title: Control OE, Run5, scRNA-seq

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: 10x Genomics 3'

data_processing:
Raw 10x Genomics data were processed using the Cellranger count command (v3.1.0), mapping to the GRCm38 assembly (ensembl 97 annotation). Filtered gene expression matrices were loaded into Scanpy (v.1.8.1) and further filtered to remove cells expressing less than 500 genes or with greater than 15% of UMIs being assigned to mitochondrial genes, Scrublet was then used to remove cells likely to be doublets (doublet_score > 0.25), and finally, samples were then combined into two datasets, miR-132 OE and miR-132 KD.
Following QC and filtering, samples were normalized to a total of 10000 UMIs per cell and log normalized; highly variable genes were detected using default parameters and the data were scaled to unit variance with a mean of 0, values greater than 10 were clipped. A principal component analysis was performed on the highly variable gene matrix and Harmony was used for batch correction between runs, 50 and 40 components were used respectively for miR-132 OE and miR-132 KD for downstream dimensionality reduction and clustering analyses
Clustering was performed at various resolutions using the Leiden algorithm and clusters were annotated with cell types based on their marker gene expression. Infiltrating immune cells segregated as distinct clusters and were removed from the analysis based on the expression of markers for monocytes (Cd44, Fn1, Gda), macrophages (Atf3, Cfp, Serpinb8), dendritic cells (Flt3) and lymphocytes (Lck). Cells from cell types we did not intend to sort per RUN, were excluded from further analysis [RUN 1: all hippocampal cells; RUN 2: only neurons and astrocytes; RUN 3: all hippocampal cells; RUN 4: only neurons and astrocytes; RUN 5: only neurons and astrocytes (Table S3)]. After removal of these cells, the analysis was repeated starting with the detection of highly variable genes, 46 and 42 principal components were used respectively for miR-132 OE and miR-132 KD for filtered datasets.
Assembly: mm10
Supplementary files format and content: Comma-separated matrix files, tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Mice received an overdose of pentobarbital and were perfused with ice-cold artificial CSF (aCSF). The aCSF was composed of (in mM): 93 NMDG, 2.5 KCl, 1.2 NaH2PO4, 30 NaHCO3, 20 HEPES, 25 glucose, 5 sodium ascorbate, 2 thiourea, 3 sodium pyruvate, 10 MgSO4, 0.5 CaCl2, and was adjusted to pH 7.4 and equilibrated in 95% O2 5% CO2. After perfusion, right hippocampi were microdissected and placed in cold Hibernate A Low Fluorescence (BrainBits), supplemented with 5 μM Actinomycin D (Cat#A1410-5MG, Sigma-Aldrich). Hippocampi were dissociated enzymatically using the Adult Brain Dissociation Kit, mouse and rat (Cat#130-107-677, Miltenyi Biotec) for 15 min at 37°C, with 5 μM Actinomycin D added. Subsequently mechanical dissociation was performed, cells were passed through a 70 µm cell strainer and washed with 10 ml ice-cold D-PBS supplemented with 0.5% BSA. Next, cells were centrifuged for 10 min at 300 g at 4°C and myelin and debris removal was performed according to manufacturer’s instructions. Afterwards, cells were resuspended in D-PBS (0.5% BSA) and labeled with the eBioscience™ Fixable Viability Dye eFluor™ 780 (1:2000, Cat#65-0865-14, Thermo Fisher Scientific, irreversibly labels dead cells) and in run 2, 4, 5 also with Anti-mouse ACSA-2-APC (1:20, Cat#130-116-142, Miltenyi Biotec) and BV421 Rat Anti-CD11b (1:10, Cat#562605, BD). Cells were incubated for 30 min in the dark at 4°C, washed with 1 ml D-PBS (0.5% BSA) and spun down for 10 min at 300 g at 4°C. Subsequently, cells were suspended in 200 μl D-PBS (0.5% BSA) for FACsorting. Only alive cells were sorted, as dead cells were excluded based on their staining with the eFluor™ 780 dye. Neurons were sorted based on YFP expression. For astrocyte isolation, ACSA-2 positive microglia were excluded by selection based on both CD11b and ACSA-2 expression. According to the run, an Influx (BD) or MACSQuant Tyto (Miltenyi Biotec) were used for sorting and different cell types were isolated.
10000-20000 cells were sorted per sample and further processing was conducted following manufacturer’s instructions (CG000183 ChromiumSingleCell3 v3 for RUN 1, 2, 3 and CG000204 ChromiumNextGEMSingleCell3 v3.1 for RUN 4, 5). Briefly, cells were loaded onto the Chromium Single Cell Chip B (RUN 1, 2, 3) or Chromium Next GEM Chip G (RUN 4, 5) for GEM formation and after consecutive steps of reverse transcription, cDNA clean-up and amplification, DNA libraries were generated. Libraries were loaded in an equimolar pool for sequencing on the HiSeq4000 or NovaSeq6000 platform (Illumina) aiming for 50000 reads/cell.

treatment_protocol: Mice were anesthetized using isoflurane and fixed in a stereotactic frame. A cannula was implanted unilaterally in the right hemisphere at position of injection (AP-0.1 mm, ML-1.0 mm, and DV-3.0 mm) and mice were left to recover for approximately 1 week. For miR-132 knockdown (miR-132 KD), mice were injected with 3 μl (0.33 nmol/μl) of miR-132 antagomiR (locked nucleic acid (LNA)-, 3′-cholesterol-modified oligonucleotide) (Exiqon, QIAGEN) resuspended in artificial cerebrospinal fluid (aCSF) (Harvard Apparatus). Control mice received a scrambled LNA oligonucleotide in aCSF. For miR-132 overexpression (miR-132 OE), mice received 150 pmol of either a miR-132 mimic or a negative control oligonucleotide (Dharmacon, Horizon Discovery) in a 3 μl mix with lipofectamine 2000 (at a 1:1 volume ratio) (Cat#11668019, Thermo Fisher Scientific). One week (miR-132 KD) or 48 h (miR-132 OE) after injection, mice were sacrificed and the injected right hippocampus was microdissected.

value: Hippocampus

value: Neurons, astrocytes

tag: genotype

value: negative control oligonucleotide


title: SB/AKT/c-Met + TAA 4

status: Public on May 31 2023

type: SRA

city: Sydney

first: Vincent

middle: Lok Hang

last: Chiu

state: NSW

address: 1 Campbell St Liverpool

country: Australia

institute: Ingham Institute for Applied Medical Research

library_source: transcriptomic

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al. 2013 ) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GRCm38 was used with transgenes appended into the reference
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts, text file, tab separated

molecule: total RNA

organism: Mus musculus

source_name: Mouse liver

extract_protocol:
Liver tissue was snap-frozen in liquid nitrogen; RNA extracted using RNAzol reagent.
Library was prepared as described in Grubman et al. (2021). Briefly, index was added during initial pA priming and pooled samples amplified using template switching oligo. P5 is added by PCR and P7 by Nextera transposase. Sequencing was performed according to Illumina protocols using NextSeq 550 v2.5 kit.

treatment_protocol: 14-15 wk old male C57BL/6JAusb mice received HTVI of 0.8 µg SB plasmid, alone or with AKT (10 µg) and c-Met (10 µg) plasmids (SB/AKT/c-Met), or AKT (10 µg) and NRas (10 µg) plasmids (SB/AKT/NRas). 8-10 days post-HTVI, mice received 10-11 i.p. injections of TAA dissolved in saline, or equal volume of saline. The first i.p. injection was 100 mg/kg TAA body weight dissolved in 0.5% body weight saline, with subsequent injections 200 mg/kg TAA body weight dissolved in 1% body weight saline. i.p. injections were given twice per week for 5-6 weeks.

tag: strain

tag: tissue

value: Liver

tag: Sex

value: male

tag: plasmid-htvi treatment

value: Sleeping Beauty (SB) + myr-AKT + c-Met

tag: injury treatment

value: thioacetamide

tag: mouse id


title: hair follicle, FP, 50

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

country: South Korea

institute: Korea Brain Research Institute

description: MA user_50

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt.
Trimmed reads were aligned to the GRCh38 human reference genome using STAR (version 2.7.9a).
Gene-level read counts were generated using featureCounts function from the Subread package (version 2.0.3).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file include raw counts for each sample.

organism: Homo sapiens

source_name: hair follicle

extract_protocol:
Total RNA was extracted from hair samples of all subjects using TRIzol RNA Isolation Reagents (Life technologies).
The extracted total RNA was used to prepare the mRNA-sequencing library using a TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

value: hair follicle

tag: state

value: former patients with methamphetamine use disorders


title: hair follicle, FP, 44

description: MA user_44


title: miR-132 OE, Run5, scRNA-seq

description: 10x Genomics 3'

library_source: transcriptomic single cell

tag: cell type

tag: treatment

value: miR-132 mimic


title: Platelet Sample from Subject 182331, 2 Days Post Vaccination

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

country: USA

institute: Yale University

data_processing:
Raw data was demultiplexed and converted to FASTQ format using bcl2fastq.
FASTQ files were quality trimmed using Trimmomatic.
FASTQ files were quality assessed with FASTQC.
Quality-trimmed FASTQ files were aligned against human reference with STAR aligner.
Read counts for each gene were genereated with htseq-count.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Each processed file contains the read counts for each gene for one sample. The format is plain text, gzip compressed.

source_name: platelet

extract_protocol:
Whole blood was collected in a yellow-cap tube and stored at room temperature. The tube was centrifuged and the platelet-rich plasma (PRP) was collected. The PRP was aliquoted and further centrifuged to isolate the platelet pellet. The platelet pellet was dissolved in 700 microliter Qiasol/TRISol. RNA was extracted using the Qiagen miRNA Easy Kit (Cat. # 217004) following the manufacturer’s instructions using a QIACUBE.
RNA-seq libraries were prepared using the Takara Bio SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian per the manufacturer’s instructions.

tag: subject id

tag: gender

value: Female

value: Young

tag: time point relative to flu vaccination

value: 2 Days Post-Vaccination


title: LCMV2: ArmD8, scATAC

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description: P14 CD8 T cells from LCMV Armstrong infection 8 days post infection

library_source: genomic

data_processing:
scRNA-seq and scATAC-seq sample demultiplexing, barcode processing, alignment, filtering, unique molecular identifier (UMI) counting and aggregating sequencing runs were performed using 10x Cell Ranger pipeline (6.0.0) and mm10 genome.
Downstream scRNA-seq amd scATAC-seq analysis was performed in R (version 4.0.2) using Signac and Archr packages
Union peak list was generated using peaks called in ArchR and using macs2 with sample bam files.
Assembly: GRCm38/mm10
Supplementary files format and content: Filtered feature-barcode matrices containing only cellular barcodes corresponding to gene expression and chromatin accessibility

molecule: genomic DNA

source_name: P14 CD8 T cells

extract_protocol:
Cells were loaded onto the Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells.
The scRNAseq and scATACseq libraries were generated using 10x Genomics multiome coAssay according to the manufacturer’s protocol.

treatment_protocol: PD1 blockade was performed with 5 treatments of 200ug aPD-L1 antibody (10F.9G2, BioXCell) i.p. every 3 days starting 16 days after infection with LCMV Cl13. Analysis was performed one day after final treatment. For control treatments, phosphate-buffered saline (PBS) was administered i.p.

