title: WT PYE + 9.3 mM gln log phase - rep 3


title: OMM2.3_shA3B_V5_ABCAM

status: Public on Jun 07 2023

type: SRA

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
Raw data was firstly processed using FastQC 0.11.9.
Clean data was obtained by removing adapters using Cutadapt 4.1 with default parameters.
Paired-end reads were aligned to genome GRCh38 using Bowtie2 v2.2.5.
After removing the duplicated reads with Picard 2.27.3, the read coverage and depth was calculated with Samtools 1.15.1.
Data were then filtered with minQualityScore＞2 using Samtools 1.15.1.
Peak calling was performed with SEACR 1.3. EdgeR package was used to get differential peaks.
BigWig file and reads distributions across genes were acquired using Deeptools 3.5.1.
Peak annotation was performed with ChIPseeker and ChIPpeakAnno package.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: RPMI1640, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were treated according to Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme)
Libraries were prepared using Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme). Libraries were amplified using 15 cycles on the thermocycler. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell line

tag: cell type

value: Uveal melanoma cells

tag: chip antibody


title: IFNAR 3 - Wt Macrophages, dsDNA+IFNARab, 2 biol replicates (cell culture), scRNA-seq

city: La Jolla

first: Kevin

middle: Robert

last: King

email: krking@health.ucsd.edu, krking@ucsd.edu

state: CA

address: 9500 Gilman Dr

department: Bioengineering; Medicine

country: USA

institute: University of California San Diego

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The alignments, filtering, and demultiplexing of generated fastq files were run with the 10X Genomics Cell Ranger analysis pipeline using standard configurations (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Variations in sequencing depth were accounted for by scaling each cell's total transcript count to 10,000 molecules and normalizing raw counts for each gene to the total transcript count for that cell followed by natural log transformation. Cells with between 200 and 2000 uniquely expressed genes and < 1% mitochondrial counts were retained for analysis. Highly variable genes were identified using the FindVariableFeatures method from seurat R package (version 3.0) to select 3000 genes with the highest variance after variance-stabilizing transformations.
Multiple single-cell RNA-seq datasets were integrated in Seurat to allow harmonized clustering and downstream analysis across conditions. Anchoring cell pairs between the datasets were identified with Canonical Correlation Analysis (CCA) and Mutual Nearest Neighbors (MNN) methods with the Seurat FindIntegrationAnchors function.
After scaling and centering expression values for each variable gene, the integrated data underwent linear dimensionality reduction using principal component analysis (PCA). Clustering was performed through the Shared Nearest Neighbor (SNN) clustering algorithm with Louvain method for modularity optimization using the Seurat FindNeighbors and FindClusters functions. Two-dimensional data visualization was done by performing Uniform Manifold Approximation and Projection (UMAP) demensional reduction, and differentially expressed genes (DEGs) between clusters were identified with the Wilcoxon Rank Sum test. Wherever specified, subsets of cells were bioinformatically isolated and reclustered to identify DEGs.
Assembly: GRCm38.p5
Supplementary files format and content: Tab-separated values files and counts matrix files consisting of matrix.mtx, features.tsv, barcodes.tsv

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Femurs and tibia were harvested from C57BL6 or IFNAR-/- mice. Bone marrow cells were flushed from femurs with ice-cold PBS and filtered through a 40 µm nylon mesh. The filtered solution was treated with red blood cell (RBC) lysis buffer (BioLegend). Bone marrow cells were flushed from femurs with ice-cold PBS and filtered through a 40 µm nylon mesh. The filtered solution was treated with red blood cell (RBC) lysis buffer (BioLegend).
Single cell libraries were prepared according to standard 10X Genomics protocols
Dual index Illumina single cell RNA sequencing

tag: tissue

value: Bone Marrow

value: Bone marrow derived monocytes

tag: treatment

value: M-CSF (Peprotech), HT DNA (Invivogen), MAR1-5A3 IFNAR neutralizing antibody (BioXCell)


title: OMM2.3_shCtrl_V5_ABCAM


title: PN5_KO_F6K_6

city: Bethesda

first: Guanghui

last: Yang

state: Maryland

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file, then mapped to the reference genome using STAR ver. 2.7.6a. The reference genome contains sequences of GRCm38 and ERCC spike-ins.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 101) and from ERCC spike-in product page.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM, TPM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: single embryo

extract_protocol:
Zygotes were collected from 6-8-week-old female mice after hormone simulation and mating. The zygotes were cultured in vitro to collect embryos at different developmental stages. M2 eggs were collected from hormone simulated females without mating. M2 eggs or embryos were washed in PBS and transferred into acidic Tyrodes solution to remove zonae pellucidae. Single zona-free eggs or embryos were finally lysed and processed following the scNMT-seq protocol.
G&T-Seq protocol was used to construct single embryo RNA-Seq libraries.

tag: strain

tag: developmental stage

tag: female mouse donor genotype


title: ∆ntrC PglnBA::IS3 PYE log phase - rep 3

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Reads were mapped to NA1000 Caulobacter crescentus genome and normalized using default settings for RNA-seq workflow in CLC Genomics Workbench v 21
Assembly: NA1000 Caulobacter crescentus
Supplementary files format and content: processed data file contains normalized counts (counts per million (CPM)) for each annotated gene in NA1000 Caulobacter crescentus genome

organism: Caulobacter vibrioides NA1000

source_name: cultures

growth_protocol: Starter cultures were grown for 18 hours at 30˚C in PYE or PYE plus 9.3mM (final concentration) glutamine. Cultures were then diluted to OD660 0.1 in their respective medium and grown for 2 h to get the cultures in similar (logarithmic) phase of growth. Once again, cultures were diluted to OD660 0.1 in their respective medium and grown another 3.25 h (OD660 < 0.4) to capture mRNA in similar log-phase growth.

extract_protocol:
6 ml of each culture were pelleted via centrifugation (1 min at 17,000 x g). Pellets were immediately resuspended in 1ml TRIzol and stored at -80˚C until RNA extraction. To extract RNA, thawed samples were incubated at 65˚C for 10 min. After addition of 200 µl of chloroform, samples were vortexed for 20 s and incubated at RT for 5 min. Phases were separated by centrifugation (10 min at 17,000 x g). The aqueous phase was transferred to a fresh tube and an equal volume of isopropanol was added to precipitate the nucleic acid. Samples were stored at 80˚C (1 h to overnight), then thawed and centrifuged at 17,000 x g for 30 min at 4˚C to pellet the nucleic acid.  Pellets were washed with ice-cold 70% ethanol then centrifuged for at 17,000 x g for 5 min at 4˚C.  After discarding the supernatant, pellets were air-dried at RT, resuspended in 100 µl RNAse-free water, and incubated at 60˚C for 10 min. Samples were treated with TURBO DNAse (Invitrogen) following manufactures protocol for 30 min at RT and then column purified using RNeasy Mini Kit (Qiagen).  RNA samples were sequenced at SeqCenter (Pittsburgh, PA). Briefly, sequencing libraries were prepared using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and custom rRNA depletion probes.  50 bp paired end reads were generated using the Illumina NextSeq 2000 platform (Illumina).
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices

treatment_protocol: For glutamine treatment conditions, 9.3 mM (final concentration) glutamine was added to growth medium

value: cultures

value: untreated


title: WT PYE + 9.3 mM gln log phase - rep 2

value: 9.3 mM (final concentration) glutamine


title: 92.1_A3B_ABCAM

data_processing:
Raw data of fastq format was processed using FastQC 0.11.9 software.
Clean reads were aligned to the reference genome GRCh38 using Bowtie2 v2.2.5 to generate bam files.
After removing PCR duplicates with Sambamba 0.8.2 software, MACS2 2.2.7.1 was used to identify regions of IP enrichment over background.
Deeptools 3.5.1 was used to transfer deduplicated bam file to BigWig format and to generate heatmaps and density plot figures.
ChIPseeker package and ChIPpeakAnno package were used for peak annotation and visualization.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using an ultrasonicator (Thermo Fisher).
ChIP-seq libraries were constructed by Novogene Corporation (Beijing, China). DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 3.0Flurometer(LifeTechnologies,CA,USA). Pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: 92.1_IgG_CST

value: normal rabbit IgG (CST, #2729)


title: IFNAR 2 - Wt Macrophages dsDNA, 2 biol replicates (cell culture), scRNA-seq

description: 10X Genomics

value: M-CSF (Peprotech), HT DNA (Invivogen)


title: 16HBE14o- CFTRhigh #4 rep2 [RNA-seq]

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.7 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using DAVID 2021.
Assembly: hg19
Supplementary files format and content: CSV file includes normalized count values for each sample

growth_protocol: Cells were grown in DMEM + 10% FBS using standard methods

extract_protocol:
Confluent 16HBE14o- cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and Bioanalyzer. Samples stored at -80oC under ethanol.
Oligo-dt mRNA directional

value: human bronchial epithelial cells

tag: genotype

value: CFTRhigh


title: WT PYE + 9.3 mM gln log phase - rep 1


title: ∆ntrC PglnBA::IS3 PYE log phase - rep 2


title: IFNAR KO dsDNA, 5 biol replicates (cell culture), scRNA-seq

description: 10X Genomics


title: PN5_KO_F6K_5


title: ∆ntrC PYE log phase - rep 3


title: PN5_KO_F6K_4


title: OMM2.3_A3B_ABCAM


title: mouse brain coronal tissue section 4, PCI

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

library_source: other

data_processing:
bcl2fastq v2.20.0.422
spaceranger count (spaceranger-1.3.1)
spaceranger mat2csv (spaceranger-1.3.1)
Assembly: Mouse reference, mm10 (GENCODE vM23/Ensembl 98); pre-build for Cell Ranger (2020-A)
Supplementary files format and content: Tagged Image File Format
Supplementary files format and content: filtered feature-barcode matrix
Library strategy: 10X Visium Spatial Transcriptomics

source_name: brain

extract_protocol:
According to Visium Spatial Gene Expression User Guide (CG000239, Rev E).
Tissue permeabilization time: 8 min. After transfer of cDNA from slide, cDNA was amplified with 14 cycles and after adapter ligation, sample index PCR was performed in dependence of the sample with 16 to 17 cycles.

treatment_protocol: Improved immunostaining protocol presented in the accompanying publication Hahn et al.

value: brain

value: PCI


title: PN5_KO_F6K_3


title: mouse brain coronal tissue section 3, PCI


title: IFNAR 1 - Wt Control Macrophages, 2 biol replicates (cell culture), scRNA-seq

description: 10X Genomics

value: M-CSF (Peprotech), Isotype Antibody Control (BioXCell)


title: OMM2.3_IgG_CST


title: ∆ntrC PYE log phase - rep 1


title: ∆ntrC PYE log phase - rep 2


title: mouse brain coronal tissue section 2, PCI


title: PN5_KO_F6K_2


title: PN5_KO_F6K_1


title: PN5_KO_F5K_8


title: WT PYE log phase - rep 3


title: AV HCT116 miRTar3p-2

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

data_processing:
Sequenced reads were mapped to hg38 human genome using Tophat and bowtie2
raw counts were calculated by HTSeq
Assembly: hg38
Supplementary files format and content: Excel sheet with normalized read counts for each sample comparison of interest, along with log2FoldChange values, p-values and adjusted p-values.

