title: N19-0411

description: N19-0411_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: steroid/anti-epileptic

value: Mixed

value: Female


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-172]

status: Public on Feb 16 2024

type: SRA

city: Lyon

first: Anne-Pierre

last: Morel

state: Rhone-Alpes

address: 28, rue Laennec, Cheney D 2nd floor

country: France

institute: Cancer Research Center of Lyon

library_source: transcriptomic

data_processing:
Raw reads were aligned on the human genome with STAR.
Gene expression was quantified with STAR gene count, following the annotations of gencode v29.
Samples with less than 50000 reads were excluded.
Assembly: GRCh38
Supplementary files format and content: STAR gene count

molecule: total RNA

organism: Homo sapiens

source_name: HME-RASi

extract_protocol:
Briefly, freshly harvested single cells were sorted into 96-well plates containing the lysis buffer (0.2% Triton X-100, 1U/  l RNase inhibitor, Thermo Fisher Scientific). RT was performed using SuperScript II (Thermo Fisher Scientific) in the presence of 1   M oligo-dT30VN (IDT), 1   M Template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Full-length scRNAseq libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) with minor modifications. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Roche) and IS PCR primer (IDT), with 23 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end reads of 75 bp length (PE75) with library indexes corresponding to cell barcodes.

tag: cell line

value: HME-RASi

tag: cell type

value: mammary epithelial cells RAS inductible

tag: sequencing plate

tag: nbcells

tag: time


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-184]


title: S43-P018-I-120m

city: Melbourne

first: Rochelle

last: Davis

state: VIC

address: 264 Ferntree Gully Rd, Notting Hill

country: Australia

institute: Monash University

data_processing:
fastq files were processed by Cutadapt (V1.9.1) to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and bases of a quality lower than 20.
Filtered data were aligned to the reference genome, GRCh37, using Hisat2(v2.0.1)
Assembly: GRCh37
Supplementary files format and content: Count table includes raw read counts and FPKM values for each Sample

molecule: polyA RNA

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA was isolated from PBMC samples using the RNeasy Plus Mini Kit (QIAGEN GmbH, Hilden, Germany) and eluted in 60µL RNase-Free water
1μg total RNA was used for library preparation. Poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module. The mRNA fragmentation and priming were performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, before PCR amplification and validation of PCR products by Qsep100 (Bioptic, Taiwan, China) and quantification by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA)

tag: tissue

value: Peripheral Blood Mononuclear Cells

tag: condition

value: abdominal obesity

tag: subject id

tag: treatment

value: Intervention

tag: timepoint

value: 120 minutes


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-160]


title: N18-0648

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

description: N18-0648_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

data_processing:
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment and FeatureCount for expression count.The reads were aligned to CanFam3  reference genome and mapping to the canine transcriptome  annotations. We then normalized the RNA-seq read counts for genes, applied a variance stabilizing transformation, and identified differentially expressed genes using the DESeq2 package. Differential gene expression determined by a false discovery rate cutoff of 0.05.
Assembly: canFam3
Supplementary files format and content: raw expression count matrix

organism: Canis lupus familiaris

source_name: Meningioma

extract_protocol:
Tissue samples from canines with spontaneous meningioma were acquired as surgical biopsies or from immediate post-mortem necropsies and archived as formalin-fixed, paraffin-embedded (FFPE) samples at Texas A&M University between 2011 and 2022. Following histopathological diagnosis, 5-10 25um thickness scrolls were collected from each meningioma for RNA sequencing. Scrolls were deparaffinized with xylene at room temperature, re-hydrated with an ethanol series, and subject to total RNA extraction using TRIzol reagent (Thermofisher, manufacturer’s instructions). RNA quantity and quality was evaluated on a TapeStation and all samples with a concentration of 10 ng/µl between 200-1,000nts were used for library preparation (n=62). Illumina library preparation was performed to manufacturer’s specification and 150 nt paired-end sequencing was performed.
RNA libraries were prepared for sequencing using standard Illumina protocols.Paired-end RNA sequencing was performed.

tag: library name

tag: survival

tag: breed

value: English Mastiff

tag: Sex

value: Male

value: Neutered


title: S39-P015-C-0m

value: Control

value: 0 minutes (fasting)


title: BAT_i75_HFD_Control

city: Tokyo

first: Motoharu

last: Awazawa

address: 1-21-1 Toyama, Shinjuku

country: Japan

institute: National Institute for Global Health and Medicine

data_processing:
QC and adopter trimming were done by fastq.Raw sequencing reads were aligned to mouse reference genome(GRCm39) by STAR, and gene-level read counts were calculated by RSEM.
The raw read counts were normalized with transcripts per million (TPM).
Assembly: GRCm39
Supplementary files format and content: xlsx

organism: Mus musculus

source_name: BAT

extract_protocol:
RNA extrantion by FavorPrep Tissue Total RNA Mini Kit
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module for PolyA selection and NEB NEXT Directional Ultra RNA Library Prep Kit for Illumina for strand specific library follwing manufacturer's protocols.

value: BAT

tag: genotype

value: HFD


title: S45-P018-C-0m


title: N20-0001

description: N20-0001_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Dachshund


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-148]


title: BAT_i76_HFD_Control


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-124]


title: PVA sponge, WT

city: La Jolla

first: Brian

last: Eliceiri

state: CA

address: 9500 Gilman Drive MC 8236

department: Surgery

institute: University of California San Diego Health

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were all performed using Cell Ranger pipelines Cell Ranger Count v7.0.0 and Cell Ranger Aggr v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Each H5 file contains the scRNA-seq raw feature count matrix outputted from running Cell Ranger Count (v7.0.0) on the respective sample of single cells. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

source_name: wound fluid

growth_protocol: Collect pellets after havesting cells from implant PVA sponges in dermal layers

extract_protocol:
Centrifugation
Library was constructed following the manufacturer's instructions.
scRNA-sequencing of cells from sponge implants of homozygous null vs. wild types of the Jackson 000697 strain

value: wound fluid

value: Wildtype


title: S40-P015-C-120m


title: S38-P015-I-240m

value: 240 minutes


title: PVA sponge - KO3 - miRNA

description: Within the processed data file (Table5_All_Expressed_miRNA.xlsx), the column labeled KO3(raw) contains the raw expression values of the corresponding miRNAs (rows) present in this sample. The column labeled KO3(norm) contains the normalized expression values of the corresponding miRNAs (rows) present in this sample.

data_processing:
To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. References: MARTIN, Marcel. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, [S.l.], v. 17, n. 1, p. pp. 10-12, may 2011. ISSN 2226-6089. Thompson O, von Meyenn F, Hewitt Z, Alexander J, Wood A, Weightman R, Gregory S, Krueger F, Andrews S, Barbaric I, Gokhale PJ, Moore HD, Reik W, Milo M, Nik-Zainal S, Yusa K, Andrews PW. Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions. Nat Commun.2020 Mar 23;11(1):1528. doi: 10.1038/s41467-020-15271-3(FastQC)
Reads were aligned to the mm10 mus musculus reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions. References: Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019). Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015. Pertea M, Kim D, Pertea G, Leek JT and Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 2016.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value. References: Pertea M, Kim D, Pertea G, Leek JT and Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 2016. Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M Transcriptome assembly from long-read RNA-seq alignments with StringTie2, Genome Biology 20, 278 (2019), doi:10.1186/s13059-019-1910-1. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015, doi:10.1038/nbt.3122. 3.4 Differentially expressed genes (DEGs) Analysis
Assembly: mm10
Supplementary files format and content: The processed data file (Table5_All_Expressed_miRNA.xlsx) contains the raw and normalized expression counts of the miRNAs that were present in the samples listed. The miRNA expression data for all samples can be found in the same processed file (Table5_All_Expressed_miRNA.xlsx). Please refer to the "descriptions" that were written for each sample above, as they describe which columns (containing raw or normalized expression values) of the processed data file (Table5_All_Expressed_miRNA.xlsx) correspond to which sample. Each expression value in a given row/column corresponds to the miRNA/sample that is indicated on the left/top side of the table in the same row/column. Please note that there are 2 columns worth of expression values for each sample: 1 column contains raw expression values (indicated at the top of the column by [...](raw); 1 column contains the normalized expression values (indicated at the top of the column by [...](norm).

growth_protocol: Collect supernatant after havesting cells from implant PVA sponges in dermal layers

extract_protocol:
Size exclusion Chromatography
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94°C 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScriptTM II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95°C for 3 min; 8 cycles of denaturation at 98°C for 15 sec, annealing at 60°C for 15 sec, and extension at 72°C for 30 sec; and then final extension at 72°C for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.
miRNA sequencing of extracellular vesicles isolated from sponge implants of homozygous null vs. wild types of the Jackson 000697 strain

value: Lept KO mice


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-112]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: N18-0609

description: N18-0609_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Labrador Retriever

value: Female


title: N18-0560

description: N18-0560_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: steroid

value: Shih Tzu


title: PVA sponge - KO2 - miRNA

description: Within the processed data file (Table5_All_Expressed_miRNA.xlsx), the column labeled KO2(raw) contains the raw expression values of the corresponding miRNAs (rows) present in this sample. The column labeled KO2(norm) contains the normalized expression values of the corresponding miRNAs (rows) present in this sample.


title: S37-P015-I-120m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: Intervention

value: 120 minutes


title: N18-0399

description: N18-0399_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Miniature Schnauzer

value: Neutered


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-100]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-183]


title: PVA sponge, db/db

description: 10x Genomics

value: Lept KO mice (db/db)


title: PVA sponge - KO1 - miRNA

description: Within the processed data file (Table5_All_Expressed_miRNA.xlsx), the column labeled KO1(raw) contains the raw expression values of the corresponding miRNAs (rows) present in this sample. The column labeled KO1(norm) contains the normalized expression values of the corresponding miRNAs (rows) present in this sample.

value: wound fluid


title: S36-P015-I-0m

value: 0 minutes (fasting)


title: N18-0613

description: N18-0613_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Standard Poodle

value: Male


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-136]

value: HME-RASi


title: N18-0338

description: N18-0338_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: RT

value: Cane Corso Mastiff


title: N18-0352

description: N18-0352_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Boxer

value: Female


title: S33-P012-C-0m

value: Control


title: PVA sponge - WT3 - miRNA

description: Within the processed data file (Table5_All_Expressed_miRNA.xlsx), the column labeled WT3(raw) contains the raw expression values of the corresponding miRNAs (rows) present in this sample. The column labeled WT3(norm) contains the normalized expression values of the corresponding miRNAs (rows) present in this sample.

