title: NSP2-H1299-2_rnaseq

city: Austin

first: Hakan

last: Ozadam

state: TX

address: Department of Molecular Biosciences Moffett Molecular Biology Building 2.122 2500 Speedway

department: Department of Molecular Biosciences

institute: University of Texas at Austin

description: RNA-Seq from NSP2 expressing cells

data_processing:
Ribosome profiling and RNA-Seq data were processed using RiboFlow (source code and documentation are available at https://github.com/ribosomeprofiling/riboflow). A detailed description of the data processing steps can be found in https://academic.oup.com/bioinformatics/article/36/9/2929/5701654
Genome_build: Ribosome Profiling and RNA-Seq data were mapped to a transcriptome assembly available in https://github.com/ribosomeprofiling/references_for_riboflow/tree/master/transcriptome/human/v1/riboflow_annot_and_ref
Supplementary_files_format_and_content: Processed data are compiled in a single ribo file (H1299.ribo). The format specification can be found in https://ribopy.readthedocs.io/en/latest/ribo_file_format.html

growth_protocol: HEK293T cell line were obtained from ATCC and maintained in Dulbecco’s modified Eagle’s media (DMEM, GIBCO) supplemented with 10% Fetal Bovine Serum (FBS, GIBCO, Life Technologies) and 1% Penicillin and Streptomycin (GIBCO, Life Technologies) at 37°C in 5% CO2 atmosphere. Cell lines were tested for mycoplasma contamination every six months and were consistently found negative

extract_protocol:
RNA-Seq: Total RNA was extracted with QIAzol and ethanol precipitation from 10% of the lysate volume (see above). Sequencing libraries were generated using the SMARTer Stranded RNA-Seq Kit which uses a template switching reverse transcriptase (Takara Bio 634837). Briefly, 100 ng of total RNA were mixed with 1 µL of a 1:10 dilution of ERCC RNA Spike-In Mix controls (Thermo Fisher 4456740). ERCC mix 1 was added to HEK293T and HEK293T-NSP1 and mix 2 was added to HEK293T-NSP2 samples. RNA hydrolysis was done for 4 min and half of the cDNA was amplified for 10 cycles. Samples were sequenced with NovaSeq 6000 S1 PE 100 (Illumina).
Sequencing libraries were generated using the SMARTer Stranded RNA-Seq Kit which uses a template switching reverse transcriptase.

treatment_protocol: pLVX-EF1alpha-SARS-CoV-2-nsp1-2XStrep-IRES-Puro plasmid (Addgene, 141367), pLVXEF1alpha-SARS-CoV-2-nsp2-2XStrep-IRES-Puro plasmid (Addgene, 141368) and pLVXEF1alpha-SARS-CoV-2-N-2XStrep-IRES-Puro (Addgene, 141391) were obtained from Addgene. The IRES-Puro elements in the above plasmids were replaced with IRES-TagBFP from TRE-KRAB-dCAS9-IRES-BFP (Addgene, 85449) to make them compatible with the MeTAFlow assay. Briefly, IRES-Tag BFP was PCR amplified (Fp 5’-TCCGCAGTTTGAAAAGTAAGCCCCTCTCCCTCCCCCCC-3’ and Rp 5’-CAGAGGTTGATTGTTCCAGATTAATTAAGCTTGTGCCCCAGTTTGCTAGGG-3’). The pLVXEF1alpha-SARS-CoV-2-nsp1/nsp2-2XStrep-IRES-Puro plasmids were digested with BamHI (NEB) and MluI (NEB) to remove the IRES-Puromycin fragment followed by gel purification. The purified vector was ligated with the IRES-TagBFP PCR amplified product using Gibson assembly cloning (NEB). For pLVX-EF1alpha-SARS-CoV-2-N-2XStrep-IRES-Puro plasmid, due to presence of internal MluI site in N ORF, a three fragment Gibson cloning was performed. The plasmid was digested with MluI and two PCR amplified products corresponding to a fragment of N ORF and IRES-Tag BFP were PCR amplified using the following oligos. (Fragment 1 Fp 5’ 5’CTCTTGAATAAACACATAGACGCGTATAAGACGTTTCC 3′ and RpGGGAGAGGGGCGGGATCCTTACTTTTCAAAC 3′ and Fragment 2 5’AAGGATCCCGCCCCTCTCCCTCCCCCCC 3′ and Rp 5’CAGAGGTTGATTGTTCCAGATTAATTAAGCTTGTGCCCCAGTTTGCTAGGG3′ The sequences of the resulting plasmid clones were confirmed by Sanger sequencing.

value: NSP2 expressing

tag: cell line

tag: rna population

value: Total RNA


title: Knockout Rep 6

status: Public on May 28 2021

type: SRA

city: Ann Arbor

first: Dave

last: Bridges

state: MI

address: 1415 Washington Heights

department: Nutritional Sciences

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
Paired-end reads were aligned using Salmon v 1.3.0 to GRCm38.p6 with the parameters --validateMappings and --gcBias
Transcripts were merged into genes using tximeta and txiimport, then quantified using DESeq2 v1.28.1
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Salmon transcript quantification files, containing transcript id's (ENSEMBL), transcript length, reads, and transcripts per million

molecule: total RNA

organism: Mus musculus

source_name: Mammary Glands

extract_protocol:
Total RNA was extracted using PureLink RNA Kit (Life Technologies)
Followed manufacturers instructions forNEBNext®Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Animals were provided ad libitum access to milk and normal chow diet.  16 days post-delivery mice were sacrificed and mammary glands were extracted.

tag: strain

value: Adipocyte Tsc1 Knockout

tag: tissue

value: Inguinal Mammary Gland

tag: genotype

value: KO

tag: diet

value: Normal Chow Diet

tag: postnatal day

value: Tsc1-fl/fl; Adipoq-Cre-Tg/+


title: B73_seedling_rep2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
cellranger count (v4.0.0)
filter barcodes with less than 1000 UMIs and 500 expressed genes
filter barcodes below 1 standard deviation from the mean fraction of nuclear derived UMIs
filter barcodes above 1 standard deviation from the mean fraction of mitocondrial and chloroplast derived UMIs
Genome_build: B73 AGP v4
Supplementary_files_format_and_content: Binary triplet matrix format of geneIDs (column 1), nuclei ID (column 2), and UMI counts (column 3)

organism: Zea mays

extract_protocol:
16,000 nuclei were used to construct each library via nuclei lysis, wash, and centrifugation steps.
10X Genomics scRNA-seq Chromium Next GEM Single Cell 3' v3.1

tag: developmental stage

value: Seedling


title: Developing_Root_Vascular at time 24 ammonium 3 mM experiment 1 [A1T24_3_RDV]

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

data_processing:
Base calling was made with the NovaSeq 6000 RTA3 software (Illumina). Conversion of cbcl files to fastq files were made with bcl2fastq2 Conversion Software (Illumina)
The raw reads were trimmed (quality and contamination) using SeqTrimBB software (https://github.com/rafnunser/seqtrimbb). Only the pairs in which both reads passed the quality test were further analysed (Q>20).
The reads were assembled using Trinity 2.11.0 (Haas et al., 2013, Nature Protocols 8:1494-512). Contigs lower than 400 pb were eliminated, for the rest of contigs the redundancy was reduced using CD-HIT-EST software (Fu et al., 2012, Bioinformatics 28: 3150-3152).
The final transcriptome was used as the reference for the read mapping that was performed with BWA using the MEM option (Li and Durbin, 2009, Bioinformatics 25: 1754-1760). The read count was obtained with the phyton script sam2counts (https://github.com/vsbuffalo/sam2counts).
The transcript expression was normalised by cpm. Finally the transcripts were filtered; 2 cpm in at least 2 samples (Robinson et al., 2010, Bioinformatics 26: 139-140).
Genome_build: Assemble reference transcriptome
Supplementary_files_format_and_content: Tab-delimited text files include CPM normalized counts for each sample.The column id is the sequence/sample identifier.

organism: Pinus pinaster

growth_protocol: Seeds from maritime pine (Pinus pinaster Ait.) from “Sierra Segura y Alcaraz” (Albacete, Spain) were provided by from the Área de Recursos Genéticos Forestales of the Spanish Ministerio de Agricultura, Pesca y Alimentación. Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were grown in vermiculite in plant growth chambers under 16 h light photoperiod, a luminal intensity of 100 μmol m−2 s−1, a constant temperature of 25 °C and watered twice a week with distilled water.

extract_protocol:
All the RNA extractions from the microdissection procedure were carried out using manufacturer’s instruction protocol (non‐LCM) for the RNAqueous‐Micro RNA Isolation Kit (Ambion, USA). RNA quality, DNA contamination and first quantification were performed via RNA Pico Assay for the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Quantification was verified via a Qubit RNA BR (Broad-Range) Assay Kit (Invitrogen, Paisley, UK).  RNA samples with RNA integrity number (RIN) higher than 7 were used for subsequent RNA sequencing, mRNA amplification and cDNA synthesis.
The low input RNA-seq was carried out by Novogen (HK). The cDNA synthesis and amplification, and the library preparation was made with the SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Takara, Mountain View, CA, USA) following the manufacturer’s instructions. RNA sequencing was made in a NovaSeq 6000 sequencer according to the manufacturer’s instructions for paired-end reads (Illumina, San Diego, CA, USA). The 24 samples were sequenced producing paired-end reads of 150 bp length.

treatment_protocol: One-month old maritime pine seedlings were used for this experiment. Pine seedlings were randomly subdivided into three different groups, relocated into forestall seedbeds and irrigated with 80 mL of a solution that contains macro- and micronutrients without any nitrogen source (1.16 mM KCl; 0.63 mM KH2PO4; 0.35 mM MgSO4·7H2O; 0.17 mM CaCl2·H2O; 80 μM EDTA-FeSO4; 25.9 μM H3BO3; 10.2 μM MnCl2·4H2O; 1.3 μM ZnSO4·7H2O; 0.7 μM CuSO4·5H2O; 0.1 μM Na2MoO4·2H2O). After three days of acclimation, the control group was irrigated with 80 mL of water (C), the second group was supplied with 80 mL of 3 mM NH4Cl. Root samples were collected 24 houres after the irrigation. Seedling’s root tips were cut and tissues of 5 - 6 mm were imbibed in a specimen holder with Tissue‐Tek optimal cutting temperature embedding medium (Sakura Finetek, Alphen aan den Rijn, The Netherlands) and immediately frozen in liquid nitrogen for cryostat sectioning. LCM procedure:  1 day before cryosectioning, root tip samples were tempered at -20°C. Thirty micrometers thick sections were cut using a cryostat (CM1950, Leica Biosysyems, Wetzlar, Germany) at -20°C and mounted on PET-membrane 1.4 µm steel frame (Leica Biosysyems, Wetzlar, Germany). The PET-membrane containing samples were stored at −80°C until use.  Before microdissection, samples were fixed in cold 70% ethanol for 30 seconds, embedding medium was removed in DEPC-treated water for 2 minutes and refixed in cold 100% ethanol for 2 minutes. Afterwards, samples were air dried and used for microdissection. A laser microdissector (LMD 7000, Leica, Wetzlar, Germany) was used for microdissection. The samples obtained were placed into 0.5 mL tube caps containing 20 μL of lysis buffer from the RNAqueous-Micro RNA Isolation Kit (Ambion, USA) and all samples were placed at −80°C. Four different tissue areas were isolated by microdissection approximatively corresponding to the root cap (RC), meristem (RM), developing cortex (RDC) and developing vessels (RDV) areas.

tag: provenance

value: Segura-Alcaraz

value: 1 month-old seedling

tag: treatment

value: Ammonium 3 mM

tag: time

value: 24 hours

tag: experimental replicate


title: NSP1_H1299-3_rnaseq

description: RNA-Seq from NSP1 expressing cells

organism: Homo sapiens

value: NSP1 expressing


title: NSP2-H1299-3_rnaseq

description: RNA-Seq from NSP2 expressing cells


title: Wild-Type Rep 5

value: WT

value: Tsc1-fl/fl; Adipoq-Cre-+/+


title: Developing_Root_Vascular at time 24 control experiment 4 [A4T24_C_RDV]


title: NSP1_H1299-2_rnaseq

description: RNA-Seq from NSP1 expressing cells


title: NSP2-H1299-1_rnaseq

description: RNA-Seq from NSP2 expressing cells


title: Knockout Rep 4


title: PDX1-CD276-low/EpCAM+

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

data_processing:
RNAs were single-end sequenced on Illumina HiSeq 3000 machines
Reads was aligned using Tophat with the hg18 build of the human genome.
Transcript assembly and differential expression were determined using Cufflinks with Refseq mRNAs.
RNA-seq data was analyzed using the cummeRbund package in R.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Head and neck squamous cell carcinoma cells

growth_protocol: Two cases of Human HNSCC PDXs were maintined in NOD/SCID mice. The discarded human HNSCC primary tissues were obtained from the UCLA Translational Pathological Core and subcutaneously inoculated into flank of 6-week-old NOD/SCID mice to generate the PDXs of HNSCC.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen, cat#74104).
Sequencing libraries were generated using a KAPA RNA-Seq Library Preparation Kits (KAPA Biosystems, cat#07960140001)

treatment_protocol: To isolate single cells from HNSCC PDXs, mice were euthanized and tumors were dissected and isolated.  Tumors were chopped into small pieces with scalpels in petri dishes on ice, and then dissociated in to single cell suspension using Tumor Dissociation Kit (Miltenyi, cat# 130-095-929). The cell suspension was filtered through a 100 micro meter mesh filter and then followed by a 40 micro meter mesh filter. Red blood cells were removed using a RBC Lysis Buffer (Santa Cruz Biotechnology, cat#sc-296258). Subsequently, tumor cells were stained with the anti-CD276-PE and anti-EpCAM-APC antibodies. The CD276+/EpCAM+ and the CD276+/EpCAM- cells were isolated throug FACS sorting.