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.
RNA-Seq; sequenced on an NovaSeq SP PE150 using Illumina provided reagents and protocols

treatment_protocol: HCT116 cells were plated in 6-well plates and transfected with 10nM of miRNA mimic using RNAiMax. Total RNA was isolated after 24 hrs.

tag: biomaterial provider

value: Korean Collection for Type Cultures (KCTC)

value: Transfected with 10 nM miR-TAR-3p for 24hrs

value: wt


title: AV HCT116 NC1-2

value: Transfected with 10 nM NC1 for 24hrs


title: AV HCT116 miRTar3p-1


title: WT PYE log phase - rep 2


title: mouse brain coronal tissue section 1, SHAM

value: SHAM


title: PN5_KO_F5K_7


title: AV HCT116 NC1-1


title: PN5_KO_F5K_6


title: BMMCs, Pulsed, 4

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
Quality control of reads was perfromed using fastqc v.0.11.9 and RSeQC v.4.0.0 and mapped to reference mouse genome build Mus_musculus.GRCm39.107 using HiSat2 v.2.2.1.
Gene expression counts were generated using featureCounts v.2.0.1 and corrected for batch effect using the removeBatchEffect function in R.
Differenatial expression analysis was performed using the Omics Playground platform.
Assembly: GRCm39
Supplementary files format and content: *.gene.counts.txt files contain raq read counts for each samples.

source_name: BMMCs

extract_protocol:
Mettl3KO or Pulsed control cells were resuspended in Trizol and total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)
RNA libraries for RNA-seq were prepared using Tecan Revelo mRNA Library Prep Kit following manufacturer's protocols.

value: BMMCs

value: Mettl3 WT


title: BMMCs, Pulsed, 3


title: BMMCs, Pulsed, 2


title: FACS Motor neurons, mnx1, rep 2

city: Portland

first: Paul

last: Brehm

state: OR

address: 3232 SW Research Drive

department: Vollum

institute: Oregon Health and Science University

description: Cells dissociated from ~150 zebrafish spines and FACS sorted for GFP expression

data_processing:
Barcode processing and gene counting were preformed using Cell ranger software v6.1.1 (10X Genomics). Reads were aligned to a reference genome made using cellrangers mkref command using the GRCz11.fa and the zebrafish_custom_ref.GTF provided as a supplimental file. The zebrafish_custom_ref.GTF is a lightly modified version of the Lawson v 1.4.3 annotation (Lawson et al, 2020, eLife) in which GFP has been added and a number of naming mistakes have been corrected.
Normalization, integration, and quality control were preformed using Seurat. Clustering of the data was preformed using the Lieden algorithm implemented in Seurat with varying parameters depending on the sample. Clusters with markers indicating contamination (hindbrain and muscle) were removed as were clusters where over 90% of cells came from only one experimental run.
Neurons and glia were isolated based on the expression of markers within clusters, snap25a and elavl4 for neurons and slc1a2b, gfap, myrf and sox10 for glia. Neurons were then sub-clustered into 33 clusters and identities were assigned to 21 of them based on both established markers in the literature and a number of novel markers we were able to validate.
Motor neurons were isolated in the dataset based on the expression of motor neuron markers  mnx1, mnx2b, isl1, and cholinergic markers slc18a3a ,and chata within clusters. Motor neurons isolated this way were then integrated together using Seurat.
Assembly: GRCz11
Supplementary files format and content: Tab seperated value files, and matrix files providing the processed count matrices for each sample
Supplementary files format and content: RDS file providing the Seurat data object for the integrated spinal samples
Supplementary files format and content: RDS file providing the Seurat data object for the annotated set of clustered neurons from the integrated spinal samples
Supplementary files format and content: RDS file providing the Seurat data object for the integrated set of isolated motor neurons from all samples
Supplementary files format and content: GTF format record of the reference genome used in the creation of this data set

organism: Danio rerio

source_name: motor neurons

extract_protocol:
About 150 4-dpf larva were euthanized in 0.02% tricaine, and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase in bath solution (134 mM NaCl, 2.9 mM KCl, 1.2 mM MgCl2, 2.1 mM CaCl2, and 10 mM Na-HEPES, pH 7.8, ∼290 mOsm) at 28 °C for 1.5 hr, with intermittent trituration using a p200 pipette aid at 0, 0.5 hr and1 hr of the incubation. For the purpose of isolating spinal cords from remaining tissue, the final trituration was done using fire-polished Pasteur pipettes with decreased opening sizes (300, 200, 100 μm respectively).  Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution (in 1xPBS containing 1 mM EDTA) at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution (L15 with 1% fetal bovine serum). The tissue was collected by spinning at 400 g for 3 min at 4°C, washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire-polished Pasteur pipettes with 80-100 μm opening. The solution was filtered through a 35μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count, Trypan blue staining based - viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing. For FACS sorted samples single cell suspension was prepared as above from Tg(mnx1:GFP) fish and were FAC sorted for EGFP+ cells using a 100 μm nozzle on a BD inFlux cell sorter (Flow Cytometry Shared Resource, OHSU)
Single cell capture, cDNA synthesis and library preparation were performed by the Massive Parallel Sequencing Shared Resource at OHSU using the 10x Genomics Chromium v3.0 reagent kit. Single cell suspension for the two full spinal cord replicates targeted 10,000-15,000 cells, for the two FACS sorted samples 4,000-5,000 cells were targeted.

value: motor neurons

value: FACS sorted motor neurons

value: 4 dpf


title: PN5_KO_F5K_5


title: FACS Motor neurons, mnx1, rep 1


title: in vitro, lycorine treated CD8+ T, 4

city: NEW BRUNSWICK

first: Xiaosheng

last: Tan

state: NJ

address: 89 French St

institute: RUTGERS

description:
HUMAN All_samples_rpkm.txt
D4_CD8T_ly400

data_processing:
Illumina NovaSeq 6000 or DNBSEQ-T7 were used for basecalling. Samples are sequenced on the platform to get image files, which are transformed by the software  of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Sequencing data contains a number of connectors, low-quality Reads, fastp (v0.21.0) software was used to filter the sequencing data to get high quality sequence for further analysis .
Trimmed sequence reads were mapped to GRCh38 and GRCm38 using HISAT2 v2.1.0. (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
StringTie(v2.1.5) statistics were used to compare the Read Count values on each gene as the original expression of the gene, and FPKM were used to standardize the expression.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: RPKMs

source_name: PBMC

extract_protocol:
RNA was harvested using TRIzol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: sample type

value: in vitro

value: PBMC

value: primary

value: CD8+ T

value: WT


title: in vitro, lycorine treated CD8+ T, 3

description:
HUMAN All_samples_rpkm.txt
D3_CD8T_ly400


title: BMMCs, Pulsed, 1


title: in vitro, lycorine treated CD8+ T, 2

description:
HUMAN All_samples_rpkm.txt
D2_CD8T_ly400


title: PN5_KO_F5K_4


title: BMMCs, Mettl3-RNP, 4

value: Mettl3 KO


title: Spinal cord, saig, rep 1

description: Cells dissociated from ~150 zebrafish spines

source_name: spine

value: spine

value: mixed spinal cells


title: in vitro, lycorine treated CD8+ T, 1

description:
HUMAN All_samples_rpkm.txt
D1_CD8T_ly400


title: PN5_KO_F5K_2


title: in vitro, control CD8+ T, 4

description:
HUMAN All_samples_rpkm.txt
D4_CD8T


title: AGS cells, Gtr_3 [RNA-seq]

city: Jinan

first: Xin

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

description:
Gt_3
rRNA-free RNA-Seq

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, and b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Assembly: GRCh38 / miRBase 22.0
Supplementary files format and content: All.counts.txt: Tab-delimited text file contains counts for each sample.

source_name: AGS

growth_protocol: AGS cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After the MKN-28 cells were incubated with Fn49256-GCEx or GCEx in an anaerobic environment for another 24 hours, exosomes were extracted from the collected supernatant and added to the RPMI-1640 medium of AGS cells for co-culture.

value: AGS

value: gastric cancer cells

tag: condition

value: exosomes from F. nucleatum-infected MKN-28 cells (Fn49256-GCEx)


title: PN5_KO_F5K_1


title: AGS cells, Gtr_2 [RNA-seq]

description:
Gt_2
rRNA-free RNA-Seq


title: AGS cells, Gtr_1 [RNA-seq]

description:
Gt_1
rRNA-free RNA-Seq


title: in vitro, control CD8+ T, 3

description:
HUMAN All_samples_rpkm.txt
D3_CD8T


title: BMMCs, Mettl3-RNP, 2


title: PN5_KO_F4K_8


title: in vitro, control CD8+ T, 2

description:
HUMAN All_samples_rpkm.txt
D2_CD8T


title: BMMCs, Mettl3-RNP, 1


title: PN5_KO_F4K_7


title: 1154_ARccF_liver

city: Los Angeles

first: Jing

last: Liu

state: California

address: 1425 San Pablo St.

department: Department of Regenerative Medicine  & Stem Cell Biology

institute: University of Southern California

data_processing:
For sample 1- 145, RNA-seq reads from fastq with length lower than 20, average quality lower than 20 were filtered through Fastp version 0.20.1. Filtered reads were then aligned to the Ensembl release 103 primary assembly by STAR version 2.7.9a. Gene counts were derived from featureCount version 2.0.1.
For sample 146 - 188, RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa; For sample 1 - 145: Mus_musculus.GRCm39.103.gtf; For sample 146 - 188: Mus_musculus.GRCm39.101.gtf
Supplementary files format and content: 1_WashU_50SE_counts.txt; 2_BGI_PE150_counts.txt; 3_WashU_PE150_counts.txt
Supplementary files format and content: 146_155_all.gene_counts.txt, 156_188_all.gene_counts.txt

source_name: liver

extract_protocol:
Whole kidney total RNA were extracted using Qiagen’s RNeasy Mini Kit.
Sample 1- 67 and sample 98 - 188 were submitted to the Genome Access Technology Center at the McDonnell Genome Institute at University of Washington in St. Louis. Samples 1- 67, sample 98 - 145 were prepared according to Clontech SMARTer library kit manufacturer’s protocol, sample 146 - 188 were prepared according to polyA selection library kit manufacturer’s protocol. Sample 1- 67 were indexed, pooled, and sequenced on Illumina HiSeq2500 platform for 50-bp single-end. Sample 98 - 188 were indexed, pooled, and sequenced on llumina NovaSeq S4 2X150 (4 lanes). Sample 68 to Sample 97 were indexed, pooled and sequenced at BGI genomics with DNBseq platform according to the manufacturer's protocol. For sample 146 - 188, Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

value: liver

tag: Sex

value: F

value: Ar c/c

tag: age

tag: time

tag: fragment length

tag: library kit

value: mRNA Direct kit, Life Technologies


title: in vitro, control CD8+ T, 1

description:
HUMAN All_samples_rpkm.txt
D1_CD8T

tag: cell line


title: AGS cells, G3 [RNA-seq]

description:
G_3
rRNA-free RNA-Seq

tag: cell type

value: exosomes from control MKN-28 cells (GCEx)


title: AGS cells, G2 [RNA-seq]

description:
G_2
rRNA-free RNA-Seq


title: in vitro, lycorine treated CD4+ T, 4

description:
HUMAN All_samples_rpkm.txt
D4_CD4T_ly400

value: CD4+ T


title: Spinal cord, saig, rep 2

value: 4 dpf


title: AGS cells, G1 [RNA-seq]

description:
G_1
rRNA-free RNA-Seq


title: PN5_KO_F5K_3


title: in vitro, lycorine treated CD4+ T, 3

description:
HUMAN All_samples_rpkm.txt
D3_CD4T_ly400

value: in vitro

value: PBMC


title: 1152_ARccF_liver


title: in vitro, lycorine treated CD4+ T, 2

description:
HUMAN All_samples_rpkm.txt
D2_CD4T_ly400

value: primary


title: PN5_KO_F4K_4


title: 1151_ARccF_liver


title: in vitro, lycorine treated CD4+ T, 1

description:
HUMAN All_samples_rpkm.txt
D1_CD4T_ly400

value: WT


title: AGS cells, tr_2 [miRNA-seq]

