title: retransplant baseline scRNAseq mouse 6 spleen

data_processing:
Barcode sequences were extracted from fastq files based on the known constant sequences flanking the random barcodes and subsequently trimmed to remove these regions such that only the random barcode sequences remained.
Barcode containing reads were further filtered to keep only those barcodes that (a) showed a correct upstream constant region (5’- CGATTGACTA-3’), (b) showed the expected barcode pattern (c) did not contain N residues, and (d) possessed an average phred quality of 30 or higher across the length of the barcode.
Barcode reads were then mapped to the respective SPLINTR reference library using bowtie v1.2.2 allowing up to 2 mismatches.
Barcode count data were imported into R v3.6 for further analysis.
Genome_build: SPLINTR mCHERRY reference library
Supplementary_files_format_and_content: 10X  output files (barcodes, features, matrix)

extract_protocol:
Viable cells were sorted on the BD FACSAria III directly into Eppendorf tubes. The cells were then washed twice with PBS + 0.04% BSA. Cells were then spun down and resuspended in PBS + 0.04% BSA + 0.4 U/ uL RNase Inhibitor (Roche) to a final cell concentrationof >1500 cells per uL. The final cell suspension was put through a cell strainer then onto a 10X Chromium Chip
10X Genomics 3' V3 scRNA-seq chemistry
scRNA seq

value: spleen

tag: mouse id

value: mouse 6

value: baseline


title: BCLP24h1

status: Public on Nov 08 2021

type: SRA

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

country: Switzerland

institute: University of Bern

library_source: transcriptomic

data_processing:
Sequencing was performed on a NovaSeq 6000 S2 flow cell.
The function cellranger count from Cell Ranger31was used to transform the fastq files.
The functioncellranger mat2csv was used to generatethe UMI matrix.
Genome_build: The reference genome was the mm10 available at Illumina Cell Ranger webpage.
Supplementary_files_format_and_content: barcode sequences
Supplementary_files_format_and_content: gene expression features
Supplementary_files_format_and_content: UMI matrix

molecule: total RNA

organism: Mus musculus

source_name: Peritoneal buttons plus cecal ligation and puntcure 24h post-injury

growth_protocol: Mice were kept under SPF condition wich free access to food and water

extract_protocol:
After 24h mice were euthanized by injection anesthesia and subsequent intracardial perfusion with ice cold PBS with 2mM EDTA. Peritoneal buttons were excised and digested for 30 minutes at 37°C in IMDM containing Ca, 25mM Hepes, 2% FCS, 1mg/mL Colagenase 1a (Sigma C9891-1g) and 0.1mg/mL DNAseI (Roche 10104159001). IMDM with 2mM EDTA was used to stop the reaction and wash the cells. Then, samples were resuspended in 40% Percoll and pipetted on top of 80% Percoll solution to create a gradient. After centrifugation (2000rpm, 20min), the interface was transferred again and washed in DPBS + 0.04% BSA. Finally, the sample was resuspended in DPBS + 0.04% BSA for library preparation.
Library preparationscRNA-seq libraries were prepared from 10000cells using the Chromium Single Cell 3’ Library & Gel Bead Kit v3(10xGenomics). Libraries were prepared according to the manufacturers protocol.

treatment_protocol: Mice (C57/Bl6) underwent surgery to receive injury alone (PB) or in combination with bacterial contamination (PB + CLP).

tag: strain

tag: Sex

value: female

tag: protocol

value: peritoneal injury

tag: time pont

value: intervention 24h


title: BCLP24h2


title: CPF3_36-3y

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

institute: ETH Zurich / University of Zurich

description: Litter 36, pup no. 3y

data_processing:
Expression values were computed using STAR and featureCounts
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: text files holding kallisto expression estimates

organism: Rattus norvegicus

source_name: Hippocampus

extract_protocol:
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.
Illumina TruSeq stranded mRNA protocol

value: Long Evans

value: Male

tag: tissue

value: Dorsal Hippocampus

tag: developmental stage

value: Postnatal day 6

tag: time of day (lights on 07.00-19.00)

tag: experimental group

value: Chlorpyrifos 3 mg/kg body wt, injected subcutaneously to dam during pregnancy and lactation.


title: CONFN2-2y

description: Litter N2, pup no. 2y

value: Feeding vehicle control


title: retransplant baseline scRNAseq mouse 6 bone marrow

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

molecule: polyA RNA

growth_protocol: c-Kit positive hematopoietic progenitor cells were cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng/mL), human IL-6 (10 ng/mL), mouse SCF (50 ng/mL) 20% fetal bovine serum (FBS), streptomycin (100 ug/mL), penicillin (100 units/mL) and 2 mM glutamax in 5% CO2 at 37 °C.

treatment_protocol: Cells were transduced with SPLINTR barcode libraries in polybrene (8.5 mg/mL) via spinfection (90 minutes at 1250 g).

value: bone marrow

tag: timepoint


title: NSG_mouse6_spleen

library_source: genomic

data_processing:
Barcode sequences were extracted from fastq files based on the known constant sequences flanking the random barcodes and subsequently trimmed to remove these regions such that only the random barcode sequences remained.
Barcode containing reads were further filtered to keep only those barcodes that (a) showed a correct upstream constant region (5’- CGATTGACTA-3’), (b) showed the expected barcode pattern (c) did not contain N residues, and (d) possessed an average phred quality of 30 or higher across the length of the barcode.
Barcode reads were then mapped to the respective SPLINTR reference library using bowtie v1.2.2 allowing up to 2 mismatches.
Barcode count data were imported into R v3.6 for further analysis.
Genome_build: SPLINTR GFP reference library
Supplementary_files_format_and_content: Table of barcode counts

molecule: genomic DNA

source_name: Spleen

extract_protocol:
Viable cells were sorted on the BD FACSAria III directly into Eppendorf tubes. The cells were then washed twice with PBS + 0.04% BSA.
Cells were lysed in 40 uL Viagen lysis buffer containing 0.5 mg/mL Proteinase K (Invitrogen) and split into technical replicates. Barcodes in cell lysate were then amplified following two rounds of PCR using Q5 polymerase (NEB). The first PCR amplified barcode specific DNA and added partial Illumina sequencing primer binding sites. PCR primers containing staggers to account for low sequence diversity during sequencing. In the second round PCR, the sequencing primer binding sites were completed, P5 and P7 flow cell regions were added and samples received a well-specific 8bp dual index (96 different indices in total).
DNA-Seq

value: Spleen

tag: mouse

value: NSG

value: Disease


title: BPA5_91-6y

description: Litter 91, pup no. 6y

value: Bisphenol A 5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: Ptprca Disease mouse 1

data_processing:
Count matrices were generated from demultiplexed scRNA-seq fastq files using the 10X Genomics Cell Ranger v3.1.0 count pipeline against the mm10/GRCm38 genome.
scRNA-seq quality control was performed using Seurat v3.2 in R. Low quality cells were removed by filtering out cells that had fewer than 500 genes or 1000 unique molecular identifiers (UMIs). Cells with greater than 15% mitochondrial content were also removed.
For detection of the SPLINTR barcodes from single cell data, unmapped reads (which contain reads corresponding to barcode transcripts) were extracted from BAM alignment files for each scRNAseq library using SAMtools v1.9.
BAM entries containing SPLINTR barcode reads were identified and extracted using a regular expression specific to the barcode structure.
Barcode reads were mapped to the corresponding reference library using Bowtie v1.2.2 end-to-end alignment allowing a maximum of two mismatches.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of gene counts
Supplementary_files_format_and_content: matrix of gene names
Supplementary_files_format_and_content: matrix of 10x cell barcodes

source_name: Bone marrow and spleen cells

growth_protocol: Secondary bone marrow cells from MLL-AF9 KRASG12D (KRAStm4Tyj/J) mice were cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng/mL), human IL-6 (10 ng/mL), mouse SCF (50 ng/mL) 20% fetal bovine serum (FBS), streptomycin (100 ug/mL), penicillin (100 units/mL) and 2 mM glutamax in 5% CO2 at 37 °C.

extract_protocol:
Viable cells were sorted on the BD FACSAria III directly into Eppendorf tubes. The cells were then washed twice with PBS + 0.04% BSA. Cells were then spun down and resuspended in PBS + 0.04% BSA + 0.4 U/ uL RNase Inhibitor (Roche) to a final cell concentrationof >1500 cells per uL. The final cell suspension was put through a cell strainer then onto a 10X Chromium Chip
Single cells were captured in droplet emulsions using the 10X Chromium Single-Cell Instrument and reverse transcription, cDNA amplification and library preparation were performed based on the manufacturer’s protocol using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics)

treatment_protocol: Cells were transduced with GFP SPLINTR barcode libraries in polybrene (8.5 mg/mL) via spinfection (90 minutes at 1250 g). After the expansion period, barcoded cells were transplanted into either sub-lethally irradiated (5.5 Gy) Ptprca or non-irradiated NSG mice via lateral tail vein injection. Each mouse received 1x106 barcoded cells.

value: bone marrow and spleen cells

value: Ptprca


title: CPF3_35-5y

description: Litter 35, pup no. 5y


title: MLL-AF9 baseline

source_name: Bone marrow cells

value: haematopoietic progenitors

value: Baseline


title: BPA5_90-2y

description: Litter 90, pup no. 2y


title: Baseline KF08

source_name: haematopoietic progenitors


title: chemo baseline scRNAseq tech rep 2

description: baseline scRNAseq

data_processing:
Count matrices were generated from demultiplexed scRNA-seq fastq files using the 10X Genomics Cell Ranger v3.1.0 count pipeline against the mm10/GRCm38 genome.
scRNA-seq quality control was performed using Seurat v3.2 in R. Low quality cells were removed by filtering out cells that had fewer than 500 genes or 1000 unique molecular identifiers (UMIs). Cells with greater than 15% mitochondrial content were also removed.
For detection of the SPLINTR barcodes from single cell data, unmapped reads (which contain reads corresponding to barcode transcripts) were extracted from BAM alignment files for each scRNAseq library using SAMtools v1.9.
BAM entries containing SPLINTR barcode reads were identified and extracted using a regular expression specific to the barcode structure.
Barcode reads were mapped to the corresponding reference library using Bowtie v1.2.2 end-to-end alignment allowing a maximum of two mismatches.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of gene names, matrix of gene names, matrix of 10x cell barcodes
Supplementary_files_format_and_content: matrix of gene counts - hashtag libraries, matrix of gene names - hashtag libraries, matrix of 10x cell barcodes - hashtag libraries