value: HNSCC PDX1

value: Head and neck squamous cell carcinoma


title: Developing_Root_Vascular at time 24 control experiment 1 [A1T24_C_RDV]


title: NSP2-H1299-3_ribo

description: Ribosome profiling from NSP2 expressing cells

data_processing:
Library strategy: Ribosome profiling
Ribosome profiling and RNA-Seq data were processed using RiboFlow (source code and documentation are available at https://github.com/ribosomeprofiling/riboflow). A detailed description of the data processing steps can be found in https://academic.oup.com/bioinformatics/article/36/9/2929/5701654
Genome_build: Ribosome Profiling and RNA-Seq data were mapped to a transcriptome assembly available in https://github.com/ribosomeprofiling/references_for_riboflow/tree/master/transcriptome/human/v1/riboflow_annot_and_ref
Supplementary_files_format_and_content: Processed data are compiled in a single ribo file (H1299.ribo). The format specification can be found in https://ribopy.readthedocs.io/en/latest/ribo_file_format.html

extract_protocol:
Ribosome Profiling: Three million HEK293T or H1299 cells were plated in a 10 cm2 flask followed by transfection to express SARS-CoV-2 NSP1 and NSP2 (see above). Untransfected and transfected cells (~8 million) were washed twice with 10 mL of ice-cold PBS. The plates were immediately placed on ice and 400 μL of lysis buffer (Tris-Cl, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL Cycloheximide, 1% Triton-X) was added to each plate, cells were scraped and transferred to 1.5 ml tubes. Cells were lysed on ice by pipetting up and down ~5 times every five minutes for a total of 10 min. All experiments were done in triplicate. The lysate was clarified by centrifugation at 160 x g for 10 min at 4°C. Ten percent of the clarified lysate by volume was separated, mixed with 700 μl QIAzol and stored at -20°C for RNA-Seq experiments (see below). The rest of the supernatant was immediately processed for ribosome profiling. Briefly, 7 μL of RNaseI (Invitrogen AM2249) was added to the clarified lysates and digestion was done for 1 h at 4 °C. The digestions were stopped with ribonucleoside vanadyl complex (NEB S1402S) at a final concentration of 20 mM. Digested lysates were layered on a 1 M sucrose cushion (Tris, pH 7.4, NaCl 150 mM, MgCl 2 5 mM, DTT 1 mM, 1 M sucrose) and the ribosomes were pelleted by centrifugation in a SW 41 Ti rotor (Beckman Coulter) at 38K rpm and 4°C for 2.5 h. RNA was extracted from the ribosome pellets with the addition of 700 μl QIAzol followed by chloroform and ethanol precipitation. RNA isolated from the pellets were size-selected by running 5 µg of each sample in a 15% polyacrylamide TBEUREA gel. The 21-34 nt RNA fragments were excised and extracted by crushing the gel fragment in 400 µL of RNA extraction buffer (NaOAc [pH 5.5] 300 mM, EDTA 1 mM, SDS 0.25% v/v) followed by a 30 min incubation on dry ice and an overnight incubation at room temperature. The sample was passed through a Spin X filter (Corning 8160) and the flow through was ethanol precipitated in the presence of MgCl2 5 mM and 1 µL of Glycoblue (Invitrogen AM9516). The RNA pellet was resuspended in 10 µL of RNase-free water and immediately processed for library preparation.
Ribosome profiling libraries were prepared with the D-Plex Small RNA-Seq Kit (Diagenode). This method incorporates a 3′ end dephosphorylation step, 5′ unique molecular identifiers (UMI) and a template switching reverse transcriptase that improves the quality of our libraries. Briefly, 25 ng of size-selected ribosome footprints were prepared following the manufacturer’s instructions with some modifications. The cDNA was amplified for 9 cycles and the resulting DNA libraries were pooled in equimolar amounts (~425 nM each). The library pool was cleaned with the AMPure XP beads (Beckman Coulter A63880) and eluted with 30 µL of RNase-free water. To enrich for ~30 bp fragments in the libraries, 3 µg of the cleaned libraries were size-selected in a 3% agarose precast-gel (Sage Science) with the BluePippin system (Sage Science) using 171-203 nt range with tight settings. The resulting size-selected libraries were analyzed with the Agilent High Sensitivity DNA Kit (Agilent) and sequenced with the NovaSeq 6000 S1 SE 75 (Illumina).

value: NSP2 expressing

value: RNA from ribosome footprint


title: Root meristem at time 24 ammonium 3 mM experiment 4 [A4T24_3_RM]

source_name: Root meristem at time 24 ammonium 3 mM

value: Root meristem


title: Wild-Type Rep 3

value: Adipocyte Tsc1 Knockout

value: Inguinal Mammary Gland


title: Root meristem at time 24 ammonium 3 mM experiment 3 [A3T24_3_RM]


title: Knockout Rep 5

value: KO

value: Normal Chow Diet


title: Root meristem at time 24 ammonium 3 mM experiment 1 [A1T24_3_RM]


title: NSP2-H1299-1_ribo


title: Developing_Root_Vascular at time 24 control experiment 3 [A3T24_C_RDV]


title: Wild-Type Rep 4


title: NSP1_H1299-1_rnaseq

description: RNA-Seq from NSP1 expressing cells

value: Total RNA


title: NSP1-H1299-3_ribo

description: Ribosome profiling from NSP1 expressing cells


title: Wild-Type Rep 2


title: Knockout Rep 2

value: Tsc1-fl/fl; Adipoq-Cre-Tg/+


title: Root meristem at time 24 control experiment 3 [A3T24_C_RM]

source_name: Root meristem at time 24 control

value: Segura-Alcaraz

value: 1 month-old seedling


title: Root meristem at time 24 control experiment 4 [A4T24_C_RM]

value: 24 hours


title: Derlin-1_KO_4PBA_b

type: RNA

city: Miyazaki

first: Takashi

last: Sugiyama

address: 5200 Kihara, Kiyotake

department: Department of Medical Sciences

country: Japan

institute: University of Miyazaki

description: Gene expression

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented and hybridized onto the Agilent SurePrint G3 mouse GE 8 × 60K slide (design ID-074809), with rotating incubation at 65˚C for 17 h.

scan_protocol: Slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation, and scanned by the Agilent DNA Microarray scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  The data files were subjected to the GeneSpring (ver. 13.0 and 14.9) for analysis.

source_name: mouse cerebellum

label_protocol: For RNA amplification and labeling, we used Agilent Low-Input QuickAmp labeling kit (Agilent) according to the manufacture’s guidance.  150 ng of total RNA of each sample was amplified T7-RNA polymerase and simultaneously incorporated Cy3-labeled CTP.

growth_protocol: C57BL/6 mice were raised under specific pathogen-free conditions.

extract_protocol: Total RNA from mouse cerebellum were extracted using NucleoSpin RNA kit (TaKaRa Bio) according to the instructions. This included an on-column DNase digestion with the RNase-free Dnase (TaKaRa Bio)

treatment_protocol: Derlin-1_control was Derlin-1flox/flox, and Derlin-2_control was Derlin-2flox/flox. Mice expressing Cre recombinase driven by the nestin promoter were intercrossed with Derl1flox/flox mice and Derl2flox/flox mice respectively to generate Derlin-1_KO and Derlin-2_KO mice. 200 mg/kg 4-phenylbutyrate (4PBA) or water (vehicle) were administrated by intraperitoneal injections once a day from postnatal day 14 to day 28.

tag: case/control

value: case


title: NSP1-H1299-2_ribo

value: NSP1 expressing


title: Derlin-2_KO_1

description: Gene expression

scan_protocol: Slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately, and scanned by the Agilent DNA Microarray scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  The data files were subjected to the GeneSpring (ver. 14.9.1) for analysis.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit.

treatment_protocol: Derlin-2_control was Derlin-2flox/flox. Mice expressing Cre recombinase driven by the nestin promoter were intercrossed with Derl2flox/flox mice to generate Derlin-2_KO mice.

value: Case


title: Derlin-2_KO_2

description: Gene expression


title: Root meristem at time 24 control experiment 1 [A1T24_C_RM]


title: Derlin-2_control_2

description: Gene expression

value: Control


title: Derlin-1_control_4PBA_b

description: Gene expression

value: control


title: NSP2-H1299-2_ribo

value: NSP2 expressing


title: Derlin-1_KO_4PBA_a

description: Gene expression


title: Wild-Type Rep 1

value: WT

value: Tsc1-fl/fl; Adipoq-Cre-+/+


title: Derlin-2_control_1

description: Gene expression


title: Derlin-1_control_4PBA_a

description: Gene expression


title: NSP1-H1299-1_ribo

value: RNA from ribosome footprint


title: Knockout Rep 3

value: Adipocyte Tsc1 Knockout

value: Inguinal Mammary Gland


title: Root cap at time 24 ammonium 3 mM experiment 4 [A4T24_3_RC]

source_name: Root cap at time 24 ammonium 3 mM

value: Ammonium 3 mM

value: Root cap


title: Derlin-1_KO_b

description: Gene expression


title: Root cap at time 24 ammonium 3 mM experiment 3 [A3T24_3_RC]


title: Derlin-1_KO_a

description: Gene expression


title: Derlin-1_control_a

description: Gene expression


title: Root cap at time 24 ammonium 3 mM experiment 1 [A1T24_3_RC]


title: Derlin-1_control_b

description: Gene expression


title: MALAT1-/- pancreatic islet-04-TCDD-treated

city: College Station

first: Qian

last: Xu

state: texas

address: 660 Raymond Stotzer Pkwy College Station 77843

department: College of Veterinary Medicine & Biomedical Sciences

institute: Texas A&M

data_processing:
For the mapping of reads to transcripts and cells, sample demultiplexing, barcode processing, and unique molecular identifier (UMI) countings were performed using the 10x Genomics pipeline CellRanger v.2.1.0 with default parameters.
Genome_build: mm10

source_name: pancreatic islet

growth_protocol: The pancreas was inflated with 3 mL of cold collagenase solution (0.3 mg/mL) (Collagenase type 4, Worthington Biochemical Corporation) through the common bile duct with a 20 G needle, starting at the gallbladder. The pancreas was then removed from the body and placed in a siliconized vial containing 2 mL of 1 mg/mL collagenase solution, and digested at 37°C in a water bath for 12∼15 min. After three washes of the digested pancreas with centrifugation (97 × g at 4°C for 1 min) to collect the tissues, islets were purified by density gradient centrifugation (cold polysucrose/sodium diatrizoate solution 1.1119 g/ml, 560 × g at 4 °C for 15 min) and then dispersed in 96 well plates and cultured in RPMI (Gibco) with 10% FBS for further experiments.

extract_protocol:
Single cell GEMs (Gel bead in EMulsion) and sequencing libraries were prepared using the 10x Genomics Chromium Controller in conjunction with the single-cell 3′ v3 kit.
The cDNA synthesis, barcoding, and library preparation were then carried out according to the manufacturer’s instructions.

treatment_protocol: The islets were washed in 10 ml of PBS and dissociated using 2ml of Accutase (Sigma-Aldrich, Cat#A6964) and incubated at room temperature for 20 mins with gentle intermittent mixing by pipetting. The dissociated islets were confirmed using microscopy and were stopped with islet culture media (RPMI with 10% FBS). The dissociated islets were then filtered through a 40-mm filter to remove disassociated tissue and obtain a single-cell suspension of pancreatic islet cells. A total of approximately 20,000 cells were resuspended in 30 ml PBS with 0.05% BSA.

tag: cell type

value: beta cell

value: TCDD


title: Knockout Rep 1

value: KO

value: Normal Chow Diet

value: Tsc1-fl/fl; Adipoq-Cre-Tg/+


title: MALAT1-/- pancreatic islet-03-DMSO-treated

value: DMSO


title: Root cap at time 24 control experiment 4 [A4T24_C_RC]

source_name: Root cap at time 24 control

value: Segura-Alcaraz

value: 1 month-old seedling

value: 24 hours


title: Root cap at time 24 control experiment 3 [A3T24_C_RC]


title: WT-pancreatic islet-01-DMSO-treated

value: wild type


title: GM12878 [s3-WGS]

city: Portland

first: Ryan

middle: M

last: Mulqueen

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular and Medical Genetics

institute: Oregon Health and Science

description:
s3-WGS on GM12878
s3WGSands3GCC_PDCLandGM12878_500kbbin_rawreadcount.tsv
s3WGSands3GCC_PDCLandGM12878.bed
The raw data contains patient information so we were not going to upload to GEO/SRA

library_source: genomic

data_processing:
Library strategy: s3-WGS and s3-GCC
After sequencing, data was converted from bcl format to FastQ format using bcl2fastq (v 2.19.0, Illumina Inc.) with the following options with-failed-reads, no-lane-splitting, fastq-compression-level=9, create-fastq-for-index-reads
FastQ reads were assigned to their expected primer index sequence allowing for sequencing error (Hamming distance ≤2) and indexes were concatenated to form a “cellID”.
Reads that could be assigned unambiguously to a cellID were then aligned to reference genomes. For both s3-WGS and s3-GCC libraries, paired reads were aligned with bwa mem (v0.7.15-r1140) to hg38.
For whole exome data (WES): The data was processed following the best practices workflow for the GATK pipeline (v4.1.9.0). Exome regions annotated as “protein-coding” were extracted from GenCode (v35) and used as the intervals for processing. The following commands were then used for WES data normalization and segmentation with additional options were specified: PreprocessInvertals, CollectReadCounts, AnnotateIntervals, FilterIntervals, CreateRedCountPanelOfNormals (using the matched blood sample as the normal, with minimum-interval-median-percentile set to 5.0), and finally PlotDenoisedCopyRatios.
For s3-WGS processing: The genome was split into 500 kbp bins with each bin being assigned a GC content and mappability score (generated through CODEX2). Reads with a mapping quality of Q ≥ 10 were counted in bins per cellID. Bins with a mappability score < 0.9 or GC content ≤ 20% or ≥ 80% were removed (5449 bins passing filter). Additionally, cellIDs with low coverage were removed (1268 samples passing filter). A bed file is also supplied of read alignments generated with bedtools bamtobed function.
For s3-GCC processing: GCC cells passing the s3-WGS processing filter were filtered to only include insert sizes >= 1kbp with samtools. This was then output as a pairix file for futher processing.
Genome_build: GRCh38 (“hg38”,Genome Reference Consortium Human Reference 38 (GCA_000001405.2))
Supplementary_files_format_and_content: Pairix: modified paired read tab-separated bed file with columns readID (containing the cellID) chr1 pos1 chr2 pos2 strand1 strand2. See https://github.com/4dn-dcic/pairix for further file format details.   rawreadcount.tsv is a tab-separated matrix with columns as cellIDs and rows as genomic bins (chr:start_end). Values are read counts passing filter.   denoisedCR.tsv files are a tab-separated format file output in the GATK CNA calling pipeline. These files are read count bin scores normalized to matched patient WES on blood. Columns are chr start end normalized_count.   Bed file is the standard bed format (chr, start, end) of single-cell read alignments passing filter. A metadata column contains cellID:read_identifier#0 for discrimination of cells.