value: Wild type


title: PVA sponge - WT1 - miRNA

description: Within the processed data file (Table5_All_Expressed_miRNA.xlsx), the column labeled WT1(raw) contains the raw expression values of the corresponding miRNAs (rows) present in this sample. The column labeled WT1(norm) contains the normalized expression values of the corresponding miRNAs (rows) present in this sample.


title: N18-0313

description: N18-0313_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: anti-epileptic

value: Dachshund


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-147]

value: mammary epithelial cells RAS inductible


title: S32-P012-I-240m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: Intervention

value: 240 minutes


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-171]


title: S34-P012-C-120m

value: 120 minutes


title: PVA sponge - WT2 - miRNA

description: Within the processed data file (Table5_All_Expressed_miRNA.xlsx), the column labeled WT2(raw) contains the raw expression values of the corresponding miRNAs (rows) present in this sample. The column labeled WT2(norm) contains the normalized expression values of the corresponding miRNAs (rows) present in this sample.

value: wound fluid


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-123]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-159]


title: S31-P012-I-120m


title: N18-0225

description: N18-0225_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Miniature Schnauzer

value: Male

value: Intact


title: S30-P012-I-0m

value: 0 minutes (fasting)


title: Tumor-bearing Gprc5a-/-  lung tissue 2 [ST-b4]

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Raw scRNA-seq data were pre-processed (demultiplex cellular barcodes, read alignment, and generation of gene count matrix) using Cell Ranger Single Cell Software Suite (version 3.0.1) provided by 10X Genomics. For read alignment of human and mouse scRNA-seq data, the human reference GRCh38 (hg38) and mouse reference GRCm38 (mm10) genomes were used, respectively. Detailed quality control (QC) metrics were generated and evaluated, and cells were carefully and rigorously filtered to obtain high-quality data for downstream analyses. Briefly, for basic quality filtering, cells with low complexity libraries (in which detected transcripts are aligned to < 200 genes such as cell debris, empty drops, and low-quality cells) were filtered out and excluded from subsequent analyses. Likely dying or apoptotic cells where > 15% of transcripts derived from the mitochondrial genome were also excluded.  For scRNA-seq data of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mice, we further removed potential droplets/dead cells with nFeature smaller than or equal to 500 and mitochondrial gene fraction larger than or equal to 15% using Seurat.
For scRNA-seq data, likely doublets or multiplets were identified and carefully removed through a multi-step approach. Briefly, doublets or multiplets were identified based on library complexity, whereby cells with high-complexity libraries in which detected transcripts are aligned to > 6,500 genes were removed, and also, based on cluster distribution and marker gene expression, whereby doublets or multiplets forming distinct clusters with hybrid expression features and/or exhibiting an aberrantly high gene count were also removed. Expression levels and proportions of canonical lineage-related marker genes in each identified cluster were carefully reviewed. Clusters co-expressing discrepant lineage markers were identified and removed. Doublets or multiplets were also identified using the doublet detection algorithm DoubletFinder. The proportion of expected doublets was estimated based on cell counts obtained prior to scRNA-seq library construction. Data normalization was then performed using Seurat on the filtered gene-cell matrix. Statistical assessment of possible batch effects was performed on non-malignant epithelial cells using the R package k-BET48 as described in our previous studies and Harmony was run with default parameters to remove batch effects present in the PCA space.  For ST profiling data, demultiplexed clean reads were aligned against the GRCm38 (mm10) mouse reference genomes by Spaceranger (version 2.0.0 for mouse ST data) with the Visium transcriptome probe set (mouse data probeset v1.0) and default parameter settings. Generated ST gene expression count matrices were then analyzed using Seurat v4.1.0 to perform unsupervised clustering analysis.
Assembly: mm10
Supplementary files format and content: Comma-separated values and matrix files

source_name: Lung

extract_protocol:
Murine lung single cells were  stained with a cocktail of antibodies (1:250 each) against CD45-PE/Cy7 (103114, BioLegend), Icam2-A647 (A15452, Life Technologies), Epcam-BV421 (118225, BioLegend), and Ecad-A488 (53-3249-80, eBioscience). Stained cells were then washed, filtered using 40 μm filters, stained with SYTOX Blue and processed on a FACS Aria I instrument. Doublets and dead cells were eliminated, and viable (SYTOX-negative) epithelial singlets were collected in PBS containing 2% FBS. Cells were washed again to eliminate ambient RNA, and a sample was taken for counting by Trypan Blue exclusion before loading on 10XGenomics Chromium microfluidic chips. Spatial transcriptomic (ST) profiling of FFPE tissues of three Gprc5a-/- mouse samples was performed using the Visium platform from 10X Genomics according to manufacturer’s recommendations and as previously reported by our group.
Up to 10,000 cells per sample were partitioned into nanoliter-scale Gel beads-in-emulsion (GEMs) using Chromium Next GEM Single Cell 5' Gel Bead Kit v1.1 (1000169, 10XGenomics, ) and by loading onto Chromium Next GEM Chips G (1000127, 10XGenomics, Pleasanton, CA). GEMs were then recovered to construct single-cell gene expression libraries using the Chromium Next GEM Single Cell 5’ Library kit (1000166, 10XGenomics) according to the manufacturer’s protocol. Briefly, recovered barcoded GEMs were broken and pooled, followed by magnetic bead clean-up (Dynabeads MyOne Silane, 37002D, Thermo Fisher Scientific). 10X-barcoded full-length cDNA was then amplified by PCR and analyzed using Bioanalyzer High Sensitivity DNA kit (5067-4626, Agilent). Up to 50 ng of cDNA was carried over to construct gene expression libraries and was enzymatically fragmented and size-selected to optimize the cDNA amplicon size prior to 5’ gene expression library construction. Further, samples were subject to end-repair, A-tailing, adaptor ligation, and sample index PCR using Single Index Kit T Set A (2000240, 10XGenomics) to generate Illumina-ready barcoded gene expression libraries. Library quality and yield was measured using Bioanalyzer High Sensitivity DNA (5067-4626, Agilent) and Qubit dsDNA High Sensitivity Assay (Q32854, Thermo Fisher Scientific) kits. Indexed libraries were normalized by adjusting for the ratio of the targeted cells per library as well as individual library concentration and then pooled to a final concentration of 10 nM. Library pools were then denatured and diluted as recommended for sequencing on the Illumina NovaSeq 6000 platform. For ST profiling, regions of interest per tissue/sample, each comprising a 6.5 x 6.5 mm capture area, were selected based on careful annotation of Hematoxylin and Eosin (H&E)-stained slides that were digitally acquired using the Aperio ScanScope Turbo slide scanner (Leica Microsystems Inc., Buffalo Grove, IL). HALO software (Indica Labs, Albuquerque, NM) was used for pathological annotation (tumour areas, blood vessels, bronchioles, lymphoid cell aggregates, macrophages, muscle tissue, normal parenchyma, and reactive pneumocytes) of H&E histology images. Spot-level histopathological annotation visualization was generated using loupe browser (v6.3.0). Briefly, cloupe file generated from Spaceranger was loaded into loupe browser along with the annotation table file , the annotation visualization was then generated in svg format using the export plot tool. Spatial transcriptomic RNA-seq libraries were generated according to manufacturer’s instructions, each with up to ~3,600 uniquely barcoded spots. Libraries were sequenced on Illumina NovaSeq 6000 platform to achieve a depth of at least 50,000 mean read pairs/spot and at least 2,000 median genes/spot
For scRNA-seq analysis of lung tissues from Gprc5a-/- mice, lung single cells were stained with a cocktail of antibodies (1:250 each) against CD45-PE/Cy7 (103114, BioLegend), Icam2-A647 (A15452, Life Technologies), Epcam-BV421 (118225, BioLegend), and Ecad-A488 (53-3249-80, eBioscience) to sort out epithelial and non-epithelial cells. Stained cells were then washed, filtered using 40 μm filters, stained with SYTOX Blue and processed on a FACS Aria I instrument. Doublets and dead cells were eliminated, and viable (SYTOX-negative) epithelial singlets were collected in PBS containing 2% FBS. Cells were washed again to eliminate ambient RNA, and a sample was taken for counting by Trypan Blue exclusion before loading on 10X Genomics Chromium microfluidic chips. Cells from Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mice were processed similarly except for sorting by GFP. Spatial transcriptomic (ST) profiling of FFPE tissues was performed using the Visium platform from 10X Genomics according to manufacturer’s recommendations.

value: Formalin-fixed paraffin embedded mouse lung tissue

value: Lung

tag: age

value: 11 months


title: Tumor-bearing Gprc5a-/-  lung tissue 3 [ST-c4]


title: N18-0136

description: N18-0136_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: steroid/anti-epileptic

value: Siberian Husky

value: Female

value: Neutered


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-111]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: S29-P016-C-240m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: Control


title: N18-0034

description: N18-0034_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Boxer


title: S35-P012-C-240m

value: 240 minutes


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-99]


title: Tumor-bearing Gprc5a-/-  lung tissue 1 [ST-a4]


title: GFP- cells from lungs of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mouse 4 at 3 months post-saline [8-SGGplussaline-GfpNeg]

value: GFP- sorted mouse lung cells

value: Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+

value: 7 months


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-182]


title: S28-P016-C-120m

value: 120 minutes


title: S26-P016-I-240m

value: Intervention


title: N17-0998

description: N17-0998_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Labrador Retriever

value: Male


title: GFP+ cells from lungs of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mouse 3 at 3 months post-saline [5-SGGplussaline-GfpPos]

value: GFP+ sorted mouse lung cells

value: Lung


title: N16-0990

description: N16-0990_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Australian Shepherd

value: Female

value: Neutered


title: N17-0960

description: N17-0960_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Dachshund


title: GFP- cells from lungs of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mouse 3 at 3 months post-saline [7-SGGplussaline-GfpNeg]


title: N18-0206

description: N18-0206_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam


title: S25-P016-I-120m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity


title: GFP+ cells from lungs of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mouse 4 at 3 months post-saline [6-SGGplussaline-GfpPos]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-158]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: N16-0629

description: N16-0629_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Cardigan Welsh Corgi


title: S27-P016-C-0m

value: Control

value: 0 minutes (fasting)