source_name: chemo baseline scRNAseq tech rep 2

tag: disease state

value: baseline

tag: molecule type

value: poly A mRNA


title: BPA5_88-3y

description: Litter 88, pup no. 3y

value: Long Evans


title: NSG_mouse5_spleen


title: NSG Disease mouse 4


title: chemo baseline scRNAseq tech rep 1

description: baseline scRNAseq

source_name: chemo baseline scRNAseq tech rep 1


title: BPA5_86-9y

description: Litter 86, pup no. 9y

value: Male


title: chemo disease endpoint scRNA-seq pool 2

source_name: chemo disease endpoint scRNA-seq pool 2

value: disease endpoint


title: BPA5_81-1y

description: Litter 81, pup no. 1y

value: Dorsal Hippocampus

value: Postnatal day 6


title: Aro5_120-2y

description: Litter 120, pup no. 2y

value: Aroclor 1254 5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: Ptprca_mouse3_spleen


title: NSG_mouse4_spleen


title: NSG_mouse4_BM

source_name: Bone Marrow

value: Bone Marrow


title: chemo disease endpoint scRNA-seq pool 1

source_name: chemo disease endpoint scRNA-seq pool 1

value: bone marrow


title: WT_3

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

country: USA

institute: Indiana University

data_processing:
Fastq files were generated using Bcl2Fastq software.
Fastq files were assessed for QC using FastQC.
Fastq files were trimmed for quality using options: -b CTGTCTCTTATA -B CTGTCTCTTATA --nextseq-trim=20 --minimum-length 50
Trimmed fastq files were aligned to the mouse genome using STAR alignment with options: --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within
Aligned files were counted using HTSeq-count using options: -s no -r pos -f bam
The R package "DESeq2" was used to determine gene level differences. FGSEA was used to determine changes in gene programs.
Genome_build: GRCm38 vM25 (GENCODE)
Supplementary_files_format_and_content: tab delimited count files

source_name: bone marrow_WT

extract_protocol:
Bone marrow cells were flushed from mouse femurs and tibiae. Lineage+ cells were depleted from each sample using Milltenyi Direct Lineage Depletion Kit. Samples were stained with fluorochrome conjugated antibodies (BD Biosciences) for lineage cocktail, CKIT, and LY6A/E (SCA1). Cells were sorted on a BD FACS Aria SORP into RLT plus Lysis buffer (Qiagen). RNA was isolated using Qiagen RNeasy Micro Plus Kit and eluted into RNAse free water
Smart-Seq v4 Ultra Low Input RNA Library preparation kit was used as described by manufacturer to prepare high quality libraries.

tag: strain background

tag: genotype/variation

value: wild type

tag: cell type

value: LSK


title: BPA5_80-1y

description: Litter 80, pup no. 1y

value: Bisphenol A 5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: BrmKO_2

source_name: bone marrow_BrmKO

value: BrmKO


title: BrmKO_1


title: BPA5_79-2y

description: Litter 79, pup no. 2y


title: BrmKO_3


title: Ptprca_mouse2_spleen

value: Spleen

value: Ptprca

value: Disease


title: Aro5_117-4y

description: Litter 117, pup no. 4y


title: WT_2


title: NSG_mouse6_BM

value: NSG


title: Aro5_120-1y

description: Litter 120, pup no. 1y


title: WT_1


title: Ptprca_mouse2_BM


title: KS--02

city: Oklahoma City

first: Lorin

middle: E.

last: Olson

state: OK

address: 825 NE 13th St,

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

description: SSC culture for 2 weeks with hypoxia

data_processing:
Sequences were demultiplexed to extract cellular barcodes, cDNA inserts and UMIs using Cellranger (v3).
The cDNA sequences were alinged to the murine mm10 genome reference to count UMIs.
Genome_build: mm10
Supplementary_files_format_and_content: H5 or HDF5 file format which contains barcodes, cDNA inserts and counts.

source_name: PDGFRa+/Sca1+ skeketal stem cells

growth_protocol: PDGFRa+/Sca1+ skeletal stem cells were isolated from 3-weeks-old limbs of four genotypes (S+/-, S-/-, KS+/-, and KS-/-) by FACS and cultured on a plastic dish for 2 weeks with hypoxia (5% oxygen) for colony formation.

extract_protocol:
Polyclonal colonies were trypsinized to prepare single-cell supension.
Cells (maximum 20,000 cells per sample) were loaded into the 10x Genomics Chromium platform, barcoded, reverse-transcribed into cDNA, and sequenced on the Illumina Nova Seq SP flowcell platform at a depth of 400 million reads per sample.
Single-cell RNA sequencing

value: Polyclonal colonies of skeletal stem cells

tag: genotype

tag: age

value: 3 weeks old


title: Aro5_116-6y

description: Litter 116, pup no. 6y

tag: strain

value: Long Evans

value: Male


title: NSG_mouse5_BM


title: Ptprca_mouse1_spleen


title: MA_IP5-2 (ORF57-CLIP 3)

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Library strategy: CLIP-seq
Samples were sequenced with Illumina HiSeq2500 platform with a 2 × 50 bp modality
CLIP-seq reads were aligned to the rRNA reference (U13369) using STAR 2.7.6a.
Also, the same reads were aligned to the chimeric genome hg19-KSHV using the same approach.
Finally, reads from the three samples were merged together, mapped to the human genome sequence (hg19) using STAR aligner 2.7.6a and then analyzed using Piranha software with default settings.
Annotation were performed by intersection with GenCode v19 GTF (genome and transcriptome).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing gene names, coordinates, read counts value and statistics

organism: Homo sapiens

source_name: BCBL-1 cells

growth_protocol: BCBL-1 cells were maintained at exponential growth in in RPMI1640 medium supplemented  with 10% FBS and 1x penicillin, streptomycin, glutamine (Thermo Fisher Scientific). Before induction the cells were diluted to 0.5x10e6 cells/ml and treated with 1 mM final concentration of valproic acid (Sigma-Aldrich). After the induction the cells were washed with PBS and exposed to UV light (254 nm, 480,000 uJ/cm2), followed by cell lysis and immunoprecipitation with an anti-ORF57 antibody. The immunoprecipitated complexes were treated with RNase A/T1 and the CLIPed RNAs were relased by proteinase K treatment.

extract_protocol: RNA was extracted by Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) followed by sodium acetate precipitation.

treatment_protocol: After induction of BCBL-1 cells with 1mM VA (Sigma) the cells were crosslinked with UV and then the complexes containing ORF57 were immunoprecipitated with antibody anti-ORF57, followed by RNA A/T1 digestion and proteinase K digestion.

tag: cell line

tag: treatment

value: 1 mM VA/24 h

tag: gender

value: male

tag: cancer type

value: primary effusion lymphoma, PEL


title: KS--01

description: SSC culture for 2 weeks with hypoxia

tag: Sex

value: Female


title: MA_IP5-1 (ORF57-CLIP 2)


title: Ptprca_mouse3_BM

tag: tissue

value: Bone Marrow


title: Ptprca_mouse1_BM


title: Aro5_115-14y

description: Litter 115, pup no. 14y

value: Dorsal Hippocampus

tag: developmental stage

value: Postnatal day 6

tag: time of day (lights on 07.00-19.00)

tag: experimental group

value: Aroclor 1254 5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: MA_IP4 (ORF57-CLIP 1)


title: KS+-02

description: SSC culture for 2 weeks with hypoxia


title: Aro5_108-1y

description: Litter 108, pup no. 1y


title: MLL-AF9 + Kras G12D/+ rep2

data_processing:
Reads were aligned with BWA (v0.7.13) to reference genome GRCm38.78 and duplicates marked with picard (v2.17.3).
Variant calling was performed with Strelka2 somatic workflow (v2.9.10), which includes structural variant calling with Manta (v1.5). PASS variants from variant calling were annotated with VEP (v92).
Compiled variants were filtered by variant allele frequency with respect to the initiating variant of their respective groups (~30%) to filter out sub-clonal mutations.
Genome_build: mm10

source_name: cKit + progenitors

extract_protocol:
Genomic DNA was isolated from mouse whole bone marrow cells using the Qiagen DNeasy Blood and Tissue Kit
Exonic DNA fragments were captured from genomic DNA using the Agilent SureSelectXT Mouse All Exon kit.
Exome-Seq

value: haematopoietic progenitors

tag: mutation

value: MLL-AF9 + Kras G12D/+


title: KS+-01

description: SSC culture for 2 weeks with hypoxia


title: MLL-AF9 + Kras G12D/+ rep1


title: HealthyControl_21

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: small RNAsequencing analysis

data_processing:
BCL basecall files were converted to FASTQ per sample using CASAVA v1.8.2 (Illumina) with default parameters to generate demultiplexed per sample fastq raw sequencing data files.
Per sample read quality was assessed using FastQC.
Trimming, quality filtering, mapping and raw read counting data processing steps were performed with XICRA pipeline  (Sanchez Herrero JF, et al,  https://github.com/HCGB-IGTP/XICRA), using sRNAbench (E. Aparicio-Puerta et al., 2019 Nucleic Acids Res., 47:(W1):W530–W535) to map, assign and count reads and miRTOP standard isomir naming (T. Desvignes et al. 2020 Bioinformatics 36(3):698-703).
Statistically significant differences in miRNA expression were determined both by DESeq2 (Love, 2014) with multiple testing adjustment. A dataset consistency step was perfomed by principal components analysis (PCA) to detect outliers. Data were renormalized after outlier removal prior to the final analysis.
Genome_build: Reads were mapped to GRCh38.87  and annotated with miRBase 21 mature database.
Supplementary_files_format_and_content: Processed miRNA expression profiling data table is provided as a supplementary file in excel workbook (.xlsx) format. It includes a single worksheet. This contains DESeq2 outputs. Column headers: FC or FoldChange (fold changes), pvalue (nominal p value), padj (adjusted pvalue by default Benjamini and Hochberg method) for all 7 comparisons presented in the publication, followed by baseMean (average normalized counts), and normalized counts for all samples.

source_name: plasma

extract_protocol:
Blood samples were collected in EDTA tubes, then, plasma samples were obtained by a single centrifugation (1000g, 15min. at room temperature). For RNA extraction from 200ul of plasma, miRCURY RNA insolation kit-Biofluids (#300112) was used following manufacturer indications with modifications that included using glycogen as carrier and a 1:50 dilution of spike in RNA.
Barcoded sequencing libraries were prepared using the TruSeq SmallRNA library kit (Illumina) with slight modifications from the default recommendations (Part # 15004197 Rev. F, February 2014). Modifications included using all RNA extracted from 200 ul of plasma, in the subnanogram range, and increasing the number of cycles in the final PCR reaction (from 12 to 15).
Libraries were quality assessed with Bioanalyzer DNA 1000 assays (Agilent). Bioanalyzer concentration estimates were used to generate an equimolar library mix. The library pool was automatically size selected (135-160bp) using 3% agarose dye free cassettes with 3% DF marker F on a Pippin Prep system with software v.6.0 (Sage Science). QIAquick (Qiagen) column purifications were performed prior and after to size selection. The library pool was quantifiedby PCR with theKAPA Library Quantification Kit following manufacturer’s instructions (Roche). The library pool was run on 4 lanes of 1x50 bp sequencing was performed on HiSeq2500 platform (Illumina) using adapted protocols for TruSeq SR cluster kit v3 (Part#15023335) following cBot™ (Part#15006165) and HiSeq2500 System (Part#15035786) user guidelines. Raw data were analysed by Real Time Analysis software v. 1.17.21.3 and Sequence Analysis Viewer software v. 1.8.20 (Illumina.).

