title: K562 Hemin Nilotinib replica3

city: Elche

first: Alicia

last: Martinez Lopez

state: Alicante

address: Avenida Candalix 42, 5A

institute: IMIB

description: Library name: NILO_24_3_1.fq

data_processing:
After the gene expression is quantified, statistical analysis of the expression data is required to screen the genes whose expression levels are significantly different in different conditions. The differential analysis is mainly divided into three steps
First, the raw readcount is normalized, mainly to correct the sequencing depth
Next, the statistical model is used to calculate the hypothesis test's probability (pvalue);
Finally, multiple hypothesis test corrections are used to obtain FDR values (false discovery rate)(Anders et al., 2010).
For different experimental conditions, we selected appropriate software for gene expression differential analysis: Biological Replicates DESeq2(Anders et al., 2014), DESeq
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: Excel, comparation between samples

source_name: erythroleukemia cell line

extract_protocol:
Total RNA was extracted from K562 cells  with TRIzol reagent (Invitrogen) and Invitroge RNA Mini Kit (12183018A)
Sequencing was performed on an Illumina NovaSeq platform, generating 150 bp paired-end reads

treatment_protocol: K562 cells were pretreated with 0.1 μM nilotinib, followed by differentiation with 50 μM hemin for 24 h. Three biological replicates (15 μl at 200 ng/μl)

value: erythroleukemia cell line

value: leukemia cell line


title: Cycling cells, DMSO treated, biol rep 3

status: Public on Sep 01 2025

type: SRA

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: Fermin Caballero 56, 3D

country: Spain

institute: CNIO

description: Library name: HT-P-NT-3

library_source: transcriptomic

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program.
STAR (2.7.9a) was used to index the human genome (Homo sapiens, GRCh38) obtained from Ensembl and then map the fastq files.
featureCounts (v1.5.1) was used to count mapped reads in annotated exons using gene annotations from Ensembl (Homo_sapiens.GRCh38.101.gtf).
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file that contains Ensembl gene IDs and the gene raw counts, one column for each sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: HT-1080 cells were grown in DMEM supplemented with 10% tet-free serum and 1% Penicilin-Streptomycin, at 37C with 5% oxygen and 5% carbon dioxide

extract_protocol:
RNA was extracted from a cell pellet using a Purelink RNA Mini Kit (Invitrogen #12183025) following manufacturer’s instructions
Illumina stranded mRNA prep ligation sample preparation protocol was used with a starting concentration of total RNA between 25-1000 ng

treatment_protocol: Human fibrosarcoma cancer cell line HT-1080 was treated for 6 or 24 hours with the compound (GNF7) or a vehicle control (DMSO).

tag: cell line

tag: cell type

value: human fibrosarcoma cells

tag: treatment

value: cycling

tag: time

value: 6 h


title: WT/WT;RAD23AKD bio rep 2

city: London

first: Ravindra

middle: Singh

last: Prajapati

state: UK

address: 2nd floor, Maurice Wohl Clinical Neuroscience Inst, 5 Cutcombe Road

department: BCN, Maurice Wohl Clinical Neuroscience Ins

country: United Kingdom

institute: King's College London

data_processing:
Low-quality reads (Phred<20), and adapters were removed using Trim-galore (V0.6.7)
Reads were aligned to the GRCm38/mm10 build using RNA STAR Gapped-read mapper (V-2.7.11a+galaxy1 or V-2.7.8a+galaxy1)
To quantify expressed genes, mapped reads were we counted on exons (GRCm38.99.gtf) using featureCounts(V 2.0.1+galaxy2)
Assembly: GRCm38/mm10
Supplementary files format and content: tabular
Supplementary files format and content: read counts

molecule: polyA RNA

organism: Mus musculus

source_name: motor cortex

extract_protocol:
Total RNA was extracted (Qiagen cat. No. 1023539)
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, following the manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: The motor cortices of WT, Tar4/Tar4 and Rad23 ASOs treated mice were dissected from left hemispheres of mice

tag: tissue

value: motor cortex

tag: genotype

value: WT/WT

value: Rad23a KD ASOs


title: K562 Hemin Nilotinib replica2

description: Library name: NILO_24_2_1.fq


title: WT/WT;RAD23AKD bio rep 1


title: K562 Mock Nilotinib replica3

description: Library name: NILO_0_3_1.fq


title: MDA-MB-231 CM S6

city: Turku

first: Sirpa

last: Jalkanen

address: Tykistökatu 6a

department: Medical Microbiology and Immunology

country: Finland

institute: Univeristy of Turku

description:
Read length 2x50bp
200004_11_HLEC_MDAMB

data_processing:
The raw sequencing data was uploaded to the BaseSpace Sequence Hub (Illumina) as fastq files for further analysis. The quality control was performed using the FastQC application of BaseSpace and subsequently, the sequences were aligned against the human reference genome hg19 (UCSC, RefSeq gene annotation) with the RNA-Seq Alignment application, which uses the STAR aligner for read mapping and salmon for quantification of reference genes and transcripts. The differences in gene expression between the samples were identified with the RNA-Seq Differential Expression application using DESeq2. The genes exhibiting a fold change (FC) >2 (log2ratio ≥1 and ≤-1) and q-values (FDR) < 0.05 were selected as differentially expressed genes (DEG)
Assembly: hg19
Supplementary files format and content: Excel file with normalized abundance measurements

extract_protocol:
RNA was extracted with the NucleoSpin RNA kit (Macherey-Nagel), 300ng were used for library preparation
TruSeq® Stranded mRNA Sample Preparation, Illumina (15031047)

value: Human Lymphatic Endothelial Cells


title: WT/WT;RAD23ASCR bio rep 10

value: scramble ASOs


title: WT/WT;RAD23ASCR bio rep 9


title: K562 Mock Nilotinib replica1

description: Library name: NILO_0_1_1.fq


title: MCF-7 CM S9

description:
Read length 2x50bp
200004_5_HLEC_MCF7


title: K562 Hemin DMSO replica3

description: Library name: DMSO_24_3_1.fq


title: Senescent cells, GNF7 treated 6 hrs, biol rep 2

description: Library name: HT-S-C1-6-2

value: senescent


title: HLEC CM S7

description:
Read length 2x50bp
200004_4_HLEC_HLEC

source_name: HLEC

value: HLEC


title: WT/WT;RAD23ASCR bio rep 8


title: K562 Hemin DMSO replica1

description: Library name: DMSO_24_1_1.fq


title: K562 Mock DMSO replica3

description: Library name: DMSO_0_3_1.fq


title: WT/WT;RAD23ASCR bio rep 7


title: WT/WT;RAD23AKD bio rep 3


title: HLEC CM S5

description:
Read length 2x50bp
200004_3_HLEC_HLEC


title: HLEC CM S3

description:
Read length 2x50bp
200004_2_HLEC_HLEC


title: K562 Mock DMSO replica1

description: Library name: DMSO_0_1_1.fq


title: PC3_GNS5_R3

city: Worcester

first: Emma

middle: V.

last: Watson

state: MA

address: AS7-1045 Albert Sherman Center, 368 Plantation St

department: Systems Biology

country: USA

institute: UMass Chan Medical School

description: Library name: Sample10

data_processing:
Reads were aligned using BWA (v 0.7.17) to the T2T-CHM13 human reference genome for samples from human cell lines and GRCm39 mouse reference genome for samples from mouse cell line.
The aligned reads were sorted using SAMtools (v1.16.1), and gene-level read counts were obtained using featureCounts (subread, v1.6.2).
Assembly: T2T-CHM13 for human, GRCm39 for mouse
Supplementary files format and content: csv file with TPM values for each gene in each sample

extract_protocol:
1 ug of RNA was utilized for mRNA isolation per sample, which was completed using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA Library Prep Kits for Illumina kit.

value: Prostate cancer cell line


title: PC3_DMSO_R2

description: Library name: Sample7

value: DMSO


title: PC3_GNS5_R1

description: Library name: Sample8


title: MCF-7 CM S11

description:
Read length 2x50bp
200004_6_HLEC_MCF7


title: WT/WT;RAD23ASCR bio rep 6


title: HLEC CM S1

description:
Read length 2x50bp
200004_1_HLEC_HLEC


title: PC3_DMSO_R1

description: Library name: Sample6


title: K562 Hemin Nilotinib replica1

description: Library name: NILO_24_1_1.fq


title: WT/WT;RAD23ASCR bio rep 5


title: PC3_GNS5_R2

description: Library name: Sample9


title: WT/WT;RAD23ASCR bio rep 4


title: K562 Mock Nilotinib replica2

description: Library name: NILO_0_2_1.fq


title: A1847_GNS5_R3

description: Library name: Sample5

value: Ovarian cancer cell line


title: K562 Hemin DMSO replica2

description: Library name: DMSO_24_2_1.fq


title: A1847_GNS5_R1

description: Library name: Sample3


title: Endometrial Cancer_ET19-44 [D09]

city: Chengdu

first: Xue

last: Xiao

state: Sichuan

address: 32# W. Sec 2, 1st Ring Rd

department: Department of Pathology

country: China

institute: Sichuan provincial people's hospital

data_processing:
The raw reads (raw sequencing FASTQ files) are selected for a DSP pipeline run
The raw reads are processed for high quality(if more than 50% base's Phred Q <=19), the adapters(for SE,if the adapter contamination length is greater than 5bp; for PE, if one read has adapter contamination, then both reads are removed) are removed, and the paired-end reads are merged
The reads are aligned to the DSP readout tag sequence identifier barcodes, then PCR duplicates are removed by matching on the Unique Molecular Index (UMI)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every Regions of Interest (ROIs)

source_name: Endometrial Tumor

extract_protocol: After the GeoMx DSP system has completed collection, each GeoMx DSP aspirate in the collection plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. When PCR is performed on the aspirates, Illumina adapter sequences and unique dual sample indices are added. Following a pooling purification and quality control process, the final library is ready for sequencing on an Illumina NGS platform using a dualindex workflow.

