title: YO0894.M0.PAX

tag: vl copies

tag: hospitalized


title: LAS256A1721

status: Public on Jul 23 2023

type: SRA

city: London

first: Vassilis

last: Pachnis

address: 1 Midland Rd

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

library_source: transcriptomic

data_processing:
Reads were aligned to the Ensembl GRCm38 genome using Tophat2.
Transcript counts, including counts for spliced and unspliced reads were obtained using the program Velocyto.
Quality control, normalisation and downstream analysis were performed using the software SCANPY.
Cells expressing more than 2000 genes and less than 10 percent mitochondrial genes were retained for further analysis. Contaminating epithelial cells (n = 9) were filtered from the data based on Cdh1 counts (>= 10 counts). Likewise, mesenchymal cells (n = 39) were filtered based on the expression of the marker Meis2 (>= 10 counts) and macrophages (n = 6) were filtered using expression of the marker Cd14 (>= 10 counts). After filtering 904 cells were retained, 143 cells (E13.5), 20 cells (E12.5 → E15.5), 129 cells (E17.5), 432 cells (P1), 11 cells (P26) and 169 cells (P61).
Genes detected in fewer than 3 cells or with total counts < 10 were omitted from further analysis (23299 genes were retained). Counts were normalised to counts per million (CPM) and log transformed (after the addition of a pseudocount of 1).
Counts were normalized to 1 million counts per cell, natural-log transformed using log1p, and scaled.
2954 genes identified as taking part in gene modules identified using the Antler algorithm were used as input for PCA analysis in SCANPY. The first 15 PCs were selected for dimensionality reduction and clustering using the Louvain algorithm (resolution 1.5). The resulting clustering was manually curated and those clusters with similar transcriptional profiles that separated purely based on the expression of cell-cycle associated markers were merged.
Assembly: GrCM38
Supplementary files format and content: Scanpy object containing normalised data and UMAP. Matrices containing spliced and unspliced counts (CSV format). Gene and cell metadata (CSV format).

molecule: total RNA

organism: Mus musculus

source_name: Enteric nervous system

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
Tissue was incubated with Collagenase I (1 mg/ml, Sigma, C0130) for 30-45 min and enzyme activity was terminated by rinsing cells with ice cold PBS. The cell suspension was centrifuged and filtered through 40 μm nylon cell strainers (Falcon, 352340). tdT+ cells were isolated by flow cytometry (BD Biosciences Aria Fusion sorter equipped with Diva V8 software) with a 100 μm nozzle and collected in 2% FBS in OptiMEM without phenol red (Thermo Fisher Scientific, 11058021). Dead cells were excluded by labelling with the cell viability dye Zombie Aqua (2 ng/ml, BioLegend, 423101) that was added to the single cell suspension before sorting. For the P0 stage, we also sorted the cells directly into 96-well plates to increase the yield.
The SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System, IFCs was used to reverse transcribe and amplify cDNA. cDNA was quantified using the Glomax (Promega). Libraries were prepared from cDNA generated from single cells using the Nextera XT kit from Illumina. Final libraries were pooled and sequenced on the HiSeq 4000.

treatment_protocol: All mice were injected with tamoxifen 24 hours prior to single cell isolation apart from E12.5_E15.5 time points (these were injected with tamoxifen 72 hours prior to single cell isolation).

tag: sample type

tag: Stage

tag: strain


title: VA0735.M0.PAX

city: Durham

first: Matthew

middle: Scott

last: Kelly

state: NC

address: 3 Genome Court, MSRB3, Room 4200

department: Pediatrics

country: USA

institute: Duke University

data_processing:
Raw sequencing reads were checked for quality using FastQC v0.11.9 and trimmed using Trimmomatic v0.39 with the following parameters in the command line: PE; threads 16; phred33; path/sampleid_R1.fastq.gz path/sampleid_R2.fastq.gz; ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True; LEADING:3; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:36
Genome index files were generated using STAR v2.7.1b with parameters in the command line: runMode: genomeGenerate; runThreadN: 16; genomeDir: path/index; genomeFastaFiles: path/GRCh38.primary_assembly.genome.fa; sjdbGTFfile: path/gencode.v43.basic.annotation.gtf; sjdbOverhang 100
Reads were mapped to the genome using STAR v2.7.1b with parameters in the command line: quantMode: GeneCounts; genomeDir: path/index; runThreadN: 16; readFilesIn: path/sampleid_R1.fastq.gz path/sampleid_R2.fastq.gz; outFileNamePrefix: path/sampleid; readFilesCommand: gunzip -c; outSAMtype BAM SortedByCoordinate; outSAMunmapped Within; outSAMattributes Standard
Assembly: Homo_sapiens.GRCh38 (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GRCh38.primary_assembly.genome.fa.gz and https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.basic.annotation.gtf.gz)
Supplementary files format and content: csv file containing raw read counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Total RNA was extracted from nasal and nasopharyngeal swabs using QIAsymphony RNA kits and from peripheral blood preserved in PAXgene Blood RNA tubes using QIAGEN PAXgene miRNA Extraction Kits according to manufacturer's instructions.
Libraries were prepared using TECAN Universal Plus mRNA-seq with AnyDeplete Globin Kits according to manufacturer's instructions.
Libraries were sequenced on an Illumina NovaSeq 6000 instrument as 100 bp PE reads.