value: plasma

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

value: HIV negative

value: HCV negative

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: CPF3_43-3x

description: Litter 43, pup no. 3x

tag: strain

tag: Sex

value: Chlorpyrifos 3 mg/kg body wt, injected subcutaneously to dam during pregnancy and lactation.


title: MLL-AF9 + Flt3 ITD/ITD rep2

tag: tissue

value: MLL-AF9 + Flt3 ITD/ITD


title: CPF3_45-6x

description: Litter 45, pup no. 6x

value: Long Evans

tag: developmental stage

tag: time of day (lights on 07.00-19.00)


title: S--02

description: SSC culture for 2 weeks with hypoxia

tag: cell type

value: Polyclonal colonies of skeletal stem cells

tag: genotype

tag: age

value: 3 weeks old


title: MLL-AF9 + Flt3 ITD/ITD rep1

tag: mutation


title: HealthyControl_20

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

tag: gender

value: female


title: HealthyControl_19

description: small RNAsequencing analysis

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id


title: CPF3_38-5x

description: Litter 38, pup no. 5x

tag: strain

tag: Sex

tag: tissue

tag: experimental group


title: S+-02

description: SSC culture for 2 weeks with hypoxia

tag: cell type

tag: genotype


title: HealthyControl_18

description: small RNAsequencing analysis

tag: library batch

tag: size selection and sequencing pool


title: CPF3_35-3x

description: Litter 35, pup no. 3x

tag: developmental stage

tag: time of day (lights on 07.00-19.00)


title: S+-01

description: SSC culture for 2 weeks with hypoxia

tag: age

value: Male


title: MLL-AF9 rep2

tag: mutation


title: HealthyControl_17

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

tag: gender

tag: age (in years)


title: HealthyControl_16

description: small RNAsequencing analysis

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id


title: S--01

description: SSC culture for 2 weeks with hypoxia

tag: cell type

tag: genotype

tag: Sex


title: MOUSE15 BM

data_processing:
Barcode sequences were extracted from fastq files based on the known constant sequences flanking the random barcodes and subsequently trimmed to remove these regions such that only the random barcode sequences remained.
Barcode containing reads were further filtered to keep only those barcodes that (a) showed a correct upstream constant region (5’- CGATTGACTA-3’), (b) showed the expected barcode pattern (c) did not contain N residues, and (d) possessed an average phred quality of 30 or higher across the length of the barcode.
Barcode reads were then mapped to the respective SPLINTR reference library using bowtie v1.2.2 allowing up to 2 mismatches.
Barcode count data were imported into R v3.6 for further analysis.
Genome_build: SPLINTR reference library

source_name: MOUSE15 BM

tag: tissue

value: BM

tag: mouse

tag: timepoint

value: DISEASE


title: HealthyControl_15

description: small RNAsequencing analysis

value: male

tag: library batch

tag: size selection and sequencing pool


title: CONFN4-3x

description: Litter N4, pup no. 3x

source_name: Hippocampus

tag: strain

value: Female

value: Dorsal Hippocampus

tag: developmental stage

value: Postnatal day 6

tag: time of day (lights on 07.00-19.00)

tag: experimental group

value: Feeding vehicle control


title: CONSC-8-2x

description: Litter 8, pup no. 2x

value: s.c. injection control (saline)


title: MOUSE14 SPL

source_name: MOUSE14 SPL

value: SPL


title: CONFN8-1x

description: Litter N8, pup no. 1x


title: HealthyControl_13

description: small RNAsequencing analysis

value: plasma

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

value: HIV negative

value: HCV negative

tag: gender

tag: age (in years)


title: BPA5_91-9x

description: Litter 91, pup no. 9x

value: Long Evans

value: Bisphenol A 5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: MOUSE14 BM

source_name: MOUSE14 BM


title: MOUSE18 SPL

source_name: MOUSE18 SPL


title: C_R4

city: Shanghai

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

country: China

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase 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, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: danRer11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Danio rerio

source_name: spinal cord

extract_protocol:
Spinal cord segments were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB

value: 5 spinal segment rostral to the injury site

tag: disease state

value: uninjured


title: KRAS_MOUSE8_BM

value: BM

tag: mutation

value: KRAS

value: Disease


title: HealthyControl_11

description: small RNAsequencing analysis

tag: tissue

value: female

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id


title: CONFN1-8x

description: Litter N1, pup no. 8x

tag: strain

tag: Sex

value: Female

value: Dorsal Hippocampus


title: Baseline KF05

source_name: Baseline

tag: timepoint

value: Baseline


title: HealthyControl_14

description: small RNAsequencing analysis

tag: library batch

tag: size selection and sequencing pool


title: HealthyControl_12

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

value: male


title: HealthyControl_10

description: small RNAsequencing analysis

tag: clinical grouping

tag: hcv infection status


title: BPA5_85-4x

description: Litter 85, pup no. 4x

tag: developmental stage

value: Postnatal day 6

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: CONSC6-7x

description: Litter 6, pup no. 7x

tag: tissue

value: s.c. injection control (saline)


title: MOUSE18 BM

source_name: MOUSE18 BM

tag: mouse

value: DISEASE


title: BPA5_81-6x

description: Litter 81, pup no. 6x


title: MOUSE17 SPL

source_name: MOUSE17 SPL

value: SPL


title: HealthyControl_9

description: small RNAsequencing analysis

value: plasma

value: HIV negative

value: HCV negative

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl


title: MLL-AF9 rep1

value: haematopoietic progenitors

tag: mutation


title: HealthyControl_8

description: small RNAsequencing analysis

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id


title: MOUSE15 SPL

source_name: MOUSE15 SPL

tag: timepoint


title: MOUSE17 BM

source_name: MOUSE17 BM


title: Aro5_120-3x

description: Litter 120, pup no. 3x

tag: strain

value: Long Evans

tag: Sex

value: Aroclor 1254 5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: BPA5_79-4x

description: Litter 79, pup no. 4x

value: Bisphenol A 5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: CONFN3-1x

description: Litter N3, pup no. 1x

value: Feeding vehicle control


title: HealthyControl_7

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

value: female

tag: library batch

tag: size selection and sequencing pool


title: IFNAR.16

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description: d0 KL25HL B cell transfer and LCMV infection, analysis d4 pi

data_processing:
Reads were aligned to the mouse genome (UCSC version mm10) with STAR (version 2.5.2a) using the multi-map settings '-outFilterMultimapNmax 10 --outSAMmultNmax 1'.
Mapped reads were assigned to genes based on the UCSC refGene annotation (downloaded 2015-12-18) using the function qCount of the R/Bioconductor package QuasR (R version 3.4.0, Bioconductor version 3.5).
Genes with zero counts were removed resulting in n=18824 genes.
Genome_build: mm10
Supplementary_files_format_and_content: counts.tsv.gz; gzipped tab-separated values text file with columns: 1. Entrez gene id, 2. gene symbol, 3. gene name, 4. gene length (exon-union model), 5. - 20. counts per sample

source_name: KL25HL splenocytes

extract_protocol:
KL25HL B cells (CD45.1+ B220+CD138-) were FACS sorted on day 4 days directly into Trizole LS; RNA was extracted using the Direct-Zol RNA Microprep Kit, Zymo Research
Library preparation was performed, starting from 100ng total RNA, using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Cat# RS-122-2103, Illumina, San Diego, CA, USA) and the TruSeq RNA CD Index Plate (Cat# 20019792, Illumina). 15 cycles of PCR were performed. Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical). Samples were pooled to equal molarity and sequenced using single-reads 76 bases on an Illumina NextSeq 500.

treatment_protocol: On day -9, recipient mice were pre-immunized with either LM61 (mice 1-4) or control (LM, mice 5-8)). Another group of wt recipients (mice 9-12) and IFNAR-/- recipients (mice 13-16) were not pre-immunized. On day 0, all mice received KL25HL B cells by adoptive transfer and were challenged with LCMV. Mice 9-12 additionally were given SM CD4 T cells on day -1 by adoptive transfer. On day 4, KL25HL B cells (CD45.1+B220+CD138-) were purified by FACS-sorting and were subject to RNAseq.

tag: cell type

value: KL25HL B cells

tag: treatment

value: IFNAR-/- B6

tag: genotype

tag: ID


title: HealthyControl_6

description: small RNAsequencing analysis

tag: tissue

tag: hcv infection status

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)


title: Aro5_117-6x

description: Litter 117, pup no. 6x

value: Female

value: Dorsal Hippocampus

tag: developmental stage

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: Aro5_116-1x

description: Litter 116, pup no. 1x

tag: strain

tag: Sex

value: Postnatal day 6


title: IFNAR.15


title: IFNAR.13


title: IFNAR.14


title: Aro5_115-7x

description: Litter 115, pup no. 7x


title: CPF1_63-5Y

description: Litter 63, pup no. 5y

value: Male

value: Chlorpyrifos 1 mg/kg body wt, injected subcutaneously to dam during pregnancy and lactation.


title: SM.tf.11

value: SM transfer on d-1


title: HealthyControl_3

description: small RNAsequencing analysis

value: plasma

tag: individual unique id

tag: sample id

tag: clinical grouping

value: male

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id


title: HealthyControl_5

description: small RNAsequencing analysis

value: HIV negative

value: HCV negative

tag: library batch

tag: size selection and sequencing pool


title: Aro5_115-13x

description: Litter 115, pup no. 13x

value: Long Evans

tag: tissue


title: CPF1_60-6Y

description: Litter 60, pup no. 6y


title: GKO-3

first: Zhuning

last: Wang

address: 280 Chong Qing Nan Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Filtered Reads were aligned to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml ), an upgraded version of TopHat2. HISAT2 uses an improved BWT algorithm (Sirén et al. 2014) which is faster and less resource intensive. HISAT2 uses default parameters for non-strand-specific libraries, while strand-specific libraries need to specify the library type (i.e. --rna-strandness RF for first and --rna-strandness FR for second).
The distribution of reads compared to the genome was counted and the localized regions were classified into CDS (coding region), Intron (intron), Intergenic (intergenic region) and UTR (5' and 3' untranslated region).
We used HTSeq statistics to compare to the read counts on each gene as the raw expression of the gene. To make the gene expression levels comparable across genes and samples, we used FPKM (Fragments Per Kilo bases per Million fragments) to normalize the expression, which is the number of fragments per kilobase per million fragments from a given gene. For Pair-End sequencing, each Fragment will have two Reads, and FPKM only counts the number of Fragments that can be compared to the same transcript by two Reads. In the reference transcriptome, we generally consider the genes with FPKM>1 to be expressed.
Supplementary_files_format_and_content: Matrix table with raw gene counts and fpkm for every gene and every sample

source_name: Kidney

extract_protocol:
The mice were euthanized 31 weeks after injection. Mice were anesthetized and kidneys were excised. Kidneys from different groups of mice were used for total RNA isolation with TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female mice (4 week) were intraperitoneally injected once with 0.5 ml of pristane oil (2,6,10,14-tetramethylpentadecane, Sigma-Aldrich). Control mice were treated with 0.5 ml of saline.