value: Endometrial Tumor

tag: ec molecular_subtype

value: MMRd

tag: area of_analysis

value: Stroma area


title: WT/WT;RAD23ASCR bio rep 3


title: Endometrial Cancer_ET19-53 [D11]


title: Endometrial Cancer_ET19-53 [D10]

tag: cd8+t cell_inifltration_status

value: TILs-high

value: Tumor area


title: WT/WT;RAD23ASCR bio rep 2


title: K562 Mock DMSO replica2

description: Library name: DMSO_0_2_1.fq

value: erythroleukemia cell line

value: leukemia cell line


title: A1847_DMSO_R1

description: Library name: Sample1


title: Endometrial Cancer_ET19-44 [D08]


title: A1847_DMSO_R2

description: Library name: Sample2


title: WT/WT;RAD23ASCR bio rep 1

value: motor cortex


title: Endometrial Cancer_ET19-35 [D07]


title: HeLa cells with UBOX-UBL and RNA was extracted after 72 hours biorep2

city: Stockton

first: Joseph

middle: S

last: Harrison

state: CA

address: 3601 Pacific Ave

department: Chemistry

institute: University of the Pacific

description: Library name: UU-2

data_processing:
RANAseq pipeline
Assembly: GRCh38
Supplementary files format and content: Tab delimited files with raw counts for each sample
Supplementary files format and content: Tab delimited files with RPM for each sample

source_name: HeLa

growth_protocol: 72 hours post electroporation

extract_protocol:
Total RNA extraction; llumina Stranded mRNA Prep with Illumina Unique Dual Indexes
Illumina Unique Dual Indexes

treatment_protocol: Electroporation with designed proteins

value: HeLa


title: HeLa cells with UBOX-UBL and RNA was extracted after 72 hours biorep1

description: Library name: UU-1


title: HeLa cells with UBOX-UBLcontrol and RNA was extracted after 72 hours biorep2

description: Library name: UC-2


title: lung, Smad4iko, sample 4

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Preprocessing of the FASTQ sequencing data was performed using the fastp preprocessor tool with default parameters. To improve quantification accuracy, sequencing errors in the UMI sequence were modeled and eliminated using the UMI-Tools method. Thereafter, the clean reads were mapped to the mouse genome (Ensemble version 100) to yield gene expression matrices (UMI counts per gene per cell).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Mouse lung tissue at the peripheral region distal to the pulmonary hilum was collected from mice at age 8 weeks. To prepare single-cell suspension, tissue blocks were minced and digested in an enzyme-containing buffer (1 mg/ml type I collagenase; 0.5 mg/ml type IV collagenase; DNase I, 1 U/ml; 2 mM MgCl2; 2 mM CaCl2) for 50 min at 37°C with occasional shaking. Thereafter, heat-inactivated fetal bovine serum (FBS, 10% v:v) was added to neutralize the enzymes. The tissue digest was further dissociated by repeated pipetting and gentle mincing and then filtered through a 70-μm strainer and a 40-μm strainer to remove undigested cell aggregates. After lysing red blood cells, the remaining pulmonary single cells were collected, rinsed and re-suspended in 0.04% BSA/PBS, followed by Acridine Orange/Propidium Iodide staining for cell count and viability test. In each preparation, we obtained approximately 1X10^6 cells per mL and the viability was more than 80%.
Library construction were performed according to manufacter's instruction for single cell 3' 10x genomic and prepared for sequencing using standard Illumina protocols.
Library were sequenced using the NovaSeq System (Illumina) with a 150 bp paired-end run according to the manufacture’s instruction.

treatment_protocol: To induce gene deletion, young adult mice received five intraperitoneal (i.p.) injections of tamoxifen (75 mg/kg body weight) on postnatal days 21, 22, 23, 25 and 26. Tamoxifen-injected, Cre-negative floxed littermates were used as controls.

value: Lung


title: HeLa cells with UBOX-UBLcontrol and RNA was extracted after 72 hours biorep1

description: Library name: UC-1


title: Endometrial Cancer_ET19-35 [D06]

value: TILs-low


title: lung, Smad4iko, sample 3

description: 10X Genomics


title: Endometrial Cancer_ET19-34 [D05]


title: PC3_shTT3, rep 2

city: Saint Petersburg

first: Ranjan

last: Perera

state: FL

address: 600 5th St S

department: Oncology Center

institute: Johns Hopkins All Childrens Hospital

description: Library name: PC3_shTT2

data_processing:
Paired end reads were quality checked and trimmed to remove low quality bases using trim_galore.
High quality trimmed reads were filtered to remove ribosomal reads using sortmerna.
Ribosomal rna reference was derived from silva-arc-16s,silva-arc-23s , silva-bac-16s, silva-bac-23s, silva-euk-18s, silva-euk-28s, rfam-5s and rfam-5.8s databases.
Filtered reads were aligned to human reference genome hg38 (v42) using splicing aware short reads aligner STAR.
Genes and isoforms read counts were derived using stringtie and gencode gtf (v42) from the aligned reads.
Assembly: hg38
Supplementary files format and content: CSV - Genes and isoforms read counts

source_name: Human prostate cancer

growth_protocol: Human PC3 cell lines were obtained from the American Type Culture Collection and cultured in Ham's F-12K media (Gibco) with 10% FBS and 1% penicillin/streptomycin at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was isolated from cell lines using the RNeasy Mini Kit (Qiagen). The quality of RNA was determined with the High Sensitivity RNA ScreenTape assay in TapeStation (Agilent Technologies).
Libraries were prepared using NEBNext rRNA Depletion Kit v2 followed by the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following the manufacturer's instructions. The quality of DNA libraries was evaluated using the KAPA library qualification kit (Roche) and Agilent 4200 TapeStation (Agilent Technologies).

value: Human prostate cancer

value: TTC3 knockdown


title: PC3_shTT3, rep 3

description: Library name: PC3_shTT3


title: A1847_GNS5_R2

description: Library name: Sample4


title: PC3_shTT3, rep 1

description: Library name: PC3_shTT1


title: lung, Smad4iko, sample 2

description: 10X Genomics


title: Endometrial Cancer_ET19-34 [D04]


title: PC3_shNC, rep 3

description: Library name: PC3_shNC3

value: WT


title: PC3_shNC, rep 2

description: Library name: PC3_shNC2

value: Prostate cancer cell line


title: PC3_shNC, rep 1

description: Library name: PC3_shNC1


title: Day4 TS-EVT ATAC

city: Pittsburgh

first: Leah

last: Cabo

state: PA

address: 4249 Fifth Avenue

institute: University of pittsburgh

library_source: genomic

data_processing:
Resulting fastq files were processed with 10X Genomics cellranger  and aggregated using aggr
Assembly: Homo sapiens hg38
Supplementary files format and content: processed data files contain aggr and cellranger outputs
Library strategy: single nuclei multiome ATAC _ Gene Expression

molecule: genomic DNA

source_name: trophoblast stem cells

growth_protocol: Human trophoblast stem cells were maintained as published in Okae et. al 2018 Cell Stem Cell. TS-CTB were plated at 70,000 cells per well of a 6 well plate and grown for 24-48 hours in TS-CTB media before treatment. TS-EVT were differentiated for 4 (intermediate) or 8 (terminal) days according to published protocols.

extract_protocol:
Adherent cells from CTB and EVT samples were trypsinized for 12 minutes with 1:1 TrypLE and PBS. Nonadherent 3D STB were collected from wells. Trypsinized cells were collected by pipetting and centrifuged for 250 x g for 5 minutes. Nuclear extraction was performed according to 10x Genomics Chromium Single Cell Nuclei Isolation protocols. Nuclei viability was tested prior to use in library preparation
Library construction was performed according to 10X Genomics Chromium single nuclei multiome ATAC _ Gene Expression protocols

treatment_protocol: After 24-48 hours of growth, TS-CTB were switched to 2 mL TS-basal medium + Y27632 and either mock-infected or infected with T. gondii. T. gondii parasites were cultured in HFFs (human foreskin fibroblasts), syringe lysed, filtered with 5.0 um syringe filter to remove host cell debris, centrifuged at 800 x g for 10 minutes, pellet was resuspended in new TS-basal + Y27632 media, and parasites were counted via hemocytometer. Tg-infected TS-CTB were infected with a 3:1 ratio of parasites (70,000 TS-CTB plated, 210,000 parasites used for infection) in 200 uL media per well. Remaining parasite suspension was filtered through 0.2 um syringe filter to remove all parasites. The same volume (200 uL) of filtered parasite suspension was used to mock-infected TS-CTB. TS-EVT were differentiated according to published protocols

value: trophoblast stem cells

value: EVT

value: intermediately differentiated


title: Day8 TS-EVT ATAC

value: terminally differentiated


title: lung, Smad4iko, sample 1

description: 10X Genomics


title: Endometrial Cancer_ET19-33 [D03]

value: Endometrial Tumor

value: MMRd

value: Stroma area


title: Endometrial Cancer_ET19-33 [D02]

value: TILs-high

value: Tumor area


title: lung, Smad4fl/fl, sample 2

description: 10X Genomics


title: mock-infected TS-CTB ATAC

value: CTB

value: mock-infected


title: Tg-infected TS-CTB ATAC

value: Tg-infected


title: Endometrial Cancer_ET19-31 [D01]


title: lung, Smad4fl/fl, sample 1

description: 10X Genomics

value: Lung


title: Endometrial Cancer_ET19-31 [C12]


title: D150L150-3

city: Shanghai

first: Jiayi

last: Mao

address: Zhi Zao Ju road

institute: shanghai ninth people's hospital

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar . Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: mm10

source_name: Skin

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Skin

tag: group

value: The flaps were treated with spacers after modeling


title: D150L150-2


title: Endometrial Cancer_ET19-23 [C11]


title: D150L150-1


title: Endometrial Cancer_ET19-23 [C10]

value: TILs-low


title: lung, Smad4fl/fl, sample 3

description: 10X Genomics


title: Endometrial Cancer_ET19-15 [C09]


title: Endometrial Cancer_ET19-15 [C08]


title: Endometrial Cancer_ET19-11 [C07]


title: D100L150-2


title: D100L150-1


title: FM79 Cells, siMEK5 72h, Trametinib 5nM 48h, biol rep 3

city: Wuerzburg

first: Rupesh

last: Paudel

state: Bavaria

address: Josef-Schneider Straße 2

department: Department of Dermatology, Venerology und Allergology

country: Germany

institute: University Hospital Wuerzburg

description: Library name: Sample 9

data_processing:
quality/adapter trimming of FASTQ files with Cutadapt
Reads alignment to Human reference genome (GCF_000001405.39_GRCh38.p13) primary assembly and mitochondrion, read quantification on gene level based on annotated exons via featureCounts using both, uniquely and multimapping reads.
Differentially expressed genes between different groups were compared in two arms: siScr vs Tram/SiScr =(Tram-regulated genes) or Tram/siScr vs Tram/siMEK5 (=siMEK5-regulated genes) using DeSeq2 (Bioconductor)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab delimited CSV file includes original and normalized FPKM values

growth_protocol: Cells were grown at 37°C with 5% CO2 in RPMI1640 GlutaMAX medium (ThermoFisher Scientific), supplemented with 10% fetal calf serum (Capricorn) and 30 µg/ml Gentamycin (Sigma Aldrich)

extract_protocol:
Toral RNA was extracted using RNAeasy Kit (Qiagen).
cDNA library preparation was done using TruSeq Kit, (Illumina) according to manufacturers protocol.

treatment_protocol: Day 0 : Cells seeded, Day 1:  cells were either transfected with siScr or siMEK5 Day 2:  Cells were either treated with vehicle or Trametinib 5nM Day 4: Cells were lysed

value: melanoma cell lines

value: MEK5 knockdown

value: Trametinib 5nM 48h


title: Endometrial Cancer_ET19-11 [C06]


title: Contemporary cow 1111

type: RNA

city: Jouy-en-Josas

first: Mariam

last: Raliou

address: Allée de Vilvert

department: PHASE

country: France

institute: INRAE

description:
The endometrial biopsy samples were collected, after peridural anaesthesia, using a uterine biopsy probe on Day 15 of estrous cycle
Custom bovine slide consisting of 61,325 nucleotides (including 23,926 unique transcripts) as described previously (Carvalho et al., 2017)
this cow was excluded from the analysis because its phenotype is divergent compared to the others in the same group

hyb_protocol: Cyanine-3 (Cy-3) labeled cRNAs were prepared using 100 ng of total RNA with the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies). Specific activities and cRNA yields were determined using the NanoDrop ND-1000 (Thermo Fisher Scientific). RNA labeling and microarray processing were carried out as described above (Carvalho et al., 2017). All the hybridization procedures were performed by CRB GADIE facility (INRA Jouy-en-Josas, France, http://crb-gadie.inra.fr/).

