title: C3H_wt_sham_-483_L3


title: 36_r6_1

status: Public on Mar 22 2023

type: SRA

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

description:
sample name: 313
Embryonic blastomere transcriptome

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases).
CEL-seq2 (Hashimshony, et a. 2016) demultiplexing of second mate, using first mate barcode, allowing no mismatches in the barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting.
Genome_build: WS230
Supplementary_files_format_and_content: Expression matrix, number of transcript molecules

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: embryo

extract_protocol:
Egg shells were removed from a C. elegans embryo, blastomeres were separated manually, collected and individually frozen
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence RNA from collected blastomeres. CEL-seq2 multiplexing barocdes were used.

tag: developmental stage

tag: cell type

value: embryonic cells


title: C3H_WT_-24_L3.D711

city: Birmingham

first: Mariame Selma

last: Kane

state: Alabama

address: 901 19th Street South

department: Medicine

country: USA

institute: University of Alabama at Birmingham

data_processing:
Basecalls were performed using CASAVA v1.8.2 following the company's EA-Quntiles analysis pipeline
Sequence reads were trimmed and clipped: we remove any residual Illumina adapter sequence and low quality bases from the ends of reads. The remaining se quence must be at least 25 nt in length to be included in subsequent analysis.  We remove entire sequences that are of low quality (less than an average of Q25), those which are clipped below the threshold length or those which are entirely homopolymers. For clipper code: http://code.google.com/p/ea-utils/wiki/FastqMcf
EA-Quintiles’ mRNAv8 pipeline: Trimmed samples were aligned using Bowtie versino 0.12.9 and quantified using RSEM version 1.2.0
Assembly: UCSC mm9
Supplementary files format and content: tab delimited TXT file containing expected counts from RSEM output for each gene in each sample.

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Cardiomyocytes were isolated from sham and ACF mice from each of the different strains. The hearts were perfused with perfusion buffer (120 mmol/L NaCl, 15 mmol/L KCl, 0.5 mmol/L KH2PO4, 5 mmol/L NaHCO3, 10 mmol/L HEPES, and 5 mmol/L glucose, at pH 7.0) for 8 min and digested with perfusion buffer containing 2% collagenase II for 25 min at 37°C. The right ventricle and atria were removed before the perfused-heart was minced. The cell suspension was then mixed with stop buffer containing 10% fetal bovine serum (FBS). After filtered, the flow-through was spun at 300 rpm for 3 min to pelletize the cardiomyocytes. After calcium re-introduction, only cardiomyocytes with purity and viability (rod-shaped) >95% or 80%, respectively, were used.Cardiomyocytes were isolated from sham and ACF surgery mice for RNA sequence analysis and stored in RNAlater RNA Stabilization Reagent (Qiagen) and flash-frozen in liquid nitrogen for storage. For these studies, the effect of different mtDNA and nuclear background combinations on gene expression was assessed by RNA sequence analysis from RNA isolated with the RNEasy kit (Qiagen). Reverse transcribed cDNA libraries were sequenced with an Illumina HiSeq 2000. Read mapping was conducted with a proprietary algorithm by Expression Analysis (www.q2labsolutions.com), and read counts were used as input for differential expression analysis in DESeq2 version 1.10.1, using default settings. Genes were interpreted as differential expressed if the adjusted p value was reported as less than 0.05.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).

tag: tissue

value: heart

value: cardiomyocyte

tag: genotype

value: WT C3H

tag: treatment


title: 36_r10_1

description:
sample name: 317
Embryonic blastomere transcriptome


title: 36_r9_1

description:
sample name: 316
Embryonic blastomere transcriptome


title: C3H_WT_-23_L3.D710


title: C3H_wt_ACF_-470_L2.D710


title: 36_r5_1

description:
sample name: 312
Embryonic blastomere transcriptome


title: C3H_WT_-21_L3.D708


title: C3H_WT_-22_L3.D709


title: 36_r2_1

description:
sample name: 309
Embryonic blastomere transcriptome


title: 36_r4_1

description:
sample name: 311
Embryonic blastomere transcriptome


title: 36_r3_1

description:
sample name: 310
Embryonic blastomere transcriptome


title: 30_r30_3

description:
sample name: 882
Embryonic blastomere transcriptome


title: C3H_MNX_sham_-6661_L2.D709

value: MNX C57n:C3Hmt


title: C3H_WT_-19_L3.D706


title: C3H_WT_-20_L3.D707


title: 36_r1_1

description:
sample name: 308
Embryonic blastomere transcriptome


title: C3H_MNX_sham_-6652_L8.D708


title: 30_r29_3

description:
sample name: 881
Embryonic blastomere transcriptome


title: 30_r27_3

description:
sample name: 879
Embryonic blastomere transcriptome


title: C3H_MNX_ACF_-6662_L8.D711


title: C3H_MNX_ACF_-6756_L8.D712


title: C3H_MNX_ACF_-6650_L8.D710


title: 30_r25_3

description:
sample name: 877
Embryonic blastomere transcriptome


title: 30_r24_3

description:
sample name: 876
Embryonic blastomere transcriptome


title: 30_r23_3

description:
sample name: 875
Embryonic blastomere transcriptome


title: Egg yolk vesicles sample 2

city: Daejeon

first: Islam

last: Saadeldin

address: Dehak ru

country: South Korea

institute: Chungnam National University

data_processing:
The reads were subjected to standard quality control (QC) criteria according to the following parameters: (1) trimming and cleaning reads that aligned to primers and/or adaptors, (2) reads with over 50% of low-quality bases (quality value ≤5) in one read, and (3) reads with over 10% unknown bases (N bases).
Clean reads were mapped to reference Gallus gallus genome (NCBI bGalGal1.mat.broiler.GRCg7b), and small RNA sequences from miRBase (version 22.1) with bowtie1 software within miRDeep2.pl software.
Using miRDeep2.pl script, read number of each of known miRNAs and predicted novel small RNAs of each sample were counted.
Assembly: NCBI bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: tab-delimited text files include read counts for each sample

organism: Gallus gallus

source_name: Egg yolk

extract_protocol:
Exosomal total RNA was isolated from exosomes of 3 chicken samples using Total Exosome RNA & Protein Isolation Kit (Invitrogen, Cat.No. 4478545) according to manufacturer's protocol.
small RNA UMI library; Small RNA sequencing libraries were prepared according to the manufacturer’s protocol (BGISEQ-500 Small RNA UMI Library Construction Protocol).

value: Egg yolk

value: exosome

value: WT

tag: molecule type

value: small RNA


title: Egg yolk vesicles sample 3


title: 30_r26_3

description:
sample name: 878
Embryonic blastomere transcriptome


title: 30_r22_3

description:
sample name: 874
Embryonic blastomere transcriptome


title: Egg yolk vesicles sample 1


title: 30_r20_3

description:
sample name: 872
Embryonic blastomere transcriptome


title: CD4_DFN0_4_AB2962

city: Bethesda

first: Timothy

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description:
TPM_all.csv
clc_mapping_stats.csv

data_processing:
Paired-end sequencing was completed on an illumina NextSeq 500 system, running illumina NextSeq Control Software System Suite version 2.1.0 and RTA version 2.4.11.  The final library pool was sequenced via 2 x 76 bp run configuration using the product NextSeq 500/550 High Output Kit v2.5 (150 Cycles
From Fastq files, reads were trimmed and mapped and normalized to TPM using CLC Genomics workbench
read mapping parameters:  Mismatch cost=2;Insertion cost=3;Deletion cost=3;Length fraction=0.8;Similarity fraction=0.8;Global alignment=TRUE;Color space alignment=TRUE;Color error cost=3;Auto-detect paired distances=TRUE;Strand specific=Both;Maximum number of hits for a read=10;Count paired reads as two=FALSE;Expression value=TPM;Calculate expression for genes without transcripts=TRUE;Minimum read count fusion gene table=5;
Assembly: GCF_000772875.2_Mmul_8.0.1
Supplementary files format and content: Mapping statistics and raw read counts, per gene, per sample "clc_mapping_stats.csv"
Supplementary files format and content: Table of gene expression (TPM) "TPM_all.csv"

organism: Macaca mulatta

source_name: Lung

extract_protocol:
single cell suspensions of individual pulmonary granulomas were stained with antibodies (clone) CD11b (ICRF44), CD3 (SP34-2), CD4 (SK3), CD8 (RPA-T8), and CD95 (DX2) for 30 minutes at 4°C (Foreman et al., 2016; Kauffman et al., 2021). Samples were washed and stained with Fixable viability dye eFluor780 from eBioscience/ThermoFisher Scientific (Massachusetts, USA) for 20 minutes at 4°C and thoroughly washed using 1X PBS with 1% fetal bovine serum (FBS). Samples were sorted using a BD FACS Aria in a biosafety cabinet inside a BSL3 laboratory. Sorted cell populations were pelleted and stored in Trizol at -80°C until RNA isolation. RNA was isolated using Direct-zol RNA kit from Zymo Research (California, USA) according to the manufacturers protocol. RNA was assessed for quality and degradation using the 2100 Bioanalyzer System from Agilent (Santa Clara, CA), with the product Bioanalyzer RNA 6000 pico assay.
Library preparation was completed with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing from Takara Bio Inc. (Shiga, Japan) according to manufacturer’s protocol to create full-length cDNA,  using an input of 2 ul of total RNA for each sample.  Quantification of cDNA was performed using Qubit 2.0 from ThermoFisher Scientific (Waltham, MA) with the Qubit dsDNA HS Assay Kit.  The resultant full-length cDNA was used to create final sequencing libraries with the Nextera XT DNA Library Preparation Kit from illumina (San Diego, CA) and the Nextera XT Index Kit v2 Set A from illumina, using 150pg of each cDNA product as input

treatment_protocol: Briefly, 3-4 year old animals were housed and maintained in biocontainment racks in accordance with the Animal Welfare Act in a biosafety level 3 (BSL3) vivarium that is accredited by AAALAC International. Primates were bronchoscopically infected with 40-80 CFU of mCherry-reporter Mycobacterium tuberculosis strain Erdman and cared for until termination of study five weeks later.  All animal procedures were approved by the National Institute of Allergy and Infectious Disease (NIAID) Division of Intramural Research (DIR) Animal Care and Use Committee under animal study LPD-25E. Other data from the rhesus macaques used in this study appeared in a previously study

