title: HIV TFH med_H75

city: Rome

first: Nicola

last: Cotugno

address: via Montpellier 1

department: Department of Systems Medicine

country: Italy

institute: University of Rome "Tor Vergata"

description:
legenda: HIV= study group; NR= Non responder to Influenza Vaccination; R=Responder to Influenza vaccination; Rem/AM/PBMC/DN/Naïve/Total B/CD4/TFH/NTF= cell subset identifier (please check source name for acronym interpretetion); med=unstimulated sample; stim= stimulated sample with H1N1 peptides for 16 hours; _HX= identifier of the subject. When patient responsiveness is not referenced please refer to this list: NR= H19  H37  H38  H40  H46  H48  H55  H58  H60  H69  H70  H83;                                                                                and Responder (R)= H3  H7  H8  H26  H41  H44  H47  H56  H75  H80  H52.
500 fixed numbers of live cell sorted by ARIA IICs, derived from human PBMCs from frozen samples.Every sample is identified according to study group, cell subset, condition and patient identifier.

data_processing:
Previously amplified samples were loaded on a Fluidigm 96.96 standard chip following manufacturer’s instructions. Briefly, assay pre-mix was prepared 1:1 20X TaqMan Gene Expression Assay (Applied Biosystems) and Assay Loading Reagent (Fluidigm). The sample pre-mix was prepared with TaqMan Universal PCR Master Mix (2X)(Applied Biosystems), 20XGE Sample Loading Reagent (Fluidigm), and cDNA. Full list of the two panels of gene probes (B subsets and T subsets is shown in supplemental table 1 and 2). 5ul of Assay and Sample mix were loaded into the chip according to manufacturers instructions. Genes’ selection has been made according to previous analysis on RNA Sequencing on HIV infected children from a different cohort (data not shown), the literature and online gene banks and biological queries.  Cycle threshold value (Ct) deriving from exported files was corrected according to number of cells sorted if lower than 500. Calculations were made following the expression 67,5 / 500 = Y / X where X is the number of cells sorted and Y is the cells equivalent cDNA of cell sorted. The dilution factor (n) was calculated as n= 67,5/Y, and base 2 log of n was subsequently subtracted to Ct value in order to get Corrected Cycle Threshold (c-Ct). Expression threshold (Et), which was  used for the main analysis was finally obtained with 40-cCT. Once exported and corrected, data were analyzed through Fluidigm SingluaR (SingulaR analysis toolset 3.0) package, loaded on R (software R 3.0.2 GUI 1.62). As previously described (De Armas LR, 2017) gene expression differences between different groups within same subset and condition were used to identify Differentially Expressed Genes (DEGs). Alternatively, paired gene expression differences between stimulated (stim) and unstimulated samples (med) (stim-med) within the same subset were used to define Differentially Induced Genes (DIGs).
Cycle threshold value (Ct) deriving from exported files was corrected according to number of cells sorted if lower than 500. Calculations were made following the expression 67,5 / 500 = Y / X where X is the number of cells sorted and Y is the cells equivalent cDNA of cell sorted. The dilution factor (n) was calculated as n= 67,5/Y, and base 2 log of n was subsequently subtracted to Ct value in order to get Corrected Cycle Threshold (c-Ct). Expression threshold (Et), which was  used for the main analysis was finally obtained with 40-cCT. Once exported and corrected, data were analyzed through Fluidigm SingluaR (SingulaR analysis toolset 3.0) package, loaded on R (software R 3.0.2 GUI 1.62). As previously described (De Armas LR, 2017) gene expression differences between different groups within same subset and condition were used to identify Differentially Expressed Genes (DEGs). Alternatively, paired gene expression differences between stimulated (stim) and unstimulated samples (med) (stim-med) within the same subset were used to define Differentially Induced Genes (DIGs).

label: FAM-MGB

source_name: HIV TFH med_H75

growth_protocol: PBMC were thawed and cells were counted with Countess Automated Cell counter (Life technology). Cells were resuspended in complete RPMI medium at a concentration of 5 x 106 PBMCs/mL and left at 37°C for 16 hours in the presence or absence of of H1N1 A/California /09 HA peptides in a final concentration 20uL/mL. PMBCs were stained for surface markers, Vivid (Pacific Blue), CD10 (PECy7), CD20 (PE), CD27 (APC), IgD (FITC), CD21 (PECy5) for the B cell panel for 15 minutes and for CD3 (AmCyan), CD4 (PerCP Cy5.5), CD45RO (ECD), CCR7 (Alexa Fluor 700), and CXCR5 (Alexa Fluor 647) and a live/dead marker (ViViD; Molecular Probes) for the T cell panel for 15 minutes. Subsequently, stained PBMCs were washed twice in PBS, finally filtered with a 40 uM mesh and sorted by FACSAriaII (BD Biosciences). The purity of the sorted cell populations were typically >99%. All antibodies were previously titrated. Viable lymphocytes were identified as live dead amine dye negative (ViViD-) cells (Invitrogen).   500 live cells per B and T cell subset were sorted into tubes previously loaded with 9uL of PCR buffer (see also Figure 1 for gating strategy). After sorting, cells were immediately centrifuged (3000RPM for 3 minutes) and kept on ice. Samples were subsequently transferred in PCR tubes and 18 PCR cycles were performed on a C1000 Thermal Cycler (Bio Rad) with the following scheme (50°C for 20’, 95°C for 2’, 95°C 15’’, 60°C for 4’. Last step repeated 18 times). Cells were finally kept at -20 until further analysis. PCR buffer premix for cell sorting contained the following: Cells Direct Reaction mix 5uL, DEPC water 1,4, Superscript III + Taq 1ul, 0.2x diluted assay (96 primer mix) 2,5uL, Superasein 0,1uL.

extract_protocol: 500 live cells per B and T cell subset were sorted into tubes previously loaded with 9uL of PCR buffer for RNA extraction. After sorting, cells were immediately centrifuged (3000RPM for 3 minutes) and kept on ice. Samples were subsequently transferred in PCR tubes and 18 PCR cycles were performed on a C1000 Thermal Cycler (Bio Rad) with the following scheme (50°C for 20’, 95°C for 2’, 95°C 15’’, 60°C for 4’. Last step repeated 18 times). Cells were finally kept at -20 until further analysis. PCR buffer premix for cell sorting contained the following: Cells Direct Reaction mix 5uL, DEPC water 1,4, Superscript III + Taq 1ul, 0.2x diluted assay (96 primer mix) 2,5uL, Superasein 0,1uL.

treatment_protocol: PBMCs were isolated by Ficoll

tag: group

value: HIV R TFH med


title: HIV TFH med_H83

status: Public on Oct 29 2020

type: RNA

molecule: total RNA

organism: Homo sapiens

source_name: HIV TFH med_H83

label_protocol: After sorting, cells were immediately centrifuged (3000RPM for 3 minutes) and kept on ice. Samples were subsequently transferred in PCR tubes and 18 PCR cycles were performed on a C1000 Thermal Cycler (Bio Rad) with the following scheme (50°C for 20’, 95°C for 2’, 95°C 15’’, 60°C for 4’. Last step repeated 18 times). Cells were finally kept at -20 until further analysis. PCR buffer premix for cell sorting contained the following: Cells Direct Reaction mix 5uL, DEPC water 1,4, Superscript III + Taq 1ul, 0.2x diluted assay (96 primer mix) 2,5uL, Superasein 0,1uL.

value: HIV TFH med


title: iKD AP2IX-5 -Auxin 1

type: SRA

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

country: France

institute: CNRS

library_source: transcriptomic

data_processing:
Clusters were generated on a flow cell within a cBot using the Cluster Generation Kit (Illumina), and libraries were sequenced as 50-bp reads on a HiSeq 2000 using a Sequence By Synthesis (SBS) technique (Illumina).
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina’s conversion software (bcl2fastq 2.17). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software Sequence Analysis Viewer (SAV). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
RNASeq reads were aligned to the Toxoplasma gondii genome (ToxoDB-25_TgondiiGT1_Genome.fasta from the ToxoDB Toxoplasma Genomics Resource, downloaded on 08/31/15) with a set of gene model annotations (ToxoDB-25_TgondiiGT1.gff from the ToxoDB Toxoplasma Genomics Resource, downloaded on 08/31/15) using the splice junction mapper TopHat 2.0.13. Final read alignments having more than three mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode). Because the data come from a strand-specific assay, the read must be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 15 reads (combining all the analyzed samples) were filtered out. Differentially expressed genes were identified using the Bioconductor package edgeR 3.6.7. The data were normalized using the Relative Log Expression (RLE) normalization factors. Genes with adjusted p-values less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.

organism: Toxoplasma gondii

source_name: HFF cell culture infected with T. gondii

growth_protocol: Intracellular parasite were grown 6 hours with or without Auxin.

extract_protocol:
Total RNA was extrated using TRIzol reagent according to manufacturer’s protocol.
Library preparation was performed using the TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s instructions. Libraries were validated using a Fragment Analyzer and quantified by qPCR (ROCHE LightCycler 480).

tag: strain

value: RH delta-Ku80 Tir1 iKD AP2IX-5


title: HIV TFH med_H70

source_name: HIV TFH med_H70


title: iKD AP2IX-5 -Auxin 2


title: HIV TFH med_H64

source_name: HIV TFH med_H64


title: HIV TFH med_H80

source_name: HIV TFH med_H80


title: HIV TFH med_H60

source_name: HIV TFH med_H60


title: HIV TFH med_H69

source_name: HIV TFH med_H69


title: HIV TFH med_H7

source_name: HIV TFH med_H7


title: genomic DNA sperm donor rep 4

type: genomic

city: North Brunswick Township

first: Jia

last: Xu

state: NJ

address: 675 US Highway One

country: USA

institute: Genomic Prediction, Inc.

description: sperm donor rep 4

data_processing:
Affymetrix UK Biobank Axiom Array Manufacturer's Protocol
processed data files include DNA copy number and genotyping

label: biotin

molecule: genomic DNA

source_name: semen from subject with homozygous frame shift mutation at rs758109813

growth_protocol: fertilization of human metaphaseII oocytes was performed using standard intracytoplasmic sperm injection (ICSI), followed by culture in GlobalTotal (LifeGlobal)

extract_protocol: single cells were placed into single PCR tubes containing 2microliter of PBS or other hypotonic collection buffer. Genomic DNA amplification was performed using amplification kit as indicated for each sample.

treatment_protocol: Cas9 guide RNA ribonucleoprotein complex was assembled in vitro and injected either with sperm at MII stage, or at the 2-cell stage on day2 after ICSI

tag: tissue

value: sperm

tag: gender

value: male


title: HIV TFH med_H58

source_name: HIV TFH med_H58


title: HIV TFH med_H56

source_name: HIV TFH med_H56


title: HIV TFH med_H47

source_name: HIV TFH med_H47


title: HIV TFH med_H46

source_name: HIV TFH med_H46


title: HIV TFH med_H48

source_name: HIV TFH med_H48


title: HIV TFH med_H44

source_name: HIV TFH med_H44


title: HIV TFH med_H55

source_name: HIV TFH med_H55


title: HIV TFH med_H40

source_name: HIV TFH med_H40


title: HIV TFH med_H41

source_name: HIV TFH med_H41


title: AP2IX-5 IP 1

description:
RH ∆Ku80 AP2IX-5-HA
AP2IX-5.merged.cleaned.bowtie2_ME49.mark_duplicates.macs2_callpeak_extsize220_controlAP2IX5_peaks.narrowPeak

library_source: genomic

data_processing:
Clusters were generated on a flow cell within a cBot using the Cluster Generation Kit (Illumina), and libraries were sequenced as 50-bp reads on a HiSeq 2000 using a Sequence By Synthesis (SBS) technique (Illumina).
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina’s conversion software (bcl2fastq 2.17). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software Sequence Analysis Viewer (SAV). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
genome build: T. gondii_ ME49 genome from ToxoDB-39
Supplementary_files_format_and_content: narrowPeak

source_name: HFF cell culture infected with T. gondii

growth_protocol: Intracellular parasite were grown 30h on HFF cells.

extract_protocol:
Genomic DNA was sonicated and process for immunoprecipitation. DNA was purified on Qiagen Minielute columns.
Library preparation was performed using the Nugen Ovation® Ultralow System V2 kit according to the manufacturer’s instructions. Libraries were validated using a Fragment Analyzer and quantified by qPCR (ROCHE LightCycler 480).