tag: tissue

value: Whole blood

tag: subject id

tag: batch

tag: sample timing

value: acute

tag: age

tag: Sex

value: Female

tag: covid

value: Positive

tag: covid cat

tag: research pcr

value: Not Tested

value: No

tag: year

tag: vaccine doses

tag: timing sx

tag: timing dx


title: LAS256A1707


title: LAS256A1679


title: YP4954.M0.PAX

value: Male

tag: vl copies

tag: hospitalized


title: UY0636.M0.PAX


title: WQ9247.M0.PAX


title: UP6626.M0.PAX


title: XI2762.M0.PAX


title: LAS256A1648

tag: sample type

tag: Stage


title: UI9611.M0.PAX

tag: tissue


title: LAS256A1594

tag: strain


title: LAS256A1630


title: UE4555.M0.PAX

tag: subject id

tag: batch

value: Negative


title: LAS250A97

value: P1, plate SCS_A00201


title: LAS250A99


title: UH8093.M0.PAX

tag: sample timing

tag: age

value: Yes


title: LAS256A1590


title: LAS250A967

value: P1, plate ASF_A00539


title: TX5656.M0.PAX

tag: Sex

tag: covid


title: LAS256A1688


title: UD7001.M1.PAX

tag: covid cat

tag: research pcr


title: TW5706.M0.PAX

tag: year

tag: vaccine doses


title: TV4923.M0.PAX

tag: timing sx

tag: timing dx


title: LAS250A966


title: LAS250A968


title: LAS250A963


title: LAS250A964


title: LAS250A965


title: TN6246.M0.PAX

tag: vl copies

tag: hospitalized


title: TU3350.M0.PAX


title: TL9437.M0.PAX


title: UH8093.M1.PAX


title: LAS250A961

tag: sample type

tag: Stage


title: LAS250A962

tag: strain


title: TH1406.M1.PAX

tag: tissue

tag: subject id


title: LAS250A960


title: LAS250A959


title: TH1406.M0.PAX

tag: batch

tag: sample timing


title: LAS250A958


title: UD7001.M0.PAX

tag: age

tag: Sex


title: TG2740.M0.PAX

tag: covid

tag: covid cat


title: TH8758.M0.PAX

tag: research pcr

tag: year


title: TC6050.M0.PAX

tag: vaccine doses

tag: timing sx


title: LAS250A955


title: TE7914.M0.PAX

tag: vl copies

tag: timing dx


title: LAS250A957

tag: sample type


title: LAS250A954

tag: Stage


title: LAS250A953

tag: strain


title: SO3251.M0.PAX

tag: tissue

tag: hospitalized


title: LAS250A951


title: SE3356.M1.PAX

tag: subject id

tag: batch


title: LAS250A950


title: SG4756.M1.PAX

tag: sample timing

tag: age


title: LAS250A948


title: LAS250A947


title: SD2421.M0.PAX

tag: Sex

tag: covid


title: SD0040.M0.PAX

tag: covid cat

tag: research pcr


title: LAS250A946


title: SC1834.M0.PAX

tag: year

tag: vaccine doses


title: LAS250A944


title: SA3829.M0.PAX

tag: vl copies

tag: timing sx


title: RX6352.M0.PAX

tag: timing dx


title: LAS250A943

tag: sample type

tag: Stage


title: LAS250A942

tag: strain


title: SY3034.M0.PAX

tag: tissue

tag: hospitalized


title: RX3601.M0.PAX

tag: subject id

tag: batch


title: SG4756.M0.PAX

tag: sample timing

tag: age


title: LAS250A949


title: RU6817.M0.PAX

tag: Sex

tag: covid


title: LAS250A940


title: SE3356.M0.PAX

tag: covid cat

tag: research pcr


title: LAS250A938


title: RX1597.M0.PAX

tag: year

tag: vaccine doses


title: LAS250A945


title: RF0171.M0.PAX

tag: vl copies

tag: timing sx


title: RI8890.M0.PAX

tag: timing dx


title: LAS250A937

tag: sample type

tag: Stage


title: RI3275.M0.PAX

tag: tissue


title: LAS250A934

tag: strain


title: LAS250A936


title: LAS250A935


title: QS9335.M0.PAX

tag: subject id

tag: hospitalized


title: QW4655.M0.PAX

tag: batch

tag: sample timing


title: LAS250A933


title: QK2775.M0.PAX

tag: age

tag: Sex


title: QR5656.M0.PAX

tag: covid

tag: covid cat


title: LAS250A941


title: QQ4295.M0.PAX

tag: research pcr

tag: year


title: RK7680.M0.PAX

tag: vl copies

tag: vaccine doses


title: LAS250A931


title: LAS250A928


title: LAS250A939


title: QH3620.M0.PAX

tag: timing sx

tag: timing dx


title: LAS250A932

tag: sample type

tag: Stage


title: LAS250A925

tag: strain


title: LAS250A930


title: PZ1823.M0.PAX

tag: tissue

tag: subject id


title: LAS250A926


title: PJ5876.M0.PAX

tag: batch

tag: hospitalized


title: QD5866.M0.PAX

tag: sample timing

tag: age


title: PJ4720.M0.PAX

tag: Sex

tag: covid


title: LAS250A924


title: LAS250A922


title: PB7187.M0.PAX

tag: covid cat

tag: research pcr


title: LAS250A920


title: PT4963.M0.PAX

tag: vl copies

tag: year


title: LAS250A921


title: OY8888.M0.PAX

tag: vaccine doses

tag: timing sx


title: OT9187.M0.PAX

tag: timing dx


title: OQ9062.M0.PAX


title: LAS250A919

tag: sample type

tag: Stage


title: LAS250A929

tag: strain


title: OM8987.M0.PAX

tag: tissue

tag: subject id


title: LAS250A916


title: PN6346.M0.PAX

tag: batch

tag: hospitalized


title: LAS250A918


title: LAS250A914


title: LAS250A915


title: OH5644.M0.PAX

tag: sample timing

tag: age


title: OK7852.M0.PAX

tag: Sex

tag: covid


title: LAS250A913


title: LAS250A912


title: OF4658.M0.PAX

tag: covid cat

tag: research pcr


title: OE2132.M0.PAX

tag: vl copies

tag: year


title: OF7032.M0.PAX

tag: vaccine doses

tag: timing sx


title: LAS250A911

tag: sample type


title: OB1593.M0.PAX

tag: timing dx


title: NZ1261.M0.PAX


title: LAS250A908

tag: Stage

tag: strain


title: LAS250A907


title: LAS250A906


title: NO7567.M0.PAX

tag: tissue

tag: subject id


title: NM9596.M1.PAX

tag: batch

tag: hospitalized


title: LAS250A904


title: LAS250A903


title: NM9596.M0.PAX

tag: sample timing

tag: age


title: LAS250A901


title: LAS250A923


title: LAS250A902


title: NK1464.M0.PAX

tag: Sex

tag: covid


title: MW3235.M0.PAX

tag: covid cat

tag: research pcr


title: LAS250A910


title: MT0776.M0.PAX

tag: vl copies

tag: year


title: LAS250A899


title: LAS250A896


title: MS0072.M0.PAX

tag: vaccine doses

tag: timing sx


title: LAS250A909

tag: sample type


title: LAS256A1669

tag: Stage


title: LAS250A898

tag: strain


title: NY5696.M0.PAX

tag: tissue

tag: timing dx


title: NT0329.M0.PAX

tag: subject id

tag: batch


title: LAS250A895


title: LAS250A894


title: LAS250A893


title: MJ2952.M0.PAX

tag: sample timing

tag: hospitalized


title: MZ2666.M0.PAX

tag: age

tag: Sex


title: LAS250A892


title: MI4012.M0.PAX

tag: covid

tag: covid cat


title: LAS250A891


title: MH6120.M1.PAX

tag: research pcr

tag: vl copies


title: LAS250A900


title: MC2708.M0.PAX

tag: year

tag: vaccine doses


title: LAS250A890

tag: sample type


title: LAS250A889

tag: Stage


title: MH6120.M0.PAX

tag: timing sx


title: LAS250A887

tag: strain


title: ML5199.M0.PAX

tag: tissue

tag: timing dx


title: MB0117.M0.PAX

tag: subject id

tag: batch


title: LZ7554.M0.PAX

tag: sample timing

tag: hospitalized


title: LAS250A886


title: LX3468.M0.PAX

tag: age

tag: Sex


title: LAS250A885


title: LO7091.M0.PAX

tag: covid

tag: covid cat


title: LAS250A884


title: LAS250A888


title: LAS250A883


title: LH4091.M0.PAX

tag: research pcr

tag: vl copies


title: LL792.M0.PAX

tag: year

tag: vaccine doses


title: MK4460.M0.PAX


title: MI9133.M0.PAX


title: LAS250A882

tag: sample type

tag: Stage


title: LG1702.M0.PAX

tag: timing sx


title: LAS250A881

tag: strain


title: LG0250.M0.PAX

tag: tissue

tag: timing dx


title: LAS250A879


title: LAS250A880


title: LE3362.M1.PAX

tag: subject id

tag: batch


title: LF3604.M0.PAX

tag: sample timing

tag: hospitalized


title: LAS250A878


title: LB8121.M0.PAX

tag: age

tag: Sex


title: LE3362.M0.PAX

tag: covid

tag: covid cat


title: LAS250A875


title: LAS250A876


title: KZ6310.M0.PAX

tag: research pcr

tag: vl copies


title: ON7836.M0.PAX

tag: year

tag: vaccine doses


title: LAS250A877

tag: sample type

tag: Stage


title: LAS250A873

tag: strain


title: LAS250A872

value: P1, plate ASF_A00538


title: KW4113.M0.PAX

tag: tissue

tag: timing sx


title: LAS250A874


title: LAS250A871


title: LAS250A870


title: KV1465.M0.PAX

tag: subject id

tag: timing dx


title: LAS250A869


title: KR3482.M0.PAX

tag: batch

tag: sample timing


title: LAS250A868


title: LAS250A867


title: Combined acidity+water deficit+low phosphate+salinity+cadmium flowers replicate 1

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Christopher S. Bond Life Sciences Center

institute: The Division of Plant Sciences and Technology

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to G_max V2.1 whole genome using Hisat2 V2.2.1
Assembly: Glycine_max_v2.1.51
Supplementary files format and content: Matrix table FPKM values for all samples

organism: Glycine max

source_name: flowers

growth_protocol: Soybean (Glycine max, cv Magellan) seeds were coated with Bradyrhizobium japonicum inoculum and germinated in pots containing 1.5 kg mixture of Promix BX and perlite mixed in ratio of 10:1 and soaked with 3 L of nutrient solution containing the different stress/stresses conditions. Plants were grown under short-day conditions (1000 µmol photons m-2 s-1, 14-h light/10-h dark) at 28/24 °C day/night temperature. Once a week the control or low phosphate nutrient solution alone or in combination with other stresses was applied as fertilizer according to each treatment.

extract_protocol:
For each biological repeat, leaves or flowers were pooled together from 5-7 different plants and flash frozen in liquid nitrogen. RNA from samples was isolated using RNeasy plant mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: All the stresses except for water deficit were applied in the nutrient solution from the beginning of the experiment. The plants under water deficit regime were irrigated with only 30% of the water available for transpiration, while for the rest of the tretaments plants  were irrigated with 100% of the water available for transpiration. Salinity treatment (15 mM) alone or in combination with other stresses was added just once at the beginning of the experiment. Cadmium (300 µM) as single stress or in the five stresses condition was included in the nutrient solution every two weeks.

value: flowers

tag: genotype

value: Magellan

tag: treatment


title: Combined acidity+water deficit+low phosphate+salinity+cadmium flowers replicate 3


title: Combined acidity+water deficit+low phosphate+salinity flowers replicate 2


title: LAS250A866


title: KQ7168.M0.PAX

tag: age

tag: Sex

tag: covid

tag: hospitalized


title: LAS250A865


title: Combined acidity+water deficit+low phosphate+salinity flowers replicate 1


title: KN1525.M0.PAX

tag: covid cat

tag: research pcr

tag: vl copies

tag: year


title: LAS250A864

tag: sample type

tag: Stage

tag: strain


title: Combined acidity+water deficit+low phosphate+salinity+cadmium flowers replicate 2

tag: tissue


title: LAS250A863


title: Combined acidity+water deficit+low phosphate+salinity flowers replicate 3


title: UO2994.M0.PAX

tag: subject id

tag: vaccine doses

tag: timing sx

tag: timing dx


title: Combined acidity+water deficit+low phosphate flowers replicate 3

tag: genotype

tag: treatment

value: Acidity+water deficit+low phosphate


title: LAS250A862


title: KA9831.M0.PAX

tag: batch

tag: sample timing

tag: age

tag: Sex


title: Combined acidity+water deficit+low phosphate flowers replicate 2


title: KI0978.M0.PAX

tag: covid

tag: covid cat

tag: research pcr

tag: hospitalized


title: Combined acidity+water deficit+low phosphate flowers replicate 1


title: LAS250A859

tag: sample type

tag: Stage


title: LAS250A861

tag: strain


title: JV7184.M0.PAX

tag: tissue

tag: subject id

tag: vl copies

tag: year


title: LAS250A860


title: Combined salinity+water deficit+low phosphate flowers replicate 3

tag: genotype

value: Salinity+water deficit+low phosphate


title: JI3265.M0.PAX

tag: vaccine doses

tag: timing sx

tag: timing dx


title: LAS250A857


title: LAS250A858


title: LAS250A856


title: Combined salinity+water deficit+low phosphate flowers replicate 2

tag: treatment


title: IT4990.M1.PAX

tag: batch

tag: sample timing

tag: age

tag: Sex


title: IT4990.M0.PAX

tag: covid

tag: covid cat

tag: research pcr

tag: hospitalized


title: LAS250A853

tag: sample type

tag: Stage

tag: strain


title: LAS250A855


title: LAS250A852


title: Combined salinity+acidity+low phosphate flowers replicate 3

tag: tissue

value: Salinity+acidity+low phosphate


title: LAS250A849


title: IT0931.M0.PAX

value: Whole blood

tag: subject id

tag: vl copies

tag: year


title: IR5536.M0.PAX

value: acute

tag: vaccine doses

tag: timing sx

tag: timing dx


title: Combined salinity+acidity+low phosphate flowers replicate 2

tag: genotype

tag: treatment


title: LAS250A847


title: LAS250A846


title: LAS250A848


title: Combined salinity+acidity+low phosphate flowers replicate 1


title: IO2962.M0.PAX

tag: batch

tag: sample timing

tag: age

tag: Sex

value: Female


title: LAS250A845


title: IM4862.M1.PAX

tag: covid

value: Positive

tag: covid cat

tag: research pcr

tag: hospitalized


title: Combined salinity+acidity+water deficit flowers replicate 3

tag: tissue

value: Salinity+acidity+water deficit


title: LAS250A844

tag: sample type

tag: Stage

tag: strain


title: LAS250A841


title: Combined salinity+acidity+water deficit flowers replicate 2


title: Combined salinity+acidity+water deficit flowers replicate 1


title: IM4862.M0.PAX

tag: subject id

tag: vl copies

value: No

tag: year

tag: vaccine doses


title: LAS250A839


title: LAS250A840


title: Combined salinity+water deficit+low phosphate flowers replicate 1

tag: genotype

tag: treatment


title: LAS250A854


title: IJ0554.M0.PAX

tag: batch

tag: sample timing

tag: timing sx

tag: timing dx


title: LAS250A838


title: LAS250A851


title: II7900.M0.PAX

tag: age

tag: Sex

value: Male

tag: covid

tag: covid cat

value: Not Tested


title: LAS250A836

tag: sample type


title: Combined low phosphate+water deficit flowers replicate 3

tag: tissue

value: Low phosphate+water deficit


title: Combined low phosphate+water deficit flowers replicate 2


title: IG7453.M0.PAX

value: Negative

tag: research pcr

tag: hospitalized


title: LAS250A835

tag: Stage

tag: strain


title: LAS250A842


title: Combined low phosphate+water deficit flowers replicate 1


title: LAS250A834


title: LAS250A833


title: HU8221.M1.PAX

tag: subject id

tag: vl copies

tag: year

tag: vaccine doses


title: HU8221.M0.PAX

tag: batch

tag: sample timing


title: LAS250A831


title: LAS250A832


title: LAS250A829


title: LAS250A830


title: Combined acidity+low phosphate flowers replicate 2

tag: genotype

tag: treatment

value: Acidity+low phosphate


title: Combined acidity+low phosphate flowers replicate 1


title: Combined acidity+low phosphate flowers replicate 3


title: LAS250A826

value: P1, plate ASF_A00538


title: LAS250A827


title: HP1718.M0.PAX

tag: age

tag: Sex

tag: timing sx

tag: timing dx


title: LAS250A825

tag: sample type


title: LAS250A824


title: LAS250A837


title: Combined acidity+water deficit flowers replicate 3

tag: tissue

value: flowers

value: Acidity+water deficit


title: HF2521.M0.PAX

tag: covid

tag: covid cat

tag: research pcr

tag: hospitalized


title: HE8769.M0.PAX

tag: subject id

tag: vl copies


title: LAS250A821

tag: Stage

tag: strain


title: LAS250A823


title: Combined acidity+water deficit flowers replicate 2

value: Magellan


title: Combined acidity+water deficit flowers replicate 1


title: LAS250A820


title: LAS250A818


title: GW5371.M0.PAX

tag: batch

tag: sample timing

tag: year

tag: vaccine doses


title: GT7397.M0.PAX

tag: age

tag: Sex


title: LAS250A817


title: Combined salinity+low phosphate flowers replicate 3

tag: genotype

tag: treatment

value: Salinity+low phosphate


title: Combined salinity+low phosphate flowers replicate 2

tag: tissue


title: HR2557.M0.PAX

tag: covid

tag: timing sx

tag: timing dx


title: GS1960.M0.PAX

tag: covid cat

tag: research pcr

tag: hospitalized


title: LAS250A813

tag: sample type

tag: Stage


title: LAS250A814

tag: strain


title: Combined salinity+low phosphate flowers replicate 1


title: LAS250A811


title: Combined salinity+water deficit flowers replicate 3

value: Salinity+water deficit


title: LAS250A812


title: LAS250A810


title: GN5032.M0.PAX

value: Whole blood

tag: subject id

tag: batch

tag: sample timing

tag: vl copies


title: GP9256.M0.PAX

value: acute

tag: age

tag: Sex

tag: year

tag: vaccine doses


title: LAS250A809


title: LAS250A822


title: Combined salinity+water deficit flowers replicate 2

tag: tissue

tag: genotype

tag: treatment


title: FZ5226.M0.PAX

tag: covid

tag: covid cat

tag: timing sx

tag: timing dx


title: LAS250A808

tag: sample type

tag: Stage


title: Combined salinity+water deficit flowers replicate 1


title: FX9488.M0.PAX

tag: subject id

value: Female

tag: research pcr

tag: hospitalized


title: Combined salinity+acidity flowers replicate 3

value: Salinity+acidity


title: LAS250A805

tag: strain


title: LAS250A806


title: LAS250A803


title: LAS250A816


title: LAS250A801


title: FX0877.M0.PAX

tag: batch

tag: sample timing

tag: age

tag: vl copies


title: FW9252.M0.PAX

tag: tissue

tag: Sex

value: Positive

tag: year

tag: vaccine doses


title: Combined salinity+acidity flowers replicate 1

tag: genotype

tag: treatment


title: LAS250A800


title: LAS250A798


title: LAS250A799


title: LAS250A797


title: Combined salinity+acidity flowers replicate 2


title: FF1165.M0.PAX

tag: covid

tag: covid cat

value: No

tag: timing sx

tag: timing dx


title: Cadmium flowers replicate 2

value: Cadmium (300 uM CdCl2)


title: LAS250A794

tag: sample type

tag: Stage


title: FC0633.M0.PAX

tag: subject id

tag: research pcr

tag: hospitalized


title: LAS250A795

tag: strain


title: LAS250A807


title: Cadmium flowers replicate 3


title: LAS250A793


title: FR8148.M0.PAX

tag: batch

tag: sample timing

tag: age

value: Not Tested

tag: vl copies


title: FB7566.M0.PAX

tag: tissue

tag: Sex

value: Male

tag: year

tag: vaccine doses


title: LAS250A792


title: Water deficit flowers replicate 3

tag: genotype

tag: treatment

value: Water deficit (30% of the water available for transpiration)