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20, and c) 15bp < read length < 30bp.
Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Homo sapiens miRNA database and GRCh38 genome.
Count counting.
Assembly: GRCh38 / miRBase 22.0
Supplementary files format and content: process_data_file.txt: Tab-delimited text file contains counts for each sample.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: PN5_KO_F4K_2


title: in vitro, control CD4+ T, 4

description:
HUMAN All_samples_rpkm.txt
D4_CD4T


title: AGS cells, tr_1 [miRNA-seq]


title: AGS cells, 3 [miRNA-seq]


title: PN5_KO_F4K_3


title: 1150_Sox2CRE_ARcy_M_liver

value: M

value: Sox2Cre/+; Ar c/y


title: 1149_Sox2CRE_ARcy_M_liver


title: 1153_ARccF_liver


title: PN5_KO_F4K_6


title: in vitro, control CD4+ T, 3

description:
HUMAN All_samples_rpkm.txt
D3_CD4T


title: AGS cells, 2 [miRNA-seq]


title: 1147_Sox2CRE_ARcy_M_liver


title: BMMCs, Mettl3-RNP, 3

value: BMMCs

value: Mettl3 KO


title: AGS cells, 1 [miRNA-seq]

value: AGS

value: gastric cancer cells


title: PN5_KO_F3K_8


title: PN5_KO_F4K_5


title: 1146_Sox2CRE_ARcy_M_liver

value: liver


title: in vitro, control CD4+ T, 2

description:
HUMAN All_samples_rpkm.txt
D2_CD4T


title: AGS cells, tr_3 [miRNA-seq]

value: exosomes from F. nucleatum-infected MKN-28 cells (Fn49256-GCEx)


title: PN5_KO_F3K_7


title: in vitro, control CD4+ T, 1

description:
HUMAN All_samples_rpkm.txt
D1_CD4T


title: Lu134A_RNA

first: Masafumi

last: Horie

address: 2011 Zonal Ave

data_processing:
ATAC-seq: Reads were aligned against GRCh38 by Bowtie2 (version 2.3.5.1) with the following parameters: --very-sensitive --local --no-mixed --no-discordant -I 10 -X 2000. Duplication reads were removed by picard MarkDuplicates (version 2.23.8) and peak calling was performed with Genrich (version 0.6, available at https://github.com/jsh58/Genrich) with default parameters.
CUT&Tag: Quality control, alignment and removal of duplication reads was performed using the same pipeline with ATAC-seq. Peak calling was performed by SEACR (version 1.4) for H3K27ac (relaxed mode with using non-normalized IgG control track), H3K4me3 (stringent mode with using non-normalized IgG control track) and ELF3 (stringent mode without IgG control track with following parameter: -c 0.01))  and SICER2 (version 1.0.3) for H3K27me3.
ChIP-seq: Reads were mapped to GRCh38 using Bowtie2. Peak calling was performed using MACS2 with the following parameters: -q 0.0001. The input DNA sequence was used as a control.
RNA-seq: STAR (version 2.7.0f) was used for alignment against GRCh38 and read counts were calculated by RSEM (version 1.2.28) with TPM normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: gene.result

growth_protocol: ATAC-seq: 50,000 nuclei were prepared for each cell and incubated with transposition buffer containing Tagment DNA Enzyme1 and Tagment DNA Buffer. The transposed fragment was amplified by PCR and the PCR product was purified using AMPure XP beads. The sequence library was pooled at 5 nM.

extract_protocol:
ChIP-seq: 5.0 × 107 fixed cells were lysed to prepare nuclear extracts. Chromatin was sheared by sonication and the lysates were incubated overnight at 4°C with Dynabeads protein A coupled with anti-H3K4me3 and anti-H3K27ac antibody. After immunoprecipitation, beads were recovered using a magnet and washed; next, chromatin was eluted, and cross-links were reverted overnight at 65°C. DNA was purified and quantified with the Agilent Bioanalyzer.
RNA-seq: Total RNA was extracted using a RNeasy Mini kit. Libraries were prepared using TruSeq stranded mRNA Sample Preparation Kit according to manufacturer's protocol.

treatment_protocol: CUT&Tag: 100,000 cells were prepared and bound to concanavalin-coated magnetic beads. After permeabilizing the cells with digitonin, a primary antibody was added and incubated at room temperature for 2 hours. Next, a secondary antibody was added and incubated at room temperature for 1 hour. The beads were washed and CUTANA pAG-Tn5 for CUT&Tag was bound to the secondary antibody. After incubated with a solution containing Mg2+ to cleave the target DNA, the DNA was extracted and amplified by PCR. The PCR product was purified using AMPureXP magnetic beads. Sequence libraries were pooled at 5 nM.

value: SCLC (ASCL1 positive)


title: 1145_Sox2CRE_ARcy_M

source_name: kidney

value: kidney

value: mRNA Direct kit, Life Technologies


title: PN5_KO_F3K_6


title: WA-hT_RNA

source_name: WA-hT


title: 1148_Sox2CRE_ARcy_M_liver


title: 1144_Sox2CRE_ARcy_M


title: ES2-SRMS-cis8h-Rep3

city: San Antonio

first: Yunhan

last: Jiang

state: TX

address: 7703 Floyd Curl Dr

institute: University of Texas Health Science Center at San Antonio

data_processing:
CleanData (fastq format): Remove low quality readsthat contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). [Software: perl scripts in house, cutadapt]
Mapping to genomethe genome of ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/: Map the reads of each sample to the reference genome, [Software: HISAT2]
Transcripts assembly (gtf format): Assemble transcripts of each sample independently, [Software: StringTie]
Merged all assemblies to create a StringTie merged gtf, [Software: StringTie, gffcompare]
mRNAs expression profiling: StringTie was used to perform expression level for mRNAs by calculating FPKM [Software: StringTie]
Assembly: Differentially expressed mRNAs: The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR [Software: Rpackage - edgeR]
Supplementary files format and content: Homo sapiens GRCh38 DNA, release 96
Supplementary files format and content: tab-delimited text file include logCPM for each sample and each gene

growth_protocol: ES-2 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
High quality total RNA was extracted using RNeasy Plus micro kit  with  gDNA removed  (Cat: #74034, Qiagen, Hilden, Germany). The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.  Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: Ovarian cancer ES-2 cells expressing control vector or SRMS shRNA were treated with 15μM cisplatin for 8 hours.

value: human ovarian cancer cell

value: SRMS knockdown

value: cisplatin


title: DMS454_RNA


title: ES2-SRMS-cis8h-Rep2


title: PN5_KO_F4K_1


title: PN5_KO_F3K_5


title: 1143_Sox2CRE_ARcy_M


title: DMS53_RNA


title: ES2-SRMS-cis8h-Rep1


title: PN5_KO_F3K_4


title: 1142_Sox2CRE_ARcy_M


title: ES2-PLKO-cis8h-Rep3


title: PN5_KO_F3K_3


title: ES2-PLKO-cis8h-Rep2


title: 1141_Sox2CRE_ARcy_M


title: ES2-PLKO-cis8h-Rep1


title: PN5_KO_F3K_1


title: ECC12_RNA

value: GIS-NEC (ASCL1 positive)


title: TYUC-1_RNA


title: TCC-NECT-2_RNA


title: 1137_Six2TGC_Neurog2cc_F

value: F

value: Six2TGC/+, Neurog2c/c


title: 1140_Six2TGC_Neurog2cc_M

value: M


title: ES2-SRMS-cis0h-Rep3

value: PBS


title: 1134_Six2TGC_Neurog2cc_F


title: PN5_Het_E6W_7


title: ECC10_RNA


title: ES2-SRMS-cis0h-Rep2


title: ECC4_RNA


title: 1131_Six2TGC_Tbx10_Tm1a1c_M

value: Six2TGC/+, Tbx10Tm1a/1c


title: A99_RNA


title: ES2-SRMS-cis0h-Rep1


title: PN5_Het_E6W_4


title: DMS53_ATAC


title: 1132_Six2TGC_Tbx10_Tm1a1c_M


title: PN5_KO_F3K_2


title: PN5_Het_E6W_6


title: 1130_Six2TGC_Tbx10_Tm1a1c_F


title: PN5_Het_E6W_3


title: A99_ATAC


title: ES2-PLKO-cis0h-Rep2

value: WT


title: 1128_Six2TGC_Neurog2cc_M


title: PN5_Het_E6W_8


title: ECC4_ATAC


title: ES2-PLKO-cis0h-Rep1


title: 1129_Six2TGC_Tbx10_Tm1a1c_F


title: CD56dim, controller, rep10

city: Worcester

first: Ozkan

last: Aydemir

state: Massachusetts

address: 366 Plantation Street, Paul J. DiMare Center  N4-1085

institute: UMass Medical School

data_processing:
cutadapt v2.9 was used to trim and move the first 6 bases (UMIs) of the reads to the read header; demultiplex fastq files based on the inline sample barcodes to generate per-sample fastq files and remove adapter sequences.
Star v2.6.1 was used to align reads to human genome hg38 assembly.
UMI-tools v1.1.2 was used to deduplicate PCR duplicates based on the UMI sequences.
Deduplicated bam files were converted to fastq using samtools v1.9.
Kalliso v0.46.0 was used to quantify gene expression from deduplicated fastq files.
Assembly: hg38
Supplementary files format and content: Tab separated values and matrix file.

source_name: blood

growth_protocol: CD56hi, CD56dim, CD56negNK cells and ILCs were sorted from the PBMCs of HIV-1 negative people, HIV-1+ viremic people, HIV-1+ people under ART, and HIV-1+ spontaneous controllers.

extract_protocol:
The RNA of sorted cells were extracted with Trizol.
The mRNA library was constructed by CEL-Seq2 method.

value: blood

value: CD56dim NK cells

value: HIV positive spontaneous controller


title: CD56dim, controller, rep9


title: 1127_Six2TGC_Neurog2cc_F


title: PN5_Het_E6W_1


title: A99_WCE_ChIP


title: PN5_Het_E6W_2


title: 1126_Six2TGC_Neurog2cc_F


title: PN5_Het_E5W_7


title: ES2-PLKO-cis0h-Rep3


title: CD56dim, controller, rep8


title: A99_H3K27ac_ChIP

tag: antibody catalog/vendor

value: ab4729, Abcam

tag: antibody


title: 1124_Six2TGC_Neurog2cc_M

tag: tissue

tag: treatment


title: 1125_Six2TGC_Neurog2cc_F


title: CD56dim, controller, rep7


title: CD56dim, controller, rep6


title: DMS53_ELF3_CUT

data_processing:
Library strategy: CUT&Tag
ATAC-seq: Reads were aligned against GRCh38 by Bowtie2 (version 2.3.5.1) with the following parameters: --very-sensitive --local --no-mixed --no-discordant -I 10 -X 2000. Duplication reads were removed by picard MarkDuplicates (version 2.23.8) and peak calling was performed with Genrich (version 0.6, available at https://github.com/jsh58/Genrich) with default parameters.
CUT&Tag: Quality control, alignment and removal of duplication reads was performed using the same pipeline with ATAC-seq. Peak calling was performed by SEACR (version 1.4) for H3K27ac (relaxed mode with using non-normalized IgG control track), H3K4me3 (stringent mode with using non-normalized IgG control track) and ELF3 (stringent mode without IgG control track with following parameter: -c 0.01))  and SICER2 (version 1.0.3) for H3K27me3.
ChIP-seq: Reads were mapped to GRCh38 using Bowtie2. Peak calling was performed using MACS2 with the following parameters: -q 0.0001. The input DNA sequence was used as a control.
RNA-seq: STAR (version 2.7.0f) was used for alignment against GRCh38 and read counts were calculated by RSEM (version 1.2.28) with TPM normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: gene.result

value: SCLC (ASCL1 positive)

value: HPA003479, Sigma-Aldrich


title: 1121_Six2TGC_Tbx10_Tm1a1c_M

value: kidney

value: mRNA Direct kit, Life Technologies


title: PN5_Het_E5W_6

tag: strain

tag: developmental stage


title: PN5_Het_E5W_5

tag: female mouse donor genotype


title: PN5_Het_E5W_3


title: PN5_Het_E5W_8


title: 1119_Six2TGC_Tbx10_Tm1a1c_F

tag: genotype


title: PN5_Het_E5W_2


title: CD56dim, controller, rep4


title: CD56dim, controller, rep5


title: PN5_Het_E5W_4


title: CD56dim, controller, rep3


title: CD56dim, controller, rep2


title: A99_H3K4me3_ChIP

value: ab1012, Abcam


title: DMS53_H3K27ac_CUT


title: DMS53_H3K4me3_CUT

value: 39159, Active Motif


title: PN5_Het_E5W_1


title: 1120_Six2TGC_Tbx10_Tm1a1c_M


title: A99_IgG_CUT

value: GIS-NEC (ASCL1 positive)