value: RH deltaKu80 AP2IX-5-HA

tag: cell type

value: HFF cells


title: HIV TFH med_H38

source_name: HIV TFH med_H38


title: HIV TFH med_H26

source_name: HIV TFH med_H26


title: HIV TFH med_H52

source_name: HIV TFH med_H52


title: HIV R Total B stim_H8

source_name: HIV R Total B stim_H8

value: HIV R Total B stim


title: HIV R Total B stim_H56

source_name: HIV R Total B stim_H56


title: HIV R Total B stim_H80

source_name: HIV R Total B stim_H80


title: HIV R Total B stim_H75

source_name: HIV R Total B stim_H75


title: HIV R Total B stim_H26

source_name: HIV R Total B stim_H26


title: HIV R Total B stim_H47

source_name: HIV R Total B stim_H47


title: HIV R Total B med_H75

source_name: HIV R Total B med_H75

value: HIV R Total B med


title: HIV R Total B med_H8

source_name: HIV R Total B med_H8


title: HIV R Total B med_H80

source_name: HIV R Total B med_H80


title: HIV R Total B med_H56

source_name: HIV R Total B med_H56


title: HIV R Total B med_H26

source_name: HIV R Total B med_H26


title: HIV R Total B med_H47

source_name: HIV R Total B med_H47


title: HIV R TFH stim_H8

source_name: HIV R TFH stim_H8

value: HIV R TFH stim


title: HIV R TFH stim_H64

source_name: HIV R TFH stim_H64


title: HIV R TFH stim_H80

source_name: HIV R TFH stim_H80


title: HIV R TFH stim_H52

source_name: HIV R TFH stim_H52


title: HIV R TFH stim_H47

source_name: HIV R TFH stim_H47


title: HIV R TFH stim_H44

source_name: HIV R TFH stim_H44


title: HIV R TFH stim_H56

source_name: HIV R TFH stim_H56


title: HIV TFH med_H37

source_name: HIV TFH med_H37


title: HIV R TFH stim_H41

source_name: HIV R TFH stim_H41


title: HIV TFH med_H3

source_name: HIV TFH med_H3


title: HIV R TFH stim_H3

source_name: HIV R TFH stim_H3


title: HIV TFH med_H19

source_name: HIV TFH med_H19


title: HIV R Total B stim_H7

source_name: HIV R Total B stim_H7


title: HIV R Total B med_H7

source_name: HIV R Total B med_H7


title: HIV R TFH stim_H75

source_name: HIV R TFH stim_H75


title: HIV R Rem stim_H56

source_name: HIV R Rem stim_H56

value: HIV R Rem stim


title: HIV R TFH stim_H7

source_name: HIV R TFH stim_H7


title: HIV R Rem stim_H8

source_name: HIV R Rem stim_H8


title: HIV R Rem stim_H52

source_name: HIV R Rem stim_H52


title: HIV R Rem stim_H7

source_name: HIV R Rem stim_H7


title: HIV R Rem stim_H80

source_name: HIV R Rem stim_H80


title: HIV R Rem stim_H26

source_name: HIV R Rem stim_H26


title: HIV R Rem stim_H47

source_name: HIV R Rem stim_H47


title: HIV R Rem med_H75

source_name: HIV R Rem med_H75

value: HIV R Rem med


title: HIV R Rem med_H8

source_name: HIV R Rem med_H8


title: HIV R Rem med_H80

source_name: HIV R Rem med_H80


title: HIV R Rem stim_H41

source_name: HIV R Rem stim_H41


title: HIV R Rem stim_H3

source_name: HIV R Rem stim_H3


title: HIV R Rem med_H52

source_name: HIV R Rem med_H52


title: HIV R Rem med_H47

source_name: HIV R Rem med_H47


title: HIV R Rem med_H44

source_name: HIV R Rem med_H44


title: HIV R Rem med_H41

source_name: HIV R Rem med_H41


title: HIV R Rem med_H56

source_name: HIV R Rem med_H56


title: HIV R Rem med_H3

source_name: HIV R Rem med_H3


title: HIV R Rem med_H26

source_name: HIV R Rem med_H26


title: HIV R TFH stim_H26

source_name: HIV R TFH stim_H26


title: HIV R PBMC stim_H80

source_name: HIV R PBMC stim_H80

value: HIV R PBMC stim


title: HIV R Rem stim_H75

source_name: HIV R Rem stim_H75


title: HIV R Rem stim_H64

source_name: HIV R Rem stim_H64


title: HIV R PBMC stim_H8

source_name: HIV R PBMC stim_H8


title: HIV R Rem stim_H44

source_name: HIV R Rem stim_H44


title: HIV R Rem med_H7

source_name: HIV R Rem med_H7


title: HIV R PBMC stim_H75

source_name: HIV R PBMC stim_H75


title: HIV R PBMC stim_H7

source_name: HIV R PBMC stim_H7


title: HIV R Rem med_H64

source_name: HIV R Rem med_H64


title: HIV R PBMC stim_H64

source_name: HIV R PBMC stim_H64


title: HIV R PBMC stim_H3

source_name: HIV R PBMC stim_H3


title: HIV R PBMC stim_H44

source_name: HIV R PBMC stim_H44


title: HIV R PBMC stim_H47

source_name: HIV R PBMC stim_H47


title: HIV R PBMC stim_H41

source_name: HIV R PBMC stim_H41


title: HIV R PBMC stim_H56

source_name: HIV R PBMC stim_H56


title: HIV R PBMC stim_H52

source_name: HIV R PBMC stim_H52


title: HIV R PBMC med_H8

source_name: HIV R PBMC med_H8

value: HIV R PBMC med


title: HIV R PBMC med_H75

source_name: HIV R PBMC med_H75


title: HIV R PBMC med_H52

source_name: HIV R PBMC med_H52


title: HIV R PBMC med_H56

source_name: HIV R PBMC med_H56


title: HIV R PBMC med_H7

source_name: HIV R PBMC med_H7


title: HIV R PBMC med_H80

source_name: HIV R PBMC med_H80


title: HIV R PBMC med_H64

source_name: HIV R PBMC med_H64


title: HIV R PBMC med_H47

source_name: HIV R PBMC med_H47


title: HIV R PBMC med_H3

source_name: HIV R PBMC med_H3


title: HIV R PBMC med_H44

source_name: HIV R PBMC med_H44


title: HIV R PBMC med_H41

source_name: HIV R PBMC med_H41


title: HIV R PBMC med_H26

source_name: HIV R PBMC med_H26


title: HIV R NT stim_H80

source_name: HIV R NT stim_H80

value: HIV R NT stim


title: HIV R NT stim_H75

source_name: HIV R NT stim_H75


title: HIV R NT stim_H8

source_name: HIV R NT stim_H8


title: HIV R NT stim_H7

source_name: HIV R NT stim_H7


title: HIV R NT stim_H64

source_name: HIV R NT stim_H64


title: HIV R NT stim_H56

source_name: HIV R NT stim_H56


title: HIV R PBMC stim_H26

source_name: HIV R PBMC stim_H26


title: HIV R NT stim_H52

source_name: HIV R NT stim_H52


title: HIV R NT stim_H47

source_name: HIV R NT stim_H47


title: HIV R NT stim_H44

source_name: HIV R NT stim_H44


title: HIV R NT stim_H41

source_name: HIV R NT stim_H41


title: HIV R NT stim_H3

source_name: HIV R NT stim_H3


title: HIV R Naive stim_H75

source_name: HIV R Naive stim_H75

value: HIV R Naive stim


title: HIV R Naive stim_H56

source_name: HIV R Naive stim_H56


title: HIV R Naive stim_H8

source_name: HIV R Naive stim_H8


title: HIV R NT stim_H26

source_name: HIV R NT stim_H26


title: HIV R Naive med_H47

source_name: HIV R Naive med_H47

value: HIV R Naive med


title: HIV R Naive stim_H7

source_name: HIV R Naive stim_H7


title: HIV R Naive stim_H80

source_name: HIV R Naive stim_H80


title: HIV R Naive med_H80

source_name: HIV R Naive med_H80


title: HIV R Naive med_H26

source_name: HIV R Naive med_H26


title: HIV R Naive med_H8

source_name: HIV R Naive med_H8


title: HIV R DN stim_H80

source_name: HIV R DN stim_H80

value: HIV R DN stim


title: HIV R Naive med_H56

source_name: HIV R Naive med_H56


title: HIV R DN stim_H75

source_name: HIV R DN stim_H75


title: HIV R Naive med_H7

source_name: HIV R Naive med_H7


title: HIV R DN stim_H64

source_name: HIV R DN stim_H64


title: HIV R DN stim_H56

source_name: HIV R DN stim_H56


title: HIV R DN stim_H7

source_name: HIV R DN stim_H7


title: HIV R DN stim_H52

source_name: HIV R DN stim_H52


title: HIV R DN stim_H47

source_name: HIV R DN stim_H47


title: HIV R DN stim_H44

source_name: HIV R DN stim_H44


title: HIV R Naive stim_H47

source_name: HIV R Naive stim_H47


title: HIV R DN stim_H3

source_name: HIV R DN stim_H3


title: HIV R DN stim_H41

source_name: HIV R DN stim_H41


title: HIV R Naive stim_H26

source_name: HIV R Naive stim_H26


title: HIV R DN stim_H26

source_name: HIV R DN stim_H26


title: HIV R Naive med_H75

source_name: HIV R Naive med_H75


title: HIV R DN med_H80

source_name: HIV R DN med_H80

value: HIV R DN med


title: HIV R DN stim_H8

source_name: HIV R DN stim_H8


title: HIV R DN med_H8

source_name: HIV R DN med_H8


title: HIV R DN med_H75

source_name: HIV R DN med_H75


title: HIV R DN med_H52

source_name: HIV R DN med_H52


title: HIV R DN med_H7

source_name: HIV R DN med_H7


title: HIV R DN med_H64

source_name: HIV R DN med_H64


title: HIV R DN med_H26

source_name: HIV R DN med_H26


title: HIV R CD4 stim_H75

source_name: HIV R CD4 stim_H75

value: HIV R CD4 stim


title: HIV R CD4 stim_H8

source_name: HIV R CD4 stim_H8


title: HIV R CD4 stim_H7

source_name: HIV R CD4 stim_H7


title: HIV R CD4 stim_H52

source_name: HIV R CD4 stim_H52


title: HIV R CD4 stim_H56

source_name: HIV R CD4 stim_H56


title: HIV R CD4 stim_H47

source_name: HIV R CD4 stim_H47


title: HIV R CD4 stim_H44

source_name: HIV R CD4 stim_H44


title: HIV R DN med_H41

source_name: HIV R DN med_H41


title: HIV R CD4 stim_H41

source_name: HIV R CD4 stim_H41


title: HIV R DN med_H47

source_name: HIV R DN med_H47


title: HIV R DN med_H44

source_name: HIV R DN med_H44


title: HIV R CD4 stim_H3

source_name: HIV R CD4 stim_H3


title: HIV R CD4 stim_H26

source_name: HIV R CD4 stim_H26


title: HIV R AM stim_H80

source_name: HIV R AM stim_H80

value: HIV R AM stim


title: HIV R AM stim_H8

source_name: HIV R AM stim_H8


title: HIV R DN med_H3

source_name: HIV R DN med_H3


title: HIV R DN med_H56

source_name: HIV R DN med_H56


title: HIV R AM stim_H75

source_name: HIV R AM stim_H75


title: HIV R AM stim_H7

source_name: HIV R AM stim_H7


title: HIV R CD4 stim_H64

source_name: HIV R CD4 stim_H64


title: HIV R AM stim_H64

source_name: HIV R AM stim_H64


title: HIV R CD4 stim_H80

source_name: HIV R CD4 stim_H80


title: HIV R AM stim_H56

source_name: HIV R AM stim_H56


title: HIV R AM stim_H52

source_name: HIV R AM stim_H52


title: HIV R AM stim_H47

source_name: HIV R AM stim_H47


title: HIV R AM stim_H44

source_name: HIV R AM stim_H44


title: HIV R AM med_H80

source_name: HIV R AM med_H80

value: HIV R AM med


title: HIV R AM stim_H26

source_name: HIV R AM stim_H26


title: HIV R AM stim_H41

source_name: HIV R AM stim_H41


title: HIV R AM stim_H3

source_name: HIV R AM stim_H3


title: HIV R AM med_H75

source_name: HIV R AM med_H75


title: HIV R AM med_H7

source_name: HIV R AM med_H7


title: HIV R AM med_H56

source_name: HIV R AM med_H56


title: HIV R AM med_H64

source_name: HIV R AM med_H64


title: HIV R AM med_H52

source_name: HIV R AM med_H52


title: HIV R AM med_H26

source_name: HIV R AM med_H26


title: HIV R AM med_H41

source_name: HIV R AM med_H41


title: HIV R AM med_H47

source_name: HIV R AM med_H47


title: HIV R AM med_H44

source_name: HIV R AM med_H44


title: HIV R AM med_H3

source_name: HIV R AM med_H3


title: HIV PBMC med_H83

source_name: HIV PBMC med_H83

value: HIV PBMC med


title: HIV PBMC med_H80

source_name: HIV PBMC med_H80


title: HIV PBMC med_H8

source_name: HIV PBMC med_H8


title: HIV PBMC med_H70

source_name: HIV PBMC med_H70


