_int

description: FFPE spatial profiling

value: synovial tissue


title: 016_lining

description: FFPE spatial profiling

value: more pain


title: Leiomyoma cell culture transfected with control siRNA for 48 h then treated with vehicle  for 24h

description: Library name: E1 (Cont siRNA)

value: Uterine Leiomyoma

value: leiomyoma smooth muscle cells


title: RAW-LPS-MCB-1 (RNA-seq)

value: macrophages

value: wt


title: 1528_79

description: Library name: Sample 79

value: liver

value: male

value: WT


title: RAW-LPS-2 (RNA-seq)

description: RAW 264.7 cells were collected for total RNA extraction with LPS treatment for 12 hours.

value: LPS


title: 501-Mel GRPR, GRP+RC, rep4

city: Orsay

first: Lionel

last: Larue

address: Centre universitaire Bat 101B-110-111-112 Rue Henri Becquerel CS 90030

department: CNRS UMR3347, INSERM  U1021

country: France

institute: Institut Curie

description:
Library name: 501GRPR-GRP+RC-4
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

data_processing:
Quality control: sequenced reads quality were assessed using fastqc v0.11.5
Reads were mapped to the mouse reference genome hg38 (gencode 42 version-GRCh38.p13) using STAR.
STAR was also used to create the expression matrixes.
Batch were corrected using ComBat.
Raw counts were normalized to the TPM-level.
Assembly: Assembly: hg38 (gencode 42 version-GRCh38.p13)
Supplementary files format and content: Supplementary files format and content: four tab-delimited text files. two per cell lines, one for the raw counts and one for the TPM-normalised values for each Sample

source_name: 501-Mel GRPR

growth_protocol: Cells were starved overnight 24 hours after seeding in 10% FCS. When the cells were treated, confluence was about 80%.

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit according to manufacturer protocol.

treatment_protocol: Cells were treated with vehicle or 10nM GRP and/or 1µM RC-3095 for 4 hours

value: 501-Mel GRPR

value: Melanoma cell line

value: GRP+RC


title: 501-Mel GRPR, RC, rep4

description:
Library name: 501GRPR-RC-4
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: RC


title: 1528_78

first: Melissa

last: Heintz

address: 31 College Place, Suite B118

institute: ToxStrategies

description: Library name: Sample 78

value: oral

value: 5 days

value: 30 mg/kg/day HFPO-DA


title: 012_lining

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

value: synovial tissue


title: RAW-LPS-1 (RNA-seq)


title: 1528_77

description: Library name: Sample 77


title: 011_vessel

description: FFPE spatial profiling

value: less pain


title: 1528_76

description: Library name: Sample 76


title: RAW-DMSO-2 (RNA-seq)

description: RAW 264.7 cells were collected for total RNA extraction with DMSO treatment for 12 hours.

value: DMSO


title: 501-Mel GRPR, MOCK, rep4

description:
Library name: 501GRPR-Mock-4
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: DMSO-MOCK


title: RAW-DMSO-1 (RNA-seq)

value: macrophages

value: wt


title: 501-Mel GRPR, GRP, rep4

description:
Library name: 501GRPR-GRP-4
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: GRP


title: 010_sub_int

description: FFPE spatial profiling


title: 1528_75

description: Library name: Sample 75

value: liver

value: male

value: WT

value: 15 mg/kg/day HFPO-DA


title: 501-Mel GRPR, GRP+RC, rep3

description:
Library name: 501GRPR-GRP+RC-3
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: 501-Mel GRPR

value: Melanoma cell line

value: GRP+RC


title: RAW-MCB (CUT&Tag-seq)

description: RAW 264.7 cells were collected for CUT&Tag  with MCB treatment for 12 hours.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to mouse mm10 genome using Bowtie2, which produced the BAM type file directly.
The peaks was called using MACS3 software.
Then the peaks was annotated by the ChIPseeker R package.
The TOBIAS software was used to perform the footprint analysis.
Assembly: UCSC mm10 genome was used as reference genome.
Supplementary files format and content: narrowPeak file includes the peaks was identified for each sample.
Supplementary files format and content: bw file includes the peaks signal intensity for each sample.
Library strategy: CUT&Tag

extract_protocol:
Total DNA was extracted using CUT&Tag Library Prep Kit (Transgen, KP172) for library following the manufacturer’s recommendations.
CUT&Tag library for sequencing was generated using CUT&Tag Library Prep Kit (Transgen, KP172) following the manufacturer’s recommendations