title: Water deficit flowers replicate 2


title: LAS250A789


title: EY5612.M1.PAX

tag: covid

tag: covid cat

tag: timing sx

tag: timing dx


title: LAS250A790

tag: sample type

tag: Stage


title: LAS250A791

tag: strain


title: LAS250A788


title: EY5612.M0.PAX

tag: subject id

tag: batch

tag: research pcr

tag: hospitalized


title: Water deficit flowers replicate 1

tag: tissue


title: EW5232.M0.PAX

tag: sample timing

tag: age

tag: Sex

value: Negative

tag: vl copies


title: LAS250A786

value: P1, plate ASF_A00538


title: Acidity flowers replicate 3

value: flowers

tag: genotype

tag: treatment

value: Acidity (pH 4)


title: LAS250A796


title: LAS250A785


title: LAS250A784


title: ET5122.M0.PAX

tag: covid

tag: covid cat

tag: year

tag: vaccine doses


title: LAS250A783

tag: sample type

tag: Stage


title: EL1974.M0.PAX

tag: subject id

tag: timing sx

tag: timing dx


title: Acidity flowers replicate 2

value: Magellan


title: Acidity flowers replicate 1


title: LAS250A781

tag: strain


title: LAS250A780


title: EF9688.M0.PAX

tag: tissue

tag: batch

tag: research pcr

tag: hospitalized


title: LAS250A779


title: Low phosphate flowers replicate 3

value: Low phosphate (phosphate concentration was reduced by 90%)


title: EE8681.M0.PAX

tag: sample timing

tag: age

tag: Sex

tag: vl copies


title: LAS250A778


title: LAS250A787


title: Low phosphate flowers replicate 2

tag: genotype

tag: treatment


title: LAS250A776

value: P1, plate ASF_A00537


title: Low phosphate flowers replicate 1


title: LAS250A774


title: DY4620.M0.PAX

value: Whole blood

tag: covid

tag: covid cat

tag: year

tag: vaccine doses


title: Cadmium flowers replicate 1


title: LAS250A773

tag: sample type

tag: Stage


title: Salinity soybean flowers replicate 3

value: Salinity (15 mM NaCl)


title: DW7012.M0.PAX

tag: subject id

value: acute

tag: timing sx

tag: timing dx


title: LAS250A771

tag: strain


title: DU3535.M0.PAX

tag: tissue

tag: batch

value: Female

tag: research pcr

tag: hospitalized


title: LAS250A768


title: LAS250A782


title: Salinity soybean flowers replicate 1


title: Control soybean flowers replicate 3

value: No treatment


title: DR1087.M0.PAX

tag: sample timing

tag: age

tag: Sex

value: Positive

tag: vl copies

value: No


title: LAS250A763


title: LAS250A765


title: LAS250A777


title: Control soybean flowers replicate 2

tag: genotype

tag: treatment


title: LAS250A775


title: LAS250A761


title: ED1053.M0.PAX

tag: covid

tag: covid cat

tag: year

tag: vaccine doses


title: LAS250A759

tag: sample type

tag: Stage


title: DN4608.M0.PAX

tag: subject id

value: Not Tested

tag: timing sx

tag: timing dx


title: LAS250A758

tag: strain


title: LAS250A757


title: DK2656.M0.PAX

tag: tissue

tag: batch

tag: research pcr

tag: hospitalized


title: LAS250A772


title: Control soybean flowers replicate 1


title: LAS250A766


title: Combined acidity+water deficit+low phosphate+salinity+cadmium leaves replicate 2

source_name: leaves

value: leaves


title: LAS250A756


title: LAS250A755


title: LAS250A764


title: Combined acidity+water deficit+low phosphate+salinity+cadmium leaves replicate 3


title: DD1781.M0.PAX

tag: sample timing

tag: age

tag: Sex

value: Male

tag: vl copies


title: LAS250A753


title: LAS250A754


title: LAS250A751


title: Salinity soybean flowers replicate 2

tag: genotype

tag: treatment


title: Combined acidity+water deficit+low phosphate+salinity+cadmium leaves replicate 1


title: DH5958.M0.PAX

tag: covid

value: Negative

tag: covid cat

tag: year

tag: vaccine doses


title: CW9613.M0.PAX

tag: subject id

tag: timing sx


title: LAS250A750

tag: sample type

tag: Stage

tag: strain


title: DU0506.M0.PAX

tag: tissue

tag: batch

tag: research pcr

tag: timing dx


title: Combined acidity+water deficit+low phosphate+salinity leaves replicate 3


title: CQ0962.M0.PAX

tag: sample timing

tag: age

tag: Sex

tag: hospitalized


title: LAS250A747


title: Combined acidity+water deficit+low phosphate+salinity leaves replicate 2

tag: genotype

tag: treatment


title: LAS250A746


title: LAS250A745


title: CP6021.M0.PAX

tag: covid

tag: covid cat

tag: vl copies

tag: year


title: Combined acidity+water deficit+low phosphate+salinity leaves replicate 1


title: LAS250A744

tag: sample type


title: LAS250A743

tag: Stage


title: CN8830.M0.PAX

tag: subject id

tag: vaccine doses

tag: timing sx


title: Combined acidity+water deficit+low phosphate leaves replicate 3

tag: tissue

value: Acidity+water deficit+low phosphate


title: LAS250A742

tag: strain


title: LAS250A741


title: LAS250A739


title: LAS250A737


title: CC7682.M0.PAX

tag: batch

tag: sample timing

tag: research pcr

tag: timing dx


title: CC8448.M0.PAX

tag: age

tag: Sex

tag: hospitalized


title: LAS250A734


title: LAS250A736


title: LAS250A740


title: Combined acidity+water deficit+low phosphate leaves replicate 2

tag: genotype

tag: treatment


title: CN2955.M0.PAX

tag: covid

tag: covid cat

tag: vl copies

tag: year


title: LAS250A733

tag: sample type

tag: Stage


title: LAS250A749


title: Combined salinity+water deficit+low phosphate leaves replicate 2

tag: tissue

value: Salinity+water deficit+low phosphate


title: LAS250A735

tag: strain


title: LAS250A732


title: Combined salinity+water deficit+low phosphate leaves replicate 3


title: BR8508.M0.PAX

tag: subject id

tag: batch

tag: vaccine doses

tag: timing sx


title: LAS250A730


title: LAS250A729


title: BO9315.M0.PAX

tag: sample timing

tag: age

tag: research pcr

tag: timing dx


title: LAS250A728


title: BO7420.M0.PAX

tag: Sex

tag: hospitalized


title: LAS250A727


title: Combined salinity+acidity+low phosphate leaves replicate 2

tag: genotype

tag: treatment

value: Salinity+acidity+low phosphate


title: Combined acidity+water deficit+low phosphate leaves replicate 1

value: Magellan


title: LAS250A725


title: BT4345.M0.PAX

tag: covid

tag: covid cat

tag: vl copies

tag: year


title: LAS250A723

tag: sample type

tag: Stage

tag: strain


title: AU4133.M0.PAX

tag: tissue

tag: subject id

tag: batch

tag: vaccine doses


title: LAS250A720


title: LAS250A724


title: LAS250A721


title: Combined salinity+acidity+water deficit leaves replicate 2

value: Salinity+acidity+water deficit


title: LAS250A722

value: P1, plate ASF_A00537


title: LAS250A719


title: AY8549.M0.PAX

value: Whole blood

tag: sample timing

tag: age

tag: research pcr

tag: timing sx


title: Combined salinity+water deficit+low phosphate leaves replicate 1

tag: genotype


title: AP2168.M0.PAX

tag: Sex

tag: hospitalized

tag: timing dx


title: Combined salinity+acidity+low phosphate leaves replicate 3

tag: treatment


title: LAS250A715


title: LAS250A716


title: LAS250A718


title: Combined low phosphate+water deficit leaves replicate 3

value: Low phosphate+water deficit


title: AO9858.M0.PAX

value: acute

tag: covid

tag: covid cat

tag: vl copies

tag: year


title: AR3216.M0.PAX

tag: tissue


title: Combined low phosphate+water deficit leaves replicate 2


title: LAS250A714

tag: sample type

tag: Stage

tag: strain


title: LAS250A726


title: AO5787.M0.PAX

tag: subject id

tag: batch

tag: sample timing

tag: vaccine doses


title: LAS250A713


title: AJ2232.M0.PAX

tag: age

tag: research pcr

tag: timing sx


title: LAS250A712


title: Combined salinity+acidity+low phosphate leaves replicate 1

tag: genotype


title: Combined salinity+acidity+water deficit leaves replicate 3

tag: treatment


title: Combined acidity+low phosphate leaves replicate 3

value: Acidity+low phosphate


title: AH5367.M1.PAX

tag: Sex

value: Female

tag: covid

tag: hospitalized

tag: timing dx


title: LAS250A717


title: Combined low phosphate+water deficit leaves replicate 1

tag: tissue


title: LAS250A710

tag: sample type


title: LAS250A707

tag: Stage


title: LAS250A711

tag: strain


title: AC9270.M0.PAX

tag: subject id

tag: covid cat

tag: vl copies

tag: year


title: Combined acidity+low phosphate leaves replicate 2


title: Combined salinity+acidity+water deficit leaves replicate 1


title: LAS250A709


title: LAS250A708


title: AH5367.M0.PAX

tag: batch

tag: sample timing

tag: age

tag: vaccine doses


title: Combined acidity+low phosphate leaves replicate 1

tag: genotype

tag: treatment


title: LAS250A706


title: LAS250A704


title: ZY4788.M0.NSB

source_name: Nasopharyngeal swab

value: Nasopharyngeal swab

tag: Sex

tag: covid

value: Positive

tag: research pcr

tag: timing sx


title: Combined acidity+water deficit leaves replicate 3

tag: tissue

value: Acidity+water deficit


title: LAS250A701

tag: sample type

tag: Stage


title: LAS250A703

tag: strain


title: ZS4446.M0.NSB

tag: subject id

tag: covid cat

value: Not Tested

tag: hospitalized

value: No

tag: timing dx


title: LAS250A70

value: P1, plate SCS_A00200


title: Combined acidity+water deficit leaves replicate 2

value: leaves


title: ZQ3518.M0.NSB

tag: batch

tag: sample timing

value: Negative

tag: vl copies

tag: year


title: LAS250A700


title: LAS250A698


title: LAS250A697


title: ZO9902.M0.NSB

tag: age

value: Male

tag: vaccine doses


title: Combined acidity+water deficit leaves replicate 1

tag: genotype

value: Magellan

tag: treatment


title: LAS250A696


title: LAS250A695


title: ZG9202.M0.NSB

tag: Sex

tag: covid

tag: research pcr

tag: timing sx


title: Combined salinity+low phosphate leaves replicate 2

tag: tissue

value: Salinity+low phosphate


title: LAS250A693

tag: sample type

value: P1, plate ASF_A00537

tag: Stage

tag: strain


title: LAS250A694


title: ZF0029.M0.NSB

tag: subject id

tag: covid cat

tag: hospitalized

tag: timing dx


title: ZD3287.M0.NSB

tag: batch

tag: sample timing

tag: vl copies

tag: year


title: LAS250A691


title: Combined salinity+water deficit leaves replicate 3

tag: genotype

tag: treatment

value: Salinity+water deficit


title: Combined salinity+low phosphate leaves replicate 3


title: LAS250A689


title: LAS250A690


title: Combined salinity+low phosphate leaves replicate 1


title: ZC2922.M0.NSB

tag: age

tag: Sex

tag: covid

tag: vaccine doses


title: LAS250A687

tag: sample type


title: LAS250A692

tag: Stage


title: LAS250A688

tag: strain


title: ZA8926.M0.NSB

tag: tissue

tag: subject id

tag: research pcr

tag: timing sx


title: Combined salinity+water deficit leaves replicate 1


title: YX3199.M0.NSB

tag: batch

tag: covid cat

tag: hospitalized

tag: timing dx


title: Combined salinity+water deficit leaves replicate 2

tag: genotype


title: LAS250A685


title: LAS250A686


title: LAS250A684


title: YP4954.M0.NSB

tag: sample timing

tag: vl copies

tag: year


title: Combined salinity+acidity leaves replicate 3

tag: treatment

value: Salinity+acidity


title: LAS250A683


title: LAS250A682


title: LAS250A681


title: LAS250A679

value: P1, plate ASF_A00536


title: LAS250A678


title: YH1847.M0.NSB

value: acute

tag: age

tag: Sex

tag: covid

tag: vaccine doses


title: Combined salinity+acidity leaves replicate 2

tag: tissue


title: YO0894.M0.NSB

tag: subject id


title: LAS250A680

tag: sample type

tag: Stage

tag: strain


title: Cadmium leaves replicate 3

value: Cadmium (300 uM CdCl2)