title: HIV PBMC med_H64

source_name: HIV PBMC med_H64


title: HIV PBMC med_H7

source_name: HIV PBMC med_H7


title: HIV PBMC med_H75

source_name: HIV PBMC med_H75


title: HIV PBMC med_H69

source_name: HIV PBMC med_H69


title: HIV PBMC med_H58

source_name: HIV PBMC med_H58


title: HIV PBMC med_H56

source_name: HIV PBMC med_H56


title: HIV PBMC med_H55

source_name: HIV PBMC med_H55


title: HIV PBMC med_H52

source_name: HIV PBMC med_H52


title: HIV PBMC med_H60

source_name: HIV PBMC med_H60


title: HIV PBMC med_H46

source_name: HIV PBMC med_H46


title: HIV R AM med_H8

source_name: HIV R AM med_H8


title: HIV PBMC med_H47

source_name: HIV PBMC med_H47


title: HIV PBMC med_H41

source_name: HIV PBMC med_H41


title: HIV PBMC med_H40

source_name: HIV PBMC med_H40


title: HIV PBMC med_H38

source_name: HIV PBMC med_H38


title: HIV PBMC med_H44

source_name: HIV PBMC med_H44


title: HIV NT med_H80

source_name: HIV NT med_H80

value: HIV NT med


title: HIV PBMC med_H19

source_name: HIV PBMC med_H19


title: HIV NT med_H7

source_name: HIV NT med_H7


title: HIV NT med_H83

source_name: HIV NT med_H83


title: HIV NT med_H75

source_name: HIV NT med_H75


title: HIV PBMC med_H3

source_name: HIV PBMC med_H3


title: HIV NT med_H70

source_name: HIV NT med_H70


title: HIV NT med_H69

source_name: HIV NT med_H69


title: HIV NT med_H64

source_name: HIV NT med_H64


title: HIV NT med_H58

source_name: HIV NT med_H58


title: HIV NT med_H60

source_name: HIV NT med_H60


title: HIV NT med_H56

source_name: HIV NT med_H56


title: HIV NT med_H55

source_name: HIV NT med_H55


title: HIV NT med_H46

source_name: HIV NT med_H46


title: HIV NT med_H47

source_name: HIV NT med_H47


title: HIV NT med_H52

source_name: HIV NT med_H52


title: HIV NT med_H41

source_name: HIV NT med_H41


title: HIV NT med_H48

source_name: HIV NT med_H48


title: HIV NT med_H40

source_name: HIV NT med_H40


title: HIV NT med_H26

source_name: HIV NT med_H26


title: HIV NT med_H37

source_name: HIV NT med_H37


title: HIV NT med_H44

source_name: HIV NT med_H44


title: HIV NT med_H38

source_name: HIV NT med_H38


title: HIV NT med_H19

source_name: HIV NT med_H19


title: HIV NR Total B stim_H60

source_name: HIV NR Total B stim_H60

value: HIV NR Total B stim


title: HIV NR Total B stim_H69

source_name: HIV NR Total B stim_H69


title: HIV NR Total B stim_H55

source_name: HIV NR Total B stim_H55


title: HIV NR Total B stim_H58

source_name: HIV NR Total B stim_H58


title: HIV NR Total B stim_H40

source_name: HIV NR Total B stim_H40


title: HIV NR Total B stim_H48

source_name: HIV NR Total B stim_H48


title: HIV NR Total B stim_H38

source_name: HIV NR Total B stim_H38


title: HIV NR Total B stim_H37

source_name: HIV NR Total B stim_H37


title: HIV NR Total B stim_H19

source_name: HIV NR Total B stim_H19


title: HIV NR Total B med_H69

source_name: HIV NR Total B med_H69

value: HIV NR Total B med


title: HIV NR Total B med_H40

source_name: HIV NR Total B med_H40


title: HIV NR Total B med_H37

source_name: HIV NR Total B med_H37


title: HIV NR Total B med_H60

source_name: HIV NR Total B med_H60


title: HIV NR Total B med_H55

source_name: HIV NR Total B med_H55


title: HIV NR Total B med_H58

source_name: HIV NR Total B med_H58


title: HIV NR Total B med_H48

source_name: HIV NR Total B med_H48


title: HIV NR Total B med_H38

source_name: HIV NR Total B med_H38


title: HIV NR Total B med_H19

source_name: HIV NR Total B med_H19


title: HIV NR TFH stim_H70

source_name: HIV NR TFH stim_H70

value: HIV NR TFH stim


title: HIV NR TFH stim_H83

source_name: HIV NR TFH stim_H83


title: HIV NT med_H3

source_name: HIV NT med_H3


title: HIV NR TFH stim_H60

source_name: HIV NR TFH stim_H60


title: HIV NR TFH stim_H69

source_name: HIV NR TFH stim_H69


title: HIV NR TFH stim_H58

source_name: HIV NR TFH stim_H58


title: HIV NR TFH stim_H55

source_name: HIV NR TFH stim_H55


title: HIV NR TFH stim_H48

source_name: HIV NR TFH stim_H48


title: HIV NR TFH stim_H46

source_name: HIV NR TFH stim_H46


title: HIV NR TFH stim_H38

source_name: HIV NR TFH stim_H38


title: HIV NR TFH stim_H40

source_name: HIV NR TFH stim_H40


title: HIV NR TFH stim_H37

source_name: HIV NR TFH stim_H37


title: HIV NR TFH stim_H19

source_name: HIV NR TFH stim_H19


title: HIV NR Rem stim_H83

source_name: HIV NR Rem stim_H83

value: HIV NR Rem stim


title: HIV PBMC med_H26

source_name: HIV PBMC med_H26


title: HIV NR Rem stim_H70

source_name: HIV NR Rem stim_H70


title: HIV NR Rem stim_H46

source_name: HIV NR Rem stim_H46


title: HIV NR Rem stim_H48

source_name: HIV NR Rem stim_H48


title: HIV NR Rem stim_H40

source_name: HIV NR Rem stim_H40


title: HIV NR Rem stim_H58

source_name: HIV NR Rem stim_H58


title: HIV NR Rem stim_H69

source_name: HIV NR Rem stim_H69


title: HIV NR Rem med_H70

source_name: HIV NR Rem med_H70

value: HIV NR Rem med


title: HIV NR Rem med_H58

source_name: HIV NR Rem med_H58


title: HIV NR Rem stim_H60

source_name: HIV NR Rem stim_H60


title: HIV NR Rem med_H69

source_name: HIV NR Rem med_H69


title: HIV NR Rem stim_H55

source_name: HIV NR Rem stim_H55


title: HIV NR Rem stim_H37

source_name: HIV NR Rem stim_H37


title: HIV NR Rem med_H48

source_name: HIV NR Rem med_H48


title: HIV NR Rem med_H60

source_name: HIV NR Rem med_H60


title: HIV NR Rem stim_H38

source_name: HIV NR Rem stim_H38


title: HIV NR Rem stim_H19

source_name: HIV NR Rem stim_H19


title: HIV NR Rem med_H38

source_name: HIV NR Rem med_H38


title: HIV NR Rem med_H40

source_name: HIV NR Rem med_H40


title: HIV NR PBMC stim_H83

source_name: HIV NR PBMC stim_H83

value: HIV NR PBMC stim


title: HIV NR Rem med_H19

source_name: HIV NR Rem med_H19


title: HIV NR Rem med_H46

source_name: HIV NR Rem med_H46


title: HIV NR Rem med_H55

source_name: HIV NR Rem med_H55


title: HIV NR PBMC stim_H70

source_name: HIV NR PBMC stim_H70


title: HIV NR Rem med_H37

source_name: HIV NR Rem med_H37


title: HIV NR PBMC stim_H69

source_name: HIV NR PBMC stim_H69


title: HIV NR PBMC stim_H55

source_name: HIV NR PBMC stim_H55


title: HIV NR PBMC stim_H46

source_name: HIV NR PBMC stim_H46


title: HIV NR PBMC stim_H60

source_name: HIV NR PBMC stim_H60


title: HIV NR Rem med_H83

source_name: HIV NR Rem med_H83


title: HIV NR PBMC stim_H38

source_name: HIV NR PBMC stim_H38


title: HIV NR PBMC stim_H37

source_name: HIV NR PBMC stim_H37


title: HIV NR PBMC med_H69

source_name: HIV NR PBMC med_H69

value: HIV NR PBMC med


title: HIV NR PBMC med_H58

source_name: HIV NR PBMC med_H58


title: HIV NR PBMC med_H46

source_name: HIV NR PBMC med_H46


title: HIV NR PBMC stim_H40

source_name: HIV NR PBMC stim_H40


title: HIV NR PBMC med_H48

source_name: HIV NR PBMC med_H48


title: HIV NR PBMC med_H70

source_name: HIV NR PBMC med_H70


title: HIV NR PBMC stim_H19

source_name: HIV NR PBMC stim_H19


title: HIV NR PBMC med_H40

source_name: HIV NR PBMC med_H40


title: HIV NR PBMC med_H83

source_name: HIV NR PBMC med_H83


title: HIV NR PBMC med_H38

source_name: HIV NR PBMC med_H38


title: HIV NR PBMC med_H37

source_name: HIV NR PBMC med_H37


title: HIV NR PBMC stim_H48

source_name: HIV NR PBMC stim_H48


title: HIV NR PBMC med_H60

source_name: HIV NR PBMC med_H60


title: HIV NR NT stim_H83

source_name: HIV NR NT stim_H83

value: HIV NR NT stim


title: HIV NR NT stim_H70

source_name: HIV NR NT stim_H70


title: HIV NR PBMC stim_H58

source_name: HIV NR PBMC stim_H58


title: HIV NR PBMC med_H55

source_name: HIV NR PBMC med_H55


title: HIV NR PBMC med_H19

source_name: HIV NR PBMC med_H19


title: HIV NR NT stim_H58

source_name: HIV NR NT stim_H58


title: HIV NR NT stim_H55

source_name: HIV NR NT stim_H55


title: HIV NR NT stim_H60

source_name: HIV NR NT stim_H60


title: HIV NR NT stim_H69

source_name: HIV NR NT stim_H69


title: HIV NR NT stim_H46

source_name: HIV NR NT stim_H46


title: HIV NR NT stim_H48

source_name: HIV NR NT stim_H48


title: HIV NR NT stim_H38

source_name: HIV NR NT stim_H38


title: HIV NR NT stim_H40

source_name: HIV NR NT stim_H40


title: HIV NR NT stim_H19

source_name: HIV NR NT stim_H19


title: HIV NR Naive stim_H69

source_name: HIV NR Naive stim_H69

value: HIV NR Naive stim


title: HIV NR Naive stim_H58

source_name: HIV NR Naive stim_H58


title: HIV NR Naive stim_H60

source_name: HIV NR Naive stim_H60


title: HIV NR NT stim_H37

source_name: HIV NR NT stim_H37


title: HIV NR Naive stim_H40

source_name: HIV NR Naive stim_H40


title: HIV NR Naive stim_H48

source_name: HIV NR Naive stim_H48


title: HIV NR Naive stim_H37

source_name: HIV NR Naive stim_H37


title: HIV NR Naive stim_H38

source_name: HIV NR Naive stim_H38


title: HIV NR Naive stim_H19

source_name: HIV NR Naive stim_H19


title: CTC patient 35

city: Bari

first: Domenica

last: Lovero

state: Bari

address: P.zza Giulio Cesare, 11

department: Department of Biomedical Sciences and Human Oncology

institute: University of study of Bari Aldo Modo

description:
BM_vs_BM+ES_Raw_gene_counts_matrix.txt; BM+ES_vs_ES_Raw_gene_counts.txt
BM_vs_BM+ES_normalized_count_matrix.txt;BM+ES_vs_ES_normalized_count_matrix.txt

data_processing:
RNAseq data from CTCs were analyzed by using the AmpliSeq RNA plugin available for Ion Torrent sequencing platforms and Partek Flow (Build version 9.0.20.0720; Partek Inc., St. Louis, MO).
Once the quality of FASTQ files was checked, bases and reads with low quality were filtered out, and adaptors and barcodes were extracted from the data.
Reads were aligned to the reference human genome (version hg19) and TMAP was used as aligner, default setting parameters on Partek Flow.
Normalization of read count was performed by total number of counts (count per million) plus 0.0001, and all genes with less than 10 normalized read counts were excluded from subsequent analyses.
Each gene was associated with a relative (log2) FC>2, whose statistical significance was expressed in terms of P value. Only genes whose P value was ≤0.05 were considered differentially expressed.
Statistically significant DEGs were subsequently grouped in a hierarchical manner using the correlation distance, and displayed in a heatmap. All correlation analyses were performed by calculating the Pearson coefficient and the adjustment for the multivariate analysis was conducted with the Benjamini and Hochberg method (FDR<0.25).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample and matrix table with normalized counts for every gene and every sample.