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-146]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-134]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-122]


title: S23-P010-C-240m

value: 240 minutes


title: GFP- cells from lungs of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mouse 1 at 3 months post-NNK [3-SGGplusNNK-GfpNeg]

value: GFP- sorted mouse lung cells

value: Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+

value: 7 months


title: GFP- cells from lungs of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mouse 2 at 3 months post-NNK [4-SGGplusNNK-GfpNeg]


title: S24-P016-I-0m

value: Intervention


title: N16-0607

description: N16-0607_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Weimaraner


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-181]


title: GFP+ cells from lungs of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mouse 2 at 3 months post-NNK [2-SGGplusNNK-GfpPos]

value: GFP+ sorted mouse lung cells

value: Lung


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-170]


title: N16-0024

description: N16-0024_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Miniature Schnauzer

value: Female

value: Neutered


title: S22-P010-C-120m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: 120 minutes


title: GFP+ cells from lungs of Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+ mouse 1 at 3 months post-NNK [1-SGGplusNNK-GfpPos]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-169]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: S21-P010-C-0m

value: Control

value: 0 minutes (fasting)


title: N15-1027

description: N15-1027_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: RT

value: Australian Shepherd

value: Male


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-157]


title: S20-P010-I-240m

value: Intervention

value: 240 minutes


title: Lungs from Gprc5a-/- mouse 4 at 7 months post-NNK [JJ49]

value: Mouse lung cells

value: 11 months


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-145]


title: S19-P010-I-120m


title: N15-0589

description: N15-0589_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Cavalier King Charles Spaniel


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-133]


title: N15-0169

description: N15-0169_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Bedlington Terrier


title: S18-P010-I-0m


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-121]


title: N14-0760

description: N14-0760_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Mixed

value: Neutered


title: N16-0520

description: N16-0520_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Boxer


title: S17-P001-C-240m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity


title: S16-P001-C-120m

value: 120 minutes


title: S15-P001-C-0m

value: Control


title: SHMT2 KO3

city: Detroit

first: Jian

last: Wang

state: MI

address: 6135 Woodward Ave

department: Pathology

institute: Wayne State University School of Medicine

data_processing:
The sequence reads underwent trimming to eliminate adapter and low-quality sequences using Trimmomatic version 0.36.
The trimmed reads were aligned to the Mus musculus GRCm38 ERCC reference genome using STAR v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Liver

growth_protocol: The mice were weaned at three weeks of age and kept on a chow diet.

extract_protocol:
The total RNA were extracted from livers uisng Qiagen RNAeasy mini kit
Libraries were prepared by Azenta Life Sciences.

treatment_protocol: Mice were fed the AMLN diet at 4 weeks of age and continued for 18 weeks.

value: Liver

value: KO

value: AMLN diet


title: Lungs from Gprc5a-/- mouse 11 at 7 months post-saline [KOS7_43]

value: Lung


title: Lungs from Gprc5a-/- mouse 12 at 7 months post-saline [KOS7_44]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-109]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: S13-P001-I-120m

value: Intervention


title: SHMT2 KO1


title: S14-P001-I-240m

value: 240 minutes


title: N14-0467

description: N14-0467_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: steroid/anti-epileptic

value: Male


title: Lungs from Gprc5a-/- mouse 10 at 7 months post-saline [KOS7_42]

value: Mouse lung cells

value: 11 months


title: N14-0061

description: N14-0061_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Shetland Sheepdog

value: Female

value: Neutered


title: SHMT2 KO2


title: N15-1024

description: N15-1024_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Australian Cattle Dog


title: Lungs from Gprc5a-/- mouse 9 at 7 months post-saline [KOS7_41]


title: S12-P001-I-0m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: 0 minutes (fasting)


title: N13-1011

description: N13-1011_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: American Pit Bull Terrier


title: SHMT2 WT2

value: Liver

value: WT

value: AMLN diet


title: SHMT2 WT3


title: SHMT2 WT1


title: N13-0876

description: N13-0876_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam


title: S10-P004-C-120m

value: Control

value: 120 minutes


title: N13-0747

description: N13-0747_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Golden Retriever


title: N14-0543

description: N14-0543_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: anti-epileptic

value: Boxer

value: Male


title: S9-P004-C-0m


title: RW-Fu-12S-M30

city: Chicago

first: Hua

middle: L

last: Liang

state: IL

department: Department of Radiation and Cellular Oncology

institute: University of Chicago

data_processing:
Raw reads of 51 nucleotides, paired-end filtered for quality score > 20.
Sequenced reads were aligned to mouse reference genome (mm10) with HISAT2.
Assembly: mm10
Supplementary files format and content: Read count was calculated for each gene in each sample by using HTSeq.

source_name: MC38/MC38 tumors

growth_protocol: MC38/MC38 tumors were established and MC38 tumors were irradiated.

extract_protocol: mRNA cDNA libraries were made using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit

treatment_protocol: Lung tissue was collected 3 days post IR and CD45+ cells were sorted from single cell suspension.

tag: tumor

value: MC38/MC38 tumors

value: lung

value: IR

value: lung-derived CD45+ cells


title: N13-0559

description: N13-0559_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Female

value: Neutered


title: S8-P004-I-240m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: Intervention

value: 240 minutes


title: N13-0210

description: N13-0210_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Weimaraner


title: RW-Fu-12S-M28


title: RW-Fu-12S-M27

value: ctrl


title: Lungs from Gprc5a-/- mouse 3 at 7 months post-NNK [KOK7_47]

value: Mouse lung cells

value: Lung

value: 11 months


title: N13-0069

description: N13-0069_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Shetland Sheepdog


title: S6-P004-I-0m

value: 0 minutes (fasting)


title: RW-Fu-12S-M26

value: MC38/MC38 tumors


title: N12-0789

description: N12-0789_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: American Staffordshire Terrier

value: Male


title: S5-P003-C-240m

value: Control


title: N12-0006

description: N12-0006_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: steroid/anti-epileptic

value: Golden Retriever

value: Female


title: Lungs from Gprc5a-/- mouse 1 at 7 months post-NNK [KOK7_45]


title: RW-Fu-12S-M25

value: lung

value: lung-derived CD45+ cells


title: Lungs from Gprc5a-/- mouse 2 at 7 months post-NNK [KOK7_46]


title: SK-LMS-1 cells, dsRNA RIP senescent RepB

city: Perugia

first: Elisabetta

last: Albi

state: Italy

address: Via Romana

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli studi di Perugia

description: dsRNA IP from senescent cells

data_processing:
Consensus Transposable elements quantification was performed using TespeX
Differential enrichment analysis was performed using edgeR
Assembly: hg38
Supplementary files format and content: Tab separated read count per consensus TE sequence

source_name: SK-LMS-1HDAC4-/-/HDAC4PAM-ER - 4OHT

growth_protocol: Cells were grown in DMEM plus 4OHT (0.5uM) to induce HDAC4 re-expression and incubated at 37°C, 5%CO2, in normoxia

extract_protocol:
Total RNA was extracted with Tri Reagent (Molecular Research Center) from a pellet of 35*106 SK-LMS-1HDAC4-/-/HDAC4PAM-ER cells grown for 96h with or without 4-OHT. Three biological replicates were pulled and subjected to two independent IP. IP was performed O/N in Polysomal Lysis Buffer in the presence of 3 μg of J2 antibody (Scicons). Immunocomplexes were purified by incubating O/N each sample with 16 μl magnetic protein A/G covered Dynabeads (ThermoFisher). After 3 washes of the collected immunocomplexes, RNA was recovered by phenolchloroform extraction/ethanol precipitation and resuspended in 10 μl RNase-free water (Ambion).
RNA concentration, integrity and purity were tested by Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit). 10ng RNA were DNAseI digested (NEB), rRNA depleted (using Ribo-Zero method) and reverse transcribed obtaining cDNA. Adapter were ligated to fragmented cDNA after end-repair and A-Tailing following DNBSEQ protocol (MGI-Tech). 18 rounds of PCR amplification were performed to enrich the cDNA fragments. Then the PCR products were purified with Ampure XP Beads (Agencourt). ssCirDNA was obtained after denaturation and circularization. DNA balls were generated from each library following BGI specifications (SOP-SS-025)

treatment_protocol: 4OHT was out to achieve HDAC4 KO

value: leiomyosarcoma

tag: cell line

value: HDAC4-/- +HDAC4-ER

value: Untreated (4OHT washout 96h before harvesting)

tag: growth state

value: senescent cells

tag: fraction

value: dsRNA IP


title: S11-P004-C-240m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

value: 240 minutes


title: S4-P003-C-0m

value: 0 minutes (fasting)


title: Kidney, epithelial cell, KOnormalM

city: Birmingham

first: Takamitsu

middle: at

last: Saigusa

state: AL

address: 1720 2nd Ave. South. MCLM533

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
FASTQ files were generated using Illumina's bcl2fastq software.
TrimGalore version 0.6.7 was used to trim off primer adapters using parameters --paired --trim-n --trim1
Trimmed reads were aligned using RSEM version 1.3.3 with parameters --paired-end --star --estimate-rpsd --append-names --output-genome-bam --star-gzipped-read-file
Assembly: Gencode GRCm39 Release M26
Supplementary files format and content: Excel file with FPKM values for each gene in each sample

source_name: Kidney

extract_protocol:
According to protocol using trizol from invitrogen
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina  using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially  enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand  and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and  adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition  and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent  TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer  (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems,  Wilmington, MA, USA).  The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was  loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were  sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were  conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina  HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-  match was allowed for index sequence identification.