molecule: genomic DNA

growth_protocol: For PDCL generation: Low-passage, patient-derived cell lines (PDCLs) were propagated from rapidly dissociated PDAC tumors and cultured for continuous propagation in culture medium containing ROCK inhibitor (Y-276320). Briefly, approximately 50,000 viable, disaggregated tumor cells were plated to a 35mm diameter, collagen-coated well (Gibco, A11428-02) and passaged 1:3 while subconfluent until reaching 85% confluence on a 10cm diameter dish. From a fraction of these cells, DNA was extracted to validate the presence of KRAS-G12 mutations by ddPCR (Bio-Rad, 1863506) and to validate an STR profile that matches normal leukocyte DNA from the same patient (Genetica). PDCLs exhibited morphologies consistent with epithelial tumor cells and abundant KRT expression was detected by immunocytofluorescence using the monoclonal antibodies: AE1/AE3, C-11, and Cam5.2. To ensure that only tumor cells were cultured, G-banded karyotyping was performed by the Knight Diagnostic Research Cytogenetics Lab at OHSU. Chromosome spreads from more than 20 cells were observed to ensure that the culture contained 100% tumor cells.  For GM12878 cells: Cells were cultured as described previously in Mulqueen et al. 2018. GM12878 (Coriell) were cultured in 5% CO2 at 37°C. GM12878 cells were grown in Roswell Park Memorial Institute media (RPMI, Gibco, Cat. 11875093) supplemented with 15% (v/v) fetal bovine serum (FBS, Gibco, Cat. 10082147), 1X L-glutamine (Gibco, Cat. 25030081), 1X Penicillin-Streptomycin (Gibco, Cat. 15140122), and gentamicin (Gibco, Cat. 15750060).

extract_protocol:
s3-WGS and s3-GCC library preparation was performed on cell lines as follows. For patient derived PDCL cell lines, cells were plated at a density of 1x10^6 on a T25 flask the day prior to processing. At harvest, cells were washed twice with ice cold 1X PBS (VWR 75800-986) and then trypsinized with 5mL 1X TrypLE (Thermo Fisher 12604039) for 15 minutes at 37°C. Suspended cells were then collected and pelleted at 300 rcf at 4°C for 5 minutes. For suspension-growth cell lines (GM12878), cells were pipetted from growth media and pelleted at 300 rcf at 4°C for 5 minutes.
For s3-WGS: Following the initial pellet, cells were washed with ice cold 1mL NIB HEPES twice. After the second wash, pellets were then resuspended in 300 uL NIB HEPES. Nuclei were aliquoted and quantified as described above, then aliquots of 1 million nuclei were generated based on the quantification. The aliquots were pelleted by a 300 rcf centrifugation at 4°C for 5 minutes and resuspended in 5 mL NIB HEPES. 246 uL 16% (w/v) formaldehyde (Thermo Fisher 28906) was then added to nuclear suspensions (f.c. 0.75% formaldehyde) to lightly fix nuclei. Nuclei were fixed via incubation in formaldehyde solution for 10 minutes on an orbital shaker set to 50 rpm. Suspensions were then pelleted at 500 rcf for 4 minutes at 4°C and supernatant was aspirated. Pellet was then resuspended in 1 mL of NIB Tris Buffer to quench remaining formaldehyde. Nuclei were again pelleted at 500 rcf for 4 minutes at 4°C and supernatant was aspirated. The pellet was washed once with 500uL 1X NEBuffer 2.1 (NEB B7202S) and then resuspended with 760 uL 1X NEBuffer 2.1. 40 uL 1% SDS (v/v) was added and sample was incubated on a ThermoMixer at 300 rcf set to 37°C for 20 minutes. Nucleosome depleted nuclei were then pelleted at 500 rcf at 4°C for 5 minutes and then resuspended in 50 uL NIB Tris. A 5 uL aliquot of nuclei was taken and diluted 1:10 in NIB Tris then quantified as described above. Nuclei were diluted to 500 nuclei/uL with addition of NIB Tris, based on the quantification. Dependent on experimental setup, the 420 uL of nuclei at 500 nuclei/uL were then combined with 540 uL 2X TD buffer. Following this, nuclei were tagmented, stained and flow sorted, genomic DNA was gap-filled and adapter switching was performed as described for the s3-ATAC protocol. Library amplification was performed by PCR as described for the s3-ATAC protocol with fewer total cycles (13-15) likely due to more initial capture events per library. Libraries were then cleaned, size selected, quantified and sequenced as described for the s3-ATAC protocol.   For s3-GCC: The same cultured cell line samples were harvested as described for s3-WGS library generation, and processed from the same pool of fixed, nucleosome depleted nuclei. Following quantification of nuclei, the full remaining nuclear suspensions (~2-3 million nuclei per sample) were pooled respective of sample. Nuclei were pelleted at 500 rcf at 4°C for 5 minutes and resuspended in 90 uL 1X Cutsmart Buffer (NEB B7204S). 10 uL of 10U/uL AluI restriction enzyme (NEB R0137S) was added to each sample. Samples were then digested for 2 hours at 37°C at 300 rpm on a ThermoMixer. Following digestion, nuclear fragments then underwent proximity ligation. Nuclei were pelleted at 500 rcf at 4°C for 5 minutes and resuspended in 100uL ligation reaction buffer. Ligation buffer is a mixture with final concentrations of 1X T4 DNA Ligase Buffer + ATP (NEB M0202S), 0.01 % TritonX-100, 0.5mM DTT (Sigma D0632), 200 U of T4 DNA Ligase, diluted in ultrapure H2O. Ligation took place at 16°C for 14 hours (overnight). Following this incubation, nuclei were pelleted at 500 rcf at 4°C for 5 minutes and resuspended in 100 uL NIB HEPES buffer. An aliquot of nuclei were quantified as described previously, and were then diluted, aliquoted, tagmented, pooled, DAPI stained, flow sorted, genomic DNA was gap-filled and adapter switching was performed as described for the s3-ATAC protocol. Library amplification occurred at the same rate as the s3-WGS libraries (13-15 cycles) and libraries were subsequently pooled, cleaned, quantified and sequenced as described for the s3-ATAC protocol.

tag: library generation


title: Primary tumor sample

description:
WES data generated on primary tumor sample
The raw data contains patient information so we were not going to upload to GEO/SRA

source_name: Primary tumor

value: whole exome sequencing

tag: disease state

value: PDAC primary tumor

value: pancreatic tumor


title: WT-pancreatic islet-02-TCDD-treated


title: Day 10 axially elongating human iPSC-derived organoids [Ashley4]

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

description: Human axially elongating organoids

data_processing:
Demultiplex with CellRanger v3.0.2
Align to GRCh38 with CellRanger v3.0.2
Generate raw counts matrix with CellRanger v3.0.2
Demultiplex MultiSeq barcodes with v2.20.0
Call MultiSeq barcodes with deMULTIplex v1.0.2
Subset final counts matrix corresponding to MultiSeq Barcode 9 using Seurat v3.1.5
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix Market Format final counts of the MultiSeq reads corresponding to axially elongating worms
Supplementary_files_format_and_content: Matrix Market Format raw counts for all samples before demultiplexing
Supplementary_files_format_and_content: Comma separated value formated final MultiSeq barcode assignments

source_name: Human iPSC

growth_protocol: Neural differentiation following Libby et al 2020

extract_protocol:
Multi-seq barcoding following McGinnis et al 2018 followed by 10x Chromium Single Cell Barcoding v2
10x Chromium Single Cell Library Prep v2 and Multi-seq Library Prep following McGinnis et al 2018

treatment_protocol: Differentiation following 2 uM CHIR pretreatment in 10 cm dishes for 10 days

value: elongating organoids


title: GM12878

description: single-cell whole genome data

data_processing:
Library strategy: WGS
FastQ files were generated from BCL files using bcl2fastq (v 2.19.0, Illumina Inc.) with the following options with-failed-reads, no-lane-splitting, fastq-compression-level=9, create-fastq-for-index-reads
FastQ reads were assigned to their expected primer index sequence allowing for sequencing error (Hamming distance ≤2) and indexes were concatenated to form a “cellID”. cellIDs are stored in the FastQ header
Reads that could be assigned unambiguously to a cellID were then aligned to reference genomes. For GM12878, paired reads were aligned with bwa mem (v0.7.15-r1140) to hg38. For s3-ATAC libraries, reads were first aligned to a concatenated hybrid genome of hg38 and GRCm38 (“mm10”, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)).
Reads were then de-duplicated to remove PCR and optical duplicates by a perl (v5.16.3) script aware of cellID, chromosome and read start, read end and strand. From there putative single-cells were distinguished from debris and error-generated cellIDs by both unique reads and percentage of unique reads.
For s3-ATAC libraries, cellIDs with ≥90% of reads aligning to a single reference genome were considered bona fide single-cells and fastQ files were filtered prior to realigning to the correct genome.
Pseudo-bulked data (agnostic of cellID) was then used to call read pile-ups or “peaks” via macs2 (v.2.2.7.1) with option –keep-dup all
A scitools perl script was then used to generate a sparse matrix of peaks × cellID to count occurrence of reads within peak regions per cell.
The peaks x cellID counts matrix was then used to generate Seurat Objects for Signac processing (see Online Methods for more downstream analyses).
Genome_build: GRCm38 (“mm10”, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2) and GRCh38 (“hg38”,Genome Reference Consortium Human Reference 38 (GCA_000001405.2).
Supplementary_files_format_and_content: SeuratObject.Rds files are RDS files used in Signac processing of data (see https://satijalab.org/signac/ and our Online Methods for more detail). Metadata.csv files are csv files containing metadata information per cell (each row), with relevant cell information (each column). Counts.csv files contain the CSV formatted peaks (rows) by cellIDs (columns) matrix, where each value denotes read counts overlapping peaks per cell. Bam files are standard bams with cellIDs filtered to those used in downstream analyses.

source_name: Cell line

extract_protocol:
Tissue samples were minced on dry ice and resuspended in NIB (10 mM HEPES-KOH (Fisher Scientific, BP310-500 and Sigma Aldrich 1050121000, respectively), pH 7.2, 10 mM NaCl, 3mM MgCl2 (Fisher Scientific AC223210010), 0.1 % (v/v) IGEPAL CA-630 (Sigma Aldrich I3021), 0.1 % (v/v) Tween (Sigma-Aldrich P-7949) and diluted in PCR-grade Ultrapure distilled water (Thermo Fisher Scientific 10977015)). After a 5 minute incubation in ice, tissue was dounce homogenized to isolate nuclei. For GM12878, cells were spun down and resuspended in NIB. See https://dx.doi.org/10.17504/protocols.io.bd6wi9fe and https://dx.doi.org/10.17504/protocols.io.beb3jaqn for more details.
Tagmentation plates were prepared by the combination of 420 uL of 1400 nuclei/uL solution with 540 uL 2X TD Buffer (Nextera XT Kit, Illumina Inc. FC-131-1024). From this mixture, 8uL (~5000 nuclei total) was pipetted into each well of a 96 well plate dependent on well schema (Figure 2a). 1uL of 2.5uM uniquely indexed transposase was then pipetted into each well. Tagmentation was performed at 55°C for 10 minutes on a 300 rcf Eppendorf ThermoMixer. Following this incubation, plate temperature was brought down with a brief incubation on ice to stop the reaction. Dependent on experimental schema pools of tagmented nuclei were combined and 2uL 5mg/mL DAPI (Thermo Fisher Scientific D1306) was added.  Nuclei were then flow sorted via a Sony SH800 to remove debris and attain an accurate count per well prior to PCR. A receptacle 96 well plate was prepared with 9uL 1X TD buffer (Nextera XT Kit, Illumina Inc. FC-131-1024,diluted with ultrapure water), and held in a sample chamber kept at 4°C. Fluorescent nuclei were then flow sorted gating by size, internal complexity and DAPI fluorescence for single nuclei following the same gating strategy as previously described40. Immediately following sorting completion, the plate was sealed and spun down for 5 minutes at 500 rcf and 4°C to ensure nuclei were within the buffer.  Nucleosomes and remaining transposases were then denatured with the addition 1uL of 0.1% SDS (~0.01% f.c.) per well. 4uL of NPM (Nextera XT Kit, Illumina Inc) per well was subsequently added to perform gap-fill on tagmented genomic DNA, with an incubation at 72°C for 10 minutes. 1.5 uL of 1uM A14-LNA-ME oligo was then added to supply the template for adapter switching (Supplementary Table 3). The polymerase based adapter switching was then performed with the following conditions: initial denaturation at 98°C for 30 seconds, 10 cycles of 98°C for 10 seconds, 59°C for 20 seconds and 72°C for 10 seconds. The plate was then held at 10°C. After adapter switching 1% (v/v) Triton-X 100 in ultrapure H2O (Sigma 93426) was added to quench persisting SDS. At this point, some plates were stored at -20°C for several weeks while others were immediately processed.   The following was then combined per well for PCR: 16.5 ul sample, 2.5uL indexed i7 primer at 10 uM, 2.5uL indexed i5 primer at 10 uM, 3 uL of ultrapure H2O, and 25 uL of NEBNext Q5U 2X Master mix (New England Biolabs M0597S), and 0.5uL 100X SYBR Green I (Thermo Scientific S7563) for a 50 uL reaction per well (Supplementary Table 4-5). A real time PCR was performed on a BioRad CFX with the following conditions, measuring SYBR fluorescence every cycle: 98°C for 30 seconds; 16-18 cycles of 98°C for 10 seconds, 55°C for 20 seconds, 72°C for 30 seconds, fluorescent reading, 72°C for 10 seconds. After fluorescence passes an exponential growth and begins to inflect, the samples were held at 72°C for another 30 seconds then stored at 4°C.

