title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep10]

description:
Ad5-FMDV_T0_rep10
Total blood sample (replicate 10) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m5_1912014298_Col19_S250

status: Public on Dec 10 2019

type: SRA

city: Barcelona

first: Atefeh

last: Lafzi

address: Baldiri Reixac 4

department: CNAG

country: Spain

institute: Center for Genomic Regulation

description:
cryopreserved HCA reference
C1HTmedium_human_exp_mat.tsv, C1HTmedium_human_metada.tsv, C1HTmedium_mouse_exp_mat.tsv, C1HTmedium_mouse_metada.tsv

library_source: transcriptomic

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-11); R2 = cDNA

molecule: polyA RNA

organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

growth_protocol: NIH3T3-GFP, MDCK-TurboFP650 and HEK293-RFP were cultured at 37ºC in an atmosphere of 5% (v/v) carbon dioxide in Dulbecco’s Modified Eagle’s Medium, supplemented with 10% (w/v) fetal bovine serum, 100 U penicillin, and 100 µg/L streptomycin (Invitrogen).

extract_protocol:
PBMCs were isolated according to the manufacturer’s instructions for FICOLL extraction (pluriSelect).Minced mouse colon was digested in 1X HBSS and 83 µl of collagenase IV (final concentration 166 U/ml) for 15 min at 37ºC and filtered through a 70 µm nylon mesh.
Sequencing librraries were prepared according to the respective single-cell RNA-seq protocols as detailed in the Methods and referenced in TableS1.
Library selection and sequencing was performed following recommendations of to the respective single-cell RNA-seq protocols as detailed in the Methods.

treatment_protocol: Untreated cells and donors.

tag: protocol

tag: centre

value: Stanford

tag: cell type

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: RA/CHIR-4d rep1

city: Hangzhou

first: Shihao

last: Wang

state: Zhejiang

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting RNA-seq reads were trimmed using Trimmomatic (Version 0.33, AVGQUAL:20TRAILING:20MINLEN:50) to remove the adaptor sequence and low-quality bases.
The clean paired-end reads of each sample were mapped to the annotated genome of Musmusculus (GRCm38) (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/) using HISAT2 aligner (Version 2.0.4)
Cufflinks counted the expression of each gene and reported them in FPKM (Trapnell et al., 2014), and then differentially expressed genes were assessed using Cuffdiff (cutoff, p-value≤0.05).
Genome_build: Mus musculus (GRCm38)
Supplementary_files_format_and_content: abundance measurements

molecule: total RNA

organism: Mus musculus

source_name: Differentiated ESCs

growth_protocol: Undifferentiated mESCs were cultured on mitomycin-inactivated mouse embryonic fibroblasts (MEFs) in DMEM supplemented with 15% fetal bovine serum and 1000 U/mL LIF at 37℃ in 5% CO2. SMCs and XEN cells cultured in DMEM supplemented with 15% fetal bovine serum.

extract_protocol:
Total RNA was prepared using TRIzol Reagent (ambion), Sequencing libraries were prepared from 3 μg of each RNA sample using TruSeq RNA Sample Prep Kit (Illumina).
mRNA with polyA tail was purified from total RNA with poly-T oligo attached magnetic beads and carried out fragmentation into about 200 bp using divalent cations at elevated temperature.The RNA fragments were converted into first strand cDNA using random primers, and then second strand synthesis was performed using DNA polymerase I and RNase H treatment. After end repair, Illumina PE adaptors were ligated to the ends of cDNA fragments. Adaptor-tagged cDNA fragments were size selected on low-range ultra-agarose gel and enriched using Illumina PCR Primer Cocktail and 10-cycle PCR. The qualities of the libraries were checked on a Bioanalyzer2100 system (Agilent) to ensure the proper insert length. Finally, the libraries were diluted, mixed and sequenced to a depth of ~25M 150bp paired-end reads using an Illumina HiSeq 2000 system.

treatment_protocol: ESCs were resuspended and plated onto gelatin-coated dishes at a density of 4Χ104/cm2 in DMEM+15% serum supplemented with 10 μM atRA or 10 μM atRA+5μM CHIR for 10 days, then DMEM with 10% serum for 6 days, to perform induced differentiation.

tag: strain

value: ES-derived XEN-like cells

tag: treatment

value: RA/CHIR-induced

tag: time (differentiation)


title: week0_SCbeta_ATAC_rep1

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

country: USA

institute: Harvard University

library_source: genomic

data_processing:
Sequencing reads were mapped to the human hg19 reference genome assembly using bowtie2 (Langmead and Salzberg, 2012) with default parameters. Peak calling was performed using MACS2 (Zhang et al., 2008) with default parameters, “--nomodel --shift 37 --extsize 73” to bypass building a ChIP-based shifting model and instead shift read 5’-ends and extend in the 5'->3' direction by a half-nucleosome size (73bp), and  “--broad --qvalue 0.01” to composite broad regions of read enrichment with a minimum FDR q-value cutoff of 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited file with peak coordinates

molecule: genomic DNA

organism: Homo sapiens

source_name: HUES 8 hESC line

growth_protocol: Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).

extract_protocol:
Live cells (typically ~50,000) were pelleted and tagmentation was performed at 37ºC for 30min as described in (Buenrostro et al., 2013). Briefly, cell pellets were resuspended in buffer containing Tn5 Transposase (Nextera DNA Sample Preparation kit; Illumina), incubated at 37ºC for 30min, and DNA was isolated using the MinElute PCR purification kit (Qiagen).
Tagmented DNA was PCR-amplified for 10 cycles and purified using AMPure XP magnetic beads (Beckman Coulter). Double-sided AMPure cleanup to remove high-molecular-weight fragments was conducted by incubation of double-concentrated AMPure beads added at 0.55x volume to the PCR reactions, followed by cleanup with a 1x AMPure volume. Sequencing libraries were pooled and sequenced on a HiSeq 2500 instrument.

tag: cell line

value: HUES 8 hESC line

value: hPSC-derived beta cell

tag: developmental stage

value: Stage 6 week 0


title: C1HTmedium_m5_1912014298_Col20_S249


title: SMC rep2

source_name: Smooth muscle cells

value: Smooth muscle cells

value: control


title: SMC rep3


title: C1HTmedium_m5_1912014298_Col18_S256


title: C1HTmedium_m6_1912014299_Col03_S262


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep9]

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

description:
Ad5-FMDV_T4_rep9
Total blood sample (replicate 9) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.12.
Tophat2 (v 2.1.1), with parameters "-N 2 --read-edit-dist 2 --b2-sensitive --no-coverage-search", was used for alignment on the reference genome/transcriptome (Ensembl90 database).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t exon -g gene_id -s 1).
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. Genes, whose sum of all samples counts was less than 10, were filtered out. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed.
Genome_build: Oar_v3.1 from Ensembl database version 90
Supplementary_files_format_and_content: counts_table_all_samples.txt : Tab-delimited text file containing the table of raw counts for all samples (3 vaccination types, 3 timepoints, 10 replicates), as established after mapping using TopHat and gene counts using featureCounts.

organism: Ovis aries

source_name: blood

extract_protocol:
RNA was extracted from the PAXgene Blood RNA tubes using the PAXgene Blood RNA kit and purified with the RNeasy MinElute Cleanup kit (QIAGEN). The quality of the total RNA was assessed on an Agilent Bioanalyzer 2100, using RNA 6000 pico kit (Agilent Technologies). Directional RNA-Seq Libraries were constructed from 1 µg of total RNA using the TruSeq mRNA Stranded library prep kit (Illumina), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Vaccination

tag: animal id

tag: breed

value: Prealpes

tag: tissue

value: blood

tag: Stage

value: adult (6 months)

tag: Sex

value: male

value: Adenovirus 5-FMDV (Ad5-FMDV)

tag: time point


title: C1HTmedium_m5_1912014298_Col17_S255


title: SMC rep1


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep9]

description:
Ad5-FMDV_T0_rep9
Total blood sample (replicate 9) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m5_1912014298_Col16_S254


title: ER47_Rep2

city: Philadelphia

first: Kai

last: Tan

state: PA

address: 3501 Civic Center Blvd

institute: CHOP

data_processing:
Raw FASTQ files were mapped to the human genome (hg19) using STAR aligner (v2.5.3).
Mapped reads were filtered and deduplicated using sambamba (v0.6.6).
Read counts for each genomic feature were generated using featureCounts from Subread package (v1.5.0-p1).
Genomic feature information were extracted from the RefSeq database downloaded from the UCSC genome browser on 01/05/2017.
FPKM values were computed using a custom python script.
De-novo fusion transcripts were identified using STAR-Fusion.
Genome_build: hg19

source_name: Entrectinib Resistant 47

growth_protocol: Entrectinib-resistant (ER) cell lines were established from the previously mentioned NB xenograft model. Xenografted tumors that initially responded to entrectinib therapy (tumor regression or growth arrest) and later re-grew (size change >0.2 cm3) were harvested. Cells were homogenized into a single-cell suspension and grown in medium as described above, and long-term viable cell lines were established from 5 different ER tumors (ER cell lines 5, 28, 29, 42, and 47). Three of these cell lines were obtained from mice dosed every 4 hours (ER5, ER28, ER29) and two were obtained from mice dosed every 6 hours (ER42 and ER47). Cell lines were initially grown in increasing concentrations of entrectinib (starting at 10 nM and increasing progressively to 750 nM), and then clones were maintained in concentrations of 200 nM entrectinib for harvesting with 0.2% tetrasodium EDTA in phosphate buffered saline.