value: Kidney

tag: cell type

value: epithelial cell

tag: diet

value: normal protein


title: SK-LMS-1 cells, dsRNA RIP senescent RepA

description: dsRNA IP from senescent cells

tag: tissue


title: N11-0682

description: N11-0682_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Jack Russell Terrier

value: Male

value: Intact


title: Kidney, epithelial cell, KOnormalF2


title: Kidney, epithelial cell, KOlowM

value: low protein


title: S3-P003-I-240m

tag: condition

value: Intervention


title: S2-P003-I-120m

tag: subject id

value: 120 minutes


title: 3_R6_resFOP_Day6_ex3

city: Kyoto

first: Yonghui

last: Jin

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Institute for Life and Medical Sciences

institute: Kyoto University

data_processing:
Adapter sequences and low-quality bases were trimmed from the raw reads using Cutadapt v3.4
The trimmed reads were mapped to hg38 human reference genome sequences using STAR ver 2.7.9a with the GENCODE v36 gtf file.
The number of reads mapped to each gene (the raw read counts) were calculated using htseq-count ver 0.13.5 with the GENCODE gtf file.
Gene expression levels were determined as Transcripts Per Kilobase Million (TPM) values with DESeq2 v1.30.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: resFOP

growth_protocol: iMSCs were maintained in αMEM (Nacalai tesque) supplemented with 10% (v/v) FBS (Nichirei), 5 ng/ml FGF2, and 0.5% penicillin and streptomycin (Invitrogen, Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted with  RNeasy mini kit (Qiagen) following the manufacturer`s instruction. RNA-seq libraries were generated from 200ng~300 ng of total RNA.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following the manufacturer's instructions.

treatment_protocol: Chondrogenic differentiation was induced with 100 ng/ml Activin-A in chondrogenic medium.

value: resFOP

value: iMSCs

value: Normal ACVR1

tag: treatment

value: day6 after chondrogenesis


title: N14-0518

description: N14-0518_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: Golden Retriever


title: N11-0249

description: N11-0249_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam

value: RT

value: Mixed

value: Neutered


title: 2_R6_resFOP_Day6_ex2


title: SK-LMS-1 cells, dsRNA RIP growing RepA

description: dsRNA IP from growing cells

source_name: SK-LMS-1HDAC4-/-/HDAC4PAM-ER + 4OHT

value: leiomyosarcoma

value: HDAC4-/- +HDAC4-ER

value: 4OHT (0.5uM) to induce HDAC4 expression

value: growing cells

value: dsRNA IP


title: S1-P003-I-0m

value: Peripheral Blood Mononuclear Cells

value: abdominal obesity

tag: timepoint

value: 0 minutes (fasting)


title: S7-P004-I-120m

value: Intervention

value: 120 minutes


title: Kidney, epithelial cell, KOhighM

value: Kidney

value: epithelial cell

value: high protein


title: SK-LMS-1 cells, Input senescent Rep3

description: Total RNA from senescent cells

value: Untreated (4OHT washout 96h before harvesting)

value: senescent cells

value: Total RNA


title: P5_BCa_scRNAseq

city: Guangzhou

first: Changhao

last: Chen

state: Guangdong

address: 107 Yanjiangxi Road, Yuexiu District, Guangzhou, Guangdong Province, P. R. China

department: Urology

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: 10x Genomics

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Assembly: Ensembl_release96
Supplementary files format and content: expression files and matrix files

source_name: bladder cancer tissues

extract_protocol:
Fresh bladder cancer tissues and normal adjacent tissues were obtained from patients and washed with ice-cold PBS. Then, the tissues were subjected to prepare single cell suspensions with tumor dissociation kit. Subsequently, the cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction.
R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produced Illumina-ready sequencing libraries. A Single Cell 3’ Library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing.

value: bladder cancer tissues

value: Male

tag: tumor stage


title: SK-LMS-1 cells, Input senescent Rep2

description: Total RNA from senescent cells

value: leiomyosarcoma

value: HDAC4-/- +HDAC4-ER


title: 1_R6_resFOP_Day6_ex1

value: resFOP

value: iMSCs

value: Normal ACVR1

value: day6 after chondrogenesis


title: Kidney, epithelial cell, KOhighF1


title: SK-LMS-1 cells, Input senescent Rep1

description: Total RNA from senescent cells


title: 3_R0_resFOP_Day0_ex3

value: day0 after chondrogenesis


title: 2_R0_resFOP_Day0_ex2


title: P4_BCa_scRNAseq

description: 10x Genomics


title: SK-LMS-1 cells, Input growing Rep3

description: Total RNA from proliferating cells

value: 4OHT (0.5uM) to induce HDAC4 expression

value: proliferating cells


title: SK-LMS-1 cells, dsRNA RIP growing RepB

description: dsRNA IP from growing cells

value: growing cells

value: dsRNA IP


title: Kidney, epithelial cell, KO7normal

value: Kidney

value: epithelial cell

value: normal protein


title: SK-LMS-1 cells, Input growing Rep2

description: Total RNA from proliferating cells

value: Total RNA


title: other CAFs-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:hg38) using HISAT2 (version:2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: fibroblasts

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

value: fibroblasts

value: human bladder fibroblasts

value: delepte PDGFRa+ITGA11+ CAFs


title: 1_R0_resFOP_Day0_ex1


title: P3_BCa_scRNAseq

description: 10x Genomics

value: bladder cancer tissues

value: Male


title: Kidney, epithelial cell, KOlowF2

value: low protein


title: SK-LMS-1 cells, Input growing Rep1

description: Total RNA from proliferating cells

value: leiomyosarcoma

value: HDAC4-/- +HDAC4-ER


title: 3_F6_FOP_Day6_ex3

source_name: FOP

value: FOP

value: iMSCs

value: day6 after chondrogenesis


title: other CAFs-2


title: other CAFs-1


title: 3_F0_FOP_Day0_ex3

value: day0 after chondrogenesis


title: P2_BCa_scRNAseq

description: 10x Genomics

value: Female


title: P3_NAT_scRNAseq

description: 10x Genomics

source_name: normal adjacent tissues

value: normal adjacent tissues


title: 2_F6_FOP_Day6_ex2


title: Hypo_RV1

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

data_processing:
FastQC
Alignment using Bowtie2
Counting using HT-Seq
Differential expression using DEseq2
Assembly: Ensembl ASM19595v2
Supplementary files format and content: Tabular files with raw read counts as calculated by Htseq-count

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis

growth_protocol: Mtb strains were grown in 7H9 media supplemented with10% ADC (NaCl, dextrose, bovine serum albumin, catalase, 0.2% glycerol and 0.1% Tween 80) in absence of oxygen.

extract_protocol:
Isolation of RNA was performed using TRIzolreagent (Ambion). Cells equivalent to 10 O.D. of Rv, Rv∆embR, and Rv∆embR::embRstrains were harvested and resuspended in TRIzol reagent. The cells were lysed using 0.1 mm zirconium beads, following which RNA was extracted through chloroform, precipitated, and washed using 70% Ethanol (prepared in DEPC-water). The RNA was resuspended in the nuclease-free water and further purified using the RNeasy mini kit (Qiagen). The samples were treated with DNase I to remove any leftover DNA traces.
TruSeq RNA Library Prep Kit v2

value: Mycobacterium tuberculosis

value: WT

value: Hypoxia


title: Kidney, epithelial cell, KOhighF2

value: Kidney

value: epithelial cell

value: high protein


title: PDGFRα+ITGA11+ CAFs-3

value: fibroblasts

value: human bladder fibroblasts

value: PDGFRa+ITGA11+ CAFs


title: Hypo_RV2


title: P5_NAT_scRNAseq

description: 10x Genomics

value: Male


title: P2_NAT_scRNAseq

description: 10x Genomics


title: Hypo_KO2

value: EmbR KO


title: 1_F0_FOP_Day0_ex1

value: FOP


title: P1_BCa_scRNAseq

description: 10x Genomics

value: bladder cancer tissues


title: Hypo_KO1


title: PDGFRα+ITGA11+ CAFs-1


title: PDGFRα+ITGA11+ CAFs-2


title: 2_F0_FOP_Day0_ex2

value: iMSCs


title: P4_NAT_scRNAseq

description: 10x Genomics


title: ND5 Mutant Sample 2

status: Public on Feb 15 2024

city: Bethesda

first: Pedro

middle: J

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Demultiplexed reads were aligned to the human genome (hg38) using STAR (v.2.7.6a). The presence of m1A was quantified using samtools-mpileup to create individual base-pair frequencies for every position within the mt-ND5 and 28S rRNA transcripts.
Assembly: hg38
Supplementary files format and content: csv count file

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent according to the manufacture’s protocol. Following phase separation, the aqueous phase was applied to a RNeasy Mini Kit column and RNA was purified according to kit instructions.
The 28S and mt-ND5 transcripts were reverse transcribed using transcript-specific primers downstream of the m1A sites with TGIRT following the manufacturer’s protocol. Transcripts were amplified with barcoded oligos targeting either 28S or mt-ND5. Barcoded samples were pooled and sequencing on an Illuminia Micro Miseq

value: renal cell carcinoma

value: Mutant


title: ND5 Mutant Sample 3


title: ND5 WT Sample 3


title: ND5 Mutant Sample 1


title: ND5 WT Sample 2


title: ND5 WT Sample 1


title: 28S Mutant Sample 2


title: 28S Mutant Sample 3


title: 28S WT Sample 3


title: 28S WT Sample 1


title: pH1.2::H1.2ΔIDR-eGFP_seedling_rep2

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

library_source: genomic

data_processing:
MNase-seq: Reads were mapped to TAIR10 using Bowtie2-2.3.4.1, retaining mononucleosomal fragments with using parameters -I 130 -X 200. NuMap was then performed to compute nucleosome positions.
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read.
w1: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
w50: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Hi-C: For Hi-C data assay, clean reads were mapped to TAIR10 genome using the HiC-Pro (version 2.11.1) pipeline. The bam files (bwt2merged.bam) generated by HiC-Pro containing mapping information were used as input files for Fan-C (version 0.9.8). The module ‘fanc auto’ was applied to generate 500 kb and 25 kb contact matrix (hic files).
Genome_build: TAIR10
Supplementary_files_format_and_content: MNase-seq: BED files of nucleosome positions.
Supplementary_files_format_and_content: Bisulfite-Seq: GFF files of fractional methylation data either for individual cytosines (w1) or in 50 bp windows (w50).
Supplementary_files_format_and_content: Hi-C: matrix and regions files of different resolutions generated by Fan-C contain genomic contacts and corresponding index information, respectively.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: pH1.2::H1.2ΔIDR-eGFP seedling

growth_protocol: Plants were grown under long day (16 hr light; 8 hr dark) conditions at 22 °C.

