title: Hyb_TDH3pr_freeMNase_clone2_1

city: Rehovot

first: Gat

last: Krieger

address: Herzl St 234

institute: Weizmann Institute of Science

data_processing:
Adapter trimming: Fastq reads were trimmed from adaptors with cutadapt (Martin, 2011)
Read alignment: Trimmed reads were aligned to a the hybrid genome using bowtie2 (Langmead and Salzberg, 2012) with the parameters: [-p8 --local --very-sensitive --trim-to 40 --dovetail --score-min G,16,8]. The hybrid genome is a concatenation of the genomes of S. cerevisiae S288c (R64-1-1/sacCer3) and S. paradoxus CBS432 (Yue et al., 2017), including the mitochondrial genomes.
Genome coverage: Then, a genome coverage file of the 5’ end of reads was generated using samtools (Li et al., 2009) and bedtools, with the genomcov parameters: [-5 -fs 1].

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: hybrid yeast in liquid culture

growth_protocol: Cultures were grown overnight to saturation in YPD media and diluted into 5 mL of fresh YPD media to reach OD600 of 4 the following morning after ∼10 divisions.

extract_protocol:
Cultures were pelleted at 1500 g and resuspended in 1 mL Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1 × Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF), and then transferred to DNA low-bind tubes (Eppendorf 022431021). Cells were washed twice more in 500 μL Buffer A, pelleted, and resuspended in 150 μL Buffer A containing 0.1% digitonin. Then, cells were transferred to an Eppendorf 96-well plate (Eppendorf 951020401) for permeabilization (30°C for 5 min). CaCl2 was added to a final concentration of 2 mM for 30 seconds. Next, 100 μL of stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA and 1% SDS) were mixed with 100 μL of sample. Proteinase K was then added (5 μL of 20 mg/ml), and incubated at 55°C for 30 min. Nucleic acids were extracted with an equal volume (200 μL) of ultrapure phenol/chloroform/isoamyl alcohol, and ethanol-precipitated (at −80°C for > 1 hour) with 2.5 volumes of cold EtOH 96%, 45 μg Glycoblue and sodium acetate to a final concentration of 20 mM. DNA was centrifuged (4°C for 10 min), washed with EtOH 70% and treated with RNase A in a final concentration of 2.5 mg/ml (37°C for 20 min), followed by another round of DNA cleanup and ethanol precipitation. To enrich for small DNA fragments, reverse 0.8x SPRI clean-up (right-side size selection) was carried out, following by isopropanol SPRI (left-side size selection) of 1.8x SPRI and 5.4x isopropanol. DNA samples were eluted in 20 μL 0.1xTE.
Library preparation was done similarly to a published protocol (Skene and Henikoff, 2017) with specific modifications. End-repair and A-tailing (ERA) of the small DNA fragments was done the following: [T4 DNA ligase buffer (10x), dNTPs (10 mM), ATP (10 mM), 50% PEG 4000, T4 PNK (6 U), T4 DNA Pol (0.3 U), Taq DNA Pol (0.1 μL per sample) with 14.6 μL sample] with the PCR protocol: [lid heated to 60°C , 12°C 15’, 37°C 15’,  58°C 45’]. Samples were cleaned with reverse 0.5x SPRI followed by left-side isopropanol SPRI: 1.3x SPRI (with the previous step reaches to 1.8x SPRI) and 5.4x isopropanol. Indexed adaptors (Blecher-Gonen et al., 2013) were ligated to the DNA using quick ligase (2000 U/μL ,2 μL per sample) and quick ligase buffer (2x), in 20°C for 15 minutes. Clean-up was done: 1.2x SPRI (left-side) followed by addition of 1.2x HXN buffer (24 μL 5 M NaCl, 19.2 μL 50% PEG 8000 and 4.8 μL H2O per sample), reaching 1.6x SPRI. Library amplification was carried out with library-specific enrichment primers [23 μL sample DNA, 2 μL enrichment primers, 25 μL KAPA Hifi PCR mix] with the following PCR protocol: [98°C 45’’ + 16 cycles (98°C 15’’ + 60°C 15’’) + 72°C 1’]. PCR products were cleaned with left-side 1x SPRI. Library concentration was measured with Q-bit, library size distribution was measured with TapeStation. Libraries were sequenced on Illumina NovaSeq and NextSeq500 machines, with a 51-bases paired end reads.
ChEC-seq

tag: transcription factor


title: hyb_cswi5_rep2

status: Public on Apr 29 2022

type: SRA

country: Israel

library_source: genomic

molecule: genomic DNA


title: T-MDA5-HIV1-1

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

library_source: transcriptomic

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 1.2.2 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome.
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
To compute coverage on viruses, Bowtie version 1.2.2 14 , with default parameters, was used for alignment on the reference genomes. Only first base of each read are used as input of genomeCoverageBed from Bedtools 15 . Minus and plus strand coverage are separated by a simple awk command.
For statistical analysis of NGS data, count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0 16 . The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. For each virus, a generalized linear model including the replicate, beads and protein factors as well as the beads x protein interaction was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure 17 and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Supplementary_files_format_and_content: Matrix count for each sample (after genomeCoverageBed)

molecule: total RNA

organism:
Homo sapiens
Human immunodeficiency virus 1

source_name: INPUT RNA extracted on MDA5 protein

growth_protocol: Cells were maintained in DMEM-Glutamax (GIBCO, Thermo Fisher Scientific, Waltham, Massachusetts) supplemented with 10% heat-inactivated FCS (Invitrogen, Thermo Fisher Scientific, Waltham, Massachusetts),100 U/ml/100 mg/ml of Penicillin-Streptomycin (GIBCO), and G418 at 500 mg/ml (#G8168, SIGMA, St. Louis, Missouri).

extract_protocol:
Cells were washed twice with cold PBS and lysed in 6 mL of lysis buffer (20 mM MOPS-KOH [pH 7.4], 120 mM KCl, 0.5% Igepal, 2 mM b-mercaptoethanol), supplemented with 200 U/mL RNasin (Promega) and Complete Protease Inhibitor Cocktail (Roche). Cell lysates were incubated on ice for 20 min, with gentle mixing every 5 min, and then clarified by centrifugation at 16,0003g for 15 min at 4°C. A 250-mL aliquot of each cell lysate was used to perform total RNA purification using TRI Reagent LS [Sigma]). The remaining cell lysate was incubated for 2 hr on a spinning wheel at 4°C with 200 mL StrepTactin Sepharose High Performance beads (GE Healthcare). Beads were collected by centrifugation (1,600 g) for 5 min at 4°C) and washed twice for 5 min on a spinning wheel with 5 mL washing buffer (20mMMOPS-KOH [pH 7.4], 120mMKCl, 2mMb-mercaptoethanol) supplemented with 200 U/mL RNasin and complete protease inhibitor cocktail. Precipitates were eluted using biotin elution buffer (IBA Lifesciences). RNA purification was performed using TRI Reagent LS (T3934; Sigma). RNA was dissolved in 50 mL DNase-free and RNase-free ultrapure water. Extracted RNAs were analyzed using Nanovue (GE Healthcare) and the Bioanalyser RNA nano kit (Agilent Technologies).
Before RNA-seq analysis of total and RLR-bound RNA from virus- and mock-infected cells, depletion of ribosomal RNA was done using the riboZero reagents included in the TruSeq stranded total RNA library prep kit (#20020596, Illumina). NGS libraries were generated following the manufacturer’s protocol. The indexed samples were multiplexed per 4 or 6 and sequenced on a HiSeq2500 sequencer (Illumina) to produce single-ends 65 bases reads, bearing strand specificity.

treatment_protocol: ST-RLR4X4 (tagged) cells were co-cultivated with HIV-1-infected cells MT4C5 cells .5*107 MT4C5 (donor cells) were exposed 150ng (equivalent p24) of HIV-1 NL4.3 for 2hr at 37°C. After washing the virus, the cells were grown for 48h. The infection was monitored by flow cytometry analysis by intracellular Gag staining. Infection was then performed via coculture of ST-RLR4X4 cells and MT4C5 cells at a donor:target cell ratio of 1:1. 24 h post infection, cells were lysed and affinity purification of ST-tagged proteins and RNA extraction was performed as described in DOI: 10.7554/eLife.11275

tag: cell line

tag: genotype/variation

value: MDA5 protein tagged 1-STrEP tag

tag: infection


title: T-RIG-HIV1-2

source_name: INPUT RNA extracted on RIG-I protein

value: RIG-I protein tagged 1-STrEP tag


title: Hyb_TDH3pr_freeMNase_clone1_2


title: T-Cherry-HIV1-2

source_name: INPUT RNA extracted on Cherry protein

value: Cherry protein tagged 1-STrEP tag


title: hyb_pace2_rep2


title: T-LGP2-HIV1-2

source_name: INPUT RNA extracted on LGP2 protein

value: LGP2 protein tagged 1-STrEP tag


title: hyb_cswi5_rep1


title: T-LGP2-HIV1-1


title: T-Cherry-HIV1-1


title: T-Cherry-HIV1-3


title: hyb_cace2_rep1


title: B-RIG-HIV1-3

source_name: OUTPUT RNA extracted on RIG-I protein


title: hyb_cace2_rep2


title: CFKH1_rep2


title: PFKH1_rep2


title: B-dVMV-Ch-2 [B-dVMV-Ch-2_TTAGGC]

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 1.2.2 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome.
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
To compute coverage on viruses, Bowtie version 1.2.2 14 , with default parameters, was used for alignment on the reference genomes. Only first base of each read are used as input of genomeCoverageBed from Bedtools 15 . Minus and plus strand coverage are separated by a simple awk command.
For statistical analysis of NGS data, count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0 16 . The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. For each virus, a generalized linear model including the replicate, beads and protein factors as well as the beads x protein interaction was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure 17 and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Supplementary_files_format_and_content: DESeq2 output

organism:
Homo sapiens
Measles morbillivirus

source_name: OUTPUT RNA extracted on Cherry protein

extract_protocol: Before RNA-seq analysis of total and RLR-bound RNA from virus- and mock-infected cells, depletion of ribosomal RNA was done using the riboZero reagents included in the TruSeq stranded total RNA library prep kit (#20020596, Illumina). NGS libraries were generated following the manufacturer’s protocol. The indexed samples were multiplexed per 4 or 6 and sequenced on a HiSeq2500 sequencer (Illumina) to produce single-ends 65 bases reads, bearing strand specificity.

tag: cell line background

value: measles virus (deltaV)


title: B-RIG-HIV1-1


title: B-RIG-HIV1-2


title: SUT1_rep2


title: SUT1_rep1


title: Hyb_TDH3pr_freeMNase_clone1


title: RGT1_rep2


title: MIG1_rep1


title: B-MDA5-HIV1-3

source_name: OUTPUT RNA extracted on MDA5 protein


title: B-LGP2-HIV1-3

source_name: OUTPUT RNA extracted on LGP2 protein


title: RGT1_rep1


title: B-MDA5-HIV1-1


title: ASH1_rep2


title: B-MDA5-HIV1-2


title: B-LGP2-HIV1-2


title: B-LGP2-HIV1-1


title: ASH1_rep1


title: B-Cherry-HIV1-3


title: B-Cherry-HIV1-2


title: HMS2_rep2


title: B-Cherry-HIV1-1


title: hyb_pace2_rep1


title: HMS2_rep1


title: SKN7_rep1


title: SKN7_rep2


title: SWI4_rep2


title: high_light_1

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

data_processing:
The computational pipeline MARACAS (https://greennetwork.us.es/AlgaeFUN/) was used to determine differentially expressed genes according to a log2FC of ± 1 and a q-value or FDR (False Discobery Rate) threshold of 0.05.
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using HISAT2 (http://daehwankimlab.github.io/hisat2/)
Transcript assembly was performed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Stringtie (http://ccb.jhu.edu/software/stringtie/)
Subsequent data analysis and visualization was performed using the R bioconductor package ballgown (https://www.bioconductor.org/packages/release/bioc/html/ballgown.html)
Assembly: Klebsormidium genome sequence assembly and annotation v1.0 (accession number DF236950)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

organism: Klebsormidium nitens

source_name: liquid culture

growth_protocol: Klebsormidium nitens (strain NIES-2285) was obtained from the National Institute for Environmental Studies (Japan). Cells were grown photoautotrophically in Bold’s Basal Medium  using photobioreactors containing 0.8 L of cell suspension and bubbled with air supplemented with 1% (v/v) CO2 as carbon source. Photobioreactors were continuously illuminated with white light lamps at 50 μE m-2 s-1 and maintained at 20ºC. Defoamer (Antifoam 204) was added to avoid the contamination of the aeration systems. Cultures at exponential phase with 45 μg/ml chlorophyll content were used in our experiments.

