title: chronic (C02_1) antibody derived tags

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

library_source: other

data_processing:
ATAC libraries were demultiplexed using 10X Genomics cellranger-atac (v2.0) pipeline. NovaSeq-based sequences were filtered using 10X Genomics index-hopping-filter (v1.1).
ATAC libraries were processed (demultiplexing, alignment, and counting) using 10X Genomics cellranger-atac (v2.0) pipeline
ADT libraries were demultiplexed using bcl2fastq2 (v2.20.0.422)
ADT fastq files were mapped to the TotalSeaA cocktail catalog using kallisto (v0.46.2) and bustools (v0.40.0) as documented with the kite pipeline (https://github.com/pachterlab/kite)
Assembly: chimeric hg38 with viral genome (HXB2, SUMA, or autologous sequences)
Supplementary files format and content: fragment.tsv.gz output file from 10X Genomics cellranger-atac count for ATAC data
Supplementary files format and content: tar.gz folder of kallisto bus output for ADT data
Library strategy: single cell ASAPseq

molecule: other

source_name: lymph node

growth_protocol: Cells were thawed and rested in complete RPMI supplemented with DNaseI.

extract_protocol: Refer to Mimitou et al., Nature Biotechnology 2021 for ASAPseq protocol

treatment_protocol: For in vitro sample, bulk CD4+ T-cells were negatively enriched and were activated for infection with HIV-1 (SUMA clone). For ex vivo samples, memory CD4+ T-cells were negatively enriched.

tag: component

value: ADT


title: chronic (C02_3) ATAC fragments

status: Public on Oct 25 2022

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: ATAC


title: chronic (C02_2) ATAC fragments


title: chronic (C02_1) ATAC fragments


title: chronic (C02_2) antibody derived tags


title: chronic (C02_3) antibody derived tags


title: 160669

type: RNA

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression data from nasal brushing of subject 160669.

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.54.0), using R version 3.5.1 and the Brainarray hugene10sthsentrezgcdf R package (version 22.0.0).

label: biotin

molecule: total RNA

source_name: Brushing of nasal epithelium

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

tag: Sex

value: Female

tag: age

tag: smoking status

value: Current smoker

tag: fev1 % predicted

tag: cancer status

value: Benign


title: chronic (C01_2) ATAC fragments


title: chronic (C01_3) ATAC fragments


title: 210573

description: Gene expression data from nasal brushing of subject 210573.


title: 46C5

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description: Sorted PI- CD45+ CD11B+ LY6G/SIGLECF- cells

library_source: transcriptomic

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 (v. 2.20) on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1.1).
Assembly: mm10
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

organism: Mus musculus

source_name: Tibialis Anterior (skeletal muscle)

extract_protocol:
Mice were anesthetized via intraperitoneal injection of 2,2,2-tribromoethyl alcohol (Aldrich T4840-2) and then perfused with warm PBS.  Following removing the fascia, skeletal muscle was harvested and cut into small pieces with scissors which was then followed by enzymatic digestion with a mixture of Collagenase D (Roche; 1.5 U ml-1; # 11088882001) and Dispase II (Roche; 2.4 U ml-1; # 04942078001) for an hour at 37 °C. Samples were vortexed every 20 minutes during incubation. Digested tissues were filtered through a 40-μm cell strainer (FALCON, # 352340), washed with PBS and collected by centrifugation at 545g for 7min.  Cell preparations were blocked with PBS containing 2 mM EDTA and 2% FBS (FACS buffer) + anti-Fcy receptor antibody on ice for 10 minutes and then stained with various antibodies on ice for 15 minutes (Supplementary Table 2). Stained cells were washed for cell sorting. Cell sorting was performed using a BD FACSAria (Becton Dickinson) equipped with three lasers or BD Influx cell sorter both equipped with four lasers.  RNeasy Micro Kit (Qiagen, # 74004) was used to isolate RNA from sorted cells. 10 μ of 2β-mercaptoethanol was added to 1mL of the buffer RLT (lysis buffer) before use.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Paired-end sequencing was performed on the Illumina NextSeq 2000 using the P3 100 cycle Kit (Illumina).

treatment_protocol: TAs of Ifngr1 wt/null or null/null mice were damaged with Notexin. Following injury, mice were treated daily with intraperitoneal injection of either anti-TNFa neutralizing antibody or a proper isotype control. On day 5  after injury, PI- CD45+ CD11B+ LY6G/SIGLECF- cells were sorted for RNA sequencing.

tag: treatment

value: Isotype antibody

tag: cell type

value: Macrophages

tag: genotype

value: wt/null


title: chronic (C01_1) ATAC fragments


title: chronic (C01_3) antibody derived tags


title: 50574

description: Gene expression data from nasal brushing of subject 50574.

value: Male

value: Former smoker


title: 140137

description: Gene expression data from nasal brushing of subject 140137.

value: Cancer


title: 60030

description: Gene expression data from nasal brushing of subject 60030.


title: chronic (C01_2) antibody derived tags


title: 160562

description: Gene expression data from nasal brushing of subject 160562.


title: 260507

description: Gene expression data from nasal brushing of subject 260507.


title: 130165

description: Gene expression data from nasal brushing of subject 130165.


title: 160654

description: Gene expression data from nasal brushing of subject 160654.


title: 100032

description: Gene expression data from nasal brushing of subject 100032.


title: 250520

description: Gene expression data from nasal brushing of subject 250520.


title: 220562

description: Gene expression data from nasal brushing of subject 220562.


title: 30011

description: Gene expression data from nasal brushing of subject 30011.


title: E9.5 single cell ATAC miR-302KO

city: Houston

first: Rachel

last: Keuls

state: TX

address: One baylor plaza, Alkek N1020

institute: Baylor College of Medicine

description:
filtered peak bc matrix files
E9.5_KOvWT_ATAC-2022-Signacv1.7.0.rds

library_source: genomic single cell

data_processing:
Cell Ranger mkfastq version 3.0.2 (mRNA); cellranger-atac mkfastq version 1.1.0 (E7.5 ATAC, E8.5 ATAC and E9.5 ATAC) or version 2.0.0 (E8.25 ATAC)
Cell Ranger count version 3.0.2 (mRNA); cellranger-atac count version 1.1.0 (E7.5 ATAC, E8.5 ATAC and E9.5 ATAC) or version 2.0.0 (E8.25 ATAC)
Seurat 3.1.5 (mRNA); Seurat 4.1.1 and Signac version 1.7.0 (ATAC)
Assembly: mm10
Supplementary files format and content: filtered matrix files for both mRNA and atac
Supplementary files format and content: RDS objects for both mRNA and atac

source_name: Cranial Region

extract_protocol:
E7.5 TS11d 0s whole embryo, E8.25 TS12a 3s cranial region, E8.5 TS13 8-12s cranial region, and E9.5 TS15 26-28s cranial region were harvested for single cell mRNA and single cell ATAC sequencing using a 10X Genomics platform. Embryos were dissected in PBS, the corresponding tissue (whole embryo for E7.5 and cranial region for E8.25-E9.5) was dissociated with papain, neutralized with FBS, and cells were pelleted and resuspended for partitioning on a 10X chromum controller
10x scRNA - Single Cell 3' v3; 10x scATAC v1.0 (E7.5 ATAC, E8.5 ATAC and E9.5 ATAC) or v1.1 (E8.25 ATAC)

tag: tissue

value: Cranial Region

tag: strain

value: C57BL/6J background

tag: developmental stage


title: E9.5 single cell mRNA WT

description:
filtered feature bc matrix files
E9.5_KOvWT_RNA.rds

library_source: transcriptomic single cell


title: gut microbiota，B_011

city: Dalian

first: Cong

last: Liu

address: 222 Zhongshan Road

country: China

institute: First Affiliated Hospital of Dalian Medical University

data_processing:
Trimmomatic (version 0.35) to to remove low quality base pairs using these parameters (SLIDINGWINDOW: 50:20 MINLEN: 50).
Trimmed reads were then cut adaptors using cutadapt (version:1.16)
PE reads merged using FLASH program (version 1.2.11)
Low quality contigs were removed based on screen.seqs command in mothur (V.1.39.5)
The reads were clustered at 97% sequence identity into OTUs, The chimera sequences and the singleton OTUs were deleted using the UPARSE pipeline (http://drive5.com/usearch/manual/uparse cmds.html).
Supplementary files format and content: Tab-delimited text files include sequences count values for each Sample
Library strategy: DNA-seq

organism: human feces metagenome

source_name: gut microbiota

growth_protocol: In all participants, fresh fecal samples were collected by fecal microbial DNA collection and preservation kits (TinyGene, Shanghai, China). All consumables were aseptic, and fecal samples were frozen and stored at −80°C after collection.

extract_protocol:
The genomic DNA of samples was extracted by the QIAamp DNA Stool Mini Kit.
The V4-V5 region of 16s rRNA were selected, using two step PCR, and pair-end sequencing was performed in accordance with the requirements of Illumina Miseq high-throughput sequencing, to complete the construction of an Miseq library.

value: gut microbiota

tag: disease

value: none, control


title: E8.5 single cell ATAC miR-302KO

description:
filtered peak bc matrix files
E8.5_KOvWT_ATAC-2022-Signacv1.7.0.rds

value: TS13 8s


title: E9.5 single cell mRNA miR-302KO


title: E9.5 single cell ATAC WT


title: E8.5 single cell mRNA miR-302KO

description:
filtered feature bc matrix files
E8.5_KOvWT_RNA.rds


title: 230506

description: Gene expression data from nasal brushing of subject 230506.


title: chronic (C01_1) antibody derived tags


title: E8.5 single cell ATAC WT


title: 170516

description: Gene expression data from nasal brushing of subject 170516.


title: E8.5 single cell mRNA WT


title: 250523

description: Gene expression data from nasal brushing of subject 250523.


title: 180503

description: Gene expression data from nasal brushing of subject 180503.


title: 50510

description: Gene expression data from nasal brushing of subject 50510.


title: 170506

description: Gene expression data from nasal brushing of subject 170506.


title: E8.25 single cell ATAC WT

description:
filtered peak bc matrix files
E8.25_KOvWT_ATAC-2022-Signacv1.7.0.rds

value: TS12a 3s


title: 250521

description: Gene expression data from nasal brushing of subject 250521.


title: E8.25 single cell mRNA miR-302KO

description:
filtered feature bc matrix files
E8.25_KOvWT_RNA.rds


title: E7.5 single cell ATAC miR-302KO

description:
filtered peak bc matrix files
E7.5_KOvWT_ATAC-2022-Signacv1.7.0.rds

source_name: Whole Embryo

value: Whole Embryo

value: TS11d 0s


title: 190515

description: Gene expression data from nasal brushing of subject 190515.