value: PP64B, Merck Millipore

value: IgG


title: DMS53_H3K27me3_CUT

value: 9733S, Cell Signaling Technology


title: 1118_Six2TGC_Tbx10_Tm1a1c_F

value: F


title: PN5_Het_E4W_8


title: DMS53_IgG_CUT


title: CD56dim, controller, rep1


title: A99_ELF3_CUT


title: 1116_Six2TGC_Tbx10_Tm1a1c_M

value: M

value: Six2TGC/+, Tbx10Tm1a/1c


title: PN5_Het_E4W_7


title: A99_H3K4me3_CUT


title: PN5_Het_E4W_6


title: A99_H3K27me3_CUT


title: CD56dim, ART, rep8

value: blood

value: HIV positive under ART


title: 10_1110.Liver_Arcy_M

value: liver

value: Ar c/y


title: A99_H3K27ac_CUT

value: ab4729, Abcam


title: PN5_Het_E4W_5


title: 9_1109.Liver_Arcy_M


title: 8_1108.Liver_Arcy_M


title: 7_1107.Liver_Arcy_M


title: CD56dim, ART, rep6

value: CD56dim NK cells


title: 1117_Six2TGC_Tbx10_Tm1a1c_M

value: kidney


title: PN5_Het_E4W_3


title: ECC4_IgG_CUT


title: PN5_Het_E4W_4


title: ECC4_H3K4me3_CUT


title: PN5_Het_E4W_2


title: PN5_Het_E4W_1


title: 6_1106.Liver_Arcy_M

value: mRNA Direct kit, Life Technologies


title: CD56dim, ART, rep5


title: 5_1105.Liver_AlbCRE_Arcy_M

value: AlbCRE/+, Ar c/y


title: CD56dim, ART, rep4


title: CD56dim, ART, rep10


title: 1115_Six2TGC_Tbx10_Tm1a1c_M


title: CD56dim, ART, rep9


title: CD56dim, ART, rep3


title: ECC4_H3K27ac_CUT


title: 4_1104.Liver_AlbCRE_Arcy_M


title: CD56dim, ART, rep7


title: ECC4_ELF3_CUT

value: HPA003479, Sigma-Aldrich


title: CD56dim, ART, rep2


title: 3_1103.Liver_AlbCRE_Arcy_M


title: PN5_Het_E3W_6


title: PN5_Het_E3W_5


title: Adult intestinal esg+ cells, scute overexpression batch2, rep3

city: Colchester

first: Joaquin

last: de Navascues Melero

state: Essex

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

data_processing:
map with `--readFilesCommand zcat --outMultimapperOrder Random --outSAMmultNmax 1 --runMode alignReads --outSAMtype BAM Unsorted --quantMode GeneCounts`
index with `bamtools index -in aligned.bam -out indexed.bam`
sort with `bamtools sort -out sorted.bam -in indexed.bam`
count reads per gene with `featureCounts -T 8 -p -C -F GTF -t exon -g gene_id ...`
Assembly: FB2019_03 Dmel Release 6.28
Supplementary files format and content: .featurecounts files contain the mapping of reads to each gene in plain text (tab-delimited)
Supplementary files format and content: .summary files contain summary statistics of the mapping in plain text

organism: Drosophila melanogaster

source_name: Adult midgut

growth_protocol: Flies maintained at 18ºC in normal food until adulthood.

extract_protocol:
We dissected 100 midguts/genotype in triplicate and for each sample 20,000–40,000 cells were sorted into RNAse-free 1× PBS with 5 mM EDTA. RNA was isolated using the Arcturus PicoPure™ RNA Isolation Kit.
The entire amount of isolated RNA was used as input for RNA-amplification using the Arcturus™ RiboAmp™ HS PLUS Kit. Two hundred nanograms of amplified aRNA was used as input for RNA-Seq library preparation using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Switched to 29ºC in normal food for 2 days prior to dissection.

value: Adult midgut

value: esg-positive cells

value: esg-Gal4, UAS-GFP, tub-Gal80[ts], UAS-scute

value: temperature switch 18>29C


title: 1_1101.Liver_AlbCRE_Arcy_M


title: CD56dim, ART, rep1


title: Adult intestinal esg+ cells, scute overexpression batch2, rep1


title: CD56dim, viremic, rep10

value: HIV positive viremic


title: CD56dim, viremic, rep9


title: Adult intestinal esg+ cells, scute overexpression batch2, rep2


title: 2_1102.Liver_AlbCRE_Arcy_M

value: M


title: CD56dim, viremic, rep8


title: ECC4_H3K27me3_CUT

value: GIS-NEC (ASCL1 positive)

value: 9733S, Cell Signaling Technology


title: PN5_Het_E3W_4

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file, then mapped to the reference genome using STAR ver. 2.7.6a. The reference genome contains sequences of GRCm38 and ERCC spike-ins.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 101) and from ERCC spike-in product page.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM, TPM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample


title: Adult intestinal esg+ cells, da:da overexpression batch2, rep2

value: esg-Gal4, UAS-GFP, tub-Gal80[ts], UAS-da:da


title: PN5_Het_E3W_8


title: PN5_Het_E3W_2


title: PN5_Het_E3W_3


title: CD56dim, viremic, rep7

value: blood


title: Adult intestinal esg+ cells, da:da overexpression batch2, rep3


title: Adult intestinal esg+ cells, da:da overexpression batch2, rep1


title: 81_1068_ovariectomized_C57BL/6NCrl

value: F

value: 15mg/kg Testosterone (Sigma:T1500)

value: 24 hours

value: mRNA-Seq.cDNA Amplification - Clontech SMARTer


title: PN5_Het_E3W_1


title: CD56dim, viremic, rep6

value: CD56dim NK cells


title: PN5_Het_E3W_7


title: Adult intestinal esg+ cells, control batch2, rep3

value: esg-Gal4, UAS-GFP, tub-Gal80[ts]


title: 78_1065_castrated_C57BL/6NCrl

value: kidney


title: 77_1064_castrated_C57BL/6NCrl


title: 79_1066_ovariectomized_C57BL/6NCrl


title: 80_1067_ovariectomized_C57BL/6NCrl


title: PN5_Het_E2W_8


title: PN5_Het_E2W_7


title: CD56dim, viremic, rep4


title: Adult intestinal esg+ cells, control batch2, rep2

value: Adult midgut


title: CD56dim, viremic, rep5


title: Adult intestinal esg+ cells, control batch2, rep1

value: esg-positive cells


title: PN5_Het_E2W_6


title: 76_1063_castrated_C57BL/6NCrl


title: CD56dim, viremic, rep3


title: CD56dim, viremic, rep2


title: 75_1062_ovariectomized_C57BL/6NCrl

value: corn oil


title: BAF155, DN2 thymocytes, Bcl11b WT, rep 2

first: Alexandra

last: Bradu

address: 924 East 57th Street

department: Pathology

institute: University Of Chicago

data_processing:
Adaptor sequences were trimmed using SeqPurge (v2019_11).
Trimmed reads were mapped to mm10 mouse genome assembly using Bowtie2 (v2.2.9) with settings --local --very-sensitive-local –no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700.
PCR duplicates were removed using Picard (v2.21.8) MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT.
Reads with MAPQ scores below 30 were purged using samtools (v1.9) view with settings -b -q 30 -f 2 -F 1804.
BedGraph files were generated using bedtools (v2.27.1) genomecov and normalized by the number of fragments intersecting nucleosome-depleted promoter regions (-300 bp to +100 bp) relative to transcriptional start-sites).
BedGraphs were converted to BigWig format using bedGraphToBigWig (v4)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: thymus

extract_protocol:
CUT&RUN was performed as previously described (Skene et al., eLife, 2017) with minor modifications. Briefly, 500k cells were washed 3x in Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x EDTA-free protease inhibitor cocktail (Roche)), then bound to Concanavalin-A beads (Bangs Laboratories) according to manufacturer’s instructions. Cells were incubated with 1:100 dilution of anti-BAF155 antibody (G. Crabtree) overnight at 4 °C in Digitonin Buffer (0.025% digitonin, 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x EDTA-free protease inhibitor cocktail) supplemented with 2 mM EDTA. Sample was then incubated with pA-MNase (S. Henikoff) at 1:200 dilution in Digitonin Buffer at 4 °C for 1h. Digestion was performed under high Ca2+/low salt conditions in Low-Salt Rinse Buffer (3.5 mM HEPES pH 7.5, 0.5 mM spermidine, 0.025% digitonin) at 4 °C for 15 min. The reaction was stopped by the addition of 4x Stop Buffer (final concentration 170 mM NaCl, 10 mM EDTA, 20 mM EGTA, 0.025% digitonin, 25 µg/mL glycogen, 25 µg/mL RNase A (Thermo Fisher)) and the sample was incubated at 37 °C for 30 min. Sample was centrifuged at 16,000g for 10 min at 4 °C, supernatant recovered, and proteins digested in 1x Stop Buffer with 0.1% SDS and 250 µg /mL Proteinase K (New England Biolabs) for 1 hour at 55 °C. CUT&RUN fragments were purified by phenol chloroform extraction.
CUT&RUN libraries were generated using NEBNext UltraII DNA Library Prep Kit for Illumina coupled with NEBNext Multiplex Oligos for Illumina (New England Biolabs) with modifications optimized for small fragments as detailed in dx.doi.org/10.17504/protocols.io.bagaibse.

value: thymus

value: 3-6 weeks

value: male

value: DN23 thymocytes

tag: replicate

value: Bcl11bf/f; Vav1-Cre-/-


title: BAF155, DN2 thymocytes, Bcl11b cKO, rep 1

value: Bcl11bf/f; Vav1-Cre-/+


title: 74_1061_ovariectomized_C57BL/6NCrl


title: 73_1060_ovariectomized_C57BL/6NCrl


title: PN5_Het_E2W_4

extract_protocol:
Zygotes were collected from 6-8-week-old female mice after hormone simulation and mating. The zygotes were cultured in vitro to collect embryos at different developmental stages. M2 eggs were collected from hormone simulated females without mating. M2 eggs or embryos were washed in PBS and transferred into acidic Tyrodes solution to remove zonae pellucidae. Single zona-free eggs or embryos were finally lysed and processed following the scNMT-seq protocol.
G&T-Seq protocol was used to construct single embryo RNA-Seq libraries.