extract_protocol:
RNA extraction was performed using mechanical disruption of the frozen cell pellets in a Mini Bead Beater (Biospe Products) with a mixture of 2.7 mm glass beads for filament fragmentation and 0.5 mm glass beads for individual cell lysis (ratio 1/3) in the presence of an extraction buffer consisting of phenol:chloroform (1:1, v/v). Subsequently, RNA was purified using ISOLATE II RNA Plant Kit (Bioline) following manufacturer’s instructions. RNA integrity number (RIN) was computed using an Agilent 2100 Bioanalyzer producing values greater than 8 per sample.
Sequencing libraries were generated according to Illumina TruSeq Stranded mRNA protocol and sequenced on an Illumina NextSeq 500 sequencer producing approximately 17 million 50 nt long reads per sample.

treatment_protocol: Control low light cultures were kept under a control light irradiance of 50 μE m-2 s-1 whereas experimental high light cultures were illuminated for three hours with an irradiance of 1500 μE m-2 s-1. Cells were collected by centrifugation at 3500xg for 5min at 4ºC. Cell pellets were washed with PBS, flash frozen with liquid Nitrogen and stored at -80ºC until RNA extraction.

tag: strain

tag: light irradiance


title: low_light_2


title: high_light_2


title: CKO replicate 4

city: Nashville

first: EDWARD

middle: M

last: LEVINE

state: TN

address: 1161 21st Ave S

department: Vanderbilt Eye Institute

country: USA

institute: Vanderbilt University Medical Center

description:
poly-A selection
10552_8

data_processing:
Data alignment was performed with TopHat 2 (Trapnell et al., 2009)
Gene quantification into FPKM was done with Cufflinks (Trapnell et al., 2010)
Additional read count per gene was generated using HTSeq (Anders et al., 2015)
Genome_build: MM10

organism: Mus musculus

source_name: retina

extract_protocol:
Retina tissue was rapidly dissected from all other tissues and flash frozen in liquid nitrogen. Total RNA was isolated using QIAshredder columns and RNeasy Micro kit (Qiagen, Cat#79654 and 74004).
Illumina TruSeq RNA Library Kit V2 with poly(A) selection; 50 cycle single end sequencing on Illumina Hi-Seq 2000 platform

treatment_protocol: ~0.15-0.2 mg/gram body weight of tamoxifen was gavage fed to pregnant dams at embryonic day 11.5 as predicted by single night matings.

tag: developmental stage

tag: treatment

value: tamoxifen

tag: stage of treatment

tag: condition

value: CKO


title: SWI4_rep1


title: MBP1_rep2


title: MBP1_rep1


title: P10 t+3

type: RNA

city: Bologna

first: Gloria

last: Ravegnini

state: BO

address: via irnerio 48

department: PHARMACY AND BIOTECHNOLOGY

country: Italy

institute: UNIVERSITY OF BOLOGNA

description:
Test
SAMPLE 10 (t+3)

data_processing:
miRNAs with Ct>35 were considered as not expressed and excluded from further analysis.
Matrix normalized worksheet reports normalized signals. The normalization was performed according to the manufacturers instructions and array data were normalized using the average of hsa-miR-16-5p (Assay ID: 477860_mir) as endogenous control and after the review of the Literature and the assessment of its stability in our study cohort.
Those miRNAs changing significantly (p-value at Student’s t-test≤0.05) in the two time points before starting treatment (t-3 and t0) were excluded in order to not consider those miRNAs changing for other causes independent of GH treatment.
Fold Change worksheet reports the fold change of each single miRNA. Fold change is expressed as log22-DDCt where -DDCt was calculated as - [(DCt miRNA at t+3) - (DCt miRNA at baseline)]
DCT=(Ct miRNA) - (Ct miR-16-5p);  DDCT =(DCt miRNA at t+3) - (DCt miRNA at baseline); Fold Change=log22-DDCt

label: FAM

organism: Homo sapiens

source_name: serum

label_protocol: 2 μl of RNA eluate was reverse transcribed to cDNA, using TaqMan Advanced miRNA cDNA synthesis kit (Applied Biosystems Cat No. A28007) in the Thermal Cycler T100 (Biorad).  The cDNAs were then amplified using the Universal miR-Amp Primers and Master Mix, contained in the kit and following the manufacturer’s protocol, to uniformly increase the amount of cDNA for each target, maintaining the relative differential expression levels.

extract_protocol: Whole blood was drawn in BD Vacutainer Serum Separator Tubes and serum was obtained by centrifugation at 2000 g for 10 min at 4°C. Total RNA was isolated from 400 μl of serum using miRVana PARIS kit (Invitrogen Cat No. AM1556) according to the manufacturer’s protocol.

tag: chronological age

tag: Sex

value: F

tag: time point

tag: disease

value: IIGHD


title: HAP4_rep2


title: low_light_1


title: CKO replicate 2

description:
poly-A selection
10552_6


title: PHO4_rep2


title: CKO replicate 1

description:
poly-A selection
10552_5


title: CKO replicate 3

description:
poly-A selection
10552_7


title: P9 t+3

description:
Test
SAMPLE 9 (t+3)


title: HAP4_rep1


title: PHO4_rep1


title: P7 t+3

description:
Test
SAMPLE 7 (t+3)

value: M


title: DOT6_rep2


title: RAP1_rep1


title: P6 t+3

description:
Test
SAMPLE 6 (t+3)


title: RAP1_rep2


title: Control replicate 2

description:
poly-A selection
10552_2

value: control


title: DOT6_rep1


title: MIG1_rep2


title: Control replicate 3

description:
poly-A selection
10552_3


title: REB1_rep4


title: REB1_rep2


title: P5 t+3

description:
Test
SAMPLE 5 (t+3)


title: ABF1_rep2


title: Control replicate 4

description:
poly-A selection
10552_4


title: REB1_rep1


title: P4 t+3

description:
Test
SAMPLE 4 (t+3)


title: Control replicate 1

description:
poly-A selection
10552_1


title: Root, 4h_MBZ, rep4

city: La Jolla

first: Ling

last: Zhang

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were trimmed for adaptors and masked for low-quality sequence
RNA-Seq read were mapped to A. thaliana reference genome (TAIR10) using STAR 2.7.0a
Differentially expressed genes were detected by edgeR (version 3.36.0)
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include FPKM values for all Samples
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
Samples were grind in liquid nitrogen and RNA was extracted using Quick-RNA Kits (Zymo research).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Root

tag: ecotype

value: MBZ


title: Root, 4h_MBZ, rep3


title: P3 t+3

description:
Test
SAMPLE 3 (t+3)


title: Azacitidine 2

city: Cordoba

first: Antonio

middle: Rodriguez

last: Franco

state: CORDOBA

address: Rabanales. Ed Severo Ochoa

department: Bioquímica y Biología Molecular

institute: Universidad de Córdoba

data_processing:
Sequenced in a Hiseq 4000 Illumina device as 2x100 paired end reads
Analyzed with FastQC. Sequences were filtered and trimmered with Trimmomatic when required
A multifasta file containing the coding sequences (cds) of Fragara vesca v4.0a1 was used as reference for the mapping
The fastq files were mapped with the Kallisto program
The command line used with Kallisto is described into the run_info.json text file included in each of the processed data files directory
After mapping, the abundance.h5 files were imported into R with the tximport package and analyed with DESeq2.
A threshold with a padj value <0.01 and a Log2Foldchange >=2 or <=-2 was used to obtain the up and down-regulated set of DE genes
Genome_build: Fragaria vesca v4.0a1 obtained from https://www.rosaceae.org
Supplementary_files_format_and_content: Kallisto abundance

organism: Fragaria x ananassa

source_name: fruit receptacke

growth_protocol: Green strawberry fruits were harvested from plants growing in thefield.  Then, unripen and green fruits were removed with their pedicels and grown in MS media

extract_protocol:
Tissue was grounded with a morter and pestle under liquid nitrogen. Then RNA was isolated according protocols already published by our laboratory
mRNA was isolated using poly(T) magnetic beads. Stranded libraries were constructed using the dUTP TrueSeq Illumina protocol

treatment_protocol: For each fruit, a half was treated by injecting 0,5ml of 0.1mM azacitidine disolved in water The other half of the same fruit was injected with water and used as control

tag: agent

value: Injected with 0.1mM azacitidine


title: ABF1_rep1

tag: transcription factor


title: Azacitidine 3


title: P8 t+3

description:
Test
SAMPLE 8 (t+3)


title: P2 t+3

description:
Test
SAMPLE 2 (t+3)


title: Control 3

value: Injected with water


title: Control 2


title: Root, 4h_MBZ, rep2


title: P1 t+3

description:
Test
SAMPLE 1 (t+3)


title: Root, 4h_MBZ, rep1


title: Control 1


title: P9 t0

description:
Test
SAMPLE 9 (t0)


title: Root, DMSO, rep4

value: DMSO


title: Root, DMSO, rep3


title: P120

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
Base calling and demultiplexing of the Bcl2 files was performed using the bcl2fastq program.
Indexing of the human reference genome (hg38/GRCh38) was done using STAR (Spliced Transcripts Alignment to a Reference).
The resulting fastq files were aligned and uniquely mapped reads were counted and mapped to annotated exons using data from UCSC (University of Santa Cruz) genome browser (http://genome.ucsc.edu/) as reference.
Read counts were normalized to counts per million (CPM) and log2 scale with the edgeR package in Bioconductor.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: Comma seperated files with raw gene counts and TMM-CPM-log2 normalized values respectively for each gene in each sample
Supplementary_files_format_and_content: Comma seperated file with metadata,

source_name: Ectocervix

extract_protocol:
The ectocervical biopsies that were stored in RNA-later were thawed and RNA was isolated and purified using AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) and the QIAcube Connect (QIAGEN). Poly-A containing mRNA transcripts were purified, fragmented and converted to cDNA. The cDNA fragments were amplified, barcoded and sequenced using NextSeq 550 (Illumina, San Diego, CA, USA). All ectocervical biopsies displayed good quality of isolated RNA and generated >10 million reads each.
We used the low sample (LS) library prep workflow from the TruSeq Stranded mRNA Reference Guide (1000000040498 v00). The samples were split into six seperate runs and sequenced with single end 75 bp reads

tag: design

value: DMPA

tag: subjectid

value: female


title: P119


title: P121


title: H9 naïve hTSC Organoid 1

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
Raw sequencing data were converted to fastq format using the cellranger mkfastq command (v.5.0.0).
scRNA-seq reads were aligned to the GRCh38 (hg38) reference genome and quantified using the cellranger count command.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files contain matrix with counts, barcodes and features provided as standard output by cellranger.

source_name: Naïve hTSC

growth_protocol: hTSCs were isolated from 2D culture and transferred into a matrigel droplet supplemented with trophoblst organoid medium. Medium changed daily for 10 days before single cell isolation.