value: Lung

tag: rna sample

value: CD4 granuloma T cell

tag: animal

tag: granuloma

tag: cfu

tag: cd4 t-cell_count


title: 30_r19_3

description:
sample name: 871
Embryonic blastomere transcriptome


title: CD4_DF4A_4_AB2961

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DFN0_20_AB2839

description:
TPM_all.csv
clc_mapping_stats.csv

value: CD8 granuloma T cell

tag: cd8 t-cell_count


title: CD4_DFN0_20_AB2838

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r16_3

description:
sample name: 868
Embryonic blastomere transcriptome


title: 30_r18_3

description:
sample name: 870
Embryonic blastomere transcriptome


title: 30_r17_3

description:
sample name: 869
Embryonic blastomere transcriptome


title: 30_r15_3

description:
sample name: 867
Embryonic blastomere transcriptome


title: C3H_MNX_sham_-6649_L4


title: CD8_DFN0_19_AB2837

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD4_DFN0_19_AB2836

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DFN0_18_AB2835

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r28_3

description:
sample name: 880
Embryonic blastomere transcriptome


title: CD4_DFN0_18_AB2834

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_2r14_3

description:
sample name: 866
Embryonic blastomere transcriptome


title: 30_r11_3

description:
sample name: 863
Embryonic blastomere transcriptome


title: 30_r12_3

description:
sample name: 864
Embryonic blastomere transcriptome


title: CD8_DFN0_16_AB2831

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r10_3

description:
sample name: 862
Embryonic blastomere transcriptome


title: 30_r21_3

description:
sample name: 873
Embryonic blastomere transcriptome


title: 30_r9_3

description:
sample name: 861
Embryonic blastomere transcriptome


title: CD4_DFN0_16_AB2830

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r8_3

description:
sample name: 860
Embryonic blastomere transcriptome


title: 30_r7_3

description:
sample name: 859
Embryonic blastomere transcriptome


title: CD8_DFN0_15_AB2829

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DFN0_13_AB2825

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r6_3

description:
sample name: 858
Embryonic blastomere transcriptome


title: CD4_DFN0_12_AB2822

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r3_3

description:
sample name: 855
Embryonic blastomere transcriptome


title: CD8_DFN0_10_AB2819

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r4_3

description:
sample name: 856
Embryonic blastomere transcriptome


title: 30_r5_3

description:
sample name: 857
Embryonic blastomere transcriptome


title: CD4_DFN0_11_AB2820

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r13_3

description:
sample name: 865
Embryonic blastomere transcriptome


title: 30_r1_3

description:
sample name: 853
Embryonic blastomere transcriptome


title: CD8_DFN0_11_AB2821

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD4_DFN0_10_AB2818

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DFN0_9_AB2817

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD4_DFN0_17_AB2832

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r30_2

description:
sample name: 238
Embryonic blastomere transcriptome


title: 30_r2_3

description:
sample name: 854
Embryonic blastomere transcriptome


title: CD4_DFN0_14_AB2826

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD4_DFN0_9_AB2816

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r29_2

description:
sample name: 237
Embryonic blastomere transcriptome


title: CD4_DFN0_7_AB2812

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r28_2

description:
sample name: 236
Embryonic blastomere transcriptome


title: CD4_DFN0_8_AB2814

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r27_2

description:
sample name: 235
Embryonic blastomere transcriptome


title: CD4_DFN0_6_AB2810

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DFN0_6_AB2811

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r26_2

description:
sample name: 234
Embryonic blastomere transcriptome


title: CD4_DFN0_13_AB2824

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_2r25_2

description:
sample name: 233
Embryonic blastomere transcriptome


title: CD8_DFN0_5_AB2809

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_2r24_2

description:
sample name: 232
Embryonic blastomere transcriptome


title: CD8_DFN0_3_AB2805

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r23_2

description:
sample name: 231
Embryonic blastomere transcriptome


title: CD4_DFN0_3_AB2804

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DFN0_2_AB2803

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r21_2

description:
sample name: 229
Embryonic blastomere transcriptome


title: 30_r22_2

description:
sample name: 230
Embryonic blastomere transcriptome


title: 30_r19_2

description:
sample name: 227
Embryonic blastomere transcriptome


title: CD8_0DH_15_AB2793

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r20_2

description:
sample name: 228
Embryonic blastomere transcriptome


title: CD4_DFN0_2_AB2802

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_0DH_4_AB2771

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r18_2

description:
sample name: 226
Embryonic blastomere transcriptome


title: 30_r17_2

description:
sample name: 225
Embryonic blastomere transcriptome


title: CD4_0DH_6_AB2774

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r16_2

description:
sample name: 224
Embryonic blastomere transcriptome


title: CD4_0DH_4_AB2770

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r15_2

description:
sample name: 223
Embryonic blastomere transcriptome


title: CD8_0DH_2_AB2767

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_0DH_1_AB2765

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_2r14_2

description:
sample name: 222
Embryonic blastomere transcriptome


title: 30_r12_2

description:
sample name: 220
Embryonic blastomere transcriptome


title: 30_r11_2

description:
sample name: 219
Embryonic blastomere transcriptome


title: 30_r10_2

description:
sample name: 218
Embryonic blastomere transcriptome


title: CD8_DF8B_14_AB2741

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD4_DF8B_14_AB2740

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD4_DF8B_13_AB2738

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DF4A_15_AB2715

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r9_2

description:
sample name: 217
Embryonic blastomere transcriptome


title: 30_r8_2

description:
sample name: 216
Embryonic blastomere transcriptome


title: 30_r7_2

description:
sample name: 215
Embryonic blastomere transcriptome


title: CD4_DF4A_14_AB2712

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r6_2

description:
sample name: 214
Embryonic blastomere transcriptome


title: 30_r4_2

description:
sample name: 212
Embryonic blastomere transcriptome


title: CD4_DF4A_11_AB2706

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r5_2

description:
sample name: 213
Embryonic blastomere transcriptome


title: CD4_DF4A_10_AB2704

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DF4A_9_AB2703

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r3_2

description:
sample name: 211
Embryonic blastomere transcriptome


title: CD4_DF4A_9_AB2702

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DF4A_7_AB2699

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r13_2

description:
sample name: 221
Embryonic blastomere transcriptome


title: 30_2r2_2

description:
sample name: 210
Embryonic blastomere transcriptome


title: CD4_DF8B_20_AB2750

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r1_2

description:
sample name: 209
Embryonic blastomere transcriptome


title: 30_r28_1

description:
sample name: 153
Embryonic blastomere transcriptome


title: CD4_DF4A_5_AB2694

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DF4A_4_AB2693

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r27_1

description:
sample name: 152
Embryonic blastomere transcriptome


title: CD8_DF8B_12_AB2737

description:
TPM_all.csv
clc_mapping_stats.csv


title: CD8_DF4A_1_AB2689

description:
TPM_all.csv
clc_mapping_stats.csv


title: 30_r26_1

description:
sample name: 151
Embryonic blastomere transcriptome


title: 30_2r25_1

description:
sample name: 150
Embryonic blastomere transcriptome


title: 20_9997-T56

type: genomic

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: DNA methylation was quantified using Illumina Infinium Human Methylation EPIC Bead Chip array (Illumina Inc., San Diego, CA) according to the manufacturer’s instructions at University of Minnesota Genomic Center. Briefly, 500ng of DNA from each sample was treated with sodium bisulfite, using the EZ-96 DNA Methylation-Gold kit (Zymo Research, CA, USA). The bisulfite-converted amplified DNA products were denatured into single strands and hybridized to the Illumina Infinium Human Methylation EPIC Bead Chip array (Illumina Inc., San Diego, CA). The hybridized BeadChips were stained, washed, and scanned for the intensities of the unmethylated and methylated bead types using Illumina’s iScan System.

data_processing:
The DNA methylation beta values were obtained and normalized from the raw IDAT files by using the ChAMP package in R.
normalized.csv: Normalized Beta values

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: EDTA blood

label_protocol: Standard Illumina protocol.

growth_protocol: All biosamples were collected in accordance with the guidelines of Institutional Review Boards of Icahn School of Medicine and the Naval Medical Research Center (protocol number NMRC.2020.0006) in compliance with all applicable U.S. federal regulations governing the protection of human subjects.

extract_protocol: Genomic DNA was extracted from cryopreserved PBMC or blood collected in EDTA tubes using Genfind V3 (Beckman Coulter) on a BioMek FXP Laboratory Automation Workstation (Beckman Coulter). All DNA samples were quantified using both absorbance (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA) and fluorescence-based methods (Qubit; Thermo Fisher Scientific, Waltham, MA) using standard dyes selective for double-stranded DNA, minimizing the effects of contaminants that affect the quantitation.

treatment_protocol: Blood collected in EDTA tubes and PBMCs were used for DNA extraction. All samples were frozen at -80 °C after collection prior to processing for methylation analysis.

tag: meth-plate

tag: enrollment batch

value: Longitudinal Study

tag: biocollection id

tag: participant id

tag: sample collection time point (days since t0)

tag: enrollment date t0

tag: gender

value: M

tag: age

tag: group

value: EarlyPost

value: blood


title: 20_9997-T00

scan_protocol: The hybridized BeadChips were stained, washed, and scanned for the intensities of the unmethylated and methylated bead types using Illumina’s iScan System.

value: Control

tag: tissue


title: CD4_DF4A_13_AB2710

description:
TPM_all.csv
clc_mapping_stats.csv

tag: cell type


title: 30_2r24_1

description:
sample name: 149
Embryonic blastomere transcriptome

tag: developmental stage

value: embryonic cells


title: 20_9997-T91

value: LatePost


title: 30_r23_1

description:
sample name: 148
Embryonic blastomere transcriptome


title: 20_9966-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: F

tag: ethnicity

value: Hispanic

value: SARS-CoV-2 Sero+


title: 30_r22_1

description:
sample name: 147
Embryonic blastomere transcriptome


title: 20_9943-T39


title: 20_9943-T63


title: 20_9943-T00


title: 30_r19_1

description:
sample name: 144
Embryonic blastomere transcriptome


title: 30_r20_1

description:
sample name: 145
Embryonic blastomere transcriptome


title: 30_r18_1

description:
sample name: 143
Embryonic blastomere transcriptome


title: 20_9940-T91


title: 20_9940-T63


title: 30_r17_1

description:
sample name: 142
Embryonic blastomere transcriptome


title: 20_9940-T42

value: First


title: 20_9937-T77


title: 20_9937-T56


title: 30_r16_1

description:
sample name: 141
Embryonic blastomere transcriptome


title: 20_9937-T49

value: Mid


title: 30_r15_1

description:
sample name: 140
Embryonic blastomere transcriptome


title: 30_r12_1

description:
sample name: 137
Embryonic blastomere transcriptome


title: 30_r13_1

description:
sample name: 138
Embryonic blastomere transcriptome


title: 30_r11_1

description:
sample name: 136
Embryonic blastomere transcriptome


title: 20_9997-T35


title: 30_r10_1

description:
sample name: 135
Embryonic blastomere transcriptome


title: 20_9937-T00


title: 30_r9_1

description:
sample name: 134
Embryonic blastomere transcriptome


title: 20_9931-T56


title: 20_9931-T77


title: 30_r21_1

description:
sample name: 146
Embryonic blastomere transcriptome


title: 30_r8_1

description:
sample name: 133
Embryonic blastomere transcriptome


title: 20_9918-T63

value: Non-Hispanic


title: 20_9918-T35


title: 20_9914-T77


title: 30_r7_1

description:
sample name: 132
Embryonic blastomere transcriptome


title: 30_r4_1

description:
sample name: 129
Embryonic blastomere transcriptome


title: 30_r5_1

description:
sample name: 130
Embryonic blastomere transcriptome


title: 30_r3_1

description:
sample name: 128
Embryonic blastomere transcriptome


title: 30_2r2_1

description:
sample name: 127
Embryonic blastomere transcriptome


title: 20_9914-T35


title: 20_9914-T42


title: 30_2r14_1

description:
sample name: 139
Embryonic blastomere transcriptome


title: 20_9862-T28


title: 27_r27_1

description:
sample name: 1740
Embryonic blastomere transcriptome


title: 30_r1_1

description:
sample name: 126
Embryonic blastomere transcriptome


title: 20_9914-T00


title: 27_r25_1

description:
sample name: 1738
Embryonic blastomere transcriptome


title: 20_9835-T28


title: 27_r24_1

description:
sample name: 1737
Embryonic blastomere transcriptome


title: 20_9931-T49


title: 20_9931-T00


title: 27_r22_1

description:
sample name: 1735
Embryonic blastomere transcriptome


title: 20_9746-T49


title: 20_9746-T56


title: 27_r23_1

description:
sample name: 1736
Embryonic blastomere transcriptome


title: 30_r6_1

description:
sample name: 131
Embryonic blastomere transcriptome


title: 20_9914-T91


title: 20_9746-T00


title: 20_9728-T98


title: 27_r20_1

description:
sample name: 1733
Embryonic blastomere transcriptome


title: 20_9728-T00


title: 27_r19_1

description:
sample name: 1732
Embryonic blastomere transcriptome


title: 27_r18_1

description:
sample name: 1731
Embryonic blastomere transcriptome


title: 27_r17_1

description:
sample name: 1730
Embryonic blastomere transcriptome


title: 27_r26_1

description:
sample name: 1739
Embryonic blastomere transcriptome


title: 20_9719-T91


title: 20_9836-T28


title: 20_9704-T46


title: 20_9719-T00


title: 27_r15_1

description:
sample name: 1728
Embryonic blastomere transcriptome


title: 27_r16_1

description:
sample name: 1729
Embryonic blastomere transcriptome


title: 27_r14_1

description:
sample name: 1727
Embryonic blastomere transcriptome


title: 20_9746-T77


title: 20_9719-T46


title: 27_r13_1

description:
sample name: 1726
Embryonic blastomere transcriptome


title: 20_9704-T00


title: 27_r11_1

description:
sample name: 1724
Embryonic blastomere transcriptome


title: 27_r9_1

description:
sample name: 1722
Embryonic blastomere transcriptome


title: 20_9694-T98


title: 20_9694-T56


title: 27_r21_1

description:
sample name: 1734
Embryonic blastomere transcriptome


title: 20_9694-T42


title: 20_9728-T42


title: 27_r8_1

description:
sample name: 1721
Embryonic blastomere transcriptome


title: 27_r10_1

description:
sample name: 1723
Embryonic blastomere transcriptome


title: 20_9694-T00


title: 20_9680-T91


title: 27_r5_1

description:
sample name: 1718
Embryonic blastomere transcriptome


title: 20_9680-T56


title: 20_9680-T00


title: 27_r6_1

description:
sample name: 1719
Embryonic blastomere transcriptome


title: 27_r7_1

description:
sample name: 1720
Embryonic blastomere transcriptome


title: 27_r4_1

description:
sample name: 1717
Embryonic blastomere transcriptome


title: 20_9641-T28


title: 27_r3_1

description:
sample name: 1716
Embryonic blastomere transcriptome


title: 27_r1_1

description:
sample name: 1714
Embryonic blastomere transcriptome


title: 20_9634-T91


title: 20_9634-T56


title: 27_r2_1

description:
sample name: 1715
Embryonic blastomere transcriptome


title: 20_9640-T28


title: 20_9634-T28


title: 25_r23_1

description:
sample name: 125
Embryonic blastomere transcriptome


title: 27_r12_1

description:
sample name: 1725
Embryonic blastomere transcriptome


title: 20_9614-T91


title: 20_9614-T77


title: 20_9614-T60


title: 25_2r19_1

description:
sample name: 121
Embryonic blastomere transcriptome


title: 20_9614-T00


title: 25_r20_1

description:
sample name: 122
Embryonic blastomere transcriptome


title: 25_r21_1

description:
sample name: 123
Embryonic blastomere transcriptome


title: 20_9590-T63


title: 20_9590-T39


title: 20_9590-T35


title: 20_9680-T49


title: 25_2r17_1

description:
sample name: 119
Embryonic blastomere transcriptome


title: 20_9568-T28

value: Arrival at quarantine vs Later (all uninfected)