value: Female


title: E7.5 single cell ATAC WT


title: E7.5 single cell mRNA miR-302KO

description:
filtered feature bc matrix files
E7.5_KOvWT_RNA.rds


title: FR121_macrophages HTO

description: A balanced number PI- Hoechst+ CD45+ CD11B+ LY6G/SIGLECF- cells. Hash 1 (TotalSeq™-B0301) : 34A5 CRE+ WTKO D5, Hash 2 (TotalSeq™-B0302): 34A4 CRE+ FLKO D5, Hash 3 (TotalSeq™-B0303): 33A8 CRE+ WTKO D6, Hash 4 (TotalSeq™-B0304): 33A7 CRE+ FLKO D6

data_processing:
Demultiplexed FASTQ reads were aligned to the mouse reference genome, mm10 (GRCm38.p5, primary assembly) using the 10X Genomics Cellranger v5.0.0 pipeline. Default and recommended parameters were adopted. The resulting gene-barcode matrices were processed and analyzed in Seurat (Satija Lab, v3.1.2). Further demultiplexing with hashtag oligos (using 0.99 quantile as a threshold for positivity)  was applied to remove cross-sample multiplets.
Low quality cells (< 200 genes/cell,  >5% mitocondrial UMIs/cell, < 200 or > 5000 UMIs per cell) were removed prior to principal component analysis, Louvain clustering, and dimensionality reduction with UMAP (30 PCs). Differential gene expression using the Wilcoxon rank sum test was performed on filtered and normalized counts.
Assembly: mm10 (GRCm38.p5)
Supplementary files format and content: HDF5 file containing gene count and HTO matrices.

molecule: polyA RNA

extract_protocol:
Mice were anesthetized via intraperitoneal injection of 2,2,2-tribromoethyl alcohol (Aldrich T4840-2) and then perfused with warm PBS.  Following removing the fascia, skeletal muscle was harvested and cut into small pieces with scissors which was then followed by enzymatic digestion with a mixture of Collagenase D (Roche; 1.5 U ml-1; # 11088882001) and Dispase II (Roche; 2.4 U ml-1; # 04942078001) for an hour at 37 °C. Samples were vortexed every 20 minutes during incubation. Digested tissues were filtered through a 40-μm cell strainer (FALCON, # 352340), washed with PBS and collected by centrifugation at 545g for 7min.  Cell preparations were blocked with PBS containing 2 mM EDTA and 2% FBS (FACS buffer) + anti-Fcy receptor antibody on ice for 10 minutes and then stained with various antibodies on ice for 15 minutes (Supplementary Table 2). Finally, cells were washed and stained with cell hashing antibodies against mouse CD45 and MHC class I (Biolegend, # 155801, # 155803, # 155805, # 155807) to pool up to four samples for one single-cell analysis run. Cell sorting was performed using a BD FACSAria (Becton Dickinson) equipped with three lasers or BD Influx cell sorter both equipped with four lasers. Cells were sorted twice.
Viable cells were delivered into a Chromium Controller (10X Genomics), captured and libraried with the Chromium single cell 3’ reagent kit v3 (10X Genomics) as per the manufacturer's protocol. cDNA libraries were sequenced on Illumina Nextseq 500 using the High Output 75 Cycle kits to a read depth of 65,000 mean reads per cell.

treatment_protocol: Following Tamoxifen induction, TAs of Cx3cr1creERT2 * Ifngr1 wt/null or flox/null mice were damaged with Notexin. Following injury, mice were treated daily with intraperitoneal injection of anti-TNFa neutralizing antibody. Five (n = 2 mice) or six (n = 2 mice) days after injury, PI-Hoechst+CD45+CD11b+LY6G-SIGLECF-  cells were double sorted for single cell RNA sequencing.

value: Day 5 and Day 6 post injury

value: Cre+ flox/null or Cre+ wt/null


title: 160543

description: Gene expression data from nasal brushing of subject 160543.

value: Current smoker


title: 100018

description: Gene expression data from nasal brushing of subject 100018.

value: Benign


title: E8.25 single cell mRNA WT


title: 220521

description: Gene expression data from nasal brushing of subject 220521.


title: 120540

description: Gene expression data from nasal brushing of subject 120540.


title: 140038

description: Gene expression data from nasal brushing of subject 140038.


title: 160549

description: Gene expression data from nasal brushing of subject 160549.


title: 160522

description: Gene expression data from nasal brushing of subject 160522.


title: 160542

description: Gene expression data from nasal brushing of subject 160542.


title: 50525

description: Gene expression data from nasal brushing of subject 50525.


title: 170513

description: Gene expression data from nasal brushing of subject 170513.


title: WT Male_RoomAir

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

description: 10x Genomics

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

source_name: Lung

growth_protocol: WT C57BL6 mice were subjected to timed mating. Neonatal mouse pups from different litters were randomized to the treatment (hyperoxia) or control (room air) conditions. Mice were transitioned to room air on PND7.

extract_protocol:
The right ventricle was perforated and lungs were perfusedwith 5 ml of DPBS until completely white. Lungs were removed, and shortly rinsed with DPBS (Lonza). Dissected lungs were then digested using the Miltenyi Biotec Lung Dissociation Kit (130-095-927) at 37 °C and the gentleMACS™  Dissociator (Miltenyi Biotech, Germany) using the program  gentleMACS Program m_lung_02. The suspension was then treated with red cell lysis buffer and passed throuh a 70um stariner. The cells were stained with DAPI and subjected to flow cytometric analysis to collect DAPI negative viable cells for downstream single-cell analysis.
Single cell Gene Expression Library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In Brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

treatment_protocol: C57BL6J neonatal mice were exposed to room air or hyperoxia from PND1-5 to 95% FiO2 or mainatined in room air. Mice were euthanized at PND7.

value: Lung

value: PND 7

value: Mixed

value: WT

value: Room Air


title: WT Female_RoomAir

description: 10x Genomics


title: WT Male_Oxygen

description: 10x Genomics

value: Male

value: Hyperoxia


title: WT Female_Oxygen

description: 10x Genomics


title: ABE-treated HET

city: Dallas

first: Andreas

last: Chai

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center

description: Single-End 75 bp Q30 score 91.5%. Correction efficiency ~35% as measured by NGS

data_processing:
FastQC tool (Version 0.11.8) was used for quality control of RNA-seq data to determine low quality or adaptor portions of the reads for trimming.
Read trimming was performed using Trimmomatic (Version 0.39) and strandness was determined using RSeQC (Version 4.0.0) and then reads were aligned to the mm10 reference genome using HiSAT2 (Version 2.1.0) with default settings and -rna-strandness R.
Aligned reads were counted using featureCounts (Version 1.6.2). Differential gene expression analysis was performed using R package DESeq (Version 1.38.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample in a master matrix

source_name: Heart

growth_protocol: Mice were housed in a barrier facility with a 12-hour:12-hour light:dark cycle and maintained on standard chow (2916 Teklad Global). To accelerate the onset of HCM, mice were treated with a custom chow (2916 Teklad Global base) containing Cyclosporine A (Alfa Aesar) at 1 g/kg and blue food dye at 0.2 g/kg.

extract_protocol:
For each nuclear sample, ventricular heart tissue was isolated from mice at 18 weeks of age. CM nuclei were isolated as previously described by Cui and Olson (STAR Protocols, 2021).Isolated nuclei were immediately used for downstream processing, or stored in Nuclei PURE Storage Buffer (Sigma Aldrich) at -80 °C. RNA was isolated using the RNeasy Micro Kit (Qiagen)
RNA-seq libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian kit (Takara), containing Illumina sequencing adapters. Libraries were visualized on a 2200 TapeStation System (Agilent) and quantified by QuBit dsDNA high-sensitivity assay (Invitrogen) before pooling and loading onto an Illumina NextSeq 500.

treatment_protocol: For injections (saline or dual AAV ABE), mice were genotyped at P0 and received either saline or a AAV9 dose via a single 40 μL bolus using a 31G insulin syringe through the diaphragm by a subxiphoid approach into the inferior mediastinum, avoiding the heart and the lung.

value: Heart

tag: cell line

value: CM

value: Isolated CM Nuclei

value: Myh6 hR403Q/+

value: Dual AAV ABE correction


title: E7.5 single cell mRNA Het

value: Whole Embryo

value: C57BL/6J background

value: TS11d 0s


title: HET

description: Single-End 75 bp Q30 score 91.5%

value: Saline


title: 120021

description: Gene expression data from nasal brushing of subject 120021.

value: Female

value: Current smoker

value: Cancer


title: WT

description: Single-End 75 bp Q30 score 91.5%


title: 50544

description: Gene expression data from nasal brushing of subject 50544.

value: Former smoker

value: Benign


title: 250532

description: Gene expression data from nasal brushing of subject 250532.


title: 220518

description: Gene expression data from nasal brushing of subject 220518.


title: FR121_macrophages

value: Day 5 and Day 6 post injury

value: Macrophages

value: Cre+ flox/null or Cre+ wt/null


title: MKC_iASPP_WT_ChIP_p63

city: Oxford, Oxfordshire

first: Xin

last: Lu

address: Roosevelt Drive

country: United Kingdom

institute: Ludwig Institute for Cancer Research, University of Oxford

data_processing:
FastQC v0.11.9 was used to assess sequencing quality
Truseq adapters were removed using cutadapt v2.10 (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 30).
Trimmed reads were aligned to the mm10 genome using BWA-backtrack. Reads aligning to the major autosome and sex chromosome contigs were selected, and duplicates were removed using SAMtools.
MACS2 was used to call peaks with a significance threshold of q < 0.05, and to generate ChIP-Seq bigwig files normalized to signal per million reads (SPMR) for visualization. Peaks overlapping with ENCODE Blacklist regions were discarded for downstream analysis. MAnorm was then used to calculate the average amplitude (A) values for each peak across iASPP KO and WT conditions, as well as the normalized log fold-change (M) between the two conditions and the associated p-value of differential enrichment for each peak. A p-value threshold of 5×10-3 was selected to define peaks that were significantly enriched in either iASPP WT or iASPP KO.
A publicly available genome browser session for this dataset can be found at http://genome.ucsc.edu/s/CarrollTM/iASPP_keratinocyte_p63. This session shows the supplementary files in this repository, including the bigWig files for each sample and the output wig files from MAnorm, showing the calculated M, A, and p values for each peak region.
Reproducible code for the downstream analysis can be found at github.com/t-carroll/iASPP_keratinocyte_ChIPseq_RNAseq.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files containing output tracks from MAnorm, comparing iASPP KO vs. iASPP WT ChIP-seq signal. MAnorm wig output contents are as described in https://buildmedia.readthedocs.org/media/pdf/manorm/stable/manorm.pdf. Briefly, M represents normalized fold change differences between samples (KO vs. WT), A represents average amplitude across samples, and p is the significance of differential binding between samples.
Supplementary_files_format_and_content: For each sample (both ChIP and input), a bigWig file is provided showing the density of ChIP-seq alignments with SPMR (signal per million reads) normalization. bigWig file format as described at https://genome.ucsc.edu/goldenpath/help/bigWig.html.

source_name: Primary keratinocytes

growth_protocol: Primary mouse keratinocytes were isolated as in doi: 10.1038/nprot.2008.50. Following trypsin-EDTA isolation, keratinocytes were plated on rat collagen type I-coated dishes in low-calcium FAD medium.