extract_protocol:
Qiagen AllPrep Kit per the manufacturer's instructions
Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems) following the manufacturer’s protocol using 100 ng of total RNA. RNA was fragmented to a size of 100-200 nucleotides, adapter stock concentration used was 750 nM, and libraries were amplified for 11 cycles. Final libraries were quantified on a high sensitivity bioanalyzer chip and sequenced on the Illumina HiSeq 2500 and NextSeq 550 sequencers (Illumina, San Diego).

treatment_protocol: Six-week-old athymic nu/nu mice were obtained from Jackson Laboratories. Mice were maintained at 5 per cage under humidity- and temperature-controlled conditions in a light/dark cycle that was set at 12-hr intervals. Animals were injected subcutaneously in the flank with 1x107 SY5Y-TrkB cells in 0.1 mL Matrigel (BD Bioscience, Palo Alto, CA). Tumors were measured 2 times per week in 3 dimensions, and treatment was started with entrectinib about 15-17 days after tumor inoculation when the average tumor size was 0.2 cm3. Entrectinib was dosed orally either every 4 or every 6 hours 7 days per week at 60 mg/kg. The Institutional Animal Care Committee of the Children’s Hospital of Philadelphia (CHOP) Research Institute approved the animal studies described herein.

value: neuroblastoma

tag: entrectinib dosing interval

value: 6 hours

tag: xenograft model

value: mouse

value: SY5Y_BR6 (Entrectinib Resistant)


title: ER47_Rep1


title: C1HTmedium_m5_1912014298_Col15_S253

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: RA-16d rep2

value: ES-derived SMC-like cells

value: RA-induced


title: ER42_Rep3

source_name: Entrectinib Resistant 42


title: RA-16d rep1


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep8]

description:
Ad5-FMDV_T4_rep8
Total blood sample (replicate 8) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep8]

description:
Ad5-FMDV_T24_rep8
Total blood sample (replicate 8) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m5_1912014298_Col14_S252


title: week0_SCbeta_ATAC_rep2

value: HUES 8 hESC line

value: hPSC-derived beta cell


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep9]

description:
Ad5-FMDV_T24_rep9
Total blood sample (replicate 9) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep8]

description:
Ad5-FMDV_T0_rep8
Total blood sample (replicate 8) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: ER42_Rep2


title: RA-10d rep3


title: C1HTmedium_m5_1912014298_Col13_S251


title: RA-10d rep2


title: ER47_Rep3


title: ER29_Rep3

source_name: Entrectinib Resistant 29

value: 4 hours


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep7]

description:
Ad5-FMDV_T4_rep7
Total blood sample (replicate 7) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep7]

description:
Ad5-FMDV_T24_rep7
Total blood sample (replicate 7) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m5_1912014298_Col12_S243


title: C1HTmedium_m5_1912014298_Col11_S259


title: RA-10d rep1


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep7]

description:
Ad5-FMDV_T0_rep7
Total blood sample (replicate 7) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m5_1912014298_Col10_S244


title: RA-16d rep3


title: RA-7d rep3


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep6]

description:
Ad5-FMDV_T24_rep6
Total blood sample (replicate 6) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: RA-7d rep2


title: C1HTmedium_m5_1912014298_Col09_S260


title: ER29_Rep1


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep6]

description:
Ad5-FMDV_T4_rep6
Total blood sample (replicate 6) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: ER28_Rep3

source_name: Entrectinib Resistant 28


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep6]

description:
Ad5-FMDV_T0_rep6
Total blood sample (replicate 6) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: RA-7d rep1


title: C1HTmedium_m5_1912014298_Col08_S245


title: ER42_Rep1


title: C1HTmedium_m5_1912014298_Col07_S246


title: RA-4d rep3


title: ER28_Rep1


title: RA-4d rep2


title: C1HTmedium_m5_1912014298_Col06_S247


title: ER5_Rep3

source_name: Entrectinib Resistant 5


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep5]

description:
Ad5-FMDV_T0_rep5
Total blood sample (replicate 5) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep5]

description:
Ad5-FMDV_T4_rep5
Total blood sample (replicate 5) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: RA-4d rep1


title: ER29_Rep2


title: C1HTmedium_m5_1912014298_Col05_S248


title: ER5_Rep2


title: C1HTmedium_m5_1912014298_Col04_S258


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep4]

description:
Ad5-FMDV_T24_rep4
Total blood sample (replicate 4) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: mES rep2

source_name: Embryonic stem cells

value: Embryonic stem cells

value: control


title: mES rep3


title: SY5Y_BR6_Rep3

source_name: Parental Cell line

value: SY5Y_BR6 (parental)


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep4]

description:
Ad5-FMDV_T4_rep4
Total blood sample (replicate 4) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt

value: Prealpes

value: blood

value: adult (6 months)


title: mES rep1


title: ER5_Rep1

value: neuroblastoma


title: C1HTmedium_m5_1912014298_Col03_S242

description:
cryopreserved HCA reference
C1HTmedium_human_exp_mat.tsv, C1HTmedium_human_metada.tsv, C1HTmedium_mouse_exp_mat.tsv, C1HTmedium_mouse_metada.tsv


title: ER28_Rep2


title: C1HTmedium_m5_1912014298_Col02_S257


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep5]

description:
Ad5-FMDV_T24_rep5
Total blood sample (replicate 5) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt

value: male

value: Adenovirus 5-FMDV (Ad5-FMDV)


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep4]

description:
Ad5-FMDV_T0_rep4
Total blood sample (replicate 4) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep3]

description:
Ad5-FMDV_T24_rep3
Total blood sample (replicate 3) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m5_1912014298_Col01_S241


title: SY5Y_BR6_Rep1


title: C1HTmedium_m4_1911014296_Col20_S149


title: suc-ste-res rep3

city: Beijing

first: Xiong

address: No. 17, Qinghua East Road, Haidian District, Beijing

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

data_processing:
After the library was constructed, preliminary quantification was performed using Qubit 3.0, and the library was diluted to 1 ng/uL. Then, the insert size of the library was detected using Qsep100. After the insert size was as expected, the effective concentration of the library was accurately determined by Q-PCR. Quantification (library effective concentration > 2 nM) to ensure library quality.
Filter the data to obtain Clean Data, sequence comparison with the specified reference genome, and obtain Mapped Data for library quality evaluation such as insert length test and randomness test; perform alternative splicing analysis, new gene discovery and gene Structural level analysis such as structural optimization; analysis of expression levels of differential expression analysis, functional expression of differentially expressed genes, and functional enrichment based on the expression levels of genes in different samples or different sample groups.
The sequenced raw sequence reads (Sequenced Reads) or Raw reads, which contain low-quality reads with connectors, as shown in Figure 1. In order to ensure the quality of information analysis, Raw reads must be filtered to get Clean reads, and subsequent analysis is based on Clean reads. The steps for data processing are as follows:(1) removing the reader with the adapter; (2) removing N (N means that the base information cannot be determined) is greater than 1% of the reads;(3) Remove low-quality reads (the number of bases with a mass value of sQ <= 15 accounts for more than 50% of the total read).
Alignment by reference to TopHat software, reference genome link
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Caenorhabditis elegans

source_name: nematode

extract_protocol:
L4 stage, nematodes were collected, flash frozen on dry ice, and total RNA was harvested using Trizol reagent kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body

tag: genotype/variation

value: wild type

value: 400mM sucrose-500mg/ml stearic acid & 500mg/ml resveratrol


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep3]

description:
Ad5-FMDV_T4_rep3
Total blood sample (replicate 3) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: suc-ste-res rep2


title: suc-ste-res rep1


title: C1HTmedium_m4_1911014296_Col19_S150

tag: protocol

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep3]

description:
Ad5-FMDV_T0_rep3
Total blood sample (replicate 3) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep2]

description:
Ad5-FMDV_T24_rep2
Total blood sample (replicate 2) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: ICA3_on

city: Los Angeles

first: John

middle: W.