value: MCB


title: 501-Mel GRPR, RC, rep3

description:
Library name: 501GRPR-RC-3
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: RC


title: 014_vessel

description: FFPE spatial profiling

data_processing:
NanoString GeoMX Platform was used for probe QC and Q3 normalization as recommended by NanoString. Then patient samples were grouped based on those with more pain and those with less pain for analysis and adjusted for ID and BMI. All microenvironment ROI subtypes were analyzed separately. For example, all ROIs of synovial intimal lining were included in one analysis, then all sublining ROIs, and then all microvessel ROIs.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files, PKC file, probe QC, Q3 normalization, metadata file
Library strategy: GeoMx Seq

extract_protocol:
Synovial tissue samples were processed for FFPE and constructed into a tissue microarray, so that all samples could be analyzed on a single slide. The slide was sent to NanoString for library construction and
https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/
https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/

value: late-stage knee osteoarthritis

value: more pain


title: 008_sub_int

description: FFPE spatial profiling

value: synovial tissue


title: 1528_74

description: Library name: Sample 74

value: oral

value: 5 days


title: 009_lining

description: FFPE spatial profiling

value: less pain


title: 501-Mel GRPR, GRP, rep3

description:
Library name: 501GRPR-GRP-3
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt


title: RAW-LPS-MCB (CUT&Tag-seq)

description: RAW 264.7 cells were collected for CUT&Tag  with LPS-MCB treatment for 12 hours.

value: macrophages

value: wt

value: LPS-MCB


title: 1528_73

description: Library name: Sample 73

value: liver

value: male

value: 0 mg/kg/day HFPO-DA


title: 013_sub_int

description: FFPE spatial profiling


title: 1528_72

description: Library name: Sample 72

value: WT


title: 501-Mel GRPR, MOCK, rep3

description:
Library name: 501GRPR-Mock-3
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: 501-Mel GRPR

value: Melanoma cell line

value: DMSO-MOCK


title: RAW-LPS (CUT&Tag-seq)

description: RAW 264.7 cells were collected for CUT&Tag  with LPS treatment for 12 hours.

value: LPS


title: 007_sub_int

description: FFPE spatial profiling

value: late-stage knee osteoarthritis


title: RAW-LPS-Input (CUT&Tag-seq)

description: RAW 264.7 cells were collected for CUT&Tag  with LPS treatment for 12 hours for input.


title: 1528_71

description: Library name: Sample 71

value: 3 mg/kg/day HFPO-DA


title: 501-Mel GRPR, GRP+RC, rep2

description:
Library name: 501GRPR-GRP+RC-2
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: GRP+RC


title: 005_lining

description: FFPE spatial profiling

value: synovial tissue

value: more pain


title: 004_vessel

description: FFPE spatial profiling

value: less pain


title: RAW-MCB (ATAC-seq)

description: RAW 264.7 cells were collected for ATAC-seq with MCB treatment for 12 hours.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to mouse mm10 genome using Bowtie2, which produced the BAM type file directly.
The peaks was called using MACS3 software.
Then the peaks was annotated by the ChIPseeker R package.
The TOBIAS software was used to perform the footprint analysis.
Assembly: UCSC mm10 genome was used as reference genome.
Supplementary files format and content: narrowPeak file includes the peaks was identified for each sample.
Supplementary files format and content: bw file includes the peaks signal intensity for each sample.

extract_protocol:
Total DNA was extracted using ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech, TD711)  for library following the manufacturer’s recommendations.
ATAC-seq library for sequencing was generated using Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech, TD711) following the manufacturer’s recommendations

value: macrophages

value: MCB


title: 501-Mel GRPR, GRP, rep2

description:
Library name: 501GRPR-GRP-2
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: GRP


title: RAW-DMSO (CUT&Tag-seq)

description: RAW 264.7 cells were collected for CUT&Tag  with DMSO treatment for 12 hours.

value: wt

value: DMSO


title: RAW-LPS-MCB (ATAC-seq)

description: RAW 264.7 cells were collected for ATAC-seq with LPS-MCB treatment for 12 hours.