source_name: circulating tumor cells (CTCs)

extract_protocol:
10-cell pools were lysed with 1 μl of the Reaction Buffer (19 μl of Lysis Buffer and 1 μl of RNase Inhibitor) (Takara Bio, Mountain View, USA) and incubated at 72°C in a thermal cycler for 3 minutes.
The lysed product was incubated at 50°C for 10 minutes with 1 μl of SuperScript IV Reverse Transcriptase (SuperScript™ IV One-Step RT-PCR SystemKit, Thermo Fisher Scientific, Waltham, USA), 5 μl of Ion AmpliSeq™ HiFi Mix (Thermo Fisher Scientific) and 5 µl of the primer pool. The cDNA target amplification was performed at 98°C for 15 seconds and at 60°C for 4 minutes, increasing from 17 to 25 the number of cycles indicated in the “Amplify the Targets” section of the Ion AmpliSeq™ RNA Library preparation user guide (Ion AmpliSeq™ Library Preparation, Quick Reference, Publication Number MAN0006735 Revision F.0), while the following steps were performed according to the manufacturer's instructions.  Both the quality and quantity of libraries, purified by Agentcourt AMPure XP (Beckman Coulter, Indianapolis, USA), were evaluated by the Ion Library Taq Man Quantitation Kit (Life Technologies Carlsbad, California, USA) on the StepOne Plus system (Applied Biosystem, Foster City, California, USA).
Targeted RNA-seq

tag: metastasis site

value: Bone and extra-skeletal metastases (BM+ES)


title: CTC patient 40

value: Extra-skeletal metastases (ES)


title: CTC patient 36

description:
BM_vs_BM+ES_Raw_gene_counts_matrix.txt; BM_vs_ES_Raw_gene_counts.txt
BM_vs_BM+ES_normalized_count_matrix.txt;BM_vs_ES_normalized_count_matrix.txt

value: Bone metastases (BM)


title: CTC patient 33


title: CTC patient 37


title: CTC patient 39


title: CTC patient 34


title: KO_1

city: Jupiter

first: Laura

middle: A

last: Solt

state: FL

address: 130 Scripps Way

department: Immunology and Microbiology

institute: The Scripps Research Institute

description: ribo-depleted RNA

data_processing:
BCL files from Illumina sequencing were demultiplexed and fastq data files were obtained using Illumina's bcl2fastq conversion software version 2.19. Raw data were aligned to the mouse genome (M.musculus-UCSC-mm10 ) using the STAR aligner v(2.5.2a).
Gene abundance was estimated with python version 2.7.11, and htseq version 0.9.1.
Raw counts were transformed into "Relative Log Expression” normalization (RLE) implemented in the DESeq2 package that was used to assess differential expression and perform gene set testing.
Genome_build: M.musculus UCSC mm10 build
Supplementary_files_format_and_content: Excel files (HT-seq Count raw and normalized counts)

organism: Mus musculus

source_name: KO Th17_48h

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kits on Day 2 (WT vs KO) of in vitro differentiated Th17 cells.  rRNA-depleted RNA was processd using the TruSeq Stranded Total RNA sample prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: T cells

tag: genotype

value: RORafl/fl x CD4 Cre (KO)


title: CTC patient 38


title: WT_2

description: ribo-depleted RNA

source_name: WT TH17_48h

value: RORafl/fl (WT)


title: KO_2

description: ribo-depleted RNA


title: Sample_wt

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

institute: IRCCS, Ospdale San Raffaele

data_processing:
alignment with STAR_2.5.3a (--outFilterMismatchNmax 10)
counting reads with featureCounts
Differential Gene Expression with LIMMA
Genome_build: mm10 GRCm38 (basic annotation mm10 GRCm38 M13 Gencode)
Supplementary_files_format_and_content: xls with count data

source_name: E9.5 hindbrain

extract_protocol:
Total RNA was extracted using RNA spin columns (PureLink RNA Mini Kit, Ambion). RNA quantification was carried out using Qubit Fluorimetric Quantification (Life Technologies) and 500ng of RNA were used to prepare the library.
Illumina_TruSeq_stranded
RNA-Seq;NextSeq 500;SE;1x75;Nextera Index;

value: wt littermate

tag: expressed protein

value: full length protein

tag: treatment

tag: age

value: hindbrain


title: Sample_wt-2


title: Sample_d28-30-2

value: Deletion of exons 6 and 7

value: deletion of zinc fingers 28-30


title: Sample_d9-20-2

value: Deletion of exon 4

value: deletion of zinc fingers 9-20


title: WT_1

description: ribo-depleted RNA


title: HIV NR Naive stim_H55

source_name: HIV NR Naive stim_H55


title: Sample_wt-1


title: Sample_d9-20-1


title: CTC patient 32

description:
BM+ES_vs_ES_Raw_gene_counts.txt; BM_vs_ES_Raw_gene_counts.txt
BM+ES_vs_ES_normalized_count_matrix.txt; BM_vs_ES_normalized_count_matrix.txt


title: HIV NR Naive med_H60

source_name: HIV NR Naive med_H60

value: HIV NR Naive med


title: Sample_d28-30-1


title: Sample_d28-30


title: CTC patient 31


title: Sphk2-/-_3

city: Columbia

first: Bumsuk

last: Hahm

state: Missouri

address: M331 Medical Science Bldg. One Hospital Drive

department: Surgery/MMI

institute: University of Missouri-Columbia

data_processing:
The quality of Fastq files was determined by FastQC (ver. 0.11.5, Upendra Kumar Devisetty, Cyverse Discovery Environment, Babraham Institute). Fastq files were aligned to the Mus musculus GRCm38.p6 (rel. 99) primary genome assembly (Ensembl) utilzing HiSat2 (ver 2.1, Kapeel Chougule, Cyverse Discovery Environment), generating BAM files.
Quality control of alignment files was conducted in Seqmonk (Babraham Institute, ver. 1.47.0)
Raw transcript counts were generated from BAM files in SeqMonk (Babrahahm Institute, ver. 1.47.0, RNA quantification pipeline, opposite strand mRNA)
Transcript counts were compared and normalized counts were generated utilizing DESeq2 in GenePattern (Broad Institute). Transcripts with an adjusted p value (FDR) less than 0.05 were used in downstream applications.
Genome_build: Mus musculus GRCm38.p6 (rel. 99) (Ensembl)
Supplementary_files_format_and_content: Processed data files are in .txt format and constitute the following: 1) file containing Ensembl transcript identifier, chromosome position, gene name, Ensembl gene identifier, and raw counts for each replicate; 2) file containing transcript name with ensembl identifiers, feature type, log2 fold change of Sphk2-/- values compared to Sphk2+/+ values, adjusted p value (FDR), and normalized scores for each replicate.

source_name: CD4+ T cell

growth_protocol: LCMV epitope-specific T cell receptor transgenic Sphk2+/+ or Sphk2-/- CD4+ T cells were transferred into wild-type mice followed by infection with LCMV Cl 13. After 7 days, spleen and inguinal lymph node tissues were harvested and disrupted by passing through nylon mesh. CD4+ T cells were isolated via positive column separation, and LCMV-specific cells were isolated via FACS based on the congenic marker CD45.1.

extract_protocol:
Total RNA was extracted using the Aurum Total RNA Mini Kit (Bio-Rad) according to the manufacturer's protocol and stored at -80C until used.
RNA libraries were prepared for sequencing using standard Illumina protocols by Cofactor Genomics (St. Louis, Mo)

tag: infection status

value: Inf. LCMV Cl 13

value: Spleen and Inguinal LN

value: CD4+ T cell


title: Sphk2-/-_2


title: HIV NR Naive med_H69

source_name: HIV NR Naive med_H69


title: Sample_d9-20


title: CTC patient 30


title: Sphk2+/+_2


title: HIV NR Naive med_H48

source_name: HIV NR Naive med_H48


title: Sphk2-/-_1


title: CTC patient 29

value: Bone and extra-skeletal metastases (BM+ES)


title: Sphk2+/+_3


title: HIV NR Naive med_H38

source_name: HIV NR Naive med_H38


title: CTC patient 28

value: Extra-skeletal metastases (ES)


title: CTC patient 27


title: young WT mouse 2, rep B [young_WT2_HSC_B_11]

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary University of London

data_processing:
sequenced on a NextSeq system
reads were aligned to the mm10 genome using hisat-2.0.5
Genome_build: mm10
Supplementary_files_format_and_content: a counts table is provided for SMART-seq data

molecule: polyA RNA

source_name: young WT_100 HSCs

extract_protocol: 100 cells, SMART-Seq2, as in Picelli et al, 2014 (PMID: 24385147)

treatment_protocol: deletion of a floxed Ythdf2 was induced in haematopoietic lineages by a cell type specific Cre

tag: mouse id

value: mouse 2

tag: strain background

tag: genotype/variation

value: wild type

value: young

value: haematopoietic stem cells (HSCs)


title: young WT mouse 3, rep A [young_WT3_HSC_A_4]

value: mouse 3


title: Sphk2+/+_1


title: young WT mouse 3, rep B [young_WT3_HSC_B_12]


title: CTC patient 26


title: HIV NR Naive med_H58

source_name: HIV NR Naive med_H58


title: young WT mouse 4, rep A [young_WT4_HSC_A_6]

value: mouse 4


title: young WT mouse 1, rep A [young_WT1_HSC_A_2]

value: mouse 1


title: young WT mouse 2, rep A [young_WT2_HSC_A_3]


title: HIV NR DN stim_H83

source_name: HIV NR DN stim_H83

value: HIV NR DN stim


title: CTC patient 24


title: young KO mouse 4, rep A [young_KO4_HSC_A_8]

source_name: young KO_100 HSCs

value: YTHDF2 KO


title: young KO mouse 4, rep B [young_KO4_HSC_B_16]


title: CTC patient 23


title: HIV NR Naive med_H40

source_name: HIV NR Naive med_H40


title: young WT mouse 4, rep B [young_WT4_HSC_B_14]


title: HIV NR Naive med_H37

source_name: HIV NR Naive med_H37


title: HIV NR Naive med_H55

source_name: HIV NR Naive med_H55


title: young KO mouse 3, rep B [young_KO3_HSC_B_15]


title: HIV NR DN stim_H69

source_name: HIV NR DN stim_H69


title: CTC patient 22

source_name: circulating tumor cells (CTCs)

value: Bone metastases (BM)


title: HIV NR DN stim_H70

source_name: HIV NR DN stim_H70


title: young KO mouse 3, rep A [young_KO3_HSC_A_7]