tag: background strain

tag: age

value: CD8 T cells


title: SB/AKT/c-Met + TAA 2


title: hair follicle, FP, 29

description: MA user_29


title: SB/AKT/NRas + TAA 1

value: Sleeping Beauty (SB) + myr-AKT + NRasV12


title: hair follicle, FP, 25

description: MA user_25


title: SB/AKT/c-Met + TAA 3


title: Platelet Sample from Subject 182331, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: Platelet Sample from Subject 182330, 7 Days Post Vaccination


title: Control KD, Run5, scRNA-seq

description: 10x Genomics 3'

value: scrambled LNA


title: hair follicle, FP, 43

description: MA user_43


title: hair follicle, FP, 20

description: MA user_20


title: SB/AKT/c-Met + saline 3

value: saline


title: SB/AKT/c-Met + TAA 1


title: hair follicle, FP, 18

description: MA user_18


title: miR-132 KD, Run5, scRNA-seq

description: 10x Genomics 3'

value: Hippocampus

value: Neurons, astrocytes

value: miR-132 antagomiR


title: SB/AKT/c-Met + saline 2

value: Liver

value: male


title: Platelet Sample from Subject 182331 Pre-vaccination

value: Pre-vaccination


title: Platelet Sample from Subject 182330, 2 Days Post Vaccination


title: hair follicle, FP, 14

description: MA user_14

value: hair follicle


title: Platelet Sample from Subject 182330 Pre-vaccination


title: Platelet Sample from Subject 182330, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: hair follicle, FP, 10

description: MA user_10

value: former patients with methamphetamine use disorders


title: SB + TAA 4

value: Sleeping Beauty (SB)

value: thioacetamide


title: Control KD, Run3, scRNA-seq

description: 10x Genomics 3'

value: All hippocampal cells


title: miR-132 OE, Run4, scRNA-seq

description: 10x Genomics 3'

value: miR-132 mimic


title: SB/AKT/c-Met + saline 1

value: Sleeping Beauty (SB) + myr-AKT + c-Met


title: SB + TAA 3


title: hair follicle, FP, 2

description: MA user_02


title: Platelet Sample from Subject 182329 Pre-vaccination

value: Female

value: Young


title: miR-132 KD, Run3, scRNA-seq

description: 10x Genomics 3'


title: Control OE, Run4, scRNA-seq

description: 10x Genomics 3'

value: negative control oligonucleotide


title: Control OE, Run2, scRNA-seq

description: 10x Genomics 3'

value: Hippocampus


title: hair follicle, FP, 1

description: MA user_01


title: SB + TAA 2


title: Platelet Sample from Subject 182328, 28 Days Post Vaccination

value: Male


title: Platelet Sample from Subject 182328, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: hair follicle, CP, 54

description: MA user_54

value: current patients with methamphetamine use disorders


title: miR-132 OE, Run2, scRNA-seq

description: 10x Genomics 3'

value: Neurons, astrocytes


title: SB + TAA 1

value: Liver

value: male


title: hair follicle, CP, 52

description: MA user_52

value: hair follicle


title: Platelet Sample from Subject 182328, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Control KD, Run2, scRNA-seq

description: 10x Genomics 3'

value: scrambled LNA


title: Platelet Sample from Subject 182328 Pre-vaccination

value: Pre-vaccination


title: Platelet Sample from Subject 182329, 7 Days Post Vaccination


title: hair follicle, CP, 51

description: MA user_51


title: hair follicle, CP, 49

description: MA user_49


title: Platelet Sample from Subject 182327, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: Platelet Sample from Subject 182327, 7 Days Post Vaccination


title: SB + saline 1

value: Sleeping Beauty (SB)

value: saline


title: miR-132 KD, Run2, scRNA-seq

description: 10x Genomics 3'

value: miR-132 antagomiR


title: SB + saline 3


title: SB + saline 2


title: S11.195M_d

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were trimmed by tool Trimmomatic
Surviving reads were aligned to reference genome mm10 by STAR aligner
reads were quantified by STAR
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

source_name: brain

extract_protocol:
The mutant mice were generated via CRISPR/Cas9 and genomic sequence was confirmed. Whole mouse brain were homogenized for RNA isolation.
RNA libraries were prepared using the KAPA RNA HyperPrep Kit with removal of ribosome RNAs by RiboErase (Kapa Biosystems) according to the manufacturer’s protocol, and the libraries were sequenced using NovaSeq6000 platform (Illumina).

value: C57/BL6J and DBA2 mixed background

value: brain


title: hair follicle, CP, 47

description: MA user_47


title: S12.195M_d


title: hair follicle, CP, 46

description: MA user_46


title: Platelet Sample from Subject 182327, 2 Days Post Vaccination

value: Female

value: Young


title: hair follicle, CP, 42

description: MA user_42


title: 22017_A9

city: Cambridge

first: Bryan

middle: B

last: Bryson

state: MA

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Cell barcode and UMI tagging of transcript reads was performed using DropSeqTools v1.12 (Macosko et al., 2015) and the Macaca_fascicularis_5.0 assembly
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: Seurat object containing week 10 cohort 2 data
Supplementary files format and content: Integrated myeloid object containing counts from all 3 cohorts
Supplementary files format and content: TSV containing raw barcodes for week 10 cohort 2
Supplementary files format and content: TSV containing filtered cell metadata for week 10 cohort 2
Supplementary files format and content: TSV containing raw cell metadata for week 10 cohort 2
Supplementary files format and content: TSV containing genes for week 10 cohort 2
Supplementary files format and content: MTX containing raw counts for week 10 cohort 2

organism: Macaca fascicularis

source_name: Lung tuberculosis granuloma

extract_protocol:
Individual granulomas were enzymatically dissociated using the gentleMACS dissociator system.
Single-cell suspensions were loaded onto Seq-Well arrays and processed as according to Gierahn et al., Nature Methods (2017).

value: Lung tuberculosis granuloma

tag: infection

value: Mycobacterium tuberculosis

tag: time

value: 10 weeks post-infection


title: S10.195M_d

tag: genotype


title: S9.195M_195M

tag: strain


title: Platelet Sample from Subject 182327 Pre-vaccination


title: SB + saline 4

tag: tissue

value: Liver


title: hair follicle, CP, 40

description: MA user_40

value: current patients with methamphetamine use disorders


title: S8.195M_195M


title: 22017_A7


title: hair follicle, CP, 39

description: MA user_39

value: hair follicle


title: Platelet Sample from Subject 182326, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Platelet Sample from Subject 182326 Pre-vaccination


title: 22017_A8


title: 22017_A6


title: S7.195M_195M


title: S6.WT_d


title: Platelet Sample from Subject 182325, 28 Days Post Vaccination

value: Male


title: hair follicle, CP, 38

description: MA user_38


title: hair follicle, CP, 36

description: MA user_36


title: 22017_A5


title: 22017_A4


title: S5.WT_d


title: hair follicle, CP, 34

description: MA user_34


title: Platelet Sample from Subject 182325, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: Platelet Sample from Subject 182325, 2 Days Post Vaccination


title: 22017_A3


title: Platelet Sample from Subject 182324, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: hair follicle, CP, 32

description: MA user_32


title: S3.WT_WT


title: 22017_A2


title: S4.WT_d


title: Platelet Sample from Subject 182324, 7 Days Post Vaccination


title: S2.WT_WT


title: hair follicle, CP, 31

description: MA user_31


title: 22017_A12


title: Platelet Sample from Subject 182324, 2 Days Post Vaccination


title: 22017_A11


title: Platelet Sample from Subject 182324 Pre-vaccination

value: Pre-vaccination


title: hair follicle, CP, 30

description: MA user_30


title: S1.WT_WT


title: 22017_A10


title: Platelet Sample from Subject 182323, 28 Days Post Vaccination

value: Older


title: hair follicle, CP, 28

description: MA user_28


title: hair follicle, CP, 27

description: MA user_27


title: 22017_A1

source_name: Distant lung tissue

value: Distant lung tissue


title: Lung Nb day 45

city: Maryland

first: Oyebola

last: Oyesola

address: Building 4, Room B1 05 4 Memorial Drive Bethesda, MD 20892

department: Type 2 Immunity Section

institute: National Institute of Health

description:
Primary Cells
Sample_C

library_source: genomic single cell

data_processing:
Demultiplexing was done allowing 1 mismatch in the barcodes. The analysis was performed with the Cell Ranger ATAC 2.0.0 software using the default parameters.
Assembly: mm10
Supplementary files format and content: Processed data sets are submitted as zipped files - *tar for each individual sample; Embedded within each zipped file for each sample are the various h5, matrix and tsv files
Supplementary files format and content: h5, matrix and tsv files for individual files are provided under A, B, C subfolders

source_name: Lung

extract_protocol:
Lung lobes were diced into small pieces and incubated in RPMI containing 0.33mg/mL Liberase TL and 0.1mg/mL DNase I (both from Sigma Aldrich) at 37°C for 45 minutes under agitation (150rpm). Enzymatic activity was stopped by adding FCS. Digested lung was filtered through a 70µm cell strainer and washed with RPMI. Red blood cells were lysed with the addition of ammonium-chloride-potassium buffer (Gibco) for 3 minutes at room temperature. Cells were then washed with RPMI supplemented with 10% FCS. Enrichment for CD45+ immune cell was done from lung single cell suspension using the EasySepTM Mouse CD45 positive selection kit (Stemcell Technologies) according to the manufacturer’s instruction.  The nuclei isolation was done using the Chromium Nuclei Isolation Kit (10x Genomics) according to the manufacturer’s instruction. 10,000 nuclei from each group were loaded on a 10X Genomics Next GEM chip and single cell GEMs were generated on a 10X Chromium Controller. Subsequent steps to generate the scRNA-seq libraries were prepared according to the manufacturer protocol (10x Genomics). Libraries were sequenced on an Illumina NovaSeq 6000 run.    The sequenced data were processed using Cell Ranger ATAC 2.0.0 software. The reads were aligned to Mus musculus mm10 genomes to generate count tables that were further analyzed using Seurat (version 4.1.2). Dimension reduction was performed with UMAP, and individual clusters were annotated based on expression on markers and gene sets from the single cell RNAseq analyzed data. Integration of scRNA-seq and scATAC-seq was performed from the Seurat package.
10X Genomics Next GEM chip.  All samples have sequencing yields of more than 422 million read per sample. The sequencing run was setup as a 50 cycles + 49 cycles non-symmetric run. Demultiplexing was done allowing 1 mismatch in the barcodes. Sequencing quality is good, over 86.55% of bases in the barcode regions have Q30 or above and at least 91.02% of bases in the read have Q30 or above, and 87.32% or more of bases in the sample index have Q30 or above. The analysis was performed with the Cell Ranger ATAC 2.0.0 software using the default parameters. The number of cells captured ranges from 2,703 to 5,424. The median fragments per cell ranged from 15,891 to 22,856. The percentage of reads mapped confidently to genome (>30 mapq) is above 91.33% for all the samples. The fraction of fragments (that passed all filters) overlapping TSS is above 47.48% and overlapping peaks is above 73.63%.

treatment_protocol: Animals were infected with 500 third stage N. brasilienesis larvae by subcutaneous injection.

value: Lung

value: CD45 enriched cells

value: Day 45 Nb


title: Lung Nb day 28

description:
Primary Cells
Sample_B

value: Day 28 Nb


title: 21917_A9

value: Lung tuberculosis granuloma


title: Lung Uninfected

description:
Primary Cells
Sample_A

value: Naïve


title: hair follicle, CP, 24

description: MA user_24


title: 21917_A8

value: Mycobacterium tuberculosis

value: 10 weeks post-infection


title: Platelet Sample from Subject 182322, 28 Days Post Vaccination

value: Female


title: Platelet Sample from Subject 182323, 7 Days Post Vaccination


title: Platelet Sample from Subject 182323, 2 Days Post Vaccination


title: 21917_A7


title: Bone unstimulated control, 12 days, rep3

city: Ann Arbor

first: Megan

last: Killian

state: Michigan

address: 109 Zina Pitcher Pl

institute: University of Michigan

data_processing:
We used Snakemake (Köster and Rahmann, 2012) to manage the bioinformatics workflow in a reproducible manner.
The reads were trimmed using Cutadapt v2.3 (Martin, 2011). The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011).
Alignment options followed ENCODE standards for RNA-seq (Dobin).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7 (Ewels et al., 2016).
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: tab-delimited text files include expected raw count values for each Sample

source_name: Tissue

extract_protocol:
Total RNA was isolated using PureLink™ RNA Mini kit. At least 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina's Poly-A (standard) Library Prep following manufacturer's protocols.