value: kidney

tag: genotype

value: GSDMD-/-

tag: treatment


title: HealthyControl_2

description: small RNAsequencing analysis

tag: hcv infection status

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)


title: GKO-2

tag: strain


title: PIL-3

tag: Sex

value: wild type

value: pristane


title: PIL-2

value: female


title: SM.tf.10

tag: cell type

value: KL25HL B cells

tag: ID


title: GKO-1


title: Co-infected, progressing 46

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

value: HIV positive

value: HCV positive


title: SM.tf.9


title: CPF1_21-1Y

description: Litter 21, pup no. 1y

value: Dorsal Hippocampus

tag: developmental stage

value: Postnatal day 6

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: PIL-1

tag: tissue


title: CPF1_16-7Y

description: Litter 16, pup no. 7y

value: Male

value: Chlorpyrifos 1 mg/kg body wt, injected subcutaneously to dam during pregnancy and lactation.


title: Con-3

tag: genotype


title: Co-infected, progressing 45

description: small RNAsequencing analysis

value: plasma

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: LM.wt.8

tag: treatment

value: LM immunization on d-9


title: HealthyControl_4

description: small RNAsequencing analysis

tag: hcv infection status

value: HIV negative

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)


title: SM.tf.12

tag: cell type

value: SM transfer on d-1

tag: ID


title: LM.wt.7


title: Co-infected, progressing 44

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

value: male


title: Con-2

tag: strain

tag: Sex

tag: tissue

value: kidney


title: Co-infected, progressing 43

description: small RNAsequencing analysis

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl


title: LM.wt.6

tag: genotype


title: HealthyControl_1

description: small RNAsequencing analysis

value: HCV negative

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: mll-af9 + kras g12d/+ (KF05)

value: haematopoietic progenitors

tag: mutation

value: MLL-AF9 KRAStm4Tyj/J


title: CONSC_13-1Y

description: Litter 13, pup no. 1y

value: Long Evans

tag: developmental stage

tag: time of day (lights on 07.00-19.00)

tag: experimental group

value: s.c. injection control (saline)


title: Con-1

value: female

value: wild type

tag: treatment


title: LM.wt.5

tag: cell type

value: KL25HL B cells

tag: ID


title: CONSC_11-4Y

description: Litter 11, pup no. 4y

value: Dorsal Hippocampus

value: Postnatal day 6


title: LM.gp61.4

value: LM61 immunization on d-9


title: CONSC_10-2Y

description: Litter 10, pup no. 2y

value: Male


title: Co-infected, progressing 41

description: small RNAsequencing analysis

value: plasma

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

value: HIV positive

value: HCV positive

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)


title: Co-infected, progressing 42

description: small RNAsequencing analysis

tag: tissue

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id


title: Co-infected, progressing 40

description: small RNAsequencing analysis

tag: library batch

tag: size selection and sequencing pool


title: LM.gp61.3

tag: genotype


title: SPF_8h_40

data_processing:
fastq files were aligned to the mouse reference genome with Hisat
sam files were sorted and converted to bam files with SAMtools
reads were counted with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with read count per sample

source_name: Immunopurified peritoneal mesothelium

growth_protocol: Isolated cells

extract_protocol: Mice were anesthetized. A 22-gauge catheter was inserted into the peritoneal cavity and the peritoneal cavity was flushed three times with 5mL warm PBS containing 2mM EDTA. The wash buffer was aspirated completely for each wash and discarded. Then, 5ml of digestion buffer (0.5% Trypsin, 24mM EDTA, Sigma) were injected and incubated for 10 Minutes while the mouse was kept warm under an infrared light. The digestion buffer was aspirated and the abdominal cavity was flushed three times with 5mL ice cold PBS containing 2mM EDTA and 3 % FCS to collect mesothelial cells. Cells were purified as previously described (22). In brief, cells were washed two times and then incubated with anti-mouse GPM6A (Clone Nr. 321, MBL, #D055-3) for 30 Minutes at 4°C. After centrifugation the cells were incubated with anti-rat IgG MicroBeads (Miltenyi, #130-048-502) and were purified by MACS Separation columns LS (Milteny, #130-042-401) according to their instructions.

treatment_protocol: Mice underwent laparatomy, sterile injury (peritoneal buttons) of the peritoneum, and limmited (2mm) cecal ligation and puncture (25 gauge needle) prior to injury. Time-delay between surgery and isolation is indicated per sample. Baseline mice did not receive any treatment.

tag: strain

tag: group

value: Specific pathogen free

tag: age

value: 8-10 week old

tag: agent

value: PB + CLP

tag: time point


title: SPF_8h_39


title: LM.gp61.2

tag: cell type

tag: treatment

tag: ID


title: CONSC_8-4Y

description: Litter 8, pup no. 4y

tag: Sex

tag: developmental stage

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: Co-infected, progressing 39

description: small RNAsequencing analysis

tag: tissue

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

tag: gender

value: male

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl


title: Co-infected, progressing 38

description: small RNAsequencing analysis

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: SPF_7d_05

tag: strain

tag: group

tag: age

tag: genotype

tag: agent

tag: time point


title: Co-infected, progressing 37

description: small RNAsequencing analysis

tag: tissue

tag: individual unique id

tag: sample id


title: SPF_8h_38


title: LM.gp61.1

tag: cell type

tag: treatment

tag: ID


title: CONSC_6-5Y

description: Litter 6, pup no. 5y

tag: Sex

tag: developmental stage

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: CONF_N5-2Y

description: Litter N5, pup no. 2y

value: Feeding vehicle control


title: CONF_N4-7Y

description: Litter N4, pup no. 7y

value: Long Evans


title: CONF_N3-4Y

description: Litter N3, pup no. 4y


title: CONF_N2-2Y

description: Litter N2, pup no. 2y


title: scRNA-Seq adult_cre+

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
cellranger (v3.1.0) count was used to perform sample demultiplexing, barcode processing, and single cell gene counting.
cellranger (v3.1.0) aggr was used to aggregate cellranger count runs for all three samples together (normalize=mapped).
features detected in at least 3 cells and cells with at least 200 features are kept using Seurat (v3.2.2).
Genome_build: mm10
Supplementary_files_format_and_content: h5: Filtered feature-barcode matrices containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode
Supplementary_files_format_and_content: raw counts: Matrix table with raw gene counts for every gene and every cell

source_name: CD8+ T cells

extract_protocol:
Adult or neonatal mouse spleens were isolated in complete media and CD8+ T cells were positively selected for using magnetic microbead (Miltenyi) selection according to manufacturer’s instructions. Splenic cells were then prepped for bulk naïve CD8 FACS sorting on the SONY by staining with CD8, CD4 and Viability Dye (~97% purity) and 60K CD8+ cells sorted into PBS + 0.04% BSA. Sorted cells were then counted on a TC20 to capture 8K viable CD8+ T cells.
Single cell 3′ RNA sequencing libraries were prepared by the Genomics core at Cornell University using a 10x Genomics Chromium instrument and the Chromium Single Cell 3′ Reagent kit (v3), following the manufacturer’s protocol.

value: CD4Cre+ miR-29ab1 fl/fl gBT-I

tag: cell state

value: naive

tag: animal age

value: 10 weeks

value: Untreated splenocytes


title: scRNA-Seq neonate

description: neonate

tag: strain

value: CD4Cre- miR-29ab1 fl/fl gBT-I

value: 7 days


title: scRNA-Seq adult_ctrl


title: BPA05_75-1Y

description: Litter 75, pup no. 1y

value: Dorsal Hippocampus

value: Postnatal day 6

value: Bisphenol A 0.5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: SPF_3h_25

tag: group

tag: age

value: wild type


title: SPF_7d_01

tag: genotype

tag: agent


title: Co-infected, progressing 35

description: small RNAsequencing analysis

tag: tissue

value: plasma

tag: clinical grouping

tag: hcv infection status

value: HIV positive

value: HCV positive

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: Co-infected, progressing 36

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id


title: Co-infected, progressing 34

description: small RNAsequencing analysis


title: BPA05_73-4Y

description: Litter 73, pup no. 4y

tag: strain

tag: Sex

value: Male

tag: developmental stage

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: BPA05_72-4Y

description: Litter 72, pup no. 4y

tag: tissue


title: SPF_3h_23

tag: group

value: Specific pathogen free

tag: age

value: 8-10 week old

tag: genotype

tag: agent

value: PB + CLP

tag: time point


title: RNA-Seq Neonate_TN_miR29_rep3

data_processing:
trim_galore (with cutadapt v1.18) was used to trim and filter reads.
hisat2 (v2.2.0) was used to map reads to the mouse mm10.
featureCounts (v2.0.0) was used to count  reads to exons (-s 0 -Q 50).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts: Matrix table with raw gene counts for every gene and every sample

growth_protocol: 2x105 magnetically-enriched CD8+ T cells from mouse spleen were plated per well in RPMI-1640 complete media with 10% FBS, Pen/strep and L-glut with IL-7 (2 ng/mL).

extract_protocol:
Naïve CD8+ T cell subsets (TN and VM) were FACS sorted by staining for CD8, CD4, CD44, CD122 and Viability Dye. Cells were sorted into PBS + 2% BSA  + 2mM EDTA. Cells were placed in Trizol and RNA was purified following the manufacturer's instructions, with the addition of a chloroform extraction, GlycoBlue addition when precipitating, and a second wash of the pelleted RNA in 70% ethanol. RNA integrity was confirmed on a Fragment Analyzer.
Libraries were prepared by the TREx core at Cornell University as follows: RNAseq libraries were generated with the non-directional NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) using 10 ng of total RNA that was initially polyA-selected.

treatment_protocol: 100 µL of red blood cell EVs (RBCEVs) were added per well, and incubated at 37°C for 4-5 days. The media was changed every 48 hours.

value: B6 x gBT-I

tag: cell state

value: Naive

tag: animal age

value: 6-7 days

tag: cell type

value: true naive (TN) splenocyte

tag: treatment

value: treat with EV loaded with miR-29 mimic for 4-5 days


title: RNA-Seq Neonate_VM_miR29_rep3

value: virtual memory (VM) splenocyte


title: BPA05_69-4Y

description: Litter 69, pup no. 4y

value: Long Evans

value: Dorsal Hippocampus


title: RNA-Seq Neonate_VM_NC_rep3

value: treat with EV loaded with negative control (NC) mimic for 4-5 days


title: SPF_3d_17

value: wild type


title: Co-infected, progressing 33

description: small RNAsequencing analysis

value: plasma

tag: individual unique id

tag: clinical grouping

tag: hcv infection status

tag: gender

value: male

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: Aro05_98-8Y

description: Litter 98, pup no. 8y

tag: strain

tag: Sex

tag: tissue

tag: developmental stage

value: Postnatal day 6

tag: time of day (lights on 07.00-19.00)

tag: experimental group

value: Aroclor 1254 0.5 mg/kg body wt, administered to dam in chow 2 wk premating, mating, pregnancy and lactation.