extract_protocol:
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.
GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits (v3 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3’ GEM, Library and Gel Bead Kit v3 (PN-1000075), Chromium Single Cell B Chip Kit (PN-1000153), and Dual Index Kit TT Set A (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.
Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 28x10x10x150 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library

tag: source cell type

value: Naive hTSC

tag: culture condition

value: Turco Trophoblast Organoid Medium

tag: passage


title: P114


title: P115


title: P8 t0

description:
Test
SAMPLE 8 (t0)


title: P116


title: Root, DMSO, rep2


title: P6 t0

description:
Test
SAMPLE 6 (t0)


title: Azacitidine 1


title: P112


title: P111


title: P5 t0

description:
Test
SAMPLE 5 (t0)


title: P4 t0

description:
Test
SAMPLE 4 (t0)


title: P109


title: CT30 primary hTSC Organoid 1

source_name: Primary placenta derived hTSC

value: Primary placenta derived hTSC


title: P10 t0

description:
Test
SAMPLE 10 (t0)


title: P3 t0

description:
Test
SAMPLE 3 (t0)


title: P113


title: P107


title: P110


title: P103


title: P102


title: P2 t0

description:
Test
SAMPLE 2 (t0)


title: P7 t0

description:
Test
SAMPLE 7 (t0)


title: Podocytes, NCK1/2 knockout, rep 2

city: Guelph

first: Nina

last: Jones

state: ON

address: 50 Stone Rd E

department: Molecular and Cellular Biology

country: Canada

institute: University of Guelph

description: Gene expression data from NCK1/2 knockout podocytes

hyb_protocol: cDNA was hybridized for 16 hrs at 45˚C on Affymetrix GeneChip MTA 1.0 array plate. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Fluidics Scripts FS450_001) at The Centre for Applied Genomics, Toronto, Ontario.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 at The Centre for Applied Genomics, Toronto, Ontario.

data_processing:
The probe set data was generated and processed using R/BioConductor (version 3.0) packages affy (version 1.44.0) and affyPLM (version 1.42.0).
RMA-normalized intensity values calculated from probe level data.

label: Biotin

source_name: Mouse podocytes

label_protocol: 5.5 ug of cDNA was labelled with biotin allonamide triphosphate according to the standard Affymetrix protocol at The Centre for Applied Genomics, Toronto, Ontario.

growth_protocol: Conditionally immortalized mouse podocyte cells were differentiated for 10 days on type I collagen.

extract_protocol: Total RNA was extracted using Trizol according to manufacturer's instructions.

tag: genotype

value: NCK1/2 knockout

tag: cell type

value: podocytes


title: P1 t0

description:
Test
SAMPLE 1 (t0)


title: Podocytes, NCK1/2 knockout, rep 3


title: P098


title: Root, DMSO, rep1

tag: treatment


title: P097


title: P10 t-3

description:
Test
SAMPLE 10 (t-3)


title: P096


title: P108


title: P095


title: P9 t-3

description:
Test
SAMPLE 9 (t-3)


title: dhgd-1(tm6671)_B12_rep7 [s28]

city: Worcester

first: Olga

last: Ponomarova

state: MA

address: 386 Plantation Street

institute: UMass Chan Medical School

data_processing:
Homemade python script was used for demultiplexing
Sequenced reads were trimmed using trimmomatic-0.32
Trimmed reads were aligned to the reference genome using STAR with the following parameters: —runThreadN 4 --alignIntronMax 25000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Features were counted by ESAT (Derr et al Genome Res. 2016) with parameter “-task score3p -wLen 100 -wOlap 50 -wExt 1000 -sigTest .01 -multimap normal -scPrep -umiMin 1”. Features in “c_elegans.PRJNA13758.WS271.canonical_geneset.gtf” were used as the annotation table input for ESAT, but pseudogenes were discard
Assembly: c_elegans.PRJNA13758 (WormBase WS271)
Supplementary files format and content: comma dilimeted file containing read count matrix for all samples and all genes

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans strains were cultured on nematode growth medium (NGM) seeded with E. coli OP50 at 20 C.

extract_protocol:
Animals were treated with SDS-DTT to break cuticle and bodies (excluding eggs) were lysed for RNA extraction. Total RNA was extracted using RNeasy mini extraction kit (Qiagen).
A modified Celseq2 protocol was used.

treatment_protocol: Nematode growth medium was supplemented with 64 nM adenosylcobalamin (vitamin B12) when specified.

value: whole organism

value: vitamin B12

tag: biological replicate


title: dhgd-1(tm6671)_control_rep7 [s27]


title: P100


title: Podocytes, NCK1/2 knockout, rep 1


title: Podocytes, wildtype, rep 3

description: Gene expression data from Wildtype podocytes

value: Wildtype


title: Podocytes, wildtype, rep 1


title: P094


title: Podocytes, wildtype, rep 2


title: P8 t-3

description:
Test
SAMPLE 8 (t-3)

tag: chronological age

value: F

value: IIGHD


title: dhgd-1(tm6671)_B12_rep6 [s22]


title: P7 t-3

description:
Test
SAMPLE 7 (t-3)

tag: Sex

value: M


title: P092


title: P091


title: P099


title: P093


title: P088


title: dhgd-1(tm6671)_control_rep6 [s21]

value: control


title: P5 t-3

description:
Test
SAMPLE 5 (t-3)

tag: time point


title: P6 t-3

description:
Test
SAMPLE 6 (t-3)

tag: disease


title: dhgd-1(tm6671)_control_rep5 [s15]

tag: tissue


title: P4 t-3

description:
Test
SAMPLE 4 (t-3)


title: P085


title: P051


title: P3 t-3

description:
Test
SAMPLE 3 (t-3)


title: P101


title: dhgd-1(tm6671)_control_rep2 [olga11]


title: P2 t-3

description:
Test
SAMPLE 2 (t-3)


title: P1 t-3

description:
Test
SAMPLE 1 (t-3)


title: WT_control_rep7 [s25]

value: WT


title: WT_B12_rep6 [s20]


title: WT_B12_rep7 [s26]


title: dhgd-1(tm6671)_control_rep1 [olga5]


title: Rig-T-D4-4

organism:
Homo sapiens
dengue virus type 4

source_name: INPUT RNA extracted on RIG-I protein

extract_protocol:
Cells were washed twice with cold PBS and lysed in 6 mL of lysis buffer (20 mM MOPS-KOH [pH 7.4], 120 mM KCl, 0.5% Igepal, 2 mM b-mercaptoethanol), supplemented with 200 U/mL RNasin (Promega) and Complete Protease Inhibitor Cocktail (Roche). Cell lysates were incubated on ice for 20 min, with gentle mixing every 5 min, and then clarified by centrifugation at 16,0003g for 15 min at 4°C. A 250-mL aliquot of each cell lysate was used to perform total RNA purification using TRI Reagent LS [Sigma]). The remaining cell lysate was incubated for 2 hr on a spinning wheel at 4°C with 200 mL StrepTactin Sepharose High Performance beads (GE Healthcare). Beads were collected by centrifugation (1,600 g) for 5 min at 4°C) and washed twice for 5 min on a spinning wheel with 5 mL washing buffer (20mMMOPS-KOH [pH 7.4], 120mMKCl, 2mMb-mercaptoethanol) supplemented with 200 U/mL RNasin and complete protease inhibitor cocktail. Precipitates were eluted using biotin elution buffer (IBA Lifesciences). RNA purification was performed using TRI Reagent LS (T3934; Sigma). RNA was dissolved in 50 mL DNase-free and RNase-free ultrapure water. Extracted RNAs were analyzed using Nanovue (GE Healthcare) and the Bioanalyser RNA nano kit (Agilent Technologies).
For library preparation TruSeq stranded total RNA library prep kit (#20020596, Illumina) was used. NGS libraries were generated following the manufacturer’s protocol. The indexed samples were multiplexed per 4 and sequenced on a Illumina Hiseq 2500 sequencer (Illumina) to produce single-ends 65 bases reads, bearing strand specificity.

treatment_protocol: ST-RLR and ST-CH cells (5,3 107) were infected with DENV (DV-4)at a fluorescent infectivity unit (FIU) of 0.5 for 24 hr.

tag: cell line background

tag: genotype/variation

value: stably expressing RIG-I protein tagged 1-STrEP tag

tag: infection

value: dengue virus (DV-4)


title: P090

tag: design

value: DMPA


title: WT_control_rep6 [s19]


title: P089

tag: subjectid

value: female


title: dhgd-1(tm6671)_B12_rep5 [s16]


title: Rig-T-D4-3


title: WT_control_rep5 [s13]


title: WT_control_rep2 [olga7]


title: Rig-T-D4-1


title: Rig-B-D4-4


title: P063


title: Rig-B-D4-1


title: WT_B12_rep1 [olga2]


title: MDA-T-D4-4

source_name: INPUT RNA extracted on MDA5 protein

value: stably expressing MDA5 protein tagged 1-STrEP tag


title: T-MV-RIG-3 [T-MV-RIG-3_GGCTAC]

organism:
Homo sapiens
Measles virus strain Schwarz

value: RIG-I protein tagged 1-STrEP tag

value: measles virus (Schwarz)


title: dhgd-1(tm6671)_B12_rep2 [olga12]


title: WT_control_rep1 [olga1]


title: dhgd-1(tm6671)_B12_rep1 [olga6]


title: hyb_pswi5_rep1

source_name: hybrid yeast in liquid culture

tag: transcription factor


title: MDA-T-D4-3


title: hyb_cswi5_rep3


title: T-MV-Ch-3 [T-MV-Ch-3_CGATGT]

source_name: INPUT RNA extracted on Cherry protein

value: Cherry protein tagged 1-STrEP tag


title: T-MV-RIG-1 [T-MV-RIG-1_TAGCTT]


title: hyb_cswi5_rep4


title: T-MV-Ch-2 [T-MV-Ch-2_CAGATC]


title: MDA-B-D4-4


title: PFKH2_rep1


title: WT_B12_rep5 [s14]


title: WT_B12_rep2 [olga8]


title: PFKH2_rep2


title: MDA-B-D4-3


title: CFKH2_rep2


title: Ch-T-D4-4

value: stably expressing Cherry protein tagged 1-STrEP tag


title: Ch-T-D4-3


title: MDA-B-D4-1


title: Ch-T-D4-1


title: Ch-B-D4-4

source_name: OUTPUT RNA extracted on Cherry protein


title: GCR2_rep2


title: Rig-B-D4-3

source_name: OUTPUT RNA extracted on RIG-I protein


title: MDA-T-D4-1


title: B-MV-RIG-2 [B-MV-RIG-2_TGACCA]


title: B-MV-RIG-3 [B-MV-RIG-3_GGCTAC]


title: T-MV-RIG-2 [T-MV-RIG-2_TGACCA]


title: B-MV-RIG-1 [B-MV-RIG-1_TAGCTT]


title: B-MV-Ch-3 [B-MV-Ch-3_CGATGT]


title: MSN2_rep6


title: GCR2_rep1


title: B-MV-Ch-2 [B-MV-Ch-2_CAGATC]


title: B-MV-Ch-1 [B-MV-Ch-1_ATCACG]


title: Ch-B-D4-3


title: MSN2_rep5


title: T-MV-RIG-3 [T-MV-RIG-3_GTGAAA]