extract_protocol:
As described previously in doi: 10.15252/embr.201439941.
ChIP was conducted using the H129 anti-p63 antibody, and DNA was quantified by Qubit. 6ng ChiPped DNA or input control DNA were taken forward for Illumina library preparation as described in doi: 10.15252/embr.201439941. Briefly, following adaptor ligation, 4 cycles of pre-PCR and size selection (~300bp) were conducted, followed by 11 cycles of PCR amplification. Final libraries were sequenced on the Illumina NextSeq using a paired-end format (2x43nt).

value: Keratinocytes isolated from mouse skin

value: WT

tag: chip antibody

value: H129 anti-p63 antibody


title: 200505

description: Gene expression data from nasal brushing of subject 200505.

value: Male


title: 140105

description: Gene expression data from nasal brushing of subject 140105.


title: 140064

description: Gene expression data from nasal brushing of subject 140064.


title: MKC_iASPP_WT_ChIP_input


title: MKC_iASPP_WT3

data_processing:
FastQC v0.11.9 was used to assess sequencing quality
Truseq adapters were removed using cutadapt v2.10 (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -m 30)
Trimmed FASTQs were aligned to the mm10 genome using STAR v2.7.3. STAR index was built using GENCODE vM25 primary assembly comprehensive genome annotation set.
Gene-level counts were generated from the aligned reads and gene annotation file using featureCounts v2.0.0 (-t exon -g gene_name -s2)
Downstream analysis was conducted in R using DESeq2 (design formula: ~batch+condition, where condition is iASPP KO or WT)
Reproducible code for the downstream analysis can be found at github.com/t-carroll/iASPP_keratinocyte_ChIPseq_RNAseq.
Genome_build: mm10
Supplementary_files_format_and_content: MKC_iASPP_rawCounts.txt: output of featureCounts command
Supplementary_files_format_and_content: MKC_iASPP_DE_output.txt: Differential gene expression results produced by DESeq2 (design formula: ~batch+condition, where condition is iASPP KO or WT) following fold change moderation ('ashr' method)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), and DNA was removed with Dnase I digestion.
Library preparation was conducted as in doi: 10.15252/embr.201439941. Briefly, one microgram of RNA was ribodepleted using Ribo-Zero rRNA Removal Kit (Epicentre). Then, fragmentation and first- and second-strand reactions were conducted, and 5ng of ds-cDNA were taken forward for adapter ligation and amplification (4 cycles pre-PCR, size selection (~300bp), 11 cycles post-PCR amplification). Single-read sequencing was then conducted (1x42nt) on the Illumina NextSeq 500.

treatment_protocol: Media was replaced after 24h of culture with or without 1 mM tamoxifen to trigger iASPP KO.

value: mixed background (C57BL/6 and 129/Sv)

tag: batch


title: MKC_iASPP_KO_ChIP_p63

tag: deletion

value: specific deletion of Ppp1r13l exon8 in CK14-positive basal epithelial cells only


title: MKC_iASPP_WT2


title: E8.25 single cell ATAC miR-302KO

description:
filtered peak bc matrix files
E8.25_KOvWT_ATAC-2022-Signacv1.7.0.rds

value: Cranial Region

value: C57BL/6J background

value: TS12a 3s


title: MKC_iASPP_WT1


title: MKC_iASPP_KO_ChIP_input


title: MKC_iASPP_KO2


title: 220513

description: Gene expression data from nasal brushing of subject 220513.


title: MKC_iASPP_KO1


title: 250529

description: Gene expression data from nasal brushing of subject 250529.

value: Female


title: 50515

description: Gene expression data from nasal brushing of subject 50515.


title: 3xTg-AD wild type, 6 months old

city: Wuhan

first: Zhuo

last: Wang

state: Hubei

address: No. 169, Donghu Road, Wuchang District, Wuhan, Hubei

department: Neurology

institute: Zhongnan Hospital of Wuhan University

data_processing:
The fastp v0.21.0 was used for quality trimming and size check of the raw data
The filtered reads were mapping to the reference genome of Mus musculus (GRCm39) and Rattus norvegicus (mRatBN7.2) using HISAT2 v2.1.0
The gene expression analysis was performed using the DESeq2 package in R
GO and KEGG pathway enrichment analysis were performed using clusterProfiler software
Assembly: GRCm39; mRatBN7.2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

extract_protocol:
TRIzol (Sigma-Aldrich,USA) was used to extract total RNA from the hippocampus. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina,USA) following manufacturer's protocols.

value: hippocampus

tag: model

value: 6 months old


title: 3xTg-AD, 6 months old

value: PSEN1 M146V knockin, APPswe and TauP301L transgenes


title: 50537

description: Gene expression data from nasal brushing of subject 50537.

tag: Sex

value: Former smoker

value: Cancer


title: 110530

description: Gene expression data from nasal brushing of subject 110530.

tag: age

value: Current smoker

value: Benign


title: 120561

description: Gene expression data from nasal brushing of subject 120561.

tag: smoking status


title: 210520

description: Gene expression data from nasal brushing of subject 210520.

tag: fev1 % predicted


title: 50569

description: Gene expression data from nasal brushing of subject 50569.

tag: cancer status


title: 70508

description: Gene expression data from nasal brushing of subject 70508.


title: G7FSen_2

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

data_processing:
Sequencing reads were pre-processed using the nf-core/rnaseq v1.2 pipeline, and read quality was assessed by FastQC v0.11.8.
TrimGalore v0.5.0 was used to trim sequencing reads, eliminate Illumina adaptor remains, and discard short reads.
The resulting reads were mapped onto the mouse genome using HiSAT2 v2.1.0 and quantified using featureCounts v1.6.2.
Genome_build: GRCm38, release 81
Supplementary_files_format_and_content: Tab-delimited text file with raw read counts for each sample.

source_name: Skeletal muscles (tibialis anterior, gastrocnemius and quadriceps)

growth_protocol: Mice were housed in standard cages under 12-hour light-dark cycles and fed ad libitum with a standard chow diet.

extract_protocol:
Sequencing libraries were prepared directly from the freshly sorted lysed cells, without a previous RNA extraction step. RNA reverse transcription and cDNA amplification were held using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing from Clontech Takara.
The Illumina "Nextera XT" kit is used for the preparation of the libraries from the amplified cDNA. Libraries were sequenced in single-end mode with a read length of 51 base pairs with an average of 20 million reads for each sample by the Illumina HiSeq 2500 sequencer in the Genomic Unit of Centro Nacional de Investigaciones Cardiovasculares (CNIC).

treatment_protocol: Cells were isolated from skeletal muscle tissue (tibialis anterior, gastrocnemius and quadriceps).

value: Fibroadipogenic progenitors

tag: spider staining

value: SPiDER+

value: geriatric (28months old)

tag: muscle state

value: 7 days after injury (Cardiotoxin)


title: MKC_iASPP_KO3

tag: cell type

value: Keratinocytes isolated from mouse skin

value: mixed background (C57BL/6 and 129/Sv)

tag: genotype


title: G7FSen_1

tag: strain


title: 50572

description: Gene expression data from nasal brushing of subject 50572.

value: Male


title: G7FNSen_3

value: SPiDER-


title: G7FNSen_2


title: G7F_3

value: non-injured contralateral muscle at 7 days post injury


title: 10070

description: Gene expression data from nasal brushing of subject 10070.


title: G7F_1


title: 260513

description: Gene expression data from nasal brushing of subject 260513.


title: 230505

description: Gene expression data from nasal brushing of subject 230505.


title: 200507

description: Gene expression data from nasal brushing of subject 200507.


title: 260506

description: Gene expression data from nasal brushing of subject 260506.


title: 150507

description: Gene expression data from nasal brushing of subject 150507.

value: Female


title: G3FSen_2

value: 3 days after injury (Cardiotoxin)


title: G3FNSen_3


title: G3FSen_1


title: G3F_2

value: non-injured contralateral muscle at 3 days post injury


title: G3FNSen_1


title: G3F_1


title: G7F_2


title: 110540

description: Gene expression data from nasal brushing of subject 110540.


title: Y7FSen_3

value: young (3-6 months old)


title: Y7FSen_2


title: 220501

description: Gene expression data from nasal brushing of subject 220501.

value: Former smoker


title: 110012

description: Gene expression data from nasal brushing of subject 110012.


title: Y7FNSen_3


title: Y7FNSen_2


title: 260523

description: Gene expression data from nasal brushing of subject 260523.

value: Cancer


title: 160613

description: Gene expression data from nasal brushing of subject 160613.


title: 260505

description: Gene expression data from nasal brushing of subject 260505.


title: 170517

description: Gene expression data from nasal brushing of subject 170517.


title: 50570

description: Gene expression data from nasal brushing of subject 50570.


title: 60026

description: Gene expression data from nasal brushing of subject 60026.


title: 80527

description: Gene expression data from nasal brushing of subject 80527.


title: G3F_3


title: Y7FNSen_1


title: Y7F_3


title: 220530

description: Gene expression data from nasal brushing of subject 220530.

value: Current smoker


title: 30019

description: Gene expression data from nasal brushing of subject 30019.


title: 60022

description: Gene expression data from nasal brushing of subject 60022.


title: Y7F_2


title: 180502

description: Gene expression data from nasal brushing of subject 180502.


title: Y7F_1


title: 220510

description: Gene expression data from nasal brushing of subject 220510.


title: Y7FSen_1


title: Y3FSen_2


title: Y3FSen_3


title: Y3FSen_1


title: 70535

description: Gene expression data from nasal brushing of subject 70535.


title: 60023

description: Gene expression data from nasal brushing of subject 60023.


title: 200506

description: Gene expression data from nasal brushing of subject 200506.

value: Benign


title: 150527

description: Gene expression data from nasal brushing of subject 150527.


title: 160612

description: Gene expression data from nasal brushing of subject 160612.


title: Y3FNSen_2

value: Fibroadipogenic progenitors


title: Y3F_2


title: Y3F_3


title: Y3FNSen_1


title: Y3F_1


title: G7MSen_2

value: Myeloid cells

value: SPiDER+


title: G7MSen_1

value: geriatric (28months old)

value: 7 days after injury (Cardiotoxin)


title: G7MNSen_3


title: G7MSen_3


title: Y3FNSen_3


title: G7MNSen_1


title: G7M_3


title: G7M_2


title: 110526

description: Gene expression data from nasal brushing of subject 110526.


title: 120516

description: Gene expression data from nasal brushing of subject 120516.


title: 110515

description: Gene expression data from nasal brushing of subject 110515.


title: 70531

description: Gene expression data from nasal brushing of subject 70531.


title: 160614

description: Gene expression data from nasal brushing of subject 160614.


title: 70536

description: Gene expression data from nasal brushing of subject 70536.


title: 160580

description: Gene expression data from nasal brushing of subject 160580.


title: 50522

description: Gene expression data from nasal brushing of subject 50522.


title: 150519

description: Gene expression data from nasal brushing of subject 150519.


title: 160553

description: Gene expression data from nasal brushing of subject 160553.


title: 160531

description: Gene expression data from nasal brushing of subject 160531.


title: 130170

description: Gene expression data from nasal brushing of subject 130170.


title: 120521

description: Gene expression data from nasal brushing of subject 120521.