last: Phillips

state: California

address: 675 Charles E Young Drive South

department: MIMG

institute: UCLA

description:
Engineered cell line with doxycycline regulated Myc expression and enforced expression of myristoylated AKT1
gene_exp.diff
isoform_exp.diff
SE.MATS.JC.txt.pairadiseAppend.txt.sig0.05.txt

data_processing:
Read mapping done using STAR 2.5.3.a with a 2-pass function for better detection of splicing junctions. --sjdbOverhang 100 used to handle different read lengths.
Differential alternative splicing was done using rMATS 4.0.2. The splice junction of each event was required to be covered by no less than 10 reads. Additionally, each event was required to vary in PSI over 5% across the entire dataset, with a mean skipping or inclusion value over 5%. Events with missing values in the majority (over 99%) of samples were removed.
Gene/isoform expression quantification was done using Cufflinks, with the default paramaters.
Genome_build: hg37
Supplementary_files_format_and_content: gene_exp.diff is the output from Cuffdiff. Rows contain genes. The 3 cell lines are treated as replicates and are averaged. The columns of interest are “value_1” and “value_2” which contains the FPKM of a gene in sample 1 (myc on) or sample 2 (myc off), respectively. Log2(fold change) of gene expression between the two conditions and the significance of the change are also included.
Supplementary_files_format_and_content: isoform_exp.diff is the output from Cuffdiff. Rows contain isoforms. The 3 cell lines are treated as replicates and are averaged. The columns of interest are “value_1” and “value_2” which contains the FPKM of an isoforn in sample 1 (myc on) or sample 2 (myc off), respectively. Log2(fold change) of isoform expression between the two conditions and the significance of the change are also included.
Supplementary_files_format_and_content: SE.MATS.JC.txt.pairadiseAppend.txt.sig0.05.txt, is the rMATS-PAIRADISE output matrix. Rows are splicing (skipped exon) events. Columns 1-8 contain information about the exon event: HUGO gene name, chromosome, strand, start and end coordinates of the cassette exon, and start and end coordinates of the upstream and downstream exons. Read counts supporting of inclusion of a cassette exon in each replicate sample (ICA1,2 and 3) are separated by comma in IJC_Sample_1 and IJC_Sample_2. Read counts supporting skipping of a cassette exon are included in SJC_Sample_1 and SJC_Sample_2. Sample_1 includes the replicates in the myc-on condition. Sample_2 includes the replicates in the myc-off condition. IncLevel1 (Myc on) and IncLevel2(Myc off) gives the percent spliced in (PSI) values of the cassette exon for each of the replicates in each condition separated by comma. IncLevelDifference is the average(IncLevel1) – average(IncLevel2). FDR and p-Value are calculated by PAIRADISE for the splicing difference between the two groups.
Supplementary_files_format_and_content: [third-party reanalysis]  In stdNull.na0.99.cov10.splcing.merged_matrix.tissue.txt (Prostate rMATS PSI matrix), rows are splicing (skipped exon) events. Columns 1-8 contain information about the exon event: HUGO gene name, chromosome, strand, start and end coordinates of the cassette exon, start coordinate of downstream exon, and end coordinate of the upstream exon. Beginning in column 9 is the Percent Spliced In (PSI) value for every sample, indicating the percentage of inclusion of the cassette exon.
Supplementary_files_format_and_content: [third-party reanalysis]  In exp.merged_matrix.Pca.txt (Prostate RNA expression matrix (FPKM)), rows contain samples, the columns are genes. Each cell contains the expression level  (in FPKM) of a gene in a given sample.

source_name: Prostate epithelium-derived Cell Line ICA3

growth_protocol: Grown in stem cell media with 1 ug/mL doxycycline

extract_protocol:
Total RNA was isolated by guanidinium thiocyanate-phenol-chloroform extraction followed by column clean-up. Isolated RNA was submitted for RNA integrity number (RIN) analysis and only samples with RIN > 9 were carried forward.
cDNA libraries were prepared from isolated RNA after poly-A selection using the TruSeq RNA Sample Prep Kit v2 (Illumina).

treatment_protocol: "Off" samples are withdrawn from doxycycline for 24h

value: Prostate epithelium-derived cells

tag: myc status

value: Myc on


title: ICA3_off

tag: cell type

value: Myc off


title: C1HTmedium_m4_1911014296_Col18_S156

tag: centre


title: suc-ste rep2

description:
Gene_full_table.xls
control_vs_suc-ste.annotation.xls

tag: treatment

value: 400mM sucrose & 500mg/ml stearic acid


title: C1HTmedium_m4_1911014296_Col17_S155


title: ICA2_off

source_name: Prostate epithelium-derived Cell Line ICA2


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep2]

description:
Ad5-FMDV_T4_rep2
Total blood sample (replicate 2) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep2]

description:
Ad5-FMDV_T0_rep2
Total blood sample (replicate 2) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m4_1911014296_Col16_S154


title: C1HTmedium_m4_1911014296_Col15_S153


title: suc-ste rep1


title: ICA1_on

source_name: Prostate epithelium-derived Cell Line ICA1


title: ste rep2

description:
Gene_full_table.xls
control_vs_ste.annotation.xls

value: 500mg/ml stearic acid


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep1]

description:
Ad5-FMDV_T24_rep1
Total blood sample (replicate 1) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: ICA1_off


title: ste rep3


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep1]

description:
Ad5-FMDV_T4_rep1
Total blood sample (replicate 1) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: ste rep1


title: C1HTmedium_m4_1911014296_Col14_S152


title: Sheep whole blood - T0 - Ad5-FMDV [Ad5-FMDV_T0_rep1]

description:
Ad5-FMDV_T0_rep1
Total blood sample (replicate 1) collected 0h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m4_1911014296_Col12_S143


title: suc-ste rep3


title: NSC_KI_B1

city: Rotterdam

first: Tahsin Stefan

last: Barakat

state: South Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: The Erasmus University Medical Center

data_processing:
Sequenced reads were trimmed for adapter sequence using Trimmomatic (version 0.38).
Read quality was checked for each sample using FastQC (version 0.11.8).
Trimmed reads were mapped against the human GRCh38 reference sequence using HiSat2 (version 2.1.0).
Count table were generated using htseq-count  (version 0.9.1).
Genome_build: GRCH38
Supplementary_files_format_and_content: bigWig files were generated by converting .Bam files to .bdg using  genomeCoverageBed, then .bdg files to .bw files using bedGraphToBigWig.

source_name: Neural stem cells

growth_protocol: Human embryonic stem cells were maintained in feeder-free conditions in mTeSR medium on Matrigel (Corning) coated culture dishes, as previously described (Barakat et al Cell Stem Cell 2018, PMID: 30033119). For NSC differentiation, we used a modified dual SMAD inhibition protocol, as described in our publication.

extract_protocol:
RNA was obtained from 6-well cultures using Trizol, and purified using a purification column (Qiagen, #74204).
Libraries were prepared with the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting libraries were sequenced according to the Illumina TruSeq Rapid  v2 protocol on an Illumina HiSeq2500 sequencer.

value: NSCs

tag: sample type

value: Knock-In A>G


title: suc rep3

description:
Gene_full_table.xls
control_vs_suc.annotation.xls

value: 400mM sucrose


title: NSC_KI_B2

tag: cell line


title: suc rep2


title: NSC_KO_B2

value: Knock-out


title: NSC_KO_B1


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep10]

description:
iFMDV_T24_rep10
Total blood sample (replicate 10) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

value: Prealpes

value: blood

value: adult (6 months)

value: inactivated FMDV (iFMDV)


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep10]

description:
iFMDV_T4_rep10
Total blood sample (replicate 10) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

value: male


title: suc rep1

value: whole body

value: wild type


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep10]

description:
iFMDV_T0_rep10
Total blood sample (replicate 10) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: NSC_WT_B2

value: Wild-Type


title: Control  rep3


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep9]

description:
iFMDV_T24_rep9
Total blood sample (replicate 9) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Control  rep2


title: C1HTmedium_m4_1911014296_Col13_S151

description:
cryopreserved HCA reference
C1HTmedium_human_exp_mat.tsv, C1HTmedium_human_metada.tsv, C1HTmedium_mouse_exp_mat.tsv, C1HTmedium_mouse_metada.tsv

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: C1HTmedium_m4_1911014296_Col08_S145


title: C1HTmedium_m4_1911014296_Col10_S144


title: Control rep1


title: SY5Y_BR6_Rep2

value: neuroblastoma

value: SY5Y_BR6 (parental)


title: C1HTmedium_m4_1911014296_Col07_S146


title: H9_KI_B1

source_name: embryonic stem cells


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep9]

description:
iFMDV_T4_rep9
Total blood sample (replicate 9) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: H9_KI_B2


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep9]

description:
iFMDV_T0_rep9
Total blood sample (replicate 9) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m4_1911014296_Col06_S147


title: C1HTmedium_m4_1911014296_Col11_S159


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep8]

description:
iFMDV_T4_rep8
Total blood sample (replicate 8) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep8]

description:
iFMDV_T24_rep8
Total blood sample (replicate 8) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: H9_WT_B2


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep7]

description:
iFMDV_T24_rep7
Total blood sample (replicate 7) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m4_1911014296_Col03_S142


title: C1HTmedium_m4_1911014296_Col05_S148


title: NSC_WT_B1


title: C1HTmedium_m4_1911014296_Col04_S158


title: H9_WT_B1


title: 2_B3_visit 0 (baseline)

type: RNA

city: Oslo

first: Stine

middle: Marie

last: Ulven

address: Sognsvannsveien 9

department: Department of Nutrition

country: Norway

institute: University of oslo

hyb_protocol: Illumina HumanHT-12 v4 Expression BeadChip (Illumina Inc., California, USA)

scan_protocol: Illumina HiScan System (Illumina Inc., California, USA)

data_processing: The data was normilised using the Illumina GenomeStudio software, version 1.7.0. Genome Studio Illumina was used to calculate and report a detection p-value, which represents the confidence that a given transcript is expressed above the background. A gene was defined as expressed when relevant probes with a p-value below 0.01 were found in more than five samples. After hybridization and scanning, a manual quality control was performed investigating density plots and hierarchical clustering of raw probe densities. One probe per gene (max IQR) was selected for further analysis.