title: PN5_Het_E2W_3


title: CD56dim, viremic, rep1

value: blood

value: HIV positive viremic


title: CD56dim, HIVneg, rep10

value: HIV negative


title: DN3 thymocytes, Runx1 cKO, rep 2

data_processing:
Adaptor sequences were trimmed using SeqPurge (v2019_11).
Trimmed reads were mapped to mm10 mouse genome assembly using Bowtie2 (v2.2.9) with settings --very-sensitive -X 2000.
PCR duplicates were removed using Picard (v2.21.8) MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT.
Reads with MAPQ scores below 30 were purged using samtools (v1.9) view with settings -b -q 30 -f 2 -F 1804.
Peaks were called for each sample using MACS2 (v2.2.7.1) with settings --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01 --min-length 100. For each sample, a 501 bp fixed-width peak set was generated by extending the MACS2 summits by 250 bp in both directions. Peaks were ranked by significance (MACS2 peak score) and overlapping peaks with lower peak scores were removed iteratively to create non-overlapping sample peak sets. To facilitate comparison of peaks across samples, each peak’s ‘score-per-million’ (SPM) was calculated by dividing the peak score by the sum of all peak scores in the sample, divided by 1 million. All sample peak sets were merged, less significant overlapping peaks removed, and remaining peaks were filtered for those that were observed in at least two samples with an SPM value > 5. We removed peaks mapping to chrY as well as any that spanned genomic regions containing “N” nucleotides. We then removed any peak that overlapped with those called in activated B cell samples to create a “Total T cell” merged peak set. To identify T effector-specific peaks, sample peak sets from only peripheral T effector samples were merged and processed as above for non-overlapping, robust, reproducible peaks purged of activated B cell peaks. To account for less robust but significant T effector peaks which were robustly accessible in early thymocyte development, we added filtered sample peaks from DN1-DN4 stages (reproducible, SPM > 5) that overlapped with reproducible T effector peaks at SPM > 2 to this initial filtered T effector merged set. This merged set was again filtered for non-overlapping, robust (SPM > 5), reproducible peaks purged of activated B cell peaks to generate the final union peak set referred to as “T effector loci”.
To generate peak-by-sample count matrices, ATAC fragment counts within each peak were normalized by the number of inserts intersecting nucleosome-depleted promoter regions (-300 bp to +100 bp relative to transcriptional start-sites).
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing TSS-normalized fragment counts over all T effector loci (n = 65253) for each ATAC-seq sample

source_name: bone marrow

extract_protocol:
ATAC-seq was performed as described previously (Buenrostro et al., Nature Methods, 2013) with minor modifications. For nuclei isolation, 50,000-60,000 FACS-sorted cells were lysed in Thymocyte Hypotonic Buffer (25 mM HEPES, 5 mM MgCl2, 0.05 mM EDTA, 10% Glycerol, 0.1% NP40. Tagmentation reactions were performed for 30 minutes at 37 °C using reagents from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit. Tagmented DNA samples were purified with DNA Clean & Concentrator-5 kit (Zymo Research).
Libraries were quantified by qPCR, amplified accordingly, and purified using DNA Clean & Concentrator kit (Zymo Research).

value: bone marrow

value: 2-4 months

value: female

value: hematopoetic stem cell derived DN3

value: Runx1f/f; Rosa26nTnG/CreERT2

value: Tamoxifen


title: BAF155, DN2 thymocytes, Bcl11b WT, rep 1


title: CD56dim, HIVneg, rep9

value: CD56dim NK cells


title: 72_1059_castrated_C57BL/6NCrl

value: kidney

value: M

value: corn oil

value: 24 hours

value: mRNA-Seq.cDNA Amplification - Clontech SMARTer


title: DN3 thymocytes, Runx1 cKO, rep 1


title: 71_1058_castrated_C57BL/6NCrl


title: PN5_Het_E2W_1


title: 70_1057_castrated_C57BL/6NCrl


title: CD56dim, HIVneg, rep8


title: DN3 thymocytes, Runx1 WT, rep 1

value: Ethanol


title: CD56dim, HIVneg, rep7


title: DN3 thymocytes, Runx1 WT, rep 2


title: PN5_Het_E1W_8


title: PN5_Het_E1W_7


title: 69_1056_C57BL/6NCrl_M


title: PN5_Het_E2W_5


title: PN5_Het_E1W_6


title: DN2 thymocytes, Runx1 cKO, rep 2

value: hematopoetic stem cell derived DN2a


title: CD56dim, HIVneg, rep5

value: blood


title: CD56dim, HIVneg, rep6


title: DN2 thymocytes, Runx1 cKO, rep 1


title: PN5_Het_E1W_5


title: CD56dim, HIVneg, rep4


title: DN2 thymocytes, Runx1 WT, rep 2


title: PN5_Het_E2W_2


title: PN5_Het_E1W_4


title: 68_1055_C57BL/6NCrl_M


title: CD56dim, HIVneg, rep3


title: PN5_Het_E1W_3


title: DN2 thymocytes, Runx1 WT, rep 1


title: 66_1053_C57BL/6NCrl_M


title: 65_1052_C57BL/6NCrl_M


title: CD56dim, HIVneg, rep2


title: 64_1051_C57BL/6NCrl_M


title: DN1 thymocytes, Runx1 cKO, rep 2

value: hematopoetic stem cell derived DN1


title: CD56dim, HIVneg, rep1

value: HIV negative


title: PN5_Het_E1W_2


title: 63_1050_C57BL/6NCrl_F

value: F


title: DN1 thymocytes, Runx1 cKO, rep 1

value: bone marrow

value: 2-4 months


title: ILCs, controller, rep10

value: ILCs

value: HIV positive spontaneous controller


title: PN5_Het_E1W_1


title: DN1 thymocytes, Runx1 WT, rep 2

value: female

value: Runx1f/f; Rosa26nTnG/CreERT2


title: 67_1054_C57BL/6NCrl_M

value: kidney


title: 62_1049_C57BL/6NCrl_F


title: ILCs, controller, rep9


title: DN1 thymocytes, Runx1 WT, rep 1


title: 61_1048_C57BL/6NCrl_F


title: M2_Het_B8W_6

source_name: single M2 egg


title: ILCs, controller, rep7


title: ILCs, controller, rep8


title: DN3 thymocytes, Bcl11b cKO, rep 1

value: thymus

value: 3-6 weeks

value: DN3 thymocytes

value: Bcl11bf/f; Vav1-Cre-/+


title: DN3 thymocytes, Bcl11b cKO, rep 2

value: male


title: ILCs, controller, rep6


title: 60_1047_C57BL/6NCrl_F

value: mRNA-Seq.cDNA Amplification - Clontech SMARTer


title: 59_1046_C57BL/6NCrl_F


title: 58_1045_C57BL/6NCrl_F


title: M2_Het_B8W_4


title: DN3 thymocytes, Bcl11b WT, rep 1

value: Bcl11bf/f; Vav1-Cre-/-


title: DN3 thymocytes, Bcl11b WT, rep 2


title: ILCs, controller, rep4

value: blood


title: M2_Het_B8W_8


title: DN2 thymocytes, Bcl11b cKO, rep 2

value: DN2a thymocytes


title: M2_Het_B8W_3


title: M2_Het_B8W_2


title: 24_1061_Esr1c/c_F

value: F


title: ILCs, controller, rep3


title: 22_1055_Esr1c/c_F


title: DN2 thymocytes, Bcl11b cKO, rep 1


title: 23_1057_Esr1c/c_F


title: M2_Het_B8W_7


title: M2_Het_B8W_1


title: ILCs, controller, rep2


title: DN2 thymocytes, Bcl11b WT, rep 2


title: M2_Het_B7W_8


title: M2_Het_B8W_5


title: ILCs, controller, rep5


title: DN2 thymocytes, Bcl11b WT, rep 1


title: ILCs, controller, rep1


title: 20_1063_Esr1c/c_M

value: M


title: 21_1064_Six2TGC/+, Esr1c/c_F

value: Six2TGC/+, Esr1c/c


title: ILCs, ART, rep10

value: ILCs

value: HIV positive under ART


title: DN3 thymocytes, Smarca4 cKO, rep 2

value: bone marrow

value: 2-4 months

value: hematopoetic stem cell derived DN3

value: Smarca4f/f; Rosa26nTnG/CreERT2

value: Tamoxifen


title: 19_1062_Esr1c/c_M

value: kidney


title: M2_Het_B7W_6


title: M2_Het_B7W_7


title: ILCs, ART, rep9


title: DN3 thymocytes, Smarca4 cKO, rep 1


title: M2_Het_B7W_5


title: 18_1059_Esr1c/c_M


title: 17_1060_Six2TGC/+, Esr1c/c_M


title: DN3 thymocytes, Smarca4 WT, rep 2

value: Ethanol


title: ILCs, ART, rep8


title: 16_1058_Six2TGC/+, Esr1c/c_M


title: M2_Het_B7W_4


title: DN3 thymocytes, Smarca4 WT, rep 1

value: male


title: DN2 thymocytes, Smarca4 cKO, rep 3

value: hematopoetic stem cell derived DN2a


title: ILCs, ART, rep7


title: 15_1054_Six2TGC/+, Esr1c/c_M

value: mRNA-Seq.cDNA Amplification - Clontech SMARTer


title: M2_Het_B7W_3


title: M2_Het_B7W_2


title: 14_1037_Six2TGC/+, Ar_c/y_M

value: Six2TGC/+, Ar_c/y


title: M2_Het_B7W_1


title: DN2 thymocytes, Smarca4 cKO, rep 2


title: ILCs, ART, rep4

value: blood


title: 13_1036_Six2TGC/+, Ar_c/y_M


title: DN2 thymocytes, Smarca4 cKO, rep 1


title: ILCs, ART, rep3


title: M2_Het_B6W_8


title: DN2 thymocytes, Smarca4 WT, rep 2


title: ILCs, ART, rep2


title: DN2 thymocytes, Smarca4 WT, rep 3


title: ILCs, ART, rep1


title: 11_1031_Arc/c_F

value: F

value: Arc/c


title: DN2 thymocytes, Smarca4 WT, rep 1


title: ILCs, ART, rep6


title: M2_Het_B6W_5


title: M2_Het_B6W_7


title: M2_Het_B6W_6


title: DN1 thymocytes, Smarca4 cKO, rep 3

value: hematopoetic stem cell derived DN1


title: ILCs, ART, rep5

value: ILCs


title: 9_1029_Arc/c_F


title: M2_Het_B6W_4


title: ILCs, viremic, rep9

value: HIV positive viremic


title: DN1 thymocytes, Smarca4 cKO, rep 2

value: bone marrow


title: M2_Het_B6W_3


title: 8_994_Arc/c_F


title: ILCs, viremic, rep8


title: 7_991_Arc/c_F


title: DN1 thymocytes, Smarca4 cKO, rep 1

value: 2-4 months


title: M2_Het_B6W_2


title: ILCs, viremic, rep7


title: DN1 thymocytes, Smarca4 WT, rep 3


title: 5_1035_Six2TGC/+, Ar c/c_F

value: Six2TGC/+, Ar c/c


title: M2_Het_B6W_1


title: ILCs, viremic, rep6


title: DN1 thymocytes, Smarca4 WT, rep 2

value: Smarca4f/f; Rosa26nTnG/CreERT2


title: 4_1034_Six2TGC/+, Ar c/c_F


title: ILCs, viremic, rep5


title: 10_1030_Arc/c_F


title: ILCs, viremic, rep10


title: 3_1033_Six2TGC/+, Ar c/c_F


title: DN1 thymocytes, Smarca4 WT, rep 1


title: ILCs, viremic, rep4


title: M2_KO_B14K_7


title: M2_KO_B14K_6


title: ILCs, viremic, rep3


title: DN3 thymocytes, DMSO-treated, rep 1

value: hematopoetic stem cell derived DN3

value: WT

value: DMSO


title: M2_KO_B14K_5


title: 12_1032_Arc/c_F

value: kidney


title: SCHW00297

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Sequences were de-multiplexed using bcl2fastq and aligned to mouse mm10  genome (with Cre and tdTomato genes added).
Paired-end reads from Illumina were trimmed for adapters by  cutadapt(v1.15) and aligned to mm9 (MGSCv37, NCBI) by STAR(v2.5.2b, parameters "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix SCHW00296. --outSAMstrandField intronMotif --genomeLoad NoSharedMemory --outSAMattributes NH HI NM MD AS nM XS --outSAMunmapped Within KeepPairs --outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --outReadsUnmapped Fastx").
LiftOver was performed on GENCODE(vM9) gene database (from mm10 to mm9) by CrossMap(v0.1.5) to improve gene annotation.
Aligned reads were then counted by HTSEQ (v 0.6.1p1) for genes annotated in GENCODE database.  Trimmed reads were also run through FastQ Screen(v0.9.5) against Human, Mouse, Adapters, Univec  databases (Dec 2016) to check for contamination and doublets. Samples with larger unique hits to human over  mouse genomes were considered putative doublets and excluded from analysis. We further excluded samples  with less than 1M reads and those that did not express Dbh.
Assembly: mm9
Supplementary files format and content: raw counts table and quality control matrix