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 1.2.2 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome.
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
To compute coverage on viruses, Bowtie version 1.2.2 14 , with default parameters, was used for alignment on the reference genomes. Only first base of each read are used as input of genomeCoverageBed from Bedtools 15 . Minus and plus strand coverage are separated by a simple awk command.
For statistical analysis of NGS data, count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0 16 . The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. For each virus, a generalized linear model including the replicate, beads and protein factors as well as the beads x protein interaction was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure 17 and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Supplementary_files_format_and_content: DESseq2 ouput file

extract_protocol:
Cells were washed twice with cold PBS and lysed in 6 mL of lysis buffer (20 mM MOPS-KOH [pH 7.4], 120 mM KCl, 0.5% Igepal, 2 mM b-mercaptoethanol), supplemented with 200 U/mL RNasin (Promega) and Complete Protease Inhibitor Cocktail (Roche). Cell lysates were incubated on ice for 20 min, with gentle mixing every 5 min, and then clarified by centrifugation at 16,0003g for 15 min at 4°C. A 250-mL aliquot of each cell lysate was used to perform total RNA purification using TRI Reagent LS [Sigma]). The remaining cell lysate was incubated for 2 hr on a spinning wheel at 4°C with 200 mL StrepTactin Sepharose High Performance beads (GE Healthcare). Beads were collected by centrifugation (1,600 g) for 5 min at 4°C) and washed twice for 5 min on a spinning wheel with 5 mL washing buffer (20mMMOPS-KOH [pH 7.4], 120mMKCl, 2mMb-mercaptoethanol) supplemented with 200 U/mL RNasin and complete protease inhibitor cocktail. Precipitates were eluted using biotin elution buffer (IBA Lifesciences). RNA purification was performed using TRI Reagent LS (T3934; Sigma). RNA was dissolved in 50 mL DNase-free and RNase-free ultrapure water. Extracted RNAs were analyzed using Nanovue (GE Healthcare) and the Bioanalyser RNA nano kit (Agilent Technologies).
For library preparation TruSeq stranded total RNA library prep kit (#20020596, Illumina) was used. NGS libraries were generated following the manufacturer’s protocol. The indexed samples were multiplexed per 12 and sequenced on a HiSeq2000 sequencer (Illumina) to produce single-ends 51 bases reads, bearing strand specificity.

treatment_protocol: ST-RLR and ST-CH cells (5x107) were infected at an MOI of 1 for 24 hr with either mesles virus Schwarz or SchwarzdeltaV strains.


title: T-MV-Ch-1 [T-MV-Ch-1_ATCACG]


title: PHD1_rep2


title: T-MV-RIG-2 [T-MV-RIG-2_GTGAAA]


title: CFKH2_rep1


title: SOK2_rep1


title: T-MV-MDA5-3 [T-MV-MDA5-3_CTTGTA]

value: MDA5 protein tagged 1-STrEP tag


title: Adipocyte WT 1

city: Jinan

first: Junjun

last: Liu

address: 18877 Jingshi road

country: China

institute: Shandong First Medical University

data_processing:
We used Hisat2(version:2.0.4) to map the cleaned reads
Stringtie（version:1.3.0) was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using edgeR
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR)
Assembly: mm10
Supplementary files format and content: count and fpkm

source_name: WAT

extract_protocol:
Total RNA was extracted using Rneasy mini kit(Qiagen)
mRNA were purified using poly-T beads and sequenced on the Illumina HiSeq X-ten after QC

treatment_protocol: The WAT were removed from 3 OTUD3 KO mice and 2 WT mice

value: WAT

value: wildtype

value: Adipocyte


title: PHD1_rep1


title: T-MV-RIG-1 [T-MV-RIG-1_GTGAAA]


title: Adipocyte KO 3

value: OTUD3 KO


title: Adipocyte KO 1


title: Adipocyte WT 2


title: PHO2_rep2


title: PHO2_rep1


title: T-MV-MDA5-2 [T-MV-MDA5-2_CCGTCC]


title: Adipocyte KO 2


title: T-MV-LGP2-3 [T-MV-LGP2-3_GCCAAT]

source_name: INPUT RNA extracted on LGP2 protein

value: LGP2 protein tagged 1-STrEP tag


title: T-MV-LGP2-2 [T-MV-LGP2-2_GCCAAT]


title: T-MV-MDA5-1 [T-MV-MDA5-1_CCGTCC]


title: db/m mouse hippocampus

city: Lanzhou

first: renjun

last: lv

address: 222 Tianshui South Road, Chengguan District

institute: lanzhou university

description: Control

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10 (GRCm38)
Supplementary files format and content: barcodes.tsv: gene-barcode counts.
Supplementary files format and content: features.tsv: gene file.
Supplementary files format and content: matrix.mtx: cell barcode file.

source_name: hippocampus

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: background

value: BKS

tag: strain

value: db/m

value: hippocampus

tag: age

value: 18 weeks


title: STB3_rep1


title: TBF1_rep1


title: SOK2_rep2


title: TBF1_rep2


title: Ch-B-D4-1

value: dengue virus (DV-4)


title: FHL1_rep1


title: T-MV-Ch-3 [T-MV-Ch-3_AGTTCC]


title: db/db mouse hippocampus

value: db/db


title: T-MV-Ch-1 [T-MV-Ch-1_TGACCA]


title: FHL1_rep2


title: TOD6_rep2


title: TOD6_rep1


title: B-MV-RIG-2 [B-MV-RIG-2_GTCCGC]


title: 20210309_Mouse_Meninges_SJL_3pr_v3_1

city: Toronto

first: Michelle

last: Zuo

address: 1 King's College Circle

department: Immunology

institute: University of Toronto

description: Meninges D11 post A/T

library_source: transcriptomic single cell

data_processing:
Naïve SJL/J Young mouse: TotalSeq B Hashtag 1    ACCCACCAGTAAGAC
Naïve SJL/J Old mouse: TotalSeq B Hashtag 2    GGTCGAGAGCATTCA
EAE SJL/J Young mouse: TotalSeq B Hashtag 3    CTTGCCGCATGTCAT
EAE SJL/J Old mouse: TotalSeq B Hashtag 4    AAAGCATTCTTCACG
All mice: Anti-PE barcode TGACCAGTTCCGCAT
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as barcode library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10

source_name: Meninges

extract_protocol: Prior to euthanasia, old and young EAE and naïve SJL/J mice were injected intravenously with 3µg of anti-CD45-PE (eBioscience) to label blood-derived and blood vessel-adjacent immune cells. Leptomeninges and cortices were dissected and single-cell suspensions were prepared as previously described. Cells from each individual mouse were stained using BioLegend TotalSeq B hashtags (Hashtags 1-4, CAT#s 155831, 155833, 155835, 155837) and an anti-PE oligonucleotide barcode (BioLegend, CAT#408113). Cells from each compartment (i.e. leptomeninges) were mixed in a 1:1 ratio, resuspended to a concentration of 1,300 cells/µL, and submitted for sequencing on the 10X Genomics platform using 5’ chemistry at the Princess Margaret Genomics Centre in Toronto, ON, Canada.

value: Meninges

tag: cell type

value: All cells

tag: genotype

value: WT SJL/J

value: EAE vs unimmunized

tag: strategy

value: CITE-seq


title: B-MV-MDA5-3 [B-MV-MDA5-3_CAGATC]

source_name: OUTPUT RNA extracted on MDA5 protein

value: MDA5 protein tagged 1-STrEP tag

value: measles virus (Schwarz)


title: 20210224_Mouse_Meninges_SJL_3pr_v3_1

description: Meninges D11 post A/T

tag: treatment


title: H1N1 Day 7, RNA-seq

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

description: 10x Genomics

data_processing:
Alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting were performed using Cellranger with default settings.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
After perfusing PBS 20 ml through the left and right ventricular chambers, mouse lungs were minced and digested. The isolated cells were treated with red blood cell lysis buffer (Biolegend, Cat#: 420301) for 5 minutes to lyse red blood cells. After washing with PBS twice, cells were incubated with DAPI (1 mg/ml) in suspension buffer (Ca2+ and Mg2+ free PBS, 5% BSA, 2mM EDTA) at 4 ºC for 30 mins with gentle tilting. After centrifuging, the lung cells from three mice at Day 7 post-inocuation were mixed and incubated in buffer (Ca2+ and Mg2+ free PBS,10% BSA, 2mM EDTA).  The sample was subjected to single-cell fluorescence-activated cell sorting (FACS) of DAPI- cells (live ECs) in the MoFlow Astrios machine.
The DAPI- lung cells were loaded into a 10x Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium controller using v3 kit according to the manufacturer’s instructions.
Library of lung cells was sequenced on NovaSeq 6000 S4 (~100k reads per cell and per lane 2x150bp Paired-Read) at a depth of ~200,000 reads per cell.

treatment_protocol: The C57BL/6J mice were inoculated with sublethal dose of H1N1 (50 pfu, influenza A/Puerto Rico/8/34) to induce acute viral lung injury with a 30% mortality.

value: lung

value: Endothelial cells


title: B-MV-RIG-3 [B-MV-RIG-3_CAGATC]

value: RIG-I protein tagged 1-STrEP tag


title: STB3_rep2

data_processing:
Adapter trimming: Fastq reads were trimmed from adaptors with cutadapt (Martin, 2011)
Read alignment: Trimmed reads were aligned to a the hybrid genome using bowtie2 (Langmead and Salzberg, 2012) with the parameters: [-p8 --local --very-sensitive --trim-to 40 --dovetail --score-min G,16,8]. The hybrid genome is a concatenation of the genomes of S. cerevisiae S288c (R64-1-1/sacCer3) and S. paradoxus CBS432 (Yue et al., 2017), including the mitochondrial genomes.
Genome coverage: Then, a genome coverage file of the 5’ end of reads was generated using samtools (Li et al., 2009) and bedtools, with the genomcov parameters: [-5 -fs 1].

extract_protocol:
Cultures were pelleted at 1500 g and resuspended in 1 mL Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1 × Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF), and then transferred to DNA low-bind tubes (Eppendorf 022431021). Cells were washed twice more in 500 μL Buffer A, pelleted, and resuspended in 150 μL Buffer A containing 0.1% digitonin. Then, cells were transferred to an Eppendorf 96-well plate (Eppendorf 951020401) for permeabilization (30°C for 5 min). CaCl2 was added to a final concentration of 2 mM for 30 seconds. Next, 100 μL of stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA and 1% SDS) were mixed with 100 μL of sample. Proteinase K was then added (5 μL of 20 mg/ml), and incubated at 55°C for 30 min. Nucleic acids were extracted with an equal volume (200 μL) of ultrapure phenol/chloroform/isoamyl alcohol, and ethanol-precipitated (at −80°C for > 1 hour) with 2.5 volumes of cold EtOH 96%, 45 μg Glycoblue and sodium acetate to a final concentration of 20 mM. DNA was centrifuged (4°C for 10 min), washed with EtOH 70% and treated with RNase A in a final concentration of 2.5 mg/ml (37°C for 20 min), followed by another round of DNA cleanup and ethanol precipitation. To enrich for small DNA fragments, reverse 0.8x SPRI clean-up (right-side size selection) was carried out, following by isopropanol SPRI (left-side size selection) of 1.8x SPRI and 5.4x isopropanol. DNA samples were eluted in 20 μL 0.1xTE.
Library preparation was done similarly to a published protocol (Skene and Henikoff, 2017) with specific modifications. End-repair and A-tailing (ERA) of the small DNA fragments was done the following: [T4 DNA ligase buffer (10x), dNTPs (10 mM), ATP (10 mM), 50% PEG 4000, T4 PNK (6 U), T4 DNA Pol (0.3 U), Taq DNA Pol (0.1 μL per sample) with 14.6 μL sample] with the PCR protocol: [lid heated to 60°C , 12°C 15’, 37°C 15’,  58°C 45’]. Samples were cleaned with reverse 0.5x SPRI followed by left-side isopropanol SPRI: 1.3x SPRI (with the previous step reaches to 1.8x SPRI) and 5.4x isopropanol. Indexed adaptors (Blecher-Gonen et al., 2013) were ligated to the DNA using quick ligase (2000 U/μL ,2 μL per sample) and quick ligase buffer (2x), in 20°C for 15 minutes. Clean-up was done: 1.2x SPRI (left-side) followed by addition of 1.2x HXN buffer (24 μL 5 M NaCl, 19.2 μL 50% PEG 8000 and 4.8 μL H2O per sample), reaching 1.6x SPRI. Library amplification was carried out with library-specific enrichment primers [23 μL sample DNA, 2 μL enrichment primers, 25 μL KAPA Hifi PCR mix] with the following PCR protocol: [98°C 45’’ + 16 cycles (98°C 15’’ + 60°C 15’’) + 72°C 1’]. PCR products were cleaned with left-side 1x SPRI. Library concentration was measured with Q-bit, library size distribution was measured with TapeStation. Libraries were sequenced on Illumina NovaSeq and NextSeq500 machines, with a 51-bases paired end reads.
ChEC-seq


title: Scramble control

city: wuhan

first: Mengna

state: State...