tag: age

tag: condition


title: Derlin-2_KO_4PBA_1

description: Gene expression

value: case


title: Derlin-2_KO_4PBA_2

description: Gene expression


title: PDCLs

description:
s3-WGS, s3-GCC, and WES data generated on cell lines.
s3WGSands3GCC_PDCLandGM12878_500kbbin_rawreadcount.tsv
s3WGSands3GCC_PDCLandGM12878.bed
The raw data contains patient information so we were not going to upload to GEO/SRA

source_name: Low passage cell culture from primary tumor

value: whole exome sequencing, s3-WGS and s3-GCC


title: Invivo-6

first: Keerthikka

last: Ravi

state: Michigan

address: 1105 N University st

department: Molecular, Cellular and Developmental Biology

data_processing:
FastQC version 0.11.9 used to check quality of sequenced reads
Trimmomativ version 0.6.5 used to trim reads of poor quality, estting the parameters as LEADING and TRAILING set at 20 and MINLEN set at 100
Trimgalore version 0.6.5 used to remove adapter reads from the in vivo  sample reads.
Fastx_trimmer to trim the adapter sequences at the 3' end of the in vitro sample reads.
Bowtie2 version 2.3.4.3 used to align the sequenced reads to the reference genome
samtools verison 1.7 used to covert the SAM alignmnet output files to BAM format
Bioconductor packages GenomicAlignments and GenomicFeatures were used to generate the count file for the reads
DESeq2 used for analysing differnetial gene expression generating an FPKM file for all smaples as well as significanr log2 fold change in expression.
Genome_build: Reference sequence used for alignemnet - GenBank accession no CP017687
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Diffential gene expression for all genes, expression at 37°C vs expression at 4°C
Supplementary_files_format_and_content: Diffential gene expression for all genes, in vivo expression  vs expression at 37°C in vitro

organism: Pseudomonas lundensis

source_name: Cecal content from GF Balb/c mice

growth_protocol: AU1044 was innoculated in LB broth from frozen stock and grown overnight aerobically at 37°C. 4 20mL flasks of LB broth each at 4°C and 37°C aerobic conditions were innoculated with the 100µl of cells from the over night culture. Cells were harvested for RNA isolation once thery reached early stationary phase (OD of 2.1 at 600nm). For the in vivo samples, 6 germ free Balb/c mice went through gastric colonisation of AU1044 through oral gavage. Cecal content of the mice was harvested after 14 days of innoculation and used for Bacterial RNA isolation.

extract_protocol:
For the in vitro samples, protease treament followed by RNA isolation was performed as per the bacterial RNA isolation protocol from Qiagen Rneasy Kit. For the in vivo samples, Trizol/Rneasy hybrid protocol by Mauricio Rodriguez-Lanetty was followed
NEBNext Ultra II DNA library prep was used for cDNA library preperation.

tag: culture method

value: Cecal content from GF Balb/c mice


title: Root cap at time 24 control experiment 1 [A1T24_C_RC]

value: Root cap


title: HNSCC_anti-CD276

city: Guangzhou

first: Cheng

last: Wang

address: 56 Lingyuan Road West

country: China

institute: Sun Yat-sen University

data_processing:
scRNA-seq data generated from the 10× Genomics platform were processed using CellRanger (version 3.1.0) pipeline
Gene expression matrix was created by using Seurat (V3.1.5) pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: tongue

extract_protocol:
HNSCC samples were harvested from the tongue of mice and single cell suspensions were prepared for 10× genomics processing.
scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to manufacturer’s protocol

treatment_protocol: Mice were induced with 4NQO to establish murine HNSCC model and then treated with anti-CD276 or control antibodies for 4 weeks.

tag: strain

value: 4NQO to establish murine HNSCC model

value: anti-CD276 antibody


title: Pulmonary artery endothelial cells - ST _HiChIP_RepC

city: Stanford

first: Jan-Renier

last: Moonen

address: 269 Campus Drive, CCSR 1220

department: Pediatrics

institute: Stanford University

data_processing:
library strategy: HiChIP
Basecalls were performed using Bcl2fastq.
Data were filtered for duplicate reads, aligned to the hg19 genome, and filtered for valid interactions using the HiC-Pro pipeline v.2.11.1 (https://github.com/nservant/HiC-Pro) using the default settings.
FitHiChIP (https://github.com/ay-lab/FitHiChIP) was used to determine statistically significant interactions using default settings, with the exception of allowing interactions with a minimum size of 1 Kb.
Genome_build: hg19
Supplementary_files_format_and_content: bedpe files with the enhancer-promotor loops for the individual replicates
Supplementary_files_format_and_content: tsv file containing enhancer-promotor loop counts of all replicates combined with their target genes.

growth_protocol: PAEC were grown in commercial EC media containing 5% FBS (Sciencell) in a 5% CO2 air atmosphere and used at passages 3–7.

extract_protocol:
Cells were trypsinized, washed with ice-cold PBS, and lysed to isolate the nuclei.
Libraries were constructed as previously described (Mumbach et al. Nat Methods. 2016) using 1000,000 cells.

treatment_protocol: PAEC were exposed to 15 dyn/cm2 of LSS, or static culture conditions, for 24h.

value: Pulmonary artery endothelial cells (PAEC)

value: static control


title: HNSCC_Ctrl

value: control antibody

tag: tissue


title: Invivo-5


title: Pulmonary artery endothelial cells - ST _HiChIP_RepB


title: Invivo-4


title: Pulmonary artery endothelial cells - ST _HiChIP_RepA


title: 4um surface

city: Houston

first: H. Courtney

last: Hodges

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: mRNA in non-adherent cells from fibrotic capsule

data_processing:
All RNA-seq reads were processed using the 10x Cell Ranger pipeline v5.0.1. Fragments were aligned to the mm10 genome assembly using STAR aligner v2.7.2a.
Reads within coding regions were counted and normalized using Cell Ranger v5.0.1
Genome_build: mm10
Supplementary_files_format_and_content: TSV and MTX files are tab-delimited text files specifying total numbers of reads overlapping each gene for each unique cell barcode (altogether in MEX format). H5 files are binary files in H5 format containing the matrix of transcript read counts for each barcode.

molecule: polyA RNA

source_name: Peri-capsular immune cells

growth_protocol: Implants were manufactured to 1.3-cm size in molds according to established manufacturing methods equivalent to untextured, SmoothSilk™, or VelvetSurface™ implants. All implants were patched, filled, packaged and dry-heat-sterilized.

extract_protocol:
Non-adherent cells were obtained by irrigation of the resulting fibrotic capsule and processed using the 10x Chromium droplet-based scRNA-seq platform using manufacturer's instructions.
All libraries were barcoded and prepared for sequencing using standard 10x protocols (Single cell 5' RNA-seq) and Illumina protocols.

treatment_protocol: Silicone implants were implanted into the mammary fat pad of mice and tissues were collected after 2 weeks.

tag: surface topology

value: 4 um


title: 90um surface

value: 90 um


title: Invivo-3


title: Invivo-2


title: 0um surface

value: 0 um


title: Pulmonary artery endothelial cells - LSS _HiChIP_RepC

value: 15 dyne/cm2 of LSS


title: Derlin-2_KO_vehicle_2

description: Gene expression


title: Derlin-2_control_4PBA_1

description: Gene expression

value: control


title: Invivo-1


title: Derlin-2_KO_vehicle_1

description: Gene expression


title: Derlin-2_control_4PBA_2

description: Gene expression


title: Derlin-2_control_vehicle_1

description: Gene expression


title: Derlin-2_control_vehicle_2

description: Gene expression


title: Pulmonary artery endothelial cells - LSS _HiChIP_RepA


title: E80 Macaque MGE IgG Go-CaRT Rep 1

first: Tomasz

last: Nowakowski

state: Ca

institute: UCSF

data_processing:
Library strategy: GO-CaRT
150bp paired-end sequencing of GO-CaRT libraries was performed on the Illumina HiSeq 4000. Low quality reads and adaptors were removed with BBduk (http://jgi.doe.gov/data-and-tools/bb-tools/), and resulting reads were aligned to the mouse (UCSC mm10), macaque (USCS rheMac8) or human (UCSC hg38) genome using bowtie2 and the following settings: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700. Duplicate reads were removed with Picard tools

organism: Macaca mulatta

source_name: Embryonic Macaque Telencephalon

extract_protocol:
75,000-100,000 acutely isolated cells from mouse, macaque, and human forebrain (or cultured 3T3 and HEK293T cells) were used for each experiment. Cells were resuspended in 500 mL ice cold Nuclei Isolation Buffer (NIB) (10 mM HEPES-KOH, Ph 7.9. 10 mM KCl, 0.1% NP40, 0.5 mM Spermidine and 1X Halt protease inhibitor cocktail) and incubated for 10 min in ice. Nuclear pellet was collected by centrifuging at 600xg for 3 min at 40C and again washed with 500 mL NIB. Nuclear pellet was collected by centrifugation at 600xg for 3 and resuspended in 100 mL of NIB. Successful nuclei isolation was confirmed by visual inspection under a phase contrast microscope. Next, 10 mL Concanavalin A lectin beads (Bio-Mag Plus) washed and resuspended in Binding Buffer (BiB) (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2) were added to each sample and rotated for 10 min at room temperature. Nuclei bound Concanavalin A beads were pulled by placing the tubes on a magnetic stand to remove the supernatant. For LaminB GO-CaRT, anti LaminB1 antibody (Abcam# ab16048) was used and for SON GO-CaRT, anti-SON antibody (Atlas antibodies #HPA031755) was used at 1:100 dilution in Blocking Buffer (BlocB) (Wash buffer containing 2mM EDTA). Same steps were followed for histone marks using anti-H3K9me2 (Active Motif #39239, 1:100), anti-H3K9me3 (Abcam# ab8898; 1:100), anti-H3K27me3 (Cell signaling technologies #9733; 1:100). An IgG control was run in parallel for all experiments (Cell signaling technologies #2729; 1:100). To each sample 50 mL of BlocB containing primary antibody was added and incubated overnight on a rotator at 40C. Next day, samples were briefly spun and placed on magnetic stand to clear off the liquid. Samples were washed twice with 1mL Wash Buffer (WaB) (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.1% BSA, 0.5 mM Spermidine and 1X Halt protease inhibitor cocktail). At the end of two washing steps, Concanavalin A bound nuclei were resuspended in 50 mL of WaB and gently mixed. To each tube, 2.5 mL of pA-MNase (diluted 1:10 in WaB from 140 mg/mL stock) kindly provided by Steven Henikoff (Fred Hutchison Cancer Research Center) was added and rotated for 1 hour at 40C. Samples were briefly spun and placed on magnetic stand to remove the liquid. Samples were washed twice with 1mL WaB. At the end of two washing steps, Concanavalin A bound nuclei were resuspended in 100 mL of WaB and gently mixed. The tubes were placed in pre-chilled metal blocks sitting in ice. While gently vortexing, 2 mL of 100 mM CaCl2 was added to initiate MNase digestion and returned to pre-chilled metal blocks. Digestion was carried out for 30 min and stopped by adding 100 mL of 2XSTOP (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/mL RNAseA, 40 mg/mL Glycogen and 10 pg/mL of heterologous DNA) while gently vortexing. To release pA-MNase cleaved fragments, samples were incubated at 370C for 15 min. DNA was extracted using Phenol: Chloroform extraction method. We considered the possibility that the pA-MNase cleaved DNA-protein complexes might be too large to diffuse out of the nucleus and enter the “soluble” fraction.  To test this, we recovered DNA from both soluble and total fractions (soluble + insoluble).  LaminB profiles were highly similar (Pearson= 0.94) between soluble and total fractions, indicating that DNA-protein complexes released by LaminB GO-CaRT can readily diffuse out of the nucleus.
Sequencing libraries were prepared from GO-CaRT DNA fragments using KAPA HyperPlus with amplification DNA library preparation kit (#KK8512) following manufacturer instructions. The library was amplified for 13-15 PCR cycles and larger DNA fragments were depleted by doing a 0.55X size selection using Agencourt AMPure XP beads (Beckman #A63881).