title: young KO mouse 2, rep A [young_KO2_HSC_A_5]


title: HIV NR Naive med_H19

source_name: HIV NR Naive med_H19


title: HIV NR DN stim_H60

source_name: HIV NR DN stim_H60


title: young WT mouse 1, rep B [young_WT1_HSC_B_10]


title: CTC patient 25


title: young KO mouse 1, rep A [young_KO1_HSC_A_1]


title: young KO mouse 2, rep B [young_KO2_HSC_B_13]


title: young KO mouse 1, rep B [young_KO1_HSC_B_9]


title: aged WT mouse 65, rep B [aged_WT65_HSC_B]

source_name: aged WT_100 HSCs

value: mouse 65

value: aged (1 year old)


title: aged WT mouse 99, rep A [aged_WT99_HSC_A]

value: mouse 99


title: aged WT mouse 99, rep B [aged_WT99_HSC_B]


title: aged WT mouse 65, rep A [aged_WT65_HSC_A]


title: HIV NR DN stim_H55

source_name: HIV NR DN stim_H55


title: aged WT mouse 124, rep B [aged_WT124_HSC_B]

value: mouse 124


title: CTC patient 18


title: HIV NR DN stim_H48

source_name: HIV NR DN stim_H48


title: aged WT mouse 124, rep A [aged_WT124_HSC_A]


title: CTC patient 17


title: HIV NR DN stim_H46

source_name: HIV NR DN stim_H46


title: aged WT mouse 114, rep B [aged_WT114_HSC_B]

value: mouse 114


title: HIV NR DN stim_H58

source_name: HIV NR DN stim_H58


title: CTC patient 21

value: Bone and extra-skeletal metastases (BM+ES)


title: aged WT mouse 114, rep A [aged_WT114_HSC_A]


title: CTC patient 20

value: Extra-skeletal metastases (ES)


title: CTC patient 16


title: aged KO mouse 94, rep B [aged_KO94_HSC_B]

source_name: aged KO_100 HSCs

value: mouse 94


title: CTC patient 14


title: aged KO mouse 81, rep A [aged_KO81_HSC_A]

value: mouse 81


title: HIV NR DN stim_H37

source_name: HIV NR DN stim_H37


title: HIV NR DN stim_H40

source_name: HIV NR DN stim_H40


title: aged KO mouse 78, rep A [aged_KO78_HSC_A]

value: mouse 78


title: CTC patient 19


title: HIV NR DN stim_H38

source_name: HIV NR DN stim_H38


title: CTC patient 15


title: aged KO mouse 94, rep A [aged_KO94_HSC_A]

value: haematopoietic stem cells (HSCs)


title: aged KO mouse 78, rep B [aged_KO78_HSC_B]


title: aged KO mouse 81, rep B [aged_KO81_HSC_B]


title: HIV NR DN stim_H19

source_name: HIV NR DN stim_H19


title: HIV NR DN med_H83

source_name: HIV NR DN med_H83

value: HIV NR DN med


title: aged KO mouse 122, rep A [aged_KO122_HSC_A]

value: mouse 122


title: aged KO mouse 121, rep B [aged_KO121_HSC_B]

value: mouse 121


title: CTC patient 12


title: aged KO mouse 121, rep A [aged_KO121_HSC_A]


title: aged KO mouse 122, rep B [aged_KO122_HSC_B]


title: HIV NR DN med_H70

source_name: HIV NR DN med_H70


title: COVID-19 Lib_CGA-17_S7

city: Pieve Emanuele

first: sarah

middle: natalia

last: mapelli

state: Milan

address: Via Rita Levi Montalcini 4

department: Experimental Immunopathology

institute: Humanitas research

data_processing:
Demultiplexing with “bcl2fastq2”  Software (version 2.19.0)
Alignment with STAR (version 2.6.1)
Gene summarized counts were processed in R (version 3.5.2).Genes whose expression was major than 2 reads were filtered and vst normalized with the R package DESeq254 (version 1.22.2).
Genome_build: GRCh38 genome guided by GENCODE annotation (version 33)

source_name: Peripheral monocytes

extract_protocol:
Monocytes were enriched from Ficoll-isolated PBMCs by positive selection using CD14 Microbeads kit (Miltenyi Biotec), RNA was purified with the Direct-zol RNA Microprep or Miniprep Kit (Zymosan)
Total-RNA-sequencing library preparation was performed starting from 1 ng of total-RNA with the SMART-Seq Stranded Kit (Clontech-Takara). Libraries obtained were qualitatively assessed by using TapeStation 4200 (Agilent) and quantified by Qubit Fluorimeter (Thermo Fisher Scientific). Afterwards, they were multiplexed in equimolar pools and sequenced on a NextSeq-550 Illumina Platform generating at least 80 million 75-bp-PE reads per sample

tag: condition

value: COVID-19 hospitalized patient


title: HIV NR DN med_H69

source_name: HIV NR DN med_H69


title: CTC patient 10

source_name: circulating tumor cells (CTCs)


title: COVID-19 Lib_CGA-15_S5


title: COVID-19 Lib_CGA-14_S4


title: COVID-19 Lib_CGA-16_S6


title: COVID-19 Lib_CGA-12_S2


title: CTC patient 9


title: CTC patient 8


title: CTC patient 13


title: COVID-19 Lib_CGA-13_S3


title: HIV NR DN med_H55

source_name: HIV NR DN med_H55


title: HIV NR DN med_H60

source_name: HIV NR DN med_H60


title: Healthy Control Lib_CGA-10_S10

description: Healthy Control

value: Healthy Control individual


title: Healthy Control Lib_CGA-08_S8

description: Healthy Control


title: HIV NR DN med_H48

source_name: HIV NR DN med_H48


title: CTC patient 7


title: CTC patient 6


title: Healthy Control Lib_CGA-09_S9

description: Healthy Control


title: HIV NR DN med_H58

source_name: HIV NR DN med_H58


title: H3K27ac T_ALL4

city: South San Francisco

first: Juliette

last: Roels

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Library strategy: ChIPmentation
Reads were trimmed by Trimmomatic and aligned to the reference genome hg38 with Bowtie2.
Peaks were called with MACS2 with the respective input control for each donor pool. Options for MACS2 were set to --extsize 73 –nomodel –broad
A matrix containing all significant peaks was made as reference for counting reads from BAM files using the function summarizeOverlaps from the R package GenomicAlignments.
Normalization of counts was done using DESeq2
Genome_build: hg38

source_name: PDX derived T-ALL blasts

extract_protocol:
50-100 000 CD45+ sorted, fixed cells were lysed in lysis buffer complemented with 20mM NaBU HDAC inhibitor and sheared on the Bioruptor Pico (Diagenode). Sheared chromatin was magnetically immunoprecipitated and tagmentated using the Auto ChIPmentation Kit for Histones (Diagenode).
Libraries were constructed with the Auto ChIPmentation Kit for histones (Diagenode). Libraries were sequenced with the Nextseq500 (SR75, High Output).

value: PDX derived T-ALL blasts

tag: cosme subgroup

tag: antibody


title: H3K27ac T_ALL5


title: CTC patient 11


title: CTC patient 4

value: Bone metastases (BM)


title: H3K27ac T_ALL1


title: HIV NR DN med_H40

source_name: HIV NR DN med_H40

tag: group


title: CTC patient 3


title: HIV NR DN med_H38

source_name: HIV NR DN med_H38


title: H3K27ac T_ALL6


title: CTC patient 2


title: HIV NR DN med_H37

source_name: HIV NR DN med_H37


title: BMT#63_+/-_SR_KIR-

city: Rozzano, Milan

first: Sara

last: Terzoli

address: Via Alessandro Manzoni, 56

institute: Humanitas Clinical and Research Center

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR- NK cells
Lib_CDV_14

data_processing:
Basecalls performed using RTA v2 version 2.4.11
RNA-seq reads were aligned to the GRCh38.p12 genome assembly using STAR version 2.6.1d
Differential Gene Expression analysis was performed using Deseq2 version 1.24.0
GRCh38.p12
Genes Raw counts

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA was purified with the MicroRNAeasy KitTM with DNAse (Qiagen®), according to the manufacturer’s instructions and quantified by Nanodrop 2000 (Thermo Fisher Scientific®, Waltham, Massachusetts, USA). Purified RNA was retro-transcribed using High Capacity cDNA Reverse transcription Kit (Thermo Fisher Scientific®).
Total-RNA-sequencing library preparation was performed starting from 0,5 ng of total-RNA with the SMART-Seq Stranded Kit (Clontech-Takara). Libraries obtained were qualitatively assessed by using TapeStation 4200 (Agilent) and quantified by Qubit Fluorimeter (Thermofisher). Multiplexed in equimolar pools and sequenced on a NextSeq-550 Illumina Platform generating at least 60 million 75bp-paired-end reads per sample

value: NK

tag: donor/recipient hcmv serostatus

tag: hcmv reactivation

value: reactivated, single reactivation

tag: days post-h-hsct


title: BMT#76_-/+_MR_KIR-

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR- NK cells
Lib_CDV_27

tag: cell type

value: reactivated, multiple reactivation


title: BMT#26_+/+_SR_KIR-

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR- NK cells
Lib_CDV_23


title: BMT#65_-/+_MR_KIR-

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR- NK cells
Lib_CDV_17


title: HIV NR DN med_H19

source_name: HIV NR DN med_H19


title: BMT#13_+/+_SR_KIR-

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR- NK cells
Lib_CDV_20


title: CTC patient 5

tag: metastasis site


title: BMT#27_+/+_SR_KIR-

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR- NK cells
Lib_CDV_11


title: BMT#105_-/-_NR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_37

value: not reactivated


title: BMT#18_+/+_NR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_29


title: HIV NR CD4 stim_H83

source_name: HIV NR CD4 stim_H83

value: HIV NR CD4 stim


title: H3K27ac T_ALL2

tag: tissue


title: BMT#25_+/-_MR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_07


title: HIV NR DN med_H46

source_name: HIV NR DN med_H46


title: BMT#65_-/+_MR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_16


title: DS50d

city: 重庆市

first: Yangyang

last: Li

state: 重庆

address: 中国重庆

country: China

institute: 农学与生物科技学院

data_processing:
Low-quality reads were filtered out using NGS QC toolkit v2.2.3 (https://omictools.com/ngs-qc-toolkit-tool)
clean reads were mapped in the reference genome of “Darmor-bzh” (http://www.genoscope.cns.fr/brassicanapus/)
The obtained genes obtained from the previous step were quantitatively analyzed using Cluffquant and Cluffnorm of Cufflinks2.0.0 (http://cole-trapnell-lab.github.io/cufflinks/releases/v2.0.0/)
The FPKM (fragments per kilobase of transcript per million fragments mapped) was employed to measure transcription
A fold change more than 2 and a false discovery rate (FDR) less than 0.01 were the conditions for screening differentially expressed genes (DEGs)
Genome_build: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica napus

source_name: seed

growth_protocol: the six lines were planted under a waterproof shed with normal experimental management until the initial flower stage.

extract_protocol:
the total RNA was extracted using a Trizol kit (Invitrogen, USA)
Biomarker Technologies Co, Ltd, Beijing, China, subjected the qualified libraries to cluster generation on cBot and sequencing on a Hiseq 2000 platform (Illumina) with paired-end 100-bp reads.

treatment_protocol: drought stress treatments and control treatments were employed in each line

value: 50d after flowering under drought stress from initial flowering stage


title: HIV NR CD4 stim_H69

source_name: HIV NR CD4 stim_H69


title: HIV NR CD4 stim_H70

source_name: HIV NR CD4 stim_H70


title: H3K27ac T_ALL3


title: DS30d

value: 30d after flowering under drought stress from initial flowering stage


title: BMT#88_+/-_NR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_35


title: BMT#76_-/+_MR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_26


title: DS40d

value: 40d after flowering under drought stress from initial flowering stage


title: BMT#63_+/-_SR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_13


title: BMT#25_+/-_MR_KIR-

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR- NK cells
Lib_CDV_08


title: HIV NR CD4 stim_H60

description:
legenda: HIV= study group; NR= Non responder to Influenza Vaccination; R=Responder to Influenza vaccination; Rem/AM/PBMC/DN/Naïve/Total B/CD4/TFH/NTF= cell subset identifier (please check source name for acronym interpretetion); med=unstimulated sample; stim= stimulated sample with H1N1 peptides for 16 hours; _HX= identifier of the subject. When patient responsiveness is not referenced please refer to this list: NR= H19  H37  H38  H40  H46  H48  H55  H58  H60  H69  H70  H83;                                                                                and Responder (R)= H3  H7  H8  H26  H41  H44  H47  H56  H75  H80  H52.
500 fixed numbers of live cell sorted by ARIA IICs, derived from human PBMCs from frozen samples.Every sample is identified according to study group, cell subset, condition and patient identifier.

