title: GCN2 mutant YAA rep 3

description:
processed files column: GCN2_YAA.Rep_3
GCN2_AA 15

value: YAA control food for 3 days


title: GCN2 mutant YAA-M rep 2

status: Public on Jun 03 2022

type: SRA

city: Cologne

first: Dennis

middle: Said

last: Gadalla

state: NRW

address: Joseph-Stelzmann-Straße 26

department: Systems Biology

country: Germany

institute: CECAD Research Center

description:
processed files column: GCN2_YAAM.Rep_2
GCN2_AA 17

library_source: transcriptomic

data_processing:
Raw reads were mapped to BDGP6.32 ENSEMBL build 103 using kallisto (v0.46.2). Genes counts were quantified in the same step.
Differential gene expression was calculated using DESeq2 (v1.24.0) in R (v3.6.3).
All steps were automated by utilizing the FLASKI RNA-Seq analysis pipeline (v fb00137)
Assembly: BDGP6.32 of ENSEMBL build 103
Supplementary files format and content: DESeq2 normalized abundances, RPKM, differential expression results of all samples: comma separated file
Supplementary files format and content: DESeq2 differential expression results files for treatment vs control: comma separated files

molecule: total RNA

organism: Drosophila melanogaster

source_name: Head and thorax

growth_protocol: Flies were maintained in culture bottles at 25 °C on a 12:12 h light:dark cycle at constant humidity (65%) on indicated diets.

extract_protocol:
Total RNA was extracted from head and thorax of 25 frozen flies using standard Trizol-Chloroform based protocol (Invitrogen). DNase treatment was done with RNase free DNase kit (Qiagen). 2 μg RNA in a total of 20 μl was sent for sequencing.
Libraries for sequencing were generated using the polyA purification method.

treatment_protocol: Once mated female flies per genotype were kept for 3 days on the Yaa, -R, -M, and -All diets and were then snap-frozen in liquid nitrogen.

tag: tissue

value: Head and thorax

tag: genotype

value: GCN2 null

tag: treatment

value: M-deprived food for 3 days

tag: Sex

value: female


title: GCN2 mutant YAA rep 1

description:
processed files column: GCN2_YAA.Rep_1
GCN2_AA 13


title: ControlIGG_Rep1

city: New York

first: Emiliano

last: Hergenreder

state: NY

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Sequenced reads were trimmed for adaptor and low-quality sequence, then mapped to Hg38  genome assembly using Bowtie2 default parameters
BAM files were filtered for unmapped and upaired reads
Peaks were called using MACS: lower mfold (5), upper mfold (50), band width (180), minimum FDR (0.05). Broad peaks were called for H3K79me2 with broad region cutoff (0.1)
Genome_build: Hg38
Supplementary_files_format_and_content: Peak text files (csv)

molecule: genomic DNA

organism: Homo sapiens

source_name: hESC-derived cortical neurons

growth_protocol: hESC-derived cortical neurons were plated at a density of 150,000/cm2 on poly-L-ornithine and laminin-coated 6-well plates, and maintained in Neurobasal medium supplemented with B27 and GlutaMAX

extract_protocol:
Standard CUT&RUN protocol, 100,000 cells were used per antibody, all antibodies used at 1 to 100 dilution, phenol chloroform extraction
Samples were sent to MSKCC Integrated Genome Operations (IGO). Libraries were prepared using standard Illumina protocols

tag: cell line

tag: cell type

value: hESC-derived cortical neurons

tag: antibody

value: Mouse IGG (ab46540)


title: GCN2 mutant YAA-R rep 2

description:
processed files column: GCN2_YAAR.Rep_2
GCN2_AA 20

value: R-deprived food for 3 days


title: GCN2 mutant YAA-All rep 1

description:
processed files column: GCN2_YAAa.Rep_1
GCN2_AA 22

value: All-deprived food for 3 days


title: wDah control YAA-R rep 3

description:
processed files column: wDah_YAAR.Rep_3
GCN2_AA 9

value: wDah


title: GCN2 mutant YAA-R rep 3

description:
processed files column: GCN2_YAAR.Rep_3
GCN2_AA 21


title: GCN2 mutant YAA rep 2

description:
processed files column: GCN2_YAA.Rep_2
GCN2_AA 14


title: GCN2 mutant YAA-M rep 1

description:
processed files column: GCN2_YAAM.Rep_1
GCN2_AA 16


title: wDah control YAA-All rep 2

description:
processed files column: wDah_YAAa.Rep_2
GCN2_AA 11


title: wDah control YAA-All rep 1

description:
processed files column: wDah_YAAa.Rep_1
GCN2_AA 10


title: wDah control YAA-All rep 3

description:
processed files column: wDah_YAAa.Rep_3
GCN2_AA 12


title: wDah control YAA-R rep 2

description:
processed files column: wDah_YAAR.Rep_2
GCN2_AA 8


title: wDah control YAA-R rep 1

description:
processed files column: wDah_YAAR.Rep_1
GCN2_AA 7


title: GFP-medium

city: Shanghai

first: Xiaojuan

last: Fan

address: 320 Yue Yang Road

country: China

institute: CAS-MPG Partner Institute of Computational Biology

description: sequencing libraries were generated by using RT-PCR

data_processing:
More than 20 million reads were obtained from cells with different levels of GFP fluorescence, generating 10-nt sequences from each cell fraction. The inserted 10-nt sequences were recovered when the flanking sequences have exact match to the minigene reporter (24-nt upstream sequences and 30-nt downstream sequences were used for comparison).
Each inserted 10-mer was extended into a 14-mer by appending 2-nt of the vector sequence at each end to allow for cases in which IRES activity derived from sequences overlapping the vector.  The resulting 14-nt sequences were broken into overlapping hexamers and the occurrences of different hexamers were counted from sequences recovered in cells with mid-high fluorescence vs. no fluorescence.
The enrichment score of each 6-mer between two datasets was calculated using Z-test
Genome_build: None
Supplementary_files_format_and_content: Matrix table with Z-score of all hexamers

source_name: HEK293T cell

growth_protocol: 293T human embryonic kidney cell line was cultured in DMEM (high glucose) medium containing 10% fetal bovine serum (FBS, Hyclone)

extract_protocol:
The RNAs were isolated with TRIzol reagent following the manufacturer’s instructions.
The Amplicon sequencing libraries were generated through RT-PCR using mutiplexed PCR primers (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCGGCATGGACGAGCTGTACAAG and CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCCGGTGGTGCAGATGAACTTCAG) NNNNNN is the sample barcode.

treatment_protocol: To transient transfect plasmids into cells, 2μg of mini-gene reporters were transfected into cells in 6 well plate, using lipofectamine 3000 (Invitrogen) according to the manufacturer’s instruction. After 48 h, cells were collected for further analysis of RNA and protein levels. Then cells were collected for FACS sorting using BD FACSAria II.

value: HEK293T cell

tag: group

value: GFP-medium


title: wDah control YAA rep 2

description:
processed files column: wDah_YAA.Rep_2
GCN2_AA 2


title: wDah control YAA-M rep 1

description:
processed files column: wDah_YAAM.Rep_1
GCN2_AA 4


title: wDah control YAA-M rep 2

description:
processed files column: wDah_YAAM.Rep_2
GCN2_AA 5


title: wDah control YAA rep 3

description:
processed files column: wDah_YAA.Rep_3
GCN2_AA 3


title: GCN2 mutant YAA-M rep 3

description:
processed files column: GCN2_YAAM.Rep_3
GCN2_AA 18


title: GCN2 mutant YAA-R rep 1

description:
processed files column: GCN2_YAAR.Rep_1
GCN2_AA 19


title: control [N03]

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health, School of Medicine

institute: Shanghai Jiaotong University

data_processing:
Raw ATAC-seq reads were mapped to hg38 reference genome  using Bowtie
Duplicates were removed with MarkDuplicates function from Picard Tools (version:2.26.11) with default parameters
Low quality reads with mapping quality (mapQ) lower than 30 were removed using samtools. Reads mapped to ChrX, Y and Random were filtered.
MACS2 (version: 2.2.7.1) was used for peak calling with parameters -nomodel -shift -100 -extsize 200.
HTseq-count(version: 1.99.2) was used for counting reads within each peak.
Assembly: hg38

source_name: cord blood

extract_protocol:
Cord blood (approximately 50-75ml) were collected from each donor during delivery. Lymphoprep (Serumwerk Bernburg cat.1858) was used to isolate mononuclear cells (MNCs) from the cord blood. Red blood cells were lysed using RBC lysing buffer (Biolegend cat. 420310). Cells were recovered from liquid nitrogen.
Approximately 10K cells were processed following the established ATAC-Seq protocol [Buenrostro et al. Nat. Methods 2013]

value: cord blood

tag: disease state

value: healthy


title: control [N01]


title: control [N04]


title: patient with superimposed preeclampsia [P02]

value: superimposed preeclampsia


title: EI046_3

city: Würzburg

first: Eslam

middle: S.

last: Ibrahim

address: Josef-Schneider-Straße 2, Bau D15

institute: Institut für Molekulare Infektionsbiologie (IMIB)

data_processing:
cleaning the adaptor sequence from nextseq sequencers using cutadapt
reademption.v.0.4.3 align function with the following parameters (-c -l 20 -q -S -g)
reademption.v.0.4.3 coverage function
reademption.v.0.4.3 gene_quanti function with the following parameters (-l -a -t CDS,tRNA,rRNA,tmRNA,SRP_RNA)
reademption.v.0.4.3 deseq function for DESeq normalization and calculations
Genome_build: NC_007793.1
Supplementary_files_format_and_content: wig files after DESeq2 normalization

organism: Staphylococcus aureus

source_name: bacteria

growth_protocol: 1:100 dilution of independent overnight cultures in RPMI until OD600=0.5

extract_protocol:
Rneasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols by the Core Unit Systems Medicine facility at the University Hospital Würzburg

tag: strain

value: JE2 delta_ofrA

value: Mutant


title: EI046_2


title: wDah control YAA-M rep 3

description:
processed files column: wDah_YAAM.Rep_3
GCN2_AA 6


title: EI046_1


title: Hospitalized_COVID-19 [COVID5304]

type: genomic

city: Abu Dhabi

first: Habiba

last: Alsafar

address: Al Saada St. Muroor Road

department: Center of Biotechnology

country: United Arab Emirates

institute: Khalifa University

hyb_protocol: Genotyping was performed using the Infinium Global Screening Array-24 v3.0 BeadChip (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s protocol, which contained 654,027 genetic markers and developed by Avera Institute for Huma Genetics (South Dakota, USA). The Infinium Global Screening Array-24 v3.0 BeadChip would be best suited for this ethnically diverse cohort because it features a broad spectrum of diverse exonic content, including both cross population and population specific markers (EUR: 52,980 markers; EAS: 31,375 markers; AMR: 45,977 markers; AFR: 43,122 markers; SAS: 40,298 markers).

scan_protocol: PLINK (version 1·9), R (version 3·4), SPSS (version 16·0), Haploview Software (version 4.2).

data_processing:
The matrix processed and matrix signal intensity files form Genome studio are uploaded.
The statistical analysis was conducted as a case-control panel, with controls characterized as non-hospitalized symptoms and cases characterized as hospitalized symptoms. Case-control association tests of the genotyped and imputed SNPs in the cohort were performed using PLINK (logistic regression). Two different analysis including covariates from the PCA without 1000 Genomes reference samples were run to control for potential population stratification (analysis I), as well as population stratification, age, and gender effects (analysis II).