extract_protocol:
DNA was extracted from ten-day-old seedlings by CTAB method
follow the instructions of NEBNext® Ultra™ II DNA Library Prep Kit and EZ DNA Methylation-Lightning Kit

tag: ecotype

value: ten-day-old seedlings


title: pH1.2::H1.2ΔIDR-eGFP_seedling_rep1


title: pH1.2::H1.2ΔIDR-eGFP_seedling_MNase_rep2

extract_protocol:
0.5 g of ten-day-old seedlings were ground with mortar and pestle in liquid nitrogen and homogenized in 10 mL of nuclei isolation buffer (0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% Triton X-100, 1 mM PMSF, 1 X proteinase inhibitors Cocktail) for 15 min on ice. Debris were filtered through two layers of miracloth to get nuclei suspension, which was then cold centrifuged at 4,000 g for 10 min. Nuclei were resuspended in 500 µL of TM2 (50 mM Tris-HCl, 2 mM MgCl2, 0.25 M sucrose, 1 mM PMSF, 1 X proteinase inhibitors Cocktail). After cold centrifugation at 4,000 g for 5 min, nuclei were resuspended in 400 µL of MNase digestion buffer (50 mM Tris-HCl pH 7.5, 5 mM CaCl2, 0.25 M sucrose, 1 mM PMSF, 1X proteinase inhibitors Cocktail) with 1000 U/mL final concentration of MNase (New England Biolabs) and incubated at 37°C with agitation (1000 rpm on Thermomixer) for 10 min. Digestion was stopped by adding 40 µL of  0.5 mM EDTA and 20 µL of  10% SDS. Proteinase K and RNase A were added to remove proteins and RNAs before Phenol-chloroform extraction to get DNA.
follow the instructions of Ovation Ultralow System V2 (Nugen) kit


title: pH1.1::H1.1G18IDR-eGFP_seedling_MNase_rep2

source_name: pH1.1::H1.1G18IDR-eGFP seedling


title: h1_seedling

source_name: h1 seedling


title: pH1.2::H1.2ΔIDR-eGFP_seedling_MNase_rep1


title: WT_seedling

source_name: WT seedling


title: pH1.1::H1.1G18IDR-eGFP_seedling_MNase_rep1


title: WT_seedling_MNase_rep1


title: WT_seedling_MNase_rep2


title: MF_11

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

data_processing:
CLC Genomics Workbench 10.0.1 & FastQC & centrifuge, quality control
CLC Genomics Workbench 10.0.1, adapter and polyA tail trimming
CLC Genomics Workbench 10.0.1, mapping to the genome with 'RNA-Seq analysis' tool (parameters: Mismatch cost 2, Insertion cost 3, Deletion cost 3, Length fraction 0.9, Similarity fraction 0.9, Global alignment No, Auto-detect paired distances Yes, Strand specific Reverse, Maximum number of hits for a read 1, Count paired reads as two Yes, Expression value Unique counts) and export of 'Expression Browser' count table
R version 3.4.2 with packages edgeR_3.20.9, filtering genes with raw counts below 10 in less than 4 samples
R version 3.4.2 with packages edgeR_3.20.9, TMM normalization
R version 3.4.2 with packages limma_3.34.9, voom transformation, linear model fit, adj.p.val calculation (BH correction)with eBayes function, DE table export
Genome_build: Pcitri.v1 (draft genome available at request at ensembl.mealybug.org)
Supplementary_files_format_and_content: Pcitri_totalCounts.txt - table with raw gene counts for all genes and all samples
Supplementary_files_format_and_content: Pcitri_lcpm.txt - table with logCPM values for all genes and all samples
Supplementary_files_format_and_content: Pcitri_logFC_PAdj.xlsx - Differential gene expression table with logFC and adj.p.val for the comparison virgin vs mated females; includes InterPro domain gene annotations

organism: Planococcus citri

source_name: whole animal from laboratory colony

growth_protocol: The colony of Planococcus citri was established at the Universitat Politècnica de València (UPV, Valencia, Spain) using starting specimens from Servicio de Sanitat Vegetal (Generalitat Valenciana, Silla, Valencia, Spain). Mealybugs were reared on organic green lemons. These were previously covered with paraffin around the midsection to delay their desiccation. Insects were maintained in a rearing chamber (darkness, at 24 ± 2 °C and 40−60% relative humidity) in plastic boxes.

extract_protocol:
Trizol total RNA extraction and DNase I treatment
Illumina TrueSeq RNA-Seq strand-specific library prep

treatment_protocol: Mated females were collected from the main P. citri stock colony described in the rearing protocol. These were collected after checking for the presence of ovisacs with fertilized eggs, which means that females were effectively mated. Virgin females were obtained as described in Vacas et al (2019). New lemons infested with P. citri first instars from the main stock colony were maintained in different plastic boxes. After the second instar stage, males produce a cottony cocoon that covers their bodies to pupate. Then, those lemons were periodically checked for the presence of cocoons, which were manually removed with an entomological needle to avoid matings and leave lemons infested only with virgin females.

tag: developmental stage

value: adult

tag: status

value: mated

value: female

value: whole animal


title: h1_seedling_MNase_rep1

tag: genotype


title: VF_6

value: virgin

tag: Sex


title: MF_10


title: VF_3


title: VF_5


title: 28S Mutant Sample 1


title: Sample 410_Oncocytoma

type: genomic

first: Kenneth

last: Aldape

state: Maryland

address: Building 10, Room 2S235

department: NCI, LABORATORY OF PATHOLOGY (HNC7Z18)

institute: National Institute of Health

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC array Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software
matrix processed value definition: Beta values were caluclated using single sample Noob method
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Kidney tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from kidney tissue samples using illumina EPIC array kit according to standard instructions