extract_protocol:
Fresh brain tissue was placed in ice-cold aCSF (2.5 mM KCl, 7 mM MgCl2, 0.5 mM CaCl2, 1.3 mM NaH2PO4, 110 mM choline chloride, 25 mM NaHCO3, 1.3 mM sodium ascorbate, 20 mM glucose, 0.6 mM sodium pyruvate, bubbled in 95% O2 /5%CO2). 200 μm coronal slices that included the LC were collected. Slices were transferred to a 32°C holding chamber containing oxygenated aCSF, where they recovered for at least 1 hour. tdTomato-expressing LC neurons were manually extracted from the slice using glass pipettes pulled from borosilicate glass (World Precision Instruments) to create an ~50 µm tip. The ends of glass pipette tips containing picked cells were snapped into individual wells of a 96 well plate containing 4µl lysis buffer: 0.1µl RNase inhibitor (Thermo Scientific), 0.1µl ERCC RNA spike-in (Invitrogen), 0.02µl 10% Triton (Sigma), 1µl 10mM dNTP (Invitrogen), 0.1µl 100µM dT (IDT; 5'-AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), and 2.68µl H2O.
Samples underwent primer annealing (72℃ for 3min) before placing on ice. Next, 6µl reverse transcription reagent was added to each sample: 0.14µl H2O, 0.25µl RNase inhibitor, 2µl 5X First Strand Buffer (Clontech), 0.5µl 100mM DTT (Invitrogen), 2µl 5M Betaine (Sigma), 0.06µl 1M MgCl2 (Invitrogen), 0.1µl 100µM TSO (Qiagen; 5'-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G), 0.95µl SmartScribe enzyme (Clontech). Samples were incubated at 42℃ for 90min, 70℃ for 5min, then held at 4℃. DNA preamplification solution (15µl) was next added to each sample: 2.1375µl H2O, 12.5µl 2X Kapa HiFi Hot Start Ready Mix (Kapa Biosystems), 0.25µl 10µM IS_PCR Primer (IDT; 5'-AAGCAGTGGTATCAACGCAGAGT), 0.1125µl Lambda Exonuclease (NEB). Samples were incubated at 37℃ for 30min, 95℃ for 3min, 21 cycles of [98℃ for 20s, 67℃ for 15sec, 72℃ for 4min], 72℃ for 5min, and then held at 4℃. DNA cleanup, quantification, dilution, tagmentation, and barcoding were performed by the Hartwell Center at St. Jude Children’s Research Hospital using standard methods.
Smart-seq2

value: brain

value: Dbh-Cre; Ai14 Neuron


title: DN2 thymocytes, FK506-treated, rep 1

value: male

value: hematopoetic stem cell derived DN2a


title: 1_992_Six2TGC/+, Ar c/c_F

value: F

value: mRNA-Seq.cDNA Amplification - Clontech SMARTer


title: ILCs, viremic, rep1

value: blood


title: M2_KO_B14K_4


title: SCHW00296


title: ILCs, HIVneg, rep10

value: ILCs

value: HIV negative


title: M2_KO_B14K_3


title: SCHW00295


title: M2_KO_B14K_8


title: M2_KO_B14K_2


title: DN1 thymocytes, FK506-treated, rep 2

value: bone marrow

value: hematopoetic stem cell derived DN1


title: ILCs, HIVneg, rep9


title: DN1 thymocytes, FK506-treated, rep 1

value: 2-4 months


title: ILCs, HIVneg, rep8


title: DN3 thymocytes, FK506-treated, rep 1


title: SCHW00294


title: 2_993_Six2TGC/+, Ar c/c_F

value: Six2TGC/+, Ar c/c


title: M2_KO_B14K_1


title: M2_KO_B13K_8


title: SCHW00292


title: DN1 thymocytes, DMSO-treated, rep 1


title: M2_KO_B13K_7


title: ILCs, HIVneg, rep6


title: ILCs, HIVneg, rep5


title: CD4 Activated T cells, rep 1

source_name: spleen

value: spleen

value: 3-6 weeks

value: female

value: activated CD4 T cells


title: SCHW00291

value: brain


title: SCHW00293

value: Dbh-Cre; Ai14 Neuron


title: SCHW00290


title: M2_KO_B13K_5


title: DN2 thymocytes, DMSO-treated, rep 1

value: male

value: WT

value: DMSO


title: CD4 Naïve T cells, rep 1

value: naive CD4 T cells


title: ILCs, HIVneg, rep7

value: blood


title: ILCs, HIVneg, rep4

value: ILCs


title: CD4 SP T cells, rep 1

value: thymus

value: CD4 single positive thymocytes


title: ILCs, HIVneg, rep3

value: HIV negative


title: M2_KO_B13K_4


title: SCHW00289


title: CD8 Activated T cells, rep 2

value: activated CD8 T cells


title: DN1 thymocytes, DMSO-treated, rep 2

value: bone marrow

value: 2-4 months

value: hematopoetic stem cell derived DN1


title: ILCs, HIVneg, rep2


title: M2_KO_B13K_3


title: CD8 Activated T cells, rep 1

value: spleen

value: 3-6 weeks

value: female


title: SCHW00288

value: brain

value: Dbh-Cre; Ai14 Neuron


title: SCHW00287


title: ILCs, HIVneg, rep1


title: CD8 Naïve T cells, rep 2

value: naive CD8 T cells

value: WT


title: M2_KO_B13K_2


title: SCHW00286


title: M2_KO_B13K_1


title: M2_KO_B13K_6


title: CD56neg, controller, rep10

value: CD56neg NK cells

value: HIV positive spontaneous controller


title: M2_KO_B12K_8


title: SCHW00285


title: CD8 SP T cells, rep 1

value: CD8 single positive thymocytes


title: CD56neg, controller, rep8

value: blood


title: M2_KO_B12K_6


title: M2_KO_B12K_7


title: SCHW00283


title: CD56neg, controller, rep9


title: SCHW00282


title: CD56neg, controller, rep7


title: DP thymocytes, rep 2

value: thymus

value: double positive thymocytes


title: M2_KO_B12K_4


title: SCHW00281


title: DP thymocytes, rep 1


title: CD56neg, controller, rep6


title: M2_KO_B12K_5


title: CD56neg, controller, rep5


title: CD8 Naïve T cells, rep 1


title: SCHW00280


title: M2_KO_B12K_3


title: CD56neg, controller, rep4


title: DN4 thymocytes, rep 2

value: DN4 thymocytes


title: DN4 thymocytes, rep 1


title: SCHW00279


title: CD56neg, controller, rep3


title: DN3 thymocytes, rep 2

value: DN3 thymocytes


title: CD8 SP T cells, rep 2


title: SCHW00278


title: SCHW00284


title: ILCs, viremic, rep2

value: ILCs

value: HIV positive viremic


title: CD56neg, controller, rep2


title: M2_KO_B12K_1


title: M2_KO_B10K_8


title: CD56neg, controller, rep1


title: DN2a thymocytes, rep 2

value: DN2a thymocytes


title: M2_KO_B10K_6


title: CD56neg, ART, rep9

value: HIV positive under ART


title: M2_KO_B10K_5


title: SCHW00275


title: SCHW00274


title: DN1 thymocytes, rep 2

value: 3-6 weeks

value: female

value: DN1 thymocytes


title: M2_KO_B12K_2


title: CD56neg, ART, rep8


title: M2_KO_B10K_3


title: SCHW00276

value: brain

value: Dbh-Cre; Ai14 Neuron


title: CD56neg, ART, rep7

value: CD56neg NK cells


title: SCHW00273


title: DN1 thymocytes, rep 1

value: WT


title: M2_KO_B10K_4


title: SCHW00272


title: CD56neg, ART, rep6


title: DN3 thymocytes, rep 1


title: R1021.12.C241_NKX_3

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
Sequencing reads were mapped using STAR against the Mus musculus genome (UCSC mm10), and gene level quantification was performed with featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file with featureCounts for all the samples combined

growth_protocol: All cell lines used in this study were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
ribosomal RNA depletion was performed using KAPA RiboErase kit (Roche) and libraries were prepared using KAPA Hyperprep kit (Roche) following manufacturer's protocols.

value: IPMN-associated cancer cells

value: Nkx6-2 overexpression


title: SCHW00277


title: SCHW00271


title: CD56neg, ART, rep5

value: blood


title: R1021.11.C241_NKX_2


title: DN2a thymocytes, rep 1

value: thymus


title: M2_KO_B10K_1

first: Guanghui

address: 50 South Drive


title: CD56neg, ART, rep10


title: R1021.9.C241_Ctrl_3

value: Control (WT)


title: SCHW00270


title: CD56neg, ART, rep4


title: M2_KO_A9K_8


title: R1021.8.C241_Ctrl_2


title: CD56neg, ART, rep3


title: M2_KO_A9K_7


title: M2_KO_A9K_6


title: R1021.7.C241_Ctrl_1


title: SCHW00267


title: M2_KO_B10K_2


title: CD56neg, ART, rep1


title: M2_KO_A9K_4


title: CD56neg, viremic, rep10


title: SCHW00266


title: SCHW00265


title: M2_KO_A9K_3


title: CD56neg, viremic, rep9


title: 3-HAA, replicate 2, scRNAseq

city: Hangzhou

first: Xue

last: Chen

state: Zhejiang

address: No.79, Qingchun Road, Shangcheng Distric

department: The First Affiliated Hospital

institute: Zhejiang University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: h5, raw count matrix generated by Cell Ranger count

source_name: mouse liver

extract_protocol:
Freshly collected Liver cancer from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was digested in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30-60 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive immune cells were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of CD45+ signal using a C57Bl6 mouse as negative control.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: immune cells

value: hepatocellular carcinoma (HCC)

value: 6-8 weeks old


title: 3-HAA, replicate 1, scRNAseq

description: 10x Genomics


title: 3-HAA, replicate 3, scRNAseq

description: 10x Genomics


title: M2_KO_A9K_5

last: Yang

institute: National Institutes of Health


title: R1021.10.C241_NKX_1


title: CD56neg, viremic, rep8

value: HIV positive viremic


title: M2_KO_A9K_2


title: SCHW00269


title: M2_KO_A9K_1


title: SCHW00263


title: SCHW00268


title: CD56neg, viremic, rep7


title: CD56neg, ART, rep2

value: HIV positive under ART


title: HCC, replicate 2, scRNAseq

description: 10x Genomics


title: HCC, replicate 3, scRNAseq

description: 10x Genomics


title: M2_Het_A4W_8


title: SCHW00262


title: CD56neg, viremic, rep6


title: HCC, replicate 1, scRNAseq

description: 10x Genomics


title: CD56neg, viremic, rep5


title: SCHW00261


title: F3.oil.D3651.2_F

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

data_processing:
Paired-end (75 + 75) FASTQ files were subjected to trimGalore pre-processing to remove Illumina adaptor sequences and low quality reads (Q<30).
Trimmed FASTQ files were subjected to alignment to mouse mm10 reference sequence using the STAR aligner to generate BAM files.
Expression of mRNA transcripts were determined using the R/Bioconductor package Rsubread.
The raw RNA counts were normalized using the negative binominal trimmed mean of M-values (TMM) algothem implemented by the R/Bioconductor package edgeR.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TMM-normalized values for each Sample.

source_name: embryonic gonad

extract_protocol:
cDNA was synthesized directlly from FACS-enriched mouse primordial germ cells (20,000 - 30,000 cells) using TAKARA SMARTer Ultra Low Input RNA kit (using a oligo-dT primer) following manurfacturer's instructions.
Illumina libraries were synthesized using TAKARA Low Input DNA Library Prep Kit following manufacturer's instructions.