source_name: Hospitalized for COVID-19

label_protocol: DNA was extracted using the automated MagPurix 12 system according to the manufacturer’s protocol. DNA was quantified using the DS-11 Series of Spectrophotometer/Fluorometer (DeNovix).

tag: gender

value: male

tag: age


title: JE2_2

value: WT


title: Hospitalized_COVID-19 [COVID5357]

extract_protocol: DNA was extracted using the automated MagPurix 12 system according to the manufacturer’s protocol. DNA was quantified using the DS-11 Series of Spectrophotometer/Fluorometer (DeNovix).


title: Hospitalized_COVID-19 [COVID5342]


title: JE2_3


title: Hospitalized_COVID-19 [COVID5356]


title: Hospitalized_COVID-19 [COVID5341]


title: JE2_1


title: Hospitalized_COVID-19 [COVID5300]


title: Hospitalized_COVID-19 [COVID5303]


title: Hospitalized_COVID-19 [COVID5298]


title: Hospitalized_COVID-19 [COVID5299]


title: Hospitalized_COVID-19 [COVID5302]


title: Hospitalized_COVID-19 [COVID5301]


title: Hospitalized_COVID-19 [COVID5296]


title: Hospitalized_COVID-19 [COVID5295]


title: Hospitalized_COVID-19 [COVID5293]


title: Hospitalized_COVID-19 [COVID5290]


title: wDah control YAA rep 1

description:
processed files column: wDah_YAA.Rep_1
GCN2_AA 1

value: Head and thorax

value: YAA control food for 3 days


title: Hospitalized_COVID-19 [COVID5288]


title: Hospitalized_COVID-19 [COVID5286]


title: Hospitalized_COVID-19 [COVID5289]

value: female


title: Hospitalized_COVID-19 [COVID5284]


title: Hospitalized_COVID-19 [COVID5283]


title: Hospitalized_COVID-19 [COVID5281]


title: Hospitalized_COVID-19 [COVID5297]


title: Hospitalized_COVID-19 [COVID5282]


title: Hospitalized_COVID-19 [COVID5258]


title: Hospitalized_COVID-19 [COVID5254]


title: Hospitalized_COVID-19 [COVID5294]


title: Hospitalized_COVID-19 [COVID5280]


title: Hospitalized_COVID-19 [COVID5256]


title: Hospitalized_COVID-19 [COVID5251]


title: Hospitalized_COVID-19 [COVID5248]


title: Hospitalized_COVID-19 [COVID5250]


title: Hospitalized_COVID-19 [COVID5246]


title: Hospitalized_COVID-19 [COVID5247]


title: Hospitalized_COVID-19 [COVID5252]


title: Hospitalized_COVID-19 [COVID5244]


title: Hospitalized_COVID-19 [COVID5243]


title: Hospitalized_COVID-19 [COVID5245]


title: Hospitalized_COVID-19 [COVID5287]


title: Hospitalized_COVID-19 [COVID5242]


title: Hospitalized_COVID-19 [COVID5241]


title: Hospitalized_COVID-19 [COVID5255]


title: Hospitalized_COVID-19 [COVID5209]


title: Hospitalized_COVID-19 [COVID5206]


title: Hospitalized_COVID-19 [COVID5207]


title: Hospitalized_COVID-19 [COVID5202]


title: Hospitalized_COVID-19 [COVID5210]


title: Hospitalized_COVID-19 [COVID5253]


title: Hospitalized_COVID-19 [COVID5249]


title: Hospitalized_COVID-19 [COVID5200]


title: Hospitalized_COVID-19 [COVID5208]


title: Hospitalized_COVID-19 [COVID5201]


title: Hospitalized_COVID-19 [COVID5199]


title: Hospitalized_COVID-19 [COVID5203]


title: Hospitalized_COVID-19 [COVID5198]


title: Hospitalized_COVID-19 [COVID5196]


title: Hospitalized_COVID-19 [COVID5193]


title: Hospitalized_COVID-19 [COVID5195]


title: Hospitalized_COVID-19 [COVID5194]


title: Hospitalized_COVID-19 [COVID5190]


title: Hospitalized_COVID-19 [COVID5186]


title: Hospitalized_COVID-19 [COVID5189]


title: Hospitalized_COVID-19 [COVID5197]


title: Hospitalized_COVID-19 [COVID5192]


title: Hospitalized_COVID-19 [COVID5187]


title: Hospitalized_COVID-19 [COVID5183]


title: Hospitalized_COVID-19 [COVID5188]


title: Hospitalized_COVID-19 [COVID5184]


title: Hospitalized_COVID-19 [COVID5204]


title: Hospitalized_COVID-19 [COVID5181]


title: Hospitalized_COVID-19 [COVID5180]


title: Hospitalized_COVID-19 [COVID5182]


title: Hospitalized_COVID-19 [COVID5179]


title: Hospitalized_COVID-19 [COVID5174]


title: Hospitalized_COVID-19 [COVID5175]


title: Hospitalized_COVID-19 [COVID5177]


title: Hospitalized_COVID-19 [COVID5150]


title: Hospitalized_COVID-19 [COVID5178]


title: Hospitalized_COVID-19 [COVID5176]


title: Hospitalized_COVID-19 [COVID5151]


title: Hospitalized_COVID-19 [COVID5147]


title: Hospitalized_COVID-19 [COVID5149]


title: Hospitalized_COVID-19 [COVID5148]


title: Hospitalized_COVID-19 [COVID5146]


title: Hospitalized_COVID-19 [COVID5043]


title: Hospitalized_COVID-19 [COVID5040]


title: Hospitalized_COVID-19 [COVID5042]


title: Hospitalized_COVID-19 [COVID5045]


title: Hospitalized_COVID-19 [COVID5041]


title: Hospitalized_COVID-19 [COVID4824]


title: Hospitalized_COVID-19 [COVID4821]


title: Hospitalized_COVID-19 [COVID4822]


title: Hospitalized_COVID-19 [COVID4823]


title: Hospitalized_COVID-19 [COVID4825]


title: Hospitalized_COVID-19 [COVID4519]


title: Hospitalized_COVID-19 [COVID4820]


title: Hospitalized_COVID-19 [COVID4469]


title: Hospitalized_COVID-19 [COVID4463]


title: Hospitalized_COVID-19 [COVID4468]


title: Hospitalized_COVID-19 [COVID4465]


title: Hospitalized_COVID-19 [COVID4464]


title: Hospitalized_COVID-19 [COVID5044]


title: Hospitalized_COVID-19 [COVID4466]


title: Hospitalized_COVID-19 [COVID4462]


title: Hospitalized_COVID-19 [COVID4467]


title: Hospitalized_COVID-19 [COVID4826]


title: Hospitalized_COVID-19 [COVID4453]


title: Hospitalized_COVID-19 [COVID4450]


title: Hospitalized_COVID-19 [COVID4458]


title: Hospitalized_COVID-19 [COVID4457]


title: Hospitalized_COVID-19 [COVID4451]


title: Hospitalized_COVID-19 [COVID4452]


title: Hospitalized_COVID-19 [COVID4454]


title: Hospitalized_COVID-19 [COVID4460]


title: Hospitalized_COVID-19 [COVID4459]


title: Hospitalized_COVID-19 [COVID4456]


title: Hospitalized_COVID-19 [COVID4455]


title: Hospitalized_COVID-19 [COVID4449]


title: Hospitalized_COVID-19 [COVID4446]


title: Hospitalized_COVID-19 [COVID4444]


title: Hospitalized_COVID-19 [COVID4445]


title: Hospitalized_COVID-19 [COVID4448]


title: Hospitalized_COVID-19 [COVID4433]


title: Hospitalized_COVID-19 [COVID4440]


title: Hospitalized_COVID-19 [COVID4434]


title: Hospitalized_COVID-19 [COVID4436]


title: Hospitalized_COVID-19 [COVID4441]


title: Hospitalized_COVID-19 [COVID4437]


title: Hospitalized_COVID-19 [COVID4435]


title: Hospitalized_COVID-19 [COVID4442]


title: Hospitalized_COVID-19 [COVID4439]


title: Hospitalized_COVID-19 [COVID4443]


title: Hospitalized_COVID-19 [COVID4438]


title: Hospitalized_COVID-19 [COVID4461]


title: Hospitalized_COVID-19 [COVID4427]


title: Non-Hospitalized_COVID-19 [COVID4428]

source_name: Not Hospitalized for COVID-19


title: Hospitalized_COVID-19 [COVID4431]


title: Hospitalized_COVID-19 [COVID4429]


title: Hospitalized_COVID-19 [COVID4447]


title: Hospitalized_COVID-19 [COVID4430]


title: Hospitalized_COVID-19 [COVID4426]


title: Hospitalized_COVID-19 [COVID4425]


title: Hospitalized_COVID-19 [COVID4424]


title: Hospitalized_COVID-19 [COVID4423]


title: Hospitalized_COVID-19 [COVID4422]


title: Hospitalized_COVID-19 [COVID4419]


title: Hospitalized_COVID-19 [COVID4420]


title: Hospitalized_COVID-19 [COVID4414]


title: Hospitalized_COVID-19 [COVID4416]


title: Hospitalized_COVID-19 [COVID4412]


title: Hospitalized_COVID-19 [COVID4413]


title: Hospitalized_COVID-19 [COVID4410]


title: Hospitalized_COVID-19 [COVID4411]


title: Hospitalized_COVID-19 [COVID4432]


title: Hospitalized_COVID-19 [COVID4415]


title: Hospitalized_COVID-19 [COVID4421]


title: Hospitalized_COVID-19 [COVID4417]


title: Hospitalized_COVID-19 [COVID4418]


title: Hospitalized_COVID-19 [COVID4408]


title: Hospitalized_COVID-19 [COVID4405]


title: Non-Hospitalized_COVID-19 [COV661]


title: Non-Hospitalized_COVID-19 [COV660]


title: Hospitalized_COVID-19 [COVID4407]


title: Hospitalized_COVID-19 [COVID4409]


title: Hospitalized_COVID-19 [COVID4403]


title: Non-Hospitalized_COVID-19 [COV658]


title: Hospitalized_COVID-19 [COVID4404]


title: Hospitalized_COVID-19 [COVID4406]


title: Hospitalized_COVID-19 [COVID4401]


title: Non-Hospitalized_COVID-19 [COV657]


title: Hospitalized_COVID-19 [COVID4402]


title: Hospitalized_COVID-19 [COV622]


title: Non-Hospitalized_COVID-19 [COV656]


title: Non-Hospitalized_COVID-19 [COV659]


title: Hospitalized_COVID-19 [COVID5285]


title: Hospitalized_COVID-19 [COV665]


title: Non-Hospitalized_COVID-19 [COV621]


title: Non-Hospitalized_COVID-19 [COV617]


title: Hospitalized_COVID-19 [COV618]


title: Non-Hospitalized_COVID-19 [COV664]


title: Hospitalized_COVID-19 [COV616]


title: Non-Hospitalized_COVID-19 [COV619]


title: Non-Hospitalized_COVID-19 [COV620]


title: Non-Hospitalized_COVID-19 [COV612]


title: Non-Hospitalized_COVID-19 [COV614]


title: Non-Hospitalized_COVID-19 [COV611]


title: Non-Hospitalized_COVID-19 [COV613]