value: Later


title: 25_2r18_1

description:
sample name: 120
Embryonic blastomere transcriptome


title: 20_9509-T91


title: 20_9509-T77


title: 25_r16_1

description:
sample name: 118
Embryonic blastomere transcriptome


title: 20_9509-T00


title: 20_9509-T49


title: 25_2r14_1

description:
sample name: 116
Embryonic blastomere transcriptome


title: 25_2r15_1

description:
sample name: 117
Embryonic blastomere transcriptome


title: 25_r22_1

description:
sample name: 124
Embryonic blastomere transcriptome


title: 20_9454-T56


title: pskmt3-6hpi-1

city: nanjing

first: Han

last: Chen

state: jiangsu

address: weigang no.1,xuanwu district

country: China

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to Phytophthora sojae whole genome using hisat2 with default parameters
Gene expression values were calculated using stringtie and featureCounts with default parameters
Assembly: P. sojae V1.1
Supplementary files format and content: csv files include FPKM values for each sample

organism: Phytophthora sojae strain P6497

source_name: mycelium

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mycelium

tag: strain

tag: genotype

tag: treatment

value: 6 hour post incubation with soybean


title: pskmt3-3hpi-2

value: 3 hour post incubation with soybean


title: pskmt3-3hpi-1


title: 25_2r13_1

description:
sample name: 115
Embryonic blastomere transcriptome


title: 20_9454-T42

value: Longitudinal Study

value: M


title: 20_9424-T70

value: blood


title: wt-6hpi-1

value: WT


title: wt-6hpi-2


title: 25_2r12_1

description:
sample name: 114
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_9424-T56

value: LatePost


title: 20_9415-T77


title: 20_9424-T28


title: 25_P4_1

description:
sample name: 113
Embryonic blastomere transcriptome


title: pskmt3-6hpi-2


title: 25_r10_1

description:
sample name: 112
Embryonic blastomere transcriptome


title: wt-3hpi-2


title: 20_9590-T00

value: Control


title: 20_9415-T46


title: 20_9415-T00


title: wt-3hpi-1


title: 20_9409-T00

value: Arrival at quarantine


title: 25_2r9_1

description:
sample name: 111
Embryonic blastomere transcriptome


title: 20_9401-T70

value: EarlyPost


title: 20_9401-T00


title: 20_9401-T35


title: 20_9454-T70

value: Hispanic


title: 25_r8_1

description:
sample name: 110
Embryonic blastomere transcriptome


title: pskmt3_MY_rep1

value: V8 medium


title: 20_9388-T42


title: 20_9388-T63


title: 25_r7_1

description:
sample name: 109
Embryonic blastomere transcriptome


title: pskmt3_input

library_source: genomic

data_processing:
Clean reads were aligned to Phytophthora sojae whole genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Assembly: Phytophthora sojae V1.1
Supplementary files format and content: Bigwig files, scores represent enriched value(log2(fold-change))

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and precipitated using ethanol followed by twice washes, finally the samples was dried and dissolved in 33 μl ddH2O
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

value: no antibody


title: 20_9388-T35

value: Mid


title: pskmt3_H3K36me3IP-rep2

value: H3K36me3 antibody


title: 20_9373-T91


title: 25_r5_1

description:
sample name: 107
Embryonic blastomere transcriptome


title: 20_9373-T77


title: 20_9373-T42


title: pskmt3_H3K36me3IP-rep1

value: mycelium


title: 20_9388-T00


title: 20_9359-T84

value: Non-Hispanic


title: 20_9373-T00


title: 25_r6_1

description:
sample name: 108
Embryonic blastomere transcriptome


title: WT-input-rep2


title: 25_r3_1

description:
sample name: 105
Embryonic blastomere transcriptome


title: 20_9359-T77


title: WT-input-rep1


title: 25_r4_1

description:
sample name: 106
Embryonic blastomere transcriptome


title: 25_r2_1

description:
sample name: 104
Embryonic blastomere transcriptome


title: 20_9359-T00


title: pskmt3_MY_rep2


title: 20_9359-T74

value: First


title: 20_9343-T39

value: Longitudinal Study


title: 20_9343-T00

value: M


title: WT-H3K36me3IP-rep2


title: WT-H3K36me3IP-rep1


title: 20_9331-T00

value: Arrival at quarantine vs Later (all uninfected)

value: blood


title: 24_r23_2

description:
sample name: 1378
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_9356-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: 25_r1_1

description:
sample name: 103
Embryonic blastomere transcriptome


title: 20_9302-T28

value: Later


title: nor-like1 mutant tomato exocarp, MG 3

city: beijing

first: zhijian

last: liu

address: Last Olympic Century Center, Xisanqi, Changping

institute: boyunhuakang

description: WT-VS-nor-like1-1.DEseq2_Method.GeneDiffExp.txt

data_processing:
DNBSEQ-T7 platform used for sequence
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence
using HISAT2 and StringTie to mapping reads to human genome and to reconstruct transcirpts
using bowtie2 and RSEM to mapping reads to gene and to calculate gene expression
Functional enrichment analyses including Gene Ontology (GO) and KEGG were performed to identify which DEGs were signifcantly enriched in GO terms or metabolic pathways
Assembly: SL4.0
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample
Supplementary files format and content: tab-delimited text files include DEGs information

organism: Solanum lycopersicum

source_name: exocarp

extract_protocol:
Total RNA was extracted from cell sample tube using Trizol reagent according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard MGI protocols

value: exocarp

value: exocarp cells

value: SlNOR-like1 knockout


title: 24_r22_2

description:
sample name: 1377
Embryonic blastomere transcriptome


title: 20_9249-T77

value: Hispanic

value: LatePost


title: nor-like1 mutant tomato exocarp, MG 2


title: 20_9249-T56

value: EarlyPost


title: 24_r21_2

description:
sample name: 1376
Embryonic blastomere transcriptome


title: 20_9249-T00

value: Control


title: 20_9248-T28

value: Non-Hispanic


title: 20_9249-T35

value: Mid


title: nor-like1 mutant tomato exocarp, MG 1


title: 24_r20_2

description:
sample name: 1375
Embryonic blastomere transcriptome


title: WT tomato exocarp, MG 3

value: WT


title: 20_9244-T28

value: M


title: 20_9241-T84

value: Longitudinal Study


title: 24_r19_2

description:
sample name: 1374
Embryonic blastomere transcriptome


title: 20_9241-T46

value: blood


title: 24_r18_2

description:
sample name: 1373
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_9241-T00


title: 20_9235-T56


title: WT tomato exocarp, MG 1


title: WT tomato exocarp, MG 2


title: 20_9235-T00


title: 20_9235-T46


title: 24_r17_2

description:
sample name: 1372
Embryonic blastomere transcriptome


title: 24_2r16_2

description:
sample name: 1371
Embryonic blastomere transcriptome


title: ScaO2

city: Loma Linda

first: Charles

last: Wang

state: CA

address: 11021 Campus Street

institute: Loma Linda University

description: RNA-seq

data_processing:
Basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
For RNA-seq, the raw reads were trimmed using TrimGalore (v.0.4.5), and then aligned to the human reference genome (GRCh38) for gene counts using STAR (--quantMode GeneCounts).
For ATAC-seq, the raw reads were mapped to human reference genome (GRCh38) using the bioinformatics pipeline snakePipes with the ATAC-seq mode. In the pipeline, fastq files were trimmed using TrimGalore, aligned with Bowtie2, and peaks are called with MACS2.
For ATAC-seq, a consensus peak set was defined by taking the intersection of peaks from both biological replicates using soGGi (v.1.18) package and regions intersecting with blacklisted regions and ChrY were excluded. The ATAC-seq count matrix was computed by counting the reads that fell into the consensus peaks using Rsubread v2.0.1.
For RRBS analysis, raw fastq reads were trimmed using TrimGalore (v.0.4.5) and Nugen RRBS trimming script (trimRRBSdiversityAdaptCustomers.py). After trimming, reads were aligned to the human reference genome (GRCh38) with Bismark54 by default parameter settings, and PCR duplicates were removed by Nugen script (nudup.py).
The methylation call files (Bismark files) including the location of each CpG sites and the methylation percentage were generated by the bismark_methylation_extractor function.
Assembly: NCBI GRCh38
Supplementary files format and content: RNAseq.ScaO.raw.count

source_name: cord blood CD34+ cells reprogrammed iMSCs

growth_protocol: After reprogramming, the cells were seeded onto fibronectin-coated plates in the mixture of erythroid medium and MSC medium (50:50 ratio) supplemented with small molecules including 3 μM CHIR99021, 10 μM Forskolin, 10 μM ALK inhibitor (SB431542), and 5 μM Tranylcypromine hydrochloride for two days, and replaced with MSC medium thereafter.

extract_protocol:
QIAGEN AllPrep DNA/RNA/miRNA Universal Kit protocol
RNA-seq libraries was constructed using the NuGEN Ovation universal RNA-seq kit (TECAN). RRBS libraries were constructed following standard protocols of the NuGEN Ovation Ultralow Methyl-seq Library Systems. ATAC-seq libraries were constructed by following the improved protocol as described by Corces et al., 2017.

tag: reprogram factors

value: SFFV-OCT4 and Sca1-OCT4

tag: reprogram day

value: day 28


title: ScaO3

description: RNA-seq


title: 20_9226-T28

tag: meth-plate

tag: enrollment batch

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: 24_r15_2

description:
sample name: 1370
Embryonic blastomere transcriptome


title: ScaO1

description: RNA-seq


title: 20_9194-T28

tag: biocollection id

tag: participant id


title: 20_9187-T28

tag: sample collection time point (days since t0)

tag: enrollment date t0


title: 24_r14_2

description:
sample name: 1369
Embryonic blastomere transcriptome


title: CFG2363 PM9_D28_5F-K_ATACseq

data_processing:
Basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
For RNA-seq, the raw reads were trimmed using TrimGalore (v.0.4.5), and then aligned to the human reference genome (GRCh38) for gene counts using STAR (--quantMode GeneCounts).
For ATAC-seq, the raw reads were mapped to human reference genome (GRCh38) using the bioinformatics pipeline snakePipes with the ATAC-seq mode. In the pipeline, fastq files were trimmed using TrimGalore, aligned with Bowtie2, and peaks are called with MACS2.
For ATAC-seq, a consensus peak set was defined by taking the intersection of peaks from both biological replicates using soGGi (v.1.18) package and regions intersecting with blacklisted regions and ChrY were excluded. The ATAC-seq count matrix was computed by counting the reads that fell into the consensus peaks using Rsubread v2.0.1.
For RRBS analysis, raw fastq reads were trimmed using TrimGalore (v.0.4.5) and Nugen RRBS trimming script (trimRRBSdiversityAdaptCustomers.py). After trimming, reads were aligned to the human reference genome (GRCh38) with Bismark54 by default parameter settings, and PCR duplicates were removed by Nugen script (nudup.py).
The methylation call files (Bismark files) including the location of each CpG sites and the methylation percentage were generated by the bismark_methylation_extractor function.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: For ATAC-seq datasets, narrowpeak files were generated. For RRBS datasets, CpG coverage report in text format were generated.