title: AGGAA, 3H, rep2

city: Paris

first: David

last: Bikard

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Bowtie2, 2.3.4
featureCounts, 1.6.1
Supplementary files format and content: csv file with counts data. Columns are: locus_tag,gene_name,con_r1,con_r2,con_r3,ACCCA_r1,ACCCA_r2,ACCCA_r3,AGGAA_r1,AGGAA_r2,AGGAA_r3

organism: Escherichia coli

growth_protocol: LB +  1 nM aTc + 50ug/ml Kanamycin

extract_protocol:
Trizol
TruSeq Stranded mRNA


title: 140141

description: Gene expression data from nasal brushing of subject 140141.


title: ACCCA, 3H, rep2


title: ACCCA, 3H, rep1


title: ACCCA, 3H, rep3


title: AGGAA, 3H, rep3


title: G3MSen_2


title: AGGAA, 3H, rep1


title: Control, 3H, rep3


title: G3MSen_1


title: G7M_1


title: 160558

description: Gene expression data from nasal brushing of subject 160558.


title: 120534

description: Gene expression data from nasal brushing of subject 120534.


title: Control, 3H, rep2


title: Control, 3H, rep1


title: G3MSen_3


title: G3MNSen_2


title: G3MNSen_3


title: G3MNSen_1


title: 190506

description: Gene expression data from nasal brushing of subject 190506.


title: 160590

description: Gene expression data from nasal brushing of subject 160590.


title: S21_20 dpa Rep3

city: Norwich

first: Martin

last: Vickers

state: Norfolk

address: Colney Ln

institute: John Innes Centre

data_processing:
Kallisto version 0.46.1 to calculate TPM values and obtain estimated counts
DESeq2 to search for differentially expressed genes
Assembly: Triticum turgidum Svevo.v1 canonical transcripts
Supplementary files format and content: tab-delimited text files include TPM values for each sample

organism: Triticum turgidum subsp. durum

source_name: endosperm

growth_protocol: Plants were grown in controlled environment rooms (CERs) at 60% relative humidity with 16 h light at 20°C and 8 h dark at 16°C. The CER light intensity was 400 μmol photons m−2 s−1.

extract_protocol:
Total RNA was extracted (n=3) from dissected endosperm tissue using the RNeasy PowerPlant kit (Qiagen).
Library preparation was carried out by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: tissue

value: endosperm

tag: cultivar/variety

value: Kronos

value: WT

tag: time

value: 20 dpa


title: S24_30 dpa Rep3

value: 30 dpa


title: S19_20 dpa Rep1


title: S22_30 dpa Rep1


title: S23_30 dpa Rep2


title: S17_18 dpa Rep2

value: 18 dpa


title: S16_18 dpa Rep1


title: S18_18 dpa Rep3


title: S15_15 dpa Rep3

value: 15 dpa


title: 120533

description: Gene expression data from nasal brushing of subject 120533.

value: Female


title: 50013

description: Gene expression data from nasal brushing of subject 50013.


title: S14_15 dpa Rep2


title: 50571

description: Gene expression data from nasal brushing of subject 50571.

value: Former smoker


title: 70537

description: Gene expression data from nasal brushing of subject 70537.

value: Cancer


title: 110506

description: Gene expression data from nasal brushing of subject 110506.

value: Current smoker


title: Y7MSen_3

value: young (3-6 months old)


title: S13_15 dpa Rep1


title: G3M_3

value: SPiDER-

value: non-injured contralateral muscle at 3 days post injury


title: 120031

description: Gene expression data from nasal brushing of subject 120031.


title: 250526

description: Gene expression data from nasal brushing of subject 250526.


title: S12_13 dpa Rep3

value: 13 dpa


title: 160619

description: Gene expression data from nasal brushing of subject 160619.

value: Male

value: Benign


title: G3M_2

value: Myeloid cells

value: geriatric (28months old)


title: S10_13 dpa Rep1

value: endosperm

value: Kronos

value: WT


title: Y7MSen_2

value: SPiDER+

value: 7 days after injury (Cardiotoxin)


title: S9_10 dpa Rep3

value: 10 dpa


title: Y7MNSen_3


title: S8_10 dpa Rep2


title: S6_8 dpa Rep3

value: 8 dpa


title: S7_10 dpa Rep1


title: Y7MSen_1


title: 160519

description: Gene expression data from nasal brushing of subject 160519.

value: Former smoker

value: Cancer


title: S4_8 dpa Rep1


title: S5_8 dpa Rep2


title: Y7MNSen_2

value: young (3-6 months old)


title: 200512

description: Gene expression data from nasal brushing of subject 200512.

value: Current smoker


title: S3_6 dpa Rep3

value: 6 dpa


title: 110024

description: Gene expression data from nasal brushing of subject 110024.


title: S2_6 dpa Rep2


title: 140133

description: Gene expression data from nasal brushing of subject 140133.

value: Female


title: Y7M_3

value: SPiDER-

value: non-injured contralateral muscle at 7 days post injury


title: S1_6 dpa Rep1


title: Y7M_2

value: Myeloid cells


title: S11_13 dpa Rep2

value: 13 dpa


title: 140118

description: Gene expression data from nasal brushing of subject 140118.

value: Benign


title: 140128

description: Gene expression data from nasal brushing of subject 140128.


title: 140094

description: Gene expression data from nasal brushing of subject 140094.

value: Male


title: Y7M_1


title: Y3MSen_3

value: 3 days after injury (Cardiotoxin)


title: 210524

description: Gene expression data from nasal brushing of subject 210524.


title: ependymoma_4

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: For each sample, 300 ng of RNA was hybridized with the PanCancer Immune Profiling probes for 17 hours at 67⁰C, following the manufacturing procedure (NanoString Technologies Inc., Seattle, WA, USA).

scan_protocol: The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).

source_name: ependymoma

extract_protocol: Samples were put at -15°C. Sections of 10µm were cut to finally have 100-200µm of each sample. These sections were put in a 42°C water batch and afterward added to a slide. The slides were dried overnight before deparaffinization was performed. The nCounter® PanCancer Immune Profiling Panel was used for NanoString targeted gene expression analysis. The total RNA was isolated from tumor tissue using the RNeasy® FFPE isolation kit (Qiagen, Leiden, The Netherlands). The RNA quantity and quality were measured using the Agilent 2100 BioAnalyzer (Santa Clara, CA, USA). RNA concentration was corrected to include fragments ≥ 300 bp.

tag: diagnosis

value: WHO III

tag: tumor location

value: IF

tag: resection location

value: Fossa cranii posterior


title: ependymoma_6

value: 4th ventricle


title: ependymoma_5


title: EAT, high fat diet, KO, rep3

city: Shaanxi

first: Xiaoming

last: Li

address: Zhuque Street

institute: xian jiaotong univercity

data_processing:
fastx_toolkit 0.0.14
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastx_toolkit
The raw data were mapped to the Mus_musculus (GRCm38.p6) reference genome using FASTX formatted files to build a STAR-v2.7 index
Supplementary files format and content: mm10
Supplementary files format and content: file includes FPKM values for all samples

source_name: eWAT

extract_protocol:
All mice were fed a control diet of standard 5% fat rodent chow (Xietong Shengwu, Nanjing, China). At 5 weeks of age and thereafter, HFD mice were fed 60% fat rodent chow (Research Diets, New Brunswick, NJ, USA). Body weight (BW) was measured weekly.
Total RNA was isolated from eWAT tissue samples from 21-week-old mice (n = 4 per group) using TRIzol.
The cDNA libraries were constructed from total RNA templates using the MGIEasy RNA Library Prep Set (MGI Tech; Shenzhen, Guangdong, China).

value: eWAT

value: ApoA4 knockdown

tag: treatment

value: high fat diet


title: EAT, high fat diet, KO, rep4


title: Y3MSen_2

value: SPiDER+

value: young (3-6 months old)


title: Y7MNSen_1

value: 7 days after injury (Cardiotoxin)


title: ependymoma_3

tag: Sex


title: ependymoma_1

tag: age

value: Female

value: ST

value: Supratentorial right frontal


title: EAT, high fat diet, KO, rep2


title: ependymoma_2

value: Supratentorial left frontal


title: 190509

description: Gene expression data from nasal brushing of subject 190509.

tag: smoking status

value: Former smoker

value: Benign


title: EAT, high fat diet, KO, rep1


title: Y3MSen_1

value: Myeloid cells

value: 3 days after injury (Cardiotoxin)


title: EAT, high fat diet, WT, rep4

value: WT


title: 160563

description: Gene expression data from nasal brushing of subject 160563.

value: Male

tag: fev1 % predicted


title: Y3MNSen_3

value: SPiDER-


title: EAT, high fat diet, WT, rep2

value: eWAT


title: 50078

description: Gene expression data from nasal brushing of subject 50078.

tag: cancer status

value: Cancer


title: 140076

description: Gene expression data from nasal brushing of subject 140076.

value: Current smoker


title: 10044

description: Gene expression data from nasal brushing of subject 10044.


title: Y3MNSen_2

tag: spider staining


title: EAT, high fat diet, WT, rep1

value: high fat diet


title: EAT, chow diet, KO, rep3

value: ApoA4 knockdown

value: chow diet


title: Y3MNSen_1

value: young (3-6 months old)

tag: muscle state


title: EAT, chow diet, KO, rep2


title: EAT, chow diet, WT, rep4


title: EAT, chow diet, KO, rep1


title: 110514

description: Gene expression data from nasal brushing of subject 110514.

value: Female


title: Y3M_3

tag: cell type

value: non-injured contralateral muscle at 3 days post injury


title: EAT, chow diet, WT, rep3

tag: genotype


title: EAT, chow diet, WT, rep2


title: EAT, high fat diet, WT, rep3


title: Y3M_2

tag: strain


title: Y3M_1


title: EAT, chow diet, WT, rep1

tag: tissue


title: 230507

description: Gene expression data from nasal brushing of subject 230507.


title: HEK-293T, Torin1-3

city: Beijing

first: Xing

last: Chen

address: Capital Medical University

institute: Capital Medical University

description: Control vs Torin1 _Gene_differential_expression

data_processing:
Raw sequencing data was preprocessed using fastp v0.19.6
Alignment of the clean sequencing data was conducted using STAR v2.4.0 (RNA-seq)
Abundance measurements of genes in RNA-seq was performed by using HTSeq-Count v0.12.4
Differential gene expression analysis of RNA-seq was conducted using DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: Excel files report gene relative expression values from RNA-seq

source_name: Embryonic kidney

growth_protocol: HEK-293T cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
For RNA-seq assay, total RNAs were extracted from HEK-293T cells using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq assay, HEK-293T cells that were untreated or treated with siCon, siGal3, DMSO or Torin1 250nM.

value: Embryonic kidney

tag: cell line

value: Human embryonic kidney cells


title: 260501

description: Gene expression data from nasal brushing of subject 260501.

value: Former smoker


title: G7SSen_3

value: Satellite cells

value: SPiDER+

value: geriatric (28months old)

value: 7 days after injury (Cardiotoxin)


title: HEK-293T, Torin1-1


title: HEK-293T, Control-3

value: DMSO


title: 60031

description: Gene expression data from nasal brushing of subject 60031.


title: 250512

description: Gene expression data from nasal brushing of subject 250512.