title: Hospitalized_COVID-19 [COV615]


title: Non-Hospitalized_COVID-19 [COV609]


title: Hospitalized_COVID-19 [COV610]


title: Non-Hospitalized_COVID-19 [COV602]


title: Hospitalized_COVID-19 [COV599]


title: Hospitalized_COVID-19 [COV597]


title: Hospitalized_COVID-19 [COV592]


title: Hospitalized_COVID-19 [COV596]


title: Hospitalized_COVID-19 [COV586]


title: Hospitalized_COVID-19 [COV593]


title: Non-Hospitalized_COVID-19 [COV603]


title: Non-Hospitalized_COVID-19 [COV585]


title: Non-Hospitalized_COVID-19 [COV606]


title: Hospitalized_COVID-19 [COV605]


title: Hospitalized_COVID-19 [COV600]


title: Hospitalized_COVID-19 [COV591]


title: Hospitalized_COVID-19 [COV588]


title: Hospitalized_COVID-19 [COV580]


title: Hospitalized_COVID-19 [COV583]


title: Hospitalized_COVID-19 [COV584]


title: Hospitalized_COVID-19 [COV579]


title: Non-Hospitalized_COVID-19 [COV577]


title: Hospitalized_COVID-19 [COV578]


title: Hospitalized_COVID-19 [COV576]


title: Hospitalized_COVID-19 [COV575]


title: Hospitalized_COVID-19 [COV572]


title: Non-Hospitalized_COVID-19 [COV589]


title: Non-Hospitalized_COVID-19 [COV571]


title: Hospitalized_COVID-19 [COV573]


title: Hospitalized_COVID-19 [COV587]


title: Hospitalized_COVID-19 [COV569]


title: Hospitalized_COVID-19 [COV568]


title: Non-Hospitalized_COVID-19 [COV559]


title: Hospitalized_COVID-19 [COV582]


title: Non-Hospitalized_COVID-19 [COV557]


title: Non-Hospitalized_COVID-19 [COV560]


title: Hospitalized_COVID-19 [COV555]


title: Non-Hospitalized_COVID-19 [COV558]


title: Hospitalized_COVID-19 [COV561]


title: Hospitalized_COVID-19 [COV565]


title: Hospitalized_COVID-19 [COV562]


title: Hospitalized_COVID-19 [COV556]


title: Hospitalized_COVID-19 [COV567]


title: Hospitalized_COVID-19 [COV554]


title: Hospitalized_COVID-19 [COV548]


title: Non-Hospitalized_COVID-19 [COV549]


title: Hospitalized_COVID-19 [COV552]


title: Hospitalized_COVID-19 [COV547]


title: Non-Hospitalized_COVID-19 [COV546]


title: Hospitalized_COVID-19 [COV544]


title: Hospitalized_COVID-19 [COV551]


title: Hospitalized_COVID-19 [COV543]


title: Hospitalized_COVID-19 [COV545]


title: Non-Hospitalized_COVID-19 [COV539]


title: Non-Hospitalized_COVID-19 [COV541]


title: Hospitalized_COVID-19 [COV542]


title: Hospitalized_COVID-19 [COV540]


title: Hospitalized_COVID-19 [COV564]


title: Hospitalized_COVID-19 [COV553]


title: Non-Hospitalized_COVID-19 [COV537]


title: Hospitalized_COVID-19 [COV538]


title: Hospitalized_COVID-19 [COV550]


title: Non-Hospitalized_COVID-19 [COV535]


title: Non-Hospitalized_COVID-19 [COV536]


title: Non-Hospitalized_COVID-19 [COV534]


title: Hospitalized_COVID-19 [COV533]


title: Hospitalized_COVID-19 [COV528]


title: Hospitalized_COVID-19 [COV529]


title: Hospitalized_COVID-19 [COV532]


title: Hospitalized_COVID-19 [COV526]


title: Hospitalized_COVID-19 [COV527]


title: Hospitalized_COVID-19 [COV530]


title: Non-Hospitalized_COVID-19 [COV531]


title: Hospitalized_COVID-19 [COV525]


title: Non-Hospitalized_COVID-19 [COV499]


title: Hospitalized_COVID-19 [COV498]


title: Hospitalized_COVID-19 [COV517]


title: Non-Hospitalized_COVID-19 [COV497]


title: Non-Hospitalized_COVID-19 [COV506]


title: Non-Hospitalized_COVID-19 [COV514]


title: Non-Hospitalized_COVID-19 [COV516]


title: Non-Hospitalized_COVID-19 [COV505]


title: Non-Hospitalized_COVID-19 [COV495]


title: Non-Hospitalized_COVID-19 [COV500]


title: Non-Hospitalized_COVID-19 [COV507]


title: Non-Hospitalized_COVID-19 [COV524]


title: Non-Hospitalized_COVID-19 [COV510]


title: Hospitalized_COVID-19 [COV521]


title: Non-Hospitalized_COVID-19 [COV508]


title: Non-Hospitalized_COVID-19 [COV509]


title: Hospitalized_COVID-19 [COV520]


title: Hospitalized_COVID-19 [COV519]


title: Non-Hospitalized_COVID-19 [COV511]


title: Non-Hospitalized_COVID-19 [COV504]


title: Hospitalized_COVID-19 [COV518]


title: Non-Hospitalized_COVID-19 [COV494]


title: Non-Hospitalized_COVID-19 [COV502]


title: Non-Hospitalized_COVID-19 [COV501]


title: Hospitalized_COVID-19 [COV522]


title: Non-Hospitalized_COVID-19 [COV512]


title: Non-Hospitalized_COVID-19 [COV513]


title: Hospitalized_COVID-19 [COV493]


title: Hospitalized_COVID-19 [COV496]


title: Non-Hospitalized_COVID-19 [COV503]


title: Non-Hospitalized_COVID-19 [COV471]


title: Non-Hospitalized_COVID-19 [COV487]


title: Non-Hospitalized_COVID-19 [COV491]


title: Non-Hospitalized_COVID-19 [COV490]


title: Non-Hospitalized_COVID-19 [COV486]


title: Non-Hospitalized_COVID-19 [COV485]


title: Non-Hospitalized_COVID-19 [COV466]


title: Non-Hospitalized_COVID-19 [COV489]


title: Non-Hospitalized_COVID-19 [COV484]


title: Non-Hospitalized_COVID-19 [COV472]


title: Non-Hospitalized_COVID-19 [COV480]


title: Non-Hospitalized_COVID-19 [COV478]


title: Non-Hospitalized_COVID-19 [COV488]


title: Non-Hospitalized_COVID-19 [COV474]


title: Non-Hospitalized_COVID-19 [COV481]


title: Non-Hospitalized_COVID-19 [COV483]


title: Non-Hospitalized_COVID-19 [COV467]


title: Hospitalized_COVID-19 [COV479]


title: Non-Hospitalized_COVID-19 [COV482]


title: Hospitalized_COVID-19 [COV473]


title: Non-Hospitalized_COVID-19 [COV470]


title: Non-Hospitalized_COVID-19 [COV477]


title: Non-Hospitalized_COVID-19 [COV469]


title: Non-Hospitalized_COVID-19 [COV476]


title: Non-Hospitalized_COVID-19 [COV492]


title: Non-Hospitalized_COVID-19 [COV465]


title: Non-Hospitalized_COVID-19 [COV464]


title: Non-Hospitalized_COVID-19 [COV468]


title: Non-Hospitalized_COVID-19 [COV475]


title: Non-Hospitalized_COVID-19 [COV462]


title: Non-Hospitalized_COVID-19 [COV452]


title: Non-Hospitalized_COVID-19 [COV461]


title: Hospitalized_COVID-19 [COV451]


title: Non-Hospitalized_COVID-19 [COV458]


title: Non-Hospitalized_COVID-19 [COV453]


title: Non-Hospitalized_COVID-19 [COV459]


title: Hospitalized_COVID-19 [COV440]


title: Non-Hospitalized_COVID-19 [COV444]


title: Hospitalized_COVID-19 [COV442]


title: Hospitalized_COVID-19 [COV441]


title: Non-Hospitalized_COVID-19 [COV455]


title: Hospitalized_COVID-19 [COV439]


title: Non-Hospitalized_COVID-19 [COV456]


title: Hospitalized_COVID-19 [COV437]


title: Hospitalized_COVID-19 [COV438]


title: Hospitalized_COVID-19 [COV435]


title: Hospitalized_COVID-19 [COV446]


title: Hospitalized_COVID-19 [COV443]


title: Non-Hospitalized_COVID-19 [COV454]


title: Hospitalized_COVID-19 [COV445]


title: Non-Hospitalized_COVID-19 [COV457]


title: Hospitalized_COVID-19 [COV434]


title: Non-Hospitalized_COVID-19 [COV447]


title: Non-Hospitalized_COVID-19 [COV449]


title: Hospitalized_COVID-19 [COV433]


title: Non-Hospitalized_COVID-19 [COV463]


title: Non-Hospitalized_COVID-19 [COV448]


title: Non-Hospitalized_COVID-19 [COV460]


title: Non-Hospitalized_COVID-19 [COV450]


title: Hospitalized_COVID-19 [COV344]


title: Hospitalized_COVID-19 [COV348]


title: Hospitalized_COVID-19 [COV339]


title: Non-Hospitalized_COVID-19 [COV400]


title: Hospitalized_COVID-19 [COV397]


title: Hospitalized_COVID-19 [COV350]


title: Hospitalized_COVID-19 [COV349]


title: Hospitalized_COVID-19 [COV336]


title: Hospitalized_COVID-19 [COV345]


title: Hospitalized_COVID-19 [COV330]


title: Non-Hospitalized_COVID-19 [COV387]


title: Hospitalized_COVID-19 [COV335]


title: Hospitalized_COVID-19 [COV333]


title: Hospitalized_COVID-19 [COV331]


title: Hospitalized_COVID-19 [COV334]


title: Non-Hospitalized_COVID-19 [COV325]


title: Hospitalized_COVID-19 [COV329]


title: Hospitalized_COVID-19 [COV347]


title: Hospitalized_COVID-19 [COV328]


title: Hospitalized_COVID-19 [COV327]


title: Hospitalized_COVID-19 [COV338]


title: Non-Hospitalized_COVID-19 [COV324]


title: Hospitalized_COVID-19 [COV337]


title: ΔbapR, LCA, biological replicate 3

city: Boston

first: Aimee

last: Shen

state: MA

address: 136 Harrison Ave

institute: Tufts University

data_processing:
Geneious Prime 2022.1.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk (parameters- Kmer length: 27; maximum substitutions: 1; minimum quality: 30; minimum length: 30)
Trimmed sequence reads were mapped to the C. difficile 630 genome using Geneious mapper (parameters- sensitivity: medium-low)
Expression levels were calculated using DEseq2
Assembly: NC_009089
Supplementary files format and content: csv files include raw counts, raw transcript, RPKM, and TPM for each gene

organism: Clostridioides difficile

source_name: Bacterial

growth_protocol: Cultured swirling anaerobically in BHIS broth

extract_protocol:
Cells were lysed using Lysing Matrix B (MP Bio); DNA was removed in two treatments with DNase I (NEB) and using an RNeasy kit (Qiagen)
mRNA libraries were made using Illumina Stranded Total RNA with Ribo Zero Plus kit

treatment_protocol: 20 μM LCA or DMSO vehicle was added to log-phase cultures for 1 hour before harvesting RNA