tag: cell line

value: Tissue

value: Calcaneus bone

value: 12-day opto stim control

value: Day 12


title: Bone stimulated control, 12 days, rep3

value: 12-day stim


title: Platelet Sample from Subject 182322, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: Bone stimulated control, 12 days, rep2


title: hair follicle, CP, 23

description: MA user_23

value: hair follicle

value: current patients with methamphetamine use disorders


title: 21917_A6


title: Platelet Sample from Subject 182322, 2 Days Post Vaccination

value: Older

value: 2 Days Post-Vaccination


title: hair follicle, CP, 21

description: MA user_21


title: hair follicle, CP, 5

description: MA user_05


title: Bone unstimulated control, 12 days, rep2


title: 21917_A5


title: Bone stimulated control, 12 days, rep1


title: hair follicle, CP, 4

description: MA user_04


title: 21917_A4


title: hair follicle, CP, 26

description: MA user_26


title: Bone unstimulated control, 12 days, rep1


title: Platelet Sample from Subject 182321, 7 Days Post Vaccination

value: Male


title: 21917_A3


title: hair follicle, control, 29

description: Healthy control_29

value: healthy


title: Platelet Sample from Subject 182321, 2 Days Post Vaccination


title: 21917_A2

value: Lung tuberculosis granuloma


title: Bone stimulated control, 5 days, rep3

value: 5-day stim

value: Day 5


title: hair follicle, control, 30

description: Healthy control_30


title: hair follicle, control, 28

description: Healthy control_28


title: Bone unstimulated control, 5 days, rep3

value: 5-day opto stim control


title: 21917_A12

value: Mycobacterium tuberculosis

value: 10 weeks post-infection


title: Platelet Sample from Subject 182320, 2 Days Post Vaccination

value: Female


title: hair follicle, control, 27

description: Healthy control_27


title: Bone stimulated control, 5 days, rep2

value: Tissue

value: Calcaneus bone


title: Platelet Sample from Subject 182320, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: 21917_A11


title: hair follicle, control, 26

description: Healthy control_26


title: 21917_A10


title: Platelet Sample from Subject 182321, 28 Days Post Vaccination


title: 21917_A1


title: Bone unstimulated control, 5 days, rep1


title: Bone unstimulated control, 5 days, rep2


title: hair follicle, control, 25

description: Healthy control_25


title: Bone stimulated control, 5 days, rep1


title: Platelet Sample from Subject 182319, 28 Days Post Vaccination


title: Platelet Sample from Subject 182319, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: hair follicle, control, 23

description: Healthy control_23

value: hair follicle


title: hair follicle, control, 24

description: Healthy control_24


title: 21817_A8


title: Platelet Sample from Subject 182319, 2 Days Post Vaccination


title: hair follicle, control, 22

description: Healthy control_22


title: Bone, naïve, rep3

value: Naïve

value: Day 0


title: Bone, naïve, rep2


title: 21817_A7


title: Platelet Sample from Subject 182319 Pre-vaccination

value: Older

value: Pre-vaccination


title: hair follicle, control, 21

description: Healthy control_21

value: healthy


title: Platelet Sample from Subject 182318, 28 Days Post Vaccination

value: Male


title: 21817_A6

value: Lung tuberculosis granuloma


title: Platelet Sample from Subject 182320 Pre-vaccination


title: Tendon stimulated control, 12 days, rep3

value: Achilles tendon

value: 12-day stim

value: Day 12


title: Bone, naïve, rep1


title: 21817_A5

value: Distant lung tissue

value: Mycobacterium tuberculosis

value: 10 weeks post-infection


title: hair follicle, control, 20

description: Healthy control_20


title: hair follicle, control, 19

description: Healthy control_19


title: 21817_A2


title: Platelet Sample from Subject 182318 Pre-vaccination


title: Platelet Sample from Subject 182317, 28 Days Post Vaccination


title: Platelet Sample from Subject 182318, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Tendon unstimulated control, 12 days, rep3

value: Tissue

value: 12-day opto stim control


title: hair follicle, control, 18

description: Healthy control_18

value: hair follicle


title: hair follicle, control, 16

description: Healthy control_16


title: Tendon stimulated control, 12 days, rep2


title: Tendon unstimulated control, 12 days, rep2


title: hair follicle, control, 17

description: Healthy control_17


title: 21817_A3


title: 21217_A8


title: hair follicle, control, 15

description: Healthy control_15


title: 21217_A9


title: Platelet Sample from Subject 182318, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: Tendon unstimulated control, 12 days, rep1


title: 21817_A1


title: Platelet Sample from Subject 182317, 2 Days Post Vaccination


title: 21817_A4


title: Platelet Sample from Subject 182317 Pre-vaccination


title: Tendon stimulated control, 12 days, rep1


title: 21217_A7


title: Tendon stimulated control, 5 days, rep3

value: 5-day stim

value: Day 5


title: hair follicle, control, 13

description: Healthy control_13


title: Tendon unstimulated control, 5 days, rep3

value: 5-day opto stim control


title: hair follicle, control, 14

description: Healthy control_14

value: healthy


title: 21217_A6


title: Platelet Sample from Subject 182316, 7 Days Post Vaccination

value: Female

value: Older


title: hair follicle, control, 12

description: Healthy control_12


title: Tendon stimulated control, 5 days, rep2

value: Achilles tendon


title: Platelet Sample from Subject 182317, 7 Days Post Vaccination

value: Male


title: Platelet Sample from Subject 182316, 2 Days Post Vaccination


title: Platelet Sample from Subject 182315, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: 21217_A5

value: Distant lung tissue


title: hair follicle, control, 11

description: Healthy control_11


title: 21217_A4

value: Lung tuberculosis granuloma

value: Mycobacterium tuberculosis


title: Tendon unstimulated control, 5 days, rep2


title: 21217_A3

value: 10 weeks post-infection


title: hair follicle, control, 9

description: Healthy control_9


title: Tendon unstimulated control, 5 days, rep1

value: Tissue


title: 21217_A2


title: Platelet Sample from Subject 182316, 28 Days Post Vaccination


title: Platelet Sample from Subject 182315, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Platelet Sample from Subject 182315, 7 Days Post Vaccination


title: hair follicle, control, 7

description: Healthy control_7

value: hair follicle


title: 21217_A12


title: hair follicle, control, 6

description: Healthy control_6


title: Tendon, naïve, rep3

value: Naïve

value: Day 0


title: hair follicle, control, 5

description: Healthy control_5


title: Tendon, naïve, rep2


title: Platelet Sample from Subject 182314, 28 Days Post Vaccination


title: Platelet Sample from Subject 182314, 7 Days Post Vaccination

value: 7 Days Post-Vaccination


title: hair follicle, control, 4

description: Healthy control_4


title: Tendon, naïve, rep1


title: 21217_A10


title: 21217_A11


title: Platelet Sample from Subject 182314, 2 Days Post Vaccination


title: ABI5_2X180ibm1ddcc (Bisulfite-Seq)

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

data_processing: Raw reads were trimmed with Trimmomatic-0.39 and then mapped to Arabidopsis reference genome (TAIR10) with BSMAP v2.90 (parameter: -q 20 -v 5 -w 10 -n 1). The mapping results were filtered to keep uniquely mapped reads and then remove duplicates with samtools-v1.9. Methylation was then quantified with methyratio.py in BSMAP and only cytosine sites with >4 reads covered were kept.

organism: Arabidopsis thaliana

source_name: Seedling, long day condition (16h light and 8h dark), 1-week old

growth_protocol: Plants were grown on 1/2 X MS agar (0.7%) + 1% sucrose

extract_protocol:
DNA was extracted via conventional cetyl trimethylammonium bromide (CTAB) method
For bisulfite-sequencing libraries, the genomic DNA was fragmented to a mean size of 100-300 bp by sonication using a Covaris S220 focused-ultrasonicator (Covaris), followed by end-repair, 3’-end adenylation and methylated adaptor ligation using Illumina TruSeq DNA kit (Illumina). Then bisulﬁte conversion was performed using a Zymo EZ DNA Methyl-ation-Lightning kit (Zymo Research). The bisulfite-converted, adaptor-ligated DNA was enriched by PCR for 12-15 cycles using KAPA HiFi HotStart Uracil+ Kit  (KAPA Biosystems), purified with Agencourt beads (NuGen).

value: whole seedling

value: ibm1-5, drm1-2, drm2-2, cmt2-7, cmt3-11 T-DNA quintuple knock-out mutant in ABI5 with 2xCEN180 knock-in background


title: Tendon stimulated control, 5 days, rep1

value: 5-day stim

value: Day 5


title: hair follicle, control, 2

description: Healthy control_2

value: healthy


title: Platelet Sample from Subject 182313, 28 Days Post Vaccination

value: Male

value: Older


title: ABI5_2X180_IBM1_#7-F3 (Bisulfite-Seq)

value: #7 F3 progeny from ABI5_2X180ibm1 crossing with Col-0 in ABI5 with 2xCEN180 knock-in and wild-type IBM1 background


title: hair follicle, control, 1

description: Healthy control_1


title: ABI5_2X180_IBM1_#5-F3 (Bisulfite-Seq)

value: #5 F3 progeny from ABI5_2X180ibm1 crossing with Col-0 in ABI5 with 2xCEN180 knock-in and wild-type IBM1 background


title: ECh_Abcg2N_K27me3_2_052721

city: New York

first: Yang

last: Lin

state: NY

address: 455 Main Street 06W

institute: Weill Cornell Medicine

description: Abcg2- EC K27me3 2

data_processing:
Sequencing service was performed on an Illumina Hiseq 4000  sequencer
ChIP-seq reads were aligned to the Mus musculus genome (mm9, NCBI Build 37) using the BWA  program (version 0.5.9), and PCR duplicates were removed by Picard (version 1.69)  (http://picard.sourceforge.net/).
Unique reads that mapped to a single best-matching location with  no more than 4% of the read length of mismatches were kept and used to study genome-wide  enrichment of specific histone modification.
Sequence data was visualized with IGV by  normalizing to 1 million reads
The SICER (version 1.1) algorithm was applied to the ChIP-seq data, with sequencing data from  input DNA as control to identify genomic enrichment (peak) of specific histone modifications  (FDR<0.01). To identify differentially enriched regions, SICER-df was used with FDR<0.01.
Promoters were defined as fragments between upstream 2 kb and transcription start site (TSS). The ChIP-seq read counts within promoters were quantified by HOMER (version 4.10.4)
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Heart