value: Embryonic Macaque Telencephalon

value: Embryonic Day 80


title: L3mbtl3 KO/+ #2

first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using Trimmomatic v0.39 (Bolger et al. Bioinformatics. 2014) with parameters ILLUMINACLIP: TruSeq3-PE.fa:2:30:10:2:true LEADING:3 TRAILING:3 MINLEN:35 SLIDINGWINDOW:4:15. Paired-end alignments and gene level counts were obtained using RSEM v1.3.1 (Li and Dewey. BMC Bioinformatics. 2011). STAR v2.5.2a was the aligner called by RSEM and the default parameters were used (Dobin et al. Bioinformatics. 2013.)
The mouse reference sequence mm10/GRCm38 and annotations, including gene IDs, were obtained from Gencode vM21 (Frankish et al. Nucleic Acids Res. 2018).
Genome_build: mm10
Supplementary_files_format_and_content: The per-sample genes and isoforms text files are the original output from RSEM.  For counts, TPM, and FPKM (all determined by RSEM), a sample matrix (tab-delimites text) is provided.  For the genes matrices (e.g. genes.counts.txt) the first 8 columns are gene annotations.  For isoforms matrices (e.g. isoforms.counts.txt) the first 4 columns contain transcript annotations. All TSV files contain headers.

source_name: cerebellum

extract_protocol:
Mouse cerebella were harvested from L3mbtl3WT versus L3mbtl3KO/+ pups at postnatal day 15 (P15). The cerebella were homogenized in Trizol with VWR Pellet Mixers (VWR, Logan, NJ, Cat# 47747-370), purified using RNeasy Mini kit (Qiagen, Germantown, MD, Cat# 74106), treated with DNase I (New England Biolab, Ipswich, MA, Cat# M0303) and processed using the Monarch RNA Cleanup Kit (New England Biolab, Ipswich, MA, Cat# T2050). RNA samples were then assessed for quality using the TapeStation (Agilent, Santa Clara, CA).
Samples with RINs (RNA Integrity Numbers) of seven or greater were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolab, Ipswich, MA, Cat# E7760L) with Poly(A) mRNA Magnetic Isolation Module (New England Biolab, Ipswich, MA, Cat# E7490L) and NEBNext Multiplex Oligos for Illumina Unique Dual (New England Biolab, Ipswich, MA, Cat# E6440L). The mRNA is then fragmented 10 minutes and copied into first strand cDNA using reverse transcriptase and dUTP mix. Samples undergo end repair and dA-tailing step followed by ligation of NEBNext adapters. The products are then purified and enriched by PCR (11 cycles) to create the final cDNA library. Final cDNA libraries were checked for quality and quantity by TapeStation (Agilent, Santa Clara, CA) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (Kapa Biosystems, Wilmington, MA, Cat# KK4835).

tag: genotype

value: L3mbtl3 KO/+

value: P15 (postnatal day 15)

value: cerebella


title: E80 Macaque MGE LaminB Go-CaRT Rep 1


title: L3mbtl3 KO/+ #3


title: Sample_cst2

city: Beijing

first: Shenglong

last: Ding

state: Beijing

address: No. 1, Dongjiaomin Lane, Dongcheng District

institute: Beijing TongRen Hospital, Capital Medical University

data_processing:
High throughput sequencing service was provided by CloudSeq Biotech (Shanghai, China). Transcriptome high throughput sequencing and subsequent bioinformatics analysis were all done by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA).
10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse mRNAs.
The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of mRNA, and fold change, p-value and FDR were calculated with DeSeq.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Nucleus Pulposus

extract_protocol:
The RNA were extracted by TRIZol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nucleus pulposus cells  were stretched using a FX-5000T Flexcell tension plus system (Flexcell International Corp., USA)  with 18% elongation (0.2 Hz) for 24 h

value: Nucleus Pulposus

tag: classification

value: cyclic tensile strain

value: Sprague Dawley Rat


title: Sample_cst1


title: L3mbtl3 KO/+ #4


title: E80 Macaque V1 IgG Go-CaRT Rep 1

tag: developmental stage


title: Pulmonary artery endothelial cells - LSS _HiChIP_RepB


title: Derlin-1_KO_4PBA_1

description: Gene expression

value: case


title: WT #3

value: WT


title: Derlin-1_KO_4PBA_2

description: Gene expression


title: Derlin-1_control_4PBA_1

description: Gene expression


title: Derlin-1_KO_vehicle_1

description: Gene expression


title: Derlin-1_KO_vehicle_2

description: Gene expression


title: Sample_cst3


title: E80 Macaque V1 LaminB Go-CaRT Rep 1

description:
MacqE80_Cortex_LmnB_log2ratio.bedGraph
EPIC2_MacqE80_Cortex_LmnBC.bed


title: Sample_con3

value: Control


title: Sample_con2


title: huFL LMPP 3

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

description: huFL LMPP 3

data_processing:
Initial quality control of ATAC-seq fastq read files generated in this study was carried out using the FastQC toolkit (https://github.com/s-andrews/FastQC).
The Tn5 transposase sequence 5’- CTGTCTCTTATACACATCT-3’ was then trimmed from reads using Cutadapt (Martin et al., https://doi.org/10.14806/ej.17.1.200).
Following trimming, samples were aligned to the mouse and human reference genomes MGSCv37 (mm9) and GRCh38 (hg38) respectively using Bowtie2 (Langmead et al., PMID: 22388286) version 2.3.4.1, with a –very-sensitive –local call and paired-end settings.
The generated sam files containing aligned read pairs were then sorted and converted to bam format using the samtools suite (Li et al., PMID: 19505943). Duplicated reads were filtered using the Picard tools function MarkDuplicates (https://github.com/broadinstitute/picard). Replicate samples were subsequently merged using the samtools merge function (Li et al., PMID: 19505943). Coverage and insert size distribution was then measured for both individual replicates and merged samples using Qualimap (Okonechnikov et al., PMID: 26428292). The aligned reads (bam files) were normalised for sequencing coverage to a 1x genome depth (reads per genome coverage, RPGC), using an effective genome size of either 2150570000 base pairs for mm9 or 3049315783 base pairs for hg38, with the bamCoverage function from deepTools (PMID: 27079975) using a bin size of 10 base pairs, the extendReads parameter, chromosome X ignored for normalisation and ENCODE blacklist regions excluded (Amemiya et al., PMID: 31249361).
The resulting normalised bigwig files were visualised using Integrative Genomics Viewer (IGV) (Robinson et al., PMID: 21221095).
Genome_build: MGSCv37 (mm9) and GRCh38 (hg38)
Supplementary_files_format_and_content: normalised bigwig files

source_name: Lineage- CD34+ CD38- CD19- CD45RA+ cells

extract_protocol:
cells were sorted from freshly isolated mouse tissues or previously frozen human tissues; single cell preparations were stained with cell surface markers and directly sorted into transposition buffer
Following the discarding of supernatant the nuclei pellet was resuspended in 50 μl transposition mix with the following Tn5 volumes according to cellular input (1000-5000 (0.5 μl Tn5), 5000-10,000 (1.0 μl Tn5), 10,000-15,000 (1.5 μl Tn5) with the remainder of the total reaction adjusted with water (25 μl 2× TD buffer, x μl transposase, 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, x μl H2O) and incubated at 37 °C for 30 min in a thermomixer with 1,000 rpm shaking. All reactions were cleaned up using the Zymo DNA Clean and Concentrator-5 Kit (Cat# D4014) with DNA eluted in 11 μl of elution buffer and PCR amplified with the NEBNext Hi-Fidelity PCR Master Mix (Cat# M0541L) with a custom dual barcoding strategy as previously described (Mezger et al. PMID: 30194434). The amplification reaction was stopped at 5 cycles and 5 μl of the pre-amplified mixture was run in a 15 μl qPCR reaction to determine the optimal number of additional cycles that corresponded to 1/3 of the maximum fluorescent intensity up to a total of 13 cycles (Buenrostro et al. PMID: 25559105). A final clean up was performed, libraries were eluted in 20 μl and quantified using the NEBNext Library Kit for Illumina (Cat# E7645L), assessed using the Agilent Bioanalyzer High Sensitivity DNA Analysis kit (Cat# 5067-4627) and finally double size selected with the Zymo Select-a-Size DNA Clean & Concentrator kit (Cat# D4084).

value: wild-type

value: foetal liver

value: 10-20 weeks of gestation


title: L3mbtl3 KO/+ #1


title: Sample_con1


title: E80 Macaque PFC LaminB Go-CaRT Rep 1


title: Derlin-1_control_vehicle_2

description: Gene expression


title: huFL LMPP 1

description: huFL LMPP 1


title: Derlin-1_control_4PBA_2

description: Gene expression


title: Control_rep3

status: Public on May 27 2021

city: Nanjing

first: Shiyu

last: Song

state: China

address: Nanjing University, Nanjing, JiangSu Province, Kejiguan 210

institute: Nanjing University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter;
(2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;
(3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: gastrocnemius muscle

extract_protocol:
The gastrocnemius muscles were removed, flash frozen on dry ice, and RNAThe total RNA extraction was prepared from M.tb infected THP-1 cells with RNA Miniprep kit reagent as described by the manufacturer Vazyme biotech, Nanjing, China.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: muscle

value: Balb/c

tag: model


title: C26_rep1


title: WT #2


title: Control_rep2


title: C26_rep2


title: E80 Macaque PFC IgG Go-CaRT Rep 1


title: RIG_Case_32

type: genomic

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: At least 300 ng of DNA was used per sample for the subsequent bisulfite conversion using the Zymo EZ-96 DNA Methylation kit. Next, the Infinium HD FFPE Restoration kit was used to restore degraded FFPE DNA to a state that is amplifiable by the Infinium HD FFPE methylation whole-genome amplification kit. Restored DNA was then plate-purified (with the Zymo ZR-96 DNA Clean & Concentrator-5), amplified, fragmented, precipitated, re-suspended, and hybridized to an Illumina Infinium Methylation EPIC 850K BeadChip array for 22 h and 30 min (by using the Illumina Infinium Methylation EPIC assay kit).

scan_protocol: After hybridization, arrays were manually disassembled and washed. Subsequent X-Staining of array features was processed on a Tecan Freedom Evo robotics system. Arrays were then manually coated and imaged using an Illumina iScan system with autoloader.

data_processing: DNA methylation data analysis was performed using the open source statistical programming language R (R Core Team, 2016). Raw data files generated by the iScan array scanner were read and pre-processed using the minfi Bioconductor package50. With the minfi package, the same preprocessing steps as in Illumina’s Genomestudio software were performed. In addition, the following filtering criteria were applied: removal of probes targeting the X and Y chromosomes, removal of probes containing nucleotide polymorphism (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, and removal of probes not mapping uniquely to the human reference genome (hg19), allowing for one mismatch. In total, 394,848 common probes of Illumina 450K and EPIC arrays were kept for clustering analysis.

label: Cy5 and Cy3

source_name: RIG tumor

label_protocol: Not provided

extract_protocol: Tumor DNA was extracted from FFPE material by using the Maxwell16 FFPE Plus LEV purification kit and the Maxwell 16 instrument (Promega, Madison, WI) according to the manufacturer’s instructions.

value: Radiation-induced high-grade glioma (RIG)


title: RIG_Case_33


title: WT #1


title: Derlin-1_control_vehicle_1

description: Gene expression

source_name: mouse cerebellum

value: control


title: Aging mice with allulose supplement, re3 [ALL7]

city: Daegu

first: Youngji

last: Han

address: Daehakro 80

country: South Korea

institute: Kyungpook National University

data_processing:
Trimmomatic-0.38 software used for filtering
fastQC v0.11.7 software used for data quality check
HISAT2 v2.1.0 software used for alignment
featureCounts software used to quantify gene expression (gene-based)
Genome_build: mm10
Supplementary_files_format_and_content: tab deliminated text file containing each gene expression (in raw count) for the sample in the file name

source_name: Aging mice with allulose supplement_Gastrocnemius

growth_protocol: 21 male C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) at 12 months of age and 8 weeks of age. All the mice were individually housed under a constant temperature (24°C) and 12-hour light/dark cycle, fed the AIN-93 semi-purified diet for a one-week acclimation period after arrival

extract_protocol:
Total RNA was extracted from the adipose tissue and liver using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.
TruSeq Stranded mRNA Sample Preparation Guide, Part #  15031047 Rev. E

treatment_protocol: The mice were fed a normal diet or normal diet with 3% (w/w) D-allulose (Sigma Chemical, MO) for 12 weeks.