title: LAS250A677


title: Combined salinity+acidity leaves replicate 1


title: LAS250A676


title: LAS250A673


title: Cadmium leaves replicate 2


title: LAS250A672


title: Water deficit leaves replicate 3

value: Water deficit (30% of the water available for transpiration)


title: LAS250A670


title: XI2762.M0.NSB

value: Nasopharyngeal swab

tag: batch

value: Female

value: Positive

tag: covid cat

tag: research pcr

tag: timing sx


title: Water deficit leaves replicate 2

tag: genotype


title: LAS250A675


title: YD8439.M0.NSB

tag: sample timing

tag: vl copies

tag: hospitalized

value: No

tag: timing dx


title: Cadmium leaves replicate 1

tag: treatment


title: XU1619.M0.NSB

tag: age

tag: Sex

tag: covid

tag: year


title: XM2821.M0.NSB

tag: tissue

tag: subject id

value: Not Tested

tag: vaccine doses


title: LAS250A669

tag: sample type

tag: Stage

tag: strain


title: LAS250A665


title: LAS250A666


title: LAS250A667


title: LAS250A663


title: WQ9247.M0.NSB

tag: batch

tag: covid cat

tag: research pcr

tag: timing sx


title: LAS250A671


title: LAS250A668


title: Acidity leaves replicate 3

value: leaves

tag: genotype

value: Acidity (pH 4)


title: WQ7051.M0.NSB

tag: sample timing

value: Male

value: Negative

tag: vl copies

tag: hospitalized

tag: timing dx


title: WM7261.M0.NSB

tag: age

tag: Sex

tag: covid


title: LAS250A664


title: Acidity leaves replicate 1

tag: tissue

value: Magellan

tag: treatment


title: LAS250A660

tag: sample type


title: VV9796.M0.NSB

tag: subject id

tag: year

tag: vaccine doses


title: Water deficit leaves replicate 1


title: Acidity leaves replicate 2


title: VZ0734.M0.NSB

tag: batch

tag: covid cat


title: LAS250A656

tag: Stage

tag: strain


title: LAS250A662


title: LAS250A655


title: LAS250A661


title: LAS250A653


title: LAS250A657


title: Low phosphate leaves replicate 2

tag: genotype

value: Low phosphate (phosphate concentration was reduced by 90%)


title: VT3754.M0.NSB

tag: sample timing

tag: research pcr

tag: vl copies

tag: timing sx


title: VT1389.M0.NSB

tag: age

tag: Sex

tag: hospitalized

tag: timing dx


title: Low phosphate leaves replicate 1

tag: tissue

tag: treatment


title: LAS250A659

tag: sample type


title: VI0592.M0.NSB

tag: subject id

tag: covid

tag: year

tag: vaccine doses


title: LAS250A654

tag: Stage

tag: strain


title: Salinity soybean leaves replicate 3

tag: genotype

value: Salinity (15 mM NaCl)


title: Salinity soybean leaves replicate 1


title: LAS250A647


title: LAS250A651


title: LAS250A658


title: VF7018.M0.NSB

tag: batch

tag: sample timing

tag: covid cat

tag: research pcr


title: UO2994.M0.NSB

tag: age

tag: Sex

tag: vl copies

tag: timing sx


title: LAS250A650


title: LAS250A644


title: Salinity soybean leaves replicate 2

tag: tissue

tag: treatment


title: Control soybean leaves replicate 2

value: No treatment


title: LAS250A649

tag: sample type

value: P1, plate ASF_A00536


title: Control soybean leaves replicate 1


title: VB2611.M0.NSB

tag: subject id

value: acute

tag: covid

tag: hospitalized

tag: timing dx


title: LAS250A639

tag: Stage

tag: strain


title: LAS250A648


title: UD7001.M0.NSB

tag: batch

tag: year

tag: vaccine doses


title: LAS250A636


title: LAS250A646


title: Low phosphate leaves replicate 3

tag: genotype


title: LAS250A634


title: VA0735.M0.NSB

tag: sample timing

tag: age

tag: covid cat

tag: research pcr


title: Control soybean leaves replicate 3

tag: tissue


title: LAS250A645


title: LAS250A632


title: LAS250A641


title: LAS250A631


title: LAS250A643


title: UI9611.M0.NSB

tag: Sex

tag: vl copies

tag: timing sx


title: LAS250A630

tag: sample type


title: LAS250A642


title: UH8093.M0.NSB

tag: subject id

tag: covid

tag: hospitalized

value: Yes


title: LAS250A640

tag: Stage

tag: strain


title: LAS250A63

value: P1, plate SCS_A00200


title: TW5706.M0.NSB

value: Nasopharyngeal swab

tag: batch

tag: year

tag: timing dx


title: UE4555.M0.NSB

tag: sample timing

tag: vaccine doses


title: WL2H9

city: Shanghai

first: Ze-guang

last: Han

address: 800 Dongchuan Road

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

description: infected with Ad-Cre

data_processing:
Raw sequencing reads were trimmed by Trimmomatic (v0.36) to remove adapters and low quality sequences.
The filtered reads were aligned to the Mus musculus genome GRCm38 UCSC annotated transcripts via Tophat (v2.1.0) with default parameters.
HTSeq (v0.8.0.) was used for transcripts counting for the subsequent statistical analyses were based on negative binomial distribution which requires integer counts. ERCC expressions were used to remove unwanted variation using R Bioconductor package RUVSeq (v1.16.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

growth_protocol: Primary hepatocytes were first isolated from Arid1af/f mice. Isolated cells were then immortalized with SV40LT-expressing lentivirus and then transformed by HrasV12D-expressing lentivirus to generate a cell line named AB17. The AB17 cells were cultured in DMEM medium supplied with 10% fetal bovin serum (FBS) and 100 µg/ml penicillin-streptomycin at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Single cell was captured by the 10-17 µm C1 Single-Cell Auto Prep System (Fluidigm).
Sequencing libraries were constructed using SMARTer (Clontech) whole-transcriptome amplification (WTA) on 73 Ad-GFP infected cells and 76 Ad-Cre infected cells, according to the manufacturer’s instruction. An ERCC Spike-in mix (Ambion) was used as the technical control.

treatment_protocol: AB17 cells were infected with Ad-GFP or Ad-Cre, respectively. 48 hours after infection, GFP-positive cells were sorted by flow cytometer (BD FACSJazz).