label: biotin

source_name: PBMC, baseline

label_protocol: Illumina Total Prep RNA Amplification Kit (Illumina Inc., California, USA)

extract_protocol: mRNA was extracted using RNeasy Mini Kit (Qiagen) acording to the protocol provided. RNA quantity was measured using NanoDrop-1000 (NanoDrop Technologies, Inc., Delaware, USA), while RNA quality was checked with Aglient 2100 Bioanalyzer (Agilent Technologies, Inc., California, USA).

treatment_protocol: PBMCs were isolated, pellets were stored at -80 °C before mRNA was extracted.

tag: group

value: Protein

value: week 0


title: 2_B4_visit 1 (end of intervention)

source_name: PBMC, end of intervention

value: week 12


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep7]

description:
iFMDV_T4_rep7
Total blood sample (replicate 7) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

source_name: blood

tag: animal id


title: C1HTmedium_m4_1911014296_Col01_S141


title: C1HTmedium_m4_1911014296_Col02_S157


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep7]

description:
iFMDV_T0_rep7
Total blood sample (replicate 7) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

tag: breed


title: C1HTmedium_m3_1911014277_Col20_S129


title: H9_KO_B2


title: 2_D2_visit 1 (end of intervention)


title: single-cell RNA-seq dataset: mock-infected A549 cells

city: New York

first: Chang

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

data_processing:
For the single-cell RNA-seq datasets generated in the time course infection assay, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment and gene counting with the processed UMIs for each cell. Then the UMI counts for all the viral reads including the gapped reads with the CIGAR string containing a large gap (i.e., “MNM”) were merged into the expression matrix.
For the bulk RNA-seq datasets, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment.
For the single-cell RNA-seq datasets generated from PR8-infected A549 and MDCK cells at different MOIs, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment.
Genome_build: hg19 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1)
Supplementary_files_format_and_content: For the single-cell RNA-seq datasets generated in the time course infection assay, each tab-delimited text file contains the raw gene expression matrix for individual cells harvested at a given time point. For the bulk RNA-seq datasets, each tab-delimited text file contains the raw gene counts for a given sample.

source_name: adenocarcinomic human alveolar basal epithelial cells

growth_protocol: A549 cells (ATCC) were maintained in Kaighn’s modified Ham’s F-12 medium (F-12K) supplemented with 10% fetal bovine serum (FBS) prior to infection. A549 cells were infected in A549 infection media (F-12K supplemented with 2% bovine serum albumin (BSA) and 1% antibiotic-antimycotic).

extract_protocol:
Cells were trypisinized, extensively washed, and re-suspended in PBS containing 0.04% BSA.
Cells were subject to 10X Genomics single cell library preparation with Chromium 3’ v2 chemistry following the manufacturer’s protocol.

treatment_protocol: Mock-infection

tag: cell types

tag: infection time points

value: No infection

tag: virus strain


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep6]

description:
iFMDV_T24_rep6
Total blood sample (replicate 6) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

tag: tissue

tag: Stage

tag: Sex

tag: time point


title: H9_KO_B1

value: Knock-out


title: C1HTmedium_m4_1911014296_Col09_S160

tag: protocol


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep8]

description:
iFMDV_T0_rep8
Total blood sample (replicate 8) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

value: Prealpes


title: 2_D1_visit 0 (baseline)


title: C1HTmedium_m3_1911014277_Col19_S130


title: 2_E2_visit 1 (end of intervention)

value: Carbohydrate


title: single-cell RNA-seq dataset: mock-infected HBEpC cells

source_name: primary human bronchial epithelial cells

growth_protocol: HBEpC cells (PromoCell) were maintained and infected in PromoCell airway epithelial cell growth media with SupplementMix.

value: HBEpC


title: C1HTmedium_m3_1911014277_Col18_S136


title: 2_C2_visit 1 (end of intervention)


title: Patient4-N rep1

city: Shanghai

first: Guang

last: Zhou

address: No. 600, Yishan Road

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

description: Normal tissue

data_processing:
Clean data(clean reads) were obtained by removing reads containing adapter, low quality reads from raw data by fastx_toolkit (0.0.14) software
The quality control analysis of preprocessed data was performed using the seqtk (1.0-r82-dirty) and  R (3.x.x) scripts.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6
New miRNA prediction using mirdeep2 (2.0.0.5) software
Target genes were predicted using miRanda (v3.3a) software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include expression values for each Sample. A FASTA file with the miRNA sequences is available on the series record.

source_name: Normal bile duct tissue

extract_protocol:
Fresh frozen cholangiocarcinoma and normal bile duct tissues were sampled, flash frozen on dry ice, and total RNA was harvested using Trizol reagent.
microRNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease state

value: Normal

value: intrahepatic bile duct

value: Fresh tissue


title: Patient5-N rep1

description: Normal tissue


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep6]

description:
iFMDV_T4_rep6
Total blood sample (replicate 6) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

value: blood

value: adult (6 months)

value: male

value: inactivated FMDV (iFMDV)


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep6]

description:
iFMDV_T0_rep6
Total blood sample (replicate 6) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep5]

description:
iFMDV_T24_rep5
Total blood sample (replicate 5) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: 2_E1_visit 0 (baseline)


title: Patient3-N rep1

description: Normal tissue


title: C1HTmedium_m3_1911014277_Col16_S134

value: Stanford

tag: cell type

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: C1HTmedium_m3_1911014277_Col17_S135

tag: centre


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep5]

description:
iFMDV_T4_rep5
Total blood sample (replicate 5) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

tag: treatment


title: Patient2-N rep1

description: Normal tissue

tag: sample type


title: 2_C1_visit 0 (baseline)


title: 2_B2_visit 1 (end of intervention)

value: Protein


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep5]

description:
iFMDV_T0_rep5
Total blood sample (replicate 5) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Patient1-N rep1

description: Normal tissue


title: Patient5-T rep1

description: tumor

source_name: Intrahepatic cholangiocarcinoma

value: Intrahepatic cholangiocarcinoma


title: C1HTmedium_m3_1911014277_Col14_S132


title: C1HTmedium_m3_1911014277_Col13_S131


title: Patient4-T rep1

description: tumor


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep4]

description:
iFMDV_T4_rep4
Total blood sample (replicate 4) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Patient3-T rep1

description: tumor


title: 2_B1_visit 0 (baseline)

value: week 0


title: C1HTmedium_m3_1911014277_Col12_S123


title: ICA2_on

description:
Engineered cell line with doxycycline regulated Myc expression and enforced expression of myristoylated AKT1
gene_exp.diff
isoform_exp.diff
SE.MATS.JC.txt.pairadiseAppend.txt.sig0.05.txt

tag: cell line

value: Prostate epithelium-derived cells

tag: myc status

value: Myc on


title: Patient2-T rep1

description: tumor


title: C1HTmedium_m3_1911014277_Col11_S139

description:
cryopreserved HCA reference
C1HTmedium_human_exp_mat.tsv, C1HTmedium_human_metada.tsv, C1HTmedium_mouse_exp_mat.tsv, C1HTmedium_mouse_metada.tsv


title: Patient1-T rep1

description: tumor


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep4]

description:
iFMDV_T0_rep4
Total blood sample (replicate 4) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

tag: animal id

value: Prealpes


title: 2_C12_visit 1 (end of intervention)

tag: group

value: week 12


title: 2_B12_visit 1 (end of intervention)

value: Carbohydrate


title: C1HTmedium_m3_1911014277_Col10_S124


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep3]

description:
iFMDV_T24_rep3
Total blood sample (replicate 3) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

tag: breed


title: Liver, Shp Hep-/- HFCF 3

city: kansas city

first: Yuxia

last: Zhang

state: KS

address: 3901 Rainbow Blvd, Hemenway 4001

department: Pharmacology, Toxicology, and Therapeutics

institute: University of Kansas Medical Center

description: HSKO HF 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm10 whole genome using CLCBio Genomics Workbench 11 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes counts, FPKM values for each Sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Zymogen Research Direct-zol RNA Miniprep Plus (Cat#R2072) was used. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded RNA Kit wit Ribo-Zero Gold

tag: strain

tag: age

value: 5 months

tag: genotype

value: Shp Hep-/-

value: HFCF

value: liver


title: 2_B11_visit 0 (baseline)


title: C1HTmedium_m3_1911014277_Col09_S140


title: Liver, Shp Hep-/- HFCF 2

description: HSKO HF 2

tag: tissue


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep3]

description:
iFMDV_T0_rep3
Total blood sample (replicate 3) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

value: blood

tag: Stage

value: adult (6 months)

tag: Sex


title: 2_C11_visit 0 (baseline)

tag: time point


title: C1HTmedium_m3_1911014277_Col15_S133

tag: protocol


title: 2_D12_visit 1 (end of intervention)


title: C1HTmedium_m3_1911014277_Col08_S125

tag: cell type


title: 2_E11_visit 0 (baseline)


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep4]

description:
iFMDV_T24_rep4
Total blood sample (replicate 4) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

value: male

value: inactivated FMDV (iFMDV)


title: 2_D11_visit 0 (baseline)