address: Donghu Road, No. 115, Wuchang District

institute: wuhan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then FPKMs were calculated.
Assembly: Mus_musculus.GRCm38.94
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

source_name: mammary basal cells

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mammary gland

tag: disease state

value: normal

tag: shRNA

value: Scramble control


title: T-MV-Ch-2 [T-MV-Ch-2_TGACCA]

value: Cherry protein tagged 1-STrEP tag


title: H9 naïve hTSC Organoid 2

data_processing:
Raw sequencing data were converted to fastq format using the cellranger mkfastq command (v.5.0.0).
scRNA-seq reads were aligned to the GRCh38 (hg38) reference genome and quantified using the cellranger count command.
Assembly: hg38
Supplementary files format and content: Processed data files contain matrix with counts, barcodes and features provided as standard output by cellranger.

source_name: Naïve hTSC

tag: source cell type

value: Naive hTSC

tag: culture condition

value: Turco Trophoblast Organoid Medium

tag: passage


title: CT30 primary hTSC Organoid 2

source_name: Primary placenta derived hTSC

value: Primary placenta derived hTSC


title: Cdk14-sh

tag: tissue


title: exp2-DE_72h-WT

city: New York

first: Dapeng

last: Yang

state: NY

address: 1275 YORK AVE

institute: Memorial Sloan Kettering Cancer Center

description:
in vitro WT human ESC differentiated to DE at 72h.
cell-meta-data.tsv.gz

data_processing:
FASTQ files from the 14 samples were individually pre-processed with Cell Ranger v6.0.0. The counts were aggregated without depth normalization.
The count matrix was filtered (QC: #transcripts>3000 & #genes>1500 & mito.<12%) and split into two batches: samples 1-4 (experiment 1) and samples 5-14 (experiment 2).
Data normalization, dimensionality reduction, and clustering of each batch was performed using Seurat v4.0.0.
The two batches (i.e. experiments) were integrated using Seurat v4.0.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: The count matrices (tab-delimited tsv files) include raw single-cell RNA-seq counts for each sample.
Supplementary_files_format_and_content: The cell meta-data matrix (tab-delimited tsv file) includes UMAP/FDL embeddings and clusters/annotations visualized in the manuscript.

source_name: Human Embryonic Stem Cells (hESC)

growth_protocol: All differentiation experiments were performed on hESCs grown on vitronectin. 2 days prior to differentiation, hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. Cells were washed with PBS once and differentiated to definitive endoderm (DE) using S1/2 media supplemented with 100 ng/ml Activin A for three days. 5 μM and 0.5 μM CHIR99021 were added at the first and second day, respectively. Endoderm cells were rinsed with 1X DPBS and then exposed to gut tube (GT) culture condition with S1/2 media supplemented with 50 ng/ml of KGF (FGF7) and 0.25mM vitamin C for 2 days. Two conditions were used during the early pancreatic progenitor (PP1) and late pancreatic progenitor (PP2) stage differentiation. Condition 1, Cultures were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1uM retinoic acid (RA) for 2 days (PP1 stage). Cultures were continued with S3/4 media supplemented with 2 ng/ml of FGF7, 0.25 mM vitamin C, 0.1 uM RA, 200 nM LDN, 0.25 uM SANT-1, 100 nM, and 1:200 ITS-X for 4 days to reach PP2 stage. Condition 2, cells were cultured with S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, 1 uM RA, 100 nM LDN, 0.25 uM SANT-1, 200 nM TPB, and 1:200 ITS-X for 2 days (PP1). Cultures were continued with S3/4 media supplemented with 2 ng/ml of FGF7, 0.25 mM vitamin C, 0.1 uM RA, 200 nM LDN, 0.25 uM SANT-1, 100 nM, and 1:200 ITS-X for 4 days to reach PP2 stage. S1/2 media: MCDB 131 medium further supplemented with 1.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM Glucose, 0.5% BSA. S3/4 media: MCDB 131 medium further supplemented with 2.5 g/l sodium bicarbonate, 1× Glutamax, 10 mM Glucose, 2% BSA.

extract_protocol:
Single cells were counted and diluted to a final concentration in PBS-/- + 0.04% BSA and then load into Single Cell Master Mix (10x Genomics). Cellular suspensions were loaded on a Chromium Controller targeting a 5,000–7,000 cell range collection.
Single-cell 3′ RNA-seq libraries were generated following the manufacturer’s instructions (10x Genomics Chromium Single Cell 3′ Reagent Kit v3 User Guide). cDNA libraries were then quantified on the Agilent Bioanalyzer with a high-sensitivity chip (Agilent), and Kapa DNA quantification kit for Illumina platforms (Roche). Sequencing setup is following the manufacturer’s instructions (10x Genomics Chromium Single Cell 3′ Reagent Kit v3 User Guide).

tag: hhex status

value: WT

tag: Stage

value: DE (Definitive Endoderm) at 72h


title: B-MV-MDA5-2 [B-MV-MDA5-2_ATGTCA]

tag: cell line background

tag: genotype/variation

tag: infection


title: young brain, sham, 24hours, biol rep3

city: Chongqing

first: Xinhui

last: Li

address: NO1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using in-house perl scripts.
Trimmed sequence reads were mapped to GRCm38.p6 using HISAT2 software (http://daehwankimlab.github.io/hisat2/).
Read count extraction and normalization were performed using FeatureCounts (http://subread.sourceforge.net/).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Perihematomal tissues in ipsilateral caudate putamen

extract_protocol:
RNA was harvested using TRIzol reagent. 3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: developmental stage

value: 8-10 weeks

tag: Sex

value: male

value: saline injection sham controls

tag: disease

value: sham controls

tag: disease stage

value: 24 hours after intracerebral hemorrhage


title: young brain, sham, 24hours, biol rep2

value: Perihematomal tissues in ipsilateral caudate putamen

tag: genotype


title: exp2-DE_60h-WT

description:
in vitro WT human ESC differentiated to DE at 60h.
cell-meta-data.tsv.gz

value: DE (Definitive Endoderm) at 60h


title: young brain, sham, 24hours, biol rep1

tag: treatment


title: B-MV-LGP2-3 [B-MV-LGP2-3_AGTCAA]

city: Paris

first: Rachel

address: 28, rue du docteur Roux

institute: Institut Pasteur

source_name: OUTPUT RNA extracted on LGP2 protein

value: LGP2 protein tagged 1-STrEP tag

value: measles virus (Schwarz)


title: exp2-PP2-HHEX_KO-cond2

description:
in vitro HHEX KO human ESC differentiated to PP2 under condition 2.
cell-meta-data.tsv.gz

value: HHEX KO

value: PP2 (Late Pancreatic Progenitor)


title: young brain, ICH, 24hours, biol rep3

value: type Ⅳ collagenase-induced intracerebral hemorrhage

value: Intracerebral hemorrhage


title: exp2-PP2-HHEX_KO-cond1

description:
in vitro HHEX KO human ESC differentiated to PP2 under condition 1.
cell-meta-data.tsv.gz


title: young brain, ICH, 24hours, biol rep2


title: T-MV-LGP2-1 [T-MV-LGP2-1_GCCAAT]


title: young brain, ICH, 24hours, biol rep1


title: B-MV-LGP2-1 [B-MV-LGP2-1_ACAGTG]


title: B-MV-RIG-1 [B-MV-RIG-1_GTCCGC]

value: RIG-I protein tagged 1-STrEP tag


title: exp2-PP2-WT-cond2

description:
in vitro WT human ESC differentiated to PP2 under condition 2.
cell-meta-data.tsv.gz


title: aged brain, sham, 24hours, biol rep3

value: 20-22 months


title: B-MV-Ch-2 [B-MV-Ch-2_CGATGT]

value: Cherry protein tagged 1-STrEP tag


title: aged brain, sham, 24hours, biol rep2

value: WT


title: aged brain, sham, 24hours, biol rep1


title: exp2-PP1-HHEX_KO-cond1

description:
in vitro HHEX KO human ESC differentiated to PP1 under condition 1.
cell-meta-data.tsv.gz

value: PP1 (Early Pancreatic Progenitor)


title: exp2-PP1-WT-cond2

description:
in vitro WT human ESC differentiated to PP1 under condition 2.
cell-meta-data.tsv.gz


title: B-MV-Ch-1 [B-MV-Ch-1_CGATGT]


title: aged brain, ICH, 24hours, biol rep2

value: male


title: B-MV-MDA5-1 [B-MV-MDA5-1_ATGTCA]

value: MDA5 protein tagged 1-STrEP tag


title: exp2-PP1-WT-cond1

description:
in vitro WT human ESC differentiated to PP1 under condition 1.
cell-meta-data.tsv.gz


title: aged brain, ICH, 24hours, biol rep1


title: exp1-GT-HHEX_KO

description:
in vitro HHEX KO human ESC differentiated to GT.
cell-meta-data.tsv.gz

value: GT (Gut Tube)


title: exp1-GT-WT

description:
in vitro WT human ESC differentiated to GT.
cell-meta-data.tsv.gz


title: h96WMJA1

city: Yangzhou

first: chen

last: xiang

address: 48 wenhui eastroad, Yangzhou, Jiangsu , China

institute: Yangzhou University

description: Pepino

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using Hisat2v2.0.5
Supplementary_files_format_and_content: FPKM,expected number of Fragments Per Kilo base of transcript sequence per Millions base pairs sequenced,considers the effect of  sequencing depth and gene length for the reads count at the same time

organism: Cucumis sativus

source_name: hypocotyl

extract_protocol:
hypocotyls were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pepino


title: h96WMJA3

description: Pepino


title: Microglia_KO1

city: Montreal

first: Stephane

last: Richard

address: 3755 Côte Ste-Catherine Road

institute: McGill University

data_processing:
Cell barcodes and UMI (unique molecular identifiers) barcodes were demultiplexed and paired-end reads were first aligned to the mouse genome (mm10) using the Cell Ranger software v3.1.0
Pre-processing was then carried out with the Seurat v3.2.0 R package (Butler et al., 2018). Genes detected in less than 3 cells as well as cells containing less than 200 genes detected were removed.
Cells were further filtered out for each sample based on the distribution of genes detected as well as the percentage of mitochondrial counts to balance the number of cells per sample to ~4000, and the raw count matrices of all samples were merged. Read counts for each cell were then normalized by the cell total, multiplied by 10000 and natural-log transformed.
The expression of the 2000 genes with highest cell-to-cell variation was standardized and the heterogeneity associated with mitochondrial contamination was regressed out. Principal component analysis was performed on the scaled data and the top 10 principal components were used to construct a K-nearest neighbor cell graph. Clustering of cells was carried out through the Louvain algorithm with the granularity parameter set to 0.4 and visualized with the Uniform Manifold Approximation and Projection (UMAP) (Becht et al., 2019) dimensional reduction technique using the Scanpy v1.5.2 python module (Wolf et al., 2018).
Cluster biomarkers were identified using the Wilcoxon Rank Sum test. Cell trajectories across pseudotime were analyzed by the Monocle v2.16.0 R package (Trapnell et al., 2014). Cell progress was defined by differentially expressed genes based on the clusters identified by Seurat. The dimensionality of the data was reduced through the Discriminative Dimensionality Reduction with Trees (DDRTree) algorithm to two dimensions and the cells were ordered along the trajectory according to pseudotime. Genes with branch-dependent expression were identified through the branched expression analysis modeling (BEAM) test. RNA velocity analysis was performed by the scVelo v0.2.2 python module (Bergen et al., 2020). Spliced and unspliced mRNAs were first distinguished through the velocyto v0.17.17 python module (La Manno et al., 2018). Velocities representing the direction and speed of cell motion were then computed and projected onto the UMAP embedding.
Assembly: mm10
Supplementary files format and content: mtx

source_name: FACS sorted quiescent microglia

growth_protocol: Microglia were FACs purified using CD11b and CD45 markers

extract_protocol: scRNA libraries were generated using the GemCode Single- Cell Instrument (10x Genomics, Pleasanton, CA, USA) and Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit (P/N 120236 P/N 120237 10x Genomics). The sequencing ready libraries were purified with SPRIselect, quality controlled for sized distribution and yield (LabChip GX Perkin Elmer), and quantified using qPCR (KAPA Biosystems Library Quantification Kit for Illumina platforms P/N KK4824) as previously described(Couturier et al., 2020). Libraries were subsequently shipped and sequenced using Illumina NovaSeq6000 at IGM Genomics Center, UCSD, San Diego, CA.

