title: TM1 alone replicate B

city: Boston

first: William

middle: P

last: Robins

address: 77 Avenue Louis Pasteur NRB 1039

department: Microbiology

institute: Harvard Medical School

data_processing:
CLC Genomics Workbench v8
Reads were trimmed for quaility (quality score 0.05 cutoff) and made reverse complement for mapping due to strand specific sequencing
Mapped reads were analyzed using the CLC DGE tool
Assembly: Asembled and annnotated TaMai1 and A603 genomes provided in manuscript
Supplementary files format and content: Excel sheet with subsheets for comparisons
Supplementary files format and content: Mapping depth and RPKM provided in processed files

organism: Vibrio parahaemolyticus

source_name: bacterial

growth_protocol: Mono or mixed culture spotted on agar

extract_protocol:
Zymo Direct-zol RNA extraction kit
NEB Ultra RNA directional library kit and Epicentre Ribozero bacterial rRNA depletion

value: bacterial

value: rRNA depleted mRNA


title: T75A_18h_Caf, rep3

status: Public on Jul 05 2024

type: SRA

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

description:
R40_T75A_18_Caf.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

library_source: transcriptomic

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
Raw data was quality trimmed and clipped for Illumina universal adapter. Potential sequencing errors were detected and corrected using Rcorrector and rRNA fragments have been depleted using SortMeRNA.
Reads were mapped on GRCm38 (mm10) genome reference using segemehl, if applicable deduplicated for over-amplified PCR fragments via Unique Molecular Identifiers using UMI-tools and quantified on Ensembl v102 derived gene annotation utilizing featureCounts. Variance stabilized counts were inferred by DESeq2.
Assembly: mm10 (Ensembl v102)
Supplementary files format and content: Tab delimited text files include raw, variance stabilized and TPM normalized read counts for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Mice were at least 8 weeks old and were housed in a 12L:12D light cycle.

extract_protocol:
RNA extraction involved resuspension in Trizol and chloroform precipitation, followed by washing with isopropanol and 75% ethanol. Subsequently, cDNA conversion was performed using the GoScript™ Reverse Transcriptase kit (#A5001, Promega).
1) Library was prepared using Novogene NGS RNA Library Prep Set (PT042) according to manufacturer instructions. 2) Libraries were prepared from 500 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA) following the manufacturer's instructions (NewEngland Biolabs).

treatment_protocol: 1) At four time points (4h, 10h, 16h, 22h), mice were intraperitoneally (i.p.) injected with 7.5 mg/kg caffeine (#, C0750, Sigma) or saline at an injection volume of 10ml/kg body weight and tested 2h later. NPB ((#CSB-MP015971HU-100, Cusabio) was injected at doses of 1, 3, and 10 nM into the NAc. NPB was diluted in ddH2O up to 100 nM and then diluted with artificial cerebrospinal fluid, which also served as a control. CYM50769 (#1067-25mg, Sigma Aldrich) was injected into the NAc at doses of 0.1 – 10 μM. CYM50769 was diluted in DMSO up to 100 μM and then diluted in artificial cerebrospinal fluid, which also served as a control solution containing the proper concentration of DMSO (#3525, Tocris). 2) Bilateral stereotaxic surgery into the NAc was essentially performed as described (doi: 10.1038/nm.4386). Viruses were utilized at concentrations from 2 x 10^10 (OE) to 6 x 10^11 (GFP ctrl) particles * 0.1ml: pAAV.1-CAG-GFP (#37825, Addgene), OE-Npbwr1-GFP: pAAV-CAG-GFP-P2A-Npbwr1-WPRE1. Npbwr1-regulating AAVs were custom-made by Charitè viral vector core, Berlin, Germany. All AAVs were serotype 1.

tag: tissue

value: Brain

tag: region

value: Nucleus accumbens

tag: strain

tag: genotype

tag: treatment

value: 6h dark, Caffeine

tag: Sex

value: male


title: Sample49

type: genomic

city: Aurora

first: Sunita

last: Sharma

state: CO

address: 13001 East 17th Place

department: Anschutz Campus - Sch of Med - Pulmonary Sciences

country: USA

institute: University of Colorado - Anschutz Medical Campus

description: Nasal-epithelial Tissue Swab

scan_protocol: The labeling, hybridization, and scanning procedures were performed on the Illumina IScan system in the University of Colorado Genomics Core. This analysis was performed in 11 adolescents who self-identified as vaping in the last 6 months and 36 who had not. All samples were assayed once (no technical replicates) with 6 arrays (8 samples per array) performed in 1 batch.

data_processing:
Samples were evaluated for a low mean-intensity to identify potential outliers with low-quality methylation values.
probes were removed due to non-unique mapping, influence by SNPs, or by having a detection p-value > 0.05 in at least 10% of samples.
Background subtraction using normal-exponential deconvolution using out-of-band probes (noob) to make Type I and Type II probes comparable
BMIQ normalization was considered a priori due to a concern for lack of within-array normalization as interpreted from diagnostic plots.
A non-linear dye bias correction was used to make the red and green signal intensities (Type-I) more comparable

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Nasal-epithelial Tissue

extract_protocol: Bisulfite converted samples formed the input for the Illumina Infinium Methylation assay using the Human Methylation 850k BeadChips (Illumina Inc, San Diego, CA).

treatment_protocol: To measure methylation at approximately 850,000 single CpG sites across the genome, we used Illumina’s Infinium Human Methylation 850k BeadChip on bisulfite-treated samples. 0.85-1.00 µg DNA were bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research, Orange, CA). Each conversion assay included a commercially available positive and negative control sample.

value: Did Not Vape in Last 6 Months

tag: age

value: Female

value: CommCity/Denver


title: Sample48

description: Nasal-epithelial Tissue Swab

hyb_protocol: The labeling, hybridization, and scanning procedures were performed on the Illumina IScan system in the University of Colorado Genomics Core.

value: Male

value: Pueblo


title: T75A_18h_Caf, rep1

description:
R8_T75A_18_Caf.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_18h_Sal, rep4

description:
R55_T75A_18_Sal.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 6h dark, Saline


title: Sample47

description: Nasal-epithelial Tissue Swab

label_protocol: The labeling, hybridization, and scanning procedures were performed on the Illumina IScan system in the University of Colorado Genomics Core.