title: EAT, chow diet, KO, rep4

value: eWAT


title: HEK-293T, Control-2


title: 10027

description: Gene expression data from nasal brushing of subject 10027.

value: Male

value: Cancer


title: G7SSen_2


title: HEK-293T, Control-1


title: G7SSen_1


title: HEK-293T, siGal3-3

description: siCon vs siGal3 _Gene_differential_expression


title: HEK-293T, siGal3-2


title: G7SNSen_3

value: SPiDER-


title: HEK-293T, siCon-3

value: siCon


title: HEK-293T, siGal3-1


title: 140010

description: Gene expression data from nasal brushing of subject 140010.


title: G7SNSen_2


title: HEK-293T, siCon-2


title: HEK-293T, siCon-1


title: HEK-293T, Torin1-2


title: mouse testis 50to700nt MgR rep3

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

description:
total RNA, remove rRNA
Discover the 3'-end Nm of RNA

data_processing:
NGS raw data gained from Illumina HiSeqX10 with 150 bp paired end reads
First, Cutadapt (v2.8) was used to cut the adapters of the paired-end reads with the following parameters: cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 15 -e 0.15. Then reads were subsequently mapped to the reference genome (mm10 or dm6) and transcriptome with STAR software with the following parameters: --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 30 --outFilterMismatchNmax 15 --outFilterMismatchNoverLmax 0.1 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15 --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts.
To identify significantly enriched 3’end-Nm sites,  we first call significant 3’-end singal with following criteria: (1) upFC=endCov/upCov≥2; (2) downFC=endCov/downCov≥2; (3) p value≤-5; (4) read count≥5. A candidate 3’-end Nm site was required to bear a significant 3'-end singal in all nine samples under three conditions (i.e. inupt, MgR-treated, MgR+OED-treated).
Assembly: mm10, dm6
Supplementary files format and content: bigwig files were generated using self-developed software; Scores represent Reads per million mapped reads (RPM).

source_name: mouse testis

growth_protocol: KC167 cells were cultivated at 26℃ in serum-free medium containing 1% penicillin and streptomycin (Gibco) without CO2. Mouse testes were isolated from 3 pieces of 8 weeks sexual mature C57BL/6J mouse (GuangDong Medical Laboratory Animal Center)

extract_protocol:
RNA was collected using RNAzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MgR exoribonuclease digestion reaction: RNA samples from the previous step were firstly denatured at 65℃ for 5min and put it on ice immediately. MgR exoribonuclease (Synbio Tech) digestion reaction was conducted by using 4ug enzyme for 1μg RNA samples with MgR Reaction buffer (20mM Tris ph=8.5, 10μM Zncl2, 100mM KCl) at 37℃ for 1 hour. Purify small RNA using RNA Clean&Concentration-5 kit (Zymoresearch; R1017), according to the manufacturer’s instructions. NaIO4 oxidation-elimination-dephosphorylation (OED): MgR treatment RNA was oxidized with 20mM NaIO4 (Thermo, PI20504) under 200mM lysine-HCl buffer (ph=8.5) incubated at 37℃ for 30min with shaking in the darkness and the β-elimination reacting automatically. Quench the reaction by adding thylene glycol (Thermo, 29810). Dephosphorylate was followed by adding rSAP enzyme (NEB, M0371L) to incubate at 37℃ for 30min with shaking in the darkness. The RNA was purified using RNA Clean&Concentration-5 kit (Zymoresearch; R1017), according to the manufacturer’s instructions. Then another OED cycle was conducted for the previous purified RNA, followed by purification. Finally, the RNA samples were subjected to periodate oxidation followed β-elimination reacting automatically without the subsequent dephosphorylation step, purifying with Rnasefree water.

value: MgR-treated

tag: treatment label

value: mouse testis

value: wild type


title: 30032

description: Gene expression data from nasal brushing of subject 30032.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.54.0), using R version 3.5.1 and the Brainarray hugene10sthsentrezgcdf R package (version 22.0.0).

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

value: Female

value: Current smoker

value: Benign


title: G7S_3

value: non-injured contralateral muscle at 7 days post injury


title: mouse testis 50to700nt MgR rep1


title: 140096

description: Gene expression data from nasal brushing of subject 140096.

value: Former smoker


title: mouse testis 50to700nt MgR rep2


title: 120507

description: Gene expression data from nasal brushing of subject 120507.


title: 100501

description: Gene expression data from nasal brushing of subject 100501.


title: G7S_2

value: Satellite cells


title: mouse testis 50to700nt MgR+OED rep3

value: MgR+OED-treated

value: exoribonuclease RNase R treated


title: 60008

description: Gene expression data from nasal brushing of subject 60008.


title: G7S_1

value: geriatric (28months old)


title: mouse testis 50to700nt MgR+OED rep2


title: G3SSen_3

value: SPiDER+

value: 3 days after injury (Cardiotoxin)


title: mouse testis 50to700nt MgR+OED rep1


title: mouse testis 50to700nt Input rep3

value: non-treated


title: G3SSen_2


title: mouse testis 50to700nt Input rep2


title: mouse testis 50to700nt Input rep1


title: mouse testis 20to50nt MgR rep2


title: mouse testis 20to50nt MgR rep1


title: mouse testis 20to50nt MgR rep3


title: mouse testis 20to50nt MgR+OED rep3


title: G3SSen_1


title: 120549

description: Gene expression data from nasal brushing of subject 120549.

value: Cancer


title: 140052

description: Gene expression data from nasal brushing of subject 140052.


title: G3SNSen_2

value: SPiDER-


title: G3SNSen_3


title: 150521

description: Gene expression data from nasal brushing of subject 150521.

value: Male


title: mouse testis 20to50nt Input rep3

value: mouse testis


title: mouse testis 20to50nt MgR+OED rep1

value: wild type


title: 160564

description: Gene expression data from nasal brushing of subject 160564.


title: 100002

description: Gene expression data from nasal brushing of subject 100002.


title: G3SNSen_1


title: 60035

description: Gene expression data from nasal brushing of subject 60035.

value: Female


title: mouse testis 20to50nt Input rep1


title: 50542

description: Gene expression data from nasal brushing of subject 50542.


title: G3S_3

value: non-injured contralateral muscle at 3 days post injury


title: S20_20 dpa Rep2

value: endosperm

tag: cultivar/variety

value: Kronos

value: WT

tag: time

value: 20 dpa


title: mouse testis 20to50nt MgR+OED rep2

value: MgR+OED-treated


title: 250505

description: Gene expression data from nasal brushing of subject 250505.

value: Current smoker


title: 60017

description: Gene expression data from nasal brushing of subject 60017.


title: 60027

description: Gene expression data from nasal brushing of subject 60027.

value: Former smoker


title: 10022

description: Gene expression data from nasal brushing of subject 10022.


title: Y7SSen_2

value: Satellite cells

value: SPiDER+

value: young (3-6 months old)

value: 7 days after injury (Cardiotoxin)


title: mouse testis 20to50nt Input rep2

description:
total RNA, remove rRNA
Discover the 3'-end Nm of RNA

value: non-treated


title: SA-1_GEX

city: Ann Arbor

first: Irina

last: Grigorova

address: 1150 W MEDICAL CENTER DR

department: Microbiology and Immunology

institute: University of Michigan

description: 10x Genomics

data_processing:
10x Genomics CellRanger-6.1.2
The single cell RNA-seq libraries were prepared at the University of Michigan Advanced Genomics Core using the 10X Genomics Chromium Next GEM Single Cell 5′ R2 only following the manufacturer’s protocol.
The libraries were run on the PerkinElmer LabChip GX Touch HT for library quality control before sequencing.
Libraries were sequenced on a NovaSeq6000 with the following run configuration: R1 - 28, Index1-10, R2 - 150. The total number of cells recovered was 15514.
mm10
Assembly: comma-separated values file that is a delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: html file containing summary of the processed data

source_name: Lymph node

extract_protocol:
Single Cell 5' R2-only
Single cell libraries were generated using the 10x Genomics Chromium Controller with Immune Profiling reagents following the manufacturer’s protocol (10x Genomics)

value: Lymph node

value: Follicular T cells


title: SA-2_VDJ

description: 10x Genomics


title: SA-1_VDJ

description: 10x Genomics


title: SA-NucPr-1_GEX

description: 10x Genomics


title: SA-NucPr-2_GEX

description: 10x Genomics


title: SA-NucPr-2_VDJ

description: 10x Genomics


title: SA-2_GEX

description: 10x Genomics


title: 160552

description: Gene expression data from nasal brushing of subject 160552.

value: Male

value: Cancer


title: G3S_2

value: SPiDER-

value: geriatric (28months old)

value: non-injured contralateral muscle at 3 days post injury


title: G3M_1

value: Myeloid cells


title: SA-NucPr-1_VDJ

description: 10x Genomics

value: WT


title: Y7SSen_3


title: NoCFC_SD_HA_PELL_9

first: Lijing

state: MI

address: 1105 N University Ave

department: MCDB

data_processing:
Amplified complementary DNA libraries were prepared using Takara’s SMART-seq v4 Ultra Low Input RNA Kit (Takara 634888) and sequenced on Illumina’s NovaSEq. 6000 platform.
Reads mapped to unique transcripts were counted with featureCounts.
Libraries were run with onboard cluster generation, and together comprised 40% of a NovaSeq S4 200 cycle kit (v1.5; ~16–20 billion paired-end reads per flow cell, quality score ≥ 90% of bases higher than Q30).
Sequencing reads (50 bp, paired-end) were mapped to Mus musculus using Star v2.6.1a and quality checked with Multiqc (v1.6a0). Reads mapped to unique transcripts were counted with featureCounts.
Assembly: GRCm38.p6
Supplementary files format and content: merged_counts.txt has counts for each different GeneID for all samples

source_name: Brain

growth_protocol: Refer to: Delorme J, Wang L, Kodoth V, Wang Y, Ma J, Jiang S, Aton SJ. Hippocampal neurons' cytosolic and membrane-bound ribosomal transcript profiles are differentially regulated by learning and subsequent sleep. Proc Natl Acad Sci U S A. 2021 Nov 30;118(48):e2108534118. doi: 10.1073/pnas.2108534118. PMID: 34819370; PMCID: PMC8640746.