value: LPS-MCB


title: 1528_69

description: Library name: Sample 69

value: liver

value: male

value: WT

value: oral

value: 5 days


title: 1528_68

description: Library name: Sample 68

value: 15 mg/kg/day HFPO-DA


title: 501-Mel GRPR, RC, rep2

description:
Library name: 501GRPR-RC-2
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: 501-Mel GRPR

value: Melanoma cell line

value: RC


title: 501-Mel GRPR, MOCK, rep2

description:
Library name: 501GRPR-Mock-2
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: DMSO-MOCK


title: RAW-LPS (ATAC-seq)

description: RAW 264.7 cells were collected for ATAC-seq with LPS treatment for 12 hours.

value: LPS


title: 002_sub_int

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

value: synovial tissue

value: less pain


title: 1528_66

description: Library name: Sample 66

value: 0 mg/kg/day HFPO-DA


title: 001_lining

description: FFPE spatial profiling


title: RAW-DMSO (ATAC-seq)

description: RAW 264.7 cells were collected for ATAC-seq with DMSO treatment for 12 hours.

value: macrophages

value: wt

value: DMSO


title: 1528_67

description: Library name: Sample 67

value: liver

value: male

value: 30 mg/kg/day HFPO-DA


title: 501-Mel GRPR, RC, rep1

description:
Library name: 501GRPR-RC-1
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt


title: Exposure to imidacloprid

city: Tsukuba

first: Tomohiro

last: Ito

address: 16-2, Onogawa

institute: National Institute for Environmental Studies

description: IMI

data_processing:
Bcl2fastq (v2.17.1.14) was used to processed the original image data for base calling and preliminary quality analysis. The Illumina built-in software determines whether to keep or discard each of the sequencing fragments (namely reads) based on the quality of the first 25 bases. The raw data (Pass Filter Data) obtained from this step is stored in FASTQ format, which contains the base sequence (the second line of a FASTQ record) and the corresponding sequencing quality information (the fourth line of a FASTQ record).
During sequencing, quality concerns may arise. A small number of target sequences might be reads into adapter sequences, and bases toward the 3'-end might have low quality due to the lengthy sequencing cycles. To eliminate the negative effect of these technical issues, low-quality reads and contaminations were filtered out before data analysis. In addition, adapter sequences were removed at this step. Software: Cutadapt (version 1.9.1)
Filtered data were subsequently aligned to the reference genome. It is important to select the appropriate reference genome for optimal analysis. The alignment rate reflects the compatibility between the selected genome and data to be analyzed. Short-read alignment was performed using Hisat2 (v2.0.1) (Nat Methods. 2015 Apr; Kim D, et al.) with default parameters.
Assembly: Mus_musculus_Ensembl_GRCm38.100
Supplementary files format and content: txt

source_name: Brain

growth_protocol: Ectoderm was generated from mouse ES cells (B6G-2) through embryoid bodies for 6 days, and then neural progenitors were obtained using RHB-A medium containing bFGF and EGF on a dish coated with poly-ornithine and laminin.

extract_protocol:
After exposure, total RNA was extracted using NucleoSpin RNA (Macherey-Nagel GmbH).
RNA library preparation and sequencing was performed by Genewiz.

treatment_protocol: Neural progenitors (day 14) derived from mouse ES cells were differentiated into neural cells (nerve cells and glial cells) with BrainPhys and B27, and then exposed by each insecticide for 1 day.

value: Brain

value: mouse ES cells (B6G-2)

value: Neural progenitors

value: WT

value: exposure


title: 1528_65

description: Library name: Sample 65

value: oral

value: 5 days


title: Exposure to deltamethrin

description: DMT


title: 006_vessel

description: FFPE spatial profiling

value: late-stage knee osteoarthritis

value: more pain


title: Traumatic brain injury, fracture, callus, Patient_32, 7d post injury

city: Salzburg

first: Andreas

last: Traweger

state: Salzburg

address: Strubergasse 22

department: Tendon and Bone Regeneration

country: Austria

institute: Paracelsus Medical University

description:
Library name: Sample 36
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P032_7d