growth_protocol: Tissue samples from 8 week old ABCG2TT mice

extract_protocol:
Chromatin immunoprecipitation was performed with ULI-NChIP protocol. 10,000 FACS isolated  ECs were used per reaction. Cells were treated with the nuclei extraction buffer (10 mM Tris-HCl pH8.5, 140 mM NaCl, 5 mM  MgCl2, 0.6% NP40, 1x protease inhibitor cocktail) and chromatin was fragmented for 10 min using  MNase at 25°C and diluted in NChIP immunoprecipitation buffer (10 mM Tris-HCl pH8.0, 2 mM EDTA, 90 mM NaCl, 0.1% Triton X-100, 0.1% DOC, 1x protease inhibitor cocktail). Chromatin was incubated with 1μg of antibody bound to 11μl of protein A Dynabeads (Thermo Fisher Scientific, 10002D) and rotated overnight at 4°C. Then it was washed twice with 200 μl low-salt wash buffer (20 mM Tris-HCl pH8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% SDS), and twice with 200μl high-salt wash buffer (20mM Tris-HCl pH8.0, 2mM EDTA, 500mM NaCl, 1% Triton X-100, 0.1% SDS). DNA was eluted from chromatin in 100μl hot elution buffer (100mM NaHCO3, 1% SDS) for 2 hr at 65°C, then purified by phenol:chloroform and precipitated by  isopropanol overnight at -20°C. The DNA was resuspended in 10mM Tris-HCl pH 8.5. ChIP was  performed using the following antibodies: anti-H3K4me3 (Cell signaling Technology, 9727), anti-  H3K27me3 (Millipore, 07-449).
ChIP sequence libraries were generated using the KAPA Hyper Prep Kit

treatment_protocol: 50mg/kg tamoxifen i.p injected 1 day before TdTomato+CD31+CD45-Ter119- AbcVESC (Abcg2p) and TdTomato-CD31+CD45-Ter119- mature endothelial cells (Abcg2n) were flow sorted from Abcg2TT mice heart

value: Heart

value: Endothelial Cells

value: 50mg/kg tamoxifen injection


title: Platelet Sample from Subject 182313, 7 Days Post Vaccination


title: ECh_Abcg2N_K27me3_1_052721

description: Abcg2- EC K27me3 1


title: GM12878 LaminB1 cTSA-seq ChIP Rep2

city: Baltimore

first: Xiaobin

last: Zheng

state: MD

address: 3520 San Martin Drive

institute: Carnegie Institution for Science

description:
GM12878_lb1_vs_input_100k_hg19.bedgraph.gz
GM12878_lb1_vs_input_10k_hg19.bedgraph.gz

data_processing:
Reads were mapped to the human genome (hg19) using bowtie2 with default parameters.
The number of reads falling into 100kb (or 10kb) windows were counted. Numbers from two replicates were added together, then normalized into RPKM.
For each 100kb (or 10kb) window, a log fold enrichment of ChIP vs Input were calculated.
Assembly: hg19
Supplementary files format and content: bedgraph file

growth_protocol: GM12878 cells were cultured in T25 flasks containing RPMI-1640/15% FBS at 37ºC with 5% CO2.

extract_protocol:
One to two million cells were then fixed with 4% PFA for 10 minutes and neutralized with glycine. The cells were stained with a rabbit anti-lamin B1 antibody (Abcam, ab16048) and the tyramide signal amplification (TSA) reaction was done with the Biotin-XX-Tyramide kit (Invitrogen, #B40921). The reaction was verified by staining a fraction of the cells with Streptavidin-488. Labeled cells were lysed with RIPA buffer containing PMSF and then sonicated on Bioruptor Pico. A 1/10th volume input sample was taken, and the remainder of the lysate was used for Streptavidin pulldown using Pierce Streptavidin conjugated magnetic beads (Thermo, #88816). DNA was extracted using Ampure XP beads.
Libraries were prepared with the Takara ThruPLEX DNA-seq kit (Takara, #R400674).

tag: chip antibody

value: anti-lamin B1 antibody


title: Platelet Sample from Subject 182313, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: ECh_Abcg2N_K4me3_2_052721

description: Abcg2- EC K4me3 2


title: ABI5_5X180 (Bisulfite-Seq)

value: 5xCEN180 repeats knocked-in at ABI5 intron1 in Columbia-0 background


title: GM12878 LaminB1 cTSA-seq input Rep2


title: ECh_Abcg2N_input_1_052721

description: Abcg2- EC input 1


title: ECh_Abcg2N_input_2_052721

description: Abcg2- EC input 2


title: ECh_Abcg2N_K4me3_1_052721

description: Abcg2- EC K4me3 1


title: hair follicle, control, 3

description: Healthy control_3

value: hair follicle


title: Platelet Sample from Subject 182312, 7 Days Post Vaccination

value: Female

value: 7 Days Post-Vaccination


title: GM12878 LaminB1 cTSA-seq input Rep1


title: C2

description:
hmdm_object.rds
hmdm_metadata.tsv
hmdm_matrix.tsv

data_processing:
DGEs were generated using kallisto (kb count) by demultiplexing barcodes (0,0,12:0,12,28:1,0,0) using a prime-seq list of barcodes and pseudoalignment to hg38 index.
Assembly: hg38
Supplementary files format and content: Seurat object containing count matrices and sample metadata
Supplementary files format and content: Metadata spreadsheet containing sample information
Supplementary files format and content: Count matrix containing batch-corrected counts for each sample

molecule: polyA RNA

source_name: primary monocyte-derived macrophages

growth_protocol: Primary human monocyte-derived macrophages were cultured in RPMI + 10% FBS in the presence of 25 ng/mL GM-CSF.

extract_protocol:
RNA was harvested in RLT + 1% BME lysis buffer and extracted using RNA-SPRI beads.
RNA-seq libraries were generated using the prime-seq protocol (https://www.protocols.io/view/prime-seq-81wgb1pw3vpk/v2)

treatment_protocol: Monocytes and macrophages were treated with various ligands described in the metadata.

value: primary monocyte-derived macrophages

value: macrophages

tag: donor

value: C


title: Platelet Sample from Subject 182312, 2 Days Post Vaccination


title: ABI5_5X180_with_Donor_DNA (Bisulfite-Seq)

value: whole seedling

value: 5xCEN180 repeats knocked-in at ABI5 intron1 with donor DNA and pEC-Cas9 transgene background


title: ECh_Abcg2P_K27me3_2_052721

description: Abcg2+ EC K27me3 2


title: Platelet Sample from Subject 182314 Pre-vaccination

value: Male

value: Older

value: Pre-vaccination


title: ECh_Abcg2P_K27me3_1_052721

description: Abcg2+ EC K27me3 1

value: Heart


title: Platelet Sample from Subject 182311, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: ABI5_2X180_with_Donor_DNA (Bisulfite-Seq)

value: 2xCEN180 repeats knocked-in at ABI5 intron1 with donor DNA and pEC-Cas9 transgene background


title: ECh_Abcg2P_K4me3_2_052721

description: Abcg2+ EC K4me3 2

value: Endothelial Cells

value: 50mg/kg tamoxifen injection


title: Control (Bisulfite-Seq)

value: Donor (without CEN180 sequences) transgenic line in pEC-Cas9 background


title: ABI5_2X180ibm1 (Bisulfite-Seq)

value: ibm1-5 T-DNA knock-out mutant in ABI5 with 2xCEN180 knock-in background


title: GM12878 LaminB1 cTSA-seq ChIP Rep1

value: anti-lamin B1 antibody


title: ECh_Abcg2P_K4me3_1_052721

description: Abcg2+ EC K4me3 1


title: B2

value: B


title: Platelet Sample from Subject 182312, 28 Days Post Vaccination

value: Female


title: Platelet Sample from Subject 182311, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: ABI5_2X180 (Bisulfite-Seq)

value: 2xCEN180 repeats knocked-in at ABI5 intron1 in Columbia-0 background


title: B1

value: primary monocyte-derived macrophages

value: macrophages


title: ECh_Abcg2P_input_2_052721

description: Abcg2+ EC input 2


title: Platelet Sample from Subject 182310, 28 Days Post Vaccination


title: A2

value: A


title: ECh_Abcg2P_input_1_052721

description: Abcg2+ EC input 1


title: Platelet Sample from Subject 182310, 7 Days Post Vaccination

value: Older

value: 7 Days Post-Vaccination


title: Quadriceps, PTRF KO muscles, rep1

city: Chengdu

first: Xiaokai

last: Li

state: Sichuan

address: Huiming road #211

country: China

institute: Sichuan Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
We used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Sequence reads were aligned to the mouse reference genome (GRCm38/mm10) by STAR alignment tool (version 2.5.3a).
Sequence reads were quantified using kallisto (version 0.43.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

source_name: Quadriceps

extract_protocol:
Total RNA was isolated from indicated tissues with TRIzol reagent (Invitrogen).  1 ug of total RNA was used for the construction of sequencing libraries).
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, E7530L) following manufacturer's protocols.

value: Quadriceps

tag: developmental stage

value: 3 months old

value: PTRF knockout

tag: disease state

value: Muscular dystrophy


title: Quadriceps, PTRF KO muscles, rep3


title: Quadriceps, normal muscles, rep3

value: WT

value: Normal


title: Quadriceps, normal muscles, rep2


title: MDM biol rep #3

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

state: CA

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

data_processing:
Reads mapped to the mm10 genome assembly using Tophat (ver 2.0.14).
Reads within genes counted using HTSeq (HTSeq-1.99.2).
DESeq2 (version 1.28.1) used for analysis of differential expression.
Assembly: mm10
Supplementary files format and content: DESeq2 normalized expression and output merged in an excel sheet.

source_name: macrophages

extract_protocol:
Macrophages were isolated from mouse skeletal muscle by FACS and RNA was harvested using Rneasy micro kit (Qiagen). 2 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian following manufacturer's protocols.

tag: cell type

value: mdx


title: Platelet Sample from Subject 182309, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: C1

value: C


title: Platelet Sample from Subject 182309, 7 Days Post Vaccination

value: Female


title: MDM biol rep #2


title: MDM biol rep #1


title: Platelet Sample from Subject 182311, 7 Days Post Vaccination

value: Male


title: Quadriceps, normal muscles, rep1


title: MP2 NTC control rep1

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Mp2_NTC_raw_h3k27ac_rep.pooled_x_ctl.pooled.pval.signal.bigwig
MP2_NTC_h3k27ac_raw_idr.optimal_peak.regionPeak.bed

data_processing:
https://github.com/ENCODE-DCC/chip-seq-pipeline
Map reads with BWA-0.7.12
Post-alignment filtering steps were carried out using samtools-1.355 with MAPQ threshold of 30
Duplicate removal was performed using picard-tools-1.88
Peak enrichment were computed using phantompeakqualtools implementing the SPP algorithm
Replicate consistency and peak ranking determined by irreproducible discovery rate (IDR) using the IDR-2.0.2 tool
Assembly: hg38
Supplementary files format and content: TAR of BED of the IDR peaks for each replicate compared to the matching non-antibody control

source_name: MIA PaCa-2

growth_protocol: MiaPaCa-2 cells (ATCC #CRM-CRL-1420) were cultured in D10 media on tissure culture treated plates: DMEM (Lonza #12-614Q) supplemented with 10% FBS (GELifeSciences #SH30071.03), and 0.5% penicillin-streptomycin (ThermoFisher #15140122). All cell lines were maintained at 37 °C and 5% CO2. Cells were cryopreserved with the addition of 10% DMSO (EMD #MX1458-6).