value: Bacterial

value: deltabapR

value: 20 microM lithocholic acid

tag: time

value: 1 hour


title: Non-Hospitalized_COVID-19 [COV420]


title: Non-Hospitalized_COVID-19 [COV323]


title: Non-Hospitalized_COVID-19 [COV326]


title: Hospitalized_COVID-19 [COV343]


title: Hospitalized_COVID-19 [COV346]


title: Hospitalized_COVID-19 [COV332]


title: Non-Hospitalized_COVID-19 [COV322]


title: WT, LCA, biological replicate 3


title: Hospitalized_COVID-19 [COV321]


title: ΔbapR, LCA, biological replicate 1


title: ΔbapR, LCA, biological replicate 2


title: Non-Hospitalized_COVID-19 [COV320]


title: Non-Hospitalized_COVID-19 [COV318]


title: ΔbapR, DMSO, biological replicate 3

value: DMSO


title: Non-Hospitalized_COVID-19 [COV319]


title: WT, LCA, biological replicate 1


title: WT, LCA, biological replicate 2


title: ΔbapR, DMSO, biological replicate 2


title: Non-Hospitalized_COVID-19 [COV313]


title: Non-Hospitalized_COVID-19 [COV315]


title: WT, DMSO, biological replicate 2


title: Non-Hospitalized_COVID-19 [COV312]


title: WT, DMSO, biological replicate 3


title: ΔbapR, DMSO, biological replicate 1


title: WCH-17-huNTCP-2

city: Hershey

first: Xupeng

last: Hong

state: PA

address: 1230 York Ave

department: Laboratory of Virology and Infectious Disease

institute: The Rockefeller University

data_processing: De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0.422) allowing no mismatches in the index read. BBDuk was used to trim/filter low-quality sequences using “qtrim=lr trimq=10 maq=10”  option. Next, alignment of the filtered reads to the woodchuck reference genome (Woodchuck_1.0) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. Read counts were calculated using HTSeq by supplementing gene annotation (Woodchuck_1.0). EdgeR was used to fit the read counts to the negative binomial model along with generalized linear model (GLM) and differentially expressed genes were determined by the likelihood ratio test method implemented in the edgeR package. Significance was defined to be those with q-value < 0.05 calculated by the Benjamini-Hochberg method to control the false discovery rate (FDR) and log2 fold change is greater than 1 or smaller than -1.

organism: Marmota monax

source_name: Woodchuck

growth_protocol: WC3-huNTCP and WCH-17-huNTCP are two cell pools stably express human sodium taurocholate cotransporting polypeptide (huNTCP). Woodchuck hepatoma cell lines WC3 and WCH-17 were transduced with lentivirus encoding huNTCP (at MOI=5) and selected under 5 μg/ml puromycin for stable huNTCP-expressing cell pools. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)-F12 supplemented with 10% fetal bovine serum (FBS) (Hyclone), 50 μg/ml of penicillin-streptomycin, and 5 μg/ml puromycin.

extract_protocol: Cells were lysed in Trizol (Life Technologies). Total RNA was extracted from cultured cells using Direct-zol RNA miniprep kit (Zymo Research, USA) following the manufacturer’s instructions. Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.

value: huNTCP-expressing

value: hepatoma  cells


title: Non-Hospitalized_COVID-19 [COV311]


title: WCH-17-huNTCP-1


title: WC3-huNTCP-2


title: Non-Hospitalized_COVID-19 [COV309]


title: Non-Hospitalized_COVID-19 [COV310]


title: WC3-huNTCP-1


title: Non-Hospitalized_COVID-19 [COV308]


title: Testes_Sorting_eya_CTTGTAAT_rep2

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

data_processing:
A preprocessing of the libraries involving filtering of reads according to their quality (score>30) using FastQC tool
Genome mapping (dm6 assembly, UCSC Genome Browser) was performed using bowtie 1.2.2 with parameters allowing unique mapping and up to 2 mismatches
The htseq-count tool [Anders et al., 2015] was used to count the reads mapped to annotated parts of the genome
Differential gene expression (DE) in the libraries obtained from sorted cells compared to control libraries and between each other was analyzed using DEseq2 [Love et al., 2014
Genome_build: dm6

source_name: Testes

extract_protocol:
We performed FACS-assisted cell sorting to isolate early and mature CyCs labeled with GFP from whole testes using the UAS-GAL4 system. We purified RNA from the collected cells and prepared RNA-seq libraries of poly(A)+ RNA fractions in biological replicates to generate comprehensive transcriptome data of the isolated CyCs and samples of the total testis transcriptome.
Protocol for NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760, NEB)

value: eya-GAL4 (Leatherman and Dinardo, 2008) x UAS-GFP (#9431, Bloomington)

tag: cell population

value: sorted GFP-positive cells

value: Testes


title: Non-Hospitalized_COVID-19 [COV316]


title: Non-Hospitalized_COVID-19 [COV307]


title: Non-Hospitalized_COVID-19 [COV314]


title: Testes_Sorting_eya_TAGCTTAT_rep1


title: Testes_Input_eya_GGCTACAT_rep2

value: unsorted cell suspension


title: Non-Hospitalized_COVID-19 [COV305]


title: Testes_Input_eya_GATCAGAT_rep1


title: Non-Hospitalized_COVID-19 [COV304]


title: Testes_Sorting_tj_ACTTGA_rep1

value: tj-GAL4 (#104055 (Kyoto)) x UAS-GFP (#9431, Bloomington)


title: Non-Hospitalized_COVID-19 [COV303]

value: male


title: MAP24-N1 [203212160106_R08C01]

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

description:
203212160106_R08C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.

hyb_protocol: as per Illumina Human Infinium Omni2.5v1.4 Beadchip protocol

data_processing:
Genomic DNA was genotyped using Infinium Omni2.5-8 v1.4 Genotyping BeadChips (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

source_name: human muscle

extract_protocol: Extraction of genomic DNA from fresh bladder tissue was performed using proteinase K and Qiagen kit

value: human muscle

tag: tissue type

value: Low-grade intraurothelial neoplasia (LGIN)


title: MAP24-H7 [203212160106_R03C01]

description:
203212160106_R03C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.

scan_protocol: as per Illumina Human Infinium Omni2.5v1.4 Beadchip protocol

source_name: human bladder

value: human bladder


title: Non-Hospitalized_COVID-19 [COV300]


title: Non-Hospitalized_COVID-19 [COV302]


title: MAP24-H11 [203212160106_R05C01]

description:
203212160106_R05C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.

label_protocol: as per Illumina Human Infinium Omni2.5v1.4 Beadchip protocol


title: MAP24-I9 [203212160106_R06C01]

description:
203212160106_R06C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV317]


title: Non-Hospitalized_COVID-19 [COV299]


title: WT, DMSO, biological replicate 1

value: WT


title: MAP24-H6 [203212160106_R02C01]

description:
203212160106_R02C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Testes_Input_tj_ATCACGAT_rep2


title: Non-Hospitalized_COVID-19 [COV306]


title: Non-Hospitalized_COVID-19 [COV298]


title: Testes_Input_tj_CAGATC_rep1


title: MAP24-H9 [203212160106_R04C01]

description:
203212160106_R04C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.

value: Urolthelial carcinoma (UC)


title: MAP24-G11 [203212160106_R01C01]

description:
203212160106_R01C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-G10 [203389170048_R08C01]

description:
203389170048_R08C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Testes_Sorting_tj_CGATGTAT_rep2


title: Non-Hospitalized_COVID-19 [COV297]


title: MAP24-G5 [203389170048_R05C01]

description:
203389170048_R05C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-G9 [203389170048_R07C01]

description:
203389170048_R07C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV301]


title: MAP24-F10 [203389170048_R04C01]

description:
203389170048_R04C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-G6 [203389170048_R06C01]

description:
203389170048_R06C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-T1-(G9) [203212160106_R07C01]

description:
203212160106_R07C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-F6 [203389170048_R03C01]

description:
203389170048_R03C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-F5 [203389170048_R02C01]

description:
203389170048_R02C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV295]


title: Non-Hospitalized_COVID-19 [COV294]


title: MAP24-E9 [203389170047_R07C01]

description:
203389170047_R07C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV292]


title: MAP24-E8 [203389170047_R06C01]

description:
203389170047_R06C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.

value: High-grade intraurothelial neoplasia (HGIN)


title: MAP24-D11 [203389170047_R05C01]

description:
203389170047_R05C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-E10 [203389170047_R08C01]

description:
203389170047_R08C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV291]


title: MAP24-D9 [203389170047_R03C01]

description:
203389170047_R03C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-D10 [203389170047_R04C01]

description:
203389170047_R04C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-D6 [203389170047_R01C01]

description:
203389170047_R01C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV296]


title: MAP24-D5 [203389170033_R08C01]

description:
203389170033_R08C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-D8 [203389170047_R02C01]

description:
203389170047_R02C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV290]


title: MAP24-C9 [203389170033_R06C01]

description:
203389170033_R06C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-C10 [203389170033_R07C01]

description:
203389170033_R07C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV289]


title: MAP24-C8 [203389170033_R05C01]

description:
203389170033_R05C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-C6 [203389170033_R03C01]

description:
203389170033_R03C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV293]


title: MAP24-E11 [203389170048_R01C01]

description:
203389170048_R01C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-B7 [203389170033_R01C01]

description:
203389170033_R01C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV286]


title: Non-Hospitalized_COVID-19 [COV287]


title: MAP19-N3 [203212160029_R08C01]

description:
203212160029_R08C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV285]


title: MAP19-T3-(G8) [203212160029_R07C01]

description:
203212160029_R07C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-T2-(H8) [203212160029_R06C01]

description:
203212160029_R06C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV284]


title: MAP19-J7 [203212160029_R03C01]

description:
203212160029_R03C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-J9 [203212160029_R05C01]

description:
203212160029_R05C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-J8 [203212160029_R04C01]

description:
203212160029_R04C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV283]


title: Non-Hospitalized_COVID-19 [COV282]


title: MAP19-I10 [203212160029_R01C01]

description:
203212160029_R01C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-I6 [203389170026_R08C01]

description:
203389170026_R08C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Hospitalized_COVID-19 [COV281]


title: Non-Hospitalized_COVID-19 [COV288]


title: MAP19-J6 [203212160029_R02C01]

description:
203212160029_R02C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: 20CQ_Experiment2

city: San Diego

first: Michael

last: McHeyzer-Williams

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

data_processing:
Bcl2fastq (Illumina) was used to demultiplex sequencing libraries using plate barcodes and assort reads by well barcodes prior to sequence alignment using Bowtie2 (v2.2.9) to a custom genome consisting of the amplicon regions for the specifically targeted genes used in the experiment based on the murine genome GRCm38.p6, version R97 (Ensembl). HTseq was used for read and UMI reduced tabulation.
Quality control excluded cells that contained fewer than 24 UMI counts and had fewer than 14 unique genes detected. A secondary quality control filter included naïve B cells that contained 2 of 3 genes (Cd79a, Cd79b, Ptprc) n=158, germinal center cells containing 2 of 5 genes (Cd79a, Cd79b, Aicda, Bcl6, Fas) n=623, and plasma cells containing 2 of 5 genes (Cd79a, Cd79b, Prdm1, Irf4, Xbp1) n=266. All transcriptional data matrices across plates and treatment status were pooled into a single count matrix for processing using the R package Seurat (3.2.3). Normalizing was carried out within phenotypically defined cell subsets using the ScTransform package (v0.3.2.9002)81. This normalized count matrix was used for downstream analysis.
Assembly: GRCm38.p6
Supplementary files format and content: Processed data files consist of a cell x gene matrix of normalized UMI counts with metadata headers
Library strategy: Targeted plate based scRNA-seq