source_name: HIV NR CD4 stim_H60


title: CTC  patient 1

description:
BM_vs_BM+ES_Raw_gene_counts_matrix.txt; BM+ES_vs_ES_Raw_gene_counts.txt
BM_vs_BM+ES_normalized_count_matrix.txt;BM+ES_vs_ES_normalized_count_matrix.txt

source_name: circulating tumor cells (CTCs)

value: Bone and extra-skeletal metastases (BM+ES)


title: HIV NR CD4 stim_H58

source_name: HIV NR CD4 stim_H58


title: CK50d

value: 50d after flowering under control


title: CK40d

value: 40d after flowering under control


title: BMT#89_-/-_NR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_05


title: CK30d

value: 30d after flowering under control


title: HIV NR CD4 stim_H55

source_name: HIV NR CD4 stim_H55


title: FB2

city: Boston

first: Aristidis

last: Veves

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

data_processing:
Libraries were quality-checked using FastQC
Cutadapt was utilized for pre-processing and contaminant removal
Quantification of small RNAs was performed by employing the Manatee pipeline against GRCm38. Small RNA annotation was derived from Ensembl v93 and miRBase v22. Non-coding transcripts overlapping coding exons in sense were filtered out, so as retain an unambiguous non-coding transcriptome. All non-coding transcripts overlapping non-coding regions (UTRs, introns) of coding genes in sense or all regions in anti-sense were retained in the dataset.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts per million reads mapped

source_name: Fibroblasts derived exosomes

growth_protocol: ESCs were isolated from the dorsal skin of 3 weeks of age telogen C57BL/6 mice. Briefly, the skin was disinfected and cut into stripes. After overnight incubation in 1mg/ml Dispase II (17105041; Gibco) in DPBS the epidermal sheets were carefully separated from the dermis and minced into pieces which were digested in 0.25% trypsin (25200-056; Gibco) for 15 minutes. Cells were then filtered and centrifuged before they were resuspended in keratinocyte serum-free medium (K-SFM, 37010022; Gibco) and seeded at a density of 105 cells/cm2 in flasks coated with 100 μg/ml collagen IV (354233; Corning, USA) for 20 minutes at 37 °C. The rapidly adhering cells were collected and cultured in K-SFM at 37 °C in 5% CO2. Fb were isolated from the dorsal skin of 14 weeks db/db mice. Briefly, the dermis was minced into pieces and digested in 0.1% Collagenase P (11249002001, Sigma, USA) in 0.25% Trypsin at 37 °C for 30 min. The cells were filtered, centrifuged, and resuspended in DMEM containing 10% FBS. After cell counting and viability detection, the Fb were seeded into flasks at a density of 2x104 cells/cm2 for further study.

extract_protocol:
Three biological replicates of ESCs-Exo and Fb-Exo were processed for total RNA isolation using the SeraMir Exosome RNA Purification Column kit (Cat #RA808A-1, System Biosciences, Palo Alto, CA) according to the manufacturer’s instructions. For each sample, 1ul of the final RNA eluate was used for measurement of small RNA concentration by Agilent Bioanalyzer Small RNA Assay using Bioanalyzer 2100 Expert instrument (Agilent Technologies, Santa Clara, CA).
Small RNA libraries were constructed with the CleanTag Small RNA Library Preparation Kit (TriLink, Cat# L-3206) according to the manufacturer's protocol. The final purified library was quantified with High Sensitivity DNA Reagents (Agilent Technologies, PO# G2933-85004) and High Sensitivity DNA Chips (Agilent Technologies, PO# 5067-4626). The libraries were pooled, and the 140bp to 300bp region was size selected on an 8% TBE gel (Invitrogen by Life Technologies, Ref# EC6215). The size selected library was quantified with High Sensitivity DNA 1000 Screen Tape (Agilent Technologies, PO# 5067-5584), High Sensitivity D1000 reagents (Agilent Technologies, PO# 5067-5585), and the TailorMix HT1 qPCR assay (SeqMatic, Cat# TM-505).

treatment_protocol: To efficiently isolate exosomes, we developed a novel method based on existing extraction methods. Briefly, the culture media of 80% confluent ESCs was collected and centrifuged at 300×g for 5 min. After the centrifugation, the supernatant was filtered using a 0.22μm filter (Millipore, USA) to remove cell debris. Followed by concentrated in Amicon™ Ultra-15 (UFC901024, EMD Millipore™ Amicon™, USA) filter at 4000g for 30 min, the supernatant was then ultra-centrifuged at 120,000 x g for 70 minutes at 4 °C in 1.5ml microfuge polyallomer tube (357448, Beckman Coulter, USA) by an Optima™ TLX Ultracentrifuge with a TLA-110 rotor (347448, Beckman Coulter, USA). Afterwards, the pelleted exosomes were resuspended in PBS and stored at −80 °C for further experiments.  The extraction process of fibroblast exosomes (Fb-Exo) was similar to that of ESCs with the only difference being that that before the Fb-Exo extraction, the culture medium was changed to a serum-free medium and cultured for two days

tag: strain

tag: passages

value: Dorsal skin dermal fibroblast


title: HIV NR CD4 stim_H48

source_name: HIV NR CD4 stim_H48


title: BMT#27_+/+_SR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_10


title: FB3


title: BMT#77_+/-_NR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_33


title: BMT#26_+/+_SR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_22


title: meRIP-seq input1

data_processing:
sequenced on a HiSeq 2000 system
reads were aligned to the mm10 genome using hisat-2.0.5
peaks were called using macs2 (version 2.1.1.20160309) with the --nomodel flag
Genome_build: mm10
Supplementary_files_format_and_content: peak files are provided for meRIP-seq samples

source_name: meRIP-seq input

value: MACS-enriched Kit+ foetal liver cells


title: HIV NR CD4 stim_H46

source_name: HIV NR CD4 stim_H46


title: meRIP-seq input2


title: ESC3

source_name: Epidermal stem cells derived exosomes

value: Dorsal skin epidermal stem cell


title: FB1


title: BMT#50_-/-_NR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_03


title: HIV NR CD4 stim_H40

source_name: HIV NR CD4 stim_H40


title: BMT#48_+/+_NR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_31

source_name: Peripheral blood mononuclear cells


title: meRIP-seq IP2

source_name: meRIP-seq IP


title: ESC2


title: meRIP-seq IP1


title: ESC1


title: HIV NR CD4 stim_H37

source_name: HIV NR CD4 stim_H37


title: BMT#3_-/-_NR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_01


title: Sox2 depleted rep 3

first: Michael

last: Tolstorukov

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
RNA-seq:Tags were aligned using Tophat software package with default parameters. RNA-Seq tag frequencies were normalized for GC-content using bioconductor package EDASeq and then the expression estimates for each gene were obtained using bioconductor package DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files representing normalized coverage coverage profiles normalized to library sizes

source_name: ESC Sox2 depleted cells

extract_protocol:
Total RNA was extracted from Oct4 or Sox2 inducible ESC lines that were either untreated (wild type) or Doxycyline treated for 48hrs and 96hrs to deplete Oct4 and Sox2, respectively. Samples were DNAse treated and purified using Qiagen RNeasy mini kit (according to manufacturer’s instructions). RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Libraries were prepared with the Truseq RNA sample preparation v2 kit. Briefly, total RNA was polyA selected using poly-T oligo-attached magnetic beads, fragmented and subject to first strand cDNA synthesis using random primers and superscript II (Invitrogen). This is followed by a second strand cDNA synthesis using polymeraseI and RNAseH. The resulting cDNA fragment were end repaired, dA-tailed at their 3’end and ligated to illumina’s multiple indexing adapters. Libraries were then PCR amplified, quantified using Qubit fluorometer and their quality assessed using an Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced on Illumina HiSeq 2000 platform. On average 20 million reads were generated per library.

value: embryonic stem cells (ESCs)

value: Sox2-inducible ESC lines

tag: treated with

value: Doxycyline for 96hrs


title: HIV NR CD4 stim_H19

source_name: HIV NR CD4 stim_H19


title: Sox2 depleted rep 2


title: Sox2 depleted rep 1


title: LRCs: H2B-GFP(high) [53563]

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

description:
High3_53563
FACS-sorted

data_processing:
We downloaded the reads files and concatenated those into a single .fastq file for each sample.
We checked the quality of the raw reads data for each sample using FastQC [1] (version v0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content).
We used the Tuxedo Suite software package for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference genome including both mRNAs and lncRNAs (UCSC mm10) [5] using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We ran two different, popular techniques for differential expression analysis: Cufflinks/CuffDiff and HTSeq/DESeq2 [9], using UCSC mm10.fa as the reference genome sequence.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: DESeq2: depth_normalized_counts, raw_counts, rlog_normalized_counts, Tuxedo: Fpkm, RawCounts, ScaledCounts

source_name: Cartilage, Growth plate

extract_protocol:
Femurs and tibias were dissected, distal epiphyseal growth plates of the femur and proximal epiphyseal growth plates of the tibia were manually dislodged. Growth plate chondrocytes were enzymatically dissociated from the epiphysis by collagenase. H2B-GFP(high)tdTomato+ cells (LRCs) or H2B-GFP(mid-low)tdTomato+ cells (non-LRCs) cells were FACS-isolated. ~10,000 (LRCs) and ~50,000 (non-LRCs) cells were used for subsequent steps.
Nextera XT DNA Library Preparation Kit.

tag: genotype

value: Peli2(Col2a1-tTA/Col2a1-tTA); Col1a1(TRE-H2B-GFP/TRE-H2B-GFP); Col2a1-creER/Col2a1-creER; R26R(tdTomato/tdTomato)

value: Col2a1+ growth plate chondrocytes (LRC)

tag: age

value: Postnatal day 49

tag: treatment

value: Doxycycline P21-49; Tamoxifen P46, 47


title: Non-LRCs: H2B-GFP(low) [53564]

description:
Low3_53564
FACS-sorted

value: Col2a1+ growth plate chondrocytes (non-LRC)


title: Non-LRCs: H2B-GFP(low) [53562]

description:
Low2_53562
FACS-sorted


title: Macrophages_SARS-CoV-2_3

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Raw reads counts were extracted using htseq-count v0.11.2.
Genome_build: hg19
Supplementary_files_format_and_content: txt files storing raw read counts per gene per sample

source_name: Macrophages

growth_protocol: For monolayer-based cardiomyocyte (CMs) differentiation, hESCs were passaged at a density of 3x105cells/well of 6-well plate and grown for 48 hours to 90% confluence in a humidified incubator with 5% CO2 at 37℃. On day 0, the medium was replaced with RPMI 1640 supplemented with B27 without insulin and 6 µM CHIR99021. On day 1, the medium was changed to RPMI 1640 supplemented with B27 without insulin for 48 hr. Day 3, medium was refreshed to RPMI 1640 supplemented with B27 without insulin and 2 µM C59 for another 48 hr. On day 5, the medium was changed back to RPMI-B27 without insulin for 48 hr, and then switched to RPMI 1640 plus normal B27 until day 12 with a medium change every 2 days. On day 12, the medium was transiently changed to RPMI 1640 without D-glucose containing ascorbic acid, human albumin and DL-Lactate for two days to allow metabolic purification of CMs. From that day on, fresh RPMI 1640-B27 was changed every two days. On day 21, cells were dissociated with Accutase at 37℃ followed by resuspending with fresh RPMI 1640-B27 plus Y-27632 and reseeding into 96-well plates. After 24 hr, then switched to RMPI 1640-B27 without Y-27632 for following virus confection tests.

extract_protocol: Libraries were prepared using Illumina TruSeq RNA Sample Preparation (Non-stranded and Poly-A selection).