title: T75A_18h_Sal, rep3

description:
R39_T75A_18_Sal.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_18h_Sal, rep2

description:
R23_T75A_18_Sal.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample45

description: Nasal-epithelial Tissue Swab


title: T75A_18h_Sal, rep1

description:
R7_T75A_18_Sal.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample46

description: Nasal-epithelial Tissue Swab

value: Vaped in Last 6 Months


title: T75A_12h_Caf, rep4

description:
R52_T75A_12_Caf.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 12h light, Caffeine


title: Sample43

description: Nasal-epithelial Tissue Swab

value: Aurora


title: Sample44

description: Nasal-epithelial Tissue Swab


title: T75A_12h_Caf, rep1

description:
R4_T75A_12_Caf.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample40

description: Nasal-epithelial Tissue Swab


title: T75A_12h_Caf, rep2

description:
R20_T75A_12_Caf.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_12h_Sal, rep4

description:
R51_T75A_12_Sal.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 12h light, Saline


title: T75A_12h_Sal, rep3

description:
R35_T75A_12_Sal.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_12h_Sal, rep2

description:
R19_T75A_12_Sal.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample41

description: Nasal-epithelial Tissue Swab


title: Sample39

description: Nasal-epithelial Tissue Swab


title: TM1 alone replicate A

state: MA

molecule: total RNA

tag: cell type

tag: molecule subtype


title: Sample37

description: Nasal-epithelial Tissue Swab


title: Sample36

description: Nasal-epithelial Tissue Swab


title: T75A_12h_Sal, rep1

description:
R3_T75A_12_Sal.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_18h_Caf, rep2

description:
R24_T75A_18_Caf.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_18h_Caf, rep4

description:
R56_T75A_18_Caf.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample35

description: Nasal-epithelial Tissue Swab


title: T75A_6h_Caf, rep3

description:
R48_T75A_6_Caf.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 6h light, Caffeine


title: Sample34

description: Nasal-epithelial Tissue Swab


title: Sample38

description: Nasal-epithelial Tissue Swab


title: Sample33

description: Nasal-epithelial Tissue Swab


title: T75A_6h_Caf, rep1

description:
R16_T75A_6_Caf.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_6h_Caf, rep4

description:
R64_T75A_6_Caf.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_12h_Caf, rep3

description:
R36_T75A_12_Caf.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_6h_Sal, rep3

description:
R47_T75A_6_Sal.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 6h light, Saline


title: T75A_6h_Sal, rep4

description:
R63_T75A_6_Sal.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample31

description: Nasal-epithelial Tissue Swab


title: Sample42

description: Nasal-epithelial Tissue Swab


title: T75A_6h_Sal, rep2

description:
R31_T75A_6_Sal.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: T75A_6h_Sal, rep1

description:
R15_T75A_6_Sal.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample26

description: Nasal-epithelial Tissue Swab


title: Sample29

description: Nasal-epithelial Tissue Swab


title: Sample28

description: Nasal-epithelial Tissue Swab


title: WT_24h_Caf, rep2

description:
R26_WT_24_Caf.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: WT

value: 12h dark, Caffeine


title: Sample25

description: Nasal-epithelial Tissue Swab


title: WT_24h_Caf, rep3

description:
R42_WT_24_Caf.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: Brain

value: Nucleus accumbens


title: Sample24

description: Nasal-epithelial Tissue Swab


title: Sample30

description: Nasal-epithelial Tissue Swab


title: Sample23

description: Nasal-epithelial Tissue Swab


title: T75A_6h_Caf, rep2

description:
R32_T75A_6_Caf.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: male


title: Sample22

description: Nasal-epithelial Tissue Swab

value: Did Not Vape in Last 6 Months


title: WT_24h_Caf, rep4

description:
R58_WT_24_Caf.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: WT_24h_Sal, rep3

description:
R41_WT_24_Sal.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 12h dark, Saline


title: WT_24h_Sal, rep2

description:
R25_WT_24_Sal.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: WT_24h_Sal, rep4

description:
R57_WT_24_Sal.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample32

description: Nasal-epithelial Tissue Swab

value: CommCity/Denver


title: WT_24h_Sal, rep1

description:
R9_WT_24_Sal.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: WT_24h_Caf, rep1

description:
R10_WT_24_Caf.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample21

description: Nasal-epithelial Tissue Swab

value: Male


title: WT_18h_Caf, rep4

description:
R54_WT_18_Caf.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 6h dark, Caffeine


title: Sample19

description: Nasal-epithelial Tissue Swab

value: Female

value: Pueblo


title: Sample18

description: Nasal-epithelial Tissue Swab

value: Vaped in Last 6 Months


title: Sample20

description: Nasal-epithelial Tissue Swab


title: WT_18h_Caf, rep2

description:
R22_WT_18_Caf.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample17

description: Nasal-epithelial Tissue Swab

value: Aurora


title: WT_18h_Caf, rep3

description:
R38_WT_18_Caf.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: WT_18h_Caf, rep1

description:
R6_WT_18_Caf.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample16

description: Nasal-epithelial Tissue Swab


title: Sample27

description: Nasal-epithelial Tissue Swab


title: WT_18h_Sal, rep4

description:
R53_WT_18_Sal.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 6h dark, Saline


title: WT_18h_Sal, rep3

description:
R37_WT_18_Sal.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: WT_18h_Sal, rep2

description:
R21_WT_18_Sal.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample15

description: Nasal-epithelial Tissue Swab


title: pdox_g3_T3_2

city: Philadelphia

first: Duancheng

last: Guo

state: PA

address: 333 Cottman AVE

institute: Fox Chase Cancer Center

description: bulk transcriptome

data_processing:
Paired-end RNA sequencing fastq files were processed for adapter and low quality base call removal. Each paired-end file was split into equal read numbers across all conditions to account for library depths. Files were then mapped to either the mm39 or hg38 gencode genome index with the light-weight transcript abundance quantifier, Salmon. Variance-mean dispersions of raw counts were estimated using the negative binomial generalized linear modeling Wald test.
Assembly: mouse:mm39, human:hg38
Supplementary files format and content: Comma-separated values text file of raw counts for each sample.

source_name: MB tumor cells treated with T3

growth_protocol: Medulloblastoma cells were suspended in NB-B22 culture medium (Neurobasal, 1mmol/L sodium pyruvate, 2mml/L L-glutamine, B22 supplement, and 1% penicillin/streptomycin).

extract_protocol:
Primary cells were freshly isolated from tumor-bearing mice at 6 to 8 weeks of age. Briefly, tumor tissues were isolated from mouse brains and digested in a papain solution to obtain a single cell suspension and then centrifuged through a 35% and 65% Percoll gradient. Cells from the 35% to 65% interface were suspended in Dulbecco's PBS (DPBS) plus 0.5% BSA. Cells were then suspended in NB-B22 (Neurobasal medium with B22 supplement. Cell suspension was plated on poly-D-lysine (PDL)-coated coverslips (BD Biosciences).
Total RNA was extracted from tumor cells treated with T3 or PBS. Strand-specific mRNA-seq libraries for the Illumina platform were generated and sequenced following the manufacturer’s protocol. High-quality total RNA was used as input for the so-called dUTP library preparation method. Briefly, the mRNA fraction was purified from total RNA by polyA capture, fragmented and subjected to first-strand cDNA synthesis with random hexamers in the presence of Actinomycin D. The second-strand synthesis was performed incorporating dUTP instead of dTTP. Barcoded DNA adapters were ligated to both ends of the double-stranded cDNA and subjected to PCR amplification. The resultant library was checked on a Bioanalyzer (Agilent) and quantified. The libraries were multiplexed, clustered, and sequenced on an Illumina NovaSeq X Plus. The sequencing run was analyzed with the Illumina BCL-Convert, with demultiplexing based on sample- specific barcodes.

treatment_protocol: For in vitro experiments, 200nM of T3 was added to the culture medium for 48 hours. For EZH2i conditions, 1mM of GSK126 was added to culture. Controls were treated with PBS only.