source_name: PBMC reprogrammed iMSCs


title: 20_9153-T63

tag: gender

tag: age


title: CFG2361 PM9_D28_5F-O_ATACseq


title: 24_r13_2

description:
sample name: 1368
Embryonic blastomere transcriptome


title: 20_9153-T56

tag: group

tag: tissue


title: 24_r12_2

description:
sample name: 1367
Embryonic blastomere transcriptome

tag: developmental stage

tag: cell type


title: CFG2360 PM9_D28_5F_ATACseq


title: 24_r11_2

description:
sample name: 1366
Embryonic blastomere transcriptome


title: 20_9140-T63

value: F

tag: ethnicity


title: 24_r10_2

description:
sample name: 1365
Embryonic blastomere transcriptome


title: 20_9234-T91


title: 20_9127-T91


title: 20_9140-T28

value: First


title: 20_9131-T28


title: 24_r9_2

description:
sample name: 1364
Embryonic blastomere transcriptome


title: 20_9234-T56


title: CFG2358 PM10_D28_5F-O_ATACseq


title: 20_9127-T35


title: CFG2357 PM10_D28_5F_ATACseq


title: 20_9092-T28


title: 24_2r8_2

description:
sample name: 1363
Embryonic blastomere transcriptome


title: 20_9058-T84


title: 20_9179-T28


title: 20_9063-T28


title: SELEX PTBP1 rep2

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description: replicates were merged for processing

data_processing:
The raw reads files with fastq format are converted by Illumina bcl2fastq (v2.16).
After the sequencing of PTBP1 SELEX libraries, adapters were trimmed off using the Trim Galore program (0.6.4). The parameters used were as follows: trim_galore -q 25 --phred33 -e 0.2 --max_n 1 --length 10 --max_length 10 --stringency 4 -o outdir read.fq. The reads count and z-score  of each heptamer were calculated using homemade scripts.
Supplementary files format and content: Read count of each heptamer in txt format
Library strategy: SELEX

organism: synthetic construct

source_name: random N10 library

extract_protocol: The input ssDNA library for SELEX was synthesized. The library was amplified by PCR (5 cycles) to generate templates for the initial in vitro transcription of the ssRNA library. To pull down PTBP1 and its interacting RNA, 40 µl of protein A/G magnetic beads coupled with anti-PTBP1 antibody were added to the ssRNA pool and then rotated at room temperature for 1 h. To elute the bound RNA, the beads were washed three times with 1 ml of binding buffer and then resuspended in 50 µl of TE buffer, 50 µl of 2 × Proteinase K buffer (0.02 M Tris-HCl, pH7.8, 0.02 M EDTA, 1% SDS), and 1 µl of Proteinase K and incubated at 50 °C for 30 min. RNA was extracted with Trizol LS, reverse transcribed into cDNA, and amplified by PCR. The PCR products were fractionated on the 2% agarose gel and purified with Gel Extraction Kit (Qiagen, 28604). This whole process was performed three times. In the third round, cDNA was amplified with index-containing primers compatible with Illumina HiSeq X Ten.

tag: antibody

value: anti-PTBP1 (BB7)


title: SELEX PTBP1 rep1

description: replicates were merged for processing


title: 24_r7_2

description:
sample name: 1362
Embryonic blastomere transcriptome


title: 24_r6_2

description:
sample name: 1361
Embryonic blastomere transcriptome


title: 20_9047-T84

value: Hispanic


title: 20_9047-T77


title: 24_r5_2

description:
sample name: 1360
Embryonic blastomere transcriptome


title: 20_9153-T42


title: 20_9058-T00


title: CFG2359 PM10_D28_5F-K_ATACseq


title: 20_9140-T56

value: EarlyPost


title: 20_9047-T74


title: 20_8991-T28

value: SARS-CoV-2 Sero-


title: 24_r3_2

description:
sample name: 1358
Embryonic blastomere transcriptome


title: Liver T cells PBS Rep 8

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description: JMR18200219_S12_R1_001_JM80_XBLA32_1h_LV_T

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.95 using HISAT2 version 2.1.0
Raw counts per gene were determined using Htseq-count version 0.11.2 with the following options: -s reverse --mode=intersection-nonempty --type=exon --idattr=gene_id
Assembly: GRCm38.95
Supplementary files format and content: Matrix of raw counts

source_name: T cells

extract_protocol:
Ly6G+ neutrophils and CD3+ T cells were FACS-sorted from the peripheral blood and tumours of DEN/ALIOS mice. Purity of isolated populations was analysed by flow cytometry at ≥ 97%. RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol. RNA quality and quantity was checked on an Agilent Bioanalyser 2100 using RNA Pico 6000 chip.  Whole tumor and healthy tissue was snap frozen and stored at -80C. Tissue was homogenized using the Precellys Evolution homogenizer and bulk RNA was isolated using the Rneasy Kit (Qiagen) according to the manufacturer’s instructions, including the optional Dnase I step. RNA quality and quantity was analysed on a Nanodrop 2000 (Thermo Fisher Scientific) and an Agilent 2200 TapeStation (D1000 screentape). Only samples with a RIN value >7 were used for library preparation. Libraries were prepared using the TruSeq stranded mRNA Kit. Library quality and quantity were assessed using 2200 TapeStation (Agilent) and Qubit (ThermoFisher Scientific).
Libraries for cluster generation and DNA sequencing were prepared following the TaKaRa SMARTer Stranded Total RNA-Seq Kit- Pico Input Mammalian v2 protocol. Quality and quantity of the DNA libraries was assessed on an Agilent 2200 Tapestation (D1000 screentape) and Qubit (Thermo Fisher Scientific) respectively.
The libraries were run on the Illumina NextSeq 500 using the High Output v2.5, 75 cycles kit (2 x 36cycles, paired-end reads).

treatment_protocol: mice treated as described in each sample characteristics: treatment field

tag: source tissue

value: Liver

tag: Sex

value: Male

tag: genotype

value: WT (C57BL/6 from in-house colony)

value: T cells

tag: treatment

value: PBS


title: 20_9047-T00

tag: meth-plate

tag: enrollment batch

value: Longitudinal Study

value: M

value: Control

value: blood


title: Liver T cells PBS Rep 7

description: JMR18200218_S19_R1_001_JM72_XBLA32_1f_LV_T


title: 20_8974-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: biocollection id

tag: participant id


title: 20_8968-T35

tag: sample collection time point (days since t0)

tag: enrollment date t0

value: Non-Hispanic

value: Mid


title: Liver T cells PBS Rep 6

description: JMR18200218_S16_R1_001_JM64_XBLA32_1d_LV_T


title: 24_r2_2

description:
sample name: 1357
Embryonic blastomere transcriptome

value: embryonic cells


title: 24_r4_2

description:
sample name: 1359
Embryonic blastomere transcriptome


title: 20_8968-T42

tag: gender

tag: age


title: 20_9058-T42

tag: group

tag: tissue


title: Liver T cells PBS Rep 4

description: JMR18200218_S04_R1_001_JM48_XBLA32_1c_LV_T

tag: cell type


title: 20_8939-T28

tag: ethnicity

value: SARS-CoV-2 Sero+


title: 20_8968-T00


title: Liver T cells PBS Rep 5

description: JMR18200218_S12_R1_001_JM56_XBLA32_1a_LV_T


title: 24_r1_2

description:
sample name: 1356
Embryonic blastomere transcriptome

tag: developmental stage


title: Liver T cells PBS Rep 3

description: JMR18191128_S24_R1_001_JM24_XBLA36_1b_LV_T

tag: source tissue


title: 20_8866-T70

value: First


title: 24_r24_1

description:
sample name: 1673
Embryonic blastomere transcriptome


title: 20_8866-T74


title: 20_8800-T91

value: LatePost


title: 20_8825-T28

value: SARS-CoV-2 Sero-


title: 24_r23_1

description:
sample name: 1672
Embryonic blastomere transcriptome


title: 20_8800-T56

value: EarlyPost


title: Liver T cells PBS Rep 2

description: JMR18191128_S18_R1_001_JM18_XBLA36_1a_LV_T

value: Liver

tag: Sex

value: Male


title: 20_8800-T46


title: Liver T cells PBS Rep 1

description: JMR18191128_S12_R1_001_JM12_XBLA36_1d_LV_T

tag: genotype

value: WT (C57BL/6 from in-house colony)

value: T cells


title: 24_r22_1

description:
sample name: 1671
Embryonic blastomere transcriptome


title: 20_8775-T28

value: Hispanic


title: Liver Tissue DEN ALIOS Rep 15

source_name: Whole Tissue

value: Whole Tissue

tag: treatment

value: Normal


title: Liver Tissue DEN ALIOS Rep 14


title: 24_r21_1

description:
sample name: 1670
Embryonic blastomere transcriptome


title: 24_r20_1

description:
sample name: 1669
Embryonic blastomere transcriptome


title: 20_8730-T91

tag: meth-plate

value: Longitudinal Study

value: M

value: blood


title: 20_8730-T00

tag: enrollment batch

value: Non-Hispanic

value: Control


title: 20_8800-T00

tag: biocollection id


title: Liver Tissue DEN ALIOS Rep 13


title: 20_8708-T98

tag: participant id


title: 20_8730-T32

tag: sample collection time point (days since t0)

value: Mid


title: 24_r19_1

description:
sample name: 1668
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_8708-T56

tag: enrollment date t0


title: Liver Tissue DEN ALIOS Rep 12


title: 20_8708-T00

tag: gender


title: 20_8692-T49

tag: age


title: Liver Tissue DEN ALIOS Rep 11


title: 20_8692-T35

tag: group


title: Liver Tissue DEN ALIOS Rep 10


title: 20_8692-T00

tag: tissue


title: 24_2r16_1

description:
sample name: 1665
Embryonic blastomere transcriptome

tag: cell type


title: 20_8671-T98

tag: ethnicity

value: LatePost


title: 20_8671-T56


title: Liver Tissue DEN ALIOS Rep 9


title: 24_r15_1

description:
sample name: 1664
Embryonic blastomere transcriptome

tag: developmental stage


title: Liver Tissue DEN ALIOS Rep 8

tag: source tissue


title: 20_8730-T42


title: 20_8671-T46


title: 20_8629-T84


title: 20_8671-T00


title: 24_r13_1

description:
sample name: 1662
Embryonic blastomere transcriptome


title: 20_8629-T56


title: Liver Tissue DEN ALIOS Rep 6

tag: Sex


title: 20_8629-T00


title: 24_r14_1

description:
sample name: 1663
Embryonic blastomere transcriptome


title: 24_r12_1

description:
sample name: 1661
Embryonic blastomere transcriptome


title: Liver Tissue DEN ALIOS Rep 7

tag: genotype


title: 20_8610-T77


title: Liver Tissue DEN ALIOS Rep 5

tag: treatment


title: 24_r18_1

description:
sample name: 1667
Embryonic blastomere transcriptome


title: 24_r11_1

description:
sample name: 1660
Embryonic blastomere transcriptome


title: 24_r17_1

description:
sample name: 1666
Embryonic blastomere transcriptome


title: 20_8610-T35

tag: meth-plate


title: 20_8708-T42

tag: enrollment batch


title: Liver Tissue DEN ALIOS Rep 4


title: 20_8610-T56

tag: biocollection id


title: 20_8590-T74

tag: participant id

value: First


title: Liver Tissue DEN ALIOS Rep 3


title: 24_r9_1

description:
sample name: 1658
Embryonic blastomere transcriptome


title: Liver Tissue DEN ALIOS Rep 2


title: 20_8586-T56

tag: sample collection time point (days since t0)

value: EarlyPost


title: 20_8590-T84

tag: enrollment date t0


title: 24_r8_1

description:
sample name: 1657
Embryonic blastomere transcriptome


title: 20_8610-T00

tag: gender


title: 20_8585-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: age

value: SARS-CoV-2 Sero+


title: 20_8566-T28

value: F

tag: group


title: 24_r7_1

description:
sample name: 1656
Embryonic blastomere transcriptome


title: Liver Tissue DEN ALIOS Rep 1

value: Liver

value: Male

value: WT (C57BL/6 from in-house colony)


title: 20_8440-T28

tag: tissue


title: 20_8416-T28

value: Arrival at quarantine vs Later (all uninfected)