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep2]

description:
iFMDV_T24_rep2
Total blood sample (replicate 2) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Liver, Shp Hep-/- HFCF 1

description: HSKO HF 1


title: C1HTmedium_m3_1911014277_Col07_S126

tag: centre

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep3]

description:
iFMDV_T4_rep3
Total blood sample (replicate 3) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt

tag: treatment


title: C1HTmedium_m3_1911014277_Col06_S127


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep2]

description:
iFMDV_T0_rep2
Total blood sample (replicate 2) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Liver, WT HFCF 2

value: WT


title: 2_E10_visit 1 (end of intervention)


title: Liver, WT HFCF 1


title: C1HTmedium_m3_1911014277_Col05_S128


title: 2_E12_visit 1 (end of intervention)


title: C1HTmedium_m3_1911014277_Col04_S138


title: C1HTmedium_m3_1911014277_Col03_S122


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep1]

description:
iFMDV_T4_rep1
Total blood sample (replicate 1) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T24 - iFMDV [iFMDV_T24_rep1]

description:
iFMDV_T24_rep1
Total blood sample (replicate 1) collected 24h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T0 - iFMDV [iFMDV_T0_rep1]

description:
iFMDV_T0_rep1
Total blood sample (replicate 1) collected 0h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: 2_E9_visit 0 (baseline)

value: week 0


title: Liver, Shp Hep-/- Chow 2

description: HSKO 2

value: Chow


title: Liver, Shp Hep-/- Chow 1

description: HSKO 1


title: C1HTmedium_m3_1911014277_Col01_S121


title: C1HTmedium_m3_1911014277_Col02_S137


title: Sheep whole blood - T4 - iFMDV [iFMDV_T4_rep2]

description:
iFMDV_T4_rep2
Total blood sample (replicate 2) collected 4h after vaccination with inactivated FMDV (iFMDV).
processed data file: counts_table_all_samples.txt


title: Liver, WT Chow 3


title: 2_A12_visit 1 (end of intervention)

value: Protein


title: 2_A11_visit 0 (baseline)


title: 2_D9_visit 0 (baseline)


title: 2_F9_visit 0 (baseline)


title: Liver, WT HFCF 3


title: C1HTmedium_m2_1912014197_Col20_S29


title: Liver, WT Chow 2


title: Liver, Shp Hep-/- Chow 3

description: HSKO 3


title: 2_D10_visit 1 (end of intervention)


title: Liver, WT Chow 1


title: C1HTmedium_m2_1912014197_Col19_S30


title: C1HTmedium_m2_1912014197_Col17_S35


title: C1HTmedium_m2_1912014197_Col18_S36


title: C1HTmedium_m2_1912014197_Col16_S34


title: tibia_proximal_BMAT_13-week-old_biological_replicate_6

city: Edinburgh

first: William

middle: P

last: Cawthorn

address: 47 Little France Crescent

department: Centre for Cardiovascular Science, The Queen's Medical Research Institute

country: United Kingdom

institute: The University of Edinburgh

hyb_protocol: Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Rabbit2a520535F Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 2.15. RMA was used to fit log2 transformed expression values. The org.Ocuniculus.eg.db_1.0 package from bioconductor was used for annoation.

organism: Oryctolagus cuniculus

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

growth_protocol: The 22-week-old rabbits were fed 100 g food per day (approximately 32 g/kg body mass/day). The 13-week-old rabbits were fed ad libitum (approximately 68 g/kg body mass/day)

extract_protocol: Total RNA was isolated from tissues using RNA STAT60 reagent (Tel-Test, Inc) according to the manufacturer’s instructions. Purified RNA was digested on-column with DNase I and cleaned using the Qiagen RNeasy kit (Qiagen, Valencia, CA, USA) as recommended by the manufacturer. Samples were screened for quality prior to downstream labelling and analysis.

value: 13 weeks old

tag: diet

value: Ad libitum


title: iWAT_13-week-old_biological_replicate_6

source_name: iWAT, 13-week-old, rabbit_ID_13.12

value: iWAT


title: C1HTmedium_m2_1912014197_Col15_S33


title: tibia_distal_BMAT_13-week-old_biological_replicate_6


title: 2_C10_visit 1 (end of intervention)

value: Carbohydrate

value: week 12


title: 2_C9_visit 0 (baseline)


title: 2_F10_visit 1 (end of intervention)


title: iWAT_13-week-old_biological_replicate_5

source_name: iWAT, 13-week-old, rabbit_ID_13.8


title: tibia_proximal_BMAT_13-week-old_biological_replicate_5


title: radius_and_ulna_BMAT_13-week-old_biological_replicate_6


title: 2_F8_visit 1 (end of intervention)


title: C1HTmedium_m2_1912014197_Col14_S32


title: 2_F7_visit 0 (baseline)


title: gWAT_13-week-old_biological_replicate_5

source_name: gWAT, 13-week-old, rabbit_ID_13.8

value: gWAT


title: C1HTmedium_m2_1912014197_Col13_S31


title: 2_C8_visit 1 (end of intervention)


title: C1HTmedium_m2_1912014197_Col12_S23


title: C1HTmedium_m2_1912014197_Col11_S39


title: 2_E7_visit 0 (baseline)


title: Tobacco-wounded for 9 hr [V1 vs WS3]

city: Minamiminowa

first: Shinpei

last: Katou

state: Kamiina, Nagano

department: Faculty of Agriculture

country: Japan

institute: Shinshu University

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Tobacco Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

organism: Nicotiana tabacum

source_name: Tobacco plants transformed with empty vector

label_protocol: 100 ng of total RNA were labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Plants were grown in pots containing vermiculite in a chamber maintained at 25°C with 16 h of light.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Leaves were wounded for 9 hours.

value: 6- to 7-week-old

tag: genotype/variation

value: transformed with empty vector

value: Leaves

source_name: Tobacco plants in which expression of WIPK and SIPK is suppressed by RNAi


title: C1HTmedium_m2_1912014197_Col10_S24


title: 2_C7_visit 0 (baseline)


title: radius_and_ulna_BMAT_13-week-old_biological_replicate_5


title: iWAT_13-week-old_biological_replicate_4

source_name: iWAT, 13-week-old, rabbit_ID_13.6


title: 2_E8_ visit 1 (end of intervention)


title: tibia_distal_BMAT_13-week-old_biological_replicate_5


title: C1HTmedium_m2_1912014197_Col09_S40


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR141_rep3

city: Atlanta

first: Neda

last: Jabbari

state: GA

address: 315 Ferst Dr

institute: Georgia Institute of Technology

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-3.cel was analyzed together only with miR-141 samples

hyb_protocol: Labeled mRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays in the GeneChip Hybridization oven 640, further processed with the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner 3000.

scan_protocol: as per manufacturer's protocol using GeneChip Scanner 3000.

data_processing:
GCRMA at www.arrayanalysis.org for signals and FDR using SAM (http://www-stat.stanford.edu/~tibs/SAM/) and MAS5 from Affymetrix Expression Console for present/absent calls. Probe_sets lacking a gene symbol annotation and x_at probes are ignored.  miR-141-3.cel was not used in the study due to quality control (www.arrayanalysis.org).
normalized using log2 of GCRMA signal

source_name: HEY ovarian cancer cell, Negative Control miRNA treated, rep 3

label_protocol: mRNAs were converted to double stranded (ds)-cDNA and amplified using Applause 3’-Amp System (NuGen, San Carlos, CA). This cDNA was then biotin labeled and fragmented by using Encore Biotin Module (NuGen)

growth_protocol: HEY ovarian cancer cell lines were cultured in RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10% v/v Fetal Bovine Serum (Atlanta Biologicals, Lawrenceville, GA) and 1% v/v antibiotic-antimycotic solution (10,000 I.U. Penicillin (per mL), 10,000 µg/mL Streptomycin and 25 µg/mL Amphotericin, Mediatech-Cellgro, Manassas, VA).

extract_protocol: Total RNA was extracted from cells using the RNeasy mini RNA isolation kit (Qiagen, Valencia, CA). The integrity of RNA samples was verified using an Agilent 2100 Bioanalyzer (1.8-2.0; Agilent Technologies, Palo Alto, CA).

treatment_protocol: 60,000 cells were seeded per well on 24-well plates in growth medium and allowed to adhere overnight at 37  ͦC in a 5% CO2 atmosphere. Cells were then transfected with 30 nM miR-141 miRNA purchased as Pre-miR miRNA Precursor (Ambion, Austin, TX) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and according to the manufacturer’s instructions. For negative control, cells were transfected with negative control miRNA (nc-miR) purchased as Pre-miR miRNA Precursor Negative Control #1(Ambion, Austin, TX). Cells were allowed to grow for 48 hours before RNA isolation.

tag: original tumor type of initial cell

value: Papillary Cystadenocarcinoma of the ovary

tag: cell line

value: HEY


title: 2_B8_visit 1 (end of intervention)

tag: group


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR141_rep2

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-2.cel was analyzed together only with miR-141 samples

source_name: HEY ovarian cancer cell, Negative Control miRNA treated, rep 2


title: HEY cell_miR-141 treated_rep1

description: HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.