scan_protocol: After washing, slides were immediately scanned using G2565CA Scanner System (Agilent Technologies) as described above (Carvalho et al., 2017).

data_processing: The resulting images were analyzed with the Feature Extraction. Software v10.7.3.1 (Agilent Technologies), using GE1_107_Sep09 protocol as described above (Carvalho et al., 2017)

organism: Bos taurus

source_name: Cow was synchronized, and endometrial biopsies were collected on day 15 of the estrous cycle.

label_protocol: Labelling was carried out with the fluorochrome Cyanine 3 (Cy-3) using the One-Color Low Input Quick Amp Labelling kit (Agilent Technologies) as described above (Carvalho et al., 2017).

extract_protocol: Total RNA of Total RNA was extracted from biopsies using TRIzol Reagent (ThermoFisher Scientific) as previously described by (Mansouri-Attia et al., 2009b) and purified on Qiagen columns (RNeasy Mini kit; Qiagen, Courtaboeuf, France) according to the manufacturer's recommendations. Total RNA was quantified using Nanodrop ND-3300 spectrophotometer (Labtech, Wilmington, DE, USA). The RNA integrity number of each RNA sample ranged from 7 to 9.5 using the Agilent 2100 ® Bioanalyzer (@bridge ICE -Iso Cell Express-, INRA, France: https://www6.jouy.inra.fr/ice).

value: Uterus at day 15 of estrous cycle

tag: stage of postpartum period

value: Day 15 of estrus cycle

tag: code barre


title: Contemporary cow 1129

description:
The endometrial biopsy samples were collected, after peridural anaesthesia, using a uterine biopsy probe on Day 15 of estrous cycle
Custom bovine slide consisting of 61,325 nucleotides (including 23,926 unique transcripts) as described previously (Carvalho et al., 2017)


title: D15L200-3


title: FM79 Cells, siScr 72h, Trametinib 5nM 48h, biol rep 3

description: Library name: Sample 6

value: WT


title: FM79 Cells, siMEK5 72h, Trametinib 5nM 48h, biol rep 1

description: Library name: Sample 7


title: FM79 Cells, siMEK5 72h, Trametinib 5nM 48h, biol rep 2

description: Library name: Sample 8


title: D100L150-3


title: Old Cow 2258


title: Old Cow 0234


title: D15L200-2


title: FM79 Cells, siScr 72h, Trametinib 5nM 48h, biol rep 2

description: Library name: Sample 5


title: Young cow 1072


title: Old Cow 0233


title: Contemporary cow 1068


title: Contemporary cow 1128


title: Endometrial Cancer_ET19-9 [C04]

value: Endometrial Tumor

value: MMRd


title: Young cow 1069

description:
The endometrial biopsy samples were collected, after peridural anaesthesia, using a uterine biopsy probe on Day 15 of estrous cycle.
Custom bovine slide consisting of 61,325 nucleotides (including 23,926 unique transcripts) as described previously (Carvalho et al., 2017). Ninety-seven percent of the transcripts present on the slide were transcripts from the bovine genome Bos Bos taurus (taxid:9913) annotated by Ensembl (http://www.ensembl.org/Bos_taurus/Info/Index).


title: Young cow 1070


title: Old Cow 0245


title: Young cow 1127


title: D15L200-1


title: FM79 Cells, siScr 72h, Mock 48h, biol rep 3

description: Library name: Sample 3

value: Mock


title: FM79 Cells, siScr 72h, Mock 48h, biol rep 2

description: Library name: Sample 2


title: Endometrial Cancer_ET19-7 [C03]

value: Stroma area


title: Endometrial Cancer_ET19-9 [C05]


title: D15L150-3


title: Endometrial Cancer_ET19-7 [C02]

value: TILs-high

value: Tumor area


title: FM79 Cells, siScr 72h, Mock 48h, biol rep 1

description: Library name: Sample 1


title: D15L150-2


title: Endometrial Cancer_ET19-4 [C01]


title: FM79 Cells, siScr 72h, Trametinib 5nM 48h, biol rep 1

description: Library name: Sample 4


title: Endometrial Cancer_ET19-4 [B12]


title: D15L100-3


title: D15L150-1


title: Endometrial Cancer_ET19-3 [B11]


title: D15L100-2


title: Hippocampal in mice subjected to TST and treated with LPS_rep3

city: Tsukuba

first: Hisako

last: Iwahashi

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from hippocampal in mice subjected to TST and treated with LPS

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Mouse; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4)

label: biotin

source_name: Hippocampal in mice subjected to TST and treated with saline for 7 days followed by LPS on the final day

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: Eight-week-old male ICR mice were housed under controlled temperature and humidity conditions with unrestricted access to food and water, maintained on a 12-hour light/dark cycle.After a one-week acclimatization period to the laboratory conditions, the mice were randomly assigned to three groups, with six to seven mice in each group: the control (saline administration group with saline injection), the depression model group: LPS group (saline with LPS injection) and PN group (50mg/kg body weight, daily referred to as PN) (with LPS injection).

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: The control group received an equivalent volume of saline orally each day. PN was dissolved in saline and administered orally at a dose of 50 mg/kg body weight daily. The treatment duration was seven days.LPS was dissolved in saline and administered as a single intraperitoneal injection at a dose of 0.85 mg/kg body weight.   On the seventh day of oral administration, one hour after the final oral administration, LPS was administered intraperitoneally. Twenty-four hours following the intraperitoneal injection of LPS into the ICR mice, the tail suspension test (TST) was conducted as described in a previous study with slight modifications. Briefly, each mouse was individually suspended for 6 minutes at a point 2 cm from the tail tip using a clip (Yamashita Giken, Tokushima, Japan) in a white box measuring 30 × 15 × 50 cm (length × width × height). The immobility time, indicative of behavioral despair akin to clinical depression in humans, was recorded and measured during the final 4 minutes of the 6-minute suspension period using SMART 3.0 video tracking software (Panlab, Barcelona, Spain). Mice were considered immobile only when they ceased movement of their limbs, head, and body.

value: hippocampal tissue


title: Hippocampal in mice subjected to TST and treated with LPS_rep2


title: Endometrial Cancer_ET19-3 [B10]


title: Hippocampal in mice subjected to TST and treated with saline_rep2

description: Gene expression data from hippocampal in mice subjected to TST and treated with saline

source_name: Hippocampal in mice subjected to TST and treated with saline for 7 days


title: Hippocampal in mice subjected to TST and treated with LPS_rep1


title: D15L100-1


title: Whole worm, BPTMC, rep3

city: Jinju

first: Ho Jeong

last: Lee

address: 17 Jeigok-gil

country: South Korea

institute: Korea institute of toxicology (KIT)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to WBcel235 (NCBI) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Caenorhabditis elegans

growth_protocol: Caenorhabditis elegans was maintained at 20℃ on NGM plates seeded with Escherichia coli OP50.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: When it came to the final step of NGM, chemical plates were made with BPTMC and DMSO at a final concentration of 1 mM. Caenorhabditis elegans was exposed on each chemical plates (control and test) for 24 hrs.

tag: strain

tag: developmental stage

value: L4 to Adult

value: wild-type

value: Bisphenol TMC

value: 24 hrs


title: Hippocampal in mice subjected to TST and treated with saline_rep1


title: Whole worm, BPTMC, rep2


title: Control-3

value: Skin

value: Control

value: The flaps were not treated after modeling


title: Endometrial Cancer_ET19-2 [B09]


title: Whole worm, BPTMC, rep1


title: Whole worm, DMSO, rep1

value: Dimethyl sulfoxide


title: Hippocampal in mice subjected to TST and treated with PN_rep3

description: Gene expression data from hippocampal in mice subjected to TST and treated with PN

source_name: Hippocampal in mice subjected to TST and treated with PN for 7 days followed by LPS on the final day


title: Endometrial Cancer_ET19-2 [B08]


title: Hippocampal in mice subjected to TST and treated with PN_rep1


title: prostate_tissue_08_BPH_biol_rep_3

city: Wrocław

first: Maciej

last: Zacharski

state: dolnoslaskie

address: Norwida, 31

department: Department of Biochemistry and Molecular Biology

country: Poland

institute: Wroclaw University of Environmental and Life Sciences

description: Library name: PR8_3

data_processing:
Reads trimmed and filtered with Trimmomatic were mapped to the C. lupus familiaris genome version CanFam3.1, annotation release 101, (GeneBank accession: GCF_000002285.3) using  STAR v2.7.6a aligner. RSEM v1.2.28 was used to calculate gene count with –rsem-calculate-expression option. The gene counts were made into a count table in R, where genes with no count and low count genes were filtered out. EdgeR v3.30.3 package was used for normalization, calculating dispersion and testing for differential expression.
Assembly: C. lupus familiaris genome version CanFam3.1, annotation release 101, (GeneBank accession: GCF_000002285.3)
Supplementary files format and content: cmp_norm_pc_bph.xlsx contains the normalized counts per million. Column A lists the Ensembl gene ID. Column B lists the default RefSeq gene name. Each column from the C to Q range lists normalized counts per million for each studied sample.

organism: Canis lupus familiaris

source_name: prostate

extract_protocol:
RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions with on column Dnase digestion
The library was prepared using 350 ng of total RNA and the QuantSeq 3’ mRNA library preparation FWD kit (Lexogen) according to the manufacturer’s instructions. Briefly, the first strand of cDNA was synthesized, RNA was removed, and the second strand was synthesized using Unique Molecular Identifiers (UMI). Library preparation encompassed 13 cycles of PCR enrichment (initial denaturation: 98 °C, 30 sec; 13 cycles of 98 °C for 10 sec, 65 °C for 20 sec, 72 °C for 30 sec; final elongation: 72 °C, 1 min) followed by purification of the amplified product. Subsequent to this, a quality control assessment of the libraries was conducted using the Bioanalyser High Sensitivity DNA chip (Agilent Technologies). Thereafter, the libraries were quantitatively assessed by qPCR in accordance with the Illumina protocol. This facilitated the equimolar pooling of the libraries, which were subsequently sequenced on the NextSeq500 (Illumina) instrument using single reads of 75 base pairs on a high-output configuration.