treatment_protocol: hPSC-derived cardiomyocytes were dissociated with Accutase at 37℃ followed by resuspending with fresh RPMI 1640-B27 plus Y-27632 and reseeding into 96-well plates. After 24 hr, the medium was switched to RMPI 1640-B27 without Y-27632. After 24h recovery, macrophages were added into hPSC-derived cardiomyocytes and co-cultured for another 24 hr before following analysis. Adult cardiomyocytes were also seeded into plates for 48-96 hr and co-cultured with macrophages for 24 hr before following analysis.

value: Macrophages


title: Macrophages_SARS-CoV-2_2


title: LRCs: H2B-GFP(high) [53561]

description:
High2_53561
FACS-sorted


title: HIV NR AM stim_H70

data_processing:
Previously amplified samples were loaded on a Fluidigm 96.96 standard chip following manufacturer’s instructions. Briefly, assay pre-mix was prepared 1:1 20X TaqMan Gene Expression Assay (Applied Biosystems) and Assay Loading Reagent (Fluidigm). The sample pre-mix was prepared with TaqMan Universal PCR Master Mix (2X)(Applied Biosystems), 20XGE Sample Loading Reagent (Fluidigm), and cDNA. Full list of the two panels of gene probes (B subsets and T subsets is shown in supplemental table 1 and 2). 5ul of Assay and Sample mix were loaded into the chip according to manufacturers instructions. Genes’ selection has been made according to previous analysis on RNA Sequencing on HIV infected children from a different cohort (data not shown), the literature and online gene banks and biological queries.  Cycle threshold value (Ct) deriving from exported files was corrected according to number of cells sorted if lower than 500. Calculations were made following the expression 67,5 / 500 = Y / X where X is the number of cells sorted and Y is the cells equivalent cDNA of cell sorted. The dilution factor (n) was calculated as n= 67,5/Y, and base 2 log of n was subsequently subtracted to Ct value in order to get Corrected Cycle Threshold (c-Ct). Expression threshold (Et), which was  used for the main analysis was finally obtained with 40-cCT. Once exported and corrected, data were analyzed through Fluidigm SingluaR (SingulaR analysis toolset 3.0) package, loaded on R (software R 3.0.2 GUI 1.62). As previously described (De Armas LR, 2017) gene expression differences between different groups within same subset and condition were used to identify Differentially Expressed Genes (DEGs). Alternatively, paired gene expression differences between stimulated (stim) and unstimulated samples (med) (stim-med) within the same subset were used to define Differentially Induced Genes (DIGs).
Cycle threshold value (Ct) deriving from exported files was corrected according to number of cells sorted if lower than 500. Calculations were made following the expression 67,5 / 500 = Y / X where X is the number of cells sorted and Y is the cells equivalent cDNA of cell sorted. The dilution factor (n) was calculated as n= 67,5/Y, and base 2 log of n was subsequently subtracted to Ct value in order to get Corrected Cycle Threshold (c-Ct). Expression threshold (Et), which was  used for the main analysis was finally obtained with 40-cCT. Once exported and corrected, data were analyzed through Fluidigm SingluaR (SingulaR analysis toolset 3.0) package, loaded on R (software R 3.0.2 GUI 1.62). As previously described (De Armas LR, 2017) gene expression differences between different groups within same subset and condition were used to identify Differentially Expressed Genes (DEGs). Alternatively, paired gene expression differences between stimulated (stim) and unstimulated samples (med) (stim-med) within the same subset were used to define Differentially Induced Genes (DIGs).

source_name: HIV NR AM stim_H70

extract_protocol: 500 live cells per B and T cell subset were sorted into tubes previously loaded with 9uL of PCR buffer for RNA extraction. After sorting, cells were immediately centrifuged (3000RPM for 3 minutes) and kept on ice. Samples were subsequently transferred in PCR tubes and 18 PCR cycles were performed on a C1000 Thermal Cycler (Bio Rad) with the following scheme (50°C for 20’, 95°C for 2’, 95°C 15’’, 60°C for 4’. Last step repeated 18 times). Cells were finally kept at -20 until further analysis. PCR buffer premix for cell sorting contained the following: Cells Direct Reaction mix 5uL, DEPC water 1,4, Superscript III + Taq 1ul, 0.2x diluted assay (96 primer mix) 2,5uL, Superasein 0,1uL.

value: HIV NR AM stim


title: Sox2 wild-type rep 2

source_name: ESC cells

tag: strain background

tag: genotype/variation

value: none (untreated; wild type)


title: HIV NR AM stim_H83

source_name: HIV NR AM stim_H83


title: Macrophages_SARS-CoV-2_1


title: Sox2 wild-type rep 1


title: Non-LRCs: H2B-GFP(low) [50033]

description:
Low1_50033
FACS-sorted


title: HIV NR CD4 stim_H38

source_name: HIV NR CD4 stim_H38

value: HIV NR CD4 stim


title: Oct4 depleted

source_name: ESC Oct4 depleted cells

value: Doxycyline for 48hrs


title: LRCs: H2B-GFP(high) [50032]

description:
High1_50032
FACS-sorted


title: HIV NR AM stim_H60

source_name: HIV NR AM stim_H60


title: Macrophages_Mock_3


title: HIV NR AM stim_H69

source_name: HIV NR AM stim_H69


title: Oct4 wild-type


title: Macrophages_Mock_2


title: BMT#13_+/+_SR_KIR+

description:
FACS sorted viable/CD14-/CD3-/Lin-/KIR+ NK cells
Lib_CDV_19

value: NK

value: reactivated, single reactivation


title: Macrophages_Mock_1


title: HIV NR AM stim_H58

source_name: HIV NR AM stim_H58


title: Periodontal ligament tissue homeostasis 2

city: london

first: Paul

last: Sharpe

address: Craniofacial Development & Stem cell bio, Guy's Tower Floor 27

institute: King's college London

data_processing:
Count matrices were generated from the fastq files via CellRanger pipeline using Ensembl 97 genome annotation.
Ambient and background RNA from the count matrices were first removed using CellBender remove‐background tool.
Only cells expressing >1000 features and having mitochondria gene content of less than 5% of total cell content were maintained, leading to 2891 high‐quality cells.
Batch effect was removed by Seurat CCA approach, with default parameters and 20 dimensions for anchors search and data integration. Integrated data were subsequently scaled and PCA was performed, followed by UMAP for embedding and Louvain clustering (resolution 0.5) on knn graph.
Mesenchymal cells (495 cells) were selected and re‐clustered with similar parameters. Main cluster markers were identified using Wilcoxon Rank Sum test.
Pathway overdispersion analysis was performed by PAGODA2.
RNA velocity data were generated from the output bam files generated by CellRanger using velocyto tool.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Data1.txt and Data2.txt include raw count matrices.

source_name: Periodontal ligament tissue

extract_protocol:
Tooth were extracted and digested with collagenase P, single cells suspensions were fed into Chromium 10x.
Library was generated with Chromium Single Cell 3' v3 Kit.

value: periodontal ligament


title: HIV NR AM stim_H55

first: Nicola

last: Cotugno

institute: University of Rome "Tor Vergata"

source_name: HIV NR AM stim_H55


title: hESC-derived cardiomyocytes_SARS-CoV-2_3

source_name: hESC-derived cardiomyocytes

value: hESC-derived cardiomyocytes


title: Periodontal ligament tissue homeostasis 1


title: WT-LPS-Lung

city: Farmington

first: Vijay

last: Rathinam

state: Connecticut

address: 263 Farmington Ave

department: Immunology

institute: UConn Health School of Medicine

data_processing:
Sequencing was conducted on a high-throughput sequencing using Illumina HiSeq4000
Illumina basecall files (*.bcl) were converted to bcl2fastq
Sequence reads were mapped to mouse genome mm10 using Histat2 v2.0.5
Mapped sam files were converted to bam files and sorted using samtools v1.4
Quantification and normalization of reads were conducted using stringtie v1.3.3b
Genome_build: mm10
Supplementary_files_format_and_content: excel spreadsheets including FPKM values for each Sample

source_name: mice treated with LPS (5 mg/kg for 8 h)

growth_protocol: Mice were maintained in specific pathogen-free conditions in the animal facilities of UConn Health. Mice of 8-24 weeks old were used.

extract_protocol:
Total RNA was extracted from freshly isolated spleen or lungs from wild-type or Lgals1-/- mice treated with LPS (5 mg/kg for 8 h) using RNeasy Mini Kit (QIAGEN)
After quality check, RNA samples were subjected to library generation using the NEBNext Ultra RNA Library Prep kit with polyA selection followed by high-throughput sequencing using Illumina HiSeq4000 at Genewiz (NJ, USA).

treatment_protocol: Wild-type or Lgals1-/- mice treated with LPS (5 mg/kg for 8 h)

value: Lung

value: WT


title: HIV NR AM stim_H46

city: Rome

address: via Montpellier 1

source_name: HIV NR AM stim_H46


title: WT-LPS-Spleen

value: Spleen


title: HIV NR AM stim_H48

source_name: HIV NR AM stim_H48


title: hESC-derived cardiomyocytes_SARS-CoV-2_2


title: HIV NR AM stim_H40

source_name: HIV NR AM stim_H40


title: KO-LPS-Lung


title: HIV NR AM stim_H38

source_name: HIV NR AM stim_H38


title: hESC-derived cardiomyocytes_SARS-CoV-2_1


title: hESC-derived cardiomyocytes_Mock_3


title: KO-LPS-Spleen


title: HIV NR AM stim_H37

source_name: HIV NR AM stim_H37


title: hESC-derived cardiomyocytes_Mock_2


title: hESC-derived cardiomyocytes_Mock_1


title: HIV NR AM stim_H19

source_name: HIV NR AM stim_H19


title: PBMCs + H-1PV

city: Heidelberg

first: Matthias

last: Neulinger Munoz

address: INF 133

country: Germany

institute: Universitätsklinikum Heidelberg

data_processing:
Quality control performed with FastQC v0.11.8
obtained reads were pseudoaligned using the hg38 reference genome and quantified by Salmon v1.2 with standard parameters
resulting transcript expression levels were summarized to gene-level expression values and corrected for average transcript length by using tximport v1.10.1 and the “lengthScaledTPM“ option
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: PBMCs

growth_protocol: The cells were routinely grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 µg/mL streptomycin. All cell lines were routinely tested for mycoplasma by PCR. PBMCs from healthy donors were isolated from whole blood using Histopaque-1077 (Sigma-Aldrich, St. Louis, MO 63103 USA). The blood was mixed with an equal amount of PBS and gently layered over Histopaque-1077 in a Falcon tube, resulting in volume ratios of blood to PBS to Histopaque-1077 of 1:1:1. After centrifugation at 800g for 20 minutes at room temperature, PBMCs were recovered from their corresponding layer and resuspended in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol:
total RNA was isolated from the cell culture using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. After isolation, the total RNA was treated with Turbo DNAfree Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions to decrease the amount of contaminating genomic DNA. The RNA concentration and quality were evaluated by Nanodrop and by using the Agilent2000 Bioanalyzer.
RNAseq libraries were prepared using the TruSeq stranded total RNA kit. The RNAseq libraries were sequenced using   an Illumina HiSeq 4000 platform, resulting in 50bp single end reads in a read count number ranging from 36 to 72 million reads per sample.

treatment_protocol: Cells were infected with wildtype H-1PV with a multiplicity of infection of 10 PFU/cell and harvested 48h (for pancreatic cancer cell lines) or 24h (for PBMCs) post infection

value: PBMCs

tag: cell line

tag: infection

tag: time

value: 24 hours post infection


title: PBMCs control

value: Control


title: T3M4 + H-1PV

source_name: Pancreatic cancer cell lines

value: Pancreatic cancer cells

value: 48 hours post infection


title: Holothuria glaberrima: Day 3 regenerating intestine_Day3B

city: San juan

first: David

middle: J

last: Quispe

state: PR

address: 14, 2534 Av. Universidad Ste. 1401

department: Biology

country: Puerto Rico

institute: Universty of Puerto Rico

description:
DispersionEstimatesDay3
Day3B

data_processing:
Preprocessing steps of quality, trimming and filtering were done using FastQCv0.11.577 and Trimmomaticv0.3678 (ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDING-WINDOW:4:15 MINLEN:36)
Kmer trimming and digital normalization was applied previously to the assembly process using the khmer package.
A de novo transcriptome assembly was carried out using Trinity
Supplementary_files_format_and_content: Final dispersion estimates obtained with DESeq2 and expression tables with Log2FC of annotated genes for the comparisons.

organism: Holothuria glaberrima

source_name: regenerating intestine

growth_protocol: Organisms were kept in fish tanks with aerators.

extract_protocol:
Combination of the method established by Chomczynski (1993) using Tri-reagent® (N.93289, Sigma, USA) and the RNAeasy mini kit (Qiagen, Germany).
TruSeq Stranded mRNA Library Prep Kit (Illumina, USA).

treatment_protocol: Organisms were treated with KCl to induce the expelling of their internal organs for the regenerative process to start.

tag: regenerative stage

value: Day 3 of regeneration

value: intestine


title: T3M4 control


title: Holothuria glaberrima: Day 3 regenerating intestine_Day3C

description:
DispersionEstimatesDay3
Day3C


title: Normoxia_rep3_tech1

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

description: Genome-wide library of transposed fragments

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

growth_protocol: MCF-7 were cultured in DMEM low glucose medium (1g/l) supplemented with 10% FBS no longer than 20 passages. Cells were subjected to normoxia or 0.1% hypoxia for 48 hours using an InVivO2 chamber (Baker).