value: Later


title: 24_r6_1

description:
sample name: 1655
Embryonic blastomere transcriptome

tag: cell type


title: Liver T cells DEN ALIOS CXCR2i aPD1 Rep 4

value: T cells

value: DEN ALIOS CXCR2i aPD1


title: 20_8414-T39

value: Longitudinal Study

value: M

tag: ethnicity

value: Non-Hispanic

value: blood


title: Liver T cells DEN ALIOS CXCR2i aPD1 Rep 5

description: JMR18190809_S20_R1_001_JM32_RCN24_1a_LIV_T


title: 20_8414-T77

value: LatePost


title: Liver T cells DEN ALIOS CXCR2i aPD1 Rep 3


title: 24_r5_1

description:
sample name: 1654
Embryonic blastomere transcriptome

tag: developmental stage

value: embryonic cells


title: 24_r10_1

description:
sample name: 1659
Embryonic blastomere transcriptome


title: 20_8590-T77

value: Hispanic

value: Mid


title: 24_2r4_1

description:
sample name: 1653
Embryonic blastomere transcriptome


title: 20_8414-T00

value: Control


title: 20_8414-T35


title: 20_8378-T42

value: First


title: 20_8378-T56

value: EarlyPost


title: Liver T cells DEN ALIOS CXCR2i aPD1 Rep 2

tag: source tissue

value: Liver

value: Male


title: 20_8360-T70


title: Liver T cells DEN ALIOS CXCR2i aPD1 Rep 1

description: JMR18190810_S16_R1_001_JM36_RCN24_1b_LIV_T

tag: Sex

value: WT (C57BL/6 from in-house colony)


title: 24_r2_1

description:
sample name: 1651
Embryonic blastomere transcriptome


title: 24_r1_1

description:
sample name: 1650
Embryonic blastomere transcriptome


title: 20_8360-T00


title: 20_8359-T56

value: F


title: 20_8359-T42


title: 20_8359-T28


title: 23_r21_1

description:
sample name: 1355
Embryonic blastomere transcriptome


title: Liver Neutrophil DEN ALIOS CXCR2i aPD1 Rep 6

source_name: Neutrophils

tag: genotype

value: Neutrophils


title: 20_8349-T70


title: 23_r20_1

description:
sample name: 1354
Embryonic blastomere transcriptome


title: Liver Neutrophil DEN ALIOS CXCR2i aPD1 Rep 5

description: JMR18190810_S20_R1_001_JM44_RCN21_1a_LIV_N

tag: treatment

value: DEN ALIOS CXCR2i aPD1


title: 20_8349-T00

tag: meth-plate

value: Longitudinal Study


title: 23_r19_1

description:
sample name: 1353
Embryonic blastomere transcriptome


title: 20_8325-T49

tag: enrollment batch

value: M


title: Liver Neutrophil DEN ALIOS CXCR2i aPD1 Rep 4

description: JMR18190810_S18_R1_001_JM42_RCN17_4c_LIV_N


title: 23_r18_1

description:
sample name: 1352
Embryonic blastomere transcriptome


title: 20_8378-T00

tag: biocollection id


title: 24_r3_1

description:
sample name: 1652
Embryonic blastomere transcriptome


title: Liver Neutrophil DEN ALIOS CXCR2i aPD1 Rep 3

description: JMR18190810_S15_R1_001_JM35_RCN24_1b_LIV_N


title: 20_8267-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: participant id

value: Non-Hispanic

value: SARS-CoV-2 Sero+


title: 20_8245-T28

tag: sample collection time point (days since t0)

value: SARS-CoV-2 Sero-

value: blood


title: Liver Neutrophil DEN ALIOS CXCR2i aPD1 Rep 8


title: 23_r17_1

description:
sample name: 1351
Embryonic blastomere transcriptome

value: embryonic cells


title: 23_r16_1

description:
sample name: 1350
Embryonic blastomere transcriptome


title: Liver Neutrophil DEN ALIOS CXCR2i aPD1 Rep 1

description: JMR18190809_S22_R1_001_JM38_RCN16_2a_BLIVN


title: 20_8197-T28

tag: enrollment date t0


title: 23_r15_1

description:
sample name: 1349
Embryonic blastomere transcriptome


title: Liver Neutrophil DEN ALIOS CXCR2i aPD1 Rep 2

description: JMR18190809_S24_R1_001_JM40_RCN17_4b_LIV_N


title: 20_8349-T56

tag: gender


title: 20_8194-T28

tag: age


title: Liver Neutrophil DEN ALIOS CXCR2i aPD1 Rep 7


title: 20_8186-T28

tag: group


title: 20_8349-T46

value: Mid

tag: tissue


title: Liver T cells DEN ALIOS CXCR2i Rep 6

description: JMR18191128_S08_R1_001_JM8_RCN24_8f_LV_T

tag: cell type

value: T cells

value: DEN ALIOS CXCR2i aPD1 isotype


title: 20_8325-T77

tag: ethnicity

value: Hispanic

value: EarlyPost


title: 20_8167-T28

value: First


title: 20_8167-T56


title: Liver T cells DEN ALIOS CXCR2i Rep 5

description: JMR18191128_S04_R1_001_JM4_RCN26_4a_LV_T

value: Liver

value: Male

value: WT (C57BL/6 from in-house colony)


title: 23_r14_1

description:
sample name: 1348
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_8325-T105

value: Longitudinal Study

value: LatePost


title: 20_8325-T00

value: M

value: Control


title: 23_r13_1

description:
sample name: 1347
Embryonic blastomere transcriptome


title: Liver T cells DEN ALIOS CXCR2i Rep 4

tag: source tissue


title: 23_r12_1

description:
sample name: 1346
Embryonic blastomere transcriptome


title: 20_8122-T91

value: Non-Hispanic


title: 20_8127-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: 20_8122-T56

value: blood


title: Liver T cells DEN ALIOS CXCR2i Rep 3

tag: Sex

value: DEN ALIOS CXCR2i


title: 20_8048-T63


title: 20_8102-T28

value: SARS-CoV-2 Sero-


title: 20_8048-T35

value: Mid


title: 23_r10_1

description:
sample name: 1344
Embryonic blastomere transcriptome

value: embryonic cells


title: Liver T cells DEN ALIOS CXCR2i Rep 1

tag: genotype

value: T cells

value: DEN ALIOS CXCR2i aPD1 isotype


title: 23_r9_1

description:
sample name: 1343
Embryonic blastomere transcriptome


title: 20_8083-T28


title: 20_8048-T00


title: 20_8167-T91

value: Hispanic


title: 20_8023-T00

value: Arrival at quarantine vs Later (all uninfected)

value: F

value: Arrival at quarantine


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 10

description: XCR18190507_S22_R1_001_XC22_RCN25_1a_Liv_val

value: Liver

value: Male

value: WT (C57BL/6 from in-house colony)

value: Neutrophils

tag: treatment


title: 20_8017-T56

tag: meth-plate

value: Longitudinal Study

value: M


title: 23_r8_1

description:
sample name: 1342
Embryonic blastomere transcriptome


title: 20_8017-T49

tag: enrollment batch

value: blood


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 9

description: XCR18190507_S16_R1_001_XC16_RCN18_2c_Liv_val

value: DEN ALIOS CXCR2i


title: 23_r7_1

description:
sample name: 1341
Embryonic blastomere transcriptome


title: 20_8015-T77

tag: biocollection id

value: LatePost


title: 20_8017-T00

tag: participant id

value: Control


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 8

description: XCR18190507_S14_R1_001_XC14_RCN18_2b_Liv_val


title: 23_r6_1

description:
sample name: 1340
Embryonic blastomere transcriptome

value: embryonic cells


title: 23_r11_1

description:
sample name: 1345
Embryonic blastomere transcriptome


title: 23_r5_1

description:
sample name: 1339
Embryonic blastomere transcriptome


title: Liver T cells DEN ALIOS CXCR2i Rep 2

value: T cells


title: 20_7996-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: sample collection time point (days since t0)

value: Non-Hispanic

value: SARS-CoV-2 Sero+


title: 20_8015-T63

tag: enrollment date t0

value: EarlyPost


title: 20_7981-T91

tag: gender


title: 20_8015-T35

tag: age

value: Mid


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 6

description: JMR18191128_S03_R1_001_JM3_RCN26_4a_LV_N

value: Liver

value: DEN ALIOS CXCR2i aPD1 isotype


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 7

description: JMR18191128_S07_R1_001_JM7_RCN24_8f_LV_N

value: Male

value: WT (C57BL/6 from in-house colony)


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 5

value: Neutrophils


title: 20_7981-T56

value: Longitudinal Study

value: M

tag: group


title: 20_7981-T46

tag: tissue

value: blood


title: 20_7981-T00


title: 23_r4_1

description:
sample name: 1338
Embryonic blastomere transcriptome

tag: cell type


title: 23_r3_1

description:
sample name: 1337
Embryonic blastomere transcriptome


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 4

value: DEN ALIOS CXCR2i


title: 20_8017-T46

tag: ethnicity

value: Hispanic


title: 23_r2_1

description:
sample name: 1336
Embryonic blastomere transcriptome

tag: developmental stage

value: embryonic cells


title: 20_7871-T91

value: LatePost


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 3

tag: source tissue


title: 23_r1_1

description:
sample name: 1335
Embryonic blastomere transcriptome


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 2

tag: Sex


title: 20_7871-T00

value: Control


title: 22_r21_1

description:
sample name: 1334
Embryonic blastomere transcriptome


title: 20_7794-T42

value: Non-Hispanic


title: 20_7833-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: 22_r20_1

description:
sample name: 1333
Embryonic blastomere transcriptome


title: Liver Neutrophils DEN ALIOS CXCR2i Rep 1

description: JMR18190809_S16_R1_001_JM28_RCN25_1b_LIV_N

tag: genotype


title: 22_r19_1

description:
sample name: 1332
Embryonic blastomere transcriptome


title: 20_7766-T28

value: SARS-CoV-2 Sero-


title: 20_7690-T70


title: Liver T cells DEN ALIOS aPD1 Rep 5

value: Liver

value: T cells

tag: treatment

value: DEN ALIOS aPD1


title: Liver T cells DEN ALIOS aPD1 Rep 4

value: Male

value: WT (C57BL/6 from in-house colony)


title: 20_7794-T00

tag: meth-plate

value: Longitudinal Study


title: 20_7690-T56

tag: enrollment batch

value: M


title: 20_7794-T35

tag: biocollection id

value: Mid

value: blood


title: 22_r18_1

description:
sample name: 1331
Embryonic blastomere transcriptome


title: 20_7920-T28

tag: participant id


title: 20_7871-T53

tag: sample collection time point (days since t0)

value: EarlyPost


title: 22_r17_1

description:
sample name: 1330
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_7656-T28

tag: enrollment date t0


title: 20_7690-T28

tag: gender

value: Hispanic


title: Liver T cells DEN ALIOS aPD1 Rep 3


title: 20_7652-T28

tag: age


title: 22_r16_1

description:
sample name: 1329
Embryonic blastomere transcriptome


title: Liver T cells DEN ALIOS aPD1 Rep 2


title: 20_7647-T56

tag: group


title: Liver T cells DEN ALIOS aPD1 Rep 1


title: 22_r15_1

description:
sample name: 1328
Embryonic blastomere transcriptome


title: 20_7871-T49

tag: tissue


title: 20_7647-T28

value: First


title: 20_7647-T00

value: Non-Hispanic

value: Control


title: Liver Neutrophils DEN ALIOS aPD1 Rep 5

tag: cell type

value: Neutrophils


title: 20_7589-T91

tag: ethnicity

value: LatePost


title: 22_r14_1

description:
sample name: 1327
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_7589-T63


title: Liver Neutrophils DEN ALIOS aPD1 Rep 4

tag: source tissue

value: Liver


title: 20_7582-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: Liver Neutrophils DEN ALIOS aPD1 Rep 3

tag: Sex

value: Male

value: DEN ALIOS aPD1


title: 22_r12_1

description:
sample name: 1325
Embryonic blastomere transcriptome


title: 20_7577-T56

value: Longitudinal Study

value: F


title: Liver Neutrophils DEN ALIOS aPD1 Rep 2

tag: genotype

value: WT (C57BL/6 from in-house colony)


title: 22_r13_1

description:
sample name: 1326
Embryonic blastomere transcriptome


title: 20_7589-T00

value: M

value: blood


title: 22_r10_1

description:
sample name: 1323
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_7560-T77


title: 20_7560-T63

value: EarlyPost


title: Liver Neutrophils DEN ALIOS aPD1 Rep 1

tag: treatment


title: 20_7560-T00

tag: meth-plate


title: 20_7560-T35

tag: enrollment batch

value: Mid


title: 22_r11_1

description:
sample name: 1324
Embryonic blastomere transcriptome


title: 20_7476-T28

tag: biocollection id

value: Non-Hispanic


title: 20_7577-T63

tag: participant id


title: 22_r9_1

description:
sample name: 1322
Embryonic blastomere transcriptome


title: 20_7577-T28

tag: sample collection time point (days since t0)