tag: mouse strain

tag: genotype

value: liver


title: WL2H4

description: infected with Ad-Cre

tag: tissue


title: WL2H6

description: infected with Ad-Cre


title: WL2H8

description: infected with Ad-Cre


title: LAS250A637


title: TU3350.M0.NSB

tag: age

tag: Sex

tag: covid cat

tag: research pcr


title: LAS250A627

tag: sample type


title: TN6246.M0.NSB

tag: subject id

tag: covid

value: Positive

tag: vl copies

tag: timing sx


title: WL2H7

description: infected with Ad-Cre


title: TX5656.M0.NSB

tag: batch

tag: hospitalized

value: No


title: LAS250A635

tag: Stage

tag: strain


title: LAS250A633


title: WL2H2

description: infected with Ad-Cre


title: LAS250A625


title: WL2H5

description: infected with Ad-Cre


title: TV4923.M0.NSB

tag: sample timing

tag: year

tag: vaccine doses

tag: timing dx


title: TH8758.M0.NSB

tag: tissue

tag: age


title: LAS250A624


title: WL2H1

description: infected with Ad-Cre

tag: mouse strain

tag: genotype


title: LAS250A629

tag: sample type


title: WL2H3

description: infected with Ad-Cre


title: LAS250A628


title: LAS250A626


title: WL2G9

description: infected with Ad-Cre


title: TG2740.M0.NSB

tag: subject id

tag: Sex

value: Female

tag: covid cat

tag: research pcr

value: Not Tested


title: WL2G8

description: infected with Ad-Cre


title: LAS250A618


title: TE7914.M0.NSB

tag: batch

tag: covid

tag: vl copies

tag: timing sx


title: LAS250A617

tag: Stage

tag: strain


title: LAS250A623


title: TH1406.M0.NSB

tag: sample timing

tag: hospitalized

tag: year

tag: vaccine doses


title: LAS250A615


title: LAS250A622


title: LAS250A614


title: LAS250A621


title: SO3251.M0.NSB

tag: tissue

tag: age

tag: timing dx


title: LAS250A620

tag: sample type


title: LAS250A619


title: TC6050.M0.NSB

tag: subject id

tag: Sex


title: WL2G3

description: infected with Ad-Cre

tag: mouse strain

tag: genotype


title: SY3034.M0.NSB

tag: batch

tag: covid

tag: covid cat

tag: research pcr


title: LAS250A616

tag: Stage

tag: strain


title: LAS250A609


title: WL2G6

description: infected with Ad-Cre


title: WL2G5

description: infected with Ad-Cre


title: LAS250A613


title: SD2421.M0.NSB

tag: sample timing

tag: vl copies

tag: hospitalized

tag: timing sx


title: LAS250A612


title: LAS250A611


title: WL2G7

description: infected with Ad-Cre

tag: tissue


title: LAS250A607


title: LAS250A606


title: LAS250A610


title: WL2G4

description: infected with Ad-Cre


title: SA3829.M0.NSB

tag: age

tag: year

tag: vaccine doses

tag: timing dx


title: WL2G1

description: infected with Ad-Cre

tag: mouse strain


title: SD0040.M0.NSB

tag: subject id

tag: Sex


title: SC1834.M0.NSB

tag: batch

tag: covid


title: LAS250A608

tag: sample type


title: RX6352.M0.NSB

tag: covid cat

tag: research pcr


title: LAS250A602

tag: Stage

tag: strain


title: WL2G2

description: infected with Ad-Cre

tag: genotype


title: WL2G10

description: infected with Ad-Cre


title: LAS250A605


title: RX3601.M0.NSB

tag: sample timing

tag: vl copies

tag: hospitalized

tag: timing sx


title: LAS250A604


title: LAS250A603


title: RX1597.M0.NSB

tag: tissue

tag: age

tag: year

tag: vaccine doses


title: RU6817.M0.NSB

tag: subject id

tag: Sex

tag: timing dx


title: LAS250A596

tag: sample type


title: LAS250A600


title: LAS250A595


title: WL2F5

description: infected with Ad-Cre

tag: mouse strain


title: WL2F6

description: infected with Ad-Cre


title: LAS250A593


title: RK7680.M0.NSB

tag: batch

tag: covid

tag: covid cat

tag: research pcr


title: LAS250A589

tag: Stage

tag: strain


title: LAS250A590


title: LAS250A592


title: QW4655.M0.NSB

tag: sample timing

tag: vl copies

tag: hospitalized


title: LAS250A586


title: LAS250A585


title: QR5656.M0.NSB

tag: tissue

tag: age

tag: timing sx


title: QH3620.M0.NSB

tag: subject id

tag: year

tag: vaccine doses


title: LAS250A381

tag: sample type

value: P1, plate SCS_A00204


title: LAS250A376


title: WL2F9

description: infected with Ad-Cre

tag: mouse strain

tag: genotype


title: LAS250A375


title: WL2E7

description: infected with Ad-Cre


title: LAS250A367


title: WL2E5

description: infected with Ad-Cre


title: LAS250A36


title: PJ4720.M0.NSB

tag: batch

tag: Sex

tag: covid

tag: timing dx


title: LAS250A355

tag: Stage

tag: strain


title: LAS250A599


title: WL2F8

description: infected with Ad-Cre


title: LAS250A598


title: WL2E4

description: infected with Ad-Cre


title: PB7187.M0.NSB

tag: sample timing

value: Male

tag: covid cat

tag: research pcr

tag: vl copies


title: LAS250A594


title: LAS250A597


title: WL2F7

description: infected with Ad-Cre

tag: tissue


title: WL2F4

description: infected with Ad-Cre


title: RI8890.M0.NSB

tag: subject id

tag: age

tag: hospitalized

tag: timing sx


title: LAS250A601

tag: sample type


title: LAS250A591


title: WL2F3

description: infected with Ad-Cre

tag: mouse strain

tag: genotype


title: WL2E3

description: infected with Ad-Cre


title: LAS250A588


title: LAS250A587


title: QS9335.M0.NSB

tag: batch

tag: Sex

value: Negative

tag: year

tag: vaccine doses


title: WL2E9

description: infected with Ad-Cre


title: WL2F2

description: infected with Ad-Cre


title: LAS250A383

tag: Stage

tag: strain


title: WL2F10

description: infected with Ad-Cre


title: PA8841.M0.NSB

tag: sample timing

tag: covid

tag: covid cat

tag: timing dx


title: PZ1823.M0.NSB

tag: tissue

tag: subject id

tag: research pcr

tag: vl copies


title: WL2E8

description: infected with Ad-Cre


title: LAS250A380

tag: sample type


title: WL2E2

description: infected with Ad-Cre

tag: mouse strain


title: LAS250A314


title: LAS250A304


title: WL2E10

description: infected with Ad-Cre

tag: genotype


title: LAS250A373


title: PT4963.M0.NSB

tag: batch

tag: age

tag: hospitalized

tag: timing sx


title: LAS250A303

tag: Stage


title: WL2E6

description: infected with Ad-Cre


title: PN6346.M0.NSB

tag: Sex

tag: year

tag: vaccine doses


title: LAS250A360

tag: strain


title: WL2D9

description: infected with Ad-Cre


title: LAS250A302


title: LAS250A300


title: LAS250A336


title: LAS250A362


title: LAS250A335


title: WL2D8

description: infected with Ad-Cre


title: LAS250A292


title: RF0171.M0.NSB

tag: sample timing

tag: covid

tag: covid cat

tag: timing dx


title: WL2D7

description: infected with Ad-Cre

tag: tissue


title: LAS250A327

tag: sample type


title: OY8888.M0.NSB

tag: subject id

tag: research pcr

tag: vl copies


title: LAS250A32


title: OT9187.M0.NSB

tag: batch

tag: age


title: LAS250A192

value: P1, plate SCS_A00201


title: LAS250A185


title: OQ9062.M0.NSB

tag: hospitalized

tag: timing sx


title: LAS250A188

tag: Stage


title: OM8987.M0.NSB

tag: Sex

tag: year


title: OK7852.M0.NSB

tag: vaccine doses


title: LAS250A171

tag: strain


title: LAS250A175


title: WL2D5

description: infected with Ad-Cre

tag: mouse strain

tag: genotype


title: WL2D6

description: infected with Ad-Cre


title: ON7836.M0.NSB

tag: sample timing

tag: covid

tag: covid cat

tag: timing dx


title: WL2D4

description: infected with Ad-Cre

tag: tissue


title: OF4658.M0.NSB

tag: subject id

tag: research pcr

tag: vl copies


title: LAS250A163

tag: sample type


title: WL2D3

description: infected with Ad-Cre


title: LAS250A161


title: LAS250A158


title: LAS250A299


title: OB1593.M0.NSB

tag: batch

tag: age

tag: hospitalized

tag: timing sx


title: LAS250A155

tag: Stage


title: WL2D2

description: infected with Ad-Cre


title: OF7032.M0.NSB

tag: Sex

tag: year

tag: vaccine doses


title: LAS250A144

tag: strain


title: NZ1261.M0.NSB

tag: sample timing

tag: covid


title: LAS250A132


title: LAS250A143


title: WL2D10

description: infected with Ad-Cre

tag: mouse strain

tag: genotype


title: NY5696.M0.NSB

tag: tissue

tag: subject id

tag: covid cat

tag: timing dx


title: LAS250A174

tag: sample type


title: LAS250A135


title: WL2C9

description: infected with Ad-Cre


title: LAS250A116


title: WL2C8

description: infected with Ad-Cre


title: LAS250A108


title: LAS250A124


title: LAS250A112


title: NT0329.M0.NSB

tag: batch

tag: age

tag: research pcr

tag: vl copies


title: LAS250A106

tag: Stage


title: WL2C7

description: infected with Ad-Cre


title: LAS256A997

value: P1, plate RL2_FL260717


title: LAS256A986


title: WL2C6

description: infected with Ad-Cre


title: NM9596.M0.NSB

tag: Sex

tag: hospitalized

tag: year

tag: timing sx


title: LAS256A987

tag: strain


title: NH5340.M0.NSB

tag: sample timing

tag: covid

tag: vaccine doses


title: WL2C5

description: infected with Ad-Cre

tag: mouse strain

tag: genotype

tag: tissue


title: WL2C4

description: infected with Ad-Cre


title: LAS256A972

tag: sample type


title: LAS256A951

value: P1, plate RL1_FL260717


title: MZ2666.M0.NSB

tag: subject id

tag: batch

tag: covid cat

tag: timing dx


title: LAS256A921

tag: Stage


title: WL2C3

description: infected with Ad-Cre


title: LAS256A934


title: MW3235.M0.NSB

tag: age

tag: Sex

tag: research pcr

tag: vl copies


title: LAS256A915

tag: strain


title: LAS256A899


title: MT0776.M0.NSB

tag: sample timing

tag: hospitalized

tag: year

tag: timing sx


title: NO7567.M0.NSB

tag: covid

tag: vaccine doses


title: WL2C10

description: infected with Ad-Cre

tag: mouse strain

tag: genotype

tag: tissue


title: MS0072.M0.NSB

tag: subject id

tag: batch

tag: covid cat


title: LAS256A765

tag: sample type

value: P1, plate RL1_FL170717

tag: Stage


title: LAS256A883


title: LAS256A879


title: WL2C1

description: infected with Ad-Cre


title: LAS256A691


title: LAS256A977


title: NK1464.M0.NSB

tag: age

tag: Sex

tag: research pcr

tag: timing dx


title: LAS256A971

tag: strain


title: ML5199.M0.NSB

tag: sample timing

tag: vl copies

tag: hospitalized

tag: year


title: LAS256A1332

value: P1, plate RL-FL130917


title: MJ2952.M0.NSB

value: acute

tag: covid

tag: vaccine doses

tag: timing sx


title: LAS256A1344


title: LAS256A1315


title: WL2B8

description: infected with Ad-Cre

tag: mouse strain

tag: genotype

tag: tissue


title: MK4460.M0.NSB

tag: subject id

tag: batch

tag: covid cat


title: WL2B9

description: infected with Ad-Cre


title: LAS256A1309

tag: sample type

tag: Stage


title: WL2C2

description: infected with Ad-Cre


title: LAS256A1295


title: WL2B6

description: infected with Ad-Cre


title: MI9133.M0.NSB

tag: age

tag: Sex

tag: research pcr

tag: timing dx


title: LAS256A1485

value: P1, plate RL-FL200917

tag: strain


title: MI4012.M0.NSB

tag: sample timing

tag: vl copies

tag: hospitalized

tag: year


title: WL2B7

description: infected with Ad-Cre

tag: mouse strain


title: LAS256A1268


title: LAS256A1260


title: MH6120.M0.NSB

tag: covid

tag: vaccine doses

tag: timing sx


title: WL2B5

description: infected with Ad-Cre

tag: genotype

tag: tissue


title: LAS256A1255

tag: sample type


title: LAS256A1045

tag: Stage


title: WL2B4

description: infected with Ad-Cre


title: MC2708.M0.NSB

tag: subject id

tag: batch

tag: age

tag: covid cat


title: LAS256A1042

tag: strain


title: LAS256A1037


title: LAS256A1044


title: MB0117.M0.NSB

tag: sample timing

tag: Sex

tag: research pcr

tag: timing dx


title: WL2B3

description: infected with Ad-Cre

tag: mouse strain


title: WL2B2

description: infected with Ad-Cre


title: LAS256A1033


title: LZ7554.M0.NSB

tag: covid

tag: vl copies

tag: hospitalized

tag: year


title: LAS256A1020


title: LAS256A206


title: LAS256A1299


title: LX3468.M0.NSB

tag: tissue

tag: vaccine doses

tag: timing sx


title: LAS256A210

tag: sample type

tag: Stage


title: WL2B10

description: infected with Ad-Cre

tag: genotype


title: LAS256A203


title: LAS256A199


title: LL792.M0.NSB

tag: subject id

tag: batch

tag: age

tag: covid cat


title: LAS256A196

tag: strain


title: LAS256A195


title: LAS256A194


title: WL2B1

description: infected with Ad-Cre


title: WL2A9

description: infected with Ad-Cre


title: LH4091.M0.NSB

tag: sample timing

tag: Sex

tag: research pcr

tag: timing dx


title: LAS256A193


title: LG1702.M0.NSB

tag: covid

tag: vl copies

tag: hospitalized


title: WL2A7

description: infected with Ad-Cre

tag: mouse strain

tag: tissue


title: LAS256A191

tag: sample type


title: LAS256A192

tag: Stage


title: LG0250.M0.NSB

tag: year

tag: vaccine doses

tag: timing sx


title: WL2A8

description: infected with Ad-Cre

tag: genotype


title: LF3604.M0.NSB

tag: subject id

tag: batch

tag: age

tag: covid cat


title: WL2A6

description: infected with Ad-Cre


title: LAS256A171

tag: strain


title: WL2A5

description: infected with Ad-Cre


title: LE3362.M0.NSB

tag: sample timing

tag: Sex

tag: research pcr

tag: timing dx


title: LAS256A166


title: LAS256A170


title: LB8121.M0.NSB

tag: covid

tag: vl copies

tag: hospitalized


title: LAS256A169

tag: sample type

tag: Stage


title: WL2A3

description: infected with Ad-Cre

tag: mouse strain

tag: tissue


title: LAS256A161


title: LAS256A152


title: LAS256A160


title: KW4113.M0.NSB

tag: year

tag: vaccine doses

tag: timing sx


title: KZ6310.M0.NSB

tag: subject id

tag: batch

tag: age


title: LAS256A156

tag: strain


title: WL2A4

description: infected with Ad-Cre

tag: genotype


title: KV1465.M0.NSB

tag: sample timing

tag: Sex

tag: covid cat

tag: research pcr


title: LAS256A176


title: LAS256A180


title: WL2A1

description: infected with Ad-Cre


title: KR3482.M0.NSB

tag: covid

tag: vl copies

tag: hospitalized

tag: timing dx


title: LAS256A147

tag: sample type

tag: Stage


title: WL2A2

description: infected with Ad-Cre

tag: mouse strain

tag: tissue


title: KQ7168.M0.NSB

tag: subject id

tag: year

tag: vaccine doses

tag: timing sx


title: LAS256A141

tag: strain


title: LAS256A150


title: LAS256A142


title: LAS256A130


title: LAS256A128


title: WL1H8

description: infected with Ad-GFP

tag: genotype


title: KN1525.M0.NSB

tag: batch

tag: sample timing

tag: age

tag: Sex


title: WL1H7

description: infected with Ad-GFP


title: LAS256A119


title: LAS256A123


title: KL0666.M0.NSB

tag: covid

tag: covid cat

tag: research pcr

tag: vl copies


title: WL2A10

description: infected with Ad-Cre


title: LAS256A117

tag: sample type

tag: Stage


title: LAS256A111