treatment_protocol: Cuprizone 0.2% diet was given to 5-6weeks old mice for 5 weeks

value: microglia

value: Cuprizone 0.2% diet


title: Microglia_WT1

value: wild type


title: B-MV-LGP2-2 [B-MV-LGP2-2_ACAGTG]

last: Legendre

value: LGP2 protein tagged 1-STrEP tag

value: measles virus (Schwarz)


title: B-MV-Ch-3 [B-MV-Ch-3_AGTCAA]


title: h96WMJA2

description: Pepino


title: h96WETH2

description: Pepino


title: exp2-PP2-WT-cond1

description:
in vitro WT human ESC differentiated to PP2 under condition 1.
cell-meta-data.tsv.gz

value: PP2 (Late Pancreatic Progenitor)


title: h96WETH3

description: Pepino


title: Microglia_KO2


title: h96WNAA3

description: Pepino


title: exp1-DE-WT

description:
in vitro WT human ESC differentiated to DE.
cell-meta-data.tsv.gz

value: DE (Definitive Endoderm)


title: aged brain, ICH, 24hours, biol rep3

value: Perihematomal tissues in ipsilateral caudate putamen

value: type Ⅳ collagenase-induced intracerebral hemorrhage

value: Intracerebral hemorrhage

value: 24 hours after intracerebral hemorrhage


title: day8 RFP+GFP- iTSp4 rep2

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

description: ALPG-promoter-RFP/OCT4-ΔPE-GFP dual repoter

data_processing:
All sequenced reads were checked for quality control by using FastQC (v0.11.9) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.6.6 )with the default parameters.
The processed RNA-Seq reads were mapped to hg38 genome using STAR (v2.5.2b). Refseq genes were quantified to FPKM using Stringtie.
The processed ATAC-Seq reads were mapped to hg38 genome using Bowtie2 (v2.4.1). MACS2(v2.2.7.1) was used to call peaks
Genome_build: hg38
Supplementary_files_format_and_content: text files of counts and FPKM values

source_name: pluripotent stem cells

growth_protocol: For primed-to-naive state transition and prolong culture , cells were cultured in 5iLAF medium containing DMEM/F12: Neurobasal (1:1) (ThermoFisher), 1% N2 supplement (ThermoFisher), 2% B27 supplement (ThermoFisher), 0.5% KnockOut SR (ThermoFisher), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin (Millipore), 20 ng/ml human LIF (Milipore), 8 ng/ml bFGF (Peprotech), 50 mg/ml BSA (Sigma) and the following cytokines and small molecules: 1 mM PD0325901 (Selleck), 0.5 mM SB590885 (Selleck), 1 mM WH-4-023 (Selleck), 10 mM Y-27632 (Selleck), and 20 ng/ml Activin A (Peprotech). For TS induction, cells were cultured in TSC medium containing DMEM/F-12 supplemented with 0.3% BSA (Sigma), 0.2% FBS (ThermoFisher), 1% ITS-X supplement (ThermoFisher), 0.1 mM 2-mercaptoethanol (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin (Millipore), 1.5 μg/ml l-ascorbic acid (Sigma), 5 μM Y27632 (Selleck), 2 μM CHIR99021 (Selleck), 0.5 μM A83-01 (Sigma), 1 μM SB431542 (Selleck), 50 ng/ml EGF (Peprotech) and 0.8 mM valproic acid (VPA) (Sigma). Medium were changed daily, and cells were passaged every 2-4 days using 0.5 mM EDTA (Invitrogen).

extract_protocol:
total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions.
mRNA-seq and ATAC-seq libraries were prepared for sequencing using standard Illumina protocols
mRNA-seq and ATAC-seq

treatment_protocol: For primed-to-naive state transition, 2~3×105 dissociated single cells of RFP; GFP pESCs were seeded on the irradiated feeder layer in conventional ESC medium supplemented with Y-27632 (Selleck, 10 mM). Medium was then switched to 5iLAF medium on the second day, and was changed every day. Intermediate cells were collected at different time points during primed-to-naïve transition.

tag: source

value: H9 primed ESC

tag: library type

value: mRNA-seq

tag: condition

value: TS induction process


title: day8 RFP+GFP- iTSp4 rep1


title: h96WNAA2

description: Pepino


title: Microglia_WT2


title: day8 RFP+GFP- iTSp2 rep2


title: day8 RFP+GFP- iTSp6 rep2


title: day8 RFP+GFP- iTSp6 rep1


title: TWT2 - S7 + TGFb1 #2

city: Bronx

first: Silvia

middle: C

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

data_processing:
Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis. Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (mm10; GRCm38.p6) using TopHat2 algorithm alignment program v.2.0.9.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm.
HTSeq software v.0.6.1 was used to count the number of reads mapped to each gene.
Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length.
Genome_build: mm10
Supplementary_files_format_and_content: .txt file including raw readcounts for every gene and every sample
Supplementary_files_format_and_content: .txt file including FPKM values for every gene and every sample

source_name: Bone Marrow Macrophages

growth_protocol: Tibial Bone Marrow derived Macrophages (BMMs) were obtained from 1-2-month-old inducible Smad7 KO mice or Smad7 fl/fl mice after tamoxifen administration (20 mg/Kg for 5 days). Briefly, bone marrow cells were incubated for 24 h in α+ MEM medium supplemented with 15% fetal calf serum (GIBCO) and 12 ng/ml CSF-1 (R&D systems). Non-adherent primitive mononuclear phagocytes were reseeded in media containing 15% fetal calf serum and CSF-1 (120 ng/ml) for 48 hours, in order to allow their differentiation to adherent macrophages. Cells used for experiments were cultured until confluent, starved in media without serum for approximately 12 hours, and then stimulated  or no.

extract_protocol:
RNA was isolated using TRIzol reagent (Qiagen, #79306) according to manufacterer's instructions.
RNA samples were sent to Novogene (Sacramento, California) to construct a total of eight cDNA libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). Briefly, libraries were prepared using at least 1ug high quality total RNA input per sample. mRNA purification and enrichmes was preformed using oligo(dt)-attached magnetic beads. After fragmentation, double stranded cDNA synthesis was preformed. Sequencing adaptors were ligated and cDNA fragmets were selected (150-200bp), amplified and purified. Library concentration and quality were assessed using a Bioanalyzer 2100 system (Agilent). These librarys were sequenced on Illumina NovaSeq 6000 devices, generating 150 bp paired-end reads.

treatment_protocol: A group of samples (n=4) from each genotype group was treated with TGF-β1 (10 ng/ml) for 4 hours. After this incubation time samples were collected for RNA isolation.

tag: strain

value: Smad7 fl/fl

value: TGF-b1 (10 ng/ml) stimulation for 4 hours

value: Bone Marrow

tag: cell type

value: Macrophages


title: TWT3 - S7 + TGFb1 #3

tag: tissue


title: TWT4 - S7 + TGFb1 #4


title: TWT1 - S7 + TGFb1 #1


title: exp2-PP1-HHEX_KO-cond2

description:
in vitro HHEX KO human ESC differentiated to PP1 under condition 2.
cell-meta-data.tsv.gz

tag: hhex status

value: HHEX KO

value: PP1 (Early Pancreatic Progenitor)


title: day8 RFP+GFP- iTSp2 rep1


title: h96WETH1

description: Pepino

value: Pepino


title: day8 RFP-GFP- iTS11d rep2


title: TS7_3 - S7KO + TGFb1 #3

value: Smad7 fl/fl + CAGGCre-ER


title: TS7_4 - S7KO + TGFb1 #4


title: h96WNAA1

description: Pepino


title: day8 RFP-GFP- iTS11d rep1


title: h96W1

description: Pepino


title: TS7_2 - S7KO + TGFb1 #2


title: day8 RFP-GFP- iTS9d rep2


title: TS7_1 - S7KO + TGFb1 #1


title: day8 RFP-GFP- iTS9d rep1


title: exp1-DE-HHEX_KO

description:
in vitro HHEX KO human ESC differentiated to DE.
cell-meta-data.tsv.gz

tag: Stage


title: day8 RFP-GFP- iTS7d rep2


title: h48WETH3

description: Pepino


title: CWT4 - S7 Ctrl #4

value: untreated


title: CWT2 - S7 Ctrl #2


title: h48WMJA3

description: Pepino


title: day8 RFP-GFP- iTS5d rep1


title: h48WETH2

description: Pepino


title: day8 RFP-GFP- iTS7d rep1


title: h48WMJA2

description: Pepino


title: CWT3 - S7 Ctrl #3


title: h48WMJA1

description: Pepino


title: CWT1 - S7 Ctrl #1


title: day8 RFP-GFP- iTS5d rep2


title: day8 RFP+GFP- iTS11d rep2


title: h48WETH1

description: Pepino


title: h96W3

description: Pepino


title: CS7_4 - S7KO Ctrl #4


title: CS7_3 - S7KO Ctrl #3


title: h48WNAA3

description: Pepino


title: h48WNAA2

description: Pepino


title: day8 RFP+GFP- iTS11d rep1


title: CS7_2 - S7KO Ctrl #2


title: day8 RFP+GFP- iTS9d rep1


title: P7WT3 - S7fl/fl 7d #3

data_processing:
Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis. Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (mm10; GRCm38.p6) using TopHat2 algorithm alignment program v.2.0.9.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm.
HTSeq software v.0.6.1 was used to count the number of reads mapped to each gene.
Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: readcount_genename.txt: Tab-delimited text file includes raw read counts for every gene and every sample.
Supplementary_files_format_and_content: fpkm_genename.txt: Tab-delimited text file includes FPKM values for every gene and every sample.

source_name: Cardiac Macrophages

extract_protocol:
Macrophage and neutrophil cell suspensions were obtained from control and infarcted S7fl/fl and MyS7KO hearts after 3 and 7 days of coronary occlusion. Macrophages were magnetically sorted with a MACS separator (Miltenyi Biotec), obtaining first a Ly6G- cell suspension (No Neutrophils) and second selecting from this suspension the CD11b+ cells. RNA was isolated from Ly6G-CD11b+ cells (Macrophages) using TRIzol reagent (Qiagen, #79306) according to manufacturer's instructions.
RNA samples were sent to Novogene (Sacramento, California) to construct a total of eight cDNA libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). Briefly, libraries were prepared using at least 1ug high quality total RNA input per sample. mRNA purification and enrichment were performed using oligo(dt)-attached magnetic beads. After fragmentation, double stranded cDNA synthesis was performed. Sequencing adaptors were ligated and cDNA fragments were selected (150-200bp), amplified and purified. Library concentration and quality were assessed using a Bioanalyzer 2100 system (Agilent). These libraries were sequenced on Illumina NovaSeq 6000 devices, generating 150 bp paired-end reads.