treatment_protocol: RNA later, freezing -80 deg C

value: prostate

tag: Sex

value: male

tag: breed

tag: age

tag: hp diagnosis

value: BPH

tag: neutering status

tag: disease state


title: Control-2

tag: treatment


title: Hippocampal in mice subjected to TST and treated with PN_rep2

tag: tissue


title: Control-1


title: prostate_tissue_08_BPH_biol_rep_1

description: Library name: PR8_1


title: prostate_tissue_06_BPH_biol_rep_3

description: Library name: PR6_2_1


title: Endometrial Cancer_ET20-98 [B06]

value: Endometrial Tumor

value: MMRd


title: 48-3

city: hangzhou

first: wang

last: pengfei

address: yuhangtang road 866

institute: zhejiang university

description: Cona stimulated CD4+T cell

data_processing:
The RNA-Seq data of control and activated T cells was aligned to the mouse reference genome (GRCm38/mm10) using the STAR aligner with default parameters, and the output was saved as sorted BAM files. Gene-level count matrices were generated using FeatureCounts. Differential expression analysis was performed with the limma package in R.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: CD4+T cell

extract_protocol:
Total RNA was extracted from control and ConA stimulated CD4+ T cells using the RNAeasy Plus Mini kit (Qiagen)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature inFirst Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

tag: cell type

value: CD4+T cell

tag: genotype

value: WT

value: Cona stimulated


title: prostate_tissue_06_BPH_biol_rep_2

description: Library name: PR6_1_2


title: Endometrial Cancer_ET20-88 [B05]

tag: ec molecular_subtype

tag: area of_analysis

value: Stroma area


title: 48-2

description: Cona stimulated CD4+T cell


title: prostate_tissue_06_BPH_biol_rep_1

description: Library name: PR6_1_1


title: prostate_tissue_17_PC_biol_rep_2

description: Library name: PR17_1_2

value: Staffordshire Bull Terrier

value: carcinoma

value: No

value: PC


title: Endometrial Cancer_ET20-88 [B04]

tag: cd8+t cell_inifltration_status

value: TILs-high

value: Tumor area


title: 48-1

description: Cona stimulated CD4+T cell


title: prostate_tissue_17_PC_biol_rep_3

description: Library name: PR17_2_1


title: prostate_tissue_17_PC_biol_rep_1

description: Library name: PR17_1_1


title: prostate_tissue_16_PC_biol_rep_3

description: Library name: PR16_2_1

value: Mixed

value: adenocarcinoma

value: Yes


title: 0-3

description: control CD4+T cell

value: no treatment


title: Endometrial Cancer_ET20-98 [B07]


title: Endometrial Cancer_ET20-85 [B02]


title: prostate_tissue_16_PC_biol_rep_2

description: Library name: PR16_1_2

value: prostate

value: male


title: prostate_tissue_11_BPH_biol_rep_3

description: Library name: PR11_3

value: BPH


title: 0-1

description: control CD4+T cell

value: CD4+T cell


title: prostate_tissue_11_BPH_biol_rep_2

description: Library name: PR11_2


title: 0-2

description: control CD4+T cell

value: WT


title: Endometrial Cancer_ET20-84 [B01]

value: Endometrial Tumor

value: MMRd


title: prostate_tissue_11_BPH_biol_rep_1

description: Library name: PR11_1


title: Endometrial Cancer_ET20-84 [A12]


title: AntiSal8

city: Rockville

first: Qiaoping

last: Yuan

state: MD

address: 5625 Fishers Lane, Suite 3S32

institute: NIAAA

description:
Library name: AntiSal8
AmpliSeq

data_processing:
Alignment and gene expression count were performed using Ion Torrent AmpliSeqRNA Plugin v0.5.4.0 (Thermo Fisher) using mm10 genome.
AmpliSeq count data was analyzed using DESeq2 1.34.0
Assembly: mm10
Supplementary files format and content: rpm files: first column contains Gene Symbols; second column contains RPM of the the gene expresion value

source_name: Heart

extract_protocol:
Endpoints were collected 3 hours after alcohol gavage.
Libraries were generated using Ion AmpliSeq™ Library Kit Plus (Thermo Fisher Scientific, 4488990) per the manufacturer’s instructions.

treatment_protocol: Mice were exposed to a single alcohol gavage at a dose of 5g/kg body weight following overnight fasting . As for the control group, mice were administered saline similarly. In the second cohort, mice were treated orally with a mixture of antibiotics (Sigma-Aldrich, St. Louis, MO, USA)  before alcohol gavage to selectively eliminate intestinal Gram-negative flora, as previously described, with minor modifications. Briefly, mice were randomly assigned to control or antibiotic treatment groups, where they either received water or non-absorbable antibiotics (neomycin, polymyxin-B, and nystatin; 200 mg/kg, 150 mg/kg, and 1 mg/kg, respectively) for a 14-day pre-treatment period prior to alcohol gavage. After selective intestinal decontamination, mice were exposed to alcohol, as described above.

value: Heart

value: Wildtype

value: AntibioticSaline

tag: batch


title: AntiEtOH8

description:
Library name: AntiEtOH8
AmpliSeq

value: AntibioticEtOH


title: ConSal7

description:
Library name: ConSal7
AmpliSeq

value: ControlSaline


title: mechanical ventilated diaphragm nuclei

city: Wuhan

first: Bing

last: Yang

state: Hubei

address: No.1 Shizishan Street, Hongshan District

department: College of Vetirinary Medicine

institute: Huazhong Agricultural University

description: 10x Genomics

data_processing:
Primary analysis, including demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger software (10X Genomics).
Assembly: mm10
Supplementary files format and content: table-separated values files and matrix files

source_name: diaphragm

extract_protocol:
Mouse diaphragm cell nuclei were isolated and purified following established protocols for scRNA-seq. Briefly, the fresh or frozen diaphragm tissue are minced and combined with 1ml of nuclear lysis buffer (NST) containing 0.1% NP40, 10mM Tris-HCl, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, and 40 U/mL RNase inhibitor. The mixture is then incubated for 7 minutes to ensure complete nuclear lysis, which is confirmed by Trypan blue staining and microscopic examination. Next, 1ml of ST wash buffer (containing 10 mM Tris-HCl, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 0.01% BSA, and 40 U/mL RNase inhibitor) is added to the lysed nuclei. The suspension is filtered through a 40 µm cell strainer, and the filtrate is collected in a 15mL centrifuge tube. The cell strainer is washed with additional ST wash buffer, and the wash solution is combined with the filtered nuclear suspension. The tube is then centrifuged at 500 g for 5 minutes at 4°C. The nuclear pellet is resuspended in 5 mL of PBS + 1% BSA, followed by centrifugation and resuspension in 100 µl of PBS + 1% BSA. Trypan blue staining is performed, and the cells are counted under a microscope
The nuclei are counted, and the nuclear concentration is adjusted as needed by diluting with PBS + 1% BSA to achieve the optimal range for loading on the 10× Chromium chip. On-machine processing and cDNA library amplification are performed according to the instructions provided by the 10× Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). For DNA library construction, the Chromium™ Single Cell 3'/5' Library Construction Kit (1000020) is used. The constructed libraries are sequenced using the PE150 sequencing mode on the Illumina Nova 6000 platform.

value: diaphragm

value: wild type

value: mechanical ventilation


title: diaphragm  nuclei

description: 10x Genomics

value: unprocessed


title: Endometrial Cancer_ET20-40 [A11]

value: Stroma area


title: AntiEtOH7

description:
Library name: AntiEtOH7
AmpliSeq


title: prostate_tissue_08_BPH_biol_rep_2

description: Library name: PR8_2

value: prostate


title: Whole worm, DMSO, rep2

value: L4 to Adult

value: wild-type

value: Dimethyl sulfoxide

tag: time

value: 24 hrs


title: Endometrial Cancer_ET20-40 [A10]

value: Endometrial Tumor

value: TILs-high

value: Tumor area


title: AntiSal6

description:
Library name: AntiSal6
AmpliSeq

value: Heart

value: Wildtype


title: AntiEtOH6

description:
Library name: AntiEtOH6
AmpliSeq

value: AntibioticEtOH


title: Endometrial Cancer_ET20-85 [B03]

value: MMRd


title: prostate_tissue_16_PC_biol_rep_1

description: Library name: PR16_1_1

value: male

value: Mixed

value: adenocarcinoma

value: Yes

value: PC


title: Female, BTZ-treated, sample 2, scRNAseq

city: St. Louis

first: Valeria

last: Cavalli

state: MO

address: 1 Bookings Dr.

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
Samples were aligned to the mouse genome (mm10) and digital gene expression matrices were generated using the 10X Genomics CellRanger software (v7.1.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values (.tsv) and matrix (.mtx) files

source_name: Dorsal Root Ganglia

extract_protocol:
Whole DRG’s were dissociated with enzyme mix (Papain, Collagenase) to a single cell suspension, washed in 1X PBS+0.2%BSA solution, passed through a 70-micron cell strainer and FACS sorted using live/dead staining. Sorted cells were loaded on the 10X Chromium system.
Libraries were prepared using the 10X Genomics GemCode Single-Cell 3′ Gel Bead and Library Kit (v3) following the manufacturer's instructions

value: Dorsal Root Ganglia

value: Female

value: 13 weeks

tag: strain

value: Balb/cJ

value: BTZ


title: AntiEtOH5

description:
Library name: AntiEtOH5
AmpliSeq


title: Female, BTZ-treated, sample 1, scRNAseq

description: 10x Genomics


title: Endometrial Cancer_ET20-37 [A09]

value: Endometrial Tumor

value: Stroma area


title: AntiSal5

description:
Library name: AntiSal5
AmpliSeq

value: AntibioticSaline


title: ConEtOH6

description:
Library name: ConEtOH6
AmpliSeq

value: Heart

value: ControlEtOH


title: Female, vehicle-treated, sample 2, scRNAseq

description: 10x Genomics

value: VEH


title: ConEtOH5

description:
Library name: ConEtOH5
AmpliSeq

value: Wildtype


title: Endometrial Cancer_ET20-13 [A07]

value: MMRd


title: Endometrial Cancer_ET20-37 [A08]

value: TILs-low

value: Tumor area


title: Endometrial Cancer_ET20-13 [A06]

value: TILs-high


title: AntiSal7

description:
Library name: AntiSal7
AmpliSeq


title: Female, vehicle-treated, sample 1, scRNAseq

description: 10x Genomics


title: ConSal6

description:
Library name: ConSal6
AmpliSeq

value: ControlSaline


title: ConSal5

description:
Library name: ConSal5
AmpliSeq


title: ConSal3

description:
Library name: ConSal3
AmpliSeq


title: Male, BTZ-treated, sample 2, scRNAseq

description: 10x Genomics

value: Dorsal Root Ganglia

value: Male


title: ConSal2

description:
Library name: ConSal2
AmpliSeq


title: Endometrial Cancer_ET20-6 [A05]


title: Endometrial Cancer_ET20-6 [A04]


title: AntiEtOH2

description:
Library name: AntiEtOH2
AmpliSeq

value: AntibioticEtOH


title: Male, BTZ-treated, sample 1, scRNAseq

description: 10x Genomics

value: 13 weeks

value: Balb/cJ


title: Male, vehicle-treated, sample 1, scRNAseq

description: 10x Genomics


title: AntiSal4

description:
Library name: AntiSal4
AmpliSeq


title: AntiEtOH1

description:
Library name: AntiEtOH1
AmpliSeq


title: Endometrial Cancer_ET20-2 [A03]