tag: institue

value: UCSF

value: Kidney tissue

tag: disease state

value: Tumor

tag: diagnosis

value: Oncocytoma


title: 28S WT Sample 2

tag: cell line

value: WT


title: Sample 409_Medulla

value: Normal

value: Medulla


title: Sample 408_ccPRCC

value: NYU

value: ccPRCC


title: Sample 406_ccPRCC


title: Sample 407_ChRCC

value: ChRCC


title: pH1.1::H1.1G18IDR-eGFP_seedling


title: Sample 405_RCC_unclassifiable


title: Sample 404_RCC_unclassifiable


title: Sample 403_AML

value: AML


title: h1_seedling_MNase_rep2

value: ten-day-old seedlings


title: Sample 402_RCC_unclassifiable


title: Sample 401_ChRCC

value: NIH


title: MF_8

value: adult

value: mated


title: MF_9

value: female

value: whole animal


title: Sample 397_AML

value: UCSF


title: Sample 398_Oncocytoma

value: Kidney tissue


title: Sample 396_Reverse polarity

value: Tumor

value: Reverse polarity


title: VF_2

value: virgin


title: Sample 399_RCC_unclassifiable


title: Sample 394_AML


title: Sample 411_ChRCC


title: Sample 395_ChRCC


title: Sample 390_RCC_unclassifiable


title: Sample 393_RCC_unclassifiable


title: Sample 392_ChRCC


title: Sample 387_Cortex

value: Normal

value: Cortex


title: Sample 388_ChRCC

value: NYU


title: Sample 384_ChRCC


title: Sample 385_RCC_unclassifiable


title: Sample 382_RCC_unclassifiable


title: Sample 389_RCC_unclassifiable


title: Sample 386_ChRCC


title: Sample 383_RCC_unclassifiable


title: Sample 381_RCC_unclassifiable


title: Sample 380_ChRCC


title: Sample 379_Oncocytoma

value: Oncocytoma


title: Sample 377_ChRCC

value: ChRCC


title: Sample 375_RCC_unclassifiable


title: Sample 376_Oncocytoma


title: Sample 400_RCC_unclassifiable


title: Sample 374_Oncocytoma


title: Sample 373_RCC_unclassifiable


title: Sample 372_RCC_unclassifiable


title: Sample 365_RCC_unclassifiable


title: Sample 366_RCC_unclassifiable


title: Sample 367_RCC_unclassifiable


title: Sample 368_RCC_unclassifiable


title: Sample 391_ChRCC


title: Sample 370_RCC_unclassifiable


title: Sample 364_RCC_unclassifiable


title: Sample 369_RCC_unclassifiable


title: Sample 360_ChRCC


title: Sample 358_ChRCC


title: Sample 363_ChRCC


title: Sample 357_RCC_unclassifiable


title: Sample 355_ccRCC

value: ccRCC


title: Sample 359_RCC_unclassifiable


title: Sample 356_RCC_unclassifiable


title: Sample 353_ccRCC


title: Sample 362_ChRCC


title: Sample 352_ccRCC


title: Sample 378_RCC_unclassifiable


title: Sample 351_RCC_unclassifiable


title: Sample 354_RCC_unclassifiable


title: Sample 350_RCC_unclassifiable


title: Sample 349_ccRCC


title: Sample 347_Oncocytoma


title: Sample 348_ccRCC


title: Sample 371_RCC_unclassifiable


title: Sample 346_ccRCC


title: Sample 345_ccRCC


title: Sample 342_ccRCC


title: Sample 343_RCC_unclassifiable


title: Sample 341_ccRCC


title: Sample 361_ChRCC


title: Sample 339_Oncocytoma


title: Sample 340_RCC_unclassifiable


title: Sample 344_Oncocytoma


title: Sample 337_RCC_unclassifiable


title: Sample 335_ccRCC


title: Sample 338_RCC_unclassifiable


title: Sample 332_RCC_unclassifiable


title: Sample 328_RCC_unclassifiable


title: Sample 331_Reverse polarity


title: Sample 336_ccRCC


title: Sample 330_Cortex


title: Sample 329_RCC_unclassifiable


title: Sample 333_ccRCC


title: Sample 327_Cortex


title: Sample 334_RCC_unclassifiable


title: Sample 325_RCC_unclassifiable


title: Sample 323_Oncocytoma


title: Sample 322_RCC_unclassifiable


title: Sample 326_Medulla

value: Medulla


title: Sample 324_RCC_unclassifiable


title: Sample 319_Medulla


title: Sample 320_Oncocytoma


title: Sample 317_AML

value: AML


title: Sample 318_PRCC

value: PRCC


title: Sample 315_Cortex

value: NIH


title: Sample 316_Medulla


title: Sample 311_Medulla


title: Sample 314_Medulla


title: Sample 312_Cortex


title: Sample 309_Cortex


title: Sample 307_ccRCC


title: Sample 308_RCC_unclassifiable


title: Sample 306_ccRCC


title: Sample 305_Cortex


title: Sample 303_RCC_unclassifiable


title: Sample 299_PRCC


title: Sample 300_RCC_unclassifiable


title: Sample 301_Cortex


title: Sample 298_RCC_unclassifiable


title: Sample 304_RCC_unclassifiable


title: Sample 302_ChRCC


title: Sample 321_RCC_unclassifiable


title: Sample 293_RCC_unclassifiable


title: Sample 292_RCC_unclassifiable


title: Sample 295_Cortex


title: Sample 296_Medulla


title: Sample 291_RCC_unclassifiable


title: Sample 294_RCC_unclassifiable


title: Sample 290_RCC_unclassifiable


title: Sample 289_RCC_unclassifiable


title: Sample 288_Medulla


title: Sample 310_Cortex


title: Sample 313_Oncocytoma


title: Sample 287_RCC_unclassifiable


title: Sample 286_Oncocytoma

tag: gender

value: Male


title: Sample 283_HLRCC

value: HLRCC


title: Sample 285_RCC_unclassifiable

value: UCSF


title: Sample 284_HLRCC

value: Kidney tissue


title: Sample 282_ccRCC

value: Tumor


title: Sample 297_Cortex


title: Sample 280_HLRCC


title: Sample 281_HOCT

value: HOCT


title: Sample 278_RCC_unclassifiable


title: Sample 277_HOCT


title: Sample 275_HOCT


title: Sample 274_HOCT


title: Sample 271_HLRCC


title: Sample 270_HLRCC


title: Sample 272_HLRCC


title: Sample 276_ccRCC


title: Sample 269_HLRCC


title: Sample 273_HLRCC


title: Sample 268_ccRCC


title: Sample 264_RCC_unclassifiable


title: Sample 265_ccRCC


title: Sample 263_RCC_unclassifiable


title: Sample 261_RCC_unclassifiable


title: Sample 262_ccRCC


title: Sample 266_ccRCC


title: Sample 259_ChRCC


title: Sample 260_RCC_unclassifiable


title: Sample 256_HOCT


title: Sample 257_ccRCC


title: Sample 255_HLRCC


title: Sample 254_HOCT


title: Sample 279_HOCT


title: Sample 253_RCC_unclassifiable


title: Sample 258_HOCT


title: Sample 250_RCC_unclassifiable


title: Sample 252_HOCT


title: Sample 249_RCC_unclassifiable


title: Sample 248_HLRCC


title: Sample 251_RCC_unclassifiable


title: Sample 247_RCC_unclassifiable


title: BMDMs, LPS+HCl 1

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description:
LH_1
gene_expression.txt

data_processing:
Reads filtering by removing adaptor contamination and low quality reads from raw reads, at  least 40 M clean reads were got
HISAT was used to align the clean reads to the reference genome
Bowtie2 was used to align the clean reads to the reference genes.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: counts and fpkm values for genes

source_name: BMDMs

growth_protocol: To get BMDMs, bone marrow cells isolated from C57/BL6 mice were cultured in RPMI 1640 differentiation medium containing 10% fetal bovine serum, 1 mM sodium pyruvate, antibiotics, and 30% L929 supernatant for 7 days. BMDMs were harvested and replated in 20% L929 medium one day before treatments. All cells were cultured in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
RNA was extracted with RNeasy Kit (Qiagen) with Rnase set (Qiagen). Quality and quantity of RNA was assessed using a NanoDrop™ One (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer.
Library preparation, sequencing at 100 bp read length, and bioinformatics analysis including  genome mapping, gene expression calculation, differentially expressed gene (DEG) detection and principal component analysis (PCA), were performed by BGI (Cambridge, MA)

treatment_protocol: BMDMs were incubated with 100 ng/ml LPS with or without L-(+)-lactic acid (LA) at 10 mM, or in low pH conditions (e.g. pH 6.5) adjusted by HCl for 3 hours.

tag: strain

tag: cell type

value: BMDMs

value: LPS+HCl


title: Sample 267_ccRCC

tag: tissue


title: BMDMs, LPS+HCl 2

description:
LH_2
gene_expression.txt


title: BMDMs, LA 2

description:
A_2
gene_expression.txt

value: LA


title: BMDMs, LA 1

description:
A_1
gene_expression.txt


title: Sample 245_PRCC


title: Sample 244_HOCT


title: BMDMs, LPS+LA 1

description:
LA_1
gene_expression.txt

value: LPS+LA


title: Sample 243_HOCT


title: BMDMs, LPS 1

description:
L_1
gene_expression.txt

value: LPS


title: BMDMs, Control 2

description:
C_2
gene_expression.txt


title: Sample 240_HLRCC


title: BMDMs, Control 1

description:
C_1
gene_expression.txt


title: Sample 242_HOCT


title: BMDMs, LPS 2

description:
L_2
gene_expression.txt


title: DAY15_CHIR_ChIP_seq_Input_rep2

city: Xiamen

first: Jie

last: Ren

state: Fujian Province

address: 2999 Jinshan Road

department: Institute of Cardiovascular Diseases

institute: Xiamen Cardiovascular Hospital of Xiamen University

data_processing:
ChIP-Seq reads were mapped to the human reference genome hg19 using the default settings of bowtie2. Peaks were called with the use of MACS2. Peaks overlapping blacklist defined by ENCODE were removed.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input samples)

source_name: H1 human embryonic stem cell line

extract_protocol:
hPSC-derived cardiomyocytes were crosslinked with 1% formaldehyde at room temperature for 10 min. After quenching and cell lysis, chromatin was sonicated using  Bioruptor (Diagenode).
ChIP-seq libraries were prepared using VAHTS Universal DNA Library Prep Kit for MGI (NDM607-01).

value: H1 human embryonic stem cell line

value: Cardiac cells


title: Sample 237_Metanephric adenoma

value: Metanephric adenoma


title: Sample 239_Metanephric adenoma


title: Sample 238_Metanephric adenoma


title: Sample 241_RCC_unclassifiable


title: Sample 236_Metanephric adenoma


title: DAY15_CHIR_H3K27ac_ChIP_seq_rep1

description:
DAY15_CHIR_H3K27ac_ChIP_seq_merged.bw
DAY15_CHIR_H3K27ac_ChIP_seq_merged_peaks.narrowPeak.gz


title: Sample 246_RCC_unclassifiable


title: BMDMs, LPS+LA 2

description:
LA_2
gene_expression.txt


title: Sample 235_Metanephric adenoma


title: Sample 234_HLRCC


title: Sample 233_HLRCC


title: skin, E14.5 Wntless mutant

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: Yale University

data_processing:
We extracted dermal cell populations from the newly collected mouse embryo skin samples. Cells from the wildtype and the Wls mutant were pooled for analyses.
After standard normalization, highly-variable gene selection and scaling using Seurat, we applied PCA and retained the top 30 principal components.
Three dermal celltypes (lower dermal cells, upper dermal cells, dermal condensate cells) were stratified based on the expression of canonical dermal markers, including Sox2, Dkk1, and Dkk2.
Assembly: mm10
Supplementary files format and content: "barcodes.tsv.gz" contains cell barcodes, "dermal_barcodes.tsv.gz" contains cell barcodes for screened dermal cells, "features.tsv.gz" contains metadata for genes, "matrix.mtx.gz" contains digital expression matrix

source_name: skin

extract_protocol:
Embryonic dorsolateral/flank skin was micro-dissected from E14.5 littermate control and mutant embryos and dissociated into a single-cell suspension using 0.25% trypsin (Gibco, Life Technologies) for 20 minutes at 37◦C. After genotyping, 2-3 embryos were pooled by condition. Single-cell suspensions were then stained with DAPI (Fisher Scientific, NBP2-31156) just prior to fluorescence-activated cell sorting.
Chromium Single cell 3’ GEM Library and Gel Bead Kit v3.1 (PN-1000121) was used according to the manufacturer’s instructions in the Chromium Single Cell 3’ Reagents Kits V3.1 User Guide. After cDNA libraries were created, they were subjected to Novaseq 6000 (Illumina) sequencing. For each scRNA-seq experiment, control and littermate mutant samples were prepared in parallel at the same time, pooled, and sequenced on the same lane.

value: skin

value: Wntless mutant


title: skin, E14.5 wildtype

value: wildtype


title: Sample 232_ccRCC

value: NIH

value: ccRCC


title: Sample 231_ccRCC


title: Heart, Control, 856

city: Columbia

first: Jacob

middle: Jeffrey

last: Russell

state: MO

address: 1401 Ashland Rd, Apartment E

department: Biomedical Sciences

institute: University of Missouri

data_processing:
Read counts ranged between 32.9-52.0 million (mean=43.7 million, S.D. ±5.5 million). The expression value parameter was set to transcripts per million (TPM) and normalization is performed using trimmed mean of M values (TMM) (23). The TMM normalization assumes that most genes are not differentially expressed and accordingly adjusts the library sizes.  The program also implements cross-sample Gaussian normalization (Z-score normalization). Principle Component Analysis (PCA) was used for quality control and to visualize variation between the experimental samples. The following steps were used in the PCA: 1) Calculate log CPM using effective library size 2) Z-score normalization across samples for each gene, and 3) Remove genes with zero expression or invalid values across all samples. One Iso+Mino sample was identified as an outlier and excluded from further analysis after PCA. Differentially expressed genes (DEG) were determined using the DGE tool of the Workbench via Exact Test for two group comparison in the edgeR Bioconductor package. The tool uses multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM). Statistical significance is calculated using the Wald Chi-Squared Test and fold changes are calculated from the GLM. Correction for multiple testing was performed using an FDR threshold <0.05.
Assembly: The trimmed sequences were aligned to the Mus_musculus_ensembl_v80_reference with gene track mus_musculis_ensembl_v86_Genes and mRNA track Mus_musculus_ensembl_v86_mRNA. The following parameters were used during alignment: mismatch cost:2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction: 0.8, and maximum number of reads: 10, and read counts derived using default parameters.
Supplementary files format and content: Text file including RPKM, TPM, CPM and total counts for all genes.