tag: cell markers

value: Ly6G- CD11b+

value: Cardiac macrophages

value: Myocardial infarction

tag: time point


title: day8 RFP+GFP- iTS7d rep1


title: day8 RFP+GFP- iTS9d rep2


title: CS7_1 - S7KO Ctrl #1


title: day8 RFP+GFP- iTS5d rep1


title: P7KO5 - MyS7KO 7d #5

value: Smad7 fl/fl + LyzM-Cre (MyS7KO)


title: h24WMJA1

description: Pepino


title: P7KO4 - MyS7KO 7d #4


title: primed TSCp10 rep2


title: h48WNAA1

description: Pepino


title: P7KO1 - MyS7KO 7d #1


title: P7WT4 - S7fl/fl 7d #4


title: h48W3

description: Pepino


title: day8 RFP+GFP- iTS7d rep2


title: h48W2

description: Pepino


title: h48W1

description: Pepino


title: day8 RFP+GFP- iTS5d rep2


title: P3WT5 - S7fl/fl 3d #5


title: day8 RFP+GFP- prolong13d rep1

value: prolong culture


title: h24WMJA3

description: Pepino


title: P3WT4 - S7fl/fl 3d #4


title: h96W2

description: Pepino


title: day8 RFP-GFP- prolong13d rep2

value: H9 primed ESC


title: h24WMJA2

description: Pepino


title: P7KO3 - MyS7KO 7d #3


title: primed TSCp10 rep1

value: mRNA-seq


title: day8 RFP-GFP- prolong13d rep1


title: h24WETH2

description: Pepino


title: day8 RFP+GFP- prolong13d rep2


title: P3WT1 - S7fl/fl 3d #1


title: day8 RFP+GFP- prolong7d rep1


title: h24WNAA1

description: Pepino


title: h24WETH1

description: Pepino


title: h24WNAA2

description: Pepino


title: P3WT3 - S7fl/fl 3d #3


title: h24WETH3

description: Pepino


title: h24WNAA3

description: Pepino


title: day8 RFP+GFP- prolong7d rep2


title: P3KO5 - MyS7KO 3d #5


title: h24W3

description: Pepino


title: P3WT2 - S7fl/fl 3d #2


title: day8 RFP-GFP- prolong7d rep2


title: P7WT2 - S7fl/fl 7d #2


title: P3KO3 - MyS7KO 3d #3


title: h24W1

description: Pepino


title: P3KO4 - MyS7KO 3d #4


title: h12WMJA3

description: Pepino


title: P3KO2 - MyS7KO 3d #2


title: day14 RFP+GFP- prolong7d rep1


title: day14 RFP+GFP- prolong7d rep2


title: h12WMJA2

description: Pepino


title: P3KO1 - MyS7KO 3d #1


title: day8 RFP-GFP- prolong7d rep1


title: CWT3 - S7fl/fl #3

value: Control

value: Baseline


title: h12WMJA1

description: Pepino


title: day14 RFP-GFP- prolong7d rep1


title: day14 RFP-GFP- prolong7d rep2


title: CKO3 - MyS7KO #3


title: CWT1 - S7fl/fl #1

value: Smad7 fl/fl


title: CKO2 - MyS7KO #2


title: CWT2 - S7fl/fl #2


title: h12WETH2

description: Pepino


title: h12WETH3

description: Pepino


title: h12WNAA1

description: Pepino


title: h12WNAA3

description: Pepino


title: h12W3

description: Pepino


title: h12WETH1

description: Pepino


title: h24W2

description: Pepino


title: ATAC_PP2_HHEXKO_2

data_processing:
Align to hg19 reference genome using bowtie2 2.3.4.1
Peak calling to generate signal tracks on on individual replicates using macs2 2.1.1.20160309 with options -B -p 1e-2 --nomodel --shift -100 --extsize 200 --scale-to large
Genome_build: hg19
Supplementary_files_format_and_content: Coverage track in bigWig format

source_name: ES-derived progenitors

growth_protocol: ES cells were maintained using complete Essential 8 media, and ES-derived progenitors were generated by differentiation meida described below. When ES cells reach 80 - 90% confluence, directed differentiation was initiated (d0). ES cells were differentiated to day 3 definitive endoderm (DE) stage with 100 ng/ml of Activin A and GSK-3 inhibitor, CHIR-99021. Gut tube (GT) stage was induced by 0.25mM L-Ascorbic acid and 50ug/ml of FGF7 and harvested on day 5. Afterward, 0.25mM L-Ascorbic acid, 50ug/ml of FGF7 and 10mM of retinoic acid were used to generate PDX1+ early pancreatic progenitor 1 (PP1) cells on day 7.

extract_protocol:
50,000 cells were lysed in ATAC lysis buffer and tagmented (Illumina Nextera DNA Library Preparation Kit). After adding SDS, the samples were purified with 2X Agencourt AMPure XP beads (Beckman Coulter A63881)
Samples were amplified using NEBNext Q5 Hot Start HiFi PCR Master Mix. The concentration of samples was checked using PicoGreen and median fragment size was checked using the Agilent D1000 screentape on the Agilent Technologies 2200 TapeStation. Samples were sequenced PE50 on a HiSeq 2500.

tag: differentiation stages

value: Pancreatic progenitor 2

value: HHEX -/-


title: h12W1

description: Pepino

tag: developmental stage


title: H3 - Smad3KO+TGFb1 #3

description: Smad3 KO was documented using qPCR and Western blotting

data_processing:
Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis. Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (mm10; GRCm38.p6) using TopHat2 algorithm alignment program v.2.0.9.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm.
HTSeq software v.0.6.1[22]  was used to count the number of reads mapped to each gene.
Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files including raw readcounts for every gene and every sample
Supplementary_files_format_and_content: Excel files including FPKM values for every gene and every sample

growth_protocol: Tibial BMMs were obtained from 2-3-month-old Smad2fl/fl mice, MyS2KO mice, Smad3fl/fl mice, and MyS3KO mice. Briefly, bone marrow cells were incubated for 24 h in α+ MEM medium supplemented with 15% fetal calf serum (GIBCO), 10% WEHI-3 conditioned media, as a source of interleukin-3, and 12 ng/ml CSF-1 (R&D systems). Non-adherent primitive mononuclear phagocytes were reseeded in media containing 15% fetal calf serum and CSF-1 (120 ng/ml) for 48 hours, in order to allow their differentiation to adherent macrophages. Cells used for experiments were cultured until confluent, starved in media without serum for approximately 16 hours, and then stimulated  or no.

treatment_protocol: A group of samples (n=3) from each genotype group was treated with TGF-β1 (10 ng/ml) for 4 hours. After this incubation time samples were collected for RNA isolation.

value: Smad3 fl/fl + LyzM-Cre (MyS3KO)

value: TGF-b1 (10 ng/ml) stimulation for 4 hours


title: CKO1 - MyS7KO #1


title: H2 - Smad3KO+TGFb1 #2


title: G1 - Smad3KO Ctrl #1


title: H1 - Smad3KO+TGFb1 #1


title: h12W2

description: Pepino

value: Pepino


title: h6WMJA2

description: Pepino


title: F3 - Smad3fl/fl+TGFb1 #3

value: Smad3 fl/fl


title: h6WETH3

description: Pepino


title: ATAC_PP2_WT_2

value: wild type


title: G2 - Smad3KO Ctrl #2

value: untreated


title: ATAC day6 SSEA4+ rep3

value: ATAC-seq

value: primed-to-naive transition


title: ATAC_PP2_HHEXKO_1


title: h6WMJA3

description: Pepino


title: E3 - Smad3fl/fl Ctrl #3


title: F1 - Smad3fl/fl+TGFb1 #1


title: ATAC day6 SSEA4+ rep1


title: G3 - Smad3KO Ctrl #3


title: ATAC_GT_HHEXKO_2

value: Gut tube


title: F2 - Smad3fl/fl+TGFb1 #2


title: ATAC_PP2_WT_1


title: h6WNAA3

description: Pepino


title: ATAC_PP1_HHEXKO_2

value: Early pancreatic progenitor


title: h12WNAA2

description: Pepino


title: ATAC_PP1_WT_2


title: h6WETH2

description: Pepino


title: E1 - Smad3fl/fl Ctrl #1


title: h6WETH1

description: Pepino


title: h6WMJA1

description: Pepino


title: ATAC day6 SSEA4- rep3

value: H9 primed ESC


title: h6WNAA2

description: Pepino


title: ATAC day6 SSEA4- rep2


title: ATAC_PP1_WT_1


title: h6WNAA1

description: Pepino


title: ATAC day6 SSEA4- rep1


title: ATAC_GT_HHEXKO_1


title: ATAC day14 RFP-GFP- rep2


title: E2 - Smad3fl/fl Ctrl #2


title: ATAC day6 SSEA4+ rep2


title: h6W2

description: Pepino


title: D2 - Smad2KO+TGFb1 #2

description: Smad2 KO was documented using qPCR and Western blotting

value: Smad2 fl/fl + LyzM-Cre (MyS2KO)


title: h6W3

description: Pepino


title: h6W1

description: Pepino


title: ATAC day14 RFP-GFP- rep1


title: ATAC day14 RFP+GFP+ rep3


title: PP1_KO_rep2

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

tag: source cell type

value: ES-derived progenitors


title: C3 - Smad2KO Ctrl #3


title: h0ck2

description: Zaoer-N

value: Zaoer-N


title: ATAC day14 RFP+GFP+ rep1


title: PP1_WT_rep2


title: ATAC_GT_WT_1


title: C1 - Smad2KO Ctrl #1


title: ATAC_PP1_HHEXKO_1


title: PP1_WT_rep1


title: ATAC_GT_WT_2


title: ATAC day14 RFP+GFP+ rep2


title: h0ck1

description: Zaoer-N


title: C2 - Smad2KO Ctrl #2


title: h0ck3

description: Zaoer-N


title: D3 - Smad2KO+TGFb1 #3


title: PP1_KO_rep1


title: ATAC day14 RFP+GFP- rep4


title: SG_GFP+_9m_3

city: Groningen

first: Rob

last: Coppes

address: Ant. Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Base-calling: bcl2fastq software (Illumina Inc.) version 2.20.0.422.
QuantSeq 3′ mRNA-Seq analysis: Bluebee (Lexogen) version 015UG108V0311
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: freshly sorted GFP positive murine salivary gland cells from 9 month old H2B-GFP mice

extract_protocol:
RNA was isolated with the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer’s instructions including DNase I treatment
QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)

value: Salivary gland cells

tag: gfp status

value: positive


title: GT_WT_rep1


title: GT_KO_rep2

value: HHEX -/-


title: ATAC day14 RFP+GFP- rep6


title: SG_GFP+_9m_2


title: A3 - Smad2fl/fl Ctrl #3

value: Smad2 fl/fl


title: ATAC day14 RFP+GFP- rep5


title: B1 - Smad2fl/fl+TGFb1 #1

value: TGF-b1 (10 ng/ml) stimulation for 4 hours


title: B3 - Smad2fl/fl+TGFb1 #3


title: ATAC day14 RFP+GFP- rep2


title: ATAC day14 RFP+GFP- rep1


title: A2 - Smad2fl/fl Ctrl #2


title: Ph+AML012

type: genomic

city: Suzhou

first: Wenzhi

last: Cai

address: 296 Shizi Street

institute: The First Affiliated Hospital of Soochow University

description: Ph+AML012, processed data in the file titled "Ph+AML REPORT_ProbeBasedReport Part1&2"

hyb_protocol: Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit (Cat#5188-5380, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 65℃, 20rpm for 40 hours. Array wash was performed using Agilent Oligo aCGH Wash Buffer 1 and 2 set (Cat#5188-5226, Agilent technologies, Santa Clara, CA, US) in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) follow the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US),scan resolution=3μm, PMT 100% to generate tiff image.