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/efac5344-6834-4e12-b971-94994d992e86/@@download/attachment/ChIP-seq_Mapping_Pipeline_Overview.pdf  pipeline protocol: https://www.encodeproject.org/documents/d00ffce2-e72c-44d7-a71f-73fd163c2426/@@download/attachment/ChIP-seq_pipeline_overview.pdf  extraction protocol: https://www.encodeproject.org/documents/73c95206-fc02-41ea-93e0-a929a6939aaf/@@download/attachment/ChIP-seq%20protocol%2C%20ENCODE4%2C%20Myers%20Lab.pdf  pipeline protocol: https://www.encodeproject.org/documents/efac5344-6834-4e12-b971-94994d992e86/@@download/attachment/ChIP-seq_Mapping_Pipeline_Overview.pdf, pipeline protocol: https://www.encodeproject.org/documents/d00ffce2-e72c-44d7-a71f-73fd163c2426/@@download/attachment/ChIP-seq_pipeline_overview.pdf, extraction protocol: https://www.encodeproject.org/documents/73c95206-fc02-41ea-93e0-a929a6939aaf/@@download/attachment/ChIP-seq%20protocol%2C%20ENCODE4%2C%20Myers%20Lab.pdf
ChIP-seq protocol Myers Lab; used antibodies: Abcam, H3K27ac (ab4729)

treatment_protocol: MiaPaCa2 containg lentiMPHv2 plasmid were co-transfected with psPAX2 pMD2G and lentiSAMv2 lentiviral plasmids containing NTC or HDAC1 sgRNA using Lipofecatming 2000 Transfection Reagent (ThermoFisher)

value: MIA PaCa-2

value: epithelial cell pancreatic carcinoma

tag: condition

value: non-targeting scrableled sgRNA control


title: Platelet Sample from Subject 182309, 2 Days Post Vaccination

tag: subject id

value: 2 Days Post-Vaccination


title: Soleus, PTRF KO muscles, rep3

source_name: Soleus

value: Soleus


title: Quadriceps, PTRF KO muscles, rep2


title: Gal-3+ Mac biol rep #3

value: macrophages


title: MP2 NTC H3k27ac rep1

value: Abcam, ab4729


title: Platelet Sample from Subject 182308, 28 Days Post Vaccination

tag: gender

value: Older


title: Soleus, PTRF KO muscles, rep2

value: 3 months old

value: PTRF knockout


title: Gal-3+ Mac biol rep #4


title: MP2 NTC H3K27ac rep2


title: A1

value: primary monocyte-derived macrophages

value: A


title: MP2 HDAC1 OE H3k27ac control rep2

description:
MP2_e7_h3k27ac_rep.pooled_x_ctl.pooled.pval.signal.bigwig
Mp2_e7_h3k27ac_raw_2_idr.optimal_peak.regionPeak.bed

value: HDAC1 overexpression


title: Soleus, PTRF KO muscles, rep1

value: Muscular dystrophy


title: Platelet Sample from Subject 182308, 2 Days Post Vaccination

tag: time point relative to flu vaccination


title: MP2 NTC control rep2


title: MP2 HDAC1 OE H3k27ac control rep1


title: Gal-3+ Mac biol rep #2

value: mdx


title: Gal-3+ Mac biol rep #1


title: Soleus, normal muscles, rep3

value: WT

value: Normal


title: MP2 HDAC1 OE H3k27ac rep2

value: MIA PaCa-2


title: SkMRM biol rep #3


title: Platelet Sample from Subject 182307, 28 Days Post Vaccination

value: Male

value: 28 Days Post-Vaccination


title: Soleus, normal muscles, rep2


title: MP2 HDAC1 OE H3k27ac rep1

value: epithelial cell pancreatic carcinoma


title: Soleus, normal muscles, rep1

value: Soleus


title: Platelet Sample from Subject 182307, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: Platelet Sample from Subject 182307 Pre-vaccination

value: Pre-vaccination


title: Platelet Sample from Subject 182308, 7 Days Post Vaccination

value: Older

value: 7 Days Post-Vaccination


title: treated with 3 µM olaparib

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

data_processing:
Extract gRNA sequences from fastq files
Use bowtie2 to map gRNA to human GeCKOv2 library
Use samtools to extract mapped gRNA and caculate gRNA abundance
Extract genes with enriched gRNAs using customized R script

source_name: Breast

extract_protocol:
The genomic DNA was extracted with Qiagen Dneasy Blood & Tissue Kits and the protocol of the kit was followed.
The protocol was followed based on the previous publication by Dr. Feng Zhang's group (Science. 2014 Jan 3; 343(6166): 84–87)
The library stategy was designed based on the previous publication by Dr. Feng Zhang's group (Science. 2014 Jan 3; 343(6166): 84–87)

value: Breast

value: Breast cancer cells

tag: treatment

value: olaparib


title: Platelet Sample from Subject 182306, 2 Days Post Vaccination

value: Female


title: treated with 1 µM olaparib


title: T_IM_09 [mouse miRNA-Seq]

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced single-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 2.8) with parameters -q 20 -O 7 -m 16 –trim-n
Trimmed reads were mapped against the mouse genome (UCSC mm10) using Bowtie2 (v 2.3.5.1) with parameters -N 1
Mapped reads were summarized using featureCounts (v 2.0.0) with parameterst -p -s 1 -T 6 -t miRA -g ID and miRBase annotation (22 GRCm 38)
Differential gene expression was assessed using R/edgeR (v 3.40) using TMM normalization
Assembly: mm10
Supplementary files format and content: Comma-separated text file including CPM, log2 fold change and false discovery rate values

source_name: tumor

extract_protocol:
TRIZOL extraction
Small RNA libraries of transgenic mouse tumor samples was performed with small RNA library preparation kit after TRIzol extraction of approximately 30 mg of tissue.

value: IMP1/MYCN, CRE +

tag: tumor type

value: neuroblastoma tumor


title: Platelet Sample from Subject 182305, 28 Days Post Vaccination


title: T_IM_11 [mouse miRNA-Seq]


title: treated with 0.3 µM olaparib


title: Platelet Sample from Subject 182305, 7 Days Post Vaccination


title: T_IM_07 [mouse miRNA-Seq]


title: T_IM_08 [mouse miRNA-Seq]

source_name: tumor spine


title: T_IM_04 [mouse miRNA-Seq]


title: Platelet Sample from Subject 182305, 2 Days Post Vaccination

source_name: platelet


title: Platelet Sample from Subject 182308 Pre-vaccination


title: Platelet Sample from Subject 182305 Pre-vaccination


title: Spleen-tropic ANKL1_1

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

country: Japan

institute: Saga University

description:
Leukemic cells were purified by human CD45 expression using flow cytometer.
processed data file: gene_count_matrix_ankl1.csv

data_processing:
Gene_count_matrix_ankl1, sequenced reads were trimmed with fastp v0.19.8, mapped to GRCh38 with Hisat2 v2.2.1, and counted with StringTie v2.1.4.
Liver_niche data, sequenced reads were mapped to hg38 or mm10 with bowtie v1.1.1 and CASTIN, then counted with CASTIN.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: tab-deliminated text files including raw counts and normalized counts for every gene.

source_name: Spleen-tropic ANKL1

extract_protocol:
Livers were removed from healthy mice or PDX mice, and RNA was harvested using Sepasol-RNA I Super G (nacalai tesque, Cat#09379-55).
RNA library was constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat#E7760L) following the manufacturer's protocol.

value: Spleen

value: lymphocyte


title: Spleen-tropic ANKL1_2


title: Spleen-tropic ANKL1_3


title: SkMRM biol rep #2

value: macrophages

value: WT


title: T_IM_05 [mouse miRNA-Seq]

source_name: tumor adrenal gland


title: Liver-tropic ANKL1_3

source_name: Liver-tropic ANKL1

value: Liver


title: Platelet Sample from Subject 182304, 28 Days Post Vaccination

value: 28 Days Post-Vaccination


title: Platelet Sample from Subject 182304, 7 Days Post Vaccination


title: Liver-tropic ANKL1_2


title: SkMRM biol rep #1


title: T_IM_12 [mouse miRNA-Seq]


title: Platelet Sample from Subject 182306, 28 Days Post Vaccination


title: T_I_08 [mouse miRNA-Seq]

value: IGF2BP1 +/+, CRE +


title: T_I_05 [mouse miRNA-Seq]


title: U-2 OS KD 39°C Rep3

city: Berlin

first: Bert

last: Maier

address: Charitéplatz 1

institute: Charité Universitätsmedizin Berlin

description:
3' end RNA
cpsf639.3

data_processing:
Illumina NextSeq 500, BaseSpace©.
Sequenced reads were mapped to hg19 genome using the alignment method STAR.
DGE within 50bp windows is quantified using ESAT as further discussed in Derr et al. (2016) Genome Research 26(10): 1397-1410.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: DGE_w50_nosig_norescan_nooverlap_finalannot.window.txt

source_name: Osteosarcoma cell line

extract_protocol:
RNA was extracted using an Invitrogen Pure Link RNA Mini kit. Fragments with PolyA tails are selected by oligo-(dT) beads.
Library was constructed as described in Wittenbrink et al. (2018).

value: U-2 OS

tag: RNAi condition

value: CPSF6 knock-down

tag: temperature condition


title: Platelet Sample from Subject 182493 Pre-vaccination

data_processing:
Raw data was demultiplexed and converted to FASTQ format using bcl2fastq.
FASTQ files were quality trimmed using Trimmomatic.
FASTQ files were quality assessed with FASTQC.
Quality-trimmed FASTQ files were aligned against human reference with STAR aligner.
Read counts for each gene were genereated with htseq-count.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Each processed file contains the read counts for each gene for one sample. The format is plain text, gzip compressed.

extract_protocol:
Whole blood was collected in a yellow-cap tube and stored at room temperature. The tube was centrifuged and the platelet-rich plasma (PRP) was collected. The PRP was aliquoted and further centrifuged to isolate the platelet pellet. The platelet pellet was dissolved in 700 microliter Qiasol/TRISol. RNA was extracted using the Qiagen miRNA Easy Kit (Cat. # 217004) following the manufacturer’s instructions using a QIACUBE.
RNA-seq libraries were prepared using the Takara Bio SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian per the manufacturer’s instructions.

value: Male

value: Young

value: Pre-vaccination


title: Liver-tropic ANKL1_1


title: T_I_04 [mouse miRNA-Seq]

tag: genotype


title: T_I_07 [mouse miRNA-Seq]


title: U-2 OS KD 39°C Rep1

description:
3' end RNA
cpsf639.1


title: Platelet Sample from Subject 182492 Pre-vaccination


title: Platelet Sample from Subject 182491 Pre-vaccination


title: U-2 OS KD 39°C Rep2

description:
3' end RNA
cpsf639.2


title: T_IM_01 [mouse miRNA-Seq]


title: T_I_06 [mouse miRNA-Seq]


title: T_I_03 [mouse miRNA-Seq]


title: U-2 OS KD 37°C Rep3

description:
3' end RNA
cpsf637.3


title: T_I_01 [mouse miRNA-Seq]

value: IGF2BP1 +/-, CRE +


title: AG_03 [mouse miRNA-Seq]

source_name: adrenal gland

value: CRE -

value: mouse organ


title: U-2 OS KD 37°C Rep1

description:
3' end RNA
cpsf637.1


title: Platelet Sample from Subject 182490 Pre-vaccination

value: Female


title: Platelet Sample from Subject 182486 Pre-vaccination


title: Platelet Sample from Subject 182420 Pre-vaccination

value: Older


title: U-2 OS KD 32°C Rep2

description:
3' end RNA
cpsf632.2


title: Platelet Sample from Subject 182304, 2 Days Post Vaccination

value: 2 Days Post-Vaccination


title: AG_01 [mouse miRNA-Seq]


title: Platelet Sample from Subject 182489 Pre-vaccination


title: Platelet Sample from Subject 182415 Pre-vaccination


title: AG_02 [mouse miRNA-Seq]


title: AGH_21 [WGS]