value: Endometrial Tumor


title: Aged mouse brain, cTBS, biol rep 4

city: Perth

first: Alexander

last: Tang

state: Western Australia

address: 35 Stirling Highway, University of Western Australia

department: School of Biomedical Science

country: Australia

institute: University of Western Australia

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Raw sequencing bcl files were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were then aligned to the mm10 genome to obtain gene expression counts using the Space Ranger count pipeline
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of all detected spatial barcodes (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: features.tsv.gz: list of all detected gene IDs (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in the Matrix Market Exchange format (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: filtered_feature_bc_matrix.h5:
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of brain hemisphere tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of brain hemisphere tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Freshly dissected right mouse brain hemisphere was flash frozen in OCT using a set-up of isopentane and liquid nitrogen (as per 10xGenomics Visium Spatial Gene Expression protocols). Fresh frozen tissue was directly sectioned onto Visium Spatial Gene Expression Slides at 10μm using a cryostat.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions

value: Brain

value: cTBS


title: Endometrial Cancer_ET21-23 [D09]

value: Stroma area


title: AntiSal3

description:
Library name: AntiSal3
AmpliSeq

value: Heart

value: AntibioticSaline


title: AntiSal2

description:
Library name: AntiSal2
AmpliSeq

value: Wildtype


title: Endometrial Cancer_ET20-2 [A02]

value: MMRd


title: AntiSal1

description:
Library name: AntiSal1
AmpliSeq


title: Endometrial Cancer_ET21-23 [D08]


title: Aged mouse brain, sham, biol rep 4

value: sham


title: ConEtOH2

description:
Library name: ConEtOH2
AmpliSeq

value: ControlEtOH


title: ConEtOH4

description:
Library name: ConEtOH4
AmpliSeq


title: AntiEtOH4

description:
Library name: AntiEtOH4
AmpliSeq


title: Endometrial Cancer_ET21-14 [D07]


title: Aged mouse brain, iTBS, biol rep 3

value: iTBS


title: AntiEtOH3

description:
Library name: AntiEtOH3
AmpliSeq


title: ConSal4

description:
Library name: ConSal4
AmpliSeq

value: ControlSaline


title: RBNS, TDP-43, Synthesized construct, 1300nM, Li+

city: Hong Kong

first: Feng

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

library_source: other

data_processing:
RBNS data were analyzed using rbns_pipeline software (https://github.com/alexrson/rbns_pipeline).
Assembly: synthetic construct
Supplementary files format and content: Tab-delimited text file includes the enrichment levels of RBNS 5,6,7mers
Library strategy: RNA Bind-n-Seq

molecule: other

organism: synthetic construct

source_name: Synthesized construct

extract_protocol:
The RNAs, with a random region of 40 nt, were prepared by in vitro transcription (NEB, E2040S) and then incubated with increasing concentrations of His-tagged TDP-43 protein (0, 5, 20, 80, 320, and 1300 nM).
The RNA pool was separated using a 10% PAGE gel and purified (Zymo Research, R1016). The concentrated RNAs were heated at 85°C for 5 minutes in the presence of 150 mM KCl or LiCl and allowed to cool for at least 3 minutes to facilitate folding. A 10 µL NEBExpress® Ni-NTA Magnetic Bead (NEB, S1423L) was used to replace the Dynabeads MyOne Streptavidin T1 in the old method for pulling down the His-tagged protein-RNA complexes. All wash and binding buffers contained either 150 mM KCl or LiCl. The protein-RNA complexes were eluted in a final buffer concentration of 20 mM Tris-HCl (pH 7.5), 150 mM KCl or LiCl, 500 mM Imidazole (pH 7.4), and 8 M Urea. The RNAs were isolated and reverse transcribed for PCR amplification and sequencing.

value: Synthesized construct

value: Li+


title: Aged mouse brain, sham, biol rep 3


title: Aged mouse brain, cTBS, biol rep 3


title: ConSal1

description:
Library name: ConSal1
AmpliSeq


title: Endometrial Cancer_ET21-12 [D05]

city: Chengdu

first: Xue

address: 32# W. Sec 2, 1st Ring Rd

institute: Sichuan provincial people's hospital

data_processing:
The raw reads (raw sequencing FASTQ files) are selected for a DSP pipeline run
The raw reads are processed for high quality(if more than 50% base's Phred Q <=19), the adapters(for SE,if the adapter contamination length is greater than 5bp; for PE, if one read has adapter contamination, then both reads are removed) are removed, and the paired-end reads are merged
The reads are aligned to the DSP readout tag sequence identifier barcodes, then PCR duplicates are removed by matching on the Unique Molecular Index (UMI)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every Regions of Interest (ROIs)

source_name: Endometrial Tumor

extract_protocol: After the GeoMx DSP system has completed collection, each GeoMx DSP aspirate in the collection plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. When PCR is performed on the aspirates, Illumina adapter sequences and unique dual sample indices are added. Following a pooling purification and quality control process, the final library is ready for sequencing on an Illumina NGS platform using a dualindex workflow.


title: Endometrial Cancer_ET21-14 [D06]

value: TILs-high

value: Tumor area


title: RBNS, TDP-43, Synthesized construct, 320nM, Li+


title: RBNS, TDP-43, Synthesized construct, 1300nM, K+

value: K+


title: Aged mouse brain, iTBS, biol rep 2


title: RBNS, TDP-43, Synthesized construct, 320nM, K+


title: Endometrial Cancer_ET21-12 [D04]

value: Endometrial Tumor

value: TILs-low


title: Aged mouse brain, iTBS, biol rep 4

value: Brain


title: ConEtOH3

description:
Library name: ConEtOH3
AmpliSeq


title: RBNS, TDP-43, Synthesized construct, 80nM, K+


title: RBNS, TDP-43, Synthesized construct, 20nM, Li+


title: Endometrial Cancer_ET21-06 [D03]

value: Stroma area


title: ConEtOH1

description:
Library name: ConEtOH1
AmpliSeq

value: Heart


title: Aged mouse brain, sham, biol rep 2


title: Endometrial Cancer_ET21-06 [D02]


title: RBNS, TDP-43, Synthesized construct, 5nM, Li+


title: RBNS, TDP-43, Synthesized construct, 5nM, K+


title: Aged mouse brain, sham, biol rep 1


title: RBNS, TDP-43, Synthesized construct, 0nM, Li+


title: Aged mouse brain, cTBS, biol rep 1

value: cTBS


title: RBNS, TDP-43, Synthesized construct, 0nM, K+


title: Endometrial Cancer_ET21-01 [D01]


title: Endometrial Cancer_ET21-01 [C12]


title: Aged mouse brain, iTBS, biol rep 1


title: RBNS, TDP-43, Synthesized construct, 0.5pmol, input


title: Somatosensory cortex cells, aged mice, cTBS, replicate 5

data_processing:
First 15 base pairs of sequencerd reads were trimmed to remove low-quality sequences using fastp.
Trimmed sequence reads were mapped to GRCm39/mm39 using the STAR RNA-seq aligner. STAR-aligned SAM files were converted into BAM files.
Read counts were generated using GenomicAlignments.
Normalisation of counts was performed using the DESeq2 R package, using a variance stabilising transformation (VST) function.
Assembly: mm39
Supplementary files format and content: Comma-separated values files containing the raw read counts for each sample
Supplementary files format and content: Comma-separated values files containing the read counts that have been normalised using the variance stabilising transformation (VST) for each sample

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). A minimum of 50ng total RNA was sent to the Australian Genome Research Facility (Melbourne, Australia) for the construction of sequencing-ready libraries.
RNA libraries for whole transcriptome RNA-seq were prepared using the Illumina Stranded Total RNA Library Preparation Kit with Ribo-Zero Plus, by the technical staff at the Australian Genome Research Facility (Melbourne, Australia).


title: Endometrial Cancer_ET20-102 [C10]


title: RiboTag, AAV-shLarp1 (IP) 3

city: Daegu

first: Eunsu

last: Jang

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

institute: DGIST

description: Library name: RiboTag_HA_ip_shLarp1_3

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts
Library strategy: Ribo-Seq

source_name: Cultured adult dorsal root ganglion neurons

extract_protocol:
For RiboTag sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-HA antibody, and the RNA from the immunoprecipitated product was extracted using RNeasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB112.24))

value: Preconditioned


title: RiboTag, AAV-shLarp1 (IP) 1

description: Library name: RiboTag_HA_ip_shLarp1_1

value: Cultured adult dorsal root ganglion neurons


title: RiboTag, AAV-shLarp1 (IP) 2

description: Library name: RiboTag_HA_ip_shLarp1_2


title: Aged mouse brain, cTBS, biol rep 2


title: RBNS, TDP-43, Synthesized construct, 80nM, Li+


title: RiboTag, AAV-Control (IP) 3

description: Library name: RiboTag_HA_ip_control_3


title: RiboTag, AAV-Control (IP) 2

description: Library name: RiboTag_HA_ip_control_2


title: Endometrial Cancer_ET19-115 [C09]

last: Xiao

value: MMRd


title: RBNS, TDP-43, Synthesized construct, 20nM, K+


title: Somatosensory cortex cells, aged mice, cTBS, replicate 3


title: RiboTag, AAV-Control (IP) 1

description: Library name: RiboTag_HA_ip_control_1


title: Endometrial Cancer_ET19-115 [C08]


title: RiboTag, AAV-shLarp1 (Input) 3

description: Library name: RiboTag_Input_shLarp1_3

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts


title: Somatosensory cortex cells, aged mice, sham, replicate 4

value: sham


title: RiboTag, AAV-shLarp1 (Input) 2

description: Library name: RiboTag_Input_shLarp1_2


title: Endometrial Cancer_ET19-109 [C07]


title: RiboTag, AAV-shLarp1 (Input) 1

description: Library name: RiboTag_Input_shLarp1_1


title: Somatosensory cortex cells, aged mice, iTBS, replicate 5

value: iTBS


title: Oxford Nanopore snRNA-Seq of lung cancer cell line mixture

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Genetics and Gene Regulation

institute: The Walter and Eliza Hall Institute of Medical Research

description: Library name: Single_nuclei_ONT

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 model. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Single-nucleus RNA-seq (Illumina) data were processed using Cell Ranger (v8.0.1) with GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome.
Long-read single-nucleus reads were first demultiplexed using BLAZE (v2.5). The resulting FASTQ files were processed using the FLAMES (v2.0.1) single-cell pipeline, configured to use GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome. Further configurations included skipping novel transcript identification, and the use of Oarfish (v0.6.2) for transcript-level quantification.
Supplementary files format and content:
Count matrix prefix:  ill_sn – single-nucleus. Each matrix is stored in the standard three-file format: <prefix>_barcodes.tsv.gz | <prefix>_features.tsv.gz | <prefix>_matrix.mtx.gz
Count matrices from long-read protocols (ont, pb) are structured as follows:
Gene-level counts: genes_count_matrix.tsv.gz
•       Transcript-level counts: stored across three files which is similar to cellranger output:
•       _barcodes.tsv.gz
•       _features.tsv.gz
•       _matrix.mtx.gz

molecule: nuclear RNA

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with GlutaMAX™ (Thermo Fisher Scientific), 10% heat-inactivated fetal bovine serum (FBS; Gibco), and 1% penicillin-streptomycin (Thermo Fisher Scientific). Cultures were incubated at 37°C in a humidified atmosphere containing 5% CO2. Cells were routinely passaged at 70–80% confluency using standard culture procedures.