value: embryonic gonad

tag: generation

value: primordial germ cell

value: F

value: Exposed to vehicle control


title: M2_Het_A4W_7

city: Bethesda


title: SCHW00260

source_name: brain

value: brain

value: Dbh-Cre; Ai14 Neuron


title: CD56neg, viremic, rep4

value: CD56neg NK cells


title: M2_Het_A4W_6


title: M2_Het_A4W_5


title: SCHW00259


title: F3.oil.D3651.1_M

tag: Sex

value: M


title: SCHW00264


title: CD56neg, viremic, rep3


title: CD56neg, viremic, rep2


title: M2_Het_A4W_4


title: M2_Het_A4W_3


title: SCHW00257


title: F3.oil.D3612.2_M


title: SCHW00258


title: SCHW00256


title: F3.oil.D3612.1_F


title: F3.oil.D3523.1_M


title: F3.oil.D3526.1_F


title: M2_Het_A4W_2


title: M2_Het_A4W_1


title: CD56neg, HIVneg, rep9

value: HIV negative


title: CD56neg, HIVneg, rep10

value: blood


title: F3.oil.D3402.3_M


title: M2_Het_A3W_8


title: SCHW00255


title: SCHW00250


title: SCHW00249


title: F3.oil.D3402.1_F


title: M2_Het_A3W_7


title: CD56neg, HIVneg, rep7


title: M2_Het_A3W_6


title: F3.oil.D1388.1_M


title: CD56neg, HIVneg, rep6


title: F3.oil.D1388.3_F


title: SCHW00248


title: SCHW00247


title: M2_Het_A3W_5


title: CD56neg, HIVneg, rep5


title: CD56neg, viremic, rep1


title: SCHW00246


title: F3.oil.D1344.3_F


title: M2_Het_A3W_4


title: F3.oil.D1344.2_M


title: CD56neg, HIVneg, rep4


title: CD56neg, HIVneg, rep3


title: M2_Het_A3W_3


title: F3.mid.D4021.2_M

value: Exposed to 0.2 mg/kg/day BaP


title: CD56neg, HIVneg, rep2


title: CD56neg, HIVneg, rep8


title: M2_Het_A3W_2


title: SCHW00245


title: SCHW00244


title: SCHW00243


title: F3.mid.D4021.1_F


title: F3.mid.D1464.2_M


title: M2_Het_A3W_1


title: CD56neg, HIVneg, rep1


title: M2_Het_A10W_8


title: CD56hi, controller, rep10

value: CD56hi NK cells

value: HIV positive spontaneous controller


title: CD56hi, controller, rep9


title: M2_Het_A10W_7


title: SCHW00241


title: SCHW00240


title: F3.mid.D1464.1_F


title: M2_Het_A10W_6


title: CD56hi, controller, rep8


title: F3.mid.D1390.1_M


title: SCHW00239


title: M2_Het_A10W_5


title: F3.low.D3744.4_M

value: Exposed to 0.033 mg/kg/day BaP


title: SCHW00238


title: CD56hi, controller, rep6


title: M2_Het_A10W_3


title: SCHW00237


title: CD56hi, controller, rep5


title: F3.low.D3501.3_F


title: SCHW00235


title: SCHW00242


title: CD56hi, controller, rep4


title: M2_Het_A10W_2


title: F3.low.D3501.1_M


title: SCHW00234


title: F3.mid.D1390.5_M


title: M2_Het_A10W_1


title: CD56hi, controller, rep2


title: SCHW00232


title: F3.low.D2549.1_F


title: PSN1, H3K27Ac

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
For human samples, reads were aligned using Bowtie2 to GRCh37 and SE peaks were called using HOMER v4.11.1 default settings (-style super, Fold change >4, p-value <0.0001).
For mouse samples, reads were aligned using Bowtie2 to MGSCv37 (mm9) and differential peaks were called using HOMER’s79 default settings (Fold change >4, p-value <0.0001) using '-style factor'.
Data tracks were visualized using IGV v2.3.90.
Assembly: GRCh37 (human) and MGSCv37 (mm9) for mouse
Supplementary files format and content: bedGraph, bed

source_name: PDAC

extract_protocol:
Briefly, cells were fixed, nuclei were isolated, lysed, and sheared with a Diagenode Bioruptor to yield DNA fragment sizes of 200 –1,000 bp, and active chromatin was immunoprecipitated.
Libraries were prepped and sequenced on the Illumina HiSeq4000 using barcoded multiplexing and a single-end 100bp length.

value: PDAC

tag: treatment duration

tag: chip antibody


title: F3.low.D2549.3_M


title: CD56hi, controller, rep3


title: SU86, 86, H3K27Ac


title: CD56hi, controller, rep7


title: F3.low.D2374.5_F


title: F3.low.D3744.1_F


title: SCHW00231


title: M2_Het_A10W_4

state: Maryland


title: AA0779E, H3K27Ac


title: SCHW00233


title: F3.low.D2374.1_M


title: SCHW00229


title: CD56hi, ART, rep10


title: MiaPaca2, H3K27Ac


title: CD56hi, controller, rep1


title: CD56hi, ART, rep9


title: F3.high.E0103.2_F

value: Exposed to 2 mg/kg/day BaP


title: Panc03, 27, H3K27Ac


title: SCHW00228


title: CD56hi, ART, rep8

value: HIV positive under ART


title: F3.high.D4190.2_F

value: embryonic gonad


title: SCHW00226


title: CD56hi, ART, rep7


title: Panc02, 03, H3K27Ac


title: F3.high.D4190.1_M

value: primordial germ cell


title: SCHW00225


title: Panc1, H3K27Ac


title: CD56hi, ART, rep6


title: F3.high.D2204.1_F

value: F


title: HS766T, H3K27Ac


title: CD56hi, ART, rep5


title: HupT4, H3K27Ac


title: F3.high.D2203.2_M


title: CD56hi, ART, rep4


title: F3.high.D2032.3_M


title: SCHW00222


title: SCHW00223


title: KCIMOH1, H3K27Ac


title: CD56hi, ART, rep3


title: CD56hi, ART, rep2


title: PaTu8988T, H3K27Ac


title: SCHW00220


title: PaTu8902, H3K27Ac


title: CAPAN2, H3K27Ac


title: SCHW00219


title: F2.oil.D3133.5_M

value: Exposed to vehicle control


title: F3.high.D2032.2_F


title: F2.oil.D3133.2_F


title: SCHW00218

value: brain


title: CD56hi, viremic, rep10

value: HIV positive viremic


title: F2.oil.D3001.2_F


title: SCHW00224

value: Dbh-Cre; Ai14 Neuron


title: CAPAN1, H3K27Ac


title: F2.oil.D3001.1_M

value: M


title: CD56hi, viremic, rep9


title: SCHW00217


title: CD56hi, viremic, rep8


title: Mutj, H3K27Ac

value: Mutj


title: F2.oil.D2996.2_M


title: SCHW00215


title: YAPC, H3K27Ac

value: YAPC


title: SCHW00221


title: CD56hi, viremic, rep7

value: blood


title: MEL290 cells, A3B OE, replicate2

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence through in-house perl scripts
Short reads were aligned to the reference human genome GRCh38 using STAR
Gene expression in terms FPKM of genes overlapping with gene annotations in Ensembl release 75 was calculated by Cufflinks
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: 92.1 and MEL290 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Uveal melanoma cells

value: A3B overexpression


title: SCHW00214


title: F2.oil.D2991.3_M


title: F2.oil.D2996.1_F


title: CD56hi, viremic, rep6

value: CD56hi NK cells


title: CD56hi, ART, rep1


title: SCHW00209


title: MEL290 cells, NC, replicate2

value: Contrl


title: CD56hi, viremic, rep5


title: SCHW00213


title: SCHW00207


title: CD56hi, viremic, rep4


title: F2.oil.D2991.1_F


title: CD56hi, viremic, rep3


title: 92.1 cells, shA3B, replicate2

value: A3B knockdown


title: CD56hi, viremic, rep2


title: F2.oil.C4992.1_F


title: SCHW00205


title: F2.oil.C4988.3_F


title: SCHW00206


title: SCHW00204


title: 92.1 cells, shA3B, replicate1


title: F2.oil.C4988.2_M


title: CD56hi, viremic, rep1


title: 92.1 cells, shCtrl, replicate2


title: MEL290 cells, A3B OE, replicate1


title: 92.1 cells, shCtrl, replicate1


title: CD56hi, HIVneg, rep10

value: HIV negative


title: SCHW00200


title: SCHW00203


title: F2.mid.D3371.2_M

value: embryonic gonad

value: Exposed to 0.2 mg/kg/day BaP


title: F2.oil.C4992.2_M

value: primordial germ cell


title: CD56hi, HIVneg, rep9


title: F2.mid.D3371.1_F

value: F


title: JLAT.PMA.rep3 (DISE-56)

first: Marcus

last: Peter

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

description: Single Read

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after).  This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Supplementary files format and content: Tab-delimited file with read, seed (bp 2-7), cell viability based on seed, raw read counts for each sample, and putative source based on blast

source_name: J-Lat cells induced with 0.1 µM PMA

extract_protocol:
Cell lysates were subjected to pull down with a GW182 FLAG-GST- T6B peptide isolated using anti-FLAG M2 Magnetic beads. Bound RNA was extracted using Trizol follwing by ethanol precipitation.
Small RNA-SEQ libraries containing library fragments 140-160 bp in size were generated using Illumina TruSeq small RNA adapters the protocol described in Hafner et al. (2012) Methods 58:164. RNA of 19-35 nt in length was size selected by Urea-PAGE gel extraction after adpater ligation. The final library of ~157bp was size selected on an agarose-TBE gel. Quality of final cDNA was assessed by Agilent Bioanalyzer and DNA concentration determined by Qubit.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: RNA was isolated from cells uninfected or infected with VSVg pseudotyped HIV R9 Env 𝚫iGFP reporter virus after 28hrs

tag: biomaterial provider

value: Dr. Judd Hultquist

value: J-Lat

value: Cells induced with 0.1 µM PMA and harvested after 36 hours


title: MEL290 cells, NC, replicate1


title: JLAT.PMA.rep2 (DISE-56)

description: Single Read


title: CD56hi, HIVneg, rep7


title: JLAT.PMA.rep1 (DISE-56)

description: Single Read


title: F2.mid.D1064.4_F


title: SCHW00193

value: brain

value: Dbh-Cre; Ai14 Neuron


title: SCHW00192


title: CD56hi, HIVneg, rep6


title: F2.mid.D1040.2_F


title: JLAT.DMSO.rep3 (DISE-56)

description: Single Read

source_name: Uninduced J-Lat cells

value: Uninduced DMSO control cells


title: CD56hi, HIVneg, rep5

value: blood


title: SCHW00191


title: F2.mid.D1040.1_M

value: M


title: JLAT.DMSO.rep2 (DISE-56)

description: Single Read


title: JLAT.DMSO.rep1 (DISE-56)

description: Single Read


title: SCHW00190


title: CD56hi, HIVneg, rep3


title: F2.low.D3136.2_F

value: Exposed to 0.033 mg/kg/day BaP


title: CD56hi, HIVneg, rep8

value: CD56hi NK cells


title: SCHW00186


title: CD56hi, HIVneg, rep2


title: SCHW00187


title: F2.low.D2256.3_F


title: F2.mid.D1064.1_M


title: F2.low.D3136.1_M


title: CD56hi, HIVneg, rep1


title: F2.low.D2256.2_M


title: Jurkat.droshaKO.3F6.HIV348.rep3 (DISE-56)

description: Single Read

source_name: Jurkat Drosha k.o. clone F6 replication competent HIV-1 NL4-3 Nef:IRES:GFP infected cells

value: ATCC

value: Jurkat

value: Drosha k.o.