title: LAS256A110


title: KA9831.M0.NSB

tag: tissue

tag: hospitalized

tag: timing dx


title: WL1H5

description: infected with Ad-GFP

tag: mouse strain


title: WL1H9

description: infected with Ad-GFP


title: LAS256A479


title: JV7184.M0.NSB

tag: subject id

tag: year

tag: vaccine doses

tag: timing sx


title: LAS256A151

tag: strain


title: WL1H4

description: infected with Ad-GFP

tag: genotype


title: LAS256A143


title: JI3265.M0.NSB

tag: batch

tag: sample timing

tag: age

tag: Sex


title: LAS256A475


title: LAS256A474


title: WL1H3

description: infected with Ad-GFP


title: IT4990.M0.NSB

tag: covid

tag: covid cat

tag: research pcr

tag: vl copies


title: LAS256A470

tag: sample type

tag: Stage


title: WL1H2

description: infected with Ad-GFP

tag: mouse strain

tag: tissue


title: LAS256A469


title: IR5536.M0.NSB

tag: subject id

tag: hospitalized

tag: year

tag: timing dx


title: WL1H1

description: infected with Ad-GFP

tag: genotype


title: LAS256A461

tag: strain


title: WL1H6

description: infected with Ad-GFP


title: IO2962.M0.NSB

tag: batch

tag: sample timing

tag: vaccine doses

tag: timing sx


title: LAS256A468


title: LAS256A463


title: WL1G9

description: infected with Ad-GFP


title: LAS256A456


title: LAS256A105


title: IM4862.M0.NSB

tag: age

tag: Sex

tag: covid

tag: covid cat


title: IJ0554.M0.NSB

tag: research pcr

tag: vl copies


title: LAS256A476

tag: sample type

tag: Stage


title: LAS256A454


title: LAS256A455


title: WL1G7

description: infected with Ad-GFP

tag: mouse strain

tag: tissue


title: LAS256A453


title: LAS256A452


title: II7900.M0.NSB

tag: subject id

tag: hospitalized

tag: year

tag: timing dx


title: WL1G6

description: infected with Ad-GFP

tag: genotype


title: LAS256A449

tag: strain


title: LAS256A448


title: LAS256A447


title: HR2557.M0.NSB

tag: batch

tag: sample timing

tag: vaccine doses

tag: timing sx


title: WL1G5

description: infected with Ad-GFP


title: HY4957.M0.NSB

tag: age

tag: Sex

tag: covid

tag: covid cat


title: WL1G4

description: infected with Ad-GFP


title: LAS256A442

tag: sample type

tag: Stage


title: LAS256A438


title: LAS256A444


title: HP1718.M0.NSB

tag: tissue

tag: research pcr

tag: vl copies


title: WL1G3

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A433


title: WL1G8

description: infected with Ad-GFP


title: LAS256A435


title: LAS256A430


title: WL1G2

description: infected with Ad-GFP


title: LAS256A427


title: HE8769.M0.NSB

tag: subject id

tag: hospitalized

tag: year

tag: timing dx


title: LAS256A425

tag: strain


title: GW5371.M0.NSB

tag: batch

tag: sample timing

tag: vaccine doses


title: WL1G1

description: infected with Ad-GFP

tag: genotype


title: WL1F9

description: infected with Ad-GFP


title: LAS256A420


title: GT7397.M0.NSB

tag: age

tag: Sex

tag: covid

tag: timing sx


title: LAS256A421

tag: sample type

tag: Stage


title: GS1960.M0.NSB

tag: tissue

tag: covid cat

tag: research pcr

tag: vl copies


title: LAS256A415


title: LAS256A413


title: WL1F8

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A412


title: WL1F7

description: infected with Ad-GFP


title: GN5032.M0.NSB

tag: subject id

tag: hospitalized

tag: year

tag: timing dx


title: LAS256A409

tag: strain


title: FX9488.M0.NSB

tag: batch

tag: sample timing

tag: vaccine doses


title: LAS256A410


title: LAS256A403


title: LAS256A406


title: LAS256A402


title: WL1F5

description: infected with Ad-GFP

tag: genotype


title: FW9252.M0.NSB

tag: age

tag: Sex

tag: covid

tag: timing sx


title: LAS256A397

tag: sample type

tag: Stage


title: WL1F4

description: infected with Ad-GFP

tag: tissue


title: FR8148.M0.NSB

tag: covid cat

tag: research pcr

tag: vl copies


title: WL1F3

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A391


title: LAS256A395


title: GP9256.M0.NSB

tag: subject id

tag: hospitalized

tag: year

tag: timing dx


title: LAS256A388

tag: strain


title: FC0633.M0.NSB

tag: batch

tag: sample timing

tag: vaccine doses


title: FF1165.M0.NSB

tag: age

tag: Sex

tag: covid


title: LAS256A385

tag: sample type

tag: Stage


title: WL1F6

description: infected with Ad-GFP

tag: genotype

tag: tissue


title: FB7566.M0.NSB

tag: covid cat

tag: research pcr

tag: vl copies

tag: timing sx


title: WL1F2

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A389


title: WL1F1

description: infected with Ad-GFP


title: LAS256A377


title: EY5612.M0.NSB

tag: subject id

tag: hospitalized

tag: year

tag: timing dx


title: LAS256A375

tag: strain


title: WL1E8

description: infected with Ad-GFP


title: LAS256A368


title: EW5232.M0.NSB

tag: batch

tag: sample timing

tag: age

tag: vaccine doses


title: LAS256A365

tag: sample type

tag: Stage


title: LAS256A400


title: LAS256A398


title: LAS256A363


title: WL1E7

description: infected with Ad-GFP

tag: genotype

tag: tissue


title: LAS256A361


title: EL1974.M0.NSB

tag: Sex

tag: covid

tag: covid cat

tag: research pcr


title: WL1E6

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A359


title: LAS256A360


title: LAS256A354


title: EF9688.M0.NSB

tag: subject id

tag: vl copies

tag: hospitalized

tag: timing sx


title: LAS256A387

tag: strain


title: WL1E5

description: infected with Ad-GFP


title: ED1053.M0.NSB

tag: batch

tag: sample timing

tag: year

tag: timing dx


title: LAS256A351

tag: sample type

tag: Stage


title: WL1E4

description: infected with Ad-GFP

tag: genotype

tag: tissue


title: WL1E9

description: infected with Ad-GFP


title: WL1E3

description: infected with Ad-GFP


title: LAS256A348


title: DW7012.M0.NSB

tag: age

tag: Sex

tag: covid

tag: vaccine doses


title: LAS256A344


title: LAS256A341


title: LAS256A340


title: DU3535.M0.NSB

tag: subject id

tag: covid cat

tag: research pcr


title: WL1E2

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A338

tag: strain


title: LAS256A339


title: DR1087.M0.NSB

tag: batch

tag: vl copies

tag: hospitalized

tag: timing sx


title: LAS256A337

tag: sample type


title: WL1D9

description: infected with Ad-GFP


title: LAS256A331

tag: Stage


title: LAS256A335


title: DN4608.M0.NSB

tag: sample timing

tag: year

tag: timing dx


title: LAS256A326


title: LAS256A349


title: WL1D7

description: infected with Ad-GFP

tag: genotype

tag: tissue


title: LAS256A346


title: DY4620.M0.NSB

tag: age

tag: Sex

tag: covid

tag: vaccine doses


title: CW9613.M0.NSB

tag: subject id

tag: covid cat

tag: research pcr


title: LAS256A323

tag: strain


title: WL1D6

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A325


title: CQ0962.M0.NSB

tag: batch

tag: vl copies

tag: hospitalized

tag: timing sx


title: LAS256A320

tag: sample type

tag: Stage


title: LAS256A316


title: WL1E1

description: infected with Ad-GFP

tag: genotype


title: LAS256A312


title: LAS256A322


title: LAS256A311


title: CN8830.M0.NSB

tag: tissue

tag: sample timing

tag: year

tag: timing dx


title: WL1D5

description: infected with Ad-GFP


title: WL1D3

description: infected with Ad-GFP


title: LAS256A306


title: LAS256A310


title: WL1D4

description: infected with Ad-GFP


title: WL1D8

description: infected with Ad-GFP


title: CC8448.M0.NSB

tag: age

tag: Sex

tag: covid

tag: vaccine doses


title: LAS256A327

tag: strain


title: DH5958.M0.NSB

tag: subject id

tag: covid cat

tag: research pcr


title: LAS256A305


title: WL1D2

description: infected with Ad-GFP

tag: mouse strain


title: CC7682.M0.NSB

tag: batch

tag: vl copies

tag: hospitalized

tag: timing sx


title: LAS256A303

tag: sample type

tag: Stage


title: BT4345.M0.NSB

tag: tissue

tag: sample timing

tag: year


title: LAS256A297


title: LAS256A294


title: BO9315.M0.NSB

tag: age

tag: Sex

tag: timing dx


title: CP6021.M0.NSB

tag: covid

tag: vaccine doses


title: WL1D1

description: infected with Ad-GFP

tag: genotype


title: LAS256A293

tag: strain


title: LAS256A302


title: BO7420.M0.NSB

tag: subject id

tag: covid cat

tag: research pcr


title: WL1C7

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A291


title: LAS256A292


title: AY8549.M0.NSB

tag: batch

tag: vl copies

tag: hospitalized

tag: timing sx


title: WL1C6

description: infected with Ad-GFP

tag: tissue


title: WL1C8

description: infected with Ad-GFP


title: LAS256A290

tag: sample type

tag: Stage


title: LAS256A289


title: WL1C5

description: infected with Ad-GFP


title: WL1C4

description: infected with Ad-GFP


title: AR3216.M0.NSB

tag: sample timing

tag: age

tag: Sex

tag: year


title: AU4133.M0.NSB

tag: covid

tag: vaccine doses

tag: timing dx


title: MEF_TNRC18_WT_2

city: CHAPEL HILL

first: Gang

middle: Greg

last: Wang

state: North Carolina

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: UNC chapel hill

description:
RNAseq_GENE_MEF_KI_Tnrc18.txt
RNAseq_TRANSPOSON_MEF_KI_Tnrc18.txt

data_processing:
The fastq files of human cell and mouse cell RNA-seq data were aligned respectively to the GRCh38 human genome (GRCh38.d1.vd1.fa) and the mm10 mouse genome by using STAR v2.4.2 with the following parameters: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM. Then, transcript abundance for each sample was estimated with salmon V1.4.0 to quantify the transcriptome defined by Gencode v22. QC was performed using the Picard 2.22.4 CollectRnaSeqMetric and FastQC 0.11.9. Gene level counts were summed across isoforms, and genes with low counts (maximum expression < 10) were filtered out from the downstream analyses. We tested genes for differential expression in DESeq2 v1.38.2 in R and gene set enrichment analysis (GSEA) on Molecular Signatures Database (MsigDB) C2 curated genesets was conducted with GSVA v1.30.1 in R.  To comprehensively quantify expression by all repetitive elements including transposable elements (TEs) in RNA-seq data, we used REdiscoverTE (v1.0.1) which annotates the genes defined in Gencode and all RepeatMasker sequences in the human genome down to the TE sub-family level after the repetitive element expression quantification by salmon. TE count matrix was appended to gene expression data matrix for differential expression analysis using DESeq2 and the TE showing significant differential expression is defined by the adjusted p-value less than 0.05 and a log2 value of fold-change greater than 1 in the experimental versus control group (with a basemean value greater than 10).  Since REdiscoverTE is specific to human, we then used SalmonTE to calculate the TE abundance in the mouse samples. By performing a read mapping against the TE sequences, salmonTE reassigns multi-mapping reads using the expectation-maximization algorithm before determining the read count of each sequence. From the counts table the differentially expressed TEs were identified and the statistical analysis function of salmonTE generated the summary of each class and clade through the generalized linear model.
Assembly: human cells were mapped to hg38 and mouse cells to mm10
Supplementary files format and content: normalized abundance measurements

source_name: MEF

growth_protocol: HEK293 cells were maintained in DMEM base medium supplemented with 10% of FBS and 1% of antibiotics (penicillin and streptomycin). MEF cells were derived from embryo of mice that carried either wildtype (WT) TNRC18 or homozygous H3K9me3-binding-defective mutations (MUT) at TNRC18’s BAH domain and maintained in DMEM supplemented with 20% of FBS and 1% of antibiotics.

extract_protocol: For RNA-seq, total RNA was extracted using the RNeasy Mini Kit (Qiagen #74106); in brief, RNA was first subjected for the on-column digestion by DNase (Qiagen #79254) for 0.5 hours and then prepared by using the NEBNext rRNA Depletion Kit (NEB #E6310L).

treatment_protocol: HEK293 cells were stably expressed with either scramble shRNA (shCtl) or TNRC18-targeting shRNA (shTNRC18), or were ones with the rescued re-expression of TNRC18 (shTNRC18-resistant) in cells with KD of endogenous TNRC18; in a separate experiment, CRISPR-cas9-based editing of TNRC18’s BAH domain was conducted in HEK293 cells.

tag: cell line

value: MEF

tag: cell type

value: Mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: MEF cells generated from wild type mice


title: AP2168.M0.NSB

value: Nasopharyngeal swab

tag: subject id

tag: batch

value: Positive

tag: covid cat

tag: research pcr

tag: vl copies

value: No


title: MEF_TNRC18_WT_1


title: WL1C9

description: infected with Ad-GFP

tag: mouse strain

tag: tissue

value: liver


title: MEF_TNRC18_KI_BAH_MUT_2

value: Tnrc18 BAH mutant, W2745A/Y2747A

value: MEF cells generated from Tnrc18 W2745A/Y2747A mice


title: AO5787.M0.NSB

tag: sample timing

tag: age

value: Male

tag: hospitalized

tag: timing sx


title: mpkDCT-siHNF1B3, RNA-seq

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description:
external-LT-027-mpkDCT-siHNF1B3-18650
processed data file: mm10_counts_gene_id_Hnf1bKD.xlsx

data_processing:
RNA-sequencing data was analyzed using the seq2science pipeline (https://vanheeringen-lab.github.io/seq2science/content/workflows/rna_seq.html). Briefly, reads were aligned with to the pre-indexed mm10 transcript assembly from UCSC. Samtools was used to filter reads with a quality score lower than 20, and PCR duplicates were removed. Reads per gene were counted with the htseq-count script from the Hisat2 software suite using the GTF file corresponding to the transcript assembly. Read counts were analyzed with DESeq2 to identify significant dynamics.
Base calling was performed with CASAVA version 1.4 burrows-wheeler transformation, 0.710 -r789 , default Peak calling was executed with Macs2, q-value (False discovery rate, FDR) 0.001. BigWig files were generated using a custom bam to bigwig script.
Genome_build: RNA-seq: mm10; ChIP-seq mm9
Supplementary_files_format_and_content: RNA-seq: read counts per transcript; ChIP-seq: Bigwig and Bed files

growth_protocol: Murine distal convoluted tubule cells (mpkDCT) clone 4a were grown in DMEM/F-12 containing 2% (v/v) fetal calf serum (FCS) (Biowest, Kansas City, MO, USA), 90 nm sodium selenate; 5 μg/ml transferrin; 2 mM glutamine; 50 nM dexamethasone; 1 nM triiodothyronine; 10 ng/ml epidermal growth factor; 5 μg/ml insulin; 20 mM d-glucose; and 20 mM HEPES, pH 7.4. Cells were grown at 37 °C in a humidity-controlled incubator with 5% (v/v) CO2.