value: MB tumor cells treated with T3

tag: cell line

value: human G3 PDOX medulloblastoma cells


title: Sample13

description: Nasal-epithelial Tissue Swab


title: pdox_g3_T3_1

description: bulk transcriptome


title: pdox_g3_T3_3

description: bulk transcriptome


title: Sample12 (excluded)

description: Sample 12 did not participate in the methylation portion of the study


title: WT_18h_Sal, rep1

description:
R5_WT_18_Sal.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: WT


title: WT_12h_Caf, rep4

description:
R50_WT_12_Caf.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 12h light, Caffeine


title: pdox_g3_PBS_2

description: bulk transcriptome

source_name: MB tumor cells treated with PBS

value: MB tumor cells treated with PBS

value: PBS


title: Sample11

description: Nasal-epithelial Tissue Swab


title: pdox_g3_PBS_3

description: bulk transcriptome


title: WT_12h_Caf, rep3

description:
R34_WT_12_Caf.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: Brain

value: Nucleus accumbens

value: male


title: pdox_g3_PBS_1

description: bulk transcriptome


title: pdox_shh_T3_3

description: bulk transcriptome

value: human SHH PDOX medulloblastoma cells


title: pdox_shh_T3_2

description: bulk transcriptome


title: pdox_shh_T3_1

description: bulk transcriptome


title: Sample09

description: Nasal-epithelial Tissue Swab

value: Did Not Vape in Last 6 Months

value: Male


title: WT_12h_Caf, rep1

description:
R2_WT_12_Caf.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample08

description: Nasal-epithelial Tissue Swab

value: CommCity/Denver


title: WT_12h_Caf, rep2

description:
R18_WT_12_Caf.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: pdox_shh_PBS_2

description: bulk transcriptome


title: pdox_shh_PBS_3

description: bulk transcriptome


title: pdox_shh_PBS_1

description: bulk transcriptome


title: Sample14

description: Nasal-epithelial Tissue Swab


title: WT_12h_Sal, rep4

description:
R49_WT_12_Sal.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 12h light, Saline


title: Sample07

description: Nasal-epithelial Tissue Swab

value: Female


title: H3K27ac-shZEB1-F10

city: Erlangen

first: Yussuf

last: Hajjaj

address: Glueckstr. 6

institute: FAU

library_source: genomic

data_processing:
Raw reads were quality filtered and adapter‐trimmed using cutadapt v.1.9.1, then  aligned to GRCh38 ensemble genome assembly. using Bowtie2 v. 2.2.9.
BigWig files were generated using deeptools v 2.3.
Assembly: GRCh38
Supplementary files format and content: BigWig format.

source_name: Breast

growth_protocol: DMEM supplemented with 10% FBS.

extract_protocol:
Cells were crosslinked with 1% formaldehyde in PBS (Ca+/Mg+) at RT for 10 min. Isolated chromatin was sonicated with a Diagenode Bioruptor to a fragment size of 300–500 bp.
Library preparation was performed with the NEBNext® Ultra DNA Library Prep Kit according to the manufacturer's instructions.

value: Breast

value: Immortalized Breast Cancer

tag: antibody

value: ZEB1 knockdown


title: H3K27ac-shZEB1-13


title: WT_12h_Sal, rep3

description:
R33_WT_12_Sal.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: H3K27ac-shGFP1

value: control


title: Sample06

description: Nasal-epithelial Tissue Swab

value: Aurora


title: WT_12h_Sal, rep2

description:
R17_WT_12_Sal.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: WT


title: H3K27ac-shGFP4


title: Sample05

description: Nasal-epithelial Tissue Swab

value: Vaped in Last 6 Months

value: Pueblo


title: FD, NHEM, scRNAseq

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Foreskin

growth_protocol: NHEMs were cultured in M254 supplemented with human melanocyte growth supplement (HMGS) at 37 °C, 5% CO2

extract_protocol:
Fsk daily and alternate day NHEMs were trypsinized and spun down at 400g then washed and resuspended in 1x DPBS and taken for library preparation
Libraries was prepared according to the manufacter’s instructions (single cell 3’ v3.1 (dual index) protocol, 10x Genomics). Briefly, NHEMs 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 two sample indexes were added.

treatment_protocol: NHEMs were treated with 20µM forskolin either daily or every alternate day for 7 days

value: Melanocytes

value: Foreskin

value: Normal human epidermal melanocytes

value: Neonatal

value: 20µM forskolin daily


title: FA, NHEM, scRNAseq

description: 10x Genomics

value: 20µM forskolin alternate day


title: HP, B16, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done using the Cell Ranger software v6.1.2 (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

growth_protocol: B16 F10 cells were cultured at a very low density of 100 cells/cm2 for 7 days in DMEM high glucose supplemented with 10% fetal bovin serum at 37 °C, 5% CO2

extract_protocol:
B16 F10 cells were trypsinized at day 7, spun down at 400g, then washed and resuspended in 1x DPBS. Low and high pigmented cells were sorted using the side scatter intensity of a flow cytometer and taken for library preparation
Libraries was prepared according to the manufacter’s instructions (single cell 3’ v3.1 (single index) protocol, 10x Genomics). Briefly, B16 cells 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 sample index were added.

tag: condition

value: high pigment


title: B16, Unsorted, replicate 2, IgG

description: 10x Genomics

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NextSeq output.
ChIP-seq reads were trimmed using a sliding window of 4 bases and average quality score of >15 using Trimmomatic v0.33, discarding reads left with < 50 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie 2 version 2.5.1.
Peaks were called uing MACS3 with the significance cut-off q-value <=0.05
bigWig files were generated using the ucsc bedgraphtobigwig tool converting the SPMR normalized bedgraph files generated by MACS3. narrowPeak files were generated using MACS3 with default parameters and retaining all duplicate reads
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: B16 F10 cells were cultured at a very low density of 100 cells/cm2 in DMEM high glucose supplemented with 10% fetal bovin serum at 37 °C, 5% CO2

extract_protocol:
B16 F10 cells were trypsinized at day 5, spun down at 400g, then washed and resuspended in 1x DPBS. Low and high pigmented cells were sorted using the side scatter intensity of a flow cytometer. Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a bath sonicator (Diagenode Bioruptor).
ChIP-seq libraries were prepared using the NEB Ultra II DNA library prep kit (E7103S) complemented with NEBNext Multiplex Oligos for Illumina (E6440S). Equal ammount of DNA was used as starting material for all samples in each replicate set. Libraries were amplified using 5-7 cycles on the thermocycler. Post amplification cleanup was performed using NEBNext beads. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: chip antibody

value: IgG (Abcam #ab172730)

value: unsorted


title: Sample04

description: Nasal-epithelial Tissue Swab

value: Did Not Vape in Last 6 Months

value: Male

value: CommCity/Denver


title: Sample10

description: Nasal-epithelial Tissue Swab

value: Female


title: WT_6h_Caf, rep4

description:
R62_WT_6_Caf.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: Brain

value: Nucleus accumbens

value: 6h light, Caffeine

value: male


title: LP, B16, scRNAseq

description: 10x Genomics

value: Melanocytes

value: low pigment


title: B16, HP, replicate 2, H3K27ac

description: 10x Genomics

value: H3K27ac (Abcam #ab4729)