title: RNA-Seq Neonate_TN_NC_rep3

tag: cell state

tag: animal age

tag: cell type

tag: treatment


title: SPF_7d_04

tag: group

value: Specific pathogen free

tag: age

tag: genotype

tag: agent

tag: time point


title: Aro05_94-3Y

description: Litter 94, pup no. 3y

value: Male


title: Co-infected, progressing 31

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

value: HIV positive

value: HCV positive

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch


title: RNA-Seq Adult_VM_rep3

tag: strain

value: Thy1.1 x gBT-I

tag: cell state

value: Naive

tag: animal age

value: 8-12 weeks

tag: cell type

tag: treatment

value: untreated


title: Aro05_106-3Y

description: Litter 106, pup no. 3y

tag: Sex

tag: tissue

tag: developmental stage

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: Co-infected, progressing 30

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

tag: gender

tag: size selection and sequencing pool


title: Co-infected, progressing 29

description: small RNAsequencing analysis

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch


title: RNA-Seq Adult_TN_rep3

tag: strain

tag: cell state

tag: animal age

tag: cell type

value: true naive (TN) splenocyte

tag: treatment


title: SPF_3h_24

tag: group

tag: age

value: 8-10 week old

tag: genotype

tag: agent

value: PB + CLP

tag: time point


title: SPF_24h_33


title: Aro05_105-5Y

description: Litter 105, pup no. 5y

value: Long Evans

tag: Sex

tag: tissue

value: Dorsal Hippocampus

tag: developmental stage

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: RNA-Seq Neonate_VM_miR29_rep2

value: B6 x gBT-I

value: 6-7 days

value: virtual memory (VM) splenocyte

value: treat with EV loaded with miR-29 mimic for 4-5 days


title: SPF_24h_31

value: Specific pathogen free

value: wild type


title: Co-infected, progressing 28

description: small RNAsequencing analysis

value: plasma

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

value: HIV positive

tag: gender

value: male

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: size selection and sequencing pool


title: Co-infected, progressing 32

description: small RNAsequencing analysis

value: HCV positive

value: female

tag: library batch


title: Co-infected, progressing 27

description: small RNAsequencing analysis


title: CONSC_9-1x

description: Litter 9, pup no. 1x

tag: strain

tag: Sex

value: Female

value: Postnatal day 6

value: s.c. injection control (saline)


title: RNA-Seq Neonate_TN_miR29_rep2

tag: cell state

value: Naive

tag: animal age

tag: cell type

value: true naive (TN) splenocyte

tag: treatment


title: SPF_24h_30

tag: group

tag: age

value: 8-10 week old

tag: genotype

tag: agent

value: PB + CLP

tag: time point


title: Co-infected, progressing 26

description: small RNAsequencing analysis

tag: tissue

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)


title: RNA-Seq Neonate_VM_NC_rep2

tag: strain

value: B6 x gBT-I

tag: cell state

value: 6-7 days

value: treat with EV loaded with negative control (NC) mimic for 4-5 days


title: CONSC_13-8x

description: Litter 13, pup no. 8x

value: Long Evans

tag: Sex

value: Dorsal Hippocampus

tag: developmental stage

tag: time of day (lights on 07.00-19.00)

tag: experimental group


title: SPF_3d_16

tag: group

value: Specific pathogen free

tag: age

tag: genotype

value: wild type


title: RNA-Seq Neonate_TN_NC_rep2

tag: animal age

tag: cell type

tag: treatment


title: Co-infected, progressing 25

description: small RNAsequencing analysis

tag: tissue

value: plasma

tag: individual unique id

tag: sample id

tag: clinical grouping

value: HIV positive

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: CONSC_11-3x

description: Litter 11, pup no. 3x

tag: strain

tag: Sex

tag: developmental stage

tag: time of day (lights on 07.00-19.00)


title: SPF_3d_15

tag: group

tag: age

tag: genotype

tag: agent

tag: time point


title: SPF_0h_12

value: baseline


title: CONF_N4-3x

description: Litter N4, pup no.3x

value: Female

tag: tissue

tag: experimental group

value: Feeding vehicle control


title: SPF_0h_10


title: RNA-Seq Adult_VM_rep2

value: Thy1.1 x gBT-I

tag: cell state

tag: animal age

value: 8-12 weeks

tag: cell type

value: virtual memory (VM) splenocyte

tag: treatment

value: untreated


title: SPF_0h_13

value: 8-10 week old


title: CONF_N2-4x

description: Litter N2, pup no.4x

value: Postnatal day 6


title: GF_3h_29

value: Germ free

value: PB + CLP


title: RNA-Seq Adult_TN_rep2

value: Naive

value: true naive (TN) splenocyte


title: RNA-Seq Neonate_VM_miR29_rep1

value: B6 x gBT-I

value: 6-7 days

value: treat with EV loaded with miR-29 mimic for 4-5 days


title: seaurchin_adult_tubefeet_MethylCseq_rep2

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

data_processing:
Sequenced reads in fastq format were trimmed using Trimmomatic software (ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 MINLEN:50)
Trimmed reads were mapped to sea urchin  Spur_v3.1 reference genome (containing the λ phage genome as chrLambda) using WALT (Chen et al, 2016) with the following settings: -m 10 -t 24 -N 10000000 -L 2000.
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true (http://broadinstitute.github.io/picard/).
Reads with more than three consecutive non-converted cytosines in the CC, CA and CT context were removed using Picard Tools’ function FilterSamReads, in order to eliminate DNA molecules not efficiently deaminated by APOBEC3A
The numbers of methylated and unmethylated cytosines at each genomic CpG position were called using the MethylDackel extract genome.fasta input.bam -o output --mergeContext. Additional MethylDackel extract parameters --minOppositeDepth 5 --maxVariantFrac 0.5 were used for the genotype correction (in order to exclude C-to-T nucleotide transitions in the genomic DNA of interest, which could be incorrectly considered as unmodified cytosines) (https://github.com/dpryan79/MethylDackel)
Genome_build: sea urchin: Spur_v3.1
Supplementary_files_format_and_content: bedGraph / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting hydroxymethylated bases; 6. The number of alignments/pairs reporting unmethylated bases

organism: Strongylocentrotus purpuratus

source_name: sea urchin adult tube feet DNA subjected to MethylC-seq rep2

extract_protocol: MethylC-seq library preparation was performed as described previously (PMID: 25692984). Briefly, 1000 ng of genomic DNA extracted from sea urchin and lancelet embryos and adult tissues was spiked with unmethylated λ phage DNA (Promega) and sonicated to ~300 bp fragments using M220 focused ultrasonicator (Covaris) with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA was then purified, end-repaired using End-It™ DNA End-Repair Kit (Lucigen) and A-tailed using Klenow Fragment (3'→5' exo-) (New England Biolabs) followed by the ligation of NEXTFLEX® Bisulfite-Seq Adapters. Bisulfite conversion of adaptor-ligated DNA was performed using EZ DNA Methylation-Gold Kit (Zymo Research). Library amplification (13 PCR cycles) was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems). Library size was determined by the Agilent 4200 Tapestation system. The libraries were quantified using the KAPA library quantification kit (Roche) yielding ~10-20 nM.

treatment_protocol: no treatment

tag: tissue type

value: adult tube feet

value: tube feet


title: Co-infected, progressing 22

description: small RNAsequencing analysis

source_name: plasma

value: plasma

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

value: HIV positive

value: HCV positive

tag: gender

value: female

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: Co-infected, progressing 23

description: small RNAsequencing analysis

tag: tissue


title: Co-infected, progressing 21

description: small RNAsequencing analysis

value: male


title: seaurchin_72hpf_embryo_MethylCseq_rep2

source_name: 72 hpf sea urchin embryo DNA subjected to MethylC-seq rep2

value: 72 hpf embryo

value: embryo


title: RNA-Seq Neonate_VM_NC_rep1

tag: strain

tag: cell state

tag: animal age

value: virtual memory (VM) splenocyte

value: treat with EV loaded with negative control (NC) mimic for 4-5 days


title: Co-infected, non progressing 20

description: small RNAsequencing analysis


title: RNA-Seq Neonate_TN_miR29_rep1

tag: cell type

tag: treatment


title: GF_3d_21

tag: group

value: Germ free

tag: age

value: 8-10 week old

tag: genotype

value: wild type

tag: agent

value: PB + CLP

tag: time point


title: RNA-Seq Neonate_TN_NC_rep1

value: B6 x gBT-I

value: Naive

value: 6-7 days

value: true naive (TN) splenocyte


title: GF_3d_20


title: Co-infected, progressing 24

description: small RNAsequencing analysis

value: plasma

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

tag: gender

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)


title: Co-infected, non progressing 19

description: small RNAsequencing analysis

tag: tissue

value: HIV positive

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: RNA-Seq Adult_VM_rep1

tag: strain

value: Thy1.1 x gBT-I

tag: cell state

tag: animal age

value: 8-12 weeks

tag: cell type

tag: treatment

value: untreated


title: seaurchin_adult_tubefeet_MethylCseq_rep1

source_name: sea urchin adult tube feet DNA subjected to MethylC-seq rep1

tag: tissue type

value: adult tube feet

value: tube feet


title: Co-infected, non progressing 17

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

value: HCV positive

value: male


title: Co-infected, non progressing 18

description: small RNAsequencing analysis

tag: hcv infection status

tag: gender

tag: age (in years)


title: seaurchin_72hpf_embryo_MethylCseq_rep1

source_name: 72 hpf sea urchin embryo DNA subjected to MethylC-seq rep1

value: 72 hpf embryo

tag: tissue

value: embryo


title: GF_3d_18

tag: group

value: Germ free

tag: age

value: 8-10 week old

tag: genotype

value: wild type

tag: agent

tag: time point


title: RNA-Seq Adult_TN_rep1

tag: strain

tag: cell state

value: Naive


title: Neonate_VM_miR29_rep3

data_processing:
Raw sequencing reads were processed using ENCODE ATAC-seq pipeline (v1.1.7). Within the pipeline, trimmed adapter sequences are ‘R1: CTGTCTCTTATACACATCT; R2: CTGTCTCTTATACACATCT’; Paired-end mode is enabled and peak calling is performed using MACS2 with ‘-f BEDPE’; Irreproducibility Discovery Rate (IDR) analysis is used to generate replicable peaks for each condition acorss replicates.
reads on positive chain are shorted by 4bp from the start and reads on negative chain are shorted by 5 bp from the end.
featureCounts (v2.0.0) was used to count reads to peaks that passed IDR from all conditions (-p -s 0 -Q 38).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak: reproducible peaks generated for each sample type
Supplementary_files_format_and_content: raw counts: Matrix table with raw counts for every peak and every sample