value: 12 months

tag: treatment

value: allulose supplement

value: Gastrocnemius


title: Aging mice with allulose supplement, re4 [ALL9]


title: Aging mice, rep3 [NC4]

source_name: Aging mice_Gastrocnemius


title: Aging mice, rep6 [NC7]


title: Aging mice, rep2 [NC3]


title: Control_rep1


title: Aging mice, rep1 [NC1]


title: Aging mice with allulose supplement, re1 [ALL1]


title: C26_rep3


title: Aging mice, rep5 [NC6]


title: Young mice, rep7 [PC10]

source_name: Young mice_Gastrocnemius

value: 8 weeks


title: Aging mice, rep4 [NC5]


title: Young mice, rep3 [PC4]


title: Young mice, rep4 [PC5]


title: Young mice, rep2 [PC3]


title: Young mice, rep6 [PC9]


title: Young mice, rep1 [PC1]


title: Young mice, rep5 [PC7]


title: M_P7_hyperoxia_mesench_1_DC33_N18

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

source_name: distal lung

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

tag: gender

value: M

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: mesenchymal

tag: cell subtype

value: Early alveolar fibroblast

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_mesench_2_DC33_N22

tag: cell type


title: M_P7_hyperoxia_mesench_2_DC33_D15

value: Early adventitial fibroblast


title: M_P7_hyperoxia_mesench_1_DC33_K8


title: Aging mice with allulose supplement, re2 [ALL4]