source_name: HEY ovarian cancer cell, miR-141 treated, rep 1


title: tibia_distal_BMAT_13-week-old_biological_replicate_4


title: radius_and_ulna_BMAT_13-week-old_biological_replicate_4


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR141_rep1

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-1.cel was analyzed together only with miR-141 samples

source_name: HEY ovarian cancer cell, Negative Control miRNA treated, rep 1


title: 2_B7_visit 0 (baseline)

source_name: PBMC, baseline


title: gWAT_13-week-old_biological_replicate_4

source_name: gWAT, 13-week-old, rabbit_ID_13.6


title: HEY cell_miR-141 treated_rep2

source_name: HEY ovarian cancer cell, miR-141 treated, rep 2


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR200b_rep3

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-3.cel was analyzed together only with miR-200b samples

data_processing:
GCRMA at www.arrayanalysis.org for signals and FDR using SAM (http://www-stat.stanford.edu/~tibs/SAM/) and MAS5 from Affymetrix Expression Console for present/absent calls. Probe_sets lacking a gene symbol annotation and x_at probes are ignored.
normalized using log2 of GCRMA signal

treatment_protocol: 60,000 cells were seeded per well on 24-well plates in growth medium and allowed to adhere overnight at 37  ͦC in a 5% CO2 atmosphere. Cells were then transfected with 30 nM miR-200b miRNA purchased as Pre-miR miRNA Precursor (Ambion, Austin, TX) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and according to the manufacturer’s instructions. For negative control, cells were transfected with negative control miRNA (nc-miR) purchased as Pre-miR miRNA Precursor Negative Control #1(Ambion, Austin, TX). Cells were allowed to grow for 48 hours before RNA isolation.


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR200b_rep2

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-2.cel was analyzed together only with miR-200b samples


title: 2_A1_visit 0 (baseline)


title: 2_A2_visit 1 (end of intervention)

source_name: PBMC, end of intervention


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR200b_rep1

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-1.cel was analyzed together only with miR-200b samples


title: tibia_proximal_BMAT_13-week-old_biological_replicate_3


title: C1HTmedium_m2_1912014197_Col07_S26

description:
cryopreserved HCA reference
C1HTmedium_human_exp_mat.tsv, C1HTmedium_human_metada.tsv, C1HTmedium_mouse_exp_mat.tsv, C1HTmedium_mouse_metada.tsv

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

value: Stanford


title: C1HTmedium_m2_1912014197_Col06_S27

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: C1HTmedium_m2_1912014197_Col08_S25


title: C1HTmedium_m2_1912014197_Col05_S28


title: iWAT_13-week-old_biological_replicate_3

source_name: iWAT, 13-week-old, rabbit_ID_13.5


title: C1HTmedium_m2_1912014197_Col04_S38


title: C1HTmedium_m2_1912014197_Col03_S22


title: tibia_distal_BMAT_13-week-old_biological_replicate_3


title: gWAT_13-week-old_biological_replicate_3

source_name: gWAT, 13-week-old, rabbit_ID_13.5


title: radius_and_ulna_BMAT_13-week-old_biological_replicate_3


title: 2_D6_visit 1 (end of intervention)


title: 2_A8_visit 1 (end of intervention)


title: tibia_proximal_BMAT_13-week-old_biological_replicate_2


title: HEY cell_miR-200b treated_rep3

source_name: HEY ovarian cancer cell, miR-200b treated, rep 3


title: C1HTmedium_m2_1912014197_Col01_S21


title: 2_B9_visit 0 (baseline)


title: HEY cell_miR-200b treated_rep1

source_name: HEY ovarian cancer cell, miR-200b treated, rep 1


title: 2_B10_visit 1 (end of intervention)


title: HEY cell_miR-200b treated_rep2

source_name: HEY ovarian cancer cell, miR-200b treated, rep 2


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR205_rep3

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-3.cel was analyzed together only with miR-205 samples

treatment_protocol: 60,000 cells were seeded per well on 24-well plates in growth medium and allowed to adhere overnight at 37  ͦC in a 5% CO2 atmosphere. Cells were then transfected with 30 nM miR-205 miRNA purchased as Pre-miR miRNA Precursor (Ambion, Austin, TX) using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and according to the manufacturer’s instructions. For negative control, cells were transfected with negative control miRNA (nc-miR) purchased as Pre-miR miRNA Precursor Negative Control #1(Ambion, Austin, TX). Cells were allowed to grow for 48 hours before RNA isolation.


title: C1HTmedium_m2_1912014197_Col02_S37


title: C1HTmedium_m1_1912014195_Col20_S9


title: iWAT_13-week-old_biological_replicate_2

source_name: iWAT, 13-week-old, rabbit_ID_13.3


title: 2_A7_ visit 0 (baseline)


title: tibia_distal_BMAT_13-week-old_biological_replicate_2


title: 2_C6_visit 1 (end of intervention)


title: gWAT_13-week-old_biological_replicate_2

source_name: gWAT, 13-week-old, rabbit_ID_13.3


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR205_rep2

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-2.cel was analyzed together only with miR-205 samples


title: 2_C5_visit 0 (baseline)


title: 2_D8_visit 1 (end of intervention)


title: HEY cell_Negative Control miRNA treated_analyzed_with_miR205_rep1

description:
HEY human ovarian carcinoma cell line was derived from a human ovarian cancer xenograft (HX-62) in immunologically deprived CBA/CJ mice originally grown from a peritoneal deposit of a patient.
nc-miR-1-1.cel was analyzed together only with miR-205 samples


title: HEY cell_miR-205 treated_rep1

source_name: HEY ovarian cancer cell, miR-205 treated, rep 1


title: C1HTmedium_m1_1912014195_Col19_S10


title: C1HTmedium_m1_1912014195_Col18_S16


title: HEY cell_miR-205 treated_rep2

source_name: HEY ovarian cancer cell, miR-205 treated, rep 2


title: 2_D5_visit 0 (baseline)


title: radius_and_ulna_BMAT_13-week-old_biological_replicate_2


title: tibia_distal_BMAT_13-week-old_biological_replicate_1


title: HEALTHY15_Healthy

city: Granada

first: Pedro

last: Medina Vico

state: Granada

address: Avenida de Fuente Nueva, s/n

department: Biochemistry and Molecular Biology I

institute: University of Granada

hyb_protocol: The labeled cRNAs were hybridized onto the LncPathTM Human Cancer Array (8x15K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: Bone marrow

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies)

extract_protocol: Total RNAs were extracted from bone marrow aspirates using Trizol reagent (Invitrogen), according to manufacturer’s instructions. Quality of RNA samples was measured using Agilent 2100 Bioanalyzer system.

treatment_protocol: Bone marrow tissues were frozen upon acquisition and stored at − 80°C.

value: Healthy

tag: sample source

value: Regional Málaga Hospital

tag: phenotype

tag: snc

tag: event (dead or relapsed)


title: HEALTHY16_Healthy


title: 2_D7_visit 0 (baseline)

value: week 0


title: 2_A6_visit 1 (end of intervention)


title: HEY cell_miR-205 treated_rep3

source_name: HEY ovarian cancer cell, miR-205 treated, rep 3


title: iWAT_13-week-old_biological_replicate_1

source_name: iWAT, 13-week-old, rabbit_ID_13.1

tag: tissue

tag: age


title: C1HTmedium_m1_1912014195_Col16_S14

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-11); R2 = cDNA


title: gWAT_13-week-old_biological_replicate_1

source_name: gWAT, 13-week-old, rabbit_ID_13.1


title: 2_A5_visit 0 (baseline)

source_name: PBMC, baseline


title: C1HTmedium_m1_1912014195_Col17_S15


title: C1HTmedium_m1_1912014195_Col13_S11


title: tibia_proximal_BMAT_13-week-old_biological_replicate_1


title: ALL53_Positive

value: Positive

value: San Juan de Dios Hospital

tag: Sex

value: male

value: alive

value: B common

value: Intermediate

value: SEHOP-PETHEMA 2013


title: 2_E4_visit 1 (end of intervention)

value: Protein

tag: time point

value: week 12


title: radius_and_ulna_BMAT_13-week-old_biological_replicate_1

value: 13 weeks old

value: Ad libitum


title: C1HTmedium_m1_1912014195_Col12_S3

tag: protocol


title: ALL51_Positive


title: HEALTHY10_Healthy


title: ALL50_Positive

value: female


title: C1HTmedium_m1_1912014195_Col11_S19

value: Stanford

tag: cell type


title: ALL52_Positive


title: C1HTmedium_m1_1912014195_Col10_S4

tag: centre

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: iWAT_22-week-old_biological_replicate_5

source_name: iWAT, 22-week-old, rabbit_ID_22.5

value: iWAT

value: 22 weeks old

value: 100 g/day


title: C1HTmedium_m1_1912014195_Col15_S13


title: gWAT_22-week-old_biological_replicate_5

source_name: gWAT, 22-week-old, rabbit_ID_22.5

value: gWAT


title: HEALTHY3_Healthy

value: Healthy

value: Regional Málaga Hospital


title: C1HTmedium_m1_1912014195_Col14_S12

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK


title: 2_E3_visit 0 (baseline)

value: week 0


title: 2_C4_visit 1 (end of intervention)

source_name: PBMC, end of intervention

value: Carbohydrate


title: ALL48_Positive

value: Positive

value: San Juan de Dios Hospital

value: alive

value: B common

value: Intermediate


title: 2_C3_visit 0 (baseline)