data_processing:
Sequenced paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 2.8) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (UCSC mm39) using HiSat2 (v 2.1.0) with parameters  -q --no-spliced-alignment --dta -k 5
Secondary alignments were filtered out using samtools (v 1.10)
Copy number variatons were analysed using R/cn.MOPS (v 1.44.0) using chromosome normalization (poisson) excluding sex chromosomes
Assembly: mm39
Supplementary files format and content: Comma-separated text file including genomic regions, log ratios of read counts and copy number values for each sample

extract_protocol:
Transgenic tumors and murine organs were dissected and shock-frozen on dry ice. Approximately 30 mg of frozen tissue was lysed in 600 µl RLT lysis buffer (Qiagen) containing β-mercaptoethanol. Tumors were homogenized with Zirconium Oxide beads and Precellys 24 homogenizer (berting technologies). Lysates were subjected to the Qiagen AllPrep DNA/RNA/Protein Kit protocol, with the exception, that precipitated protein was solubilized in 5% SDS solution.
A total amount of 1 μg DNA per sample was used as input material for DNA sample preparation of human neuroblastoma and transgenic mouse tumor samples. Shallow WGS (sWGS) libraries were generated using NEBNext DNA Library Prep Kit following manufacturer's recommendations and indices were added to each sample. The genomic DNA was randomly fragmented to a size of 350 bp by shearing, then DNA fragments were end polished, A-tailed, and ligated with NEBNext adapter for Illumina sequencing, and further PCR enriched by P5 and indexed P7 oligos. The PCR products were purified (AMPure XP system) and resulting libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified using real-time PCR.
shallow whole genome sequencing (sWGS)

value: IMP1/MYCN, CRE +

value: neuroblastoma tumor


title: Platelet Sample from Subject 182419 Pre-vaccination


title: U-2 OS WT 39°C Rep3

description:
3' end RNA
nsi39.3

value: non-silencing


title: U-2 OS KD 32°C Rep1

description:
3' end RNA
cpsf632.1


title: AGH_17 [WGS]


title: U-2 OS WT 39°C Rep2

description:
3' end RNA
nsi39.2


title: AGH_145 [WGS]

source_name: tumour


title: U-2 OS WT 39°C Rep1

description:
3' end RNA
nsi39.1


title: Platelet Sample from Subject 182411 Pre-vaccination


title: Platelet Sample from Subject 182412 Pre-vaccination


title: U-2 OS KD 37°C Rep2

description:
3' end RNA
cpsf637.2


title: Platelet Sample from Subject 182410 Pre-vaccination


title: U-2 OS WT 37°C Rep3

description:
3' end RNA
nsi37.3


title: U-2 OS KD 32°C Rep3

description:
3' end RNA
cpsf632.3


title: AGH_142 [WGS]


title: AGH_144 [WGS]


title: U-2 OS WT 37°C Rep2

description:
3' end RNA
nsi37.2


title: Platelet Sample from Subject 182409 Pre-vaccination


title: AGH_141 [WGS]


title: Platelet Sample from Subject 182408 Pre-vaccination


title: U-2 OS WT 37°C Rep1

description:
3' end RNA
nsi37.1


title: Platelet Sample from Subject 182406 Pre-vaccination


title: AGH_140 [WGS]


title: U-2 OS WT 32°C Rep3

description:
3' end RNA
nsi32.3


title: AGH_20 [WGS]


title: Platelet Sample from Subject 182405 Pre-vaccination


title: U-2 OS WT 32°C Rep2

description:
3' end RNA
nsi32.2


title: AGH_138 [WGS]


title: Platelet Sample from Subject 182339 Pre-vaccination


title: SH17 [WGS]


title: SH20 [WGS]

source_name: tumour adrenal gland


title: Platelet Sample from Subject 182404 Pre-vaccination


title: SH19 [WGS]


title: Platelet Sample from Subject 182413 Pre-vaccination


title: Rheb floxp/floxp; Ribo-HA k/+; Syn-Cre, P25, 2

first: Alexander

last: Platero

address: 725 N. Wolfe st

department: Neuroscience

institute: Johns Hopkins SOM

data_processing:
Alignment with Tophat v.2.1.0
Cuffdiff v2.2.1 (with option “ -u gencode.vM5.annotation.sorted.gtf” )
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Cortex

extract_protocol:
Cortical lysate was subjected to IP with anti-HA monoclonal antibody bound Dynabeads, and then RNA was harvested using RNeasy mini kit (Qiagen).
RNA library preparation with the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to manufacturer’s user guide.

value: Cortex

value: Neuron

value: Rheb  knockdown

value: Cortical lysate to IP with anti-HA antibody bound Dynabeads


title: Rheb floxp/floxp; Ribo-HA k/+; Syn-Cre, P25, 3


title: Rheb floxp/floxp; Ribo-HA k/+; Syn-Cre, P25, 1


title: Rheb floxp/floxp; Ribo-HA k/+, P25, 2

value: Control


title: Platelet Sample from Subject 182337 Pre-vaccination

first: Steven

last: Kleinstein

address: 300 George St.

institute: Yale University


title: Rheb floxp/floxp; Ribo-HA k/+, P25, 1


title: SH18 [WGS]

value: IGF2BP1 +/+, CRE +


title: Platelet Sample from Subject 182336 Pre-vaccination

value: Young


title: Rheb floxp/floxp; Ribo-HA k/+, P25, 3


title: Platelet Sample from Subject 182333 Pre-vaccination

value: Pre-vaccination


title: Platelet Sample from Subject 182325 Pre-vaccination

value: Male


title: Platelet Sample from Subject 182334 Pre-vaccination


title: SH14 [WGS]

value: IGF2BP1 +/-, CRE +


title: SH16 [WGS]


title: Platelet Sample from Subject 182323 Pre-vaccination


title: SH15 [WGS]


title: Platelet Sample from Subject 182321 Pre-vaccination


title: db/db Dapa rep5

city: Beijing

first: yihui

last: Wang

state: Beijing

address: Haidian district

data_processing:
Raw data (raw reads) were processed using Trimmomatic
clean reads were mapped to the reference genome (GRCm39) using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count
Assembly: GRCm39
Supplementary files format and content: excel files include RPKM values for all Sample

source_name: kidney

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: kidney

tag: Sex

value: male

value: db/db

tag: strain

value: 1mg/kg dapagliflozin solving in 0.5% methylcellulose

tag: time

value: 22 week old


title: db/db Dapa rep3

tag: tissue


title: AGH_15 [WGS]

value: MYCN fl/wt, CRE +

value: mouse organ


title: AGH_16 [WGS]


title: AGH_13 [WGS]


title: AGH_14 [WGS]


title: U-2 OS WT 32°C Rep1

description:
3' end RNA
nsi32.1

tag: cell line

value: U-2 OS

value: non-silencing


title: db/db Dapa rep4


title: Platelet Sample from Subject 182322 Pre-vaccination

city: New Haven

value: Female

value: Older


title: Platelet Sample from Subject 182316 Pre-vaccination


title: db/db Dapa rep1


title: Platelet Sample from Subject 182313 Pre-vaccination


title: db/db Dapa rep2


title: Platelet Sample from Subject 182315 Pre-vaccination


title: Platelet Sample from Subject 182312 Pre-vaccination


title: db/db vehicle rep3

value: 0.5% methylcellulose


title: db/db vehicle rep2


title: db/db vehicle rep5


title: AGH_12 [WGS]


title: db/db vehicle rep4


title: SH13 [WGS]

value: CRE -


title: T_IM_12 [RNA-Seq]

data_processing:
Sequenced strand specific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 2.8) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (UCSC mm39) using HiSat2 (v 2.1.0) with parameters -q --rna-strandness RF --dta -k 5
Secondary alignments were filtered out using samtools (v 1.10)
Mapped reads were summarized using featureCounts (v 2.0.0) with parameterst -p -s 2 -T 6 -M -t exon -g gene_id and Ensembl gene annotations (GRCm 39.105)
Raw counts were corrected for batch effects using ComBat-seq from R package sva (version 3.46.0)
Differential gene expression was assessed using R/edgeR (v 3.40) using TMM normalization
Assembly: mm38
Supplementary files format and content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values

extract_protocol:
Transgenic tumors and murine organs were dissected and shock-frozen on dry ice. Approximately 30 mg of frozen tissue was lysed in 600 µl RLT lysis buffer (Qiagen) containing β-mercaptoethanol. Tumors were homogenized with Zirconium Oxide beads and Precellys 24 homogenizer (berting technologies). Lysates were subjected to the Qiagen AllPrep DNA/RNA/Protein Kit protocol, with the exception, that precipitated protein was solubilized in 5% SDS solution.
For RNA-seq library preparation of transgenic mouse tumor samples, 2 µg of total RNA served as input for polyA(+)-RNA enriched and strand-specific library preparation, performed by Novogene (Hong Kong)

value: IMP1/MYCN, CRE +

value: neuroblastoma tumor

tag: batch run


title: Platelet Sample from Subject 182309 Pre-vaccination

value: Pre-vaccination


title: Platelet Sample from Subject 182306 Pre-vaccination


title: SH12 [WGS]


title: Platelet Sample from Subject 182311 Pre-vaccination

value: Male


title: SH11 [WGS]


title: T_IM_11 [RNA-Seq]


title: T_IM_08 [RNA-Seq]


title: WT rep5

value: kidney

value: m/m


title: Platelet Sample from Subject 182310 Pre-vaccination


title: WT rep2

value: male


title: WT rep3


title: WT rep4


title: Platelet Sample from Subject 182304 Pre-vaccination


title: T_IM_09 [RNA-Seq]


title: WT rep1


title: Retinal cells, Zfp292 OE, Rep3

city: Stanford

first: Yue

last: Sun

address: 290 Jane Stanford Way

institute: Stanford University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: retina

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Control CAG-GFP or CAG-Zfp292 (Zfp292-OE) plasmids were electroporated into P0 mouse pups in vivo. We harvested the retinas 4 days later to allow for robust expression,
Retinas were dissociated into single cell preps.  GFP+ RPCs were colleted from control or Zfp292-OE samples using FACS sorting .

value: retina

value: CAG-Zfp292 electroporation


title: T_IM_07 [RNA-Seq]


title: Retinal cells, Zfp292 OE, Rep1


title: KO-2

city: Duarte

first: Zhen

last: Chen

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

description: polyA RNA enriched

data_processing:
Illumina bcl2fastq version 2.18 used for base calling
Reads were aligned to the mm10 genome assembly using STAR (2.5.4b) with parameter '--sjdbGTFfile'
featureCounts from Subread package (2.0.0) was used to count the number of uniquely mapped reads over exons (-t) per each gene. Strand specific parameter (-s) set to 2
Assembly: mm10
Supplementary files format and content: the processed counts.txt file is a tab-delimited table which includes annotation columns (‘Geneid’, ‘Chr’, ‘Start’, ‘End’, ‘Strand’ and ‘Length’) and data columns (eg. read counts for genes for each library).

source_name: KO mice infused with Angiotensin II through an osmotic pump for 2 weeks

growth_protocol: Male mice at 14-weeks old were fed with normal chow diet

extract_protocol:
CD31-enriched cells from 3 mice/group were pooled together and then subjected for total RNA extraction and construction of strand-specific mRNA-seq library
The libraries were constructed using the KAPA mRNA stranded HyperPrep kit following the user manual

treatment_protocol: Mice was infused with Angiotensin II (1000 ng/kg/min) through an osmotic pump 2 weeks.