source_name: Heart

extract_protocol:
Qiagen RNEasy Lipid Tissue Mini Kit (Cat # 74804)
A cDNA library constructed by technology from the pooled RNA from the left ventricle of mice was sequenced run with Illumina Novaseq TM 6000 sequence platform. Using the Illuminapaired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-endreads.The RNA-Seq analyses module included in the CLC Genomics Workbench v. 21.0.3 (Qiagen®) (22) was used for the analyzing transcriptome data. Briefly, the compressed Fastq files were extracted, trimmed and filtered using the software’s default parameters. The Workbench uses modified-Mott trimming algorithm for trimming sequence ends with the following trim parameters used: trim using quality scores, yes; quality limit, 0.05; trim ambiguous nucleotides, yes; maximum number of ambiguities, 2; automatic read-through adapter trimming, yes, and trim ambiguous nucleotides, yes. A total of 784,251,576 sequences were processed and the total nucleotides in the datasets were 108,840,542,046.

value: Heart

tag: tissue region

value: Left Ventricle

value: Male

value: Wild Type

value: Control


title: Heart, Isoproterenol, 858

tag: treatment

value: Iso 30


title: Heart, Isoproterenol and Minocycline, 855

value: Mino + Iso 30


title: Sample 230_RCC_unclassifiable

value: Female

value: Kidney tissue

value: Tumor


title: Heart, Isoproterenol, 854


title: Sample 229_RCC_unclassifiable


title: DAY15_CHIR_ChIP_seq_Input_rep1

value: H1 human embryonic stem cell line

value: Cardiac cells


title: Heart, Isoproterenol and Minocycline, 852


title: Sample 228_Oncocytoma

value: UCSF

value: Oncocytoma


title: Heart, Isoproterenol, 851


title: Heart, Control, 850


title: Sample 226_ChRCC

value: ChRCC


title: Sample 227_Oncocytoma

value: NIH


title: Heart, Control, 849


title: DAY15_CHIR_H3K27ac_ChIP_seq_rep2


title: Sample 225_Oncocytoma


title: Sample 224_ChRCC


title: Heart, Isoproterenol and Minocycline, 857


title: Heart, Isoproterenol, 848


title: Heart, Isoproterenol and Minocycline, 846


title: Heart, Control, 847


title: Sample 222_RCC_unclassifiable


title: Sample 220_PRCC

value: PRCC


title: Sample 223_RCC_unclassifiable


title: Heart, Control, 844

value: Heart


title: Sample 221_PRCC


title: Sample 219_Oncocytoma


title: Heart, Isoproterenol, 841

value: Left Ventricle


title: Sample 218_Oncocytoma

value: Male


title: Heart, Isoproterenol, 843

value: Wild Type


title: Sample 217_CCSK

value: CCSK


title: Heart, Control, 840

value: Control


title: Sample 216_MRT

value: MRT


title: MuSCs,old_2

city: Ann Arbor

first: Carlos

middle: A

last: Aguilar

state: Michigan

address: 2800 Plymouth Rd

department: Biomedical Engineering

institute: University of Michigan

data_processing:
The sequencing reads were demultiplexed into FASTQ files and the adapters were trimmed using the Cutadapt v2.3.
The reads were mapped to the mouse genome using Kallisto.Counts were then assigned to genes using RSEM.
Differential expression analysis of old versus young groups was performed with DESeq2 and significantly differentially expressed genes were obtained with a p adjusted value<0.05. We then used WebGestalt to perform a Gene Set Enrichment Analysis with the Reactome pathway database.
Assembly: mm39
Supplementary files format and content: tsv matrix represents est_counts and tpm values

source_name: muscle

growth_protocol: Muscle stem cells were cultured in 50% AHA-based media (DMEM-86.7%, L-cystine-0.06%, Glutamax-1%, Sodium pyruvate-0.9%, AHA-0.2%, Ascorbic acid-0.1%, FBS-10%, Pen-strep-1%), 40% F-10, 9.5% FBS, 0.2% Pen-strep and 0.02 µg/ml bFGF.

extract_protocol:
RNA was isolated following the RNease Mini Kit protocol.
cDNAs were prepared based on the SMART-Seq® Ultra® Low Input RNA Kit, and libraries prepared following the Nextera XT DNA Library Prep protocol. Libraries were sequenced on NovaSeq instrument (Illumina).

value: muscle

value: Muscle stem cells

tag: age

value: old

value: WT

tag: time


title: Sample 215_MRT

value: Kidney tissue

value: Tumor


title: MuSCs,old_1


title: Sample 214_MRT

value: UCSF

value: Female


title: MuSCs, young_2

value: young


title: Sample 212_Reverse polarity

value: NYU

value: Reverse polarity


title: MuSCs, young_1


title: Sample 213_Reverse polarity


title: Sample 211_Reverse polarity


title: Sample 210_PRCC T2

value: PRCC T2


title: BV2 cells, sh-NFAT5 RNA-2

city: 重庆

first: ailiyaer

last: palahati

address: 重庆市渝中区医学院路1号

institute: 重庆医科大学

data_processing:
Quality control: samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis. Reads mapping: the reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5. Differential expression analysis: we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: xlsx file contains all raw-count for each sample

source_name: Brain

growth_protocol: BV2 microglia cell was maintained cultivated in Dulbecco's Modified Eagle Medium (Gibco, Thermo Fisher Scientific, New York, USA) supplied with 10% FBS (VivaCell, Shanghai, China), 100 U/ml penicillin and 100 g/ml streptomycin (Thermo, USA). The cells were maintained in a humidified atmos-phere comprising 5% CO2 at a temperature of 37°C.

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina).

treatment_protocol: For the contruction of negative control and NFAT5 deficiency BV2 microglia cells, BV2 cells transfected with scrambled sh-RNA lentivirus or NFAT5 sh-RNA lentivirus, respectively.

value: Brain

value: Microglia

value: NFAT5 deficiency BV2

value: NFAT5 sh-RNA lentivirus transfection


title: BV2 cells, sh-NFAT5 RNA-3

address: 重庆市渝中区医学院路1号


title: Heart, Isoproterenol and Minocycline, 842

value: Heart

value: Left Ventricle

value: Male

value: Wild Type

value: Mino + Iso 30


title: Sample 209_PRCC T1

value: Kidney tissue

value: PRCC T1


title: BV2 cells, sh-scambled RNA-3

address: 重庆市渝中区医学院路1号

value: Negative control (NC) BV2

value: Scrambled sh-RNA lentivirus transfection


title: Sample 207_PRCC T1

value: Tumor


title: Heart, Isoproterenol and Minocycline, 839


title: BV2 cells, sh-scambled RNA-1

address: 重庆市渝中区医学院路1号


title: BV2 cells, sh-NFAT5 RNA-1

address: 重庆市渝中区医学院路1号


title: Sample 208_PRCC T1

value: NYU


title: BV2 cells, sh-scambled RNA-2

address: 重庆市渝中区医学院路1号


title: Sample 204_PRCC T1


title: Sample 205_PRCC

value: PRCC


title: ILC, D14, scRNAseq

first: Shabaana

last: Khader

state: Illinois

address: 920 East 58th Street

institute: The University of Chicago

description: 10X genomics

data_processing:
demultiplexing, alignment, raw gene expression matrices were by the Cell Ranger software (10x Genomics, version 3) available on the 10x website
Assembly: mm10
Supplementary files format and content: tab seperated values files and matrix files

source_name: Lung

extract_protocol:
Lung single cell suspension was prepared by digesting the heart. After lysing red blood cells, single cells were subjected to staining with antobodies to to ILCs. Sorted ILCs were then resuspended in 0.04% w/v BSA in PBS and sunjected to 10X pipeline.
10x 3' GEX (v2)

value: Lung

value: ILCs

value: Mtb infection d14


title: PND0-KO4

city: Seattle

first: Libin

last: Xu

state: WA

address: 1705 NE Pacific St

department: Medicinal Chemistry

institute: University of Washington

data_processing:
HISAT2 algorithm was used to align sequence reads to the reference mouse genome (mm10). SAMtools and featureCounts programs were implemented for format conversion and counting reads to genomic features (annotation file VM25). DESeq2 (using R/Bioconductor) was used for differential expression analysis comparing WT and Dhcr7-KO samples at each time point.
Assembly: mm10
Supplementary files format and content: comma-separated values (CSV) text files include raw counts for each Sample

extract_protocol:
RNA was isolated using the Qiagen Lipid RNeasy Kit following the manufacturer’s protocol.
Samples were sent to Novogene Co. Ltd (Sacramento, CA) for total RNA sequencing on their Illumina platform. RNA sample quality control was further assessed, and the mRNA library was prepared with additional polyA enrichment, RNA fragmentation, and cDNA transcription steps. Libraries were sequenced by 150 bp paired-end reads on the Illumina NovaSeq 6000 Sequencing System with a minimum sequencing read depth of 6 Gb of raw data per sample.

value: Brain

tag: genetic modification

value: KO


title: ILC, D5, scRNAseq

description: 10X genomics

value: Mtb infection d5


title: Sample 203_PRCC T1


title: Sample 202_PRCC


title: PND0-KO2


title: Sample 201_PRCC


title: PND0-KO1


title: Sample 200_PRCC T2

value: PRCC T2


title: PND0-WT4

value: WT


title: PND0-WT2


title: PND0-WT3


title: Sample 199_PRCC T1


title: Sample 206_PRCC


title: Sample 197_Oncocytoma

value: Oncocytoma


title: PND0-WT1


title: Sample 196_Oncocytoma


title: E165-KO3


title: E165-KO4


title: Sample 195_Oncocytoma


title: Sample 194_Oncocytoma


title: Sample 193_Oncocytoma


title: Sample 192_Oncocytoma


title: PND0-KO3


title: E165-KO2


title: E165-KO1


title: Sample 190_Oncocytoma

value: UCSF

value: Male


title: E165-WT4


title: E165-WT2


title: Sample 188_Oncocytoma

value: Kidney tissue


title: Sample 187_Oncocytoma


title: E145-KO4


title: E165-WT3


title: E165-WT1


title: Sample 186_Metanephric adenoma

value: Metanephric adenoma


title: E145-KO3


title: E145-KO2


title: Sample 198_PRCC T1

value: NIH

value: PRCC T1


title: Sample 184_Metanephric adenoma

value: Tumor


title: Sample 191_Oncocytoma

value: NYU


title: E145-KO1


title: Sample 183_Metanephric adenoma

value: Female


title: E145-WT4


title: E145-WT3


title: Sample 182_Metanephric adenoma


title: E145-WT2


title: Sample 181_Metanephric adenoma


title: E145-WT1


title: E125-KO3


title: Sample 179_Medulla

value: Normal

value: Medulla


title: E125-KO1

value: Brain


title: Sample 175_Medulla


title: E125-WT3


title: Sample 174_Medulla


title: Sample 178_Medulla


title: E125-KO2

value: KO


title: E125-WT4


title: Sample 176_Medulla


title: Sample 185_Metanephric adenoma


title: Sample 189_Oncocytoma


title: E125-WT1


title: Sample 177_Medulla


title: Sample 173_Medulla


title: Sample 172_Medulla


title: BAL_d30+3_FluNP+CD11a+CD8-TRM_rep3

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: txt file of RPKM normalized read counts for each detected gene