title: WT_6h_Caf, rep3

description:
R46_WT_6_Caf.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: WT


title: Sample02

description: Nasal-epithelial Tissue Swab


title: B16, Unsorted, replicate 1, IgG

description: 10x Genomics


title: B16, LP, replicate 2, H3K27ac

description: 10x Genomics


title: Sample03

description: Nasal-epithelial Tissue Swab

value: Pueblo


title: B16, HP, replicate 1, H3K27ac

description: 10x Genomics


title: WT_6h_Caf, rep2

description:
R30_WT_6_Caf.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: Sample01

description: Nasal-epithelial Tissue Swab


title: D5, B16, replicate 2, scATACseq

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done using the Cell Ranger Arc software v2.0.2 (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, matrix files, peak files and fragments files

growth_protocol: B16 F10 cells were cultured at a very low density of 100 cells/cm2 in DMEM high glucose supplemented with 10% fetal bovine serum at 37 °C, 5% CO2

extract_protocol:
Day 0, 3 and 5 B16 F10 cells were trypsinized on the same day, spun down at 400g, then washed and resuspended in 1x DPBS. All the three samples were then taken for library preparation
scMultiome (ATAC+Gene Expression):
Libraries were prepared according to the manufacter’s instructions (single cell multiome ATAC + Gene Expression protocol, 10x Genomics). Briefly, 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 sample index were added.

tag: time

value: Day 5

value: nuclear chromatin


title: WT_6h_Caf, rep1

description:
R14_WT_6_Caf.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: WT_6h_Sal, rep4

description:
R61_WT_6_Sal.N4
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 6h light, Saline


title: D5, B16, replicate 2, scRNAseq

description: 10x Genomics

molecule: nuclear RNA


title: WT_12h_Sal, rep1

description:
R1_WT_12_Sal.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz

value: 12h light, Saline


title: D5, B16, replicate 1, scRNAseq

description: 10x Genomics


title: D5, B16, replicate 1, scATACseq

description: 10x Genomics


title: WT_6h_Sal, rep3

description:
R45_WT_6_Sal.N3
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: D3, B16, scATACseq

description: 10x Genomics

value: Day 3


title: D3, B16, scRNAseq

description: 10x Genomics


title: WT_6h_Sal, rep2

description:
R29_WT_6_Sal.N2
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: WT_6h_Sal, rep1

description:
R13_WT_6_Sal.N1
NAc-caf-counts.tsv.gz
NAc-caf-tpm.tsv.gz
NAc-caf-vsc.tsv.gz


title: B16, LP, replicate 1, H3K27ac

description: 10x Genomics


title: NAc_Npbwr1-OE, rep4

description:
Npbwr1-OE.N4
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz

value: female


title: NHK_4h

type: RNA

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Hybridization was performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals were developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays were dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430. Data extraction was done for all beads individually

data_processing:
All arrays were normalized together using the quantile normalization algorithm  with background correction.
Quantile normalization based on idat file information and BGX file annotation using Limma in R

source_name: Keratinocytes in monoculture for 4h

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Normal human keratinocytes (NHK) and human dermal ﬁbroblasts (HDF) were derived from foreskin as previously described (König & Bruckner-Tuderman, 1994; Stark et al, 1999). NHK were cultivated in keratinocyte serum free medium (KSFM, Invitrogen, Carlsbad, CA, USA) supplemented with recombinant human EGF (rhEGF) and pituitary bovine extract (BPE). Cells were kept under a humidified environment with 5% CO2 and 37oC. Keratinocytes were used up to passage 4-5 and density of 4-9 x 104 cells/cm2

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: KSFM medium was added to a culture of NHK and collected after 12h to stimulate sub-confluence monolayers of HDF for 18 hours. This supernatant from the conditioned HDF culture was used to stimulate keratinocytes (NHK_DP_Xh) for the specified time in a double paracrine manner. NHK_DP_C0/4/12 samples are used as controls, wherein NHK are stimulated with KSFM medium for 12 h, then again for 18h and then again for the specified time. NHK_Xh are keratinocyte mono-cultures sampled after the specified time. After each conditioning  the collected media were centrifuged (200 xg/ 5 min) and then used to stimulate the respected other cells. Time and volume was considered to have adequate soluble factors content and sufficient medium nutrients.

tag: group

value: NHK monoculture

tag: stimulus

tag: timepoint

value: Skin

tag: gender

value: Male

value: Normal Human Epithelial Keratinocytes

tag: array id


title: NAc_Npbwr1-OE, rep3

description:
Npbwr1-OE.N3
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz

tag: tissue

value: Brain

tag: region

value: Nucleus accumbens

tag: strain


title: NHK_1h

source_name: Keratinocytes in monoculture for 1h


title: spRNA-seq_HS_areaC

city: ATHENS

first: Robert

middle: J.

last: Schmitz

state: GA

address: B416 Davison Life Sciences Department of Genetics University of Georgia 120 East Green Street

department: Genetics

institute: University of Georgia

description: Gm_atlas_Heart_stage_seeds.spRNA.obj.rds

data_processing:
We used the Space Ranger (10X Genomics) to map the spRNA-seq reads to the soybean genome and count gene expression. The filtered gene expression matrix was analyzed using the Seurat (v4) R package.87 All the datasets were analyzed using SCTransform and RunPCA. To remove the batch effect for replicates placed in different spatial capture areas, we used the Harmony R package to integrate the replicates and analyzed it using RunUMAP (reduction = "harmony", dims = 1:20) and FindNeighbors (reduction = "harmony", dims = 1:20). We used FindClusters to identify cell clusters and FindSubCluster to identify the subclusters for specific cell types. Various resolutions were used to identify the cell clusters in distinct types of tissues.
Assembly: Soybean William 82 v4 reference genome
Supplementary files format and content: processed seurat objects
Library strategy: spatial transcriptomics

organism: Glycine max

source_name: seeds at heart stage

extract_protocol:
For the spatial RNA-seq experiment, the hypocotyl tissues, the root tissues, and the seed tissues at the heart stage, cotyledon stage, and early maturation stage, matching the stages of the single-cell datasets, were sampled. The tissues were embedded in the Optimal Cutting Temperature (OCT) compound, snap-frozen in a cold 2-methylbutane bath merged in liquid nitrogen, and cryosectioned into 12 um thick slices.
We used the Visium Spatial Gene Expression Kit (10X Genomics, USA) to construct the spatial RNA-seq libraries following the manufacturer’s instructions. The tissue sections were mounted onto the spatial slides, fixed by cold methanol, and stained by 0.05% toluidine blue. The stained tissue sections were imaged using the BZ-X800 fluorescent microscope (Keyence, Japan). To determine the optimal tissue permeabilization time, we performed the Tissue Optimization workflow on a series of digestion times for each tissue type. For the spatial RNA-seq libraries, mRNA was first released according to the optimal permeabilization time, then the spatially barcoded cDNA were synthesized on the slides. Finally, cDNA were released from the slide and subjected to amplification and library construction, following the manufacturer’s specifications