extract_protocol:
Suspension cell lines (H211, H526, H146, H69, SHP-77) were prepared for fluorescence-activated cell sorting (FACS). Each cell line was collected from culture, washed twice with PBS, and re-suspended in 500 μL FACS buffer (PBS with 2% FBS). Cells were then passed through a 35 μm strainer cap into FACS tubes and were subsequently stained with 7-amino-actinomycin D for live/dead sorting. Cells were sorted on the BD Aria III to collect 250,000 cells per sample. The remaining 3 adherent lines (H1975, H2228, HCC827) were detached using TrypLE Express (Gibco), washed twice with PBS, and resuspended in FACS buffer. Cell counts were performed in triplicate per cell line on the Countess 3 (Thermo Fisher Scientific) to ensure accuracy, and then 270,000 cells per line were combined into a single mixture. Nuclei isolation was performed using a custom protocol based on the Nuclei EZ Prep kit (Sigma-Aldrich). 1.7M Cells were pelleted at 300 x g for 5 minutes at 4°C, then gently resuspended in 300 μL of cold cell lysis buffer (EZ lysis buffer supplemented with 0.2 U/μL RNaseOUT™). Lysis was carried out on ice for 2.5 minutes to release nuclei, followed by centrifugation at 300 x g for 5 minutes at 4°C. The nuclei pellet was resuspended in 500 μL of cold wash buffer(1X PBS, 1% BSA, 0.2 U/μL RNaseOUT™), incubated on ice for 1 minute, then supplimented with a second 500 μL of wash buffer. Nuclei were gently resuspended by pipetting and pelleted at 200 x g for 5 minutes at 4°C. The pellet was resuspended in 200 μL of wash buffer, topped up to 1 mL, and centrifuged at 130 x g for 5 minutes. Nuclei were finally resuspended in 500 μL of wash buffer for quality assessment via DAPI staining and microscopy using Countess 3 system. The suspension was filtered twice using FlowMi 40 μM filter tips (Sigma-Aldrich) to remove any present clumps and re-counted prior to 10X capture. The nuclei mixture was loaded onto the 10X Genomics Chromium following the same protocol as described for single-cell capture, with a target capture of 5,000 nuclei.
From the cDNA generated by the 10X Genomics single-cell 3’ kit (v3.1, 11 cycles of PCR), libraries were prepared for Illumina, nanopore and Pacbio sequencing. Illumina snRNA-seq libraries were prepared with the 10X Library Construction Kit (PN1000190). The nanopore single-nucleus library was prepared from 10 ng of input cDNA, following the ONT single-cell protocol including the artifact removal step (v9198_v114_revE_06Dec2023). 125 ng of the post-pulldown PCR product were taken to adapter ligation with the ONT SQK-LSK114 kit. The final wash was performed with a 0.5X bead ratio (adjusted from 0.4X) and the short fragment buffer. The Pacbio single-nucleus Kinnex library was prepared with the Kinnex single-cell 12-plex concatenation kit according to the manufacturer’s instructions, which also includes an artifact removal step.

tag: cell line

value: Epithelial

value: pooled male and female

tag: disease stage

value: Lung Cancer


title: Endometrial Cancer_ET20-102 [C11]


title: Somatosensory cortex cells, aged mice, iTBS, replicate 4


title: RiboTag, AAV-shControl (Input) 3

description: Library name: RiboTag_Input_control_3


title: Endometrial Cancer_ET19-108 [C05]


title: Endometrial Cancer_ET19-109 [C06]

value: TILs-high


title: Oxford Nanopore scRNA-Seq of lung cancer cell line mixture

description: Library name: Single_cell_ONT

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using the dna_r10.4.1_e8.2_400bps_sup@v5.0.0 model. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Single-cell RNA-seq (Illumina) data were processed using Cell Ranger (v8.0.1) with GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome.
Long-read single-cell reads were first demultiplexed using BLAZE (v2.5). The resulting FASTQ files were processed using the FLAMES (v2.0.1) single-cell pipeline, configured to use GENCODE v44 comprehensive annotations and the GRCh38 primary assembly reference genome. Further configurations included skipping novel transcript identification, and the use of Oarfish (v0.6.2) for transcript-level quantification.
Supplementary files format and content:
Count matrix prefix:  ill_sn – single-nucleus. Each matrix is stored in the standard three-file format: <prefix>_barcodes.tsv.gz | <prefix>_features.tsv.gz | <prefix>_matrix.mtx.gz
Count matrices from long-read protocols (ont, pb) are structured as follows:
Gene-level counts: genes_count_matrix.tsv.gz
•       Transcript-level counts: stored across three files which is similar to cellranger output:
•       _barcodes.tsv.gz
•       _features.tsv.gz
•       _matrix.mtx.gz

extract_protocol:
Suspension cell lines (H211, H526, H146, H69, SHP-77) were prepared for fluorescence-activated cell sorting (FACS). Each cell line was collected from culture, washed twice with PBS, and re-suspended in 500 μL FACS buffer (PBS with 2% FBS). Cells were then passed through a 35 μm strainer cap into FACS tubes and were subsequently stained with 7-amino-actinomycin D for live/dead sorting. Cells were sorted on the BD Aria III to collect 250,000 cells per sample. The remaining 3 adherent lines (H1975, H2228, HCC827) were detached using TrypLE Express (Gibco), washed twice with PBS, and resuspended in FACS buffer. Cell counts were performed in triplicate per cell line on the Countess 3 (Thermo Fisher Scientific) to ensure accuracy, and then 270,000 cells per line were combined into a single mixture. The cell mixture was loaded onto the 10X Genomics Chromium according to the manufacturer’s protocol using the 10X Chromium NEXT GEM single-cell 3’ kit (v3.1) with a target capture of 5,000 cells.
From the cDNA generated by the 10X Genomics single-cell 3’ kit (v3.1, 11 cycles of PCR), libraries were prepared for Illumina, nanopore and Pacbio sequencing. Illumina scRNA-seq libraries were prepared with the 10X Library Construction Kit (PN- 1000190). The nanopore single-cell library was prepared from 10 ng of input cDNA, following the ONT single-cell protocol including the artifact removal step (v9198_v114_revE_06Dec2023). 125 ng of the post-pulldown PCR product were taken to adapter ligation with the ONT SQK-LSK114 kit. The final wash was performed with a 0.5X bead ratio (adjusted from 0.4X) and the short fragment buffer. The Pacbio single-cell Kinnex library was prepared with the Kinnex single-cell 12-plex concatenation kit according to the manufacturer’s instructions, which also includes an artifact removal step.

tag: Sex


title: RiboTag, AAV-shControl (Input) 2

description: Library name: RiboTag_Input_control_2


title: Somatosensory cortex cells, aged mice, iTBS, replicate 3


title: Oxford Nanopore PCR-Barcoding RNA-Seq of lung cancer cell line H211 (SCLC-P)

description: Library name: H211_Bulk_ONT

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using rna004_130bps_sup@v5.1.0 for direct RNA and dna_r10.4.1_e8.2_400bps_sup@v5.0.0 for the cDNA datasets. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Transcript-level quantification was performed using Salmon (v1.10.2) for short-read datasets and Oarfish (v0.6.2) for long-read datasets, based on the GENCODE v44 transcriptome combined with spike-in sequences from SIRV Set 4 and Sequins.
•       Salmon uses an internal quasi-mapping approach.
•       Long-read datasets were first aligned to the transcriptome using minimap2 (v2.28), followed by quantification with Oarfish.
Supplementary files format and content:
Bulk RNA-seq count matrices follow the naming convention: <protocol>_bulk_<cell line>_matrix.tsv
Where <protocol> is one of:
•       dRNA – ONT direct RNA sequencing
•       ont – ONT PCR cDNA sequencing
•       pb – PacBio Kinnex
•       ill – Illumina

extract_protocol:
Total RNA was isolated from 1.5–2 M cells using TRIzol Reagent (Invitrogen) following the manufacturers guidelines.
llumina bulk RNA-Seq libraries we constructed using the Illumina Truseq v2 Stranded kit with polyA selection. Superscript III was used instead of SuperScript II, and the reverse transcription incubation step was accordingly adjusted to 50°C. Nanopore direct-RNA sequencing libraries were constructed using the ONT SQK-RNA004 kit, with the following modifications: input was increased to 2μg total RNA. RNA CS (calibrating strand) was omitted. NEB Induro Reverse Transcriptase was used in place of SuperScript III.
Nanopore direct-RNA sequencing libraries were constructed using the ONT SQK-RNA004 kit, with the following modifications: input was increased to 2μg total RNA. RNA CS (calibrating strand) was omitted. NEB Induro Reverse Transcriptase was used in place of SuperScript III.
Nanopore PCR-cDNA libraries were constructed using the ONT SQK-PCB114.24 kit, with the following modifications: reverse transcription was perormed for 90 minutes at 42°C, followed by 14 cycles of PCR with an extension time of 4 minutes.
Pacbio Bulk Kinnex libraries were prepared with the Iso-Seq express 2.0 kit and Kinnex PCR 8-fold kit

value: Female


title: Endometrial Cancer_ET19-108 [C04]

value: Tumor area


title: Somatosensory cortex cells, aged mice, cTBS, replicate 4


title: Endometrial Cancer_ET19-106 [C03]

value: Endometrial Tumor


title: Wildtype, DRG, Injured (IP) 3

description: Library name: wild-type_LARP1_ip_dx_3

source_name: Dorsal root ganglion(DRG)

extract_protocol:
For LARP1-IP sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-LARP1 antibody, and the RNA from the immunoprecipitated product was extracted using RNeasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB112.24))

value: Dorsal root ganglion(DRG)

value: Wildtype

value: Injury


title: Somatosensory cortex cells, aged mice, sham, replicate 3

value: Brain


title: Oxford Nanopore PCR-Barcoding RNA-Seq of lung cancer cell line SHP77 (SCLC-A)

description: Library name: SHP77_Bulk_ONT

value: Male


title: Somatosensory cortex cells, aged mice, cTBS, replicate 2

value: cTBS


title: RiboTag, AAV-shControl (Input) 1

description: Library name: RiboTag_Input_control_1

value: Cultured adult dorsal root ganglion neurons

value: Preconditioned


title: Endometrial Cancer_ET19-106 [C02]

value: MMRd

value: TILs-low


title: Oxford Nanopore PCR-BarcodingRNA-Seq of lung cancer cell line H69 (SCLC-A)

description: Library name: H69_Bulk_ONT

value: Epithelial


title: Wildtype, DRG, Injured (IP) 1

description: Library name: wild-type_LARP1_ip_dx_1


title: Endometrial Cancer_ET19-105 [B12]


title: Oxford Nanopore PCR-Barcoding RNA-Seq of lung cancer cell line H146 (SCLC-A)

description: Library name: H146_Bulk_ONT


title: Somatosensory cortex cells, aged mice, cTBS, replicate 1


title: Somatosensory cortex cells, aged mice, iTBS, replicate 2

value: iTBS


title: Wildtype, DRG, Injured (IP) 2

description: Library name: wild-type_LARP1_ip_dx_2


title: Wildtype, DRG, Uninjured (IP) 3

description: Library name: wild-type_LARP1_ip_du_3

value: Uninjury


title: Oxford Nanopore PCR-Barcoding RNA-Seq of lung cancer cell line H2228 (LUAD)