extract_protocol:
RNA was isolated using the NucleoSpin RNA plus kit following the manufacturer’s protocol (Macherey Nagel, Dueren, Germany). ChIP: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Total RNA was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Wilmington, MA, USA). In short, oligo hybridization and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94 °C for 6 min. First strand synthesis, second strand synthesis and A-tailing were performed according to protocol. For the adaptor ligation, a 1.5 mM stock was used (NextFlex DNA barcodes, Bioo Scientific, Austin, Tx, USA). First and second post-ligation cleanup was performed according to protocol. A total of 11 PCR cycles were performed for library amplification. The library amplification cleanup was done using a 0.8 x followed by a 1.0 x bead-based cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer kit, and the library concentration was measured using the dsDNA High Sensitivity Assay (DeNovix, Wilmington, DE, USA). Paired-end sequencing reads of 50 bp were generated using an Illumina NextSeq 500. ChIP-sequencing: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: MpkDCT4a cells were seeded in a 12 well plate and transiently transfected with 100 pmol of a SMARTpool of siRNAs targeting Hnf1b (Dharmacon, Lafayette, CO, USA), or non-targeting siRNAs using 3 μL RNAiMAX transfection reagent (ThermoFisher Scientific). 48 hours after transfection cells were harvested for RNA isolation using the NucleoSpin RNA plus kit following the manufacturer’s protocol (Macherey Nagel, Dueren, Germany). For ChIP-seq mpkDCT4a cells were untreated.

value: HNF1B depletion

tag: icu admission


title: WL1C3

description: infected with Ad-GFP


title: MEF_TNRC18_KI_BAH_MUT_1


title: LAS256A277

tag: sample type

tag: Stage

tag: strain


title: mpkDCT-siHNF1B2, RNA-seq

description:
external-LT-027-mpkDCT-siHNF1B2-18651
processed data file: mm10_counts_gene_id_Hnf1bKD.xlsx

tag: cell type

value: Murine distal convoluted tubule cells (mpkDCT)

tag: cell line

tag: genotype


title: AJ2232.M0.NSB

tag: subject id

tag: batch

tag: Sex

tag: covid

tag: year

tag: vaccine doses

tag: timing dx


title: LAS256A304


title: WL1C2

description: infected with Ad-GFP

tag: mouse strain

tag: tissue


title: LAS256A211


title: mpkDCT-siHNF1B1, RNA-seq

description:
external-LT-027-mpkDCT-siHNF1B1-18652
processed data file: mm10_counts_gene_id_Hnf1bKD.xlsx

tag: treatment


title: LAS256A240


title: WL1C1

description: infected with Ad-GFP


title: LAS256A157


title: mpkDCT-siMock3, RNA-seq

description:
external-LT-027-mpkDCT-siMock3-18653
processed data file: mm10_counts_gene_id_Hnf1bKD.xlsx

value: siMock

value: control

tag: icu admission


title: WL1B9

description: infected with Ad-GFP


title: AC9270.M0.NSB

tag: sample timing

value: acute

tag: age

value: Female

value: Negative

tag: covid cat

tag: research pcr

tag: vl copies

tag: hospitalized

tag: timing sx


title: LAS256A79

tag: sample type

tag: Stage

tag: strain


title: mpkDCT-siMock2, RNA-seq

description:
external-LT-027-mpkDCT-siMock2-18654
processed data file: mm10_counts_gene_id_Hnf1bKD.xlsx

tag: cell type

tag: cell line

tag: genotype


title: LAS256A245


title: WL1B8

description: infected with Ad-GFP

tag: mouse strain


title: YF5006.M0.NSB

source_name: Nasal swab

tag: tissue

value: Nasal swab

tag: subject id

tag: batch

tag: Sex

tag: covid

value: Not Tested

tag: year

tag: vaccine doses

tag: timing dx


title: mpkDCT-siMock1, RNA-seq

description:
external-LT-027-mpkDCT-siMock1-18655
processed data file: mm10_counts_gene_id_Hnf1bKD.xlsx

tag: treatment

tag: icu admission


title: XT5859.M0.NSB

tag: sample timing

tag: age

tag: covid cat

tag: research pcr

tag: vl copies

tag: hospitalized

tag: timing sx


title: WL1B6

description: infected with Ad-GFP

tag: mouse strain

tag: genotype

tag: tissue


title: Fkbp5 KO mice liver with Etoh diet plus binge-4

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

description:
IU31
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

data_processing:
Reads were mapped using the Tophat software package.
The transcripts were assembled using the Cufflinks software package and differential gene expression (DGE) levels were determined using Cuffdiff software.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx: Excel file includes FPKM values for each Sample.

source_name: Liver

extract_protocol:
RNA was isolated from snap-frozen liver tissue of wild-type and Fkbp5-/- mice (n=4) fed on ethanol and pair-fed diet using Total RNA isolation kit from Agilent (Cat# 5185, Santa Clara, CA). The RNA-sequencing services were performed by DNA Link (San Diego, CA) using Illumina NextSeq 500.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Fkbp5 KO

value: Liver

value: EtOH diet plus binge


title: WB1507.M0.NSB

tag: subject id

tag: batch

tag: Sex

tag: covid

value: Positive

value: No


title: WL1B5

description: infected with Ad-GFP

value: liver


title: LAS256A1249

tag: sample type

tag: Stage


title: RI3275.M0.NSB

tag: sample timing

tag: year

tag: vaccine doses

tag: timing dx


title: Fkbp5 KO mice liver with Etoh diet plus binge-2

description:
IU26
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: treatment


title: Fkbp5 KO mice liver with Etoh diet plus binge-3

description:
IU28
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx


title: WL1B4

description: infected with Ad-GFP


title: LAS256A1247


title: LAS256A1236


title: QQ4295.M0.NSB

tag: age

tag: covid cat

tag: research pcr

tag: vl copies

tag: hospitalized


title: PJ5876.M0.NSB

tag: tissue

tag: timing sx


title: Fkbp5 KO mice liver with Etoh diet plus binge-1

description:
IU25
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: strain

tag: genotype


title: Fkbp5 KO mice liver with control diet-3

description:
IU21
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

value: Control diet


title: WL1B3

description: infected with Ad-GFP

tag: mouse strain


title: WL1B2

description: infected with Ad-GFP


title: LAS256A1227

tag: sample type


title: OH5644.M0.NSB

tag: subject id

tag: batch

tag: Sex

tag: covid


title: IG7453.M0.NSB

tag: sample timing

tag: year

tag: vaccine doses

tag: timing dx


title: LAS256A1218

tag: Stage


title: Fkbp5 KO mice liver with control diet-2

description:
IU20
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: treatment


title: Fkbp5 KO mice liver with control diet-1

description:
IU17
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx


title: WL1B7

description: infected with Ad-GFP


title: LAS256A254


title: WL1A9

description: infected with Ad-GFP


title: AH5367.M0.NSB

value: Nasopharyngeal swab

tag: age

tag: covid cat

tag: research pcr

tag: vl copies

tag: hospitalized


title: LAS256A212

tag: strain


title: LAS256A1216

tag: sample type


title: FZ5226.M0.NSB

tag: tissue

tag: subject id

value: Male

tag: timing sx


title: WT mice liver with Etoh diet plus binge-4

description:
IU15
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: genotype


title: FX0877.M0.NSB

tag: batch

tag: sample timing

tag: Sex

tag: covid


title: WT mice liver with Etoh diet plus binge-3

description:
IU14
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

value: Wild type


title: WL1A7

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A1209

tag: Stage


title: WT mice liver with Etoh diet plus binge-2

description:
IU11
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: treatment


title: ET5122.M0.NSB

tag: age

tag: covid cat

tag: year

tag: vaccine doses

tag: timing dx


title: WL1A6

description: infected with Ad-GFP


title: LAS256A1205

tag: sample type

tag: strain


title: LAS256A1202


title: WT mice liver with Etoh diet plus binge-1

description:
IU8
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: tissue


title: WL1A5

description: infected with Ad-GFP


title: LAS256A1198


title: BR8508.M0.NSB

tag: subject id

tag: research pcr

tag: vl copies

tag: hospitalized

tag: timing sx


title: COVIRS_34_V2B_Monocytes_ATACSeq

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: ATAC Seq on human classical monocytes from participant COVIRS_34 post-vaccination

library_source: genomic

data_processing:
Reads were aligned to the hg38 human genome using Bowtie2.
Peaks were called using Genrich v0.6.
Counts per peak were generated using FeatureCounts v1.53p.
Assembly: hg38
Supplementary files format and content: FeatureCounts output; Tab-delimited text files with raw peak counts for every peak for each sample.

molecule: genomic DNA

source_name: Monocytes

extract_protocol:
Cryopreserved PBMC were thawed and stained and classical monocytes (CD3-CD19-CD56-CD14+CD16-; 50,000 per sample) were sorted via flow cytometry. Transposed DNA samples were purified using DNA Clean and Concentrator 5 columns (Zymo Research).
Libraries were prepared from transposed DNA with custom primers and subjected to double-sided cleanup with SPRI beads to enrich for fragments in the 200-700bp range. Samples were sequenced on an illumina NovaSeq using paired end (2x150pb) sequencing.

tag: cell type

value: Monocytes

tag: batch

tag: vaccine

tag: timepoint

tag: participant id


title: WL1A4

description: infected with Ad-GFP

tag: mouse strain

tag: genotype


title: WL1A3

description: infected with Ad-GFP


title: WT mice liver with control diet-3

description:
IU5
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: treatment


title: WT mice liver with control diet-2

description:
IU3
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx


title: WL1B1

description: infected with Ad-GFP


title: EE8681.M0.NSB

tag: sample timing

tag: age

tag: Sex

tag: covid

tag: covid cat

tag: year

tag: vaccine doses

tag: timing dx


title: WT mice liver with control diet-1

description:
IU2
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: strain

tag: tissue


title: WL1A2

description: infected with Ad-GFP


title: LAS256A1201

tag: sample type

tag: Stage


title: DU0506.M0.NSB

tag: subject id

tag: batch

tag: research pcr

tag: vl copies

tag: hospitalized

tag: timing sx


title: LAS256A1187


title: WT mice liver with control diet-4

description:
IU7
Fkbp5-KO-Etoh-RNA-seq-FPKM-raw.xlsx

tag: genotype

tag: treatment


title: LAS256A1188


title: COVIRS_34_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_34 pre-vaccination

tag: cell type

tag: vaccine

tag: timepoint

tag: participant id


title: LAS256A1183


title: WL1A10

description: infected with Ad-GFP

tag: mouse strain


title: LAS256A1182

tag: strain


title: WL1A1

description: infected with Ad-GFP

tag: tissue


title: WL1A8

description: infected with Ad-GFP


title: COVIRS_41_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_41 post-vaccination


title: Mus_musculus spleen by HieffNGS kit repeat4

city: wuhan

first: zaiqiao

last: sun

institute: wuhan university

data_processing:
Raw reads from sequencing were firstly subjected to Trimmomatic (v0.39) for quality control and adaptor trimming
reads were mapped to genome using STAR (v2.7.10a)
gene counts was statisticed with featurecount
Genes with FPKM >0.5 were considered to be expressed
Assembly: Homo_sapiens.GRCh38, Mus_musculus.GRCm39, Mycobacterium_smegmatis.NZ_CP054795.1
Supplementary files format and content: tab-delimited text file includes raw counts for each
Supplementary files format and content: Sampletab-delimited text files include FPKM values for each Sample mRNA Fragmentation and cDNA synthesis.

source_name: spleen

growth_protocol: HEK293T cells and Hepa1-6 cells were maintained in DMEM medium (Gibco, Cat #11965092) + 10% FBS (Gibco, Cat#16000044) and 1% penicillin/streptomycin (Gibco, Cat#15140122) at 37°C with 5%CO2, Mycobacterium smegmatis was maintained in Middlebrook 7H9 broth base medium

extract_protocol:
Total RNA was extracted from mouse tissue with TRIzol, Total RNA from Cell line or bacterium was extracted by MolPure® Cell/Tissue Total RNA Kit
RNA libraries for RNA-seq were prepared using DADCSeq, HieffNGS kit and SHERRY following manufacturer's protocols

treatment_protocol: No special treatment

value: spleen

tag: cell line

value: BALB/c

value: WT

value: Mus_musculus spleen by HieffNGS kit


title: LAS256A1181

tag: sample type

tag: Stage


title: Day9, IL-1b, Exp4

city: Stockholm

first: Kaisa

last: Hofwimmer

address: Blickagången 16

country: Sweden

institute: Karolinska Institutet

description:
Day9_IL-1b_Exp4
raw_counts.txt
normalized_counts.txt

data_processing:
BCL conversion and demultiplexing of raw data was performed using bcl2fastq (v2.20.0)
Read quality was assessed using FastQC (v0.11.8)
Reads were aligned to the Ensembl GRCh38 reference genome using STAR (v2.6.1d)
Counts for each gene were obtained using featureCounts (v1.5.1)
Bioconductor package DESEq2 (v1.22.2) was used for normalization
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for ech sample

source_name: White adipose tissue

growth_protocol: Human adipose-derived stem cells were expanded in proliferation media, consisting of low-glucose DMEM (#31885-023, Gibco) supplemented with 10% fetal bovine serum (FBS), 0.01 M HEPES buffer, 50 U/ml Penicillin, 50 ug/ml Streptomycin, and 2.5 ng/ml fibroblast growth factor 2 (FGF2).