value: First


title: 20_7466-T28

tag: enrollment date t0


title: Liver T cells DEN ALIOS Rep 4

description: JMR18190810_S04_R1_001_JM12_RCN24_2c_LIV_T

value: T cells

value: DEN ALIOS


title: 22_r8_1

description:
sample name: 1321
Embryonic blastomere transcriptome


title: Liver T cells DEN ALIOS Rep 5

description: JMR18190810_S08_R1_001_JM16_RCN24_2d_LIV_T

value: Liver


title: 20_7589-T35

tag: gender


title: 22_r7_1

description:
sample name: 1320
Embryonic blastomere transcriptome


title: 20_7451-T91

tag: age

value: LatePost


title: Liver T cells DEN ALIOS Rep 6

description: JMR18190810_S12_R1_001_JM20_RCJ22_3b_LIV_T


title: 20_7451-T49

tag: group


title: 22_r6_1

description:
sample name: 1319
Embryonic blastomere transcriptome


title: Liver T cells DEN ALIOS Rep 3

description: JMR18190809_S14_R1_001_JM26_RCN25_3h_LIV_T

value: DEN ALIOS/Vehicle


title: 20_7432-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+

tag: tissue


title: 20_7388-T28


title: 20_7382-T74

value: Longitudinal Study


title: 20_7392-T00

value: Arrival at quarantine vs Later (all uninfected)

value: Arrival at quarantine


title: 22_r5_1

description:
sample name: 1318
Embryonic blastomere transcriptome

tag: cell type


title: Liver T cells DEN ALIOS Rep 1

description: JMR18190809_S04_R1_001_JM4_RCN22_1a_LIV_T

value: Male

value: WT (C57BL/6 from in-house colony)


title: Liver T cells DEN ALIOS Rep 2

description: JMR18190809_S08_R1_001_JM8_RCN21__2b_LIV_T


title: 20_7382-T63

value: M

tag: ethnicity

value: blood


title: 22_r4_1

description:
sample name: 1317
Embryonic blastomere transcriptome

tag: developmental stage

value: embryonic cells


title: 20_7382-T00

value: Non-Hispanic

value: Control


title: 20_7253-T28


title: Liver Tumour small DEN ALIOS Rep 25

source_name: Small Primary Tumour

tag: source tissue

value: Small Primary Tumour


title: Liver Tumour small DEN ALIOS Rep 24

tag: Sex

value: DEN ALIOS


title: 22_r3_1

description:
sample name: 1316
Embryonic blastomere transcriptome


title: 20_7250-T77

value: Hispanic


title: 22_r2_1

description:
sample name: 1315
Embryonic blastomere transcriptome


title: 20_7302-T00


title: 20_7250-T63

value: EarlyPost


title: 20_7239-T91

value: LatePost


title: 20_7250-T39


title: Liver Tumour small DEN ALIOS Rep 22

value: Liver

tag: genotype


title: 20_7250-T00


title: 21_r16_1

description:
sample name: 1312
Embryonic blastomere transcriptome


title: 22_r1_1

description:
sample name: 1314
Embryonic blastomere transcriptome


title: 21_2r17_1

description:
sample name: 1313
Embryonic blastomere transcriptome


title: 20_7239-T32

value: Mid


title: 20_7239-T56

value: Longitudinal Study


title: Liver Tumour small DEN ALIOS Rep 23

tag: treatment


title: 20_7239-T00

tag: meth-plate


title: 20_7226-T00

tag: enrollment batch

value: Arrival at quarantine vs Later (all uninfected)

value: F


title: 20_7223-T70

tag: biocollection id


title: Liver Tumour small DEN ALIOS Rep 21

value: Male


title: 21_r14_1

description:
sample name: 1310
Embryonic blastomere transcriptome


title: 20_7202-T56

tag: participant id


title: 20_7223-T63

tag: sample collection time point (days since t0)


title: Liver Tumour small DEN ALIOS Rep 19

value: WT (C57BL/6 from in-house colony)


title: 21_r13_1

description:
sample name: 1309
Embryonic blastomere transcriptome


title: 20_7193-T91

tag: enrollment date t0

value: Later


title: 20_7202-T00

tag: gender

value: M

value: blood


title: Liver Tumour small DEN ALIOS Rep 17


title: Liver Tumour small DEN ALIOS Rep 16


title: Liver Tumour small DEN ALIOS Rep 20


title: 20_7193-T56

tag: age

value: Non-Hispanic


title: 21_r11_1

description:
sample name: 1307
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_7193-T63

tag: group


title: 20_7193-T42

tag: tissue


title: Liver Tumour small DEN ALIOS Rep 15

tag: cell type

value: Small Primary Tumour


title: 20_7193-T35

tag: ethnicity


title: 21_r10_1

description:
sample name: 1306
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_7193-T28


title: Liver Tumour small DEN ALIOS Rep 18

tag: source tissue

value: DEN ALIOS


title: 21_r9_1

description:
sample name: 1305
Embryonic blastomere transcriptome


title: 21_r15_1

description:
sample name: 1311
Embryonic blastomere transcriptome


title: Liver Tumour small DEN ALIOS Rep 13

tag: Sex


title: 21_r8_1

description:
sample name: 1304
Embryonic blastomere transcriptome


title: 20_7143-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: 20_7166-T28

value: SARS-CoV-2 Sero-


title: 20_7160-T91

value: LatePost


title: 20_7160-T42

value: Mid


title: 21_r7_1

description:
sample name: 1303
Embryonic blastomere transcriptome


title: Liver Tumour small DEN ALIOS Rep 12

value: Liver

tag: genotype


title: 20_7223-T00

value: Longitudinal Study

value: Control


title: 20_7121-T49


title: 20_7160-T35

value: F

value: First


title: Liver Tumour small DEN ALIOS Rep 11

value: Male

value: WT (C57BL/6 from in-house colony)

tag: treatment


title: 21_r6_1

description:
sample name: 1302
Embryonic blastomere transcriptome


title: 20_7121-T105

tag: meth-plate

value: M

value: blood


title: 20_7202-T46

tag: enrollment batch

value: Hispanic


title: Liver Tumour small DEN ALIOS Rep 10

value: Small Primary Tumour


title: 20_7121-T00

tag: biocollection id

value: Non-Hispanic


title: 21_r12_1

description:
sample name: 1308
Embryonic blastomere transcriptome

value: embryonic cells


title: Liver Tumour small DEN ALIOS Rep 9

value: DEN ALIOS


title: 20_7084-T56

tag: participant id

value: EarlyPost


title: 20_7106-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: sample collection time point (days since t0)

value: SARS-CoV-2 Sero+


title: 20_7084-T91

tag: enrollment date t0

value: LatePost


title: Liver Tumour small DEN ALIOS Rep 8

value: Liver


title: 20_7121-T60

value: Longitudinal Study

tag: gender


title: 21_r4_1

description:
sample name: 1300
Embryonic blastomere transcriptome


title: 21_r5_1

description:
sample name: 1301
Embryonic blastomere transcriptome


title: Liver Tumour small DEN ALIOS Rep 14


title: 20_7084-T46

tag: age

value: Mid


title: 20_7084-T00

tag: group

value: Control


title: 20_7037-T46

tag: tissue


title: Liver Tumour small DEN ALIOS Rep 7

value: Male

tag: cell type


title: 21_r3_1

description:
sample name: 1299
Embryonic blastomere transcriptome


title: Liver Tumour small DEN ALIOS Rep 6

value: WT (C57BL/6 from in-house colony)


title: 21_r2_1

description:
sample name: 1298
Embryonic blastomere transcriptome


title: Liver Tumour small DEN ALIOS Rep 5


title: 20_7037-T00

value: M

tag: ethnicity


title: 21_r1_1

description:
sample name: 1297
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_7037-T56

value: blood


title: 17_r17_2

description:
sample name: 1296
Embryonic blastomere transcriptome


title: 20_6991-T28

value: F


title: Liver Tumour small DEN ALIOS Rep 4

tag: source tissue

value: Small Primary Tumour


title: 20_6962-T00

value: Non-Hispanic


title: 17_r16_2

description:
sample name: 1295
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_6962-T35


title: 20_6962-T91


title: Liver Tumour small DEN ALIOS Rep 3

tag: Sex

value: DEN ALIOS


title: 17_r15_2

description:
sample name: 1294
Embryonic blastomere transcriptome


title: 17_r14_2

description:
sample name: 1293
Embryonic blastomere transcriptome


title: 20_6957-T77


title: 20_6957-T74

value: First


title: 20_6957-T84


title: 20_6956-T56

value: Hispanic

value: EarlyPost


title: 20_6956-T46


title: Liver Tumour small DEN ALIOS Rep 2

tag: genotype


title: 17_r13_2

description:
sample name: 1292
Embryonic blastomere transcriptome


title: Liver Tumour small DEN ALIOS Rep 1

tag: treatment


title: 20_6956-T00

tag: meth-plate


title: 20_6944-T28

tag: enrollment batch

value: Arrival at quarantine vs Later (all uninfected)

value: Later


title: Liver Neutrophils DEN ALIOS Rep 6

description: JMR18190810_S11_R1_001_JM19_RCJ22_3b_LIV_N

value: Liver

value: Neutrophils


title: 17_r12_2

description:
sample name: 1291
Embryonic blastomere transcriptome


title: 20_6962-T42

value: Longitudinal Study

tag: biocollection id

value: Mid


title: Liver Neutrophils DEN ALIOS Rep 5

description: JMR18190810_S07_R1_001_JM15_RCN24_2d_LIV_N

value: Male

value: WT (C57BL/6 from in-house colony)


title: 20_6939-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: participant id

value: SARS-CoV-2 Sero+

value: blood


title: 20_6911-T91

tag: sample collection time point (days since t0)

value: M

value: LatePost


title: 17_r11_2

description:
sample name: 1290
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_6911-T00

tag: enrollment date t0

value: Control


title: 20_6911-T42

tag: gender

value: Hispanic


title: Liver Neutrophils DEN ALIOS Rep 3

description: JMR18190809_S13_R1_001_JM25_RCN25_3h_LIV_N

value: DEN ALIOS/Vehicle


title: 20_6872-T28

value: F

tag: age


title: Liver Neutrophils DEN ALIOS Rep 2

description: JMR18190809_S07_R1_001_JM7_RCN21__2b_LIV_N

value: DEN ALIOS


title: 20_6871-T00

value: Arrival at quarantine vs Later (all uninfected)

value: Non-Hispanic

tag: group

value: Arrival at quarantine


title: 20_6816-T00

tag: tissue


title: 17_r9_2

description:
sample name: 1288
Embryonic blastomere transcriptome

tag: cell type


title: 17_r8_2

description:
sample name: 1287
Embryonic blastomere transcriptome


title: 20_6848-T00

tag: ethnicity


title: 20_6803-T74

value: Longitudinal Study

value: Mid


title: Liver Neutrophils DEN ALIOS Rep 1

description: JMR18190809_S03_R1_001_JM3_RCN22_1a_LIV_N

value: Liver

value: Male

value: WT (C57BL/6 from in-house colony)

value: Neutrophils


title: 17_r7_2

description:
sample name: 1286
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_6803-T70

value: M

value: First

value: blood


title: 20_6764-T60

value: EarlyPost


title: Liver Tumour large DEN ALIOS Rep 24

source_name: Large Primary Tumour

tag: source tissue

value: Large Primary Tumour


title: 17_r6_2

description:
sample name: 1285
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_6764-T49


title: Liver Tumour large DEN ALIOS Rep 25

tag: Sex


title: Liver Neutrophils DEN ALIOS Rep 4

description: JMR18190810_S03_R1_001_JM11_RCN24_2c_LIV_N

tag: genotype


title: 20_6764-T105

value: LatePost


title: 20_6764-T00

value: Control


title: 17_r5_2

description:
sample name: 1284
Embryonic blastomere transcriptome


title: Liver Tumour large DEN ALIOS Rep 23

tag: treatment

value: DEN ALIOS


title: 20_6717-T00

tag: meth-plate

value: F

value: Hispanic


title: 17_r10_2

description:
sample name: 1289
Embryonic blastomere transcriptome


title: 20_6683-T28

tag: enrollment batch

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: Non-Hispanic

value: SARS-CoV-2 Sero+


title: 17_r4_2

description:
sample name: 1283
Embryonic blastomere transcriptome


title: Liver Tumour large DEN ALIOS Rep 22

value: Liver

value: Male


title: 20_6717-T70

value: Longitudinal Study

tag: biocollection id


title: Liver Tumour large DEN ALIOS Rep 21

value: WT (C57BL/6 from in-house colony)