description: Library name: H2228_Bulk_ONT

value: Lung Cancer


title: Somatosensory cortex cells, aged mice, sham, replicate 2

value: sham


title: Endometrial Cancer_ET19-105 [C01]

value: Stroma area


title: Endometrial Cancer_ET19-102 [B11]

value: Endometrial Tumor


title: Wildtype, DRG, Uninjured (IP) 2

description: Library name: wild-type_LARP1_ip_du_2

value: Dorsal root ganglion(DRG)


title: Somatosensory cortex cells, aged mice, iTBS, replicate 1


title: Wildtype, DRG, Uninjured (IP) 1

description: Library name: wild-type_LARP1_ip_du_1

value: Wildtype


title: Oxford Nanopore PCR-Barcoding RNA-Seq of lung cancer cell line HCC827 (LUAD)

description: Library name: HCC827_Bulk_ONT

value: Female


title: Oxford Nanopore PCR-Barcoding RNA-Seq of lung cancer cell line H1975 (LUAD)

description: Library name: H1975_Bulk_ONT


title: Somatosensory cortex cells, aged mice, sham, replicate 1

value: Brain


title: Oxford Nanopore PCR-Barcoding RNA-Seq of lung cancer cell line H526 (SCLC-P)

description: Library name: H526_Bulk_ONT

value: Male


title: Endometrial Cancer_ET19-94 [B09]


title: RiboTag, adult DRG neuron, shGpr151 with e5'UTR (IP) 3

description: Library name: RiboTag_IP_shGpr151_with_e5UTR_3

source_name: Adult DRG neuron

value: Adult DRG neuron

value: AAV-shGpr151 and AAV-e5'UTR


title: RGCs from mice treated with AAV2-shLIFR, Sample3

city: Changsha

first: Qian

last: Jiang

state: 湖南省

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

institute: 中南大学湘雅二医院

description:
SHLiFR3
FPKM_allsamples-KO.txt
Raw_gene_counts_matrix-KO.txt

data_processing:
The libraries were sequenced on a llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads, which were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis was performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2. p-value <0.05 and |log2FC| > 1 was set as the threshold for significantly differential expression genes (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. Based on the hypergeometric distribution, GO pathway enrichment analysis of DEGs was performed to screen the significantly enriched term using R (v 3.2.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: retinal ganglion cells

extract_protocol:
The total RNA of each sample was extracted by RNeasy Micro Kit (QIAGEN). The purity and quantification of RNA were assessed with Nanodrop 2000 (Thermo Scientific). The integrity of RNA was evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies). 1ng of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: retinal ganglion cells

value: LIFR knowdown


title: RiboTag, adult DRG neuron, shGpr151 with e5'UTR (IP) 2

description: Library name: RiboTag_IP_shGpr151_with_e5UTR_2


title: Oxford Nanopore direct RNA-Seq of lung cancer cell line H211 (SCLC-P)

description: Library name: H211_dRNA_ONT


title: Endometrial Cancer_ET19-94 [B08]

value: MMRd

value: TILs-high

value: Tumor area


title: RGCs from mice treated with AAV2-shLIFR, Sample2

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
SHLiFR2
FPKM_allsamples-KO.txt
Raw_gene_counts_matrix-KO.txt


title: Oxford Nanopore direct RNA-Seq of lung cancer cell line H526 (SCLC-P)

description: Library name: H526_dRNA_ONT

value: Epithelial


title: Endometrial Cancer_ET19-90 [B07]


title: RiboTag, adult DRG neuron, shGpr151 with e5'UTR (IP) 1

description: Library name: RiboTag_IP_shGpr151_with_e5UTR_1


title: RGCs from mice treated with AAV2-shLIFR, Sample1

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
SHLiFR1
FPKM_allsamples-KO.txt
Raw_gene_counts_matrix-KO.txt


title: Oxford Nanopore direct RNA-Seq of lung cancer cell line SHP77 (SCLC-A)

description: Library name: SHP77_dRNA_ONT

value: Lung Cancer


title: Endometrial Cancer_ET19-90 [B06]

value: TILs-low


title: RGCs from mice treated with AAV2-shScramble, Sample3

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
CTRL-4
FPKM_allsamples-KO.txt
Raw_gene_counts_matrix-KO.txt

value: Ctrl


title: Endometrial Cancer_ET19-88 [B05]

value: Endometrial Tumor

value: Stroma area


title: Oxford Nanopore direct RNA-Seq of lung cancer cell line H69 (SCLC-A)

description: Library name: H69_dRNA_ONT


title: Oxford Nanopore direct RNA-Seq of lung cancer cell line H146 (SCLC-A)

description: Library name: H146_dRNA_ONT


title: RGCs from mice treated with AAV2-shScramble, Sample2

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
CTRL-3
FPKM_allsamples-KO.txt
Raw_gene_counts_matrix-KO.txt


title: Endometrial Cancer_ET19-102 [B10]


title: Endometrial Cancer_ET19-88 [B04]


title: RiboTag, adult DRG neuron, shGpr151 (IP) 1

description: Library name: RiboTag_IP_shGpr151_1


title: RGCs from mice treated with AAV2-shScramble, Sample1

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
CTRL-2
FPKM_allsamples-KO.txt
Raw_gene_counts_matrix-KO.txt


title: RiboTag, adult DRG neuron, shGpr151 with e5'UTR (Input) 3

description: Library name: RiboTag_input_shGpr151_with_e5UTR_3


title: RGCs from mice treated with AAV2-LIFR, Sample3

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
LIFR3
FPKM_allsamples-OE.txt
Raw_gene_counts_matrix-OE.txt

value: LIFR overexpression


title: Oxford Nanopore direct RNA-Seq of lung cancer cell line HCC827 (LUAD)

description: Library name: HCC827_dRNA_ONT

value: Female


title: RGCs from mice treated with AAV2-LIFR, Sample2

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
LIFR2
FPKM_allsamples-OE.txt
Raw_gene_counts_matrix-OE.txt


title: RiboTag, adult DRG neuron, shGpr151 with e5'UTR (Input) 1

description: Library name: RiboTag_input_shGpr151_with_e5UTR_1


title: RGCs from mice treated with AAV2-LIFR, Sample1

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
LIFR1
FPKM_allsamples-OE.txt
Raw_gene_counts_matrix-OE.txt


title: Endometrial Cancer_ET19-76 [B01]


title: BITC_RES3

city: Dalian

first: Jianan

last: Liu

state: Liaoning

address: NO.1 Light-Industry Garden, Ganjingzi Borough

institute: Dalian Polytechnic University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: ncbi_staphylococcus_aureus_gcf_000013425_1_asm1342v1
Supplementary files format and content: gene_fpkm_group.txt

organism: Staphylococcus aureus

source_name: bacterial cell

extract_protocol: Staphylococcus aureus RNA was extracted using the RNAprep Pure Cell/Bacteria Kit.

value: bacterial cell


title: RGCs from mice treated with AAV2-Ctrl, Sample3

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
ctrl3
FPKM_allsamples-OE.txt
Raw_gene_counts_matrix-OE.txt


title: RiboTag, adult DRG neuron, shGpr151 (IP) 2

description: Library name: RiboTag_IP_shGpr151_2


title: RiboTag, adult DRG neuron, shGpr151 (Input) 2

description: Library name: RiboTag_input_shGpr151_2


title: RGCs from mice treated with AAV2-Ctrl, Sample2

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
ctrl2
FPKM_allsamples-OE.txt
Raw_gene_counts_matrix-OE.txt


title: BITC_RES1


title: RiboTag, adult DRG neuron, shGpr151 (Input) 1

description: Library name: RiboTag_input_shGpr151_1


title: Endometrial Cancer_ET19-69 [A10]


title: Endometrial Cancer_ET19-67 [A09]


title: RES3

value: RES


title: Endometrial Cancer_ET19-86 [B03]


title: RiboTag, adult DRG neuron, shGpr151 (IP) 3

description: Library name: RiboTag_IP_shGpr151_3

value: Adult DRG neuron


title: RGCs from mice treated with AAV2-Ctrl, Sample1

address: 湖南省长沙市芙蓉区解放中路有色院小区研究生宿舍

description:
ctrl1
FPKM_allsamples-OE.txt
Raw_gene_counts_matrix-OE.txt


description: Library name: RiboTag_HA_ip_shGpr151_3


title: Single-cell RNA sequencing of Lgr5+ clonally cultured organoids (clone 7)

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

data_processing:
Cellranger count v6.1.1
Assembly: mm10
Supplementary files format and content: 10X count matrices

source_name: Lgr5+ clonally cultured organoids of mouse taste buds (clone 7)

extract_protocol:
10X RNA sequencing
GEX 3'

value: Tongue

value: Taste bud organoids

value: Various

value: WT


title: Endometrial Cancer_ET19-67 [A08]

value: MMRd

value: TILs-high


title: RES2


title: RiboTag, adult DRG neuron, shGpr151 with e5'UTR (Input) 2

description: Library name: RiboTag_input_shGpr151_with_e5UTR_2

value: AAV-shGpr151 and AAV-e5'UTR


title: RiboTag, adult DRG neuron, shGpr151 (Input) 3

description: Library name: RiboTag_input_shGpr151_3


title: Endometrial Cancer_ET19-76 [A12]

value: Tumor area


title: Endometrial Cancer_ET19-65 [A07]


title: RiboTag, adult DRG neuron, shGpr151 (IP) 1

description: Library name: RiboTag_HA_ip_shGpr151_1


title: BITC_RES2


title: Endometrial Cancer_ET19-69 [A11]


title: Single-cell RNA sequencing of Lgr5+ clonally cultured organoids (clone 3)

source_name: Lgr5+ clonally cultured organoids of mouse taste buds (clone 3)


title: RES1


title: BITC3

value: BITC


title: Endometrial Cancer_ET19-65 [A06]


title: Single-cell RNA sequencing of Lgr5+ clonally cultured organoids (clone 1)

source_name: Lgr5+ clonally cultured organoids of mouse taste buds (clone 1)


title: BITC2


title: Endometrial Cancer_ET19-55 [A05]


title: BITC1


title: Endometrial Cancer_ET19-55 [A04]


title: RiboTag, adult DRG neuron, control (IP) 2

description: Library name: RiboTag_HA_ip_control_2

value: AAV-control


title: Single-cell RNA sequencing of foliate papillae (n=40)

source_name: 40 resected foliate papillae from mouse tongues


title: RiboTag, adult DRG neuron, control (IP) 3

description: Library name: RiboTag_HA_ip_control_3


title: Single-cell RNA sequencing of circumvallate papillae (n=20)

source_name: 20 resected circumvallate papillae from mouse tongues


description: Library name: RiboTag_HA_ip_shGpr151_2


title: Endometrial Cancer_ET19-54 [A03]

value: Endometrial Tumor


title: LJN3

value: LJN


title: LJN2


title: control (flox/flox) fed MASH diet  for 30 weeks , three liver samples pooled