value: seeds at heart stage


title: NHK_12h

source_name: Keratinocytes in monoculture for 12h


title: spRNA-seq_HS_areaD


title: D0, B16, scATACseq

description: 10x Genomics

value: Melanocytes

value: Day 0


title: spRNA-seq_EMS_areaC

description: Gm_atlas_Early_maturation_stage_seeds.spRNA.obj.rds

source_name: seeds at early maturation stage

value: seeds at early maturation stage


title: spRNA-seq_root_areaC

source_name: root

value: root


title: spRNA-seq_HS_areaA


title: spRNA-seq_hypocotyl_areaB

source_name: hypocotyl

value: hypocotyl


title: NHK_DP_24h

source_name: Keratinocytes with double paracrine stimulation for 24h

value: Double paracrine stimulation

value: Fibroplast conditioned medium


title: spRNA-seq_hypocotyl_areaA


title: NHK_DP_6h

source_name: Keratinocytes with double paracrine stimulation for 6h


title: NHK_DP_4h

source_name: Keratinocytes with double paracrine stimulation for 4h


title: spRNA-seq_EMS_areaD


title: NHK_DP_12h

source_name: Keratinocytes with double paracrine stimulation for 12h


title: spRNA-seq_HS_areaB


title: spRNA-seq_root_areaD


title: NAc_Npbwr1-OE, rep1

description:
Npbwr1-OE.N1
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz

source_name: Brain

tag: genotype

tag: Sex


title: D0, B16, scRNAseq

description: 10x Genomics

tag: cell type


title: NAc_Npbwr1-OE, rep2

description:
Npbwr1-OE.N2
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz


title: NAc_ctrl, rep4

description:
ctrl.N4
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz

value: ctrl


title: spRNA-seq_EMS_areaA


title: spRNA-seq_CS_areaD

source_name: seeds at cotyledon stage

value: seeds at cotyledon stage


title: spRNA-seq_EMS_areaB


title: NAc_ctrl, rep3

description:
ctrl.N3
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz

value: female


title: spRNA-seq_CS_areaC


title: NHK_DP_2h

source_name: Keratinocytes with double paracrine stimulation for 2h


title: NHK_DP_1h

source_name: Keratinocytes with double paracrine stimulation for 1h


title: NHK_DP_C12h

source_name: Keratinocytes 12h after stimulation with keratinocyte-conditioned medium

value: Control for double paracrine stimulation

value: NHK conditioned medium


title: snRNA-seq_Root.rep4

description:
Gm_atlas_Root.rna.seurat.obj.rds
Gm_atlas_Root_RNA_gene_cellstate_counts.txt.gz

data_processing:
STARSolo was used to map the snRNA-seq reads and count the gene features using the soybean genome (William 82 v4).86 We specified the following parameters in STARSolo to filter the UMI, filter empty cells, and count multi-mapping reads: --soloUMIfiltering MultiGeneUMI_CR, --soloCellFilter EmptyDrops_CR, --soloMultiMappers PropUnique. The filtered expression data was analyzed using the Seurat (v4) R package.87 Potential low-quality nuclei or empty droplets were filtered. Specifically, cells with gene counts below a threshold calculated as the median gene count minus two times the median absolute deviation, and cells with UMI counts less than the lower 10% percentile of total UMI counts, were filtered out. Additionally, cells with organelle gene counts comprising more than 15% of the total gene count were excluded. The preprocessed datasets were normalized using SCTransform before the RunPCA for principal component analysis (PCA). Subsequently, the doublets were identified by the DoubletFinder R package, and removed from downstream analysis. We prepared two replicates for each library and integrated them using the Harmony R package.88 The integrated dataset was then processed using RunUMAP (reduction = "harmony", dims = 1:20) for Uniform Manifold Approximation and Projection (UMAP) dimension reduction, FindNeighbors (reduction = "harmony", dims = 1:30) to obtain the Nearest-neighbor graph, and FindClusters to identify distinct cell populations. Different resolutions were selected to classify cell types in varying tissue types. We used FindSubCluster to identify the sub-clusters according to the specificity of marker genes.
Assembly: Soybean William 82 v4 reference genome
Supplementary files format and content: Seurat object, gene count matrix for celltypes

extract_protocol:
The protocol for nuclei isolation and purification was adapted from a previously described scATAC-seq method. To minimize RNA degradation and leakage, the tissue was finely chopped on ice for approximately 1 minute using 600 μL of pre-chilled Nuclei Isolation Buffer containing 0.4 U/μL RNase inhibitor (Roche, Protector RNase Inhibitor, Cat. RNAINH-RO) and a low detergent concentration of 0.1% NP-40. Following chopping, the mixture was passed through a 40-μm cell strainer and centrifuged at 500 rcf for 5 minutes at 4°C. The supernatant was carefully decanted, and the pellet was reconstituted in 500 μL of NIB wash buffer (10 mM MES-KOH at pH 5.4, 10 mM NaCl, 250 mM sucrose, 0.5% BSA, and 0.2 U/μL RNase inhibitor). The sample was filtered again through a 10-μm cell strainer and gently layered onto 1 mL of 35% Percoll buffer (prepared by mixing 35% Percoll with 65% NIB wash buffer) in a 1.5-mL centrifuge tube. The nuclei were centrifuged at 500 rcf for 10 minutes at 4°C. After centrifugation, the supernatant was carefully removed, and the pellets were resuspended in 50 μL of NIB wash buffer. Approximately 5 μL of nuclei were diluted tenfold and stained with DAPI (Sigma Cat. D9542). The quality and density of the nuclei were evaluated using a hemocytometer under a microscope. The original nuclei were further diluted with DNB buffer to achieve a final concentration of 1,000 nuclei per μL. Ultimately, a total of 16,000 nuclei were used as input for snRNA-seq library preparation.
For scRNA-seq library preparation, we employed the Chromium Next GEM Single Cell 3'GEM Kit v3.1 from 10X Genomics (Cat# PN-1000123), following the manufacturer's instructions (10xGenomics, CG000315_ChromiumNextGEMSingleCell3-_GeneExpression_v3.1_DualIndex_RevB). The libraries were subsequently sequenced using the Illumina NovaSeq 6000 in dual-index mode with 10 cycles for the i7 and i5 indices, respectively.


title: DBP35 at 100uM concentration replicate 2

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to listed concentrations in a 80-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing:
To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. Next, the Seed-and-wobble algorithm was applied to compute enrichment scores (E-scores) and median intensities for all possible 7-mers.
value definition: Enrichment scores (E-scores), median intensities, and z-scores for 7-mers

label: Alexa 488

molecule: protein

organism: synthetic construct

source_name: DBP35 replicate 2

label_protocol: Proteins were tagged with N-terminal His by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen).

growth_protocol: DNA sequences encoding the proteins of interest were purchased as Integrated DNA Technologies (IDT) E-Blocks and incorporated into plasmids using Golden Gate assembly. The plasmids were then transformed into BL21(DE3) competent E. coli. The transformation reactions were used to inoculate starter cultures in 5 mL or 25 mL of “Terrific Broth” (TB), supplemented with 1% (w/v) glucose and 50 mg/L kanamycin. After shaking overnight at 37°C, the starter cultures were diluted 50-fold into 50 mL or 500 mL of TB with kanamycin. These cultures were incubated at 37°C, shaking, until the optical density (OD) reached 0.6-0.8, at which point protein expression was induced by the addition of IPTG. The cultures were then further incubated overnight at 18°C.