tag: strain

tag: age

tag: tissue


title: M_P7_hyperoxia_mesench_1_DC33_P10


title: M_P7_hyperoxia_mesench_2_DC33_H19

value: Vascular smooth muscle


title: M_P7_hyperoxia_mesench_1_DC33_D4

value: Myofibroblast


title: M_P7_hyperoxia_mesench_2_DC33_P13


title: M_P7_hyperoxia_mesench_2_DC33_G12


title: M_P7_hyperoxia_mesench_2_DC33_E17


title: M_P7_hyperoxia_mesench_1_DC33_M15


title: M_P7_hyperoxia_mesench_2_DC33_J4

value: Early airway smooth muscle


title: M_P7_hyperoxia_mesench_1_DC33_H6


title: M_P7_hyperoxia_mesench_2_DC33_N20


title: M_P7_hyperoxia_mesench_1_DC33_N5


title: M_P7_hyperoxia_mesench_2_DC33_C21


title: M_P7_hyperoxia_mesench_2_DC33_H11


title: M_P7_hyperoxia_mesench_1_DC33_A22


title: M_P7_hyperoxia_mesench_1_DC33_N9


title: M_P7_hyperoxia_mesench_1_DC33_C22

value: Proliferating myofibroblast


title: M_P7_hyperoxia_mesench_1_DC33_G21


title: M_P7_hyperoxia_mesench_1_DC33_F12


title: M_P7_hyperoxia_mesench_2_DC33_I20


title: M_P7_hyperoxia_mesench_2_DC33_J16

value: Male hyperoxic fibroblast


title: M_P7_hyperoxia_mesench_1_DC33_E18

value: Proliferating pericyte


title: M_P7_hyperoxia_mesench_2_DC33_P23


title: M_P7_hyperoxia_mesench_2_DC33_O10


title: M_P7_hyperoxia_mesench_2_DC33_O23


title: M_P7_hyperoxia_mesench_1_DC33_C18


title: M_P7_hyperoxia_mesench_2_DC33_C11


title: M_P7_hyperoxia_mesench_1_DC33_C17


title: M_P7_hyperoxia_mesench_2_DC33_O22


title: M_P7_hyperoxia_mesench_2_DC33_H8


title: M_P7_hyperoxia_mesench_1_DC33_H12


title: M_P7_hyperoxia_mesench_2_DC33_L23


title: M_P7_hyperoxia_mesench_2_DC33_G23


title: M_P7_hyperoxia_mesench_2_DC33_K3


title: M_P7_hyperoxia_mesench_1_DC33_A16


title: M_P7_hyperoxia_mesench_2_DC33_K9


title: M_P7_hyperoxia_mesench_1_DC33_J15


title: M_P7_hyperoxia_mesench_1_DC33_J17


title: M_P7_hyperoxia_mesench_1_DC33_K1


title: M_P7_hyperoxia_mesench_2_DC33_M5


title: M_P7_hyperoxia_mesench_1_DC33_I14


title: M_P7_hyperoxia_mesench_1_DC33_A11


title: M_P7_hyperoxia_mesench_1_DC33_E15


title: M_P7_hyperoxia_mesench_1_DC33_P4


title: M_P7_hyperoxia_mesench_1_DC33_I19


title: M_P7_hyperoxia_mesench_1_DC33_O5


title: M_P7_hyperoxia_mesench_2_DC33_E19


title: M_P7_hyperoxia_mesench_2_DC33_I9

value: Proliferating fibroblast


title: M_P7_hyperoxia_mesench_1_DC33_P13


title: M_P7_hyperoxia_mesench_2_DC33_N9


title: M_P7_hyperoxia_mesench_1_DC33_E12


title: M_P7_hyperoxia_mesench_1_DC33_D12


title: M_P7_hyperoxia_mesench_2_DC33_O18


title: M_P7_hyperoxia_mesench_1_DC33_A21


title: M_P7_hyperoxia_mesench_1_DC33_P5


title: M_P7_hyperoxia_mesench_2_DC33_L19


title: M_P7_hyperoxia_mesench_1_DC33_M22


title: M_P7_hyperoxia_mesench_2_DC33_K18


title: M_P7_hyperoxia_mesench_1_DC33_I9


title: M_P7_hyperoxia_mesench_2_DC33_F18


title: M_P7_hyperoxia_mesench_2_DC33_F19


title: M_P7_hyperoxia_mesench_2_DC33_H12


title: M_P7_hyperoxia_mesench_2_DC33_B21


title: M_P7_hyperoxia_mesench_2_DC33_D14


title: M_P7_hyperoxia_mesench_1_DC33_A15


title: M_P7_hyperoxia_mesench_1_DC33_G14


title: M_P7_hyperoxia_mesench_1_DC33_O2


title: M_P7_hyperoxia_mesench_2_DC33_I17


title: M_P7_hyperoxia_mesench_2_DC33_H3


title: M_P7_hyperoxia_mesench_2_DC33_B13


title: M_P7_hyperoxia_mesench_1_DC33_A20


title: M_P7_hyperoxia_mesench_2_DC33_F3


title: M_P7_hyperoxia_mesench_1_DC33_G16


title: M_P7_hyperoxia_mesench_1_DC33_O23


title: M_P7_hyperoxia_mesench_2_DC33_M2


title: M_P7_hyperoxia_mesench_2_DC33_B19


title: M_P7_hyperoxia_mesench_2_DC33_M11


title: M_P7_hyperoxia_mesench_2_DC33_A16


title: M_P7_hyperoxia_mesench_1_DC33_B11


title: M_P7_hyperoxia_mesench_2_DC33_O21


title: M_P7_hyperoxia_mesench_2_DC33_C3


title: M_P7_hyperoxia_mesench_1_DC33_G8


title: M_P7_hyperoxia_mesench_1_DC33_F6


title: M_P7_hyperoxia_mesench_2_DC33_H16


title: M_P7_hyperoxia_mesench_2_DC33_B6


title: M_P7_hyperoxia_mesench_2_DC33_N23


title: M_P7_hyperoxia_mesench_2_DC33_G20


title: M_P7_hyperoxia_mesench_1_DC33_O3


title: M_P7_hyperoxia_mesench_1_DC33_P12


title: M_P7_hyperoxia_mesench_2_DC33_N8


title: M_P7_hyperoxia_mesench_2_DC33_H4


title: M_P7_hyperoxia_mesench_2_DC33_I19


title: M_P7_hyperoxia_mesench_1_DC33_J21


title: M_P7_hyperoxia_mesench_2_DC33_K8


title: M_P7_hyperoxia_mesench_1_DC33_D10


title: M_P7_hyperoxia_mesench_2_DC33_M22


title: M_P7_hyperoxia_mesench_1_DC33_N19


title: M_P7_hyperoxia_mesench_1_DC33_N6


title: M_P7_hyperoxia_mesench_2_DC33_L10


title: M_P7_hyperoxia_mesench_2_DC33_E6


title: M_P7_hyperoxia_mesench_1_DC33_L11


title: M_P7_hyperoxia_mesench_1_DC33_K3


title: M_P7_hyperoxia_mesench_1_DC33_H13


title: M_P7_hyperoxia_mesench_2_DC33_J21


title: M_P7_hyperoxia_mesench_1_DC33_E11


title: M_P7_hyperoxia_mesench_2_DC33_I8


title: M_P7_hyperoxia_mesench_2_DC33_E4


title: M_P7_hyperoxia_mesench_2_DC33_D23


title: M_P7_hyperoxia_mesench_1_DC33_O20


title: M_P7_hyperoxia_mesench_2_DC33_N5


title: M_P7_hyperoxia_mesench_1_DC33_F5


title: M_P7_hyperoxia_mesench_1_DC33_H20


title: M_P7_hyperoxia_mesench_1_DC33_M3


title: M_P7_hyperoxia_mesench_2_DC33_J15


title: M_P7_hyperoxia_mesench_2_DC33_G21


title: M_P7_hyperoxia_mesench_2_DC33_H18


title: M_P7_hyperoxia_mesench_2_DC33_B11


title: M_P7_hyperoxia_mesench_2_DC33_J7


title: M_P7_hyperoxia_mesench_1_DC33_L15


title: M_P7_hyperoxia_mesench_2_DC33_D8


title: M_P7_hyperoxia_mesench_2_DC33_P19


title: M_P7_hyperoxia_mesench_1_DC33_D16


title: M_P7_hyperoxia_mesench_2_DC33_D20


title: M_P7_hyperoxia_mesench_1_DC33_K9


title: M_P7_hyperoxia_mesench_1_DC33_O18

value: Myofibroblast and smooth muscle precursor


title: M_P7_hyperoxia_mesench_2_DC33_F1


title: M_P7_hyperoxia_mesench_1_DC33_F13


title: M_P7_hyperoxia_mesench_2_DC33_E7


title: M_P7_hyperoxia_mesench_2_DC33_D16


title: M_P7_hyperoxia_mesench_1_DC33_B22


title: M_P7_hyperoxia_mesench_1_DC33_M9


title: M_P7_hyperoxia_mesench_1_DC33_N17


title: M_P7_hyperoxia_mesench_1_DC33_E6


title: M_P7_hyperoxia_mesench_2_DC33_P12


title: M_P7_hyperoxia_mesench_1_DC33_N21


title: M_P7_hyperoxia_mesench_1_DC33_C16


title: M_P7_hyperoxia_mesench_1_DC33_I6


title: M_P7_hyperoxia_mesench_2_DC33_A7


title: M_P7_hyperoxia_mesench_2_DC33_M21


title: M_P7_hyperoxia_mesench_2_DC33_E14


title: M_P7_hyperoxia_mesench_2_DC33_F20


title: M_P7_hyperoxia_mesench_1_DC33_P6


title: M_P7_hyperoxia_mesench_2_DC33_J9


title: M_P7_hyperoxia_mesench_1_DC33_E22


title: M_P7_hyperoxia_mesench_2_DC33_K17


title: M_P7_hyperoxia_mesench_2_DC33_I22


title: M_P7_hyperoxia_mesench_1_DC33_D17


title: M_P7_hyperoxia_mesench_2_DC33_B20


title: M_P7_hyperoxia_mesench_1_DC33_I18


title: M_P7_hyperoxia_mesench_1_DC33_A5


title: M_P7_hyperoxia_mesench_2_DC33_E16


title: M_P7_hyperoxia_mesench_2_DC33_L12


title: M_P7_hyperoxia_mesench_1_DC33_C4


title: M_P7_hyperoxia_mesench_1_DC33_F8


title: M_P7_hyperoxia_mesench_1_DC33_I2


title: M_P7_hyperoxia_mesench_2_DC33_J12


title: M_P7_hyperoxia_mesench_1_DC33_C15


title: M_P7_hyperoxia_mesench_1_DC33_M12


title: M_P7_hyperoxia_mesench_2_DC33_J6


title: M_P7_hyperoxia_mesench_2_DC33_C23


title: M_P7_hyperoxia_mesench_1_DC33_F10


title: M_P7_hyperoxia_mesench_2_DC33_E9


title: M_P7_hyperoxia_mesench_1_DC33_M2


title: M_P7_hyperoxia_mesench_2_DC33_O16


title: M_P7_hyperoxia_mesench_1_DC33_F16


title: M_P7_hyperoxia_mesench_2_DC33_H23


title: M_P7_hyperoxia_mesench_2_DC33_G22


title: M_P7_hyperoxia_mesench_2_DC33_H7


title: M_P7_hyperoxia_mesench_1_DC33_C14


title: M_P7_hyperoxia_mesench_2_DC33_E20


title: M_P7_hyperoxia_mesench_1_DC33_J19


title: M_P7_hyperoxia_mesench_1_DC33_L6


title: M_P7_hyperoxia_mesench_2_DC33_A13


title: M_P7_hyperoxia_mesench_2_DC33_O8


title: M_P7_hyperoxia_mesench_1_DC33_A10


title: M_P7_hyperoxia_mesench_1_DC33_M20


title: M_P7_hyperoxia_mesench_2_DC33_C2


title: M_P7_hyperoxia_mesench_1_DC33_E14


title: M_P7_hyperoxia_mesench_1_DC33_I11


title: M_P7_hyperoxia_mesench_1_DC33_M21


title: M_P7_hyperoxia_mesench_1_DC33_G22


title: M_P7_hyperoxia_mesench_1_DC33_C6


title: M_P7_hyperoxia_mesench_1_DC33_K13


title: M_P7_hyperoxia_mesench_1_DC33_C12


title: M_P7_hyperoxia_mesench_1_DC33_J4


title: M_P7_hyperoxia_mesench_1_DC33_I12


title: M_P7_hyperoxia_mesench_1_DC33_H14


title: M_P7_hyperoxia_mesench_1_DC33_C21


title: M_P7_hyperoxia_mesench_2_DC33_J10


title: M_P7_hyperoxia_mesench_1_DC33_F21


title: M_P7_hyperoxia_mesench_1_DC33_M11


title: M_P7_hyperoxia_mesench_2_DC33_E3


title: M_P7_hyperoxia_mesench_1_DC33_I1


title: M_P7_hyperoxia_mesench_1_DC33_D18


title: M_P7_hyperoxia_mesench_1_DC33_G17


title: M_P7_hyperoxia_mesench_2_DC33_I21


title: M_P7_hyperoxia_mesench_2_DC33_O5


title: M_P7_hyperoxia_mesench_1_DC33_F23


title: M_P7_hyperoxia_mesench_1_DC33_L4


title: M_P7_hyperoxia_mesench_2_DC33_M12


title: M_P7_hyperoxia_mesench_2_DC33_B4


title: M_P7_hyperoxia_mesench_2_DC33_M1


title: M_P7_hyperoxia_mesench_2_DC33_G1


title: M_P7_hyperoxia_mesench_2_DC33_M19


title: M_P7_hyperoxia_mesench_2_DC33_I18


title: M_P7_hyperoxia_mesench_1_DC33_N14


title: M_P7_hyperoxia_mesench_2_DC33_M14


title: M_P7_hyperoxia_mesench_2_DC33_O3


title: M_P7_hyperoxia_mesench_1_DC33_L7


title: M_P7_hyperoxia_mesench_2_DC33_I14


title: M_P7_hyperoxia_mesench_1_DC33_I13


title: M_P7_hyperoxia_mesench_2_DC33_J19


title: M_P7_hyperoxia_mesench_2_DC33_A10


title: M_P7_hyperoxia_mesench_1_DC33_L9


title: M_P7_hyperoxia_mesench_2_DC33_M8


title: M_P7_hyperoxia_mesench_1_DC33_G5


title: M_P7_hyperoxia_mesench_2_DC33_N6


title: M_P7_hyperoxia_mesench_2_DC33_M17


title: M_P7_hyperoxia_mesench_1_DC33_K23


title: M_P7_hyperoxia_mesench_2_DC33_M6


title: M_P7_hyperoxia_mesench_1_DC33_C13


title: M_P7_hyperoxia_mesench_1_DC33_K10


title: M_P7_hyperoxia_mesench_1_DC33_E13


title: M_P7_hyperoxia_mesench_1_DC33_J9


title: M_P7_hyperoxia_mesench_2_DC33_F6


title: M_P7_hyperoxia_mesench_1_DC33_H18


title: M_P7_hyperoxia_mesench_1_DC33_C23


title: M_P7_hyperoxia_mesench_2_DC33_B22


title: M_P7_hyperoxia_mesench_1_DC33_C10


title: M_P7_hyperoxia_mesench_2_DC33_F9


title: M_P7_hyperoxia_mesench_2_DC33_G5


title: M_P7_hyperoxia_mesench_1_DC33_E17


title: M_P7_hyperoxia_mesench_1_DC33_A2


title: M_P7_hyperoxia_mesench_1_DC33_A13


title: M_P7_hyperoxia_mesench_2_DC33_I6


title: M_P7_hyperoxia_mesench_2_DC33_I3


title: M_P7_hyperoxia_mesench_1_DC33_A14


title: M_P7_hyperoxia_mesench_2_DC33_J18


title: M_P7_hyperoxia_mesench_2_DC33_N12


title: M_P7_hyperoxia_mesench_1_DC33_O15


title: M_P7_hyperoxia_mesench_1_DC33_K21


title: M_P7_hyperoxia_mesench_1_DC33_J11


title: M_P7_hyperoxia_mesench_1_DC33_N11


title: M_P7_hyperoxia_mesench_2_DC33_G4


title: M_P7_hyperoxia_mesench_2_DC33_K19


title: M_P7_hyperoxia_mesench_1_DC33_M13


title: M_P7_hyperoxia_mesench_2_DC33_P7


title: M_P7_hyperoxia_mesench_1_DC33_K19


title: M_P7_hyperoxia_mesench_2_DC33_J23


title: M_P7_hyperoxia_mesench_2_DC33_K12


title: M_P7_hyperoxia_mesench_2_DC33_O4


title: M_P7_hyperoxia_mesench_1_DC33_B5


title: M_P7_hyperoxia_mesench_1_DC33_I7


title: M_P7_hyperoxia_mesench_1_DC33_B19


title: M_P7_hyperoxia_mesench_1_DC33_N12


title: M_P7_hyperoxia_mesench_1_DC33_O14


title: M_P7_hyperoxia_mesench_1_DC33_E2


title: M_P7_hyperoxia_mesench_2_DC33_A5


title: M_P7_hyperoxia_mesench_1_DC33_J23


title: M_P7_hyperoxia_mesench_2_DC33_D4


title: M_P7_hyperoxia_mesench_2_DC33_F17


title: M_P7_hyperoxia_mesench_2_DC33_G16


title: M_P7_hyperoxia_mesench_2_DC33_P5


title: M_P7_hyperoxia_mesench_1_DC33_H9


title: M_P7_hyperoxia_mesench_1_DC33_O7


title: M_P7_hyperoxia_mesench_2_DC33_B10


title: M_P7_hyperoxia_mesench_2_DC33_P6


title: M_P7_hyperoxia_mesench_2_DC33_H5


title: M_P7_hyperoxia_mesench_2_DC33_F16


title: M_P7_hyperoxia_mesench_1_DC33_P8


title: M_P7_hyperoxia_mesench_2_DC33_L9


title: M_P7_hyperoxia_mesench_2_DC33_N15


title: M_P7_hyperoxia_mesench_2_DC33_O12


title: M_P7_hyperoxia_mesench_1_DC33_I17


title: M_P7_hyperoxia_mesench_1_DC33_E21


title: M_P7_hyperoxia_mesench_1_DC33_O13


title: M_P7_hyperoxia_mesench_1_DC33_J8


title: M_P7_hyperoxia_mesench_2_DC33_L14


title: M_P7_hyperoxia_mesench_2_DC33_L7


title: M_P7_hyperoxia_mesench_1_DC33_D14


title: M_P7_hyperoxia_mesench_1_DC33_B17


title: M_P7_hyperoxia_mesench_1_DC33_M23


title: M_P7_hyperoxia_mesench_2_DC33_E22


title: M_P7_hyperoxia_mesench_2_DC33_D1


title: M_P7_hyperoxia_mesench_1_DC33_L20


title: M_P7_hyperoxia_mesench_2_DC33_C16


title: M_P7_hyperoxia_mesench_1_DC33_K16


title: M_P7_hyperoxia_mesench_1_DC33_M14


title: M_P7_hyperoxia_mesench_1_DC33_J13


title: M_P7_hyperoxia_mesench_1_DC33_B23


title: M_P7_hyperoxia_mesench_1_DC33_E8


title: M_P7_hyperoxia_mesench_2_DC33_O7


title: M_P7_hyperoxia_mesench_1_DC33_J2


title: M_P7_hyperoxia_mesench_2_DC33_H6


title: M_P7_hyperoxia_mesench_1_DC33_B15

value: Pericyte


title: M_P7_hyperoxia_mesench_1_DC33_K15


title: M_P7_hyperoxia_mesench_2_DC33_I15


title: M_P7_hyperoxia_mesench_2_DC33_I23


title: M_P7_hyperoxia_mesench_2_DC33_J17


title: M_P7_hyperoxia_mesench_2_DC33_E15