data_processing:
Sequencing was performed on an Illumina platform (NextSeq 550, 75bp, SR).
Analysis parameters were defined as follows: Sequencing adapter: RealSeq (cutadapt -a Realseq3P=TGGAATTCTC -u1). Minimum read length: 17nt. Reads quality cutoff: 30 (phred quality score). Significance level: 0.05. Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.9 and multiQC v1.10. Reads from all passing samples were adapter trimmed and filtered using cutadapt v3.3. Reads were then filtered for a minimum length of 17 nucleotides.
Mapping was performed with bowtie v1.3.0 and miRDeep2 v2.0.1.2, whereas reads were mapped first against the genomic reference GRCh38.p12 provided by Ensembl allowing for two mismatches and subsequently miRBase v22.1, filtered for miRNAs of hsa only, allowing for one mismatch. For a general RNA composition overview, non-miRNA mapped reads were mapped against RNAcentral and then assigned to various RNA species of interest.
Statistical analysis of preprocessed NGS data was done with R v4.0 and the packages pheatmap v1.0.12, pcaMethods v1.82 and genefilter v1.72.
Differential expression analysis with edgeR v3.32 used the quasi-likelihood negative binomial generalized log-linear model functions provided by the package. The independent filtering method of DESeq2 was adapted for use with edgeR to remove low abundant miRNAs and thus optimize the false discovery rate (FDR) correction.
Assembly: GRCh38.p12
Supplementary files format and content: csv file containing reads per million (RPM) normalized values for all samples.

source_name: Blood

extract_protocol:
Total RNA was extracted from human blood samples using miRNeasy Serum/Plasma Advanced Kit (qiagen, #217204) according to manufacturer’s protocol.
Micro-RNA-seq analysis was performed by a contractor (TAmiRNA GmbH, Leberstrasse 20, 1110 Vienna, Austria) according to their customized protocol. RNA preparation and library construction was performed using Serum/Plasma Advanced Kit (Qiagen, #217204) and Biofluids Plasma/Serum miRNA Library kit (RealSeq, #600-00048) according to manufacturer’s protocol.

value: Blood

value: Male


title: Traumatic brain injury, fracture, callus, Patient_32, 72h post injury

description:
Library name: Sample 35
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P032_72h


title: 501-Mel GRPR, GRP, rep1

description:
Library name: 501GRPR-GRP-1
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: 501-Mel GRPR

value: Melanoma cell line

value: GRP


title: 1528_70

city: Asheville

description: Library name: Sample 70

source_name: liver

value: liver

value: 3 mg/kg/day HFPO-DA


title: Traumatic brain injury, fracture, callus, Patient_32, 24h post injury

description:
Library name: Sample 34
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P032_24h


title: Exposure to carbaryl

description: CAR


title: 501-Mel GRPR, MOCK, rep1

description:
Library name: 501GRPR-Mock-1
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: DMSO-MOCK


title: 1528_64

description: Library name: Sample 64

value: PPARa KO

value: male

value: 30 mg/kg/day HFPO-DA


title: 1528_63

description: Library name: Sample 63

value: WT


title: 003_lining

description: FFPE spatial profiling

value: synovial tissue

value: less pain


title: Traumatic brain injury, fracture, callus, Patient_19, 72h post injury

description:
Library name: Sample 32
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P019_72h


title: 1528_62

description: Library name: Sample 62

value: oral

value: 5 days


title: Exposure to rotenone

description: ROT

value: Brain

value: mouse ES cells (B6G-2)

value: Neural progenitors

value: exposure


title: 501-Mel GRPR, GRP+RC, rep1

description:
Library name: 501GRPR-GRP+RC-1
501-Mel GRPR GRPR stimulation Raw counts.txt
501-Mel GRPR GRPR stimulation Normalised expression (TPM).txt

value: 501-Mel GRPR

value: Melanoma cell line

value: GRP+RC


title: MDA-MB-435S, RC, rep4

description:
Library name: MDA-RC-4
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: RC


title: Traumatic brain injury, fracture, callus, Patient_19, 7d post injury

description:
Library name: Sample 33
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P019_7d

value: Blood

value: Male


title: 1528_61

description: Library name: Sample 61

value: liver

value: PPARa KO

value: male


title: MDA-MB-435S, GRP, rep4

description:
Library name: MDA-GRP-4
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: GRP


title: Traumatic brain injury, fracture, callus, Patient_19, 24h post injury

description:
Library name: Sample 31
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P019_24h


title: 1528_60

description: Library name: Sample 60

value: WT

value: 15 mg/kg/day HFPO-DA


title: MDA-MB-435S, MOCK, rep4

description:
Library name: MDA-MOCK-4
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: DMSO-MOCK


title: Exposure to chlorpyrifos

description: CPS

value: Brain


title: Traumatic brain injury, fracture, callus, Patient_5, 7d post injury

description:
Library name: Sample 30
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P005_7d


title: control

description: Ctrl

value: mouse ES cells (B6G-2)