extract_protocol: Cells were harvested by centrifugation for 15 min at 3000g, pellets resuspended in lysis buffer (150 mM NaCl, 20 mM Tris-HCl, 0.5 mg/mL DNAse I, 1 mM PMSF, pH 8.0), the cells lysed by sonication, and the lysate clarified by further centrifugation for 30 min at 20,000g. The supernatant was passed through Ni-NTA resin in a gravity column, and then the resin was washed with 20 column volumes of high-salt wash buffer (2 M NaCl, 20 mM Tris-HCl, 20 mM Imidazole, pH 8.0). Either (A) the His-tagged protein was eluted with 2 column volumes of elution buffer (1 M NaCl, 20 mM Tris, 250 mM Imidazole, pH 8.0), or (B) the resin was further washed with 5 column volumes of SNAC buffer (100 mM CHES, 100 mM Acetone oxime, 100 mM NaCl, 500 mM GnCl, pH 8.6), incubated in 5 column volumes of SNAC buffer + 0.2 mM NiCl2 on an orbital shaker at room temperature overnight, and collected as the column flow-through. Whether cleaved or not, the protein was concentrated to about 1 mL and loaded in 500 μL samples onto a Cytiva Superdex™ 75 Increase 10/300 GL gel filtration column equilibrated in buffer (1 M NaCl, 20 mM Tris-HCl, pH 8.0). Fractions containing monomeric protein were pooled and concentrated to about 200 μL. Protein concentrations were estimated spectroscopically by absorbance at 280 nm. For proteins with no Trp, Tyr, or Cys residues, concentrations were approximated by Bradford reagent absorbance at 470 nm in comparison to BSA standards of known concentration.

tag: synthetic dna-binding protein

tag: protein concentration


title: snRNA-seq_Nodule.rep2

description:
Gm_atlas_Early_nodule.rna.seurat.obj.rds
Gm_atlas_Early_nodule_RNA_gene_cellstate_counts.txt.gz

source_name: root with 1mm nodule

value: root with 1mm nodule


title: snRNA-seq_Root.rep3


title: NAc_ctrl, rep2

description:
ctrl.N2
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz


title: NAc_ctrl, rep1

description:
ctrl.N1
NAc-Npbwr1-counts.tsv.gz
NAc-Npbwr1-tpm.tsv.gz
NAc-Npbwr1-vsc.tsv.gz


title: NHK_DP_C4h

source_name: Keratinocytes 4h after stimulation with keratinocyte-conditioned medium

value: Skin

value: Male

value: Normal Human Epithelial Keratinocytes


title: snRNA-seq_HS_seeds.rep1

description:
Gm_atlas_Heart_stage_seeds.rna.seurat.obj.rds
Gm_atlas_Heart_stage_seeds_RNA_gene_cellstate_counts.txt.gz

source_name: seeds at heart stage

value: seeds at heart stage


title: OCDC, scTCR-seq

city: chengdu

first: Hao

last: Zeng

state: sichuan

address: 37 Guoxue Alley

country: China

institute: West China Hospital

data_processing:
The Cell Ranger Software Suite v.6.1.2 was used to process the raw sequence data into gene expression profiles. The FASTQ files for each sample were processed with cell ranger count, which was used to mm10 reference genome alignment, filtering and quantifying the reads. The recovered cell parameter was set at 10,000, which is the expected number of cells for each library. The output files of Cell Ranger for each sample included the feature barcode and gene expression (in unique molecular identifier (UMI) format). Gene expression data were obtained using cellranger aggr, which performed an intersample normalization and merged the results of all samples into one file to remove potential sample variability. For the scTCR-seq data, TCR reads were aligned to the mm10 reference genome, and TCR annotation was performed using the 10x cellranger vdj pipeline. The clonotype of each T-cell was represented by the paired alpha and beta CDR3 sequences.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes all_contig annotations
Supplementary files format and content: tab-delimited text file includes consensus annotations
Supplementary files format and content: tab-delimited text file includes metrics summary

source_name: Tumor

growth_protocol: Mouse Lewis lung carcinoma (LL/2) cell lines were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) and 100 units/ml streptomycin and penicillin (PS) was used to culture the LL/2 cells. Mouse bone marrow-derived dendritic cells (BMDCs) were generated from C57BL/6J female mice according to a previous report (50). Briefly, bone marrow cells were obtained by flushing the bone marrow cavities of the femur and tibia. After treatment with red blood cell lysis buffer, these marrow cells were cultured in fresh Roswell Park Memorial Institute (RPMI)-1640 medium containing 10% FBS, 1% PS and 20 ng/ml granulocyte-macrophage colony-stimulating factor (GM-CSF) (Prime Gene Biotechnology, Shanghai, China) for 8 days. On day 3, the medium was replaced with fresh RPMI-1640 medium containing 10% FBS, 1% PS and 20 ng/ml GM-CSF. All cells were cultured at 37 °C in 5% CO2. DMEM, FBS, PS and RPMI-1640 were all purchased from Thermo Fisher Scientific (Waltham, MA, USA).

extract_protocol:
Tumor tissues were dissected into 1~2 mm pieces with scissors in PBS buffer and digested in RPMI 1640 Medium containing 1% FBS, 1% penicillin-streptomycin, 1 mg/ml Collagenase II (Sigma) and 100 μg/ml DNase I (Sigma) at 37 °C for 30 min. Subsequently, tumor tissue cells were filtered with a 70 µm cell strainer (BD Biosciences). After a 5 min centrifugation at 500 g, cells were resuspended with red blood cell lysis buffer (Beyotime) to deplete red blood cells. Thereafter, cells were washed 2~3 times and kept in RMPI1640 medium with 1% FBS and 2mM EDTA at 4°C for cell sorting.Libraries were constructed using the Single Cell %’ Library Kit V3 (10× Genomics).
Enzymatic fragmentation and size selection are used to generate variable length fragments that collectively span the V(D)J segments of the amplified TCR and/or BCR transcripts prior to library construction. P5, P7, i5 and i7 sample indexes, and an Illumina R2 sequence (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and Sample Index PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification.

treatment_protocol: Immunization of subcutaneous tumor model mice Mice were subcutaneously inoculated with 1× 105 LL/2 tumor cells on day 0. Then, these mice were randomly divided into the 0.9% NaCl saline (NS) group, DC group and OCDC group. In total, NS (100 µl), 2 × 106 DC vaccine (100 µl) and 2 × 106 OCDC vaccine (100 µl) were intradermally injected into the mice in each group (n = 9) on days 1, 4, 8 and 11. One week after tumor inoculation, tumor volume was recorded every 2 days. Mice were sacrificed on day 18, and the tumors were weighed and photographed.  Immunization of lung metastatic tumor model mice A total of 5×105 LL/2 tumor cells were injected into the mice through the tail vein on day 0. These tumor-bearing mice were randomly grouped into the NS group, DC group and OCDC group. For different treatments, NS (100 µl), 2 × 106 DC vaccine (100 µl) and 2 × 106 OCDC vaccine (100 µl) were intradermally injected into the mice in each group (n = 6) on days 4, 11 and 18 posttumor inoculation. A week after treatment, the mice were sacrificed, and the lungs were weighed and photographed.