value: lung

value: endothelial cells

tag: cell subtype

value: CD31-enriched cells

value: KO

value: infused with Angiotensin II


title: Retinal cells, Zfp292 OE, Rep2


title: T_IM_01 [RNA-Seq]


title: db/db vehicle rep1

value: db/db

value: 22 week old


title: KO-1

description: polyA RNA enriched

tag: cell type


title: T_I_07 [RNA-Seq]

value: IGF2BP1 +/+, CRE +


title: LP6599 EPZ

city: Lexington

first: Jinpeng

last: Liu

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

description:
raw counts and TPM
6599E

data_processing:
Sequencing and base-calling were performed by BGI (Beijing Genomics Institute)
Sequencing reads were trimmed and filtered using Trimmomatic(V0.39) to remove adapters and low quality reads. Reads from human and mouse samples were mapped to Ensembl GRCm38 transcripts annotation (release 82), using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.

source_name: Lung tumor organoids

growth_protocol: Patient derived tumoroids were grown in Matrigel plus cocktail media

extract_protocol:
Matrigel was dissolved by Dispase and the cell pellets were collected.  RNA was extracted using Absolutely RNA Nanoprep kits (Agilent).
RNA libraries were prepared for sequencing using BGI protocols.

treatment_protocol: Patient derived tumoroids were treated with 5uM EPZ6438 for 9 days followed by 2 days of EPZ6438 + 20 ng/mL IFNy

value: Lung tumor organoids

value: malignant epithelial

value: Lkb1/Pten null


title: LP6599 EPZ + IFNy

description:
raw counts and TPM
6599Ei

value: IFNy + EPZ6438


title: LP6599 GSK + IFNy

description:
raw counts and TPM
6599Gi

value: IFNy + GSK126


title: Retinal cells, Control, Rep2

value: CAG-GFP electroporation


title: KO-3

description: polyA RNA enriched


title: T_I_08 [RNA-Seq]

value: neuroblastoma tumor


title: LP6599 GSK

description:
raw counts and TPM
6599G


title: T_IM_04 [RNA-Seq]

value: IMP1/MYCN, CRE +


title: Retinal cells, Control, Rep1

value: retina


title: LP725 EPZ + IFNy

description:
raw counts and TPM
725Ei


title: LP6599 IFNy

description:
raw counts and TPM
6599i

value: IFNy


title: T_I_06 [RNA-Seq]


title: WT-3

description: polyA RNA enriched

source_name: WT mice infused with Angiotensin II through an osmotic pump for 2 weeks

value: lung

value: endothelial cells

value: WT


title: KOT1-589

first: 剑辉

last: 张

address: 岳阳路320号细胞楼11楼

institute: SIBCB

data_processing:
Illumina Casava1.7 software used for basecalling
Sequence reads were trimmed for adaptor sequence/low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters
Reads per kilobase of exon per megabse of library size (RPKM) were calculated using a protocol from chepelev et al., Nucleic Acids Research,
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: muscle

growth_protocol: Tarsl2 WT and KO mice were born in SPF animal room and cultured until 6 weeks.

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

treatment_protocol: Mice were feed with standard chow food and water.

value: Male

value: Tarsl2 KO

value: muscle

tag: age

value: 6 weeks


title: WT1-584

address: 岳阳路320号细胞楼11楼


title: LP725 GSK + IFNy

description:
raw counts and TPM
725Gi

value: Lung tumor organoids


title: T_IM_05 [RNA-Seq]


title: WT1-583

address: 岳阳路320号细胞楼11楼


title: T_I_02 [RNA-Seq]

source_name: tumor

value: IGF2BP1 +/+, CRE +


title: KO1-588

address: 岳阳路320号细胞楼11楼


title: LP6599 Vehicle

description:
raw counts and TPM
6599V

value: malignant epithelial

value: Lkb1/Pten null

value: Vehicle


title: LP725 GSK

description:
raw counts and TPM
725G


title: Small intestinal mucosa, wt_3

city: Iowa City

last: Riordan

state: IA

address: 375 Newton Road

institute: University of Iowa

data_processing:
Basecalling and demultiplexing with Illumina bclfastq2
Alignment with STAR version 2.5.1a
Gene counts derived with Subread:featureCount 1.4.6-p5
Assembly: Ensembl Release 76 GRCm38
Supplementary files format and content: Gene counts, CPM and RPKM in tab-delimited text format

source_name: Small intestinal mucosa

extract_protocol:
Total RNA was extracted using TRIzol and treated with DNAse. For each genotype, 3 pools were prepared, each containing RNAs from 3 separate mice (both sexes), for a total of 10 mg RNA per final pool.
RNA pools were subjected to oligo(dT) selection and cDNA library preparation and whole transcriptome sequencing on an Illumina HiSeq2000.

value: Small intestinal mucosa

value: 8-12 weeks

value: wt


title: AG_M_05 [RNA-Seq]

value: MYCN +/-, CRE +

value: mouse organ


title: WT-2

description: polyA RNA enriched

value: lung

value: CD31-enriched cells

value: infused with Angiotensin II


title: U-OEx-LE3

city: Guangzhou

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

institute: South China Agricultural University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: epithelium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 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 following manufacturer's protocols.

value: luminal epithelium

value: overexpress Notch1


title: WT1-595

address: 岳阳路320号细胞楼11楼

value: Male

value: WT

value: muscle


title: T_I_04 [RNA-Seq]

value: IGF2BP1 +/+, CRE +

value: neuroblastoma tumor


title: T_I_03 [RNA-Seq]


title: E-OEX-GE1

value: glandular epithelium


title: AG_M_03 [RNA-Seq]


title: U-OEx-LE2


title: Small intestinal mucosa, wt_2


title: LP725 EPZ

description:
raw counts and TPM
725E

value: Lung tumor organoids

value: malignant epithelial

value: Lkb1/Pten null


title: AG_M_01 [RNA-Seq]


title: E-OEX-GE3


title: T_I_01 [RNA-Seq]

value: IGF2BP1 +/-, CRE +


title: Small intestinal mucosa, wt_1

value: Small intestinal mucosa

value: 8-12 weeks

value: wt


title: E-OEX-LE1


title: LP725 Vehicle

description:
raw counts and TPM
725V

value: Vehicle


title: E-OEX-GE2


title: AG_03 [RNA-Seq]

value: CRE -

value: mouse organ


title: WT-1

description: polyA RNA enriched

value: lung

value: endothelial cells

value: CD31-enriched cells

value: infused with Angiotensin II


title: SK-Mel-28_miR-127-5p_rep3

type: RNA

city: Greifswald

first: Theresa

last: Kordaß

state: Mecklenburg-Vorpommern

address: Ferdinand-Sauerbruch Straße DZ7 5.05

department: Surgical Research Laboratory

institute: Univserity Medicine Greifswald

hyb_protocol: was performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany

data_processing: data was quantile normalized (enforces the individual hybridizations to have equal intensity distributions) across all hybridizations on BeadArray(s); performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany

label: biotin

source_name: cell line

extract_protocol: After 48 h, cells were harvested for RNA isolation using an RNAeasy kit (Qiagen, Hilden, Germany).

treatment_protocol: SK-Mel-28 cells were transfected with 50 nM miRNA, including a non-targeting control miRNA (control-1/ath-miR-416) in a 12 well plate format, performing triplicates for each format.

tag: transfected with


title: AG_M_04 [RNA-Seq]

value: MYCN +/-, CRE +


title: Small intestinal mucosa, Rbm47_IKO_2


title: 4T1-Cas9-sgTaz-tumor-4

city: Buffalo

first: Jianmin

last: Zhang

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

data_processing:
Fastq files generated with CASAVA
Sequenced reads were mapped to GRCm38 reference GENCODE annotation M22 using STAR aligner
Read counts are obtained using Subread
Assembly: GRCm38
Supplementary files format and content: Raw counts csv file format

source_name: mammary tumor

extract_protocol:
Tumor RNA was harvested using Trizol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
The RNA samples were subjected to transcriptome sequencing (RNA-seq) with an Illumina HiSeq 2000 sequencer in the RPCCC genomic shared resource.

value: mammary tumor

value: tumor cell

value: sgTaz


title: E-OEX-LE3

value: luminal epithelium

value: overexpress Notch1


title: Small intestinal mucosa, Rbm47_IKO_3


title: AG_M_02 [RNA-Seq]


title: Ctrl-GE3

value: glandular epithelium

value: WT


title: U-OEx-LE1


title: AG_02 [RNA-Seq]


title: T_I_05 [RNA-Seq]

value: IGF2BP1 +/+, CRE +

value: neuroblastoma tumor


title: E-OEX-LE2


title: 4T1-Cas9-sgTaz-tumor-3


title: Ctrl-GE2


title: AG_01 [RNA-Seq]


title: 4T1-Cas9-sgTaz-tumor-1


title: Ctrl-LE3


title: 4T1-Cas9-sgTaz-tumor-2


title: LP725 IFNy

description:
raw counts and TPM
725i

value: Lung tumor organoids

value: malignant epithelial

value: Lkb1/Pten null

value: IFNy


title: Ctrl-LE2


title: 4T1-Cas9-sgCon-tumor-4

value: sgControl


title: 4T1-Cas9-sgTaz-tumor-5


title: Ctrl-GE1


title: KO1-591

address: 岳阳路320号细胞楼11楼

tag: gender

value: Male

value: Tarsl2 KO

value: muscle

value: 6 weeks


title: 4T1-Cas9-sgCon-tumor-2

value: mammary tumor

value: tumor cell


title: Small intestinal mucosa, Rbm47_IKO_1

value: Small intestinal mucosa

value: 8-12 weeks


title: 4T1-Cas9-sgCon-tumor-3


title: 4T1-Cas9-sgCon-tumor-5


title: WT_P6, scRNAseq

first: Cheng

last: Wu

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Vitreous

extract_protocol:
Postnatal eyeballs were enucleated from mice and placed in 4% paraformaldehyde (PFA) for 15 min and then for another 45 min after corneal cutoff.  Eyeballs were then thrown into Eppendorf tube containing 5-10% gelatin (abs9357, Absin, China) for 1-2 min and invert the tube gently to allow complete immersion. Pour eyeballs out on a glass slide at R.T. for air dry. After 5-10 mins, peel the scleral, choroidal and retinal layer off with forceps. Circle and fall a drop of ddH2O on the HV buried in solidified gelatin, then melt the gelatin at 60°C and absorb ddH2O away. Air dry the HV at R.T. to make the HV attached to the slide tightly. Subsequent blocking and IHC were similar to conventional IHC of tissue section.
Cell count and viability was estimated with Trypan Blue staining and Countess II Cell Counter (ThermoFisher Scientific). Samples having ＞90% live cells were barcoded with 10x chromium system using the v3 single-cell reagent kit (10x Genomics) for library construction. Barcoded libraries were pooled and sequenced on Illumina Hi-Seq 2500 platform generating 150-bp paired-end reads.

value: Goblet cells

value: Vitreous

value: 6 days

value: wild type


title: Ctrl-LE1

value: luminal epithelium

value: WT


title: WT_P3, scRNAseq

value: 3 days


title: SK-Mel-28_miR-3116_rep3

scan_protocol: was performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany


title: SK-Mel-28_miR-3126-5p_rep3

label_protocol: was performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany


title: SK-Mel-28_miR-6514-3p_rep3


title: SK-Mel-28_miR-1293_rep3


title: SK-Mel-28_miR-34b-3p_rep3


title: FA8mg_Poly.5

city: Philadelphia

first: Margie

last: Clapper

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

description: polypoid tumor cells form colitic mice treated with 8 mg folic acid

data_processing:
Raw reads were aligned to mm10 genome using bowtie
Raw counts in each known gene from the Ensembl database were enumerated using htseq-count from the HTSeq package
Genome_build: mm10
Supplementary_files_format_and_content: raw count in tab-delimited format

source_name: polypoid tumor cells, 8mg folic acid, rep5

growth_protocol: Mice were fed a diet containing folic acid 2 mg/kg chow, followed by carcinogen azoxymethane injection. Colitis was induced in all mice using 4 cycles of DSS. Immediately after the first DSS treatment, mice were randomized to receive folic acid 0 or 8 mg/kg chow for 16 weeks. At the end of study, mice were euthanized and colons were collected and process for gene expression analyses

extract_protocol:
Cells were microdissected from paraffin-embedded tissues usig Leica LMD6500 system.  RNA was isolated using the RecoverAllTM total Nucleic Acid Isolation for FFPE kit.  RNA concentration and quality were determined on an Agilent 2100 Bioanalyzer using RNA 6000 Pico chips.
Libraries were generated using SMARTerÒ Stranded RNA-Seq Kit V2- Pico Input Mammalian with 40 ng total RNA. Libraries were quantified using a Qubit ds DNA HS kit and size distribution validated on the Agilent 2100. Bioanalyzer using the Agilent High Sensitivity DNA kit.