value: control


title: MDA-MB-435S, GRP+RC, rep3

description:
Library name: MDA-GRP+RC-3
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt


title: 1528_59

description: Library name: Sample 59

value: oral

value: 5 days


title: Traumatic brain injury, fracture, callus, Patient_5, 72h post injury

description:
Library name: Sample 29
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P005_72h


title: MDA-MB-435S, RC, rep3

description:
Library name: MDA-RC-3
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: Melanoma cell line


title: Traumatic brain injury, fracture, callus, Patient_5, 24h post injury

description:
Library name: Sample 28
Column name in RPM_All_Samples.csv: TBI_Fx_Call_P005_24h


title: MDA-MB-435S, GRP+RC, rep4

description:
Library name: MDA-GRP+RC-4
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: GRP+RC


title: RAW264.7, oxldl, E2

data_processing:
The raw reads were trimmed with Trim-Galore and aligned to the mm10 reference genome using Bowtie2
Peak calling was performed with MACS2
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: RAW264.7 cells

growth_protocol: RAW 264.7 cells, a macrophage cell line, were cultured in Dulbecco's modified eagle medium with 10% fetal bovine serum, 100 U/ml penicillin and 0.1 mg/ml streptomycin at 37°C under 5% CO2.

extract_protocol:
5 x 104 cells were washed twice in cold PBS and resuspended in 50μl of cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween, 0.1% NP40 and 0.01% Digitonin)
Lysates were centrifuged (750 x g, 10min, 4°C) and nuclei were resuspended in 50μl of transposition reaction mix with 5 μl Tn5 Transposase (TruePrep DNA Library Prep kit V2 for Illumina) and incubated for 30 min at 37°C. Transposed DNA fragments were purified using a QIAGEN Reaction MiniElute Kit, barcoded with Novo NGS Index Kit for Illumina and amplified to 240 fmol by NEBNext Ultra II Q5 Master Mix. PCR products were purified using a PCR Purification Kit  for paired-end sequencing in Novaseq 6000.

treatment_protocol: RAW264. 7 cells were treated with 25 ug/mL DIL-oxLDL and esculetin (0 or 40 ug/mL) for 24 hr.

value: RAW264.7 cells

value: macrophages

value: 40 ug/mL esculetin


title: 1528_57

description: Library name: Sample 57

value: liver


title: RAW264.7, oxldl, E1


title: MDA-MB-435S, GRP, rep3

description:
Library name: MDA-GRP-3
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt


title: 1528_56

description: Library name: Sample 56

value: PPARa KO

value: 3 mg/kg/day HFPO-DA


title: MDA-MB-435S, MOCK, rep3

description:
Library name: MDA-MOCK-3
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt


title: Exposure to DDT

description: DDT

value: Neural progenitors

value: exposure


title: Traumatic brain injury and fracture, Patient_31, 72h post injury

description:
Library name: Sample 26
Column name in RPM_All_Samples.csv: TBI_Fx_P031_72h

value: Blood

value: Female


title: MDA-MB-435S, GRP+RC, rep2

description:
Library name: MDA-GRP+RC-2
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt


title: RAW264.7, oxldl, C1

value: WT

value: DMSO


title: Traumatic brain injury and fracture, Patient_31, 24h post injury

description:
Library name: Sample 25
Column name in RPM_All_Samples.csv: TBI_Fx_P031_24h


title: tamoxifen treated, UBCCreERT2;miR-96 CKO4

city: Yangpu

first: Changgeng

last: Peng

state: Shanghai

address: Siping Road 1239

department: School of Medicine

institute: Tongji University

description:
UBCCreERT2;miR-96 CKO4_FPKM
FPKM.UBCCreERT2 and UBCCreERT2;miR-96CKO

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Inner ear

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: Inner ear

value: UBCCreERT2;miR-96 CKO

value: tamoxifen


title: 1528_54

description: Library name: Sample 54

value: male

value: oral

value: 5 days


title: tamoxifen treated, UBCCreERT2;miR-96 CKO3

description:
UBCCreERT2;miR-96 CKO3_FPKM
FPKM.UBCCreERT2 and UBCCreERT2;miR-96CKO


title: Traumatic brain injury and fracture, Patient_29, 7d post injury

description:
Library name: Sample 24
Column name in RPM_All_Samples.csv: TBI_Fx_P029_7d