value: Tumor

tag: cell line

value: lung cancer cells and immune cells

tag: treatment

value: Mouse tumor sample treated with OCDC vaccine


title: snRNA-seq_Nodule.rep1


title: snRNA-seq_HS_seeds.rep2


title: T, scTCR-seq

value: Mouse tumor sample treated with T cell transfer


title: snRNA-seq_Hypocotyl.rep2

description:
Gm_atlas_Hypocotyl.rna.seurat.obj.rds
Gm_atlas_Hypocotyl_RNA_gene_cellstate_counts.txt.gz

value: hypocotyl


title: DBP9 at 75uM concentration replicate 2

source_name: DBP9 replicate 2


title: snRNA-seq_GS_seeds.rep2

description:
Gm_atlas_Globular_stage_seeds.rna.seurat.obj.rds
Gm_atlas_Globular_stage_seeds_RNA_gene_cellstate_counts.txt.gz

source_name: seeds at globular stage

value: seeds at globular stage


title: NS, scTCR-seq

value: Mouse tumor sample with no treat


title: DBP6 at 200uM concentration replicate 2

source_name: DBP6 replicate 2


title: DBP3 at 75uM concentration replicate 2

source_name: DBP3 replicate 2


title: snRNA-seq_Hypocotyl.rep1

source_name: hypocotyl


title: snRNA-seq_GS_seeds.rep1


title: NooT, scTCR-seq

value: Neoantigen-reactive T cells treated with OCDC


title: snRNA-seq_EMS_seeds.rep2

description:
Gm_atlas_Early_maturation_stage_seeds.rna.seurat.obj.rds
Gm_atlas_Early_maturation_stage_seeds_RNA_gene_cellstate_counts.txt.gz

source_name: seeds at early maturation stage

value: seeds at early maturation stage


title: NHK_DP_C0h

source_name: Keratinocytes 0h stimulation with keratinocyte-conditioned medium


title: DBP1 at 300uM concentration replicate 2

source_name: DBP1 replicate 2


title: snRNA-seq_EMS_seeds.rep1


title: spRNA-seq_CS_areaB

source_name: seeds at cotyledon stage

value: seeds at cotyledon stage


title: spRNA-seq_CS_areaA


title: Nta RPFs, with rRNA depletion

city: Potsdam

first: Reimo

last: Zoschke

address: Am Mühlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

description:
NTa_undepleted
counts_over_CDS-Tobacco.xlsx
library_stats.xlsx

library_source: other

data_processing:
library strategy: Ribosome Profiling (Ribo-seq)
Arabidopsis:The Arabidopsis GTF gene annotations (v45) and TAIR10 genome were downloaded from ensembl (https://plants.ensembl.org/index.html). Cutadapt (Martin, 2011) was used to remove adapters and UMIs. Ribo-seq contaminants are generally defined as rRNA, tRNA and snoRNA. These sequences were extracted from the gene annotation file, and converted to fasta format using bedtools (Quinlan and Hall, 2010). Importantly, the nuclear 25S and 5S are missing from the Arabidopsis gene annotations. Thus, these sequences were obtained from the following sources: 25S rRNA (https://www.ncbi.nlm.nih.gov/nuccore/X52320.1) and the 5S rRNA database (http://combio.pl/rrna/). Contaminants were filtered out using STAR aligner (Dobin et al., 2013) with the following parameters: --outFilterMismatchNoverLmax 0.1 --outReadsUnmapped Fastx –outSAMmultNmax 1. After contaminant filtering, the remaining reads were mapped to the genome using STAR aligner using the following parameters: --outFilterMismatchNoverLmax 0.1 --alignIntronMax 8000 --outSAMmultNmax 1. Mapped reads were counted over annotated CDS using FeatureCounts (Liao et al., 2014) using the parameters: -M -s 1 -t CDS -g gene_id.
Tobacco: There are two available genomes for tobacco, which are both available from solgenomics (https://solgenomics.net/). The most recent version was used for alignment (Edwards et al., 2017) since it is conveniently assembled into chromosomes. Nuclear rRNA sequences used to filter the Ribo-seq libraries were obtained from NCBI; 26S (AF479172.1), 18S (AJ236016.1), 5.8S (AJ300215.1) and 5S (AJ222659.1). The tobacco chloroplast (NC_001879.2) and mitochondrial (NC_006581.1) genomes were also obtained from NCBI. Chloroplast and mitochondrial rRNA sequences were extracted from the respective genome annotations. The remainder of the analysis pipeline follows the same structure as what was performed for Arabidopsis.
Assembly: Arabidopsis: TAIR10 genome  (https://plants.ensembl.org/index.html) using the Arabidopsis GTF gene annotations (v45)
Assembly: Tobacco: The Edwards genome assembly was used (solgenomics (https://solgenomics.net/). The chloroplast genome (NC_001879.2) and mitochondria genome (NC_006581.1) were obtained from NCBI.
Supplementary files format and content: "library_stats.xlsx" contains information on the proportion of reads mapping to rRNA, nuclear genome, plastid genome, and mitochondria genome.
Supplementary files format and content: "counts_over_CDS-Arabidopsis.xlsx" contains the number of reads mapping to annotated Arabidopsis coding sequences (CDS)
Supplementary files format and content: "counts_over_CDS-Tobacco.xlsx" contains the number of reads mapping to annotated Tobacco coding sequences (CDS)

molecule: other

organism: Nicotiana tabacum

source_name: leaves harvested from 28-day old plants

growth_protocol: The tissue used for the comparison of RNase I and MNase digestion, was derived from 8-day old Arabidopsis seedlings (Col-0) grown on ½ Murashige and Skoog medium (Murashige and Skoog, 1962) with 6.8% agar and 1% sucrose, grown at 100 µmol m-2s-1 for 16h/8h light/dark cycles at 20 °C. The tissue used for refining RNase I treatment and rRNA depletion were derived from 14-day old Arabidopsis seedlings (Col-0), grown on ½ Murashige and Skoog media with 1% agar, grown at 100 µmol m-2s-1 for 12h/12h light/dark cycles at 20 °C. Nicotiana tabacum tissue was derived from leaves harvested from 28-day old plants grown on soil at 350 µmol m-2s-1 in 16h/8h light/dark cycles at 12 °C.