treatment_protocol: AOM was injected at 7 weeks of age and DSS treatment was initiated at 9 weeks of age for 4 cycles (each cycle = 7 days of 2% DSS in drinking water plus 14 days of untreated water). At 11 weeks of age, mice were randomly assigned to receive folic acid at 0 or 8 mg/kg chow for 16 weeks.  Mice were euthanized at 27 weeks of age.  Colons were fixed in 10% formalin and processed for embedding.

value: laser microdissected polypoid tumor cells

value: Swiss Webster

value: 8 mg folic acid


title: SK-Mel-28_miR-6859-3p_rep3


title: 4T1-Cas9-sgCon-tumor-1

value: sgControl


title: MT_P6, scRNAseq

value: mutant


title: WT mouse O4+ cells 3

city: Ann Arbor

first: Andrew

last: Lieberman

state: MI

address: 1150 W Medical Center Drive

institute: University of Michigan

description:
O4+ cells were collected from a P16 WT mouse. RNA was purified and sequenced.
5434-TK-3

data_processing:
BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files.
We use Snakemake (Köster and Rahmann, 2012) to manage the bioinformatics workflow in a reproducible manner.
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011).
Alignment options followed ENCODE standards for RNA-seq (Dobin).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7 (Ewels et al., 2016).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample
Supplementary files format and content: tab-delimited text file include TPM values for each Sample

source_name: brain

extract_protocol:
Cells were isolated from brains of 16-day-old mice by magnetic-activated cell sorting using microbeads targeting the antigen O4 and were immediately flash frozen. RNA was extracted using an Rneasy plus kit (Qiagen).
Libraries were constructed using the following kits: NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and xGen Broad-range RNA Library Prep (IDT, 1009813) with xGen Normalase UDI Primers (IDT, various).

value: brain

value: primary cells

value: O4+ oligodendrocyte

value: wt


title: MT_P3, scRNAseq


title: Npc1-/- mouse O4+ cells 2

description:
O4+ cells were collected from a P16 Npc1-/- mouse. RNA was purified and sequenced.
5434-TK-5


title: SK-Mel-28_miR-127-5p_rep2


title: SK-Mel-28_miR-3116_rep2


title: WT mouse O4+ cells 2

description:
O4+ cells were collected from a P16 WT mouse. RNA was purified and sequenced.
5434-TK-2


title: Npc1-/- mouse O4+ cells 1

description:
O4+ cells were collected from a P16 Npc1-/- mouse. RNA was purified and sequenced.
5434-TK-4


title: Arid1a_knockout_rep3

city: Goettingen

first: Zhe

state: Niedersachsen

address: Robert-Koch-Strasse 40

department: Department of Gastroenterology & GI oncology

institute: University Medical Center, Goettingen

data_processing:
Paired-end 75bp reads were aligned to mouse genome MGSCv37/mm9 by Bowtie2 (Version 2.3.4.2)
peaks were called by MACS2 Version 2.1.1 with FDR < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files cover large fraction of the genome with varing scores representing the enrichment of peaks at each genomic regions.

source_name: Pancreas

extract_protocol:
The pancreas of 8-week-old p48-Cre and Arid1afl/fl;p48-Cre mice were harvested in ice-cold HBSS, dissociated by surgical scissors in a 10 cm cell culture dish filled with 5 ml cold HBSS and centrifuged at low speed (300 rpm, 5 min) to remove blood vessels and adipose tissue. The remaining explant was digested in 5 ml solution 2 at 37 ºC for 20 min, pipetted every 2 min using a 10 ml pipette. The tissue-containing tube was washed with 10 ml solution 1 and centrifuged (300 rpm, 5 min) before adding a second time of solution 2 and cultivated at 37 ºC for 10 min. Next, tissue suspension was transferred into a new 50 ml tube by filtering through a 100 µm cell strainer and the tissue fragments were ground using a syringe plunger. The remaining cells were collected by washing the mesh with two times of 10 ml solution 1 and pelleted. Recovering was achieved by easing the acinar cells in 5 ml solution 3 containing 10% FCS for 1 hour at 37 ºC and subjected to ATAC-seq library preparation.
ATAC-seq library preparation was conducted using Nextera DNA Library Prep (Illumina) as previously described (Buenrostro et al., 2013). 10,000 cells were used for the assay. Crude nuclei preparation was achieved by incubating the cells in ATAC lysis buffer. The pelleted nuclei were incubated with transposition reaction buffer containing Tn5 transposases and incubated at 37 ºC for 30 min, followed by DNA purification using Qiagen MinElute PCR purification Kit. Further, transposed DNA was barcoded and amplified through PCR. After quality control by Agilent Bioanalyzer 2100 and size-selection, samples were prepared as 2 nmol/L and sequenced on a HiSeq 2500

value: Primary acinar cells

value: post natal 8 weeks


title: Arid1a_wt_rep2


title: Npc1-/- mouse O4+ cells 3

description:
O4+ cells were collected from a P16 Npc1-/- mouse. RNA was purified and sequenced.
5434-TK-6


title: FA8mg_Poly.3

state: PA

source_name: polypoid tumor cells, 8mg folic acid, rep3


title: SK-Mel-28_control_miRNA_rep3


title: FA8mg_Poly.4

source_name: polypoid tumor cells, 8mg folic acid, rep4


title: Arid1a_knockout_rep1


title: SK-Mel-28_miR-224-3p_rep3


title: Wild Type cntl, D7 SCV2, Lung cells, scRNAseq

city: Maryland

first: Oyebola

last: Oyesola

address: Building 4, Room B1 05 4 Memorial Drive Bethesda, MD 20892

institute: National Institute of Health

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Lung lobes were diced into small pieces and incubated in RPMI containing 0.33mg/mL Liberase TL and 0.1mg/mL DNase I (both from Sigma Aldrich) at 37°C for 45 minutes under agitation (150rpm). Enzymatic activity was stopped by adding FCS. Digested lung was filtered through a 70µm cell strainer and washed with RPMI. Red blood cells were lysed with the addition of ammonium-chloride-potassium buffer (Gibco) for 3 minutes at room temperature. Cells were then washed with RPMI supplemented with 10% FCS.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, pooled lung samples 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.

treatment_protocol:
Animals were infected with 500 third stage N. brasilienesis larvae by subcutaneous injection.
SCV2 infections were performed under BSL3 containment. Animals were anesthetized by isoflurane inhalation and a dose of 103 TCID50/mouse SCV2 WA/2020 was administered by intranasal instillation

value: Lung cells

value: Lung

value: 6-8 weeks old

value: cntl, D7 SCV2


title: SK-Mel-28_miR-4672_rep3


title: FA8mg_ND.4

description: non-neoplastic colon epithelium form colitic mice treated with 8 mg folic acid

source_name: non-neoplastic, 8mg folic acid,rep 4

value: laser microdissected non-neoplasitc colon epitheila cells


title: Wild Type N. brasiliensis d28, D7 SCV2, Lung cells, scRNAseq

description: 10x Genomics

value: N. brasiliensis d28, D7 SCV2


title: CL10_KPV_VIM_KO_3

city: Chicago

first: kishore

last: Anekalla

state: IL

address: 303 E. Superior

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
Reads were demultiplexed (bcl2fastq), and fastq files were aligned to the mm10 mouse reference genome with TopHat2.
Htseq was used to obtain counts.
The resulting data were filtered, and differentially expressed genes (DEGs) were identified using the edgeR package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing CPM for each sample; also includes FDR and fold change for pairwise comparisons

source_name: lung

extract_protocol:
Cells were cultured for one passage, then lysed using RLT lysis buffer (Qiagen), and total RNA was isolated with the RNeasy Plus Mini Kit (Qiagen). RNA quality was confirmed with a TapeStation 4200 (Agilent); all samples had an RNA integrity number (RIN) score equal to or greater than 9.8. Next, mRNA was isolated via poly(A) enrichment (NEBNext).
Libraries were prepared using NEBNext RNA Ultra chemistry (New England Biolabs).

value: lung

value: KPV-/-

value: lung adenocarcinoma


title: Arid1a_knockout_rep2


title: FA8mg_Poly.2

source_name: polypoid tumor cells, 8mg folic acid, rep2

value: laser microdissected polypoid tumor cells

value: Swiss Webster

value: 8 mg folic acid


title: WT mouse O4+ cells 1

description:
O4+ cells were collected from a P16 WT mouse. RNA was purified and sequenced.
5434-TK-1

value: brain

value: primary cells


title: Arid1a_wt_rep3


title: FA8mg_ND.5

source_name: non-neoplastic, 8mg folic acid,rep 5


title: FA8mg_Poly.1

source_name: polypoid tumor cells, 8mg folic acid, rep1


title: SK-Mel-28_miR-1293_rep2


title: SK-Mel-28_miR-134-3p_rep3


title: SK-Mel-28_miR-4672_rep2


title: SK-Mel-28_miR-6514-3p_rep2


title: FA8mg_ND.3

source_name: non-neoplastic, 8mg folic acid, rep3


title: Wild Type cntl, Lung cells, scRNAseq

description: 10x Genomics

value: cntl


title: SK-Mel-28_miR-3126-5p_rep2


title: SK-Mel-28_miR-34b-3p_rep2


title: FA8mg_ND.2

source_name: non-neoplastic, 8mg folic acid, rep2


title: SK-Mel-28_miR-6859-3p_rep2


title: CL09_KPV_VIM_KO_2


title: FA8mg_ND.1

source_name: non-neoplastic, 8mg folic acid, rep1


title: CL08_KPV_VIM_KO_1


title: CL07_KP_VIM_WT_3

value: KPV+/+


title: Wild Type N. brasiliensis d28, Lung cells, scRNAseq

description: 10x Genomics

value: N. brasiliensis d28


title: FA0mg_Poly.4

description: polypoid tumor cells form colitic mice treated with 0 mg folic acid

source_name: polypoid tumor cells, 0mg folic acid, rep4

value: 0 mg folic acid


title: FA0mg_Poly.1

source_name: polypoid tumor cells, 0mg folic acid, rep1


title: CL06_KP_VIM_WT_2


title: Arid1a_wt_rep1

value: Primary acinar cells

value: post natal 8 weeks


title: FA0mg_Poly.3

source_name: polypoid tumor cells, 0mg folic acid, rep3


title: FA0mg_Poly.2

source_name: polypoid tumor cells, 0mg folic acid, rep2


title: CL05_KP_VIM_WT_1


title: FA0mg_ND.3

description: non-neoplastic colon epithelium form colitic mice treated with 0 mg folic acid

source_name: non-neoplastic, 0mg folic acid, rep3


title: FA0mg_ND.1

source_name: non-neoplastic, 0mg folic acid, rep1