title: radius_and_ulna_BMAT_22-week-old_biological_replicate_5


title: iWAT_22-week-old_biological_replicate_4

source_name: iWAT, 22-week-old, rabbit_ID_22.9


title: 2_D4_visit 1 (end of intervention)

value: Protein

value: week 12


title: 2_F4_visit 1 (end of intervention)


title: 2_D3_visit 0 (baseline)


title: C1HTmedium_m1_1912014195_Col09_S20

value: Stanford


title: ALL47_Positive

value: female

value: SEHOP-PETHEMA 2013


title: tibia_distal_BMAT_22-week-old_biological_replicate_5

value: 22 weeks old


title: C1HTmedium_m1_1912014195_Col08_S5

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: ALL49_Positive


title: ALL46_Positive

value: male


title: C1HTmedium_m1_1912014195_Col07_S6


title: C1HTmedium_m1_1912014195_Col06_S7


title: C1HTmedium_m1_1912014195_Col04_S18


title: C1HTmedium_m1_1912014195_Col05_S8


title: tibia_distal_BMAT_22-week-old_biological_replicate_4

value: 100 g/day


title: 2_E6_visit 1 (end of intervention)


title: C1HTmedium_m1_1912014195_Col03_S2


title: 2_F3_visit 0 (baseline)


title: SMARTseq2_allLanes

description:
cryopreserved HCA reference
SMARTseq2_human_exp_mat.tsv, SMARTseq2_human_metada.tsv, SMARTseq2_mouse_exp_mat.tsv, SMARTseq2_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = cDNA; R2 = cDNA; I1 = BC (1-8); I2 = BC (1-8)

value: Karolinska


title: ALL45_Positive


title: ALL44_Positive

value: Very high


title: MARSseq_5927AA

description:
cryopreserved HCA reference
MARSseq_human_exp_mat.tsv, MARSseq_human_metada.tsv, MARSseq_mouse_exp_mat.tsv, MARSseq_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = cDNA; R2 = BC (1-6), UMI (7-14)

value: MARS-Seq

value: CNAG


title: C1HTmedium_m1_1912014195_Col02_S17


title: iWAT_22-week-old_biological_replicate_3

source_name: iWAT, 22-week-old, rabbit_ID_22.A

value: iWAT


title: radius_and_ulna_BMAT_22-week-old_biological_replicate_4


title: ALL43_Positive

value: Positive

value: Regional Málaga Hospital

value: alive

value: Pre-B

value: Low

value: PETHEMA PROTOCOLO 27/89


title: MARSseq_5926AA


title: 2_A3_visit 0 (baseline)

value: Carbohydrate

value: week 0


title: ALL40_Positive

value: B common

value: High

value: PETHEMA RIA-96


title: 2_A4_visit 1 (end of intervention)

value: week 12


title: 2_E5_visit 0 (baseline)

value: Protein


title: gWAT_22-week-old_biological_replicate_3

source_name: gWAT, 22-week-old, rabbit_ID_22.A

value: gWAT

value: 22 weeks old

value: 100 g/day


title: radius_and_ulna_BMAT_22-week-old_biological_replicate_3


title: tibia_distal_BMAT_22-week-old_biological_replicate_3


title: gWAT_22-week-old_biological_replicate_4

source_name: gWAT, 22-week-old, rabbit_ID_22.9


title: ALL41_Positive

value: male

value: Intermediate


title: ALL42_Positive

value: Positive

value: Regional Málaga Hospital


title: C1HTmedium_m1_1912014195_Col01_S1

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: MARSseq_5924AA

value: MARS-Seq

value: CNAG


title: MARSseq_5925AA


title: MARSseq_5923AA


title: REF_10X8x10Kcell25Kreads_71727

description:
cryopreserved HCA reference
10X8x10Kcell25Kreads_human_exp_mat.tsv, 10X8x10Kcell25Kreads_human_metada.tsv, 10X8x10Kcell25Kreads_mouse_exp_mat.tsv, 10X8x10Kcell25Kreads_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-16), UMI (17-91), R2 = cDNA

value: Chromium V2


title: REF_10X8x10Kcell25Kreads_71728


title: REF_10X8x10Kcell25Kreads_71726


title: ALL37_Positive

value: alive

value: B common


title: ALL36_Positive

value: Low

value: PETHEMA BR/01


title: REF_10X8x10Kcell25Kreads_71725


title: ALL35_Positive


title: Pfalciparum_D6_hour69

city: Durham

first: Steven

last: Haase

state: North Carolina

institute: Duke University

data_processing:
Reads were aligned using STAR_2.4.1d with parameters --runMode alignReads --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFilterIntronMotifs RemoveNoncanonical
Aligned, sorted SAM files were created with cuffquant v2.2.1 with parameter --library-type=fr-firststrand
Samples from each strain were normalized by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using cuffnorm v2.2.1 with parameter --library-type=fr-firststrand
Genome_build: The Sanger Institute's P. falciparum 3D7 v3.0 genome
Supplementary_files_format_and_content: Tab-delimited text files for each strain with FPKM values for all genes per timepoints, which are given in hours

organism: Plasmodium falciparum

source_name: in vitro culture

growth_protocol: Parasites were synchronized by alanine treatment and temperature cycling as decribed in Haynes and Moch 2002 (PMID:12125145). For the course of the experiment, strains were grown at 37C in RPMI 1640 with 10% human serum and 4% hematocrit. Flasks were gassed with 5% CO2, 5% O2, 90% N2. Cultures were sampled every 3 hours, and sampling began between late schizont and early ring stages.

extract_protocol:
Samples were spun down, media aspirated, and pellet snap frozen and stored at -80C. Total RNA was extracted using a phenol-chloroform protocol as described in Leman et al 2014 (PMID: 24906319), except citrate-buffered phenol was substituted for acid phenol. The ratios of reagent to sample as found in the cited protocol were retained, with the exception of the initial thawing in TES buffer, which was changed to a 2:1 ratio of TES to sample.
Libraries were prepared using Stranded Total RNA Kapa kits with rRNA Ribo-Zero Globin depletion

tag: strain


title: MARSseq_5921AA

city: Barcelona

first: Atefeh

institute: Center for Genomic Regulation

extract_protocol:
PBMCs were isolated according to the manufacturer’s instructions for FICOLL extraction (pluriSelect).Minced mouse colon was digested in 1X HBSS and 83 µl of collagenase IV (final concentration 166 U/ml) for 15 min at 37ºC and filtered through a 70 µm nylon mesh.
Sequencing librraries were prepared according to the respective single-cell RNA-seq protocols as detailed in the Methods and referenced in TableS1.
Library selection and sequencing was performed following recommendations of to the respective single-cell RNA-seq protocols as detailed in the Methods.


title: gWAT_22-week-old_biological_replicate_2

source_name: gWAT, 22-week-old, rabbit_ID_22.8

tag: diet


title: iWAT_22-week-old_biological_replicate_2

source_name: iWAT, 22-week-old, rabbit_ID_22.8

value: iWAT


title: REF_10X8x10Kcell25Kreads_71723


title: tibia_distal_BMAT_22-week-old_biological_replicate_2


title: ALL34_Positive

value: female


title: MARSseq_5920AA


title: REF_10X8x10Kcell25Kreads_71724


title: radius_and_ulna_BMAT_22-week-old_biological_replicate_2

value: 22 weeks old


title: tibia_distal_BMAT_22-week-old_biological_replicate_1

value: 100 g/day


title: Pfalciparum_D6_hour66


title: gWAT_22-week-old_biological_replicate_1

source_name: gWAT, 22-week-old, rabbit_ID_22.7

value: gWAT


title: REF_10X8x10Kcell25Kreads_71722


title: MARSseq_5571AA


title: MARSseq_5570AA


title: MARSseq_5922AA


title: Pfalciparum_D6_hour63


title: REF_10X8x10Kcell25Kreads_71721


title: ALL30_Positive

source_name: Bone marrow

value: High


title: ALL31_Positive

value: Positive

value: male

value: SEHOP-PETHEMA 2013 standard risk


title: ALL32_Positive

value: Regional Málaga Hospital

value: Intermediate

value: PETHEMA standard risk


title: MARSseq_5569AA

value: MARS-Seq

value: CNAG

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: Pfalciparum_D6_hour60


title: ALL29_Positive

value: alive

value: B common

value: RI LAL/SEHOP-PETHEMA 2013


title: Pfalciparum_D6_hour57


title: Dropseq_N705

description:
cryopreserved HCA reference
Dropseq_human_exp_mat.tsv, Dropseq_human_metada.tsv, Dropseq_mouse_exp_mat.tsv, Dropseq_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-12), UMI (13-20); R2 = cDNA

value: Drop-seq

value: DKFZ


title: 10X2x5Kcell250Kreads_64220

description:
cryopreserved HCA reference
10X2x5Kcell250Kreads_human_exp_mat.tsv, 10X2x5Kcell250Kreads_human_metada.tsv, 10X2x5Kcell250Kreads_mouse_exp_mat.tsv, 10X2x5Kcell250Kreads_mouse_metada.tsv