extract_protocol:
Naïve CD8+ T cell subsets (TN and VM) were FACS sorted by staining for CD8, CD4, CD44, CD122 and Viability Dye. Cells were sorted into PBS + 2% BSA  + 2mM EDTA. FACS sorted cells were permeabilized in lysis buffer (10 mM Tris-Cl pH 8.0, 300 mM sucrose, 10 mM NaCl, 2 mM MgAc2, 6 mM CaCl2, 0.2% NP-40 (Igepal), 0.5 mM DTT, 1x Pierce protease inhibitor (Thermo Scientific), and 40 units of RiboLock RNase inhibitor (Thermo Scientific) per 10 mL buffer) by brief aggressive pipetting, washed with buffer W (10 mM Tris-Cl pH 8.0, 300 mM sucrose, 10 mM NaCl, 2 mM MgAc2, 0.008% Tween20, 0.5 mM DTT, 1x protease inhibitor, and 40 units of RiboLock RNase inhibitor per 10 mL buffer), and resuspended in storage buffer (50 mM Tris-Cl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 0.5 mM DTT, 1x protease inhibitor, and 40 units of RiboLock RNase inhibitor per 10 mL buffer). The cells were pelleted at 1000 g for 8 minutes for each step of buffer change. The permeabilized cells were counted, snap-frozen in liquid nitrogen, and stored at -80°C.
Libraries were prepared by the TREx core at Cornell University from 25,000 permeabilized cells as described in Buenrostro et al. (2015) and Corces et al. (2017). Briefly, frozen permeabilized cells were thawed, washed twice in ATAC-RSBbuffer containing 0.1% Tween20, resuspended in Transposition Mix (Nextera DNA Sample Preparation Kit, Illumina) containing 0.1% Tween20 and PBS, and incubated for 30 minutes at 37°C with shaking (1000 rpm). After column cleanup, libraries were amplified using Nextera PCR oligos (Nextera Index Kit, Illumina) and Ultra II Q5 Master Mix (NEB) for a total of 11 PCR cycles. The libraries were cleaned up twice (in series) with a 2:1 ratio of SPRIselect beads (Beckman Coulter).

value: B6 x gBT-I

tag: animal age

value: 6-7 days

tag: cell type

value: virtual memory (VM) splenocyte


title: GF_24h_37

value: PB + CLP


title: seaurchin_48hpf_embryo_MethylCseq_rep1

source_name: 48 hpf sea urchin embryo DNA subjected to MethylC-seq rep1

tag: tissue type

value: 48 hpf embryo


title: Co-infected, non progressing 16

description: small RNAsequencing analysis

value: plasma

tag: individual unique id

value: HIV positive

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: GF_3h_28

tag: group


title: GF_24h_35

tag: age


title: seaurchin_48hpf_embryo_MethylCseq_rep2

source_name: 48 hpf sea urchin embryo DNA subjected to MethylC-seq rep2

tag: tissue


title: Neonate_TN_miR29_rep3

value: true naive (TN) splenocyte


title: GF_3h_27

tag: genotype

tag: agent


title: seaurchin_24hpf_embryo_MethylCseq_rep1

source_name: 24 hpf sea urchin embryo DNA subjected to MethylC-seq rep1

value: 24 hpf embryo


title: GF_24h_34

tag: strain

tag: time point


title: Neonate_VM_NC_rep3

tag: cell state

tag: animal age


title: GF_0h_08

value: baseline


title: seaurchin_24hpf_embryo_MethylCseq_rep2

source_name: 24 hpf sea urchin embryo DNA subjected to MethylC-seq rep2

tag: tissue type


title: Co-infected, non progressing 14

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping

tag: hcv infection status

value: HCV positive

tag: gender

value: male

tag: age (in years)


title: seaurchin_72hpf_embryo_hMeDIPseq

data_processing:
Library strategy: hMeDIP-seq
hMeDIP-seq raw data was processed using the NGSANE framework v0.5.2.0 (Buske et al, 2014). Sequenced hMeDIP-seq reads in fastq format were trimmed using Trimmomatic software (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:20).
Trimmed reads were mapped to Spur_v3.1, Bl71nemr and danRer10 reference genomes for sea urchin, lancelet and zebrafish, respectively, using bowtie2 v2.1.0 with the following parameters: bowtie2 --end-to-end -R 2 -p 10 -N 1 --very-sensitive -X 1000 --no-mixed --no-discordant (Langmead et al, 2012)
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true.
Genome_build: sea urchin: Spur_v3.1; lancelet: Bl71nemr; zabrafish: danRer10
Supplementary_files_format_and_content: bigwig

source_name: 72 hpf sea urchin embryo DNA subjected to hMeDIP-seq

extract_protocol: hMeDIP-seq library preparation for the DNA hydroxymethylation profiling was performed  according to the Active Motif protocol (hMeDIP, Cat No 55010).

value: 72 hpf embryo

value: embryo


title: GF_0h_07

value: Germ free

value: 8-10 week old


title: seaurchin_adult_tubefeet_ACEseq_rep1

data_processing:
Library strategy: ACE-seq
Adapter clipping and read quality trimming using Trimmomatic (ILLUMINACLIP:NEXTflex.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:50 CROP:140 HEADCROP:10) (Bolger et al, 2014)
Trimmed reads were mapped to Spur_v3.1, Bl71nemr, danRer10 and mm10 genome references for sea urchin, lancelet, zebrafish and mouse, respectively, (all containing the λ phage genome as chrLambda and pUC19 plasmid genome as chrPUC) using WALT (Chen et al, 2016) with the following settings: -m 10 -t 24 -N 10000000 -L 2000.
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true (http://broadinstitute.github.io/picard/).
Reads with more than three consecutive non-converted cytosines in the CC, CA and CT context were removed using Picard Tools’ function FilterSamReads, in order to eliminate DNA molecules not efficiently deaminated by APOBEC3A
The numbers of hydroxymethylated and unmethylated cytosines at each genomic CpG position were called using the MethylDackel extract genome.fasta input.bam -o output --mergeContext. Additional MethylDackel extract parameters --minOppositeDepth 5 --maxVariantFrac 0.5 were used for the genotype correction (in order to exclude C-to-T nucleotide transitions in the genomic DNA of interest, which could be incorrectly considered as unmodified cytosines) (https://github.com/dpryan79/MethylDackel)
Genome_build: sea urchin: Spur_v3.1; lancelet: Bl71nemr; zabrafish: danRer10
Supplementary_files_format_and_content: bed / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting hydroxymethylated bases; 6. The number of alignments/pairs reporting unmethylated bases

source_name: sea urchin adult tube feet DNA subjected to ACE-seq rep1

extract_protocol: ACE-seq library preparation for the DNA hydroxymethylation profiling was performed as previously described {Schutsky et al, 2018 PMID: 30295673;Wang et al, 2021 PMID: 32822044}. Briefly, 100 ng of genomic DNA extracted from sea urchin, lancelet and zebrafish embryos and adult tissues was spiked with 1ng of CpG methylated λ phage DNA (Wisegene) and 0.5 ng of all-C hydroxymethylated pUC19 plasmid DNA (Wisegene) and sonicated to ~300 bp fragments using a M220 focused ultrasonicator (Covaris) with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA (125 ul total volume) was concentrated to 16.6 ul using AMPure beads (1 volume DNA : 2 volumes AMPure beads). 5hmC protection reaction was performed using β-glucosetransferase (10U/ul, New England Biolabs) in Cutsmart Buffer according to manufacturer’s instructions at 37°C for 1 hr, followed by 10 min at 65°C. The DNA was denatured in DMSO at 95°C for 10 min and immediately placed on dry ice for 2 mins allowing the samples to freeze. C and 5mC deamination reaction was performed using the APOBEC3A enzyme (NEBNext® Enzymatic Methyl-seq Kit, New England Biolabs) with the following ramping conditions: 4°C for 10 min, 4°C - 50°C 2:15 min per degree of the ramp, 50°C for 10 min. Deaminated DNA was then purified using AMPure beads (1 volume DNA : 1 volume AMPure beads) and subjected to low input library preparation using Accel-NGS Methyl-Seq DNA kit (Swift Biosciences). Briefly, DNA was denatured and subjected to an adaptase reaction, followed by primer extension, adapter ligation, and 15 cycles of indexing PCR. Library size and consistency was determined by the Agilent 4200 Tapestation system. The libraries were quantified using the KAPA library quantification kit (Roche).

value: adult tube feet

value: tube feet


title: Neonate_TN_NC_rep3

value: B6 x gBT-I

value: Naive

value: 6-7 days

tag: cell type


title: GF_0h_06

tag: group

value: wild type


title: Adult_VM_rep3

value: Thy1.1 x gBT-I

value: 8-12 weeks

value: virtual memory (VM) splenocyte


title: Co-infected, non progressing 11

description: small RNAsequencing analysis

value: plasma

value: HIV positive

value: female

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id

tag: library batch

tag: size selection and sequencing pool


title: Neonate_VM_miR29_rep2

tag: strain

tag: cell state


title: Co-infected, non progressing 12

description: small RNAsequencing analysis

tag: tissue

value: HCV positive

value: male


title: seaurchin_72hpf_embryo_ACEseq_rep1

source_name: 72 hpf sea urchin embryo DNA subjected to ACE-seq rep1

tag: age

value: 72 hpf embryo

value: embryo


title: Adult_TN_rep3

tag: animal age

value: true naive (TN) splenocyte


title: Co-infected, non progressing 10

description: small RNAsequencing analysis

tag: individual unique id

tag: sample id

tag: clinical grouping


title: seaurchin_48hpf_embryo_ACEseq_rep1

source_name: 48 hpf sea urchin embryo DNA subjected to ACE-seq rep1

value: 48 hpf embryo


title: Co-infected, non progressing 9

description: small RNAsequencing analysis

tag: hcv infection status

tag: gender

tag: age (in years)


title: seaurchin_24hpf_embryo_ACEseq_rep1

source_name: 24 hpf sea urchin embryo DNA subjected to ACE-seq rep1

value: 24 hpf embryo


title: Neonate_TN_miR29_rep2

value: B6 x gBT-I

tag: cell type


title: seaurchin_72hpf_embryo_input

source_name: 72 hpf sea urchin embryo input DNA sequencing


title: Co-infected, non progressing 15

description: small RNAsequencing analysis

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl


title: Co-infected, non progressing 8

description: small RNAsequencing analysis

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id


title: Neonate_VM_NC_rep2

value: Naive


title: Co-infected, non progressing 13

description: small RNAsequencing analysis

tag: library batch

tag: size selection and sequencing pool


title: Co-infected, non progressing 7

description: small RNAsequencing analysis


title: Co-infected, non progressing 6

description: small RNAsequencing analysis


title: Neonate_TN_NC_rep2

tag: strain

tag: cell state

value: 6-7 days


title: Adult_TN_rep2


title: Co-infected, non progressing 5

description: small RNAsequencing analysis

tag: tissue


title: Co-infected, non progressing 4

description: small RNAsequencing analysis


title: control_s1

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Reads were aligned to the reference assembly of the Saccharomyces cerevisiae genome using the bowtie  program with  the following parameters “-m 1 --best –strata” to allow up to 1 mismatch and report only the best scoring alignment.
PCR duplicates were removed by means of the rmdup utility from the samtools package
Peak were called by means of the MACS2 program. A FDR threshold of 10E-10 was applied.
Genome_build: saccer3
Supplementary_files_format_and_content: peaks in narrowpeak format