title: 1528_58

description: Library name: Sample 58

value: 15 mg/kg/day HFPO-DA


title: MDA-MB-435S, MOCK, rep2

description:
Library name: MDA-MOCK-2
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: Melanoma cell line

value: DMSO-MOCK


title: Traumatic brain injury and fracture, Patient_29, 24h post injury

description:
Library name: Sample 22
Column name in RPM_All_Samples.csv: TBI_Fx_P029_24h


title: MDA-MB-435S, RC, rep2

description:
Library name: MDA-RC-2
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: RC


title: Traumatic brain injury and fracture, Patient_29, 72h post injury

description:
Library name: Sample 23
Column name in RPM_All_Samples.csv: TBI_Fx_P029_72h


title: MDA-MB-435S, GRP, rep2

description:
Library name: MDA-GRP-2
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: GRP


title: 1528_53

description: Library name: Sample 53

value: liver

value: PPARa KO

value: 3 mg/kg/day HFPO-DA


title: 1528_52

description: Library name: Sample 52

value: 0 mg/kg/day HFPO-DA


title: RAW264.7, oxldl, C2

value: RAW264.7 cells

value: macrophages

value: WT


title: 1528_51

description: Library name: Sample 51


title: Traumatic brain injury and fracture, Patient_16, 7d post injury

description:
Library name: Sample 21
Column name in RPM_All_Samples.csv: TBI_Fx_P016_7d

value: Blood

value: Female


title: MDA-MB-435S, RC, rep1

description:
Library name: MDA-RC-1
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt


title: tamoxifen treated, UBCCreERT2;miR-96 CKO1

description:
UBCCreERT2;miR-96 CKO1_FPKM
FPKM.UBCCreERT2 and UBCCreERT2;miR-96CKO

value: Inner ear

value: UBCCreERT2;miR-96 CKO

value: tamoxifen


title: Traumatic brain injury and fracture, Patient_31, 7d post injury

description:
Library name: Sample 27
Column name in RPM_All_Samples.csv: TBI_Fx_P031_7d


title: MDA-MB-435S, GRP+RC, rep1

description:
Library name: MDA-GRP+RC-1
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: GRP+RC


title: tamoxifen treated, UBCCreERT2-2

description:
UBCCreERT2-2_FPKM
FPKM.UBCCreERT2 and UBCCreERT2;miR-96CKO


title: 1528_49

description: Library name: Sample 49

value: male

value: oral

value: 5 days


title: tamoxifen treated, UBCCreERT2-3

description:
UBCCreERT2-3_FPKM
FPKM.UBCCreERT2 and UBCCreERT2;miR-96CKO


title: 1528_50

description: Library name: Sample 50


title: 1528_55

description: Library name: Sample 55


title: Traumatic brain injury and fracture, Patient_16, 24h post injury

description:
Library name: Sample 19
Column name in RPM_All_Samples.csv: TBI_Fx_P016_24h


title: MDA-MB-435S, GRP, rep1

description:
Library name: MDA-GRP-1
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: Melanoma cell line

value: GRP


title: MDA-MB-435S, MOCK, rep1

description:
Library name: MDA-MOCK-1
MDA-MB-435S GRPR StimulationRaw Counts.txt
MDA-MB-435S GRPR Stimulation Normalised expression (TPM).txt

value: DMSO-MOCK


title: Traumatic brain injury and fracture, Patient_16, 72h post injury

description:
Library name: Sample 20
Column name in RPM_All_Samples.csv: TBI_Fx_P016_72h


title: tamoxifen treated, UBCCreERT2;miR-96 CKO2

description:
UBCCreERT2;miR-96 CKO2_FPKM
FPKM.UBCCreERT2 and UBCCreERT2;miR-96CKO


title: Traumatic brain injury, Patient_28, 7d post injury

description:
Library name: Sample 18
Column name in RPM_All_Samples.csv: TBI_P028_7d

value: Male


title: miR-96 KO4

description:
miR-96 KO4_FPKM
FPKM. WT and miR-96 KO

value: miR-96 KO

value: non


title: 1528_47

description: Library name: Sample 47

value: liver

value: 20 mg/kg/day rosiglitazone


title: miR-96 KO3

description:
miR-96 KO3_FPKM
FPKM. WT and miR-96 KO


title: Traumatic brain injury, Patient_28, 24h post injury

description:
Library name: Sample 16
Column name in RPM_All_Samples.csv: TBI_P028_24h

value: Blood


title: 1528_46

description: Library name: Sample 46

value: WT