tag: infection

value: Cells were infected with replication competent HIV-1 for 12hrs


title: Jurkat.droshaKO.3F6.HIV348.rep2 (DISE-56)

description: Single Read

tag: cell line


title: SCHW00184

tag: cell type


title: F2.low.D1996.2_M

value: embryonic gonad


title: SCHW00185


title: Jurkat.droshaKO.3F6.HIV348.rep1 (DISE-56)

description: Single Read


title: Jurkat.parental.HIV348.rep3 (DISE-56)

description: Single Read

source_name: Jurkat wt replication competent HIV-1 NL4-3 Nef:IRES:GFP infected cells

value: wt


title: SCHW00183


title: F2.low.D1996.1_F

value: primordial germ cell

value: F


title: Jurkat.parental.HIV348.rep2 (DISE-56)

description: Single Read


title: SCHW00182


title: CD56hi, HIVneg, rep4

value: HIV negative


title: F2.high.D4028.3_M

value: Exposed to 2 mg/kg/day BaP


title: Jurkat.parental.HIV348.rep1 (DISE-56)

description: Single Read


title: in_vitro_rep4

city: Durham

first: Clare

last: Smith

state: North Carolina

address: 207 Research Drive

department: MGM

institute: Duke University

data_processing:
Basecalls performed using CASAVA version 1.8
100-base paired-end reads were trimmed and aligned to the M. tuberculosis H37Rv genome to identify sites of himar1 insertion. Custom Perl programs available at https://github.com/sassettilab/Bellerose_et_al_mSystems_TnSeq_analyses were used for the read trimming and subsequently to summarize insertion counts at each genomic TA dinucleotide (see subdirectory 'TnSeq_insertion_counts_v6' under the aforementioned Github link).
Insertion mutant counts across all libraries were normalized by beta-geometric correction (DeJesus, M.A., Ambadipudi, C., Baker, R., Sassetti, C., and Ioerger, T.R. (2015). TRANSIT--A Software Tool for Himar1 TnSeq Analysis. PLoS Comput Biol: 11, e1004401), binned by gene, and replicate values for each mouse genotype averaged.
Assembly: NC_018143.2
Supplementary files format and content: Tab-delimited text files generated in the custom data processing pipeline: col 1, genome coordinate; col 2, unique insertion counts
Library strategy: TnSeq

organism: Mycobacterium tuberculosis H37Rv

source_name: homogenized mouse spleen

extract_protocol:
Spleens from infected mice were homogenized and approximately 1.0E+06 CFU per mouse was plated on 7H10 agar with 20ug/mL kanamycin. After three weeks of growth, colonies were harvested by scraping, and genomic DNA was extracted as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling, Methods Mol Biol: 1279:79-95.
Libraries were prepared for Illumina sequencing using custom primers as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 1279:79-95. In the majority of cases, two replicate mouse libraries were used per genotype. Only a single TnSeq library was obtained for BXD48a and BXD51. Five replicate libraries were obtained for in vitro-grown libraries.

treatment_protocol: Mice were infected with 1.0E+06 CFU of saturated Himar1 transposon mutants delivered via intravenous tail vein injection. At 4 weeks post-infection, mice were euthanized and organs harvested.

tag: h37rv genotype

value: himar1 transposon library

tag: mouse strain

tag: infection length (days)


title: in_vitro_rep5


title: in_vitro_rep3


title: F2.high.D4028.2_F

tag: tissue

tag: treatment


title: Jurkat.droshaKO.3F6.UT.rep3 (DISE-56)

city: Chicago

description: Single Read

source_name: Jurkat Drosha k.o. clone F6 uninfected cells

value: Uninfected cells


title: F2.high.D3620.6_M

tag: strain


title: F2.high.D3620.3_F


title: BXD102.RwwJ_rep2


title: in_vitro_rep2


title: BXD102.RwwJ_rep1


title: F2.high.D1669.5_F


title: SCHW00174

value: brain

value: Dbh-Cre; Ai14 Neuron


title: SCHW00173


title: in_vitro_rep1


title: SCHW00176


title: SCHW00177


title: BXD93.RwwJ_rep1


title: Jurkat.parental.UT.rep3 (DISE-56)

description: Single Read

source_name: Jurkat wt uninfected cells


title: Jurkat.droshaKO.3F6.UT.rep2 (DISE-56)

description: Single Read


title: Jurkat.parental.UT.rep2 (DISE-56)

description: Single Read


title: Jurkat.droshaKO.3F6.UT.rep1 (DISE-56)

description: Single Read


title: SCHW00179


title: SCHW00172


title: BXD90.RwwJ_rep2


title: Jurkat.parental.UT.rep1 (DISE-56)

description: Single Read


title: Jurkat.DroshaKO.F6.HIV.rep2

description: Single Read

source_name: Jurkat Drosha k.o. clone F6 VSVg pseudotyped HIV-1 virus infected cells

value: Cells were infected with HIV-1 for 28hrs


title: F1.oil.D2580.1_F

value: Exposed to vehicle control


title: SCHW00169


title: F1.oil.D1961.1_F


title: SCHW00168


title: BXD90.RwwJ_rep1


title: BXD79.RwwJ_rep2


title: Jurkat.DroshaKO.F6.HIV.rep1

description: Single Read


title: BXD93.RwwJ_rep2


title: F2.high.D1669.1_M

value: M


title: F1.oil.C4605.2_F


title: SCHW00167


title: F1.oil.C4605.1_M


title: SCHW00166


title: SCHW00171


title: Jurkat.DroshaKO.F6.UT.rep1

description: Single Read

value: ATCC


title: Jurkat.DroshaKO.F6.UT.rep2

description: Single Read

value: Jurkat


title: BXD77.RwwJ_rep2


title: Jurkat.DroshaKO.E11.HIV.rep2

description: Single Read

source_name: Jurkat Drosha k.o. clone E11 VSVg pseudotyped HIV-1 virus infected cells

value: Drosha k.o.


title: F1.oil.C4321.1_M


title: Jurkat.DroshaKO.E11.HIV.rep1

description: Single Read


title: SCHW00164


title: BXD77.RwwJ_rep1


title: SCHW00165


title: F1.oil.D2580.2_M


title: BXD73b.RwwJ_rep2


title: SCHW00163


title: F1.oil.C4232.9_F


title: SCHW00162


title: Jurkat.DroshaKO.E11.UT.rep1

description: Single Read

source_name: Jurkat Drosha k.o. clone E11 uninfected cells


title: BXD73b.RwwJ_rep1


title: SCHW00161


title: BXD79.RwwJ_rep1


title: F1.oil.C4232.2_M


title: F1.mid.D2510.2_F

value: Exposed to 0.2 mg/kg/day BaP


title: F1.oil.C4321.6_F

value: embryonic gonad


title: BXD73.RwwJ_rep1


title: SCHW00160


title: F1.oil.C3774.3_M


title: Jurkat.parental.HIV.rep2

description: Single Read

source_name: Jurkat wt VSVg pseudotyped HIV-1 virus infected cells

value: wt


title: BXD69.RwwJ_rep2


title: F1.mid.D2510.1_M

value: primordial germ cell


title: Jurkat.parental.HIV.rep1

description: Single Read


title: Jurkat.parental.UT.rep2

description: Single Read


title: Jurkat.parental.UT.rep1

description: Single Read


title: F1.mid.D2506.3_M


title: BXD67.RwwJ_rep2


title: F1.mid.D2506.2_F

value: F


title: DicerKO.HIV.rep3 (DISE-42)

description: Single Read

source_name: HCT116 Dicer k.o. VSVg pseudotyped HIV-1 virus infected cells

value: Korean Collection for Type Cultures (KCTC)

value: Dicer k.o.


title: Jurkat.DroshaKO.E11.UT.rep2

description: Single Read


title: BXD73.RwwJ_rep2

value: himar1 transposon library


title: F1.mid.D1190.2_M


title: DroshaKO.HIV.rep3 (DISE-42)

description: Single Read

source_name: HCT116 Drosha k.o. VSVg pseudotyped HIV-1 virus infected cells


title: SCHW00155


title: F1.mid.D1190.1_M


title: BXD62.RwwJ_rep2


title: SCHW00153


title: SCHW00159


title: SCHW00151


title: F1.mid.C4322.2_M


title: BXD60.RwwJ_rep2


title: BXD62.RwwJ_rep1


title: F1.mid.C4322.4_F


title: SCHW00149


title: DroshaKO.UT.rep3 (DISE-42)

description: Single Read

source_name: HCT116 Drosha k.o. uninfected cells

value: Uninfected cells


title: F1.mid.C4242.1_F

source_name: embryonic gonad


title: BXD69.RwwJ_rep1


title: DicerKO.UT.rep3 (DISE-42)

description: Single Read

source_name: HCT116 Dicer k.o. uninfected cells


title: SCHW00146

source_name: brain

value: brain


title: SCHW00156

value: Dbh-Cre; Ai14 Neuron


title: SCHW00145


title: HCT116.UT.rep3 (DISE-42)

description: Single Read

source_name: HCT116 wt uninfected cells


title: BXD67.RwwJ_rep1


title: SCHW00158


title: F1.mid.C4228.3_F


title: BXD56.RwwJ_rep2


title: BXD56.RwwJ_rep1


title: F1.mid.C4228.1_M


title: DicerKO.HIV.rep2 (DISE-42)

description: Single Read

value: Cells were infected with HIV-1 for 28hrs


title: DroshaKO.HIV.rep2 (DISE-42)

description: Single Read


title: HCT116.HIV.rep3 (DISE-42)

description: Single Read

source_name: HCT116 wt VSVg pseudotyped HIV-1 virus infected cells


title: BXD54.RwwJ_rep2


title: SCHW00142


title: F1.low.D2645.2_M

value: Exposed to 0.033 mg/kg/day BaP


title: SCHW00143


title: HCT116.HIV.rep2 (DISE-42)

description: Single Read


title: BXD60.RwwJ_rep1


title: BXD54.RwwJ_rep1


title: F1.low.D2645.1_F


title: BXD51.RwwJ_rep1


title: SCHW00141


title: F1.low.D2595.1_M

value: M


title: SCHW00138


title: F1.low.D2271.1_F


title: BXD48a.RwwJ_rep1


title: HCT116.UT.rep2 (DISE-42)

description: Single Read


title: SCHW00135


title: BXD40.TyJ_rep2


title: F1.high.D2593.1_M

value: Exposed to 2 mg/kg/day BaP


title: F1.high.D2587.2_M


title: DicerKO.HIV.rep1 (DISE-42)

description: Single Read


title: SCHW00134


title: BXD40.TyJ_rep1


title: SCHW00133


title: DroshaKO.HIV.rep1 (DISE-42)

description: Single Read


title: BXD39.TyJ_rep2


title: BXD39.TyJ_rep1


title: SCHW00132


title: HCT116.HIV.rep1 (DISE-42)

description: Single Read


title: SCHW00130


title: DicerKO.UT.rep1 (DISE-42)

description: Single Read


title: F1.high.D2582.2_M


title: F1.high.D2587.1_F


title: BXD29.Ty_rep2


title: F1.high.D2582.1_F


title: F1.high.D1824.3_M


title: DroshaKO.UT.rep2 (DISE-42)

description: Single Read


title: BXD29.Ty_rep1


title: SCHW00129


title: BXD9.TyJ_rep2


title: HCT116.UT.rep1 (DISE-42)

description: Single Read


title: SCHW00127


title: DicerKO.UT.rep2 (DISE-42)

description: Single Read


title: DicerKO.HIV.rep2

description: Single Read

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after). This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Supplementary files format and content: Tab-delimited file with read, seed (bp 2-7), cell viability based on seed, raw read counts for each sample, and putative source based on blast


title: F1.high.D1824.1_F


title: F1.high.C4578.2_M


title: SCHW00121


title: HCT116.HIV.rep2

description: Single Read


title: BXD9.TyJ_rep1


title: DBA.2J_rep2


title: DroshaKO.UT.rep1 (DISE-42)

description: Single Read


title: SCHW00122


title: DicerKO.UT.rep2

description: Single Read


title: F1.high.C4258.5_M


title: DBA.2J_rep1


title: F1.high.C4258.2_F


title: HCT116.UT.rep2

description: Single Read


title: C57BL.6J_rep2


title: F1.high.C4219.4_F


title: F1.high.C4219.2_M


title: DicerKO.HIV.rep1

description: Single Read


title: SCHW00116


title: HCT116.HIV.rep1

description: Single Read


title: SCHW00115


title: F1.high.C4219.1_M


title: SCHW00114


title: DicerKO.UT.rep1

description: Single Read


title: HCT116.WT.HIV.rep2

source_name: HCT116wt VSVg pseudotyped HIV-1 virus infected cells


title: HCT116.UT.rep1

description: Single Read


title: HCT116.DroshaKO.HIV.rep2