organism: Saccharomyces cerevisiae

source_name: Overnight cell cultures pre-grown in YEP

extract_protocol:
Following lysate clarification by centrifugation at 16,000 x g for 30 minutes at 4°C, pellets were resuspended in NP-40 ChIP lysis buffer and samples were sonicated for 15 minutes, 30 seconds on, 60 seconds off, at high power at 4°C with a Bioruptor® Plus sonicator (Diagenode).
Immunoprecipitation was carried out with anti-MYC (9E10) mouse monoclonal antibody following incubation followed by incubation with Dynabeads M-280 Sheep Anti-Mouse IgG (Life Technologies). Washing steps and reverse crosslinks were performed as reported in (46)(Ferrari, PLoS Genet., 11, e1004928). Inputs and IPs were purified using Wizard® SV Gel and PCR Clean-Up System (Promega, A9281); DNA was eluted in 80-100 µl of nuclease-free water.  DNA obtained from two independent pooled ChIP experiment was quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen, Q32851). ChIP-seq libraries were generated starting from 5 ng of DNA using an in house protocol (47), quality checked on a Bioanalyzer High-Sensitivity DNA Chip (Agilent) and sequenced on an Illumina HiSeq 2000 at 50 bp read length.

treatment_protocol: Cells were cross-linked with 1% formaldehyde (Sigma) for 10 minutes at 25°C

value: cell culture

tag: chip antibody


title: vid22_s1

growth_protocol: Overnight cell cultures pre-grown in YEP

value: anti-MYC (9E10)


title: Co-infected, non progressing 3

description: small RNAsequencing analysis

tag: individual unique id


title: Neonate_TN_miR29_rep1

source_name: CD8+ T cells

tag: animal age


title: Co-infected, non progressing 2

description: small RNAsequencing analysis

tag: sample id

tag: clinical grouping


title: Colon 26_Cell culture_Cell culture [R18072464RN01]

city: Cambridge

first: Min Young

last: Lee

state: MA

address: 40 Landsdowne St

institute: Takeda Pharmaceutical Company Limited

description: Colon 26_Cell culture_Cell culture

data_processing:
To quantify transcript abundance, we calculated the raw count for each gene from RNA-seq data using “Report gene/transcript counts” in Array Studio (version 10.0.1.118) and Ensembl.R78 annotation. Then DESeq2 (version 1.24.0) with default parameters was used to determine differentially expressed genes, requiring adjusted p-value ≤0.1 and the absolute log2 fold change ≥1. Ingenuity Pathway Analysis was used to determine the significantly enriched pathways. Tumor mutational burden was calculated by dividing the number of non-synonymous mutations called using exome sequencing data by the length of mouse CDS regions. SNPs were called and annotated using “summarize variant data” and “annotate variant table report,” respectively.
Compared CT-26 and Colon 26 tumors at each size (100, 400 and 800 mm3) separately to obtain 3 sets of differentially expressed genes, and then merged these gene sets to obtain the differentially expressed genes between CT-26 and Colon 26 tumors.
Genome_build: mouse NCBI genome build 38
Supplementary_files_format_and_content: FPKM of each sample
Supplementary_files_format_and_content: Count of each sample

source_name: Cell culture

growth_protocol: To establish murine colon adenocarcinoma cancer model Colon26 and CT-26, 3 x 105 cells were implanted into the right flank of female BALB/c mice.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When the mean tumor volume reached approximately 60 mm3, animals were randomized into treatment groups (n = 10/group) and dosing was initiated on Day 0 of the study. Tumor size and body weight were measured three times weekly. During the observation period, animals bearing oversized tumor exceeding 2,000 mm3 were sacrificed. Anti-mouse CTLA-4 (10 mg/kg), anti-mouse PD-1 (10 mg/kg) and anti-mouse PD-L1 mAbs (10 mg/kg) were administered intraperitoneally on day 0, 3, 7, 10, 14 and 17.

tag: tumor size

value: Cell culture

tag: tissue type

tag: model id

value: Colon 26


title: HL-60 cells, C. trachomatis-infected replicate 3

type: RNA

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Gene expression data from C. trachomatis-infected HL-60 sample

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing: CHP files were generated using Affymetrix Expression Control.

label: biotin

source_name: C. trachomatis-infected HL-60

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA

growth_protocol: HL-60 cells were maintained in RPMI-1640 medium supplemented with 10% v/v heat-inactivated fetal bovine serum (FBS) (Gibco; Germany), 2 mmol/l of L-glutamine, 8 mmol/l HEPES, 25 μg/ml gentamycin and 1 μg/ml fungisone under humidified air containing 5% CO2 at 37 °C. HL-60 cells were differentiated in the culture medium supplemented with 12.5 l/ml dimethyl sulphoxide (DMSO) for 3 days (14).

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

treatment_protocol: Differentiated HL-60 cells were infected with C. trachomatis serovar D at a multiplicity of infection (MOI) of 4 or identical volume of mock sample for 1 h in 0.5% glucose containing the medium. After infection HL-60 cells were washed twice with PBS and the culture medium without cycloheximide

tag: cell line

tag: cell type

value: neutrophil granulocyte

tag: infection

value: C. trachomatis


title: HL-60 cells, uninfected control replicate 3

description: Gene expression data from uninfected control HL-60 sample

source_name: uninfected control HL-60

value: control


title: HL-60 cells, C. trachomatis-infected replicate 1


title: Neonate_VM_NC_rep1

value: virtual memory (VM) splenocyte


title: Co-infected, non progressing 1

description: small RNAsequencing analysis

source_name: plasma

value: plasma

tag: hcv infection status

value: HIV positive

value: HCV positive

tag: gender

value: female

tag: age (in years)

tag: hemolysis score (deltact mir451-mir-23a)

tag: hemolysis grade (high_hl

tag: hemolysis status (<5_hl

tag: geo gse141522 sample id


title: Colon 26_Cell culture_Cell culture [R18072463RN01]

description: Colon 26_Cell culture_Cell culture


title: HL-60 cells, uninfected control replicate 1


title: HL-60 cells, uninfected control replicate 2


title: Colon 26_Cell culture_Cell culture [R18072462RN01]

description: Colon 26_Cell culture_Cell culture


title: Adult_VM_rep1

tag: strain

value: Thy1.1 x gBT-I

tag: cell state

value: 8-12 weeks


title: Adult_TN_rep1

tag: animal age

value: true naive (TN) splenocyte


title: Neonate_TN_NC_rep1

value: B6 x gBT-I

value: Naive


title: Adult_VM_rep2


title: CT26_Cell culture_Cell culture [R18070990RN01]

description: CT26_Cell culture_Cell culture


title: post_mesendo_competence_loss_ATACseq_rep3

first: Sharad

last: Ramanathan

address: 52 Oxford Street, Room 402

department: Molecular and Cellular Biology

institute: Harvard University

data_processing:
Reads were trimmed using NGmerge 0.2_dev in adapter removal mode with minimum overlap (-e flag) set to 20
Reads were aligned to the hg38 build of the human genome using bowtie2 2.2.9 using the --very-sensitive preset and with a maximum fragment size of 2000, then collated with samtools 1.9
Duplicate fragments were removed with picard 2.8.0
Peaks were called with MACS2 2.1.1 in callpeak -f BAMPE mode
Differentially accessible peaks were identified using the Bioconductor package DiffBind 2.12.0 in R 3.6.1
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated with HOMER 4.9; differential binding analysis was conducted with DiffBind 2.12.0 in R 3.6.1

source_name: OCT4:RFP; SOX2:YFP H1 hESCs

growth_protocol: Cells were grown on polyester membrane filters (Sterlitech) with 3 µm pores that had been treated with Matrigel.

extract_protocol:
Accutase-dissociated cells were sorted using a BD Aria III (BD Biosciences) using a 100 µm nozzle. Cells were gated such that the pre-competence-loss population was taken as the cells with the top 10-15% OCT4:RFP to SOX2:YFP ratio, and the post-competence-loss population was the bottom 10-15% OCT4:RFP to SOX2:YFP ratio. We sorted around 250,000 cells per subpopulation in a typical experiment. Populations were sorted into 1.5 mL centrifuge tubes (Eppendorf) filled with 500 µL of mTeSR supplemented with 10 µM γ-27632; by the end of the sort, ~800 µL of sheath and sorted cells had been added to each tube. After the sort had completed, we pelleted the cells in a microcentrifuge at 250 xg for 3 minutes, then resuspended in PBS. For each sorted sample, about 10% of the sorted cells were reserved for competence testing to confirm the pre-/post-competence-loss status of the sorted population. These cells were seeded back into glass-bottom 24-well plates (Ibidi) treated with Matrigel and filled with 1 mL of mTeSR supplemented with γ-27632 and allowed to recover for 3 hours. The media was then changed to mTeSR supplemented with BMP4 and Activin A for 36 hours. Cells were fixed and stained for OCT4 and SOX2. ATAC-seq was performed as previously described (Buenrostro et al., 2015). Briefly, live cells were lysed and incubated with Tn5 transposase for 30 min at 37°C.
After DNA purification, samples were amplified as described in (Buenrostro et al., 2015) for the appropriate number of cycles as determined by qPCR to minimize PCR bias.

treatment_protocol: Differentiation towards the ectoderm lineage was effected using mTeSR supplemented with 0.5 µM A83-01 (R&D Systems), a small molecule inhibitor of Activin and Nodal signaling. BMP4 + Activin A treatment was accomplished by treating cells with mTeSR supplemented with 3 ng/mL recombinant human BMP4 protein (R&D Systems) and 100 ng/mL recombinant human Activin A protein (R&D Systems).