source_name: BAL

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: BAL

tag: day post-infection_or_challenge_(+)

tag: population

tag: infection

value: x31 influenza, PR8 influenza

tag: sorting markers

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69+ CD11a+

value: 12-13 weeks


title: Sample 180_Metanephric adenoma

tag: institue

value: UCSF


title: Sample 169_ccPRCC

tag: disease state

value: ccPRCC


title: BAL_d30+3_FluNP+CD11a+CD8-TRM_rep1

tag: genotype

tag: Sex


title: E125-KO4


title: BAL_d30+3_FluNP+CD11a-CD8-TRM_rep3

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69+ CD11a-


title: Sample 167_ccPRCC

value: Kidney tissue

tag: diagnosis


title: BAL_d30+3_FluNP+CD11a-CD8-TRM_rep2


title: E125-WT2

tag: strain

value: WT


title: Sample 165_ccPRCC


title: Sample 166_ccPRCC


title: BAL_d30+3_FluNP+CD11a-CD8-TRM_rep1


title: Sample 164_RCC_unclassifiable

tag: gender

value: Male


title: Lung_d30+3_FluNP+CD69+CD8-TEFF_rep2

tag: tissue

value: Lung

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69+


title: Lung_d30+3_FluNP+CD69+CD8-TEFF_rep3

value: Female


title: Sample 163_RCC_unclassifiable

value: Tumor


title: Sample 161_Oncocytic neoplasm

value: NYU

value: Oncocytic neoplasm


title: Sample 160_Oncocytic neoplasm


title: Lung_d30+3_FluNP+CD69-CD8-TEM_rep3

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69-


title: Lung_d30+3_FluNP+CD69-CD8-TEM_rep2


title: Lung_d30+3_FluNP+CD69-CD8-TEM_rep1


title: Sample 171_Medulla

value: Normal

value: Medulla


title: Sample 170_Medulla


title: Spleen_d30+3_FluNP+CD8-TEM_rep3

source_name: Spleen

value: Spleen

value: x31 influenza, PR8 influenza

value: CD3+ CD8a+ CD44Hi FluNP 366-374/Db+


title: Sample 159_ChRCC

value: NIH

value: ChRCC


title: Spleen_d30+3_FluNP+CD8-TEM_rep2

value: 12-13 weeks


title: Sample 168_ccPRCC

value: Kidney tissue

value: ccPRCC


title: BAL_d30+3_FluNP+CD11a+CD8-TRM_rep2

value: BAL

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69+ CD11a+


title: Sample 158_HLRCC

value: Male

value: HLRCC


title: Sample 157_Cortex

value: Female

value: Cortex


title: Spleen_d30+3_FluNP+CD8-TEM_rep1


title: BAL_d30_FluNP+CD11a+CD8-TRM_rep3

value: x31 influenza


title: Sample 156_Cortex

value: Normal


title: Sample 155_Cortex


title: Lung_d30+3_FluNP+CD69+CD8-TEFF_rep1

value: Lung

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69+


title: Sample 154_Cortex


title: BAL_d30_FluNP+CD11a+CD8-TRM_rep1


title: Sample 162_RCC_unclassifiable

value: UCSF

value: Tumor


title: BAL_d30_FluNP+CD11a-CD8-TRM_rep3

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69+ CD11a-


title: Sample 153_Cortex

value: NIH


title: BAL_d30_FluNP+CD11a-CD8-TRM_rep2

value: 12-13 weeks


title: BAL_d30_FluNP+CD11a-CD8-TRM_rep1


title: Sample 151_Cortex

value: Kidney tissue


title: Lung_d30_FluNP+CD69+CD8-TEFF_rep3


title: Sample 150_Cortex


title: Sample 147_Cortex


title: Sample 148_Cortex


title: Lung_d30_FluNP+CD69-CD8-TEM_rep3

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69-


title: Lung_d30_FluNP+CD69+CD8-TEFF_rep1


title: Lung_d30_FluNP+CD69-CD8-TEM_rep1


title: BAL_d30_FluNP+CD11a+CD8-TRM_rep2

value: BAL


title: Sample 149_Cortex


title: Lung_d30_FluNP+CD69-CD8-TEM_rep2


title: Sample 143_ChRCC

value: NYU

value: ChRCC


title: Sample 145_Cortex

value: Male


title: Spleen_d30_FluNP+CD8-TEM_rep2

value: Spleen

value: CD3+ CD8a+ CD44Hi FluNP 366-374/Db+

value: Female


title: Sample 142_ChRCC


title: Spleen_d30_FluNP+CD8-TEM_rep1

value: x31 influenza


title: Spleen_d30_FluNP+CD8-TEM_rep3


title: Sample 144_Cortex

value: Normal

value: Cortex


title: Sample 141_ChRCC


title: BAL_d10_FluNP+CD69+CD8-TEFF_rep3

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69+

value: 8-10 weeks


title: BAL_d10_FluNP+CD69+CD8-TEFF_rep2


title: Sample 140_ChRCC

value: Tumor


title: Sample 152_Cortex

value: NIH


title: Sample 139_RCC_unclassifiable

value: UCSF


title: BAL_d10_FluNP+CD69+CD8-TEFF_rep1


title: BAL_d10_FluNP+CD69-CD8-TEFF_rep3


title: BAL_d10_FluNP+CD69-CD8-TEFF_rep2


title: Lung_d30_FluNP+CD69+CD8-TEFF_rep2

value: Lung

value: 12-13 weeks


title: Sample 138_ChRCC

value: Kidney tissue


title: Sample 146_Cortex


title: Sample 136_CCSK

value: CCSK


title: BAL_d10_FluNP+CD69-CD8-TEFF_rep1

value: BAL

value: CD45 IV- CD3+ CD8a+ CD44Hi FluNP 366-374/Db+ CD69-


title: Sample 137_ChRCC

value: Male

value: ChRCC


title: Lung_d10_FluNP+CD69+CD8-TEFF_rep3

value: Female


title: Sample 135_ccRCC

value: ccRCC


title: Lung_d10_FluNP+CD69+CD8-TEFF_rep2

value: x31 influenza


title: Sample 132_ccRCC


title: Lung_d10_FluNP+CD69-CD8-TEFF_rep3


title: Sample 133_ccRCC


title: Lung_d10_FluNP+CD69+CD8-TEFF_rep1


title: Sample 134_ccRCC


title: Sample 131_ccRCC

value: NYU


title: Sample 129_ccRCC


title: Lung_d10_FluNP+CD69-CD8-TEFF_rep2


title: Spleen_d10_FluNP+CD8-TEFF_rep3

value: Spleen

value: CD3+ CD8a+ CD44Hi FluNP 366-374/Db+


title: Sample 130_ccRCC

value: Tumor


title: Spleen_d10_FluNP+CD8-TEFF_rep2

value: 8-10 weeks


title: Sample 128_ccRCC


title: Lung_d10_FluNP+CD69-CD8-TEFF_rep1


title: Spleen_d10_FluNP+CD8-TEFF_rep1


title: Sample 127_ccRCC

value: NIH


title: Sample 126_ccRCC


title: d3.IFNgR.KOrep10

source_name: Nasal cavity

value: Nasal cavity

tag: developmental stage

value: IFNg-KO


title: d3.IFNgR.KOrep8

value: 12-13 weeks


title: Sample 125_ccRCC

value: Kidney tissue


title: d3.IFNgR.KOrep7


title: Sample 123_ccRCC


title: Sample 124_ccRCC


title: d3.IFNgR.KOrep5


title: d3.IFNgR.KOrep4


title: d3.IFNgR.KOrep3


title: Sample 122_ccRCC


title: Sample 121_ccRCC


title: d3.IFNgR.KOrep1


title: d3.IFNgR.KOrep2


title: Sample 120_ccRCC


title: Sample 118_ccRCC


title: d0.IFNgR.KOrep9


title: Sample 116_ccRCC


title: Sample 117_ccRCC


title: d0.IFNgR.KOrep7


title: Sample 114_ccRCC


title: d0.IFNgR.KOrep6


title: d0.IFNgR.KOrep5


title: Sample 113_ccRCC

value: UCSF


title: Sample 112_ccRCC


title: d0.IFNgR.KOrep3


title: d0.IFNgR.KOrep4


title: d0.IFNgR.KOrep2


title: Sample 110_ccRCC


title: Sample 111_ccRCC


title: d3.WTrep10


title: Sample 109_ccRCC


title: d0.IFNgR.KOrep1


title: Sample 108_AML

value: AML


title: d3.WTrep9


title: Sample 107_AML

value: Male


title: Sample 119_ccRCC


title: d3.WTrep7


title: d3.WTrep8


title: d0.IFNgR.KOrep8


title: Sample 115_ccRCC


title: Sample 105_AML


title: d3.WTrep6


title: Sample 104_AML


title: d3.WTrep5


title: Sample 103_AML


title: d3.WTrep3


title: d3.WTrep4


title: d3.WTrep2


title: Sample 101_AML


title: Sample 102_AML


title: d0.WTrep10


title: Sample 99_AML


title: d3.WTrep1


title: d0.WTrep9


title: Sample 100_AML


title: Sample 98_AML


title: Sample 97_AML


title: d0.WTrep8


title: Sample 106_AML


title: d0.WTrep6


title: d0.WTrep7


title: d0.WTrep5


title: Sample 95_Wilms tumor

value: Wilms tumor


title: d0.WTrep4

value: Female


title: Sample 94_Wilms tumor


title: Sample 92_Wilms tumor


title: d0.WTrep3


title: Sample 93_Wilms tumor


title: d0.WTrep2


title: d0.WTrep1


title: Sample 91_Reverse polarity

value: Reverse polarity


title: Sample 90_Reverse polarity