organism: Mus musculus

source_name: Spleen

extract_protocol:
Single-cell suspensions were made from the spleen. Processing of cells and flow cytometry staining were performed on ice. Briefly, cells were lysed (ACK red cell lysis buffer, Gibco), passed through a 70μm cell strainer (Fisher Scientific), washed, and resuspended in ice cold phenol red-free DMEM (Gibco) with 2% (vol/vol) Fetal Calf Serum FACS buffer at 4 x 108 cells/mL. For surface staining, cells were incubated for 5 mins with 2% (vol/vol) normal mouse and normal rat serum (Jackson ImmunoResearch Laboratories), prior to staining with a 2X master mix containing fluorophore-labeled antibodies at pre-titrated concentrations in Brilliant Violet Staining Buffer (BD Biosciences), and added to suspended cells at a final staining concentration of 2 x 108 cells/mL for 30-45 min. Cells were washed and resuspended in FACS buffer before flow cytometry analysis and sorting
Library preparation was carried out using a custom scRNA-seq strategy described in detail in (Shuparksi et al., 2021 STAR Protocols). In brief, Single cells were sorted into 384 well plates with each well containing the necessary reagents for reverse transcription (RT). Including polyA targeting oligoDT primers with unique molecular identifiers and cell barcodes. Negative control wells without sorted cells were included to enable assessment of potential contamination. Following the completion of the sort an RT reaction was performed (42˚C for 50 mins then 80˚C for 10 mins) and wells from the same plate were pooled into a single PCR tube. To remove excess oligoDT primer, cDNA libraries were treated with ExoSAP-IT Express according to manufacturer’s instructions (Affymetrix). Libraries were then volume reduced via a 0.8x ratio of AMpure XP SPRIselect magnetic beads (BeckmandCoulter). Ensuring separation between plates to preserve barcode fidelity, two nested PCR reactions were performed utilizing external and internal mixed primer sets targeting ~500 gene transcript species of interest. A final PCR reaction was carried out to allow for the ligation of adapter sequences enabling Illumina flow cell binding. Final cDNA libraries containing the amplified targeted mRNA species were quantified using a Qubit 4 Fluorometer (Invitrogen Technologies) and 2100 BioAnalyzer (Agilent). Multiplexed plates were then sequenced on an Illumina NextSeq 500 (Read 1: 19 cycles; Index Read 1: 6 cycles; Read 2: 67 cycles)

value: Steady State or  anti-PD1

tag: molecule subtype

value: targeted mRNA; ~500 amplified mRNA targets


title: MAP24-C7 [203389170033_R04C01]

description:
203389170033_R04C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-H11 [203389170026_R06C01]

description:
203389170026_R06C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-B8 [203389170033_R02C01]

description:
203389170033_R02C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV280]


title: MAP19-G13 [203389170026_R04C01]

description:
203389170026_R04C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-G12 [203389170026_R03C01]

description:
203389170026_R03C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV279]


title: sRNA-Seq_4T1_4

first: Sohail

last: Tavazoie

data_processing:
Adaptors were removed using cutadapt.
Reads were aligned to mm10 or tRNA space using bwa (HITS-CLIP and sRNA-Seq) or STAR (RNA-Seq and Ribo-Seq).
HITS-CLIP peaks were called using Piranha.
HITS-CLIP and sRNA-Seq reads that were aligned to peaks, tRNA space were counted using featureCounts.
RNA-Seq and Ribo-Seq reads that were aligned to RefSeq transcripts and coding sequence respectively were counted using featureCounts.
Differential expressed transcripts were determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Count tables: tsv files.
Supplementary_files_format_and_content: Called peaks: bed files.

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS, sodium pyruvate, L-glutamine, Pen/Strep and Amphotericin.

extract_protocol:
Total RNAs were extracted using TRIzol and RNeasy MINI kit (Qiagen).
RNA-Seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Ribo-Seq libraries were constructed as described previously (McGlincy and Ingolia, 2017). HITS-CLIP libraries were constructed as described previously (Moore et al., 2014). small RNA-Seq libraries were constructed using RealSeq-AC (SomaGenics).

treatment_protocol: Cells were transfected with a scrambled control (Scr-LNA) or  5'-tRFCys antisense LNAs (5'-Cys-LNA1) using Lipofectamine 2000.

value: breast cancer cells

tag: clip antibody

value: total RNA


title: sRNA-Seq_4T1_3


title: MAP19-G11 [203389170026_R02C01]

description:
203389170026_R02C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.

tag: tissue


title: Non-Hospitalized_COVID-19 [COV278]


title: MAP19-G5 [203389170025_R08C01]

description:
203389170025_R08C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-G10 [203389170026_R01C01]

description:
203389170026_R01C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-H5 [203389170026_R05C01]

description:
203389170026_R05C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-F13 [203389170025_R07C01]

description:
203389170025_R07C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-I5 [203389170026_R07C01]

description:
203389170026_R07C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-F12 [203389170025_R06C01]

description:
203389170025_R06C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: sRNA-Seq_4T1_2


title: MAP19-F11 [203389170025_R05C01]

description:
203389170025_R05C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Hospitalized_COVID-19 [COV275]


title: Hospitalized_COVID-19 [COV277]


title: MAP19-F10 [203389170025_R04C01]

description:
203389170025_R04C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: 20CJ_Experiment1


title: Non-Hospitalized_COVID-19 [COV274]


title: MAP19-F5 [203389170025_R01C01]

description:
203389170025_R01C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV273]


title: MAP19-F7 [203389170025_R02C01]

description:
203389170025_R02C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-F9 [203389170025_R03C01]

description:
203389170025_R03C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-E11 [203389170012_R08C01]

description:
203389170012_R08C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: sRNA-Seq_4TO7_4


title: sRNA-Seq_4TO7_2


title: MAP19-E8 [203389170012_R06C01]

description:
203389170012_R06C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV272]


title: sRNA-Seq_4TO7_3


title: sRNA-Seq_4T1_1


title: MAP19-E9 [203389170012_R07C01]

description:
203389170012_R07C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV270]


title: sRNA-Seq_67NR_4


title: MAP19-D8 [203389170012_R02C01]

description:
203389170012_R02C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: sRNA-Seq_4TO7_1


title: MAP19-E7 [203389170012_R05C01]

description:
203389170012_R05C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-E6 [203389170012_R04C01]

description:
203389170012_R04C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: Non-Hospitalized_COVID-19 [COV271]


title: MAP19-E5 [203389170012_R03C01]

description:
203389170012_R03C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP19-D7 [203389170012_R01C01]

description:
203389170012_R01C01
Genomic DNA extracted from bladder samples was genotyped using Illumina Infinium Omni2.5v1.4 beadchip array array.


title: MAP24-NU1

description:
203219730136_R08C01
Genomic DNA extracted from ureter sample was genotyped using Illumina EPIC v1.0 Beadchip.

hyb_protocol: As per Illumina EPICv1.0 protocol.

scan_protocol: Standard Illumina protocol.

data_processing:
matrix_signal.csv includes unmethylated signals, methylated signals, and detection p-values.
matrix_processed.csv includes average beta values and detection p-values.

source_name: human ureter

label_protocol: As per Illumina EPICv1.0 protocol.

extract_protocol: Extraction of genomic DNA from fresh bladder tissue was performed using proteinase K and Qiagen kit.

value: Ureter

tag: diagnosis

value: control


title: sRNA-Seq_67NR_2

tag: treatment


title: MAP24-T1 (G9)

description:
203219730136_R07C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Bladder

value: Urothelial carcinoma (UC) Grade 3


title: MAP24-I9

description:
203219730136_R06C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: sRNA-Seq_67NR_1


title: Hospitalized_COVID-19 [COV267]


title: Non-Hospitalized_COVID-19 [COV268]


title: MAP24-H11

description:
203219730136_R05C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-H9

description:
203219730136_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV266]


title: Non-Hospitalized_COVID-19 [COV269]


title: Ribo-Seq_5'-Cys-LNA1_4

data_processing:
Library strategy: Ribo-seq
Adaptors were removed using cutadapt.
Reads were aligned to mm10 or tRNA space using bwa (HITS-CLIP and sRNA-Seq) or STAR (RNA-Seq and Ribo-Seq).
HITS-CLIP peaks were called using Piranha.
HITS-CLIP and sRNA-Seq reads that were aligned to peaks, tRNA space were counted using featureCounts.
RNA-Seq and Ribo-Seq reads that were aligned to RefSeq transcripts and coding sequence respectively were counted using featureCounts.
Differential expressed transcripts were determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Count tables: tsv files.
Supplementary_files_format_and_content: Called peaks: bed files.

molecule: polyA RNA

value: transfected with 5-Cys-LNA1

value: ribosome protected fragment


title: MAP24-H6

description:
203219730136_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-H7

description:
203219730136_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV265]

value: male


title: Ribo-Seq_5'-Cys-LNA1_2


title: Ribo-Seq_5'-Cys-LNA1_3


title: sRNA-Seq_67NR_3


title: MAP24-G9

description:
203219730081_R07C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-G10

description:
203219730081_R08C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV264]


title: MAP24-G5

description:
203219730081_R05C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Ribo-Seq_5'-Cys-LNA1_1


title: Hospitalized_COVID-19 [COV261]


title: Hospitalized_COVID-19 [COV262]


title: Ribo-Seq_Scr-LNA_4

value: transfected with Scr-LNA


title: Hospitalized_COVID-19 [COV260]


title: MAP24-G11

description:
203219730136_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Low-grade intraurothelial neoplasia (LGIN)


title: MAP24-F10

description:
203219730081_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-E9

description:
203219730080_R07C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-E11

description:
203219730081_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-E10

description:
203219730080_R08C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV259]


title: MAP24-F5

description:
203219730081_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-E8

description:
203219730080_R06C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Ribo-Seq_Scr-LNA_1


title: MAP24-D11

description:
203219730080_R05C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-G6

description:
203219730081_R06C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV258]


title: RNA-Seq_5'-Cys-LNA1_3


title: MAP24-D9

description:
203219730080_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-F6

description:
203219730081_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV256]


title: Hospitalized_COVID-19 [COV257]


title: MAP24-D8

description:
203219730080_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-D6

description:
203219730080_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: RNA-Seq_5'-Cys-LNA1_2


title: Hospitalized_COVID-19 [COV255]


title: MAP24-D5

description:
203219730044_R08C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Ribo-Seq_Scr-LNA_3


title: RNA-Seq_Scr-LNA_3


title: Ribo-Seq_Scr-LNA_2


title: MAP24-C9

description:
203219730044_R06C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: RNA-Seq_5'-Cys-LNA1_1


title: MAP24-C10

description:
203219730044_R07C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV254]


title: MAP24-C8

description:
203219730044_R05C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Non-Hospitalized_COVID-19 [COV253]


title: MAP24-C6

description:
203219730044_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-B8

description:
203219730044_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP24-B7

description:
203219730044_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: RNA-Seq_Scr-LNA_2


title: MAP24-C7

description:
203219730044_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-NU2

description:
203219730043_R08C01
Genomic DNA extracted from ureter sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV252]


title: MAP24-D10

description:
203219730080_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV251]


title: MAP19-T3-(G8)

description:
203219730043_R07C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-J9

description:
203219730043_R05C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV250]


title: MAP19-T2-(H8)

description:
203219730043_R06C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV249]


title: MAP19-J6

description:
203219730043_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-J8

description:
203219730043_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-J7

description:
203219730043_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-I10

description:
203219730043_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Patient 9247 10x VDJ Replicate 1