extract_protocol:
RiboTag TRAP was performed as previously described by indirect conjugation, separating MB and free-floating ribosomes. Following homogenization and centrifugation, the resulting supernatant (cytosolic fraction) was transferred to a new tube while the pellet (MB fraction) was resuspended in homogenization buffer. Both MB and cytosolic fractions were separated into Input, Camk2a+, and pS6+ fractions. For isolating ribosomes from Camk2a+ populations, fractions were incubated with 1:40 anti-HA antibody (Abcam, ab9110). To isolate ribosomes from highly active (pS6+) neurons, fractions were incubated with 1:25 anti-pS6 244-247 (ThermoFisher 44-923G). Homogenate-antibody solution was added directly to Protein G Dynabeads (ThermoFisher, 10009D) for incubation. After washing conjugated beads and removing the supernatant, RNA was eluted by vortexing the beads vigorously in 350 μL RLT (Qiagen, 79216). Eluted RNA was purified using RNeasy Micro kit (Qiagen).
Amplified complementary DNA libraries were prepared using Takara’s SMART-seq v4 Ultra Low Input RNA Kit (Takara 634888)

value: Brain

value: neuron

value: male

tag: cell population

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: fraction

value: membrane(PELL)

tag: treatment cfc

value: NO

tag: treatment sleep

value: SD


title: G3S_1

value: Satellite cells

tag: age


title: NoCFC_SD_Input_PELL_9

treatment_protocol: Refer to: Delorme J, Wang L, Kodoth V, Wang Y, Ma J, Jiang S, Aton SJ. Hippocampal neurons' cytosolic and membrane-bound ribosomal transcript profiles are differentially regulated by learning and subsequent sleep. Proc Natl Acad Sci U S A. 2021 Nov 30;118(48):e2108534118. doi: 10.1073/pnas.2108534118. PMID: 34819370; PMCID: PMC8640746.

tag: Sex

value: Input


title: NoCFC_SD_S6_PELL_9


title: Y7SNSen_3

value: young (3-6 months old)

value: 7 days after injury (Cardiotoxin)


title: 210513

first: Adam

address: 72 East Concord Street, E632

description: Gene expression data from nasal brushing of subject 210513.

source_name: Brushing of nasal epithelium

value: Female

tag: smoking status

value: Former smoker

tag: fev1 % predicted

tag: cancer status

value: Benign


title: 130156

description: Gene expression data from nasal brushing of subject 130156.

value: Male


title: 140039

description: Gene expression data from nasal brushing of subject 140039.

value: Cancer


title: NoCFC_SD_S6_SUP_9

tag: cell type

value: cytosolic (SUP)


title: NoCFC_SD_HA_SUP_9

value: Brain

tag: genotype


title: Y7SNSen_2

tag: strain

tag: spider staining

value: SPiDER-

tag: muscle state


title: NoCFC_SD_Input_PELL_8

tag: tissue

value: neuron

value: male


title: NoCFC_SD_Input_SUP_8

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: Y7SNSen_1


title: Y7SSen_1

value: SPiDER+


title: 160585

description: Gene expression data from nasal brushing of subject 160585.


title: Y7S_3

value: non-injured contralateral muscle at 7 days post injury


title: NoCFC_SD_S6_SUP_8

value: NO

value: SD


title: NoCFC_SD_HA_SUP_8


title: NoCFC_SD_S6_PELL_8

value: membrane(PELL)


title: 210511

description: Gene expression data from nasal brushing of subject 210511.

value: Current smoker


title: NoCFC_SD_Input_PELL_7

value: Input


title: NoCFC_SD_S6_PELL_7


title: NoCFC_SD_HA_PELL_7


title: Y7S_1

value: Satellite cells

value: young (3-6 months old)


title: NoCFC_SD_HA_SUP_7


title: NoCFC_SD_Input_SUP_7


title: 10103

description: Gene expression data from nasal brushing of subject 10103.

value: Female

value: Former smoker

value: Benign


title: Y3SSen_2

value: 3 days after injury (Cardiotoxin)


title: Y3SSen_3


title: Y7S_2

value: SPiDER-


title: NoCFC_SD_Input_SUP_9

value: Brain

value: neuron

value: cytosolic (SUP)


title: NoCFC_SD_HA_PELL_8

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: 160570

description: Gene expression data from nasal brushing of subject 160570.

value: Cancer


title: G7SNSen_1

value: geriatric (28months old)

value: 7 days after injury (Cardiotoxin)


title: 140126

description: Gene expression data from nasal brushing of subject 140126.


title: NoCFC_Sleep_Input_PELL_6

value: membrane(PELL)

value: NO

value: Sleep


title: NoCFC_Sleep_Input_SUP_6

value: Input


title: NoCFC_Sleep_S6_PELL_6


title: Y3SSen_1

value: Satellite cells

value: SPiDER+

value: young (3-6 months old)


title: NoCFC_Sleep_HA_PELL_6


title: Y3SNSen_3

value: 3 days after injury (Cardiotoxin)


title: 140059

description: Gene expression data from nasal brushing of subject 140059.

value: Male

value: Former smoker


title: 120526

description: Gene expression data from nasal brushing of subject 120526.

value: Female

value: Current smoker

value: Benign


title: NoCFC_SD_S6_SUP_7

value: Brain

value: neuron

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)

value: SD


title: 160528

description: Gene expression data from nasal brushing of subject 160528.

value: Cancer


title: Y3SNSen_2

value: SPiDER-


title: NoCFC_Sleep_S6_SUP_6

value: NO

value: Sleep


title: NoCFC_Sleep_HA_SUP_6


title: 160525

description: Gene expression data from nasal brushing of subject 160525.


title: NoCFC_Sleep_Input_SUP_5

value: Input


title: NoCFC_Sleep_S6_PELL_5

value: membrane(PELL)


title: NoCFC_Sleep_HA_PELL_5


title: NoCFC_Sleep_HA_SUP_5


title: Y3S_3

value: Satellite cells

value: young (3-6 months old)

value: non-injured contralateral muscle at 3 days post injury


title: Y3S_1


title: 100014

description: Gene expression data from nasal brushing of subject 100014.

value: Female

value: Former smoker


title: 160527

description: Gene expression data from nasal brushing of subject 160527.

value: Male

value: Current smoker


title: NoCFC_Sleep_S6_SUP_5

value: Brain

value: neuron

value: male


title: NoCFC_Sleep_Input_PELL_4

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: NoCFC_Sleep_S6_PELL_4


title: EAE SC IL17-GFP+

city: New York

first: Dan

last: Littman

state: NY

address: 430 East 29th St Room 403

institute: New York University School of Medicine

data_processing:
ATAC-seq:Bowtie2 was used to align the reads to the mm10 genome using parameters —very-sensitive. Picard tools was used to mark and remove duplicates.  Deeptools bamCoverage was used to generate a bigwig file normalized using RPGC and 10 bins.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for ATAC and ChIP, normalized count file for bulk RNAseq

source_name: Spinal cord

growth_protocol: Naïve T cells were purified from lymph nodes and spleens of six to eight week old WT or RORaKO mice, by sorting live (DAPI-), CD4+CD25-CD62L+CD44low naïve T cells using a FACSAria (BD). Cells were cultured in IMDM (Sigma) supplemented with 10% heat-inactivated FBS (Hyclone), 10U/ml penicillin-streptomycin (Invitrogen), 10g/ml gentamicin (Gibco), 4mM L-glutamine, and 50μM β-mercaptoethanol.

extract_protocol:
Samples were prepared according to (Buenrostro et al., 2013). Briefly, 50,000 sort-purified Th17 cells were pelleted in a fixed rotor centrifuge at 500xg for 5 minutes, washed once with 50 μL of cold 1x PBS buffer. Spun down again at 500xg for 5 min. Cells were gently pipetted to resuspend the cell pellet in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) for 10 minutes. Cells were then spun down immediately at 500xg for 10 min and 4 degrees after which the supernatant was discarded and proceeded immediately to the Tn5 transposition reaction. Gently pipette to resuspend nuclei in the transposition reaction mix. Incubate the transposition reaction at 37 degrees for 30 min. Immediately following transposition, purify using a Qiagen MinElute Kit. Elute transposed DNA in 10 μL Elution Buffer (10mM Tris buffer, pH 8).
The transposed nuclei were then amplified using NEBNext High-fidelity 2X PCR master mix for 5 cycles. In order to reduce GC and size bias in PCR, the PCR reaction is monitored using qPCR to stop amplification prior to saturation using a qPCR side reaction. The additional number of cycles needed for the remaining 45 μL PCR reaction is determined as following: (1) Plot linear Rn vs. Cycle (2) Set 5000 RF threshold (3) Calculate the # of cycle that is corresponded to ¼ of maximum fluorescent intensity. Purify amplified library using Qiagen PCR Cleanup Kit. Elute the purified library in 20 μL Elution Buffer (10mM Tris Buffer, pH 8).

treatment_protocol: For T cell polarization, 1 x 10^5 cells were seeded in 200μl/well in 96-well plates that were pre-coated with a 1:20 dilution of goat anti-hamster IgG in PBS (STOCK = 1mg/ml, MP Biomedicals Catalog # 55398).  Naïve T cells were primed with anti-CD3ε (0.25μg/mL) and anti-CD28 (1μg/mL) for 24 hours prior to polarization. Cells were further cultured for 48h under Th-lineage polarizing conditions; Th0 (Con. : 100U/mL IL-2, 2.5μg/mL anti-IL-4, 2.5μg/mL anti-IFNg), Th2 (20U/ml IL-2, 20ng/ml IL-4, 2.5μg/mL anti-IFNg), Th17 (0.3 ng/mL TGF-β, 20 ng/mL IL-6, 20 ng/mL IL-23, 2.5μg/mL anti-IL-4, 2.5μg/mL anti-IFNg).

value: Spinal cord

tag: isolate

tag: disease

value: EAE

tag: disease stage

value: Peak


title: 140037

last: Gower

institute: Boston University School of Medicine

description: Gene expression data from nasal brushing of subject 140037.

value: Cancer


title: 10078

description: Gene expression data from nasal brushing of subject 10078.


title: EAE SC IL17-GFP-


title: NoCFC_Sleep_Input_PELL_5

tag: cell population

value: Input

tag: fraction

value: NO

value: Sleep


title: NoCFC_Sleep_HA_PELL_4

value: membrane(PELL)

tag: treatment cfc

tag: treatment sleep


title: NoCFC_Sleep_HA_SUP_4

tag: Sex

value: cytosolic (SUP)


title: SI IL17-GFP+

source_name: Small intestinal laminapropria

value: Small intestinal laminapropria


title: CFC_SD_Input_PELL_30

value: YES

value: SD


title: SI IL17-GFP-


title: Y3SNSen_1

value: Satellite cells

value: SPiDER-

tag: age

value: young (3-6 months old)

value: 3 days after injury (Cardiotoxin)


title: 250519

description: Gene expression data from nasal brushing of subject 250519.

value: Female

tag: smoking status

value: Former smoker

tag: fev1 % predicted


title: 10110

description: Gene expression data from nasal brushing of subject 10110.

tag: cancer status

value: Benign


title: CFC_SD_S6_PELL_30

value: Brain

tag: cell type

value: neuron

value: male

tag: genotype

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: 160538

description: Gene expression data from nasal brushing of subject 160538.

value: Current smoker


title: CFC_SD_HA_PELL_30

value: membrane(PELL)


title: NoCFC_Sleep_Input_SUP_4

value: Input

value: cytosolic (SUP)

value: NO

value: Sleep


title: In vitro 48h Th17 Rep 1

source_name: lymphoid organ

value: lymphoid organ

value: Wild-type


title: NoCFC_Sleep_Input_SUP_3


title: 160536

description: Gene expression data from nasal brushing of subject 160536.


title: NoCFC_Sleep_S6_PELL_3


title: CFC_SD_HA_SUP_30

value: YES

value: SD


title: NoCFC_Sleep_S6_SUP_4


title: NoCFC_Sleep_Input_PELL_3


title: In vitro 48h Th2 Rep 2


title: 120535

description: Gene expression data from nasal brushing of subject 120535.