data_processing:
Raw data was acquired and normalized(algorithm: LOWESS) using Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).Calculate Z-score for each CNV region using DNA Analytics 4.0.81 software (Agilent technologies, Santa Clara, CA, US), window size is set to 1M and Z-score threshold is set to 4.0.
value definition: Logarithm value(log2) of test/control ratios.

source_name: mononuclear cells of bone marrow at diagnosis

label_protocol: Experimental sample and control sample were labeled with Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US) and Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) respectively, using Agilent Genomic DNA Labeling Kit PLUS (Cat#5188-5309, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions. Labeled DNA fragments were purified using Amicon Ultra-0.5, Ultracel-30 Membrane,30 kDa(Cat#UFC5030BK, Millipore, Billerica, MA, US). Measured the absorbance at A260nm (DNA),A550nm (Cyanine 3),and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.

growth_protocol: Mononuclear cells of fresh bone marrow from each patient were isolated with Ficoll following manufacturer's instructions. Cells were carefully frozen and stored in -80℃ and recovered when used.

extract_protocol: Total DNA were extracted from mononuclear cells with Invitrogen Genomic DNA Mini Kit following manufacturer's instructions. Genomic DNA was digested by two Restriction Enzymes AluI (Cat#R6281, Promega, Madison, WI, US) and RsaI (Cat#R6371, Promega, Madison, WI, US), follow the instructions provided by the manufacture.

tag: subject status

value: Ph+AML

tag: gender

value: M

tag: age

tag: status

value: Alive

tag: months

source_name: mononuclear cells from pooled healthy donors

value: healthy donor

value: mononuclear cells


title: B2 - Smad2fl/fl+TGFb1 #2

tag: genotype

tag: treatment


title: Thy_GFP+_9m_2

source_name: freshly sorted GFP positive murine thyroid gland cells from 9 month old H2B-GFP mice

tag: cell type

value: Thyroid gland cells


title: Thy_GFP+_6m_4

source_name: freshly sorted GFP positive murine thyroid gland cells from 6 month old H2B-GFP mice


title: Thy_GFP+_9m_3


title: A1 - Smad2fl/fl Ctrl #1

tag: strain

value: untreated


title: DE_KO_rep1

value: Definitive endoderm


title: Thy_GFP+_9m_1


title: SG_GFP+_9m_1


title: GT_KO_rep1

value: Gut tube


title: D1 - Smad2KO+TGFb1 #1

value: Smad2 fl/fl + LyzM-Cre (MyS2KO)


title: Ph+AML011

description: Ph+AML011, processed data in the file titled "Ph+AML REPORT_ProbeBasedReport Part1&2"

value: Dead

value: mononuclear cells of bone marrow at diagnosis


title: ATAC day12 RFP-GFP- rep3

tag: source

value: H9 primed ESC

tag: library type

value: ATAC-seq

tag: condition

value: primed-to-naive transition


title: Thy_GFP+_6m_3

value: positive


title: MISTRG_Tumor

city: Cape Town

first: Valentin

last: Voillet

state: Western Cape

address: First Floor Wembley Square, 3 McKenzie St, Gardens

country: South Africa

institute: cape town hvtn immunology laboratory

description:
MISTRG -Tumor - Gene expression
raw_countMatrix.csv

data_processing:
bam files (I6: 8bp - R1: 26bp - R2: 98bp)
Alignment and quantification have been done following the Cell Ranger Software Suite (2.1.0). The Cell Ranger Single-Cell Software Suite (version 2.1.0) was used to perform sample demultiplexing, barcode processing and single-cell 5' gene counting (http://10xgenomics.com/). First, raw base BCL files were demultiplexed using the cellranger mkfastq pipeline into sample-specific FASTQ files. Second, these FASTQ files were processed with the cellranger count pipeline. Each sample was analyzed separately. The Cell Ranger pipeline uses the STAR alignment software (Dobin et al., 2013) to align cDNA reads to the GRCh38 human reference genome. Aligned reads were then filtered for valid cell barcodes and unique molecular identifiers (UMIs). Cell barcodes with 1-Hamming-distance from a list of known barcodes were considered. UMIs with sequencing quality score > 10% and not homopolymers were retained as valid UMIs. A UMI with 1-Hamming-distance from another UMI with more reads, for a same gene and a same cell was corrected to this UMI with more reads. cellranger aggr was then used to aggregate the two samples together. A correction for sequencing depth was performed during the aggregation.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv-delimited table

source_name: Immunodeficient MISTRG mice repopulated with human CD34+ hematopoietic stem and progenitor cells, implanted in flank with human melanoma cell line Me275

extract_protocol:
Tissues we digested with an optimized protocol, and human CD45+ cells were isolated by flow cytometry (tumor) or magnetic enrichment (their tissues)
scRNAseq libraries were prepared with the 10x Genomics’ Chromium Single Cell 3’ Library & Gel Bead Kit v2, following the manufacturer’s protocol, and sequenced on the Illumina HiSeq 2500 instrument

tag: tissue

value: Tumor

value: Human CD45+ cells

tag: cellranger id


title: GT_WT_rep2

value: ES-derived progenitors

tag: differentiation stages

value: wild type


title: ATAC day14 RFP+GFP- rep3


title: ATAC day12 RFP+GFP+ rep3


title: ATAC day12 RFP-GFP- rep1


title: ATAC day12 RFP-GFP- rep2


title: Ph+AML015

description: Ph+AML015, processed data in the file titled "Ph+AML REPORT_ProbeBasedReport Part1&2"

value: Ph+AML

value: M

value: healthy donor


title: Ph+AML010

description: Ph+AML010, processed data in the file titled "Ph+AML REPORT_ProbeBasedReport Part1&2"

value: mononuclear cells


title: Thy_GFP+_6m_2

value: Thyroid gland cells


title: MISTRG_Lung

description:
MISTRG - Lung - Gene expression
raw_countMatrix.csv

value: Lung


title: DE_WT_rep2

tag: source cell type

value: Definitive endoderm


title: Thy_GFP+_3m_4

source_name: freshly sorted GFP positive murine thyroid gland cells from 3 month old H2B-GFP mice

tag: gfp status


title: MISTRG_BoneMarrow

description:
MISTRG - Bone Marrow - Gene expression
raw_countMatrix.csv

value: Bone Marrow


title: DE_KO_rep2

value: HHEX -/-


title: Thy_GFP+_3m_3


title: ATAC day12 RFP+GFP- rep3

value: H9 primed ESC


title: T-RIGI-3

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 1.2.2 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome.
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
For statistical analysis of NGS data, count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0 16 . The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. For each virus, a generalized linear model including the replicate, beads and protein factors as well as the beads x protein interaction was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure 17 and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Supplementary_files_format_and_content: FeatureCounts output

source_name: INPUT RNA extracted on RIG-I protein

extract_protocol:
Cells were washed twice with cold PBS and lysed in 6 mL of lysis buffer (20 mM MOPS-KOH [pH 7.4], 120 mM KCl, 0.5% Igepal, 2 mM b-mercaptoethanol), supplemented with 200 U/mL RNasin (Promega) and Complete Protease Inhibitor Cocktail (Roche). Cell lysates were incubated on ice for 20 min, with gentle mixing every 5 min, and then clarified by centrifugation at 16,0003g for 15 min at 4°C. A 250-mL aliquot of each cell lysate was used to perform total RNA purification using TRI Reagent LS [Sigma]). The remaining cell lysate was incubated for 2 hr on a spinning wheel at 4°C with 200 mL StrepTactin Sepharose High Performance beads (GE Healthcare). Beads were collected by centrifugation (1,600 g) for 5 min at 4°C) and washed twice for 5 min on a spinning wheel with 5 mL washing buffer (20mMMOPS-KOH [pH 7.4], 120mMKCl, 2mMb-mercaptoethanol) supplemented with 200 U/mL RNasin and complete protease inhibitor cocktail. Precipitates were eluted using biotin elution buffer (IBA Lifesciences). RNA purification was performed using TRI Reagent LS (T3934; Sigma). RNA was dissolved in 50 mL DNase-free and RNase-free ultrapure water. Extracted RNAs were analyzed using Nanovue (GE Healthcare) and the Bioanalyser RNA nano kit (Agilent Technologies).
Before RNA-seq analysis of total and RLR-bound RNA from virus- and mock-infected cells, depletion of ribosomal RNA was done using the riboZero reagents included in the TruSeq stranded total RNA library prep kit (#20020596, Illumina). NGS libraries were generated following the manufacturer’s protocol. The indexed samples were multiplexed per 4 and sequenced on a HiSeq2500 sequencer (Illumina) to produce single-ends 65 bases reads, bearing strand specificity.

treatment_protocol: no treatment

tag: cell line

tag: genotype/variation

value: RIG-I protein tagged 1-STrEP tag

tag: infection

value: mock


title: DE_WT_rep1


title: ATAC day12 RFP+GFP- rep2

value: ATAC-seq

value: primed-to-naive transition


title: MISTRG_Liver

description:
MISTRG - Liver - Gene expression
raw_countMatrix.csv

value: Liver

value: Human CD45+ cells


title: ATAC day12 RFP+GFP+ rep2


title: Ph+AML002

description: Ph+AML002, processed data in the file titled "Ph+AML REPORT_ProbeBasedReport Part1&2"

tag: subject status

tag: gender

tag: age

tag: status

value: Alive

value: mononuclear cells of bone marrow at diagnosis


title: ATAC day12 RFP+GFP+ rep1


title: Thy_GFP+_6m_1

tag: cell type

value: positive


title: ATAC day10 RFP-GFP- rep3


title: Ph+MPAL022

description: Ph+MPAL022, processed data in the file titled "Ph+MPAL-1 REPORT_ProbeBasedReport Part1&2"

value: Ph+MPAL

value: F

value: Dead

tag: months

value: healthy donor


title: Ph+MPAL014

description: Ph+MPAL014 , processed data in the file titled "Ph+MPAL-2 REPORT_ProbeBasedReport Part1&2"

value: mononuclear cells


title: Ph+MPAL020

description: Ph+MPAL020, processed data in the file titled "Ph+MPAL-1 REPORT_ProbeBasedReport Part1&2"


title: Ph+MPAL013

description: Ph+MPAL013, processed data in the file titled "Ph+MPAL-2 REPORT_ProbeBasedReport Part1&2"

value: M


title: ATAC day10 RFP-GFP- rep2

description: ALPG-promoter-RFP/OCT4-ΔPE-GFP dual repoter

tag: source


title: Thy_GFP+_3m_2

value: Thyroid gland cells


title: Thy_GFP+_3m_1


title: Ph+AML003

description: Ph+AML003, processed data in the file titled "Ph+AML REPORT_ProbeBasedReport Part1&2"

value: Ph+AML


title: T-RIGI-2

value: RIG-I protein tagged 1-STrEP tag


title: ATAC day12 RFP+GFP- rep1

value: H9 primed ESC

tag: library type


title: Ph+MPAL004

description: Ph+MPAL004, processed data in the file titled "Ph+MPAL-3 REPORT_ProbeBasedReport"

value: ND


title: T-MDA-3

source_name: INPUT RNA extracted on MDA5 protein

value: MDA5 protein tagged 1-STrEP tag

value: mock


title: T-RIGI-1


title: Ph+MPAL017

description: Ph+MPAL017, processed data in the file titled "Ph+MPAL-1 REPORT_ProbeBasedReport Part1&2"


title: T-LGP-3

source_name: INPUT RNA extracted on LGP2 protein

value: LGP2 protein tagged 1-STrEP tag


title: T-LGP-2


title: T-MDA-2


title: SG_GFP-_9m_3

source_name: freshly sorted GFP negative murine salivary gland cells from 9 month old H2B-GFP mice

value: Salivary gland cells

value: negative


title: T-LGP-1


title: Ph+ALL189

description: Ph+ALL189, processed data in the file titled "Ph+ALL-2 REPORT_ProbeBasedReport Part1&2&3"

value: Ph+ALL

value: mononuclear cells of bone marrow at diagnosis