title: 20_6682-T49

tag: participant id

value: M


title: 17_r2_2

description:
sample name: 1281
Embryonic blastomere transcriptome


title: Liver Tumour large DEN ALIOS Rep 20


title: 20_6682-T00

tag: sample collection time point (days since t0)

value: blood


title: 20_6663-T77

tag: enrollment date t0


title: Liver Tumour large DEN ALIOS Rep 19


title: Liver Tumour large DEN ALIOS Rep 18


title: 20_6663-T39

tag: gender

value: EarlyPost


title: 17_1r17_1

description:
sample name: 101
Embryonic blastomere transcriptome


title: 20_6679-T28

tag: age

value: SARS-CoV-2 Sero-


title: 17_r1_2

description:
sample name: 1280
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_6663-T00

tag: group


title: 17_1r13_1

description:
sample name: 102
Embryonic blastomere transcriptome


title: Liver Tumour large DEN ALIOS Rep 17

value: Large Primary Tumour


title: 20_6682-T42

value: Mid

tag: tissue


title: 20_6627-T00

value: Arrival at quarantine vs Later (all uninfected)

value: Arrival at quarantine


title: 17_r3_2

description:
sample name: 1282
Embryonic blastomere transcriptome

tag: cell type


title: 20_6586-T49

tag: ethnicity


title: 20_6682-T98

value: Hispanic

value: LatePost


title: Liver Tumour large DEN ALIOS Rep 15

value: DEN ALIOS


title: Liver Tumour large DEN ALIOS Rep 16


title: 20_6600-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: 17_r11_1

description:
sample name: 100
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_6586-T00

value: Non-Hispanic

value: Control


title: 20_6586-T105

value: Longitudinal Study


title: Liver Tumour large DEN ALIOS Rep 14

tag: source tissue

value: Liver

value: Male

value: WT (C57BL/6 from in-house colony)


title: 20_6544-T91

value: M

value: blood


title: 20_6663-T35


title: 17_r8_1

description:
sample name: 97
Embryonic blastomere transcriptome

value: embryonic cells


title: Liver Tumour large DEN ALIOS Rep 13

tag: Sex

value: Large Primary Tumour


title: 17_r10_1

description:
sample name: 99
Embryonic blastomere transcriptome


title: 20_6533-T28

value: F


title: Liver Tumour large DEN ALIOS Rep 12

tag: genotype


title: 20_6529-T77

value: EarlyPost


title: Liver Tumour large DEN ALIOS Rep 11

tag: treatment


title: 17_r5_1

description:
sample name: 94
Embryonic blastomere transcriptome


title: 20_6529-T00

tag: meth-plate


title: 20_6586-T56

tag: enrollment batch


title: 20_6516-T28

tag: biocollection id

value: SARS-CoV-2 Sero-


title: Liver Tumour large DEN ALIOS Rep 10


title: 17_r9_1

description:
sample name: 98
Embryonic blastomere transcriptome


title: 20_6483-T28

tag: participant id

value: Hispanic


title: 17_r4_1

description:
sample name: 93
Embryonic blastomere transcriptome


title: 20_6481-T49

tag: sample collection time point (days since t0)

value: Mid


title: 20_6481-T53

tag: enrollment date t0


title: Liver Tumour large DEN ALIOS Rep 9

value: DEN ALIOS


title: 20_6578-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

tag: gender


title: 20_6481-T00

tag: age


title: 20_6544-T49

value: Non-Hispanic

tag: group


title: Liver Tumour large DEN ALIOS Rep 8


title: 17_r7_1

description:
sample name: 96
Embryonic blastomere transcriptome


title: 17_r2_1

description:
sample name: 91
Embryonic blastomere transcriptome


title: 20_6449-T28

value: SARS-CoV-2 Sero+

tag: tissue


title: Liver Tumour large DEN ALIOS Rep 7

tag: cell type


title: 20_6424-T77

value: Longitudinal Study

value: LatePost


title: 17_r1_1

description:
sample name: 90
Embryonic blastomere transcriptome


title: 20_6532-T00

value: Arrival at quarantine vs Later (all uninfected)

tag: ethnicity

value: Arrival at quarantine


title: 20_6424-T35

value: M


title: Liver Tumour large DEN ALIOS Rep 6

value: Liver

value: Male

value: WT (C57BL/6 from in-house colony)


title: 17_r6_1

description:
sample name: 95
Embryonic blastomere transcriptome

tag: developmental stage

value: embryonic cells


title: 20_6424-T00

value: Control

value: blood


title: 14_r14_2

description:
sample name: 1279
Embryonic blastomere transcriptome


title: 20_6389-T00


title: 20_6376-T77

value: F

value: Hispanic


title: 14_r13_2

description:
sample name: 1278
Embryonic blastomere transcriptome


title: Liver Tumour large DEN ALIOS Rep 4

tag: source tissue

value: Large Primary Tumour

value: DEN ALIOS


title: 17_r3_1

description:
sample name: 92
Embryonic blastomere transcriptome


title: 20_6481-T105


title: 20_6376-T00


title: 14_r12_2

description:
sample name: 1277
Embryonic blastomere transcriptome


title: 20_6376-T49

value: Mid


title: 20_6367-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: Liver Tumour large DEN ALIOS Rep 3

tag: Sex


title: 20_6349-T77

value: Longitudinal Study

value: EarlyPost


title: Liver Tumour large DEN ALIOS Rep 2

tag: genotype


title: 14_r10_2

description:
sample name: 1275
Embryonic blastomere transcriptome


title: 20_6349-T63


title: 20_6349-T56


title: Liver Tumour large DEN ALIOS Rep 1

tag: treatment


title: 14_r9_2

description:
sample name: 1274
Embryonic blastomere transcriptome


title: 20_6250-T39

tag: meth-plate


title: 20_6349-T00

tag: enrollment batch


title: 20_6250-T77

tag: biocollection id

value: LatePost


title: Liver T cells CXCR2i Rep 6

description: JMR18200318_S24_R1_001_JM24_RCA46_1d_LV_T

value: T cells


title: 14_r8_2

description:
sample name: 1273
Embryonic blastomere transcriptome


title: Liver T cells CXCR2i Rep 5

description: JMR18200318_S20_R1_001_JM20_RCA46_1c_LV_T

value: Liver


title: 20_6250-T00

tag: participant id

value: M


title: Liver Tumour large DEN ALIOS Rep 5

value: Male

value: WT (C57BL/6 from in-house colony)


title: 20_6376-T91

tag: sample collection time point (days since t0)


title: 20_6238-T49

tag: enrollment date t0

value: First


title: 14_r7_2

description:
sample name: 1272
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_6238-T00

tag: gender

value: Control

value: blood


title: Liver T cells CXCR2i Rep 4

description: JMR18200318_S16_R1_001_JM16_RCA46_1b_LV_T


title: 14_r11_2

description:
sample name: 1276
Embryonic blastomere transcriptome


title: Liver T cells CXCR2i Rep 3

description: JMR18200318_S12_R1_001_JM12_RCA46_1a_LV_T


title: 14_r6_2

description:
sample name: 1271
Embryonic blastomere transcriptome


title: 20_6228-T91

tag: age

value: Non-Hispanic


title: 20_6215-T74

tag: group


title: 20_6228-T53

tag: tissue


title: 14_r5_2

description:
sample name: 1270
Embryonic blastomere transcriptome

tag: cell type


title: 20_6228-T49

tag: ethnicity


title: 20_6215-T70


title: Liver T cells CXCR2i Rep 2

description: JMR18200318_S08_R1_001_JM8_RCA45_1b_LV_T


title: 14_r4_2

description:
sample name: 1269
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_6207-T91


title: 14_r3_2

description:
sample name: 1268
Embryonic blastomere transcriptome


title: 20_6207-T56


title: Liver T cells CXCR2i Rep 1

description: JMR18200318_S04_R1_001_JM4_RCA45_1a_LV_T

tag: source tissue


title: 20_6238-T60

value: Hispanic


title: 20_6207-T35

value: Mid


title: Blood T cells PBS Rep 8

description: JMR18200218_S22_R1_001_JM79_XBLA32_1h_B_T

value: Blood

tag: Sex

value: PBS


title: 14_r2_2

description:
sample name: 1267
Embryonic blastomere transcriptome


title: 20_6207-T00

value: Longitudinal Study


title: Blood T cells PBS Rep 7

description: JMR18200218_S18_R1_001_JM71_XBLA32_1f_B_T

tag: genotype


title: 20_6195-T77


title: 14_r1_2

description:
sample name: 1266
Embryonic blastomere transcriptome


title: 20_6195-T84


title: 20_6195-T74


title: 20_6135-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: Blood T cells PBS Rep 6

description: JMR18200218_S15_R1_001_JM63_XBLA32_1d_B_T

value: T cells

tag: treatment


title: 14_r10_1

description:
sample name: 185
Embryonic blastomere transcriptome


title: Blood T cells PBS Rep 4

description: JMR18200218_S03_R1_001_JM47_XBLA32_1c_B_T


title: 14_r9_1

description:
sample name: 184
Embryonic blastomere transcriptome


title: 20_6132-T00

tag: meth-plate


title: Blood T cells PBS Rep 5

description: JMR18200218_S11_R1_001_JM55_XBLA32_1a_B_T


title: 20_6132-T39

tag: enrollment batch


title: Blood T cells PBS Rep 3

description: JMR18191128_S22_R1_001_JM22_XBLA36_1b_B_T


title: 20_6132-T56

tag: biocollection id

value: EarlyPost


title: 20_6116-T00

value: Arrival at quarantine vs Later (all uninfected)

tag: participant id

value: M

value: Arrival at quarantine


title: 14_r8_1

description:
sample name: 183
Embryonic blastomere transcriptome


title: 20_6114-T28

tag: sample collection time point (days since t0)


title: 20_6132-T84

tag: enrollment date t0


title: Blood T cells PBS Rep 2

description: JMR18191128_S16_R1_001_JM16_XBLA36_1a_B_T

value: Male

value: WT (C57BL/6 from in-house colony)


title: 14_r7_1

description:
sample name: 182
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_6107-T28

tag: gender

value: blood


title: Blood T cells PBS Rep 1

description: JMR18191128_S10_R1_001_JM10_XBLA36_1d_B_T


title: 20_6100-T28

tag: age

value: Non-Hispanic


title: 14_r6_1

description:
sample name: 181
Embryonic blastomere transcriptome


title: Blood T cells DEN ALIOS CXCR2i/aPD1 Rep 5

value: DEN ALIOS CXCR2i aPD1


title: 20_6092-T28

value: Hispanic

tag: group


title: 20_6068-T91

value: LatePost

tag: tissue


title: 14_r11_1

description:
sample name: 186
Embryonic blastomere transcriptome

tag: cell type


title: 20_6068-T77

tag: ethnicity


title: 20_6186-T00

value: F


title: Blood T cells DEN ALIOS CXCR2i/aPD1 Rep 4

value: Blood


title: 14_r4_1

description:
sample name: 179
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_6068-T00

value: Longitudinal Study

value: Control


title: Blood T cells DEN ALIOS CXCR2i/aPD1 Rep 3

tag: source tissue

value: T cells


title: 20_6046-T56

value: EarlyPost


title: 14_r3_1

description:
sample name: 178
Embryonic blastomere transcriptome


title: 20_6046-T42

value: Mid


title: 14_r2_1

description:
sample name: 177
Embryonic blastomere transcriptome


title: 20_6046-T00

value: M


title: Blood T cells DEN ALIOS CXCR2i/aPD1 Rep 2

description: JMR18190810_S14_R1_001_JM34_RCN24_1b_B_T

tag: Sex


title: 20_6041-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero-


title: 14_r1_1

description:
sample name: 176
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 10

value: Male

tag: genotype

value: WT (C57BL/6 from in-house colony)

value: Neutrophils


title: Blood T cells DEN ALIOS CXCR2i/aPD1 Rep 1

description: JMR18190809_S18_R1_001_JM30_RCN24_1a_B_T

tag: treatment


title: 20_6023-T28

tag: meth-plate

value: SARS-CoV-2 Sero+

value: blood


title: 20_6012-T60

tag: enrollment batch

value: Hispanic


title: 20_6012-T00

tag: biocollection id


title: 20_6012-T49

tag: participant id


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 9

value: DEN ALIOS CXCR2i aPD1


title: 13_r11_2

description:
sample name: 1265
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_6001-T28