value: Male


title: 140029

description: Gene expression data from nasal brushing of subject 140029.

value: Female

value: Cancer


title: NoCFC_Sleep_HA_PELL_3

value: Brain


title: NoCFC_Sleep_HA_SUP_3

value: neuron


title: In vitro 48h Th2 Rep 1


title: CFC_SD_Input_PELL_29

value: male


title: In vitro 48h Th0 Rep 2


title: CFC_SD_Input_SUP_30

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: NoCFC_Sleep_S6_SUP_3


title: CFC_SD_Input_SUP_29


title: In vitro 48h Th0 Rep 1


title: 120004

description: Gene expression data from nasal brushing of subject 120004.

value: Current smoker

value: Benign


title: 20023

description: Gene expression data from nasal brushing of subject 20023.

value: Former smoker


title: CFC_SD_S6_SUP_30

value: cytosolic (SUP)


title: CFC_SD_S6_PELL_29

value: membrane(PELL)


title: In vitro 48h Th17 Rep 2


title: 160540

description: Gene expression data from nasal brushing of subject 160540.


title: Sprague Dawley rat, shOpn3.5

city: Bristol

first: Ghadir

last: ElSamad

address: Whitson St.

institute: University of Bristol

data_processing:
Original .fastq files were inspected using FastQC. As all samples passed initial QC no further trimming was applied
.fastq were aligned to the rat reference genome (Rn6) using RNA-STAR mapper
Reads were counted using featureCounts at a gene level
Differential expression analysis was performed using DEseq2
Assembly: Rn6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Hypothalamic supraoptic nucleus

growth_protocol: Male Sprague-Dawley rats weighing 250–300 g (Envigo) were maintained under a 12:12 light-dark cycle at a constant temperature of 21-22°C and a relative humidity of 40%-50% with ad libitum access to food and water

extract_protocol: SON samples were collected using a 1-mm micropunch (Fine Scientific Tools) from 100 μm brain coronal sections in a cryostat. RNA from individual SONs was extracted with RNeasy Mini Kit (74106, Qiagen) according to manufacturer's instructions and eluted in a final volume of 30 µl.

treatment_protocol: Rats were injected with adeno-associated viruses delivering Opn3 shRNA in one SON and non-targeting shRNA to the opposite RNA. Two weeks after administration SON samples were collected.

value: Hypothalamic supraoptic nucleus

tag: shRNA

tag: strain

value: Sprague Dawley

tag: treatment

value: knockdown by ShRNA


title: CFC_SD_HA_PELL_29

tag: tissue

value: YES


title: Input_pooled

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

data_processing:
The 75-nt single end sequence reads were mapped to the human reference genome (GRCh37/hg19) using the BWA algorithm  with default settings.
Duplicate reads were removed and only uniquely mapped reads were used for further analysis.
Peak locations (enriched regions) for HDAC1, BRD4, H3K9Ac, H3K27ac were determined using the MACS algorithm (v1.4.2) with a cutoff p-value of 1E-7 for narrow peaks and 1E-1 for broad peaks.
Assembly: GRCh37/hg19
Supplementary files format and content: narrowPeak

source_name: Pooled Input

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. 15 ug of chromatin was immunoprecipitated per sample using antibodies against HDAC1 (Active Motif # 40967) and BRD4 (Active Motif # 91301, 4l), H3K9Ac (Active Motif # 39917), H3K27Ac (Active Motif # 39133), and RNA Pol II (Active Motif # 91151),
Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end-polishing, dA addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500.

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: del 11q

tag: disease state

value: CLL

tag: chip antibody

value: Input DNA

value: pool of Control and Abexinostat treated cells


title: Sprague Dawley rat, shOpn3.4

value: male


title: CTRL3_00251766_H3K27Ac

source_name: CLL,1766 , Control

value: H3K27Ac (Active Motif # 39133)

value: Control


title: Sprague Dawley rat, shOpn3.3


title: CFC_SD_S6_SUP_29

value: Brain

value: neuron

tag: cell population

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: SD


title: 60019

city: Boston

description: Gene expression data from nasal brushing of subject 60019.

value: Female

value: Former smoker

value: Cancer


title: 120027

description: Gene expression data from nasal brushing of subject 120027.

value: Current smoker


title: CFC_SD_HA_SUP_29

tag: fraction

value: cytosolic (SUP)

value: YES


title: Sprague Dawley rat, shOpn3.2

value: Hypothalamic supraoptic nucleus

value: Sprague Dawley

value: knockdown by ShRNA


title: Treated2_00251275_H3K27Ac

source_name: CLL,1275 Abexinostat 400mM  6h

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: del 11q

value: CLL

value: Abexinostat


title: NoCFC_SD_Input_PELL_28

value: Brain

value: neuron

value: male

value: Input

value: membrane(PELL)

tag: treatment cfc

value: NO


title: Sprague Dawley rat, shOpn3.1


title: CTRL2_00251275_H3K27Ac

source_name: CLL,1275 A, Control

value: H3K27Ac (Active Motif # 39133)

value: Control


title: NoCFC_SD_S6_PELL_28

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: treatment sleep

value: SD


title: Treated1_00251228_H3K27Ac

source_name: CLL,1228 Abexinostat 400mM 6h


title: Sprague Dawley rat, shControl4

value: Hypothalamic supraoptic nucleus

value: shControl

value: Sprague Dawley

tag: Sex


title: Sprague Dawley rat, shControl5

value: knockdown by ShRNA


title: CTRL1_00251228_H3K27Ac

source_name: CLL,1228 , Control

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: del 11q


title: NoCFC_SD_HA_PELL_28

value: Brain


title: 120029

description: Gene expression data from nasal brushing of subject 120029.

value: Male

tag: age

value: Former smoker

value: Cancer


title: Treated3_00251766_H3K27Ac

source_name: CLL,1766 Abexinostat 400mM  6h

value: CLL

value: Abexinostat


title: Treated3_00251766_BRD4

value: BRD4 (Active Motif # 91301, 4ml)


title: NoCFC_SD_Input_SUP_28

value: neuron

value: male

value: Input

value: cytosolic (SUP)

value: NO


title: 150514

description: Gene expression data from nasal brushing of subject 150514.

tag: smoking status

value: Benign


title: 250502

description: Gene expression data from nasal brushing of subject 250502.

value: Female

tag: fev1 % predicted


title: NoCFC_SD_S6_SUP_28

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: SD


title: Sprague Dawley rat, shControl2

value: Hypothalamic supraoptic nucleus

value: shControl

value: Sprague Dawley

value: knockdown by ShRNA


title: CTRL3_00251766_BRD4

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: del 11q

value: Control


title: NoCFC_SD_HA_SUP_28

value: Brain

value: neuron


title: Sprague Dawley rat, shControl1

value: male


title: 110501

description: Gene expression data from nasal brushing of subject 110501.

value: Male

value: Current smoker

tag: cancer status


title: NoCFC_SD_Input_PELL_27

tag: cell type

value: Input

value: membrane(PELL)

value: NO


title: 70016

description: Gene expression data from nasal brushing of subject 70016.

value: Cancer


title: NoCFC_SD_Input_SUP_27

tag: genotype

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)

value: SD


title: Sham, 3-4 months old

source_name: hippocampus

value: hippocampus

tag: model

value: Sham

value: WT

value: 3-4 months old


title: CTRL2_00251275_BRD4

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: del 11q

value: CLL

value: BRD4 (Active Motif # 91301, 4ml)

value: Control


title: Sprague Dawley rat, shControl3

value: Hypothalamic supraoptic nucleus

tag: shRNA

value: shControl

tag: strain

value: Sprague Dawley

value: male

value: knockdown by ShRNA


title: Treated2_00251275_BRD4

tag: tissue

tag: treatment

value: Abexinostat


title: 2VO, 3-4 months old


title: NoCFC_SD_S6_PELL_27

value: Brain

value: neuron

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: NO

value: SD


title: NoCFC_SD_HA_PELL_27


title: Treated3_00251766_H3K9Ac

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

tag: disease state

tag: chip antibody

value: H3K9Ac (Active Motif # 39917)


title: CTRL1_00251228_BRD4

value: del 11q

value: CLL

value: BRD4 (Active Motif # 91301, 4ml)


title: Treated1_00251228_BRD4

source_name: CLL,1228 Abexinostat 400mM  6h


title: 120017

description: Gene expression data from nasal brushing of subject 120017.

value: Female

value: Current smoker

value: Cancer


title: 70018

description: Gene expression data from nasal brushing of subject 70018.

value: Male

value: Former smoker


title: NoCFC_SD_S6_SUP_27

value: Brain

value: male

tag: cell population

tag: fraction

value: cytosolic (SUP)


title: Treated2_00251275_H3K9Ac

value: Abexinostat


title: CTRL3_00251766_H3K9Ac

value: Control


title: NoCFC_SD_HA_SUP_27

value: neuron

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

tag: treatment cfc

value: NO

tag: treatment sleep

value: SD


title: 120014

description: Gene expression data from nasal brushing of subject 120014.

tag: Sex

tag: age


title: CFC_Sleep_Input_PELL_26

value: Input

value: membrane(PELL)

value: YES

value: Sleep


title: 140042

description: Gene expression data from nasal brushing of subject 140042.

tag: smoking status

tag: fev1 % predicted


title: 60024

description: Gene expression data from nasal brushing of subject 60024.

tag: cancer status


title: 180501

description: Gene expression data from nasal brushing of subject 180501.

value: Female


title: 50508

description: Gene expression data from nasal brushing of subject 50508.

value: Current smoker

value: Cancer


title: 50545

description: Gene expression data from nasal brushing of subject 50545.

value: Male

value: Former smoker


title: 30030

description: Gene expression data from nasal brushing of subject 30030.


title: T48Gm-1

city: Lanzhou City

first: lu

last: zhao

state: Gansu Province

address: Yintan Road Street

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: gill tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gill tissues

value: IHNV infection

tag: genotype

value: wild-type


title: 140047

description: Gene expression data from nasal brushing of subject 140047.

value: Benign


title: 50034

description: Gene expression data from nasal brushing of subject 50034.


title: CTRL2_00251275_H3K9Ac

value: Blood, PBMC

tag: cell type

value: Human peripheral blood mononuclear cells

value: del 11q

value: CLL

value: H3K9Ac (Active Motif # 39917)

value: Control


title: CFC_Sleep_Input_SUP_26

value: Brain

value: neuron

value: male

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)

value: YES


title: 50031

description: Gene expression data from nasal brushing of subject 50031.