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

description: 5' VDJ library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
The demultiplexing, barcoded processing, TCR assembly and gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, VDJ_filtered_contig_annotations.csv
Library strategy: VDJ-seq

source_name: PBMC

extract_protocol:
PBMCs were obtained from HIV-1 infected, aviraemic individuals under ART by leukapheresis and stored on liquid nitrogen. CD4+ CD45RA- cells were isolated by magnetic-activated cell sorting. Cells were subsequently incubated with Fc blocking reagent, and stained with a combination of anti-CD3 and/or anti-CD4, anti-TRBC1, and one or a combination of various anti-TRBV antibodies. Cells were sorted for CD3 and/or CD4, a specific TRBC domain and/or a specific TRBV domain or a subset of various TRBV domains.
Library was performed according to the manufacter’s instructions (single cell 5’ and V(D)J Enrichment v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: individual

value: Patient 9247

tag: Sex

value: Male

tag: hiv-1 infected

value: Yes

tag: aviraemic

tag: art

value: PBMC

value: CD4+ T cells

tag: library type

value: VDJ RNA


title: Patient B207 10x VDJ Replicate 1

value: Patient B207

tag: cell type


title: Patient B207 10x VDJ Replicate 2


title: Hospitalized_COVID-19 [COV248]

tag: gender


title: Patient 9247 10x VDJ Replicate 2

tag: age


title: RNA-Seq_Scr-LNA_1

tag: cell line

value: breast cancer cells

value: total RNA


title: Patient 605 10x VDJ Replicate 1

value: Patient 605


title: MAP19-I6

description:
203219730042_R08C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Bladder

value: High-grade intraurothelial neoplasia (HGIN)


title: MAP19-I5

description:
203219730042_R07C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV247]


title: MAP19-H11

description:
203219730042_R06C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-G13

description:
203219730042_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Patient 603 10x VDJ Replicate 1

value: Patient 603


title: Hospitalized_COVID-19 [COV246]


title: MAP19-G12

description:
203219730042_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-G11

description:
203219730042_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Patient 5104 10x VDJ Replicate 2

value: Patient 5104


title: Hospitalized_COVID-19 [COV244]

value: male


title: MAP19-G10

description:
203219730042_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-F12

description:
203219730039_R06C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Patient 5104 10x VDJ Replicate 1


title: MAP19-G5

description:
203219730039_R08C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-F13

description:
203219730039_R07C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV243]


title: Hospitalized_COVID-19 [COV242]


title: MAP19-F9

description:
203219730039_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Sample 12_32_notet_E2_3_S24

city: Stockholm

first: Dandan

last: Song

address: Tomtebodavägen 23

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Basecall files were converted and demultiplexed to fastq files with bcl2fastq v2.20.0.422
Bcl files were converted and demultiplexed to fastq using the bcl2fastq program. STAR was used to index the human reference genome (hg38/GRCh38) and align the resulting fastq files. Mapped reads were then counted in annotated exons using featureCounts. The entrez gene annotations and reference genome were obtained from UCSC. The count table from featureCounts was imported into R/Bioconductor and differential gene expression was performed using the EdgeR package and its general linear models pipeline. For the gene expression analysis genes that had 1 count per million in 3 or more samples were used and normalized using TMM normalization. P values were adjusted for multiple hypothesis testing (FDR), and genes with and an adjusted p value under 0.05 were termed significant.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: rawCounts

source_name: Breast cancer cell line

growth_protocol: MCF7 cells are cultured with DMEM with 10%FBS and 1%P/S, sample 1-6 cultured with tetracycline (2ug/ml), 7-12 cultured with normal DMEM without tetracycline

extract_protocol:
Total RNA was extracted use RNeasy Plus Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: sample 1-3, 7-9 treated with ethanol, 4-6, 10-12 treated with E2 (10nM) for 24 h

tag: strain

value: MCF7Tet-Off cell line

tag: cell model

value: only ERβ expression

value: E2 (10nM) treated for 24h


title: MAP19-F7

description:
203219730039_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-F11

description:
203219730039_R05C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Low-grade intraurothelial neoplasia (LGIN)


title: MAP19-F10

description:
203219730039_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Sample 11_32_notet_E2_2_S23


title: Hospitalized_COVID-19 [COV241]

value: female


title: MAP19-E11

description:
203219730002_R08C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV240]


title: Sample 10_32_notet_E2_1_S22


title: MAP19-H5

description:
203219730042_R05C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Patient 5125 10x VDJ Replicate 1

description: 5' VDJ library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Patient 5125

value: Male

value: Yes

value: PBMC


title: MAP19-F5

description:
203219730039_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Sample 9_32_notet_etoh_3_S21

value: ethanol


title: Hospitalized_COVID-19 [COV239]


title: Hospitalized_COVID-19 [COV245]


title: MAP19-E8

description:
203219730002_R06C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Urothelial carcinoma (UC) Grade 3


title: MAP19-E9

description:
203219730002_R07C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-E7

description:
203219730002_R05C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV238]


title: MAP19-E6

description:
203219730002_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: MAP19-D7

description:
203219730002_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Non-Hospitalized_COVID-19 [COV237]


title: Sample 7_32_notet_etoh_1_S19


title: Hospitalized_COVID-19 [COV236]


title: MAP19-E5

description:
203219730002_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: M_D2-targeted  [3632]

first: Casey

middle: K

last: Lardner

address: 1425 Madison Avenue

department: Nash Family Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads were trimmed, aligned to the mouse reference genome mm10, and processed using NGS-Data-Charmer (https://github.com/shenlab-sinai/NGS-Data-Charmer). Briefly, reads were trimmed using trim_galore, then aligned to the mm10 genome with HISAT2.
Read alignments in SAM file format were converted to BAM files and were sorted according to chromosome number using SAMtools. Duplicate alignments were filtered using SAMtools rmdup.
Counts of reads mapped to genes were obtained using featureCounts (http://subread.sourceforge.net/) against GENCODE version M22 annotation
Differential expression analysis was carried out using the R package DESeq2 (version 1.27). Prior to processing the expression data with DESeq2, poorly expressed genes were filtered by removing those genes with less than 20 samples having a minimum of one read. Samples were sequenced in two batches, as the male D2-Cre groups were underpowered and had poor sequencing depth in the first run. A second group of samples was generated and sequenced (IDs: 2755, 3127, 3619, 3632, 3803, 1675, 3128, 1674, 3631, 3805, 2756, 3618). Sequencing batch was included in the differential expression formula, in order to account for possible batch effects.
Genome_build: mm10
Supplementary_files_format_and_content: counts_file: A tab delimited text file containing the raw read counts for all genes. Columns represent samples and rows represent the genes.

extract_protocol:
Nucleus accumbens was dissected 6 days after surgery and immediately frozen on dry ice. Total RNA was isolated using the RNeasy Mini Kit (Qiagen).
Libraries were constructed using a TruSeq Stranded Total RNA – Gold kit from Illumina.

treatment_protocol: Nucleus accumbens in male and female C57/BL6 mice was infected with two herpes simplex viruses. One contained a nuclease-dead Cas9 protein fused to a mutated, constitutively active form of CREB, CREB(S133D). The other contained a short guide RNA to direct the modified CRISPR activation system to either the Fosb locus (gRNA-Fosb or g11), or a non-targeted control gRNA (gNT).

tag: backcross strain

tag: strain genotype

tag: hsv-grna

tag: cre-dependent virus

value: yes

value: Nucleus accumbens

tag: molecule subtype

value: ribo-depleted total RNA

tag: sequencing batch


title: M_D2-control [3803]

tag: Sex

value: gNT

tag: tissue


title: Sample 5_crispr_plustet_E2_2_S17

value: only ERα expression

tag: treatment

value: cell cultured with tetracycline 2ug/ml, treated with E2 (10nM) for 24h


title: Hospitalized_COVID-19 [COV235]

value: male


title: M_D2-control [3619]


title: M_D2-control [3631]


title: Sample 8_32_notet_etoh_2_S20

value: MCF7Tet-Off cell line

value: only ERβ expression


title: M_D2-control [3618]


title: Sample 4_crispr_plustet_E2_1_S16


title: Hospitalized_COVID-19 [COV232]


title: Hospitalized_COVID-19 [COV234]


title: M_D2-control [3127]


title: M_D2-targeted  [3128]


title: Hospitalized_COVID-19 [COV233]


title: Sample 3_crispr_plustet_etoh_3_S15

value: cell cultured with tetracycline 2ug/ml


title: M_D2-control [2755]


title: Sample 1_crispr_plustet_etoh_1_S13


title: Sample 2_crispr_plustet_etoh_2_S14


title: M_D2-targeted  [2756]


title: Hospitalized_COVID-19 [COV230]

value: female


title: MAP19-D8

description:
203219730002_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Bladder

tag: diagnosis

value: Low-grade intraurothelial neoplasia (LGIN)


title: Sample 6_crispr_plustet_E2_3_S18


title: PARK2-resPD rep3 line NP PDL 1.5L-wtParkin

first: Daniil

last: Poberezhniy

address: Kurchatov sq. 2

institute: National Research Centre "Kurchatov Institute"

description:
PARK2-resPDnp_3
iPSCs from Parkinson's disease patient were transduced with lentiviral particles carrying the full-length copy of cDNA PARK2 under minimal CMV + TetO promoter and differentiated into uncommitted neural progenitors

data_processing:
RNA-seq reads were trimmed for quality, paired reads were cropped using Trimmomatic (v. 0.39).
Trimmed RNAseq reads were quantified against Homo Sapiens GRCh38.13  genome annotation at the transcript level using Salmon (v.1.4). Results were aggregated to gene level using the R package tximport.
Differentially expressed genes were identified using the R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: TPM values for every gene and every sample

source_name: neural progenitors

growth_protocol: Neural progenitors were cultivated at 37°C under humidified atmosphere with 5% CO2 in DMEM/F12 containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential amino acids (“Paneco”, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U/ml; 50 µg/ml) (“Paneco”, Russian Federation), 1%  N2 supplement (“Life Technologies”, USA), 10 µM SB431542 (“Stemgent”, USA), and 80 ng recombinant Noggin (“Peprotech”, USA).

extract_protocol:
Total RNA was isolated from neural progenitors using RNeasy Micro Kit (Qiagen, USA) followed by treatment with DNAse I (Qiagen, USA). The reaction was purifed with PureLink RNA Mini Kit (ThermoFisher, USA). RNA quality was checked by 2100 bioanalyzer (Agilent, USA). Enrichment of polyadenylated RNA and library preparation was performed with NEB Next Ultra II Directional RNA Library Prep (NEB, USA) according to the manufacturer’s protocol. Samples were sequenced on NextSeq 500 System (Illumina, USA) with NextSeq 500/550 High Output Kit v2.5 (75 Cycles).
Library preparation was performed with NEB Next Ultra II Directional RNA Library Prep (NEB, USA) according to the manufacturer’s protocol.