title: M_P7_hyperoxia_mesench_2_DC33_H21


title: M_P7_hyperoxia_mesench_1_DC33_P20


title: M_P7_hyperoxia_mesench_1_DC33_J20


title: M_P7_hyperoxia_mesench_2_DC33_E1


title: M_P7_hyperoxia_mesench_2_DC33_N3


title: M_P7_hyperoxia_mesench_2_DC33_N10


title: M_P7_hyperoxia_mesench_1_DC33_J5


title: M_P7_hyperoxia_mesench_1_DC33_M4


title: M_P7_hyperoxia_mesench_1_DC33_H8


title: M_P7_hyperoxia_mesench_2_DC33_G2


title: M_P7_hyperoxia_mesench_2_DC33_K16


title: M_P7_hyperoxia_mesench_1_DC33_D3


title: M_P7_hyperoxia_mesench_1_DC33_N10


title: M_P7_hyperoxia_mesench_2_DC33_K20


title: M_P7_hyperoxia_mesench_2_DC33_N7


title: M_P7_hyperoxia_mesench_1_DC33_I5


title: M_P7_hyperoxia_mesench_1_DC33_J10


title: M_P7_hyperoxia_mesench_2_DC33_E18


title: M_P7_hyperoxia_mesench_2_DC33_A14


title: M_P7_hyperoxia_mesench_1_DC33_P22


title: M_P7_hyperoxia_mesench_2_DC33_F10


title: M_P7_hyperoxia_mesench_2_DC33_F21


title: M_P7_hyperoxia_mesench_1_DC33_C3


title: M_P7_hyperoxia_mesench_2_DC33_A18


title: M_P7_hyperoxia_mesench_2_DC33_H1


title: M_P7_hyperoxia_mesench_1_DC33_B13


title: M_P7_hyperoxia_mesench_2_DC33_M13


title: M_P7_hyperoxia_mesench_2_DC33_J8


title: M_P7_hyperoxia_mesench_1_DC33_L13


title: M_P7_hyperoxia_mesench_2_DC33_L20


title: M_P7_hyperoxia_mesench_2_DC33_F5


title: M_P7_hyperoxia_mesench_2_DC33_K10


title: M_P7_hyperoxia_mesench_1_DC33_B4


title: M_P7_hyperoxia_mesench_2_DC33_P4


title: M_P7_hyperoxia_mesench_2_DC33_I5


title: M_P7_hyperoxia_mesench_1_DC33_C2


title: M_P7_hyperoxia_mesench_2_DC33_C17


title: M_P7_hyperoxia_mesench_2_DC33_O14


title: M_P7_hyperoxia_mesench_2_DC33_P10


title: M_P7_hyperoxia_mesench_2_DC33_B2


title: M_P7_hyperoxia_mesench_2_DC33_D6


title: M_P7_hyperoxia_mesench_1_DC33_N3


title: M_P7_hyperoxia_mesench_1_DC33_A19


title: M_P7_hyperoxia_mesench_2_DC33_P21


title: M_P7_hyperoxia_mesench_2_DC33_A22


title: M_P7_hyperoxia_mesench_2_DC33_D2


title: M_P7_hyperoxia_mesench_2_DC33_K6


title: M_P7_hyperoxia_mesench_2_DC33_A19


title: M_P7_hyperoxia_mesench_2_DC33_G11


title: M_P7_hyperoxia_mesench_1_DC33_G13


title: M_P7_hyperoxia_mesench_2_DC33_L17


title: M_P7_hyperoxia_mesench_1_DC33_N22


title: M_P7_hyperoxia_mesench_2_DC33_F11


title: M_P7_hyperoxia_mesench_2_DC33_G15


title: M_P7_hyperoxia_mesench_1_DC33_K11


title: M_P7_hyperoxia_mesench_2_DC33_M20


title: M_P7_hyperoxia_mesench_2_DC33_H10


title: M_P7_hyperoxia_mesench_2_DC33_F13


title: M_P7_hyperoxia_mesench_2_DC33_M23


title: M_P7_hyperoxia_mesench_2_DC33_B15


title: M_P7_hyperoxia_mesench_1_DC33_N2


title: M_P7_hyperoxia_mesench_2_DC33_B9


title: M_P7_hyperoxia_mesench_1_DC33_H21


title: M_P7_hyperoxia_mesench_1_DC33_E9


title: M_P7_hyperoxia_mesench_2_DC33_E21


title: M_P7_hyperoxia_mesench_1_DC33_B10


title: M_P7_hyperoxia_mesench_2_DC33_A20


title: M_P7_hyperoxia_mesench_2_DC33_F23


title: M_P7_hyperoxia_mesench_2_DC33_N13


title: M_P7_hyperoxia_mesench_1_DC33_P16


title: M_P7_hyperoxia_mesench_2_DC33_D11


title: M_P7_hyperoxia_mesench_2_DC33_C18


title: M_P7_hyperoxia_mesench_2_DC33_P8


title: M_P7_hyperoxia_mesench_1_DC33_G9


title: M_P7_hyperoxia_mesench_2_DC33_B18


title: M_P7_hyperoxia_mesench_2_DC33_L5


title: M_P7_hyperoxia_mesench_1_DC33_I15


title: M_P7_hyperoxia_mesench_2_DC33_L15


title: M_P7_hyperoxia_mesench_1_DC33_F17


title: M_P7_hyperoxia_mesench_1_DC33_F3


title: M_P7_hyperoxia_mesench_2_DC33_O17


title: M_P7_hyperoxia_mesench_1_DC33_A6


title: M_P7_hyperoxia_mesench_1_DC33_O17


title: M_P7_hyperoxia_mesench_1_DC33_B12


title: M_P7_hyperoxia_mesench_1_DC33_G4


title: M_P7_hyperoxia_mesench_1_DC33_F2


title: M_P7_hyperoxia_mesench_2_DC33_L21


title: M_P7_hyperoxia_mesench_2_DC33_C8


title: M_P7_hyperoxia_mesench_1_DC33_I23


title: M_P7_hyperoxia_mesench_2_DC33_O11


title: M_P7_hyperoxia_mesench_1_DC33_N15


title: M_P7_hyperoxia_mesench_2_DC33_C1


title: M_P7_hyperoxia_mesench_2_DC33_C10


title: M_P7_hyperoxia_mesench_1_DC33_J12


title: M_P7_hyperoxia_mesench_1_DC33_L1


title: M_P7_hyperoxia_mesench_2_DC33_B12


title: M_P7_hyperoxia_mesench_2_DC33_K13


title: M_P7_hyperoxia_mesench_1_DC33_K20


title: M_P7_hyperoxia_mesench_2_DC33_J2


title: M_P7_hyperoxia_mesench_2_DC33_N18


title: M_P7_hyperoxia_mesench_1_DC33_G2


title: M_P7_hyperoxia_mesench_2_DC33_I2


title: M_P7_hyperoxia_mesench_1_DC33_G19


title: M_P7_hyperoxia_mesench_2_DC33_F4


title: M_P7_hyperoxia_mesench_1_DC33_J3


title: M_P7_hyperoxia_mesench_2_DC33_C9


title: M_P7_hyperoxia_mesench_1_DC33_H10


title: M_P7_hyperoxia_mesench_2_DC33_B16


title: M_P7_hyperoxia_mesench_1_DC33_N13


title: M_P7_hyperoxia_mesench_1_DC33_D21


title: M_P7_hyperoxia_mesench_1_DC33_F22


title: M_P7_hyperoxia_mesench_2_DC33_P16


title: M_P7_hyperoxia_mesench_1_DC33_F7


title: M_P7_hyperoxia_mesench_1_DC33_D2


title: M_P7_hyperoxia_mesench_2_DC33_K21


title: M_P7_hyperoxia_mesench_1_DC33_K17


title: M_P7_hyperoxia_mesench_1_DC33_J7


title: M_P7_hyperoxia_mesench_1_DC33_N7


title: M_P7_hyperoxia_mesench_2_DC33_G7


title: M_P7_hyperoxia_mesench_1_DC33_F18


title: M_P7_hyperoxia_mesench_1_DC33_J22


title: M_P7_hyperoxia_mesench_1_DC33_D19


title: M_P7_hyperoxia_mesench_1_DC33_M16


title: M_P7_hyperoxia_mesench_1_DC33_B21


title: M_P7_hyperoxia_mesench_2_DC33_K1


title: M_P7_hyperoxia_mesench_1_DC33_G10


title: M_P7_hyperoxia_mesench_1_DC33_M1


title: M_P7_hyperoxia_mesench_1_DC33_D7


title: M_P7_hyperoxia_mesench_1_DC33_A17


title: M_P7_hyperoxia_mesench_1_DC33_I21


title: M_P7_hyperoxia_mesench_2_DC33_G9


title: M_P7_hyperoxia_mesench_2_DC33_B5


title: M_P7_hyperoxia_mesench_2_DC33_D3


title: M_P7_hyperoxia_mesench_1_DC33_K22


title: M_P7_hyperoxia_mesench_2_DC33_E10


title: M_P7_hyperoxia_mesench_1_DC33_H16


title: M_P7_hyperoxia_mesench_2_DC33_A4


title: M_P7_hyperoxia_mesench_2_DC33_L8


title: M_P7_hyperoxia_mesench_1_DC33_L19


title: M_P7_hyperoxia_mesench_2_DC33_O15


title: M_P7_hyperoxia_mesench_2_DC33_K23


title: M_P7_hyperoxia_mesench_2_DC33_I16


title: M_P7_hyperoxia_mesench_1_DC33_D13


title: M_P7_hyperoxia_mesench_2_DC33_C5


title: M_P7_hyperoxia_mesench_2_DC33_L16


title: M_P7_hyperoxia_mesench_2_DC33_A8


title: M_P7_hyperoxia_mesench_2_DC33_E5


title: M_P7_hyperoxia_mesench_1_DC33_H11


title: M_P7_hyperoxia_mesench_1_DC33_P14


title: M_P7_hyperoxia_mesench_2_DC33_N11


title: M_P7_hyperoxia_mesench_1_DC33_K6


title: M_P7_hyperoxia_mesench_1_DC33_D8


title: M_P7_hyperoxia_mesench_2_DC33_I1


title: M_P7_hyperoxia_mesench_1_DC33_B1


title: M_P7_hyperoxia_mesench_1_DC33_H2


title: M_P7_hyperoxia_mesench_2_DC33_L2


title: M_P7_hyperoxia_mesench_1_DC33_M19


title: M_P7_hyperoxia_mesench_1_DC33_A18


title: M_P7_hyperoxia_mesench_1_DC33_L12


title: M_P7_hyperoxia_mesench_2_DC33_O2


title: M_P7_hyperoxia_mesench_2_DC33_J22


title: M_P7_hyperoxia_mesench_1_DC33_K5


title: M_P7_hyperoxia_mesench_2_DC33_P2


title: M_P7_hyperoxia_mesench_1_DC33_I3


title: M_P7_hyperoxia_mesench_1_DC33_D5


title: M_P7_hyperoxia_mesench_2_DC33_H13


title: M_P7_hyperoxia_mesench_1_DC33_C8


title: M_P7_hyperoxia_mesench_2_DC33_O6


title: M_P7_hyperoxia_mesench_1_DC33_L18


title: M_P7_hyperoxia_mesench_2_DC33_O1


title: M_P7_hyperoxia_mesench_1_DC33_E4


title: M_P7_hyperoxia_mesench_2_DC33_C7


title: M_P7_hyperoxia_mesench_2_DC33_D17


title: M_P7_hyperoxia_mesench_1_DC33_H4


title: M_P7_hyperoxia_mesench_1_DC33_L17


title: M_P7_hyperoxia_mesench_2_DC33_G3


title: M_P7_hyperoxia_mesench_1_DC33_E3


title: M_P7_hyperoxia_mesench_1_DC33_P18


title: M_P7_hyperoxia_mesench_1_DC33_O8


title: M_P7_hyperoxia_mesench_1_DC33_A8


title: M_P7_hyperoxia_mesench_2_DC33_C12


title: M_P7_hyperoxia_mesench_1_DC33_H23


title: M_P7_hyperoxia_mesench_2_DC33_C19


title: M_P7_hyperoxia_mesench_1_DC33_J18


title: M_P7_hyperoxia_mesench_2_DC33_G8


title: M_P7_hyperoxia_mesench_1_DC33_K4


title: M_P7_hyperoxia_mesench_1_DC33_H7


title: M_P7_hyperoxia_mesench_2_DC33_H9


title: M_P7_hyperoxia_mesench_2_DC33_M3


title: M_P7_hyperoxia_mesench_2_DC33_K14


title: M_P7_hyperoxia_mesench_2_DC33_M9


title: M_P7_hyperoxia_mesench_1_DC33_O22


title: M_P7_hyperoxia_mesench_1_DC33_E5


title: M_P7_hyperoxia_mesench_2_DC33_F12


title: M_P7_hyperoxia_mesench_2_DC33_A6


title: M_P7_hyperoxia_mesench_2_DC33_J20


title: M_P7_hyperoxia_mesench_2_DC33_I12


title: M_P7_hyperoxia_mesench_1_DC33_M18


title: M_P7_hyperoxia_mesench_1_DC33_K14


title: M_P7_hyperoxia_mesench_2_DC33_O13


title: M_P7_hyperoxia_mesench_2_DC33_A12


title: M_P7_hyperoxia_mesench_2_DC33_H20


title: M_P7_hyperoxia_mesench_2_DC33_E12


title: M_P7_hyperoxia_mesench_2_DC33_H15


title: M_P7_hyperoxia_mesench_1_DC33_O9


title: M_P7_hyperoxia_mesench_2_DC33_F15


title: M_P7_hyperoxia_mesench_2_DC33_P14


title: M_P7_hyperoxia_mesench_2_DC33_L22


title: M_P7_hyperoxia_mesench_1_DC33_O11


title: M_P7_hyperoxia_mesench_1_DC33_D15


title: M_P7_hyperoxia_mesench_1_DC33_I8


title: M_P7_hyperoxia_mesench_2_DC33_M15


title: M_P7_hyperoxia_mesench_1_DC33_I4


title: M_P7_hyperoxia_mesench_2_DC33_A23


title: M_P7_hyperoxia_mesench_2_DC33_F22


title: M_P7_hyperoxia_mesench_1_DC33_B6


title: M_P7_hyperoxia_mesench_1_DC33_A4


title: M_P7_hyperoxia_mesench_2_DC33_P11


title: M_P7_hyperoxia_mesench_1_DC33_O4


title: M_P7_hyperoxia_mesench_1_DC33_I22


title: M_P7_hyperoxia_mesench_1_DC33_L16


title: M_P7_hyperoxia_mesench_2_DC33_I7


title: M_P7_hyperoxia_mesench_2_DC33_J14


title: M_P7_hyperoxia_mesench_1_DC33_G18


title: M_P7_hyperoxia_mesench_2_DC33_B17


title: M_P7_hyperoxia_mesench_2_DC33_N14


title: M_P7_hyperoxia_mesench_1_DC33_E20


title: M_P7_hyperoxia_mesench_2_DC33_C14


title: M_P7_hyperoxia_mesench_1_DC33_K12


title: M_P7_hyperoxia_mesench_1_DC33_M10


title: M_P7_hyperoxia_mesench_2_DC33_D21


title: M_P7_hyperoxia_mesench_1_DC33_C9


title: M_P7_hyperoxia_mesench_2_DC33_D5


title: M_P7_hyperoxia_mesench_2_DC33_P17


title: M_P7_hyperoxia_mesench_2_DC33_K4


title: M_P7_hyperoxia_mesench_1_DC33_C19


title: F_P7_hyperoxia_CD31_1_DC36_O22

value: F


title: M_P7_hyperoxia_mesench_1_DC33_B14


title: F_P7_hyperoxia_CD31_1_DC36_B10


title: F_P7_hyperoxia_CD31_1_DC36_B11


title: M_P7_hyperoxia_mesench_2_DC33_H17


title: F_P7_hyperoxia_CD31_1_DC36_L16


title: F_P7_hyperoxia_CD31_1_DC36_K2


title: F_P7_hyperoxia_CD31_1_DC36_B8


title: F_P7_hyperoxia_CD31_1_DC36_M17


title: F_P7_hyperoxia_mesench_1_DC34_C9


title: F_P7_hyperoxia_CD31_1_DC36_N3


title: F_P7_hyperoxia_CD31_1_DC36_M16


title: F_P7_hyperoxia_mesench_2_DC34_D12


title: F_P7_hyperoxia_mesench_1_DC34_B18


title: F_P7_hyperoxia_mesench_1_DC34_H20


title: F_P7_hyperoxia_CD31_1_DC36_K4


title: F_P7_hyperoxia_mesench_2_DC34_F15


title: F_P7_hyperoxia_CD31_1_DC36_E10


title: F_P7_hyperoxia_mesench_1_DC34_P23


title: F_P7_hyperoxia_mesench_2_DC34_G2


title: F_P7_hyperoxia_mesench_1_DC34_M14


title: F_P7_hyperoxia_mesench_2_DC34_I20


title: F_P7_hyperoxia_mesench_2_DC34_D10


title: F_P7_hyperoxia_mesench_2_DC34_L4


title: F_P7_hyperoxia_mesench_1_DC34_L2


title: M_P7_hyperoxia_mesench_2_DC33_N21


title: F_P7_hyperoxia_mesench_1_DC34_N20


title: F_P7_hyperoxia_mesench_2_DC34_M18


title: F_P7_hyperoxia_mesench_1_DC34_D6


title: F_P7_hyperoxia_mesench_1_DC34_B2


title: F_P7_hyperoxia_mesench_1_DC34_F21


title: F_P7_hyperoxia_mesench_2_DC34_A4


title: F_P7_hyperoxia_mesench_2_DC34_G10


title: F_P7_hyperoxia_mesench_1_DC34_I4


title: F_P7_hyperoxia_mesench_2_DC34_O10


title: F_P7_hyperoxia_mesench_2_DC34_L12


title: F_P7_hyperoxia_mesench_2_DC34_G14


title: F_P7_hyperoxia_mesench_1_DC34_J6


title: F_P7_hyperoxia_mesench_2_DC34_I11


title: F_P7_hyperoxia_mesench_2_DC34_G23


title: F_P7_hyperoxia_mesench_2_DC34_L3


title: F_P7_hyperoxia_mesench_1_DC34_F4


title: F_P7_hyperoxia_mesench_1_DC34_P4


title: F_P7_hyperoxia_mesench_1_DC34_J2


title: F_P7_hyperoxia_mesench_1_DC34_O20


title: F_P7_hyperoxia_mesench_1_DC34_G20


title: F_P7_hyperoxia_mesench_2_DC34_K23


title: F_P7_hyperoxia_mesench_2_DC34_D23


title: F_P7_hyperoxia_mesench_1_DC34_D14


title: F_P7_hyperoxia_mesench_1_DC34_P11


title: F_P7_hyperoxia_mesench_2_DC34_A7


title: F_P7_hyperoxia_mesench_2_DC34_D2


title: F_P7_hyperoxia_mesench_2_DC34_A8


title: F_P7_hyperoxia_mesench_2_DC34_K20


title: F_P7_hyperoxia_mesench_2_DC34_B20


title: F_P7_hyperoxia_mesench_1_DC34_A14


title: F_P7_hyperoxia_mesench_1_DC34_G3


title: F_P7_hyperoxia_mesench_2_DC34_C10


title: F_P7_hyperoxia_mesench_1_DC34_G5


title: F_P7_hyperoxia_mesench_2_DC34_N5


title: F_P7_hyperoxia_mesench_1_DC34_H13


title: F_P7_hyperoxia_mesench_2_DC34_N16


title: F_P7_hyperoxia_mesench_1_DC34_N6


title: F_P7_hyperoxia_mesench_1_DC34_E21


title: F_P7_hyperoxia_mesench_1_DC34_C18


title: F_P7_hyperoxia_mesench_1_DC34_C20


title: F_P7_hyperoxia_mesench_1_DC34_L15


title: F_P7_hyperoxia_mesench_1_DC34_L20


title: F_P7_hyperoxia_mesench_1_DC34_I1


title: F_P7_hyperoxia_mesench_2_DC34_N9


title: F_P7_hyperoxia_mesench_2_DC34_N12