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

value: breast cancer

value: Normoxia


title: Normoxia_rep3_tech2


title: Normoxia_rep2_tech2


title: HIV NR AM med_H70

source_name: HIV NR AM med_H70

tag: group

value: HIV NR AM med


title: Holothuria glaberrima: Day 3 regenerating intestine_Day3A

description:
DispersionEstimatesDay3
Day3A


title: HIV NR AM med_H69

source_name: HIV NR AM med_H69


title: MiaPaca2 + H-1PV


title: Holothuria glaberrima: Day 1 regenerating intestine_Day1C

description:
DispersionEstimatesDay1
Day1C

value: Day 1 of regeneration


title: Normoxia_rep1_tech2


title: Normoxia_rep1_tech1


title: MiaPaca2 control


title: HIV NR AM med_H60

source_name: HIV NR AM med_H60


title: HIV NR AM med_H55

source_name: HIV NR AM med_H55


title: HIV NR AM med_H58

source_name: HIV NR AM med_H58


title: AsPC1 +H-1PV


title: Holothuria glaberrima: Day 1 regenerating intestine_Day1B

description:
DispersionEstimatesDay1
Day1B


title: Holothuria glaberrima: Normal mesentery_Normal3

description:
DispersionEstimatesNormal
Normal3

source_name: mesentery

value: Non-regenerating

value: mesentery


title: AsPC1 control


title: Holothuria glaberrima: Day 1 regenerating intestine_Day1A

description:
DispersionEstimatesDay1
Day1A


title: Hypoxia_rep3_tech2

value: Hypoxia


title: HIV NR AM med_H83

source_name: HIV NR AM med_H83


title: Hypoxia_rep3_tech1


title: Hypoxia_rep2_tech2


title: HIV NR AM med_H48

source_name: HIV NR AM med_H48


title: Holothuria glaberrima: Normal mesentery_Normal2

description:
DispersionEstimatesNormal
Normal2


title: HIV NR AM med_H46

source_name: HIV NR AM med_H46


title: Hypoxia_rep2_tech1


title: HIV NR AM med_H40

source_name: HIV NR AM med_H40


title: Holothuria glaberrima: Normal mesentery_Normal1

description:
DispersionEstimatesNormal
Normal1


title: Hypoxia_rep1_tech2


title: mTEC2_thymic epithelial cells_scRNA-seq

first: Paola

last: Bonfanti

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

source_name: FACS sorted EpCAM+CD49F-

growth_protocol: Tissue was processed fresh after cardiothoracic surgery

extract_protocol:
Thymic tissue fragments were dissociated to single cells by enzymatic treatment (0.4 mg/mL Collagenase D (Roche), 0.6 mg/mL Dispase II (Roche), 40 μg/mL DNAse I (Roche)) for about 30-45 minutes at 37ºC. Cells were pelleted and re-suspended for cell counting. single cell suspension was depleted of CD45 and CD235ab (red blood) expressing cells by immunomagnetic separation. The enriched fraction was stained and sorted using FACSAria III machine for cortical (EpCAMlowCD205+) and medullary  (EpCAMhighCD205-) thymic epithelial cells (TEC)
RNA libraries were prepared for sequencing using Chromium Single Cell 3' v2 protocol (PN-120233, 10X Genomics); cDNA amplification involved 12 PCR cycles

treatment_protocol: Tissue was digsted with collagenase and dispase at single-cell level, stained form epithlial markers and 4 epithelial populations separated by FACS analysis based on surface markers expression

tag: Stage

value: 6months old human thymus

tag: condition

value: Female healthy


title: cTEC2_ thymic epithelial cells_scRNA-seq

source_name: FACS sorted CD205+CD49F-


title: HIV NR AM med_H38

source_name: HIV NR AM med_H38


title: cTEC1_thymic epithelial cells_scRNA-seq

source_name: FACS sorted CD205+CD49F+


title: Hypoxia_rep1_tech1

tag: cell type


title: HIV NR AM med_H37

source_name: HIV NR AM med_H37


title: RNA-seq HEK293T NSUN6 KO rep2

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Adapters were trimmed with cutadapt (--max-n 1 --trim-n -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAG).
Clean reads were mapped to reference genome with Tophat2 (--library-type fr-firststrand).
Aligned reads were sorted; and gene read counts were called via HTSeq-count.
DESeq2 was used in differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: TXT files generated by HTSeq-count

extract_protocol:
Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

value: NSUN6 KO


title: HIV NR AM med_H19

source_name: HIV NR AM med_H19


title: RNA-seq HEK293T NSUN6 KO rep1


title: HIV CD4 med_H83

source_name: HIV CD4 med_H83

value: HIV CD4 med


title: RNA-seq HEK293T WT rep2

value: Wildtype


title: HIV CD4 med_H8

source_name: HIV CD4 med_H8


title: RNA-seq HEK293T WT rep1


title: mTEC1_thymic epithelial cells_scRNA-seq

source_name: FACS sorted EpCAM+CD49F+


title: HD6 CD28+CD57-CD8+ N+ED (naive and early differentiated)

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description:
count.txt
HD6_N_ED

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16   --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

source_name: peripheral blood

extract_protocol:
RNA was isolated using the Qiagen RNAeasy microkit
Barcoded RNA-sequencing libraries were prepared from 100 ng total RNA using the Ovation Human RNA-Seq system for small amounts of RNA (Nugen, San Carlos, CA). For selective depletion of rRNAs, the insert-dependent adapter cleavage method from Nugen was used prior to cDNA synthesis. To control sources of variability during sample and data processing, a common set of external spike-in RNA controls, developed by the external RNA controls consortium (ERCC), was used (Ambion).

value: T cells

tag: tissue

value: peripheral blood

value: wildtype FAS

tag: diagnoses

value: healthy individual


title: HIV CD4 med_H75

source_name: HIV CD4 med_H75


title: HD4 CD28+CD57-CD8+ N+ED (naive and early differentiated)

description:
count.txt
HD4_N_ED


title: HD5 CD28+CD57-CD8+ N+ED (naive and early differentiated)

description:
count.txt
HD5_N_ED


title: HIV CD4 med_H70

source_name: HIV CD4 med_H70


title: HIV CD4 med_H7

source_name: HIV CD4 med_H7


title: HIV CD4 med_H69

source_name: HIV CD4 med_H69


title: HD5 cDNT (CD3+TCRab+CD4-CD8- NOT CD38+CD45RA+)

description:
count.txt
HD5_cDNT


title: HIV CD4 med_H60

source_name: HIV CD4 med_H60


title: HD5* FC DNT pooled with FC DNT from 3 additional HD  (CD3+TCRab+CD4-CD8-CD38+CD45RA+)

description:
count.txt
HD5_FC DNT


title: HIV CD4 med_H80

source_name: HIV CD4 med_H80


title: HD4 FC DNT (CD3+TCRab+CD4-CD8-CD38+CD45RA+)

description:
count.txt
HD4_FC DNT


title: HIV CD4 med_H56

source_name: HIV CD4 med_H56


title: HIV CD4 med_H58

source_name: HIV CD4 med_H58


title: patient 22 FC DNT (CD3+TCRab+CD4-CD8-CD38+CD45RA+)

description:
count.txt
P22_FC DNT

value: mutated FAS

value: ALPS-FAS, untreated


title: patient 3 FC DNT (CD3+TCRab+CD4-CD8-CD38+CD45RA+)

description:
count.txt
P3_FC DNT

source_name: spleen

value: spleen


title: HIV CD4 med_H52

source_name: HIV CD4 med_H52


title: HIV CD4 med_H55

source_name: HIV CD4 med_H55


title: HD6 cDNT (CD3+TCRab+CD4-CD8- NOT CD38+CD45RA+)

description:
count.txt
HD6_cDNT


title: patient 6 FC DNT (CD3+TCRab+CD4-CD8-CD38+CD45RA+)

description:
count.txt
P6_FC DNT


title: HD4 cDNT (CD3+TCRab+CD4-CD8- NOT CD38+CD45RA+)

description:
count.txt
HD4_cDNT


title: wt, hippocampus bio rep 2

city: Hershey

first: Nuno

last: Raimundo

state: PA

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

description: gene expression data from cerebellum of wt mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 60C on mouse chip. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix scanner

data_processing: The data were analyzed with GCOS 4.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.  For statistical analysis, unicaudal t-test p<0.05 was used.

source_name: hippocampus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue type

value: hippocampus

value: 24 months

tag: genome/variation

value: wild type


title: mutant Twinkle overexpressor, hippocampus bio rep 3

description: gene expression data from cerebellum of mice overexpressing mutant Twinkle

value: 21 months

value: mutant Twinkle overexpressor


title: mutant Twinkle overexpressor, hippocampus bio rep 4


title: mutant Twinkle overexpressor, hippocampus bio rep 2


title: mutant Twinkle overexpressor, hippocampus bio rep 1


title: wt, hippocampus bio rep 4

value: 23 months


title: wt, hippocampus bio rep 1

value: 26 months


title: HEK293T NSUN6 KO rep2

description:
HT-2_combined
processed data file: 293T_NSUN6_KO.csv

data_processing:
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were mapped to Ensembl GRCh37.75 genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only0. Unmapped reads were further mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to the same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with a custom script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts.
Custom scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at certain C-cutoff (mostly at 2-5) and (v) one-side binomial P value < 0.001
Genome_build: hg19
Supplementary_files_format_and_content: CSV for the position, coverage, and methylation level for the samples

source_name: HEK293T NSUN6 KO

growth_protocol: Cell lines were maintained in DMEM (Gibco) supplemented with 10% FBS (HyClone).

extract_protocol:
Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit; for cytoplasm/nuclear fractions, cells were fractionated using the PARIS kit (Ambion) according to the manufacturer’s instructions. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. The converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

tag: cell line background

tag: genotype

value: NSUN6 knockout

tag: transfected vector


title: HEK293T NSUN6 KO


title: wt, cerebellum bio rep 4

source_name: cerebellum

value: cerebellum

tag: age


title: HIV CD4 med_H47

source_name: HIV CD4 med_H47

value: HIV CD4 med


title: HIV CD4 med_H46

source_name: HIV CD4 med_H46


title: wt, hippocampus bio rep 3


title: HIV CD4 med_H48

source_name: HIV CD4 med_H48


title: HIV CD4 med_H44

source_name: HIV CD4 med_H44


title: mutant Twinkle overexpressor, cerebellum bio rep 4


title: HEK293T nuclear BS

value: wildtype


title: wt, cerebellum bio rep 1


title: wt, cerebellum bio rep 2


title: mutant Twinkle overexpressor, cerebellum bio rep 3


title: HIV CD4 med_H41

source_name: HIV CD4 med_H41


title: wt, cerebellum bio rep 3


title: HIV CD4 med_H40

source_name: HIV CD4 med_H40


title: mutant Twinkle overexpressor, cerebellum bio rep 1


title: mutant Twinkle overexpressor, cerebellum bio rep 2


title: HEK293T rescue NSUN6 K159AR181A rep2

value: NSUN6 K159AR181A