value: hESC-derived ectoderm-directed differentiation, post- mesendoderm competence loss

tag: passages


title: CT26_Cell culture_Cell culture [R18070988RN01]

description: CT26_Cell culture_Cell culture

tag: tumor size


title: CT26_Cell culture_Cell culture [R18070989RN01]

description: CT26_Cell culture_Cell culture

tag: tissue type


title: In vitro barcoding Pool 2

organism: synthetic construct

source_name: In vitro barcoding Pool 2

extract_protocol:
Viable cells were sorted on the BD FACSAria III directly into Eppendorf tubes. The cells were then washed twice with PBS + 0.04% BSA.
Cells were lysed in 40 uL Viagen lysis buffer containing 0.5 mg/mL Proteinase K (Invitrogen) and split into technical replicates. Barcodes in cell lysate were then amplified following two rounds of PCR using Q5 polymerase (NEB). The first PCR amplified barcode specific DNA and added partial Illumina sequencing primer binding sites. PCR primers containing staggers to account for low sequence diversity during sequencing. In the second round PCR, the sequencing primer binding sites were completed, P5 and P7 flow cell regions were added and samples received a well-specific 8bp dual index (96 different indices in total).
DNA-Seq

tag: sample type

value: library


title: In vitro barcoding Pool 1

source_name: In vitro barcoding Pool 1


title: Colon 26_E6 - 800mm^3_Tumor [R18070613RN01]

description: Colon 26_E6 - 800mm^3_Tumor

source_name: Tumor

value: Tumor

tag: model id

tag: exact tumor volume (mm^3)


title: pre_mesendo_competence_loss_ATACseq_rep3

tag: cell type

value: hESC-derived ectoderm-directed differentiation, pre- mesendoderm competence loss


title: Neonate_VM_miR29_rep1

value: 6-7 days


title: mCHERRY barcode reference ibrary

description: mCHERRY-barcode-library_filtered_starcode_over1_truebc.fasta

source_name: mCHERRY barcode reference ibrary


title: Colon 26_E6 - 800mm^3_Tumor [R18070612RN01]

description: Colon 26_E6 - 800mm^3_Tumor

value: Colon 26


title: BFP barcode reference ibrary

source_name: BFP barcode reference ibrary


title: Colon 26_E6 - 800mm^3_Tumor [R18070611RN01]

description: Colon 26_E6 - 800mm^3_Tumor


title: Colon 26_E6 - 800mm^3_Tumor [R18070610RN01]

description: Colon 26_E6 - 800mm^3_Tumor


title: MDA-MB-231 cells, RBI2 treated 30min rep2

city: Birmingham

first: David

middle: A

last: Schneider

state: Alabama

address: 705 20th Street South

institute: University of Alabama at Birmingham

data_processing:
Sample sequences were aligned to a single copy of the human rDNA gene sequence (GenBank: U13369.1) using STAR (ver 2.7.6a) with parameters "--alignIntronMax 1 --outMultimapperOrder Random --outSAMmultNmax 1  --outReadsUnmapped Fastx".
Aligned reads were converted from SAM to BAM, sorted, and indexed using SAMtools (ver 1.11).
BAM files were converted to BED and then used to generate coverage bedGraph files with bedtools (version 2.29.2).
Unaligned reads from the previous STAR alignment were then used with Salmon (version 1.3.0) to quantify transcripts from HG38.
Differential expression was conducted using DESeq2 (version 1.28.1) to compare treated timpoints against control samples.
Genome_build: RNA repeating unit (GenBank: U13369.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: bedGraph files were generated using bedTools. These files detail coverage of RNA-seq reads mapping to the rDNA repeat unit reference.
Supplementary_files_format_and_content: xlsx files contain DESeq2 table outputs from comparing treated timepoints vs control transcript quantifications from salmon. There are separate Excel files for each treatment type, and sheets contained within for each timepoint.

growth_protocol: One million MDA-MB-231 cells were resuspended in 1X DMEM with 10% FBS media and incubated overnight at 37°C with 5% CO2

extract_protocol:
RNA was extracted with TRIzol followed by Purelink RNA mini kit
RNA-seq libraries were prepared using KAPA Stranded mRNA-Seq kit. Briefly, mature mRNA was captured from total RNA, fragmented, and then reverse transcribed into cDNA. Illumina Tru-seq adapters were ligated to the ends of the cDNA. The library was amplified, and 25 million reads per sample were sequenced using the Illumina Sequencing Platforms HiSeq2000

treatment_protocol: One million cells were incubated overnight and were then treated with 5 µM of RBI2 or CX-5461 as a function of time (10 minutes, 30 minutes, and 120 minutes).

tag: treatment compound

tag: treatment time

value: 30 minutes

tag: cell line


title: MDA-MB-231 cells, RBI2 treated 120min rep2

value: 120 minutes


title: MDA-MB-231 cells, RBI2 treated 10min rep2

value: 10 minutes


title: Colon 26_D5 - 400mm^3_Tumor [R18070605RN01]

description: Colon 26_D5 - 400mm^3_Tumor


title: MDA-MB-231 cells, RBI2 treated 10min rep1


title: MDA-MB-231 cells, CX-5461 treated 120min rep2


title: MDA-MB-231 cells, CX-5461 treated 120min rep1


title: young_arch

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing was performed on Illumina HiSeq 4000 (Pair-end, 100 base pairs per read).
The digital expression matrix was generated by demultiplexing, barcode processing, and gene unique molecular index counting using the Cellranger count pipeline (version 2.1.2, 10X Genomics).
Multiple samples were aggregated by cellranger aggr.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: aortic arch

extract_protocol:
In summary, mice were anaesthetized and perfused with 10mLs versene buffer through the left ventricle. The adventitia was removed and aorta dissected and cut open in versene buffer so that it laid like a flat sheet, exposing the endothelium. After versene washes, the aortae were bathed in 1X trypsin and incubated for 2X 5min at 37oC. Following this, the endothelium was gently removed using a microscalpel (EMS#72046-30) and repeat pipetting, now with sc-HBSS (containing 0.04%BSA and 2%FBS to inactivate the trypsin and Actinomycin D at 1ug/ml to block transcription) was applied this helped in removing the cells and obtaining a single cell suspension. The procedures were done under a dissecting microscope. Cells were pelleted and then treated with 1X RBC lysis buffer (eBioscience, #00-4333-57) for 1 minute and then washed twice with 0.04%BSA. Schematics of intimal cell isolation is shown in Figure 2A. To obtain enough cells, 6 (aged descending) or 8 (arch) C57BL/6 mice were used per library.
scRNA-seq libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10X Genomics). Cells were loaded accordingly to 10X Genomics protocol with an estimated targeted cell recovery of 5000 cells.

tag: tissue

value: aortic arch


title: Colon 26_D5 - 400mm^3_Tumor [R18070603RN01]

description: Colon 26_D5 - 400mm^3_Tumor


title: Colon 26_D5 - 400mm^3_Tumor [R18070604RN01]

description: Colon 26_D5 - 400mm^3_Tumor


title: HL-60 cells, C. trachomatis-infected replicate 2

value: neutrophil granulocyte

tag: infection

value: C. trachomatis


title: MDA-MB-231 cells, RBI2 treated 120min rep1


title: aged_aorta_a

source_name: descending aorta

value: descending aorta


title: Colon 26_D5 - 400mm^3_Tumor [R18070602RN01]

description: Colon 26_D5 - 400mm^3_Tumor


title: MDA-MB-231 cells, CX-5461 treated 30min rep2


title: mesendo_derived_outgroup_ATACseq_rep3


title: Colon 26_A1 - 100mm^3_Tumor [R18070593RN01]

description: Colon 26_A1 - 100mm^3_Tumor


title: MDA-MB-231 cells, CX-5461 treated 30min rep1


title: MDA-MB-231 cells, RBI2 treated 30min rep1


title: Colon 26_A1 - 100mm^3_Tumor [R18070592RN01]

description: Colon 26_A1 - 100mm^3_Tumor


title: MDA-MB-231 cells, CX-5461 treated 10min rep2


title: sample5: BCBL1 VA24 (6)

data_processing:
Illumina HiSeq 4000 (Illumina, Inc) reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1
High-quality reads were then aligned with STAR version 2.5.2b to create bam files.
Normalization of counts was performed using Limma package
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing gene names, read counts and statistics

growth_protocol: BCBL-1  cells were maintained at exponential growth in in RPMI1640 medium supplemented  with 10% FBS and 1x penicillin, streptomycin, glutamine (Thermo Fisher Scientific).

extract_protocol:
The cell pellet was lysed in 0.7ml of Tripure reagent (Roche, cat. no. 11667165001) for total RNA isolation using miRNeasy Mini kit (Qiagen, cat. No. , 217004) with DNase treatment.
RNA libraries were prepared by ACGT, inc (Germantown, MD). Indexed cDNA sequencing libraries were prepared from the RNA samples using the TruSeq Stranded mRNA Sample Preparation Kit, and bar-coded with individual tags, following the manufactures recommendations. Library preparation was performed using a 96-well plate method. The libraries were quantified using Qubit fluoroscopy and also with the NGS kit for Fragment Analyzer. Any failed results from the fragment analyzer were repeated using 2100 Bioanalyzer. Indexed libraries were prepared as equimolar pools and run on HiSeq4000 (2x150 paired end runs) in order to generate 40 million paired-end reads per sample library.

treatment_protocol: Before induction to lytic infection the cell were  diluted to 0.5 x 10e6 cells/ml and 10 ml of cell suspension was plated in10 cm dishes. The half ofsamples was treated with VA (Sigma-Aldrich) at final concentration 1 mM for 24h to induce viral lytic replication. The remaining untreated samples represent paired latently-infected samples.

tag: treatment

value: 1 mM VA/24 h

tag: infection stage

value: lytic

tag: gender

value: male

tag: cancer type

value: primary effusion lymphoma, PEL


title: GFP barcode reference ibrary

data_processing:
Barcode sequences were extracted from fastq files based on the known constant sequences flanking the random barcodes and subsequently trimmed to remove these regions such that only the random barcode sequences remained.
Barcode containing reads were further filtered to keep only those barcodes that (a) showed a correct upstream constant region (5’- CGATTGACTA-3’), (b) showed the expected barcode pattern (c) did not contain N residues, and (d) possessed an average phred quality of 30 or higher across the length of the barcode.
Barcode reads were then mapped to the respective SPLINTR reference library using bowtie v1.2.2 allowing up to 2 mismatches.
Barcode count data were imported into R v3.6 for further analysis.
Genome_build: SPLINTR reference library

source_name: GFP barcode reference ibrary


title: MDA-MB-231 cells, CX-5461 treated 10min rep1


title: Colon 26_A1 - 100mm^3_Tumor [R18070591RN01]

description: Colon 26_A1 - 100mm^3_Tumor


title: sample4: BCBL1 VA24 (2)


title: MDA-MB-231 cells, Control rep2


title: aged adventitia

source_name: adventitia

value: adventitia


title: sample3: BCBL1 UNINDUCED (7)

value: untreated

value: latent


title: MDA-MB-231 cells, Control rep1


title: Colon 26_A1 - 100mm^3_Tumor [R18070590RN01]

description: Colon 26_A1 - 100mm^3_Tumor

value: Tumor


title: sample2: BCBL1 UNINDUCED (5)


title: mesendo_derived_outgroup_ATACseq_rep2


title: aged_aorta_b


title: CT26_E6 - 800mm^3_Tumor [R18070583RN01]

description: CT26_E6 - 800mm^3_Tumor


title: sample1: BCBL1 UNINDUCED (1)


title: CT26_E6 - 800mm^3_Tumor [R18070584RN01]

description: CT26_E6 - 800mm^3_Tumor


title: post_mesendo_competence_loss_ATACseq_rep2

value: hESC-derived ectoderm-directed differentiation, post- mesendoderm competence loss