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Life Sciences Institute

institute: University of Michigan

description: wt

data_processing:
FastQC was used to asses the sequencing qualtiy on fastq files; STAR was used for alignment to generate bam files; The reads aligned to each gene feature were counted by the RSEM package (version 1.3.3) ; DESeq2 pacakge was used for differential gene expression analysis
snRNA-seq fastq files were processed by CellRanger to generate aligned matrix data that were further analyzed using Seurat package (version 4.0.1).
Assembly: mm10
Supplementary files format and content: DEseq2 normalized reads counts for bulk RNA-seq data
Supplementary files format and content: average UMI counts for snRNA-seq data

source_name: Liver

extract_protocol:
Nuclei were isolated from frozen liver tissues using salt-Tris based protocol. Isolated nuclei were stained with propidium iodide before FACS sorting. Sorted nuclei were processed for snRNA sequencing. Total liver RNA was extracted from frozen tissues using RNA extract kit (Invitrogen, Cat: 12183025)
Bulk RNA libraries were prepared using high-throughput sequenicng set following the user manual; snRNA libraries were prepared using standard Illumina and 10X genomics Chromium single cell guide

value: Liver

value: control (flox/flox)

value: MASH diet  for 30 weeks


title: Endometrial Cancer_ET19-54 [A02]

value: TILs-low


description: Library name: RiboTag_Input_shGpr151_2

value: Adult DRG neuron


title: LJN1

value: bacterial cell


title: Tgfbr1 MKO (flox/flox; LysMcre) fed MASH diet  for 30 weeks, rep3

value: Tgfbr1 MKO (flox/flox; LysMcre)


description: Library name: RiboTag_Input_shGpr151_1


title: CD4+t CELLS, RA (ATPLOW)-4,CSA

city: Rochester

first: Yanyan

last: Zheng

state: Minnesota

address: 839 16th ST SW, Apt421

institute: Mayo Clinic

data_processing:
The procedure of raw reads filtering is as follows: (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
CLC genomics workbench v11.0.1
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). D
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: pbmc

extract_protocol:
rna was harvested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: pbmc

value: cd3+cd28+ stimulated cd4+t

tag: disease

value: RA (ATPlow)

value: ra

value: csa


title: Tgfbr1 MKO (flox/flox; LysMcre) fed MASH diet  for 30 weeks, rep2


title: WT_6h_r4

city: Rehovot

first: Xun

last: Liang

address: Herzl 234

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description: Library name: WT4_3h_TWEAK

data_processing:
Raw next-generation sequencing (NGS) data in the FASTQ format were analyzed using user-friendly transcriptome analysis pipeline (UTAP).
Briefly, reads were trimmed using “cutadapt” and mapped to the mouse reference genome (GRCm38/mm10) according to Gencode annotated genes using  STAR v2.7.10a .
UMI counting was done using HTSeq-count after marking duplicates in union mode. Differential gene expression analysis and normalization of the counts was performed using DESeq2 using the rld (log2 normalized) gene expression values
Assembly: mm10
Supplementary files format and content: Tab-delimited file includes raw counts for each sample
Supplementary files format and content: Tab-delimited file include processed counts for each sample

source_name: Skin

growth_protocol: Primary mouse dermal fibroblasts (MDF) were cultured in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 degree.

extract_protocol:
The RNA samples were prepared by  using either the RNeasy Mini Kit (QIAGEN) or the NucleoSpin RNA Mini Kit (MACHEREY-NAGEL). 50ng of total RNA was used for preparing sequencing library.
RNA libraries for RNA seq were prepared using a bulk version of the MARS-Seq procedure. Briefly, 50 ng of total RNA from each sample was barcoded during reverse transcription (RT) and then pooled. After cleanup with Agencourt AMPure XP beads (Beckman Coulter), the pooled samples underwent second-strand synthesis and were linearly amplified by T7 in-vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by adding Illumina sequences during ligation, RT, and PCR. Libraries were quantified using Qubit and TapeStation, as well as by qPCR for the ACTB gene.

treatment_protocol: 5th passage Primary MDF were treated or not with 100ng/ml TWEAK for 6 and 24 hours before collecting cell lysates

value: Skin

value: Primary cells

value: Dermal fibroblast

value: Wild-type

value: 100ng/ml TWEAK for 6 hours


title: RiboTag, adult DRG neuron, control (Input) 3

description: Library name: RiboTag_Input_control_3

value: AAV-control


title: Tgfbr1 MKO (flox/flox; LysMcre) fed MASH diet  for 30 weeks, rep1

value: Liver


title: RiboTag, adult DRG neuron, control (IP) 1

description: Library name: RiboTag_HA_ip_control_1


title: CD4+t CELLS, RA (ATPLOW)-2,CSA


title: control (flox/flox) fed MASH diet  for 30 weeks, rep3

value: control (flox/flox)

value: MASH diet  for 30 weeks


title: Tgfbr1 MKO (flox/flox; LysMcre) fed MASH diet  for 30 weeks,  three liver samples pooled

description: ko


title: CD4+t CELLS, RA (ATPLOW)-1,CSA


title: RiboTag, adult DRG neuron, control (Input) 1

description: Library name: RiboTag_Input_control_1

value: Adult DRG neuron


title: RiboTag, adult DRG neuron, control (Input) 2

description: Library name: RiboTag_Input_control_2


title: WT_6h_r3

description: Library name: WT3_3h_TWEAK


title: control (flox/flox) fed MASH diet  for 30 weeks, rep2


title: RiboTag, adult DRG neuron, shGpr151 (Input) 3

description: Library name: RiboTag_Input_shGpr151_3


title: e5'UTR, primary DRG neuron, Injured (CSDE1-IP) 3

description: Library name: eDRG_CSDE1_ip_e5UTR_3

source_name: Primary DRG neuron

extract_protocol:
For CSDE1-IP sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-CSDE1 antibody, and the RNA from the immunoprecipitated product was extracted using RNeasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB112.24))

value: Primary DRG neuron

value: Wild type


title: CD4+t CELLS, RA (ATPLOW)-3,CSA

value: pbmc


title: WT_24h_r3

description: Library name: WT3_24h_TWEAK

value: 100ng/ml TWEAK for 24 hours


title: CD4+t CELLS, RA (ATPint)-3,FMET

value: cd3+cd28+ stimulated cd4+t

value: RA (ATPint)

value: fmet


title: e5'UTR, primary DRG neuron, Injured (CSDE1-IP) 2

description: Library name: eDRG_CSDE1_ip_e5UTR_2


title: CD4+t CELLS, RA (ATPint)-2,FMET

value: ra


title: Itga5-Low_DM3

city: Bethesda

first: Youngjae

last: Bahn

state: Maryland

address: 10 Center Dr.

institute: NIH

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
Single-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene. RPKM of each gene was calculated based on the length of the gene and the reads count mapped to that gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include transcript counts for each gene

source_name: Primary preadipocytes

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA was further  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Primary preadipocytes

value: WT

value: Adipogenic differentiation


title: Itga5-Low_DM2


title: WT_6h_r2

description: Library name: WT2_3h_TWEAK

value: Skin

value: Primary cells

value: Dermal fibroblast

value: Wild-type

value: 100ng/ml TWEAK for 6 hours


title: CD4+t CELLS, RA (ATPint)-1,FMET


title: e5'UTR, primary DRG neuron, Injured (CSDE1-IP) 1

description: Library name: eDRG_CSDE1_ip_e5UTR_1


title: control (flox/flox) fed MASH diet  for 30 weeks, rep1

value: Liver

value: control (flox/flox)

value: MASH diet  for 30 weeks


title: WT_0h_r3

description: Library name: WT3_0h_TWEAK

value: Non-treated


title: Itga5-Low_DM1


title: WT_24h_r2

description: Library name: WT2_24h_TWEAK

value: 100ng/ml TWEAK for 24 hours


title: CD4+t CELLS, RA (ATPint)-4,CONTROL

description: H

value: pbmc

value: cd3+cd28+ stimulated cd4+t

value: vehicle


title: control, primary DRG neuron, Uninjured (CSDE1-IP) 2

description: Library name: eDRG_CSDE1_ip_control_2

value: Primary DRG neuron

value: Wild type

value: LV-control


title: CD4+t CELLS, RA (ATPint)-4,FMET

value: RA (ATPint)

value: ra

value: fmet


title: WT_0h_r2

description: Library name: WT2_0h_TWEAK

value: Skin

value: Primary cells

value: Dermal fibroblast


title: CD4+t CELLS, RA (ATPint)-3,CONTROL

description: G


title: control, primary DRG neuron, Uninjured (CSDE1-IP) 1

description: Library name: eDRG_CSDE1_ip_control_1


title: WT_6h_r1

description: Library name: WT1_3h_TWEAK

value: Wild-type

value: 100ng/ml TWEAK for 6 hours


title: Itga5-High_DM_2

value: Primary preadipocytes

value: WT

value: Adipogenic differentiation


title: CD4+t CELLS, RA (ATPint)-2,CONTROL

description: F

value: pbmc


title: Itga5-High_DM_1


title: e5'UTR, primary DRG neuron, Injured (Input) 3

description: Library name: eDRG_input_e5UTR_3


title: CD4+t CELLS, RA (ATPint)-1,CONTROL

description: E

value: cd3+cd28+ stimulated cd4+t


title: WT_24h_r1

description: Library name: WT1_24h_TWEAK

value: 100ng/ml TWEAK for 24 hours


title: HFD_mock_3

value: Mock

value: High Fat Diet


title: WT_0h_r1

description: Library name: WT1_0h_TWEAK

value: Non-treated


title: HFD_mock_2


title: e5'UTR, primary DRG neuron, Injured (Input) 1

description: Library name: eDRG_input_e5UTR_1

value: Primary DRG neuron

value: Wild type


title: control, primary DRG neuron, Uninjured (Input) 3

description: Library name: eDRG_input_control_3

value: LV-control


title: CD4+t CELLS, RA (ATPLOW)-3,CONTROL

description: C

value: RA (ATPlow)

value: ra

value: vehicle


title: control, primary DRG neuron, Uninjured (CSDE1-IP) 3

description: Library name: eDRG_CSDE1_ip_control_3


title: control, primary DRG neuron, Uninjured (Input) 2

description: Library name: eDRG_input_control_2


title: CD4+t CELLS, RA (ATPLOW)-2,CONTROL

description: B


title: CD4+t CELLS, RA (ATPLOW)-4,CONTROL

description: D


title: MUT_24h_r2

description: Library name: TAD2_24h_TWEAK

value: Skin

value: Primary cells

value: Dermal fibroblast

value: NIK X mut


title: control, primary DRG neuron, Uninjured (Input) 1

description: Library name: eDRG_input_control_1


title: CD_TGF-b/SB431542_2

value: Primary preadipocytes

value: WT

value: Control Diet


title: MUT_0h_r2

description: Library name: TAD2_0h_TWEAK


title: MUT_6h_r1

description: Library name: TAD1_3h_TWEAK

value: 100ng/ml TWEAK for 6 hours


title: shGpr151, DRG, Injured (IP) 3

description: Library name: shGpr151_CSDE1_ip_dx_3

value: Dorsal root ganglion(DRG)

value: AAV-shGpr151, Injury