tag: sample collection time point (days since t0)


title: 14_r5_1

description:
sample name: 180
Embryonic blastomere transcriptome


title: 20_6068-T60

tag: enrollment date t0


title: 20_5988-T00

tag: gender

value: Non-Hispanic


title: 13_r9_2

description:
sample name: 1263
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 7

description: JMR18190810_S19_R1_001_JM43_RCN21_1a_B_N

value: Blood


title: 20_5988-T56

value: Longitudinal Study

tag: age


title: 20_5988-T46

tag: group


title: 13_r10_2

description:
sample name: 1264
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 8


title: 20_5985-T28

tag: tissue


title: 13_r8_2

description:
sample name: 1262
Embryonic blastomere transcriptome

tag: cell type


title: 20_5972-T28

value: F

tag: ethnicity


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 6

description: JMR18190810_S17_R1_001_JM41_RCN17_4c_B_N


title: 20_5956-T77

value: LatePost


title: 20_5956-T35

value: Mid


title: 20_5951-T74

value: M

value: EarlyPost


title: 13_r6_2

description:
sample name: 1260
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_5956-T00

value: Control


title: 13_r7_2

description:
sample name: 1261
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 5

description: JMR18190810_S13_R1_001_JM33_RCN24_1b_B_N

tag: source tissue

value: Male


title: 20_5951-T63


title: 20_5951-T00


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 4

description: JMR18190809_S23_R1_001_JM39_RCN17_4b_B_N

tag: Sex

value: WT (C57BL/6 from in-house colony)


title: 20_5937-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero-


title: 20_5932-T91

value: blood


title: 13_r5_2

description:
sample name: 1259
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 3

description: JMR18190809_S21_R1_001_JM37_RCN16_2a_B_N

tag: genotype

value: Neutrophils


title: 13_r4_2

description:
sample name: 1258
Embryonic blastomere transcriptome


title: 20_5932-T56

value: Hispanic


title: 20_5932-T46


title: 13_r3_2

description:
sample name: 1257
Embryonic blastomere transcriptome

value: embryonic cells


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 2

description: XCR18190507_S23_R1_001_XC23_RCN20_1b_Bl_val

tag: treatment

value: DEN ALIOS CXCR2i aPD1


title: Blood Neutrophils DEN ALIOS CXCR2i/aPD1 Rep 1

description: JMR18190809_S17_R1_001_JM29_RCN24_1a_B_N

value: Blood


title: 20_5914-T00

tag: meth-plate

value: Arrival at quarantine vs Later (all uninfected)

value: Arrival at quarantine


title: 20_5911-T56

tag: enrollment batch

value: Longitudinal Study


title: 20_5911-T35

tag: biocollection id

value: Mid


title: 13_r1_2

description:
sample name: 1255
Embryonic blastomere transcriptome


title: Blood T cells DEN ALIOS CXCR2i Rep 6

value: T cells

value: DEN ALIOS CXCR2i aPD1 isotype


title: 13_r2_2

description:
sample name: 1256
Embryonic blastomere transcriptome


title: Blood T cells DEN ALIOS CXCR2i Rep 5


title: 20_5932-T00

tag: participant id

value: M

value: Control


title: 20_5910-T91

tag: sample collection time point (days since t0)

value: Non-Hispanic

value: LatePost


title: 20_5910-T46

tag: enrollment date t0


title: 20_5910-T00

tag: gender


title: Blood T cells DEN ALIOS CXCR2i Rep 3

value: Male

value: WT (C57BL/6 from in-house colony)

value: DEN ALIOS CXCR2i


title: 20_5894-T91

tag: age

value: Hispanic

value: blood


title: 13_r10_1

description:
sample name: 196
Embryonic blastomere transcriptome

value: embryonic cells


title: 13_r11_1

description:
sample name: 197
Embryonic blastomere transcriptome


title: 13_r8_1

description:
sample name: 194
Embryonic blastomere transcriptome


title: 20_5910-T56

tag: group

value: EarlyPost


title: 20_5891-T63

tag: tissue


title: 13_r7_1

description:
sample name: 193
Embryonic blastomere transcriptome

tag: cell type


title: 13_r9_1

description:
sample name: 195
Embryonic blastomere transcriptome


title: 20_5894-T00

tag: ethnicity


title: Blood T cells DEN ALIOS CXCR2i Rep 1

value: Blood


title: 20_5894-T35


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 10

description: XCR18190507_S21_R1_001_XC21_RCN25_1a_Bl_val

value: Neutrophils


title: 20_5891-T00

value: Longitudinal Study


title: 20_5891-T42


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 9

description: XCR18190507_S15_R1_001_XC15_RCN18_2c_Bl_val


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 8

description: XCR18190507_S13_R1_001_XC13_RCN18_2b_Bl_val


title: 13_r5_1

description:
sample name: 191
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_5879-T49

value: Mid


title: Blood T cells DEN ALIOS CXCR2i Rep 4

tag: source tissue

value: T cells


title: 20_5911-T00


title: 13_r4_1

description:
sample name: 190
Embryonic blastomere transcriptome


title: 20_5879-T00


title: 20_5864-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: SARS-CoV-2 Sero+


title: Blood T cells DEN ALIOS CXCR2i Rep 2

tag: Sex


title: 13_r3_1

description:
sample name: 189
Embryonic blastomere transcriptome


title: 20_5894-T56

value: M


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 6

tag: genotype

value: DEN ALIOS CXCR2i aPD1 isotype


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 7

tag: treatment


title: 20_5849-T28

tag: meth-plate

value: Arrival at quarantine vs Later (all uninfected)

value: Non-Hispanic

value: Later


title: 20_5844-T28

tag: enrollment batch


title: 13_r6_1

description:
sample name: 192
Embryonic blastomere transcriptome


title: 20_5812-T28

tag: biocollection id


title: 20_5837-T28

tag: participant id


title: 20_5807-T00

tag: sample collection time point (days since t0)

value: Arrival at quarantine


title: 20_5891-T39

tag: enrollment date t0


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 4

value: Male

value: WT (C57BL/6 from in-house colony)

value: DEN ALIOS CXCR2i


title: 20_5765-T91

tag: gender

value: LatePost

value: blood


title: 13_r2_1

description:
sample name: 188
Embryonic blastomere transcriptome

value: embryonic cells


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 3

value: Blood

value: Neutrophils


title: 20_5785-T10

value: Longitudinal Study

tag: age

value: EarlyPost


title: 12_r12_6

description:
sample name: 1624
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 5


title: 20_5879-T91

value: Hispanic

tag: group


title: 20_5765-T46

value: M

value: Mid

tag: tissue


title: 20_5743-T91


title: 20_5765-T00

value: Control


title: 20_5785-T60

value: Non-Hispanic


title: 12_r11_6

description:
sample name: 1623
Embryonic blastomere transcriptome

tag: cell type


title: 12_r10_6

description:
sample name: 1622
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 1

description: JMR18190809_S15_R1_001_JM27_RCN25_1b_B_N


title: 20_5743-T42


title: Blood Neutrophils DEN ALIOS CXCR2i Rep 2

value: DEN ALIOS CXCR2i aPD1 isotype


title: 20_5743-T00


title: 12_r9_6

description:
sample name: 1621
Embryonic blastomere transcriptome


title: Blood T cells DEN ALIOS aPD1 Rep 5

value: T cells

value: DEN ALIOS aPD1


title: 20_5738-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)

value: F

tag: ethnicity

value: SARS-CoV-2 Sero-


title: 12_2r8_6

description:
sample name: 1620
Embryonic blastomere transcriptome

tag: developmental stage


title: 20_5698-T28

value: blood


title: 20_5658-T28

value: SARS-CoV-2 Sero+


title: 12_2r7_6

description:
sample name: 1619
Embryonic blastomere transcriptome

value: embryonic cells


title: Blood T cells DEN ALIOS aPD1 Rep 4

tag: source tissue

value: Blood

value: Male

value: WT (C57BL/6 from in-house colony)


title: 20_5653-T28


title: Blood T cells DEN ALIOS aPD1 Rep 3

tag: Sex


title: 20_5615-T28


title: 20_5586-T00

value: Longitudinal Study


title: 13_r1_1

description:
sample name: 187
Embryonic blastomere transcriptome


title: 20_5567-T00

value: Arrival at quarantine vs Later (all uninfected)

value: M

value: Hispanic

value: Arrival at quarantine


title: 20_5586-T91

value: Non-Hispanic

value: LatePost


title: 20_5586-T49

value: Mid


title: 20_5586-T60

value: EarlyPost


title: 12_2r6_6

description:
sample name: 1618
Embryonic blastomere transcriptome


title: 12_2r5_6

description:
sample name: 1617
Embryonic blastomere transcriptome


title: 20_5483-T74

value: First


title: 20_5542-T28

value: SARS-Cov-2 Sero- vs Sero+ (approximate 10 weeks after outbreak)


title: 20_5568-T28

value: F

value: blood


title: Blood Neutrophils DEN ALIOS aPD1 Rep 3

tag: genotype

value: Neutrophils

value: DEN ALIOS aPD1


title: Blood Neutrophils DEN ALIOS aPD1 Rep 5

value: Blood

value: Male

tag: treatment


title: 12_2r4_6

description:
sample name: 1616
Embryonic blastomere transcriptome

value: embryonic cells


title: 12_2r3_6

description:
sample name: 1615
Embryonic blastomere transcriptome


title: Blood T cells DEN ALIOS aPD1 Rep 1

value: WT (C57BL/6 from in-house colony)

value: T cells


title: 12_2r1_6

description:
sample name: 1613
Embryonic blastomere transcriptome


title: 12_2r2_6

description:
sample name: 1614
Embryonic blastomere transcriptome


title: Blood Neutrophils DEN ALIOS aPD1 Rep 4


title: 20_5483-T00

tag: meth-plate

value: Longitudinal Study

value: M

value: Control


title: Blood Neutrophils DEN ALIOS aPD1 Rep 2


title: Blood T cells DEN ALIOS aPD1 Rep 2


title: 20_5482-T77

tag: enrollment batch


title: 20_5482-T63

tag: biocollection id


title: 20_5483-T84

tag: participant id

value: Non-Hispanic


title: 20_5483-T77

tag: sample collection time point (days since t0)


title: 12_r9_5

description:
sample name: 1243
Embryonic blastomere transcriptome


title: 20_5482-T00

tag: enrollment date t0


title: 20_5427-T28

value: Arrival at quarantine vs Later (all uninfected)

tag: gender

value: Later


title: Blood Neutrophils DEN ALIOS aPD1 Rep 1


title: 20_5412-T39

tag: age

value: Hispanic

value: Mid


title: 20_5482-T35

tag: group

value: First


title: 20_5427-T00

value: Arrival at quarantine

tag: tissue

value: blood


title: 20_5412-T77

value: LatePost


title: Blood T cells DEN ALIOS Rep 7

description: JMR18190810_S10_R1_001_JM18_RCJ22_3b_B_T

value: Blood

tag: cell type

value: DEN ALIOS


title: 12_r8_5

description:
sample name: 1242
Embryonic blastomere transcriptome

value: embryonic cells


title: 20_5412-T00

tag: ethnicity


title: 20_5390-T14


title: 12_r5_5

description:
sample name: 1239
Embryonic blastomere transcriptome

tag: developmental stage


title: 12_r7_5

description:
sample name: 1241
Embryonic blastomere transcriptome


title: Blood T cells DEN ALIOS Rep 5

description: JMR18190810_S02_R1_001_JM10_RCN24_2c_B_T

tag: source tissue

value: Male

value: WT (C57BL/6 from in-house colony)


title: Blood T cells DEN ALIOS Rep 6

description: JMR18190810_S06_R1_001_JM14_RCN24_2d_B_T

tag: Sex

value: T cells


title: Blood T cells DEN ALIOS Rep 4

description: JMR18190809_S12_R1_001_JM24_RCN25_3h_B_T

tag: genotype

value: DEN ALIOS/Vehicle


title: 20_5390-T20

value: Longitudinal Study

value: M

value: EarlyPost


title: 12_r3_5

description:
sample name: 1237
Embryonic blastomere transcriptome


title: 20_5346-T49

value: Non-Hispanic


title: 12_r6_5

description:
sample name: 1240
Embryonic blastomere transcriptome


title: 12_r4_5

description:
sample name: 1238
Embryonic blastomere transcriptome


title: 20_5346-T00

value: Control


title: Blood T cells DEN ALIOS Rep 3

description: JMR18190809_S10_R1_001_JM22_RCN25_3e_B_T

tag: treatment