extract_protocol:
RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel)
Libraries were constructed using the Illumina TruSeq Stranded mRNA sample preparation protocol, with 200 ng total RNA.

treatment_protocol: When proliferating cells reached confluence, FGF2 was removed from the proliferation media. The day after, cells were seeded to plates at a density of 65 000 cells/cm2 in proliferation media –FGF2. The following day (day 0), cells were washed twice with PBS and adipogenesis was induced by adding differentiation media, consisting of the proliferation media –FGF2/–FBS and Ham's F-12 Nutrient mix (#21765-029, Gibco) in equal volumes, along with the following adipogenic stimulators: 860 nM insulin, 10 ug/ml transferrin, 0.2 nM triiodothyronine, 10 uM rosiglitazone, 100 uM 3-isobutyl-1-methylxanthine (IBMX), and 1 uM dexamethasone. Media was changed on day 2, 5, and 7 of differentiation. Differentiation media –IBMX/–dexamethasone was used from day 5. Human recombinant IL-1b (10 ng/ml, #I9401, Sigma-Aldrich) or vehicle (water, 1:1000) was added to the differentiation media prior to all media changes starting from day 0.

value: White adipose tissue

value: Mesenchymal stem cells

value: Adipogenic differentiation, IL-1b

tag: time

value: Day 9


title: Day9, IL-1b, Exp3

description:
Day9_IL-1b_Exp3
raw_counts.txt
normalized_counts.txt


title: COVIRS_12_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_12 post-vaccination

tag: batch


title: COVIRS_22_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_22 pre-vaccination


title: Day9, IL-1b, Exp1

description:
Day9_IL-1b_Exp1
raw_counts.txt
normalized_counts.txt


title: LAS256A1164


title: Mus_musculus spleen by HieffNGS kit repeat3


title: Mus_musculus spleen by HieffNGS kit repeat1


title: COVIRS_12_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_12 pre-vaccination


title: LAS256A1157


title: LAS256A1180


title: Day9, IL-1b, Exp2

description:
Day9_IL-1b_Exp2
raw_counts.txt
normalized_counts.txt


title: Day9, Veh, Exp4

description:
Day9_Veh_Exp4
raw_counts.txt
normalized_counts.txt

value: Adipogenic differentiation, vehicle


title: Mus_musculus spleen by DADCSeq(dsDNase) repeat1

value: Mus_musculus spleen by DADCSeq(dsDNase)


title: LAS256A1178


title: Mus_musculus spleen by DADCSeq(dsDNase) repeat3

value: No


title: COVIRS_9_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_9 pre-vaccination


title: Mus_musculus spleen by DADCSeq(dsDNase) repeat2


title: COVIRS_33_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_33 post-vaccination


title: Mus_musculus spleen by DADCSeq(dsDNase) repeat4


title: Day5, IL-1b, Exp4

description:
Day5_IL-1b_Exp4
raw_counts.txt
normalized_counts.txt

value: Day 5


title: Day9, Veh, Exp2

description:
Day9_Veh_Exp2
raw_counts.txt
normalized_counts.txt


title: COVIRS_33_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_33 pre-vaccination


title: Day9, Veh, Exp1

description:
Day9_Veh_Exp1
raw_counts.txt
normalized_counts.txt


title: Day9, Veh, Exp3

description:
Day9_Veh_Exp3
raw_counts.txt
normalized_counts.txt


title: COVIRS_41_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_41 pre-vaccination


title: Day5, IL-1b, Exp3

description:
Day5_IL-1b_Exp3
raw_counts.txt
normalized_counts.txt


title: Dermal fibroblast, Control, rep4

city: Pathum Wan

first: Thanawat

last: Chaisirirat

state: Bangkok

address: Rama IV Rd

department: Faculty of Medicine,

country: Thailand

institute: Chulalongkorn University

data_processing:
Quality of raw reads in FASTQ files were inspected with the FASTQC program.
The Trim Galore program was used to cut adaptors and sequence reads with a Phred score lower than 30. To estimate abundance of transcript.
Trimmed reads were analyzed with Salmon v1.9.0 in mapping-based mode with defualt parameters.
Transcript abundances in estimated read counts were imported to R with tximeta v1.12.4 and aggregated to gene-level expression with gene model annotation (GRCh38) for further analysis.
Normalized counts with respect to library sizes were processed in DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include normalized count with DESeq2 for each sample

source_name: Neonatal foreskin tissue

growth_protocol: Dermal fibroblasts were cultured in medium containing DMEM supplemented with 10% FBS and gentamicin (1mL/L). The cells were incubated in a 5% CO2 incubator at 37ºC

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Next generation sequencing library preparations were constructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® in according to the manufacturer’s protocol

treatment_protocol: Dermal fibroblasts were seeded into a 6-well plate (2.5x10^5 cells/well) in DMEM containing 1% FBS overnight. The cells were treated with HNP1 (10 µM) for 24 h.

value: Neonatal foreskin tissue

value: Donor-derived

value: Dermal fibroblast

value: Control


title: COVIRS_7_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_7 post-vaccination

value: Monocytes


title: Mus_musculus spleen by DADCSeq(dT) repeat4

value: spleen

value: Mus_musculus spleen by DADCSeq(dT)


title: Mus_musculus spleen by HieffNGS kit repeat2

value: BALB/c

value: WT


title: Dermal fibroblast, Control, rep3


title: COVIRS_9_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_9 post-vaccination


title: Day5, IL-1b, Exp2

description:
Day5_IL-1b_Exp2
raw_counts.txt
normalized_counts.txt

value: White adipose tissue


title: COVIRS_7_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_7 pre-vaccination


title: COVIRS_10_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_10 post-vaccination


title: Mus_musculus spleen by DADCSeq(dT) repeat3


title: Day5, IL-1b, Exp1

description:
Day5_IL-1b_Exp1
raw_counts.txt
normalized_counts.txt

value: Mesenchymal stem cells


title: COVIRS_10_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_10 pre-vaccination


title: Day5, Veh, Exp4

description:
Day5_Veh_Exp4
raw_counts.txt
normalized_counts.txt


title: Dermal fibroblast, HNP1 treated, rep4


title: Mus_musculus spleen by DADCSeq(dT) repeat2


title: Day5, Veh, Exp3

description:
Day5_Veh_Exp3
raw_counts.txt
normalized_counts.txt


title: Dermal fibroblast, HNP1 treated, rep3


title: Mus_musculus spleen by DADCSeq(SH) repeat4

value: Mus_musculus spleen by DADCSeq(SH)


title: Dermal fibroblast, Control, rep1


title: Mus_musculus spleen by DADCSeq(SH) repeat3


title: Mus_musculus spleen by DADCSeq(dT) repeat1


title: COVIRS_11_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_11 post-vaccination


title: Mus_musculus spleen by DADCSeq(SH) repeat2


title: Day5, Veh, Exp2

description:
Day5_Veh_Exp2
raw_counts.txt
normalized_counts.txt


title: Day5, Veh, Exp1

description:
Day5_Veh_Exp1
raw_counts.txt
normalized_counts.txt


title: Dermal fibroblast, HNP1 treated, rep2


title: Dermal fibroblast, HNP1 treated, rep1


title: COVIRS_11_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_11 pre-vaccination


title: Day2, IL-1b, Exp4

description:
Day2_IL-1b_Exp4
raw_counts.txt
normalized_counts.txt

value: Adipogenic differentiation, IL-1b

value: Day 2


title: Mus_musculus spleen by DADCSeq(SH) repeat1


title: Dermal fibroblast, Control, rep2


title: DTHTPCRep3 [input]

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

description: Robert Nobel Foundation

data_processing:
The libraries were sequenced on Illumina HiSeq 2500 platform with 101 bp paired-end reads.
Read quality was assessed using FastQC (v 0.11.2) for all samples and quality trimming was done using cutadapt (v 1.13)
Histone modification peaks were detected using SICER (v 1.1)
Genome_build: The quality trimmed reads were mapped against the bowtie2-indexed Panicum virgatum reference genome (v4.1) using bowtie2 (v 2.3.1)
Supplementary_files_format_and_content: BigWig files were generated using deeptools

organism: Panicum virgatum

source_name: leaf tissue

growth_protocol: The ramets of lowland ecotype Alamo, AP13 genotype of switcghrass were transplanted in 3GP nursery pots and later transferred to the green house for optimum conditions at the Samuel Roberts Noble Foundation in Ardmore, Oklahoma.

extract_protocol:
ChIP-DNA was extracted from Proteinase-K digested samples by phenol-chloroform extraction and ethanol precipitation using glycogen.
100 ng of purified DNA was used to generate the ChIP-Seq library using Illumina HiSeq using manusfacturer instructions

treatment_protocol: The control and drought treated plants were arranged in one growth chamber and palnts with drought and heat treatment in a separate chamber

tag: developmental stage

value: leaf

value: Input


title: Day2, IL-1b, Exp3

description:
Day2_IL-1b_Exp3
raw_counts.txt
normalized_counts.txt


title: DTHTPCRep2 [input]

description: Robert Nobel Foundation


title: hapa1-6 cell WT  by DADCSeq repeat3

source_name: liver

value: liver

value: live cancel

value: hapa1-6 cell WT  by DADCSeq


title: DTHTPCRep1 [input]

description: Robert Nobel Foundation


title: COVIRS_5_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_5 pre-vaccination


title: Day2, IL-1b, Exp2

description:
Day2_IL-1b_Exp2
raw_counts.txt
normalized_counts.txt


title: COVIRS_39_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_39 pre-vaccination


title: Day2, IL-1b, Exp1

description:
Day2_IL-1b_Exp1
raw_counts.txt
normalized_counts.txt


title: hapa1-6 cell WT  by DADCSeq repeat1


title: COVIRS_3_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_3 post-vaccination


title: hapa1-6 cell WT  by DADCSeq repeat2


title: hapa1-6 cell Raf_knockdown by DADCSeq repeat3

value: hapa1-6 cell Raf_knockdown by DADCSeq


title: Day2, Veh, Exp4

description:
Day2_Veh_Exp4
raw_counts.txt
normalized_counts.txt

value: Adipogenic differentiation, vehicle


title: COVIRS_39_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_39 post-vaccination

value: Monocytes


title: COVIRS_3_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_3 pre-vaccination


title: Day2, Veh, Exp3

description:
Day2_Veh_Exp3
raw_counts.txt
normalized_counts.txt


title: COVIRS_21_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_21 pre-vaccination


title: COVIRS_21_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_21 post-vaccination


title: DTPCRep1 [input]

description: Robert Nobel Foundation


title: DTPCRep2 [input]

description: Robert Nobel Foundation


title: Day2, Veh, Exp2

description:
Day2_Veh_Exp2
raw_counts.txt
normalized_counts.txt


title: CPCRep3 [input]

description: Robert Nobel Foundation


title: hapa1-6 cell Raf_knockdown by DADCSeq repeat1


title: COVIRS_40_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_40 post-vaccination


title: COVIRS_5_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_5 post-vaccination


title: DTPCRep3 [input]

description: Robert Nobel Foundation


title: CPCRep2 [input]

description: Robert Nobel Foundation


title: hapa1-6 cell Raf_knockdown by DADCSeq repeat2


title: COVIRS_40_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_40 pre-vaccination


title: hapa1-6 cell WT  by HieffNGS kit repeat3

value: hapa1-6 cell WT  by HieffNGS kit


title: CPCRep1 [input]

description: Robert Nobel Foundation


title: COVIRS_20_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_20 post-vaccination


title: hapa1-6 cell WT  by HieffNGS kit repeat2


title: COVIRS_20_V0_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_20 pre-vaccination


title: DTHT96hRep2 [ChIP-seq]

description: Robert Nobel Foundation

value: drought and heat


title: DTHT96hRep3 [ChIP-seq]

description: Robert Nobel Foundation


title: COVIRS_14_V2B_Monocytes_ATACSeq

description: ATAC Seq on human classical monocytes from participant COVIRS_14 post-vaccination