treatment_protocol: To obtain neural progenitors from iPSCs, the culture medium was replaced with a neuronal differentiation medium containing a cocktail of factors that stimulates differentiation in the neuronal direction. After 10-14 days of culturing, neural rosettes with specific “ridges” formed by iPSCs were mechanically transferred to a 24-well plate with extremely low adhesion, where neurospheres were formed. After 3-5 days, neurospheres were collected and treated with 0.05% trypsin. Thereafter, neurospheres were resuspended in DMEM with 10% FBS, then resuspended in growth medium for neural progenitors (DMEM/F12 containing 2% serum replacement (Gibco, USA), 1 mM non-essential amino acids (Paneco, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U / ml; 50 µg / ml) (“Paneco”, Russian Federation), 1% N2 supplement (“Life Technologies” , USA), 10 μM SB431542 (Stemgent, USA), and 80 ng recombinant Noggin (Peprotech, USA), and transferred to Petri dishes coated with Matrigel.

value: neural progenitors

tag: genotype

value: PARK2:2 exon (del 202-203 AG), 1 intron (splicing mutation IVS1+1G/A) + full-length copy of cDNA PARK2 under (minimal CMV + TetO) promoter

tag: subject status

value: Parkinson's disease (PD) patient


title: F_D1-D2-control [19754]

value: Female

value: no


title: Hospitalized_COVID-19 [COV229]

tag: gender


title: F_D1-D2-targeted  [19749]

value: Nucleus accumbens


title: F_D1-D2-control [19750]

value: ribo-depleted total RNA


title: Hospitalized_COVID-19 [COV228]

tag: age


title: Hospitalized_COVID-19 [COV227]


title: F_D1-D2-control [19762]

value: gNT


title: PARK2-resPD rep2 line NP PDL 1.5L-wtParkin

description:
PARK2-resPDnp_2
iPSCs from Parkinson's disease patient were transduced with lentiviral particles carrying the full-length copy of cDNA PARK2 under minimal CMV + TetO promoter and differentiated into uncommitted neural progenitors

tag: cell type


title: F_D1-D2-targeted  [19748]


title: Hospitalized_COVID-19 [COV226]


title: F_D1-control [19755]

value: yes


title: PARK2-resPD rep1 line NP PDL 1.5L-wtParkin

description:
PARK2-resPDnp_1
iPSCs from Parkinson's disease patient were transduced with lentiviral particles carrying the full-length copy of cDNA PARK2 under minimal CMV + TetO promoter and differentiated into uncommitted neural progenitors


title: F_D1-D2-control [19719]


title: F_D1-D2-targeted  [19604]


title: Hospitalized_COVID-19 [COV223]


title: F_D1-D2-control [19598]


title: Hospitalized_COVID-19 [COV224]


title: F_D1-D2-targeted  [19597]


title: 22RV1 cell line 10B.lp3_GAATTCGT.ATAGAGGC_AH3VFYBCX2_L002_001

first: Navneet

last: Dogra

address: 1 Gustave L. Levy Pl

data_processing:
For quantification of gene expression, raw reads were aligned to the latest Ensembl GRCh38.p13 (GCA_000001405.28) using bowtie aligner (version 2.5.4b).
FeatureCounts was then used to map the aligned reads to the GENCODE v26 primary gene annotation
Normalization via trimmed mean of M-values in edgeR ensures library sizes of all samples are scaled properly to minimize the influences of external factors.
Differentially expressed genes are discerned between 1) 22RV1 cell lines versus 22RV1 cell-line- derived EVs, and 2) Prostate cancer patient serum-derived EVs isolated using nanoDLD versus the EVs isolated using UC via the standard differential expression pipeline as illustrated in limma/edgeR packages.
Assembly: hg38
Supplementary files format and content: raw and voom normalized counts provided in csv form

extract_protocol:
Total RNA was extracted from the serum bump fraction of nanoDLD, serum EVs pellet from UC using the Total EV RNA and Protein Isolation Kit (Invitrogen 4478545).
cDNA Libraries were prepared for small RNAs using the SMARTer smRNA-seq Kit for Illumina (Takara Bio 635030).

tag: aligner

tag: concentration

tag: cell line

tag: libprep

value: human prostate carcinoma epithelial cell line


title: Hospitalized_COVID-19 [COV225]

value: male


title: 22RV1 cell line 10B.lp2_ATTCAGAA.ATAGAGGC_AH3VFYBCX2_L002_001


title: F_D1-D2-targeted  [19600]

tag: backcross strain

tag: strain genotype

tag: hsv-grna


title: 22RV1 cell line 19A.30ng.lp2_TAATGCGC.CCTATCCT_AH3VFYBCX2_L002_001


title: F_D1-D2-control [19599]

tag: cre-dependent virus

tag: molecule subtype

tag: sequencing batch


title: 22RV1 cell line 19A.30ng.lp1_CTGAAGCT.CCTATCCT_AH3VFYBCX2_L001_001


title: F_D1-D2-targeted  [19596]

tag: Sex

tag: tissue


title: 22RV1 cell line 19A.30ng.lp2_TAATGCGC.CCTATCCT_AH3VFYBCX2_L001_001


title: F_D1-D2-control [19727]


title: Hospitalized_COVID-19 [COV222]


title: 22RV1 cell line 19A.30ng.lp3_CGGCTATG.CCTATCCT_AH3VFYBCX2_L002_001


title: F_D1-D2-targeted  [19610]


title: Hospitalized_COVID-19 [COV221]


title: 22RV1 cell line 10B.lp3_GAATTCGT.ATAGAGGC_AH3VFYBCX2_L001_001


title: Hospitalized_COVID-19 [COV220]


title: M_D1-D2-control [19219]

value: Male


title: M_D1-D2-control [19511]


title: M_D1-D2-control [19512]


title: F_D1-D2-targeted  [19482]


title: M_D1-D2-control [19220]


title: M_D1-targeted  [19507]


title: F_D1-D2-targeted  [19483]


title: Hospitalized_COVID-19 [COV218]


title: Hospitalized_COVID-19 [COV219]


title: 22RV1 cell line 10B.lp1_GAGATTCC.ATAGAGGC_AH3VFYBCX2_L002_001


title: M_D1-targeted  [19214]


title: M_D1-targeted  [19112]


title: M_D1-D2-control [19109]


title: 22RV1 cell line 10B.lp1_GAGATTCC.ATAGAGGC_AH3VFYBCX2_L001_001


title: M_D2-control [19099]


title: Hospitalized_COVID-19 [COV215]


title: 22RV1 cell line 19A.30ng.lp1_CTGAAGCT.CCTATCCT_AH3VFYBCX2_L002_001


title: M_D1-D2-control [19107]


title: M_D1-D2-control [18759]


title: Hospitalized_COVID-19 [COV213]


title: M_D2-targeted  [18893]


title: F_D2-control [18433]


title: Hospitalized_COVID-19 [COV214]


title: Hospitalized_COVID-19 [COV217]


title: M_D1-D2-targeted  [19211]


title: M_D1-D2-targeted  [18749]


title: COVD10 (+)

city: La Jolla

first: Nadejda

last: Beliakova-Bethell

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

data_processing:
Basecalling was performed using BCL2Fastq2 in Illumina’s Basespace workflow. Base-calling filters were minimum Q30 and minimum read length of 35
Sequenced reads were trimmed for adaptor sequence and filtered for low quality sequences using TrimGalore, then mapped to hg38 whole genome using HISAT2 with parameters: --fr  --q --x
Read counts were calculated with HTSeq (htseq-count) using the following parameters:  --stranded=reverse.  Mapped files were counted against the Gencode v37.
Data filtering, quality control and batch correction was performed before differential expression analysis with EdgeR. Batch correction was performed using library sva, function ComBat_seq. There were 2 batches in the study: batch 1, samples COVD1 – COVD5; batch 2, samples COVD6 – COVD10. Batch effect was identified and corrected. Repeated quality control (box plots and PCA analysis) identified two outliers, samples COVD1 and COVD8, which were excluded. The remaining 8 samples were re-processed. Filtering removed any gene which did not achieve 10 counts per million in at least 3 samples (size of CoV2 (-) group). Data were batch corrected and normalized using upperquartile normalization. Differential expression analysis was performed between CoV2 (+) and CoV2 (-) groups; significance was determined at either nominal p-value or an FDR corrected p-value < 0.05.
Assembly: hg38
Supplementary files format and content: Matrix of total host gene read counts

source_name: CD14+HLA DR-/lo cell RNA extract

extract_protocol:
Total RNA was extracted from cell samples using the miRNeasy Micro Kit (QIAGEN, Cat. No. 217084) with DNase treatment (RNase-free Dnase I, Invitrogen, Cat. No. AM2222).
Paired end RNA libraries were prepared for sequencing using 10 pg -1 ng total RNA and SMART-Seq HT PLUS kit kit (Takara Bio USA, Inc.).
RNA-Seq using Illumina 500 mid-output PE75 sequencer

treatment_protocol: Cells were isolated by flow cytometry from peripheral blood mononuclear cells from SARS CoV2 (+) and SARS CoV2 (-) study participants.

value: CD14+HLA DR-/lo cell

tag: infection status

value: Infected


title: 22RV1 cell line 10B.lp2_ATTCAGAA.ATAGAGGC_AH3VFYBCX2_L001_001


title: M_D2-targeted  [18777]


title: 22RV1 cell line 19A.30ng.lp3_CGGCTATG.CCTATCCT_AH3VFYBCX2_L001_001


title: Hospitalized_COVID-19 [COV216]


title: M_D1-D2-targeted  [18919]


title: M_D2-targeted  [18891]


title: M_D1-targeted  [18722]


title: Hospitalized_COVID-19 [COV212]


title: COVD7 (-)

value: Uninfected


title: F_D2-targeted  [18432]


title: M_D2-targeted  [18718]


title: Hospitalized_COVID-19 [COV211]


title: COVD8 (-)


title: Hospitalized_COVID-19 [COV209]


title: Hospitalized_COVID-19 [COV210]


title: COVD9 (+)


title: F_D2-control [18420]


title: F_D2-targeted  [18419]


title: F_D2-control [18421]


title: COVD5 (+)


title: F_D2-control [18401]


title: M_D2-control [18386]


title: F_D2-targeted  [18402]


title: COVD6 (-)


title: Hospitalized_COVID-19 [COV207]


title: M_D1-control [18383]


title: Hospitalized_COVID-19 [COV208]


title: M_D1-targeted  [18366]


title: F_D2-targeted  [18168]


title: M_D1-targeted  [18368]


title: COVD4 (+)


title: COVD2 (-)


title: COVD3 (+)


title: Hospitalized_COVID-19 [COV206]


title: F_D2-targeted  [18150]


title: F_D2-targeted  [18167]


title: COVD1 (-)


title: Hospitalized_COVID-19 [COV205]


title: F_D2-targeted  [18138]


title: Hospitalized_COVID-19 [COV204]


title: Hospitalized_COVID-19 [COV203]


title: M_D1-control [18068]


title: M_D1-control [18069]