value: Male

value: Former smoker

value: Cancer


title: CFC_Sleep_S6_SUP_26

value: Sleep


title: CFC_Sleep_S6_PELL_26

value: membrane(PELL)


title: T48Gm-2

value: gill tissues

value: IHNV infection

value: wild-type


title: Treated1_00251228_H3K9Ac

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: del 11q

value: CLL

value: H3K9Ac (Active Motif # 39917)

value: Abexinostat


title: CTRL1_00251228_H3K9Ac

value: Control


title: CFC_Sleep_HA_SUP_26

value: Brain

value: neuron

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)


title: CFC_Sleep_HA_PELL_26

value: YES

value: Sleep


title: C48Gm-2

value: gill tissues

value: control


title: Treated2_00251275_Pol2

value: RNA Pol II (Active Motif # 91151)


title: Treated3_00251766_RnaPol2

value: Blood, PBMC


title: T48Gm-3

value: IHNV infection

value: wild-type


title: CTRL2_00251275_Pol2

value: Human peripheral blood mononuclear cells

value: del 11q

value: CLL


title: 50036

description: Gene expression data from nasal brushing of subject 50036.

value: Female

value: Former smoker

value: Cancer


title: C48Gm-3


title: CTRL3_00251766_Pol2

value: Control


title: CFC_Sleep_Input_SUP_25

value: Brain

value: neuron

value: male

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line


title: 250516

description: Gene expression data from nasal brushing of subject 250516.

value: Current smoker


title: 120049

description: Gene expression data from nasal brushing of subject 120049.


title: 70002

description: Gene expression data from nasal brushing of subject 70002.


title: CFC_Sleep_Input_PELL_25

value: membrane(PELL)

value: YES

value: Sleep


title: C48Gm-1

value: gill tissues

value: control

value: wild-type


title: CTRL1_00251228_Pol2

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: del 11q

value: CLL

value: RNA Pol II (Active Motif # 91151)


title: GNAQ Q209L dox - Tram - rep 3

city: Cincinnati

first: Sandra

last: Schrenk

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

description:
tpm_all_samples.txt
DESeq2_GNAQ Q209L_Trametinib vs Vehicle.txt

data_processing:
RNA-seq reads in FASTQ format were subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments.   The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1
The trimmed reads were aligned to the reference human genome version hg38 with the program STAR v2.6.1e
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package
Raw counts were normalized as transcripts per million (TPM)
Differential gene expressions between groups of samples were assessed with the R package DESeq2 v1.26.0
Assembly: hg38
Supplementary files format and content: Matrix table (tab-delimited text file) including tpm values for all genes in all samples
Supplementary files format and content: Matrix table (tab-delimited text file) including DEseq2 normalized values. GNAQ-WT vs GNAQ-Q209L cells
Supplementary files format and content: Matrix table (tab-delimited text file) including DEseq2 normalized values.  GNAQ-Q209L cells, vehicle-treated vs trametinib-treated

source_name: Cord blood

growth_protocol: Cells were grown in low-serum media (2% FBS in Endothelial growth medium) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Illumina Stranded mRNA Prep – Ligation kit was used for library preparation

treatment_protocol: To induce gene expression prior to RNA collection, cells were treated with 1µg/mL doxycycline for 18 hours, followed by an additional 6 hours of DMSO (vehicle control) or 10nM Trametinib treatment.

value: Cord blood

tag: cell line

value: Endothelial colony forming cell

value: Endothelial

value: dox, trametinib


title: GNAQ Q209L dox - Tram - rep 4


title: Treated1_00251228_Pol2

value: Abexinostat


title: CFC_Sleep_S6_SUP_25

source_name: Brain

value: Brain

value: neuron

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: cytosolic (SUP)


title: CFC_Sleep_HA_PELL_25

value: membrane(PELL)

value: YES

value: Sleep


title: CFC_Sleep_S6_PELL_25


title: CTRL3_00251766_HDAC1

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: HDAC1 (Active Motif # 40967)

value: Control


title: GNAQ Q209L dox - Tram - rep 1

value: Cord blood


title: CFC_Sleep_HA_SUP_25


title: 160561

description: Gene expression data from nasal brushing of subject 160561.

source_name: Brushing of nasal epithelium

value: Female

value: Former smoker

value: Benign


title: 120006

description: Gene expression data from nasal brushing of subject 120006.

value: Male

value: Current smoker

value: Cancer


title: GNAQ Q209L dox, vehicle - rep 4

description:
tpm_all_samples.txt
DESEq2_GNAQ Q209L vs WT.txt
DESeq2_GNAQ Q209L_Trametinib vs Vehicle.txt

value: Endothelial colony forming cell

value: Endothelial

value: dox, vehicle


title: 160603

description: Gene expression data from nasal brushing of subject 160603.


title: GNAQ Q209L dox - Tram - rep 2

value: dox, trametinib


title: 30026

description: Gene expression data from nasal brushing of subject 30026.


title: 30028

description: Gene expression data from nasal brushing of subject 30028.


title: 50020

description: Gene expression data from nasal brushing of subject 50020.


title: GNAQ Q209L dox, vehicle - rep 3


title: Treated3_00251766_HDAC1

value: del 11q

value: CLL

value: Abexinostat


title: NoCFC_Sleep_Input_PELL_24

value: Brain

value: neuron

value: male

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: NO

value: Sleep


title: 10138

description: Gene expression data from nasal brushing of subject 10138.

value: Male

value: Former smoker


title: CTRL2_00251275_HDAC1

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: HDAC1 (Active Motif # 40967)

value: Control


title: NoCFC_Sleep_Input_SUP_24

value: cytosolic (SUP)


title: GNAQ Q209L dox, vehicle - rep 2

value: Cord blood

value: Endothelial colony forming cell

value: Endothelial

value: dox, vehicle


title: GNAQ Q209L dox, vehicle - rep 1


title: NoCFC_Sleep_S6_PELL_24

value: Brain

value: neuron

value: male


title: Treated1_00251228_HDAC1

value: del 11q

value: CLL

value: Abexinostat


title: NoCFC_Sleep_HA_PELL_24

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: NO

value: Sleep


title: CTRL1_00251228_HDAC1

value: Blood, PBMC

value: Human peripheral blood mononuclear cells

value: HDAC1 (Active Motif # 40967)


title: GNAQ WT dox, vehicle - rep 4

description:
tpm_all_samples.txt
DESEq2_GNAQ Q209L vs WT.txt

value: Cord blood

value: GNAQ-WT


title: NoCFC_Sleep_S6_SUP_24

value: cytosolic (SUP)


title: Patient 15 derived orthoxenograft (PDOX) [S30]

city: L'Hospitalet de Llobregat

last: Llobet

state: Barcelona

address: Gran Via de L'Hospitalet 199-203

department: Gynecologic cancer

institute: Bellvitge Biomedical Research Institute (IDIBELL)

description: Samples from xenografts were aligned against mouse transcriptome (mm10/GRCm38), previously indexed. We used R package XenofilteR for deconvolution of mouse and human reads on xenografts samples.

data_processing:
Raw files were merged, and quality control assessed by FastQC analysis
Trimmomatic software was used to trim Illumina adaptors and bad quality reads
Trimmed reads were mapped over human reference transcriptome (hg19/GRCh38) with STAR. An annotation file in GTF format (downloaded from the UCSC Table Browser, using RefSeq genes table)   were used for the indexing step.
Aligned sequences were quantified with RSEM
Assembly: hg19/GRCh38
Supplementary files format and content: tab delimited text file of raw count data values for each Sample

source_name: Patient derived xenograft

extract_protocol:
Total RNA was isolated from primary tumors (BX) and PDOX tumors from mice using the RNeasy Micro kit (Qiagen, 74004)
NGS libraries with polyA capture were prepared according to the manual NEBNext® Ultra™ II Directional RNA  Library Prep Kit for Illumina® (New England Biolabs) (Version 1.0, 4/17)

value: Patient derived xenograft

value: Tumor


title: GNAQ WT dox, vehicle - rep 3

value: Endothelial colony forming cell

value: Endothelial

value: dox, vehicle


title: Patient 14 derived orthoxenograft (PDOX) [S29]


title: 120015

description: Gene expression data from nasal brushing of subject 120015.

value: Female

value: Former smoker

value: Cancer


title: 50028

description: Gene expression data from nasal brushing of subject 50028.

value: Male

value: Current smoker


title: NoCFC_Sleep_Input_PELL_23

value: Brain

value: neuron

value: male

value: Input

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: NO

value: Sleep


title: 50029

description: Gene expression data from nasal brushing of subject 50029.


title: 110509

description: Gene expression data from nasal brushing of subject 110509.


title: genomic DNA from glioma patient 4

type: genomic

first: changlin

last: yang

address: No. 119 South Fourth Ring Road West

department: Department of Molecular Neuropathology

institute: Beijing Neurosurgical Institute, Capital Medical University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  IlluminaInfinium Methylation EPICBeadChip.These chips include more than 850,000 methylation sites across whole genome.

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

data_processing: DNA methylation data were analyzed using the methylation analysis module within BeadStudio software employing default parameters (Illumina, Inc., San Diego CA, USA). The raw intensity data were loaded to a biocondutor package minfi. The raw data were normalized using the subset-quantile within array normalization (SWAN) method and probes with a detection p-value >= 0.01 in at least one sample were excluded from further analysis. Methylation values, referred to as β-values, were calculated as the ratio of the methylated signal intensity to the sum of the methylated and unmethylated signals after background subtraction. The β-values were reported as a DNA methylation score ranging from 0 (completely unmethylated) to 1 (fully methylated). Differentially methylated CpGs were selected using an algorithm in IMA Bioconductor. In this study, we assessed the mean-difference β-value (Δβ) between the two sample groups for each CpG site. Specifically, we considered a probe as differentially methylated if the absolute Δβ was higher than 0.14 and the statistical test was significant (p value <0.05).

label: Cy5 and Cy3

source_name: glioma sample 4

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from glioma sample using OMEGA TISSUE DNA Kit according to the manufacturer’s instructions.

treatment_protocol: The specimens were frozen in liquid nitrogen within 5 min of resection.

tag: gender

value: glioma sample

value: CNS WHO Grade 3


title: genomic DNA from glioma patient 3

source_name: glioma sample 3

tag: tissue

value: CNS WHO Grade 2


title: genomic DNA from glioma patient 5

source_name: glioma sample 5


title: Patient 13 derived orthoxenograft (PDOX) [S28]

value: Patient derived xenograft

value: Tumor


title: Patient 12 derived orthoxenograft (PDOX) [S27]


title: 110508

description: Gene expression data from nasal brushing of subject 110508.

value: Female

value: Former smoker


title: NoCFC_Sleep_Input_SUP_23

last: Wang

value: cytosolic (SUP)


title: GNAQ WT no dox, vehicle - rep 4

value: Cord blood

value: Endothelial colony forming cell

value: Endothelial

value: GNAQ-WT

tag: treatment

value: no dox, vehicle


title: GNAQ WT dox, vehicle - rep 1

value: dox, vehicle


title: GNAQ WT dox, vehicle - rep 2


title: Patient 11 derived orthoxenograft (PDOX) [S26]


title: GNAQ WT no dox, vehicle - rep 3


title: Patient 9 derived orthoxenograft (PDOX) [S24]


title: 70527

description: Gene expression data from nasal brushing of subject 70527.

value: Male

value: Benign


title: genomic DNA from glioma patient 2

source_name: glioma sample 2


title: NoCFC_Sleep_S6_PELL_23

value: Brain

value: neuron

value: male

value: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J mice crossed B6N.129-Rpl22tm1.1Psam/J mouse line

value: membrane(PELL)

value: NO

value: Sleep