value: Chromium V2


title: ALL33_Positive

value: PETHEMA RIA-96


title: Pfalciparum_D6_hour51


title: Dropseq_N706


title: inDrop_SP021_024015

description:
cryopreserved HCA reference
inDrop_human_exp_mat.tsv, inDrop_human_metada.tsv, inDrop_mouse_exp_mat.tsv, inDrop_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = cDNA; R2 = BC (1-8,31-38), UMI (39-44)

value: inDrop (1CellBio)

value: MDC-Berlin


title: Dropseq_N704


title: ALL57_Negative

value: Negative

value: San Juan de Dios Hospital

value: female

value: SEHOP-PETHEMA 2013


title: ALL56_Negative

value: male

value: Intermediate


title: Pfalciparum_D6_hour45


title: Dropseq_N703


title: ICELL8_SP021_022

description:
cryopreserved HCA reference
ICELL8_human_exp_mat.tsv, ICELL8_human_metada.tsv, ICELL8_mouse_exp_mat.tsv, ICELL8_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-11), UMI (12-22); R2 = cDNA


title: ALL28_Positive

value: Positive

value: Regional Málaga Hospital

value: High


title: ICELL8_SP021_023

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: Dropseq_N702


title: ALL26_Negative

value: deceased

value: B common

value: SHOP-baby


title: ALL58_Negative

value: alive


title: ALL54_Negative


title: ICELL8_SP021_021


title: Dropseq_N701

value: Drop-seq

value: DKFZ


title: MARSseq_5568AA

value: MARS-Seq

value: CNAG


title: Pfalciparum_D6_hour42


title: Pfalciparum_D6_hour39


title: Pfalciparum_D6_hour54


title: ICELL8_SP021_020

value: MDC-Berlin


title: Pfalciparum_D6_hour36


title: CELseq2_HCAP4_8

description:
cryopreserved HCA reference
CELseq2_human_exp_mat.tsv, CELseq2_human_metada.tsv, CELseq2_mouse_exp_mat.tsv, CELseq2_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (7-12), UMI (1-6); R2 = cDNA

value: MPI-Germany


title: Pfalciparum_D6_hour30


title: CELseq2_HCAP4_7


title: ALL24_Negative

value: Negative

value: PETHEMA RIA-96


title: ALL23_Negative


title: Pfalciparum_D6_hour33


title: ALL22_Negative

value: female

value: PETHEMA AR-05


title: CELseq2_HCAP4_6


title: CELseq2_HCAP4_5


title: 10X2x5Kcell250Kreads_64221

value: Chromium V2


title: CELseq2_HCAP3_4


title: ALL11_Negative

value: Regional Málaga Hospital

value: Intermediate

value: RI LAL/SEHOP-PETHEMA 2013


title: Pfalciparum_D6_hour15


title: ALL10_Negative

value: male

value: B common


title: Pfalciparum_D6_hour24


title: CELseq2_HCAP3_3

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: ALL5_Negative

value: alive


title: ALL8_Negative

value: Pre-B

value: High

value: AR LAL/SEHOP-PETHEMA 2013


title: ALL17_Negative

value: Low

value: SEHOP PETHEMA 2013


title: CELseq2_HCAP3_2

value: MPI-Germany


title: Pfalciparum_D6_hour21


title: Pfalciparum_D6_hour18


title: Pfalciparum_D6_hour27


title: ALL3_Negative

value: Negative


title: CELseq2_HCAP2_8


title: CELseq2_HCAP3_1


title: Pfalciparum_D6_hour12


title: CELseq2_HCAP2_5


title: Pfalciparum_D6_hour9


title: CELseq2_HCAP2_7


title: CELseq2_HCAP1_4


title: Pfalciparum_D6_hour3


title: Pfalciparum_D6_hour6


title: ALL2_Negative

value: female


title: ALL18_Negative

value: PETHEMA BR-01


title: ALL1_Negative


title: Pfalciparum_D6_hour0


title: CELseq2_HCAP1_2


title: ALL7_Negative


title: C1HTsmall_s8_1911015030_Col19_S230

description:
cryopreserved HCA reference
C1HTsmall_human_exp_mat.tsv, C1HTsmall_human_metada.tsv, C1HTsmall_mouse_exp_mat.tsv, C1HTsmall_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-11), R2 = cDNA

value: Stanford


title: Pfalciparum_SA250_hour57


title: CELseq2_HCAP1_3


title: CELseq2_HCAP2_6


title: Pfalciparum_SA250_hour63


title: C1HTsmall_s8_1911015030_Col20_S229


title: Pfalciparum_SA250_hour60


title: Pfalciparum_SA250_hour42


title: Pfalciparum_SA250_hour54


title: Pfalciparum_SA250_hour45


title: C1HTsmall_s8_1911015030_Col17_S235


title: C1HTsmall_s8_1911015030_Col18_S236


title: Pfalciparum_SA250_hour51


title: 10XV3_AN4492

description:
cryopreserved HCA reference
10XV3_human_exp_mat.tsv, 10XV3_human_metada.tsv, 10XV3_mouse_exp_mat.tsv, 10XV3_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-16), UMI (17-28), R2 = cDNA

value: Chromium V3 without Viability sorting


title: 10XV3_AN4491

value: Chromium V3 with Viability sorting


title: C1HTsmall_s8_1911015030_Col16_S234


title: C1HTsmall_s8_1911015030_Col14_S232


title: Pfalciparum_SA250_hour36


title: C1HTsmall_s8_1911015030_Col12_S223


title: C1HTsmall_s8_1911015030_Col13_S231


title: Pfalciparum_SA250_hour33


title: C1HTsmall_s8_1911015030_Col15_S233


title: Pfalciparum_SA250_hour30


title: Pfalciparum_SA250_hour27


title: Pfalciparum_SA250_hour48


title: Pfalciparum_SA250_hour24


title: C1HTsmall_s8_1911015030_Col11_S239


title: 44104_P4 mem non-THF

city: Pittsburgh

first: Smita lab

last: Lab

address: 3550 Terrace Street

department: Pathology

institute: University of Pittsburgh

description:
44104 CD4 mem non-TFH cell
44104P4

data_processing: Prior to analysis, genes with fewer than 30 counts per million reads were filtered, leaving 6,455 genes. Differential expression analyses were conducted using the limma-voom Bioconductor pipeline.

organism: Macaca mulatta

source_name: Lymph node

extract_protocol:
CD4 T cell subsets were sorted from frozen lymph nodes. Collected cells were flash frozen in RLT buffer and extracted using the Qiagen RNA isolation kit according to manufacturers instructions.
RNA converted to ds DNA. dsDNA fragmented the ends are repaired and ‘A’ tailed, adapters are ligated on, size selection is carried out, then PCR performed to generate the final library ready for sequencing according to Illumina protocols
3′-Tag-Seq (QuantSeq) Gene Expression Profiling

value: primary sorted CD4 T cells

tag: cd4 subsets

value: CD4 mem non-TFH cell

tag: gender

tag: time point post vacc

value: Week 2 post protein+ALFQ boost


title: single-cell RNA-seq dataset: PR8-infected MDCK cells at a MOI of 5 harvested at 6hpi

data_processing:
For the single-cell RNA-seq datasets generated in the time course infection assay, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment and gene counting with the processed UMIs for each cell. Then the UMI counts for all the viral reads including the gapped reads with the CIGAR string containing a large gap (i.e., “MNM”) were merged into the expression matrix.
For the bulk RNA-seq datasets, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment.
For the single-cell RNA-seq datasets generated from PR8-infected A549 and MDCK cells at different MOIs, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment.
Genome_build: hg19 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1)
Supplementary_files_format_and_content: For the single-cell RNA-seq datasets generated in the time course infection assay, each tab-delimited text file contains the raw gene expression matrix for individual cells harvested at a given time point. For the bulk RNA-seq datasets, each tab-delimited text file contains the raw gene counts for a given sample.

organism:
Canis lupus familiaris
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: Madin-Darby canine kidney cells

growth_protocol: Madin-Darby canine kidney (MDCK) cells were maintained in minimum essential medium (MEM) supplemented with 5% FBS. MDCK cells were infected in MDCK infection media (MEM supplemented with 2% bovine serum albumin (BSA), 1% antibiotic-antimycotic, and 1.5ug/mL TPCK-Trypsin)

treatment_protocol: MDCK cells were infected with PR8 virus at a MOI of 5.

tag: cell types

value: MDCK

tag: infection time points

value: 6 hours post-infection

tag: virus strain


title: Pfalciparum_SA250_hour21


title: 44104_P3 mem- TFH

description:
44104 CD4 mem-TFH cell
44104P3

value: CD4 mem-TFH cell


title: Pfalciparum_SA250_hour18


title: C1HTsmall_s8_1911015030_Col09_S240

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: Pfalciparum_SA250_hour39


title: 44104_P2 TFH

description:
44104 CD4 TFH cell
44104P2

value: CD4 TFH cell


title: C1HTsmall_s8_1911015030_Col08_S225


title: Pfalciparum_SA250_hour12


title: 44265_P4 mem non-THF

description:
44265 CD4 mem non-TFH cell
44265P4


title: 44104_P1 Naïve Cell

description:
44104 Naive CD4 T cell
44104P1

value: Naive CD4 T cell


title: C1HTsmall_s8_1911015030_Col07_S226


title: Pfalciparum_SA250_hour15