title: P8D_neg

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

description: NEUNnegOLIG2neg nuclei

data_processing:
Bulk RNAseq: data processing was performed with the Lexogen Quantseq 2.3.1 FWD UMI pipeline on the BlueBee Genomics Platform (1.10.18). Deduplicated BAM files were used as input for ht-seq count where reads mapping to the entire gene (-t gene) were counted.
snRNAseq: data processing was performed with Cell ranger v3.0.0 with the pre-mRNA reference from 10X Genomics.
Genome_build: Homo Sapiens GRCh38.86
Supplementary_files_format_and_content: Bulk RNAseq: countfile where each column is a sample and each row is a gene. snRNAseq: one countfile per sample, where columns are barcodes and rows are genes

source_name: Brain

extract_protocol:
Nuclei were isolated from fresh frozen human brain tissue using a sucrose gradient ultracentrifugation protocol. Nuclei were separated into 3 populations using FANS: 1) NEUNpos neurons used for bulk RNAseq, 2) OLIG2pos oligodendrocytes and OPCs used for bulk RNAseq, 3) NEUNnegOLIG2neg nuclei used for single-nucleus RNAseq. For bulk RNAseq RNA was isolated with the Arcturus™ PicoPure™ RNA Isolation Kit from Thermo Fisher Scientific
Bulk: Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD with UMI) from Illumina. snRNAseq: Chromium Single Cell 3’ Reagents Kit v3 from 10X Genomics

tag: donor

tag: brain region

value: Temporal Cortex

value: F

tag: rin tissue block


title: M_D1-targeted  [18130]


title: P8A_neg

description: NEUNnegOLIG2neg nuclei

value: Frontal Cortex

tag: age


title: Hospitalized_COVID-19 [COV201]

tag: gender


title: Hospitalized_COVID-19 [COV196]


title: F_D2-control [17910]


title: M_D1-control [17789]


title: M_D1-D2-targeted  [17728]


title: P21A_neg

description: NEUNnegOLIG2neg nuclei


title: F_D2-control [17906]


title: F_D2-targeted  [17907]


title: F_D2-control [17909]


title: P20A_neg

description: NEUNnegOLIG2neg nuclei

value: M


title: F_D1-control [17719]


title: F_D2-control [18143]


title: F_D1-control [17457]


title: F_D2-targeted  [18142]


title: P18A_neg

description: NEUNnegOLIG2neg nuclei


title: Hospitalized_COVID-19 [COV193]


title: Hospitalized_COVID-19 [COV195]


title: F_D1-control [17455]


title: P8B_neg

description: NEUNnegOLIG2neg nuclei

value: Occipital Cortex


title: F_D1-targeted [17436]

value: Female


title: Hospitalized_COVID-19 [COV202]


title: F_D1-targeted [17435]


title: F_D1-targeted [17376]


title: Hospitalized_COVID-19 [COV192]


title: P19A_neg

description: NEUNnegOLIG2neg nuclei


title: Hospitalized_COVID-19 [COV191]

value: female


title: F_D1-D2-targeted  [16761]

value: no

value: Nucleus accumbens


title: P12D_neg

description: NEUNnegOLIG2neg nuclei


title: F_D1-D2-targeted  [16762]

value: ribo-depleted total RNA


title: Hospitalized_COVID-19 [COV190]


title: F_D1-D2-targeted  [16764]


title: P12B_neg

description: NEUNnegOLIG2neg nuclei


title: F_D1-D2-control [16760]

value: gNT


title: P12A_neg

description: NEUNnegOLIG2neg nuclei


title: Hospitalized_COVID-19 [COV189]


title: P11D_neg

description: NEUNnegOLIG2neg nuclei


title: F_D1-targeted [16754]

value: yes


title: P11A_neg

description: NEUNnegOLIG2neg nuclei


title: Hospitalized_COVID-19 [COV188]


title: F_D1-control [16583]


title: F_D1-control [16597]


title: P16A_neg

description: NEUNnegOLIG2neg nuclei


title: F_D1-control [16585]


title: Hospitalized_COVID-19 [COV187]

value: male


title: F_D1-control [16596]


title: F_D1-targeted [16565]


title: C4B_neg

description: NEUNnegOLIG2neg nuclei


title: C4A_neg

description: NEUNnegOLIG2neg nuclei


title: Hospitalized_COVID-19 [COV182]


title: F_D1-targeted [16564]


title: Hospitalized_COVID-19 [COV186]


title: Hospitalized_COVID-19 [COV181]


title: C4C_neg

description: NEUNnegOLIG2neg nuclei


title: Hospitalized_COVID-19 [COV179]


title: CTRL rep4 [OE]

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

data_processing:
Fastq files were aligned to human reference genome GRCh38 using STARv2.42 and gencode v25 as guide gtf
Counts were generated on the fly by STAR
QC of fastq files was done with FastQC
Genome_build: GRCh38
Supplementary_files_format_and_content: a tab separated raw count matrix file

source_name: Natural Killer Cell

growth_protocol: HPC were obtained by isolating peripheral blood monocytes from umbilical cord blood by density gradient centrifugation and by subsequently enriching CD34+ HPC using magnetic activated cell sorting (MACS). Isolated cord blood-derived CD34+ HPC were cultured in complete IMDM containing 10% FCS and supplemented with thrombopoietin (TPO) (20 ng/ml), stem cell factor (SCF) (100 ng/ml) (all from Peprotech, London, UK.) and FMS-like tyrosine kinase 3 ligand (FLT3-L) (100 ng/ml, R&D Systems, Minneapolis, MN, U.S.A.) for 48 hours. Successfully transduced HPC were sorted and co-cultured with mitomycin-inactivated EL08.1D2 cells in Dulbecco’s modified Eagle medium plus Ham’s F-12 medium (2:1 ratio), supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM glutamine, 10 mM sodium pyruvate (all from Life Technologies), 20% of heat-inactivated human AB serum (Biowest, Nuaillé, France), 24 μM β-mercaptoethanol, 20 μg/mL ascorbic acid and 50 ng/mL sodium selenite (all from Sigma-Aldrich). The following cytokines were added: IL-3 (5 ng/mL, first week only, R&D systems), IL-7 (20 ng/mL), IL-15 (10 ng/mL) (all from Miltenyi Biotec), SCF (20 ng/mL; Peprotech, London, UK.), and Flt3-L (10 ng/mL; R&D Systems, Minneapolis, MN, U.S.A.) . Culture medium was refreshed on day 7 by addition of the same volume of fresh medium with cytokines except for IL-3.

extract_protocol:
Total mRNA was extracted using the RNeasy micro kit (Qiagen). The concentration and quality of the total extracted RNA was checked using the Quant-it ribogreen RNA assay (Life Technologies) and the RNA 6000 nano chip (Agilent Technologies, Santa Clara, CA, U.S.A), respectively.
Illumina sequencing library preparation was performed using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to manufacturer's protocol. Libraries were quantified by qPCR.
RNA seq, Lexogen Quantseq FWD

treatment_protocol: CD34+ HPC underwent retroviral transduction with the RUNX2-I isoform overexpression vector or the control vector. After 48 hours, eGFP+CD34+ Lin- HPC were sorted by FACS cell sorting.

tag: day of culture

value: Donor 4

tag: transduction

value: CTRL

tag: treatment

value: Retroviral transduction


title: RUNX2-I rep4 [OE]


title: Hospitalized_COVID-19 [COV180]

data_processing:
The matrix processed and matrix signal intensity files form Genome studio are uploaded.
The statistical analysis was conducted as a case-control panel, with controls characterized as non-hospitalized symptoms and cases characterized as hospitalized symptoms. Case-control association tests of the genotyped and imputed SNPs in the cohort were performed using PLINK (logistic regression). Two different analysis including covariates from the PCA without 1000 Genomes reference samples were run to control for potential population stratification (analysis I), as well as population stratification, age, and gender effects (analysis II).


title: Hospitalized_COVID-19 [COV177]


title: CTRL rep3 [OE]

value: Donor 3


title: RUNX2-I rep3 [OE]


title: Hospitalized_COVID-19 [COV178]


title: RUNX2-I rep2 [OE]

value: Donor 2


title: Hospitalized_COVID-19 [COV176]


title: Hospitalized_COVID-19 [COV175]


title: Wether LATE gestation exposure replicate 3

city: Clemson

first: Susan

last: Duckett

state: SC

address: 112 Biosystems Research Complex

department: Animal and Veterinary Sciences

institute: Clemson University

data_processing:
Novogene's custom perl and python scripts were used to clean and filter the raw data.
Bowtie 0.12.9 without mismatch for alignment.
miRBase 20.0
mirdeep2 0.0.5
srna-tools-cli
RepeatMasker 4.0.3
miREvo v1.1
miRanda v3.3
DeSeq 1.12.0
GOSeq 2.12
KOBAS v 2.0
Genome_build: Ovis aries (TEXEL) Ensembl release 96
Supplementary_files_format_and_content: Raw_read_counts_miRNA.txt: Tab-delimited text file of raw read counts for all miRNA features for all samples.

organism: Ovis aries

source_name: Longissimus

extract_protocol:
Total RNA was extracted with Trizol according to manufacturer's specifications. Quantification and qualification were checked by 1% agarose gel, NanoPhotometer spectrophotometer, and Agilent Bioanalyzer 2100 system.
The NEBNext Multiplex Small RNA Library Prep Set for Illumina following manufacturer's recommendation and index codes were used to prepare the sequencing library.

tag: breed

value: Suffolk

value: d 250 postnatal

value: LATE gestation in utero exposure to endophyte-infected tall fescue seed

value: Longissimus muscle

tag: replicate

value: replicate 3


title: Wether MID gestation exposure replicate 3

value: MID gestation in utero exposure to endophyte-infected tall fescue seed


title: Wether LATE gestation exposure replicate 2

value: replicate 2


title: Deep Cortex rep 2 [2680 - DCx2]

type: RNA

city: Newark

first: Melinda

last: Duncan

state: DE

address: 105 The Green

department: Biological Sciences

institute: University of Delaware

description: replicate 2

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: The data was processed using the lumi package in R. The data was read into lumi using the lumiR function. The data was transformed using the default lumiT function. The data was normalized using quantile normalization with the lumiN function.

label: biotin

source_name: Mouse ocular lens

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy Micro Kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Enucleated globes were embedded in optimal cutting temperature medium and frozen in 2-methylbutane over dry ice. Sections were cut on a cryostat and mounted on glass RNase-free PEN-Membrane Slides. Sections were washed in Rnase-free water for 30 seconds and fixed in ethanol for 1 minute, and air dried for 10 minutes. Sections were laser-microdissected to obtain superficial and deep cortical samples and collected directly into lysis buffer supplied with the RNeasy Micro Kit.

value: 1 month

value: Lens Deep Cortex


title: Wether MID gestation exposure replicate 2


title: Deep Cortex rep 4 [2682 - DCx4]

description: replicate 4


title: Deep Cortex rep 1 [2672 - DCX]

description: replicate 1


title: Deep Cortex rep 3 [2681 - DCx3]

description: replicate 3


title: Epithelium rep 1 [2673 - Ep1]

description: replicate 1

value: Lens Epithelium


title: Superficial Cortex rep 3 [2678 - SCx3]

description: replicate 3

value: Lens Superficial Cortex


title: Wether LATE gestation exposure replicate 1

value: replicate 1


title: Epithelium rep 2 [2674 - Ep2]

description: replicate 2


title: RUNX2-I rep1 [OE]

value: Donor 1


title: CTRL rep1 [OE]

value: CTRL


title: Superficial Cortex rep 1 [2671 - SCX]

description: replicate 1


title: Epithelium rep 3 [2675 - Ep3]

description: replicate 3