extract_protocol:
RPF isolation: RPFs were isolated as previously described (Trösch et al., 2018) with the following modifications. The units (U) of ribonuclease used in this study are normalized to one mL of plant lysate, derived from 100 mg of plant fresh weight. 300 mg frozen plant tissue was homogenized in liquid nitrogen with a mortar and pestle followed by the addition of 3 mL ribosome extraction buffer (0.2 M sucrose, 0.2 M KCl, 40 mM Tris-OAc pH 8.0, 10 mM MgCl2, 10 mM 2-Mercaptoethanol, 2% (v/v) polyoxyethylene (10) tridecyl ether, 1% (v/v) Triton X-100, 100 μg/mL chloramphenicol, 100 μg/mL cycloheximide). After brief mixing, a 0.5 mL aliquot of the lysate was flash frozen and stored at -80 °C for later total RNA extraction using TRIzol reagent (ThermoFisher cat# 15596026). This total RNA can be used for standard RNA-seq experiments. This step is especially important if the calculation of translation efficiencies is desired (i.e., the normalization of Ribo-seq data to RNA-seq data). The remaining lysate was filtered through glass wool, followed by centrifugation for 10 min at 15,000 x g at 4 °C to remove cell debris. 2.5 mL of the clarified lysate were incubated at specified concentrations of RNase1 or MNase for 1 h at room temperature with gentle rotation to degrade mRNA regions that are not covered and protected by translating ribosomes. Since Ca2+ is a known cofactor of MNase, samples digested with MNase include 5 mM CaCl2. The ribonuclease-treated lysate contains mainly monosomes which were loaded onto a 2 mL sucrose cushion (30% (w/v) sucrose, 40 mM Tris-Acetate pH 8.0, 100 mM KCl, 15 mM MgCl2, 0.1 mg/mL chloramphenicol, 0.1 mg/mL cycloheximide, 0.2% β-MeEtOH) and centrifuged (OptimaTM L-80 XP Ultracentrifuge - Beckman Coulter) for 1.5 h at 303,800 x g at 4 °C. The supernatant was then carefully aspirated and the pelleted monosomes resuspended in 0.5 mL footprint isolation buffer (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 100 mM NaCl, 1% (w/v) SDS, 0.1 M EGTA pH 8.0). The RNA was immediately extracted from this pellet using 0.5 mL TRIzol reagent. Next RPFs were size-selected through electrophoresis on a 12% denaturing polyacrylamide gel (19:1, acrylamide:bisacrylamide) prepared in 1x TBE buffer (89 mM Tris, 89 mM Boric Acid, 2mM EDTA pH 8.0) containing 8 M urea. To this end, 25 μg RNA were resuspended in 40 μL of ribosome footprint loading buffer (90% (v/v) deionized formamide, 20 mM Tris-HCl pH 7.5, 20 mM EDTA pH 8.0, 0.04% (w/v) bromophenol blue, and 0.04% (w/v) xylene cyanol) and denatured for 10 min at 70 °C. The gel was run in 1x TBE buffer with a constant power of 30 W at constant temperature of 12 °C (achieved by a cooling unit). Co-migrating pre-stained RNA ladder (Biodynamics Laboratory cat# DM253) was used to visualize the regions of the gel to excise RPFs. All RPFs that were not rRNA-depleted were size-selected between 20-50 nt. All rRNA-depleted RPFs were size-selected between 20-35 nt. RNA was eluted from the excised gel piece in 4 mL TESS (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 0.1 M NaCl, 0.2% (w/v) SDS) by overnight incubation at 4 °C with gentle rotation. Eluted RNA was isolated with 4 mL of phenol:chloroform:isoamyl alcohol (25:24:1), followed by overnight ethanol precipitation at -20 °C. To increase purity and further narrow the volume, the RNA pellet was resuspended in 0.1 M NaCl (500 μL) and subjected to a second round of phenol:chloroform:isoamyl alcohol (25:24:1) extraction, followed by two washes with chloroform:isoamylalcohol (24:1) and overnight ethanol precipitation at -20 °C. The received RPF pellet was washed twice with 75% ethanol and resuspended in 20 μL RNase-free water.
Library preparation: T4 polynucleotide kinase (PNK; ThermoFisher, cat#EK0031) reactions were carried out in 18 µL volume with 100 ng of RPFs without ATP for 10 min at 37 °C to promote the 3’-dephosphorylation reaction. Next, 2 µL ATP (10 mM) was added, followed by another incubation for 30 min at 37 °C. PNK was inactivated by heating to 65 °C for 20 min. 20 ng RPFs were directly used as input for the NEXTflex small RNA-seq kit v3 (Perkin Elmer, cat# NOVA-5132-06) according to manufacturer’s instructions. The final libraries were PCR amplified using 15-17 PCR cycles.

value: leaves harvested from 28-day old plants

tag: nuclease treatment

value: 600 Units RNaseI

tag: rrna depletion

value: yes

value: Wild type

value: RPFs with rRNA depletion

tag: molecule type

value: ribosome protected fragment


title: NeOT, scTCR-seq

value: Mouse tumor sample with OCDC and neoantigen-reactive T cells


title: DC, scTCR-seq

value: Tumor

value: Mouse tumor sample treated with DC cell transfer


title: scATAC-seq_Root.rep3

description:
Root.soc.processed.rds
Gm_atlas_Root_metav3_gene_sparse.rds
Gm_atlas_Root_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Root_ACR_4cpm_cellstates_counts.txt.gz

library_source: genomic single cell

data_processing:
The R package Socrates was used for nuclei identification and quality control.23 The BED file containing single base-pair Tn5 integration sites was imported into Socrates along with the soybean GFF gene annotation (Phytozome, version Gmax_508_Wm82.a4.v1) and the genome index file. To identify bulk-scale ACRs in Socrates, the callACRs function was employed with the following parameters: genome size=8.0e8, shift=-75, extsize=150, and FDR=0.1. This step allowed us to estimate the fraction of Tn5 integration sites located within ACRs for each nucleus. Metadata for each nucleus were collected using the buildMetaData function, with a TSS (Transcription Start Site) window size of 1 kb (tss.window=1000). Sparse matrices were then generated with the generateMatrix function, using a window size of 500. High-quality nuclei were identified based on the following criteria: a minimum of 1,000 Tn5 insertion sites per nucleus, at least 20% of Tn5 insertions within 2 kb of TSSs, and at least 20% of Tn5 insertions within ACRs across all datasets. Additionally, a maximum of 20% of Tn5 insertions in organelle genomes was allowed.
Assembly: Soybean William 82 v4 reference genome
Supplementary files format and content: Sorate object for clustering, gene accessibility matrix, ACR accessibility matrix, ACR count matrix for celltypes

source_name: root

extract_protocol:
Briefly, the tissue was finely chopped on ice for approximately 2 minutes using 600 μL of pre-chilled Nuclei Isolation Buffer (NIB: 10 mM MES-KOH at pH 5.4, 10 mM NaCl, 250 mM sucrose, 0.1 mM spermine, 0.5 mM spermidine, 1 mM DTT, 1% BSA, and 0.5% Triton X-100). After chopping, the mixture was passed through a 40-μm cell strainer and centrifuged at 500 rcf for 5 minutes at 4°C. The supernatant was carefully decanted, and the pellet was reconstituted in 500 μL of NIB wash buffer (10 mM MES-KOH at pH 5.4, 10 mM NaCl, 250 mM sucrose, 0.1 mM spermine, 0.5 mM spermidine, 1 mM DTT, and 1% BSA). The sample was filtered through a 10-μm cell strainer and gently layered onto 1 mL of 35% Percoll buffer (35% Percoll mixed with 65% NIB wash buffer) in a 1.5-mL centrifuge tube. The nuclei were centrifuged at 500 rcf for 10 minutes at 4°C. After centrifugation, the supernatant was carefully removed, and the pellets were resuspended in 10 μL of diluted nuclei buffer (DNB, 10X Genomics Cat# 2000207). Approximately 5 μL of nuclei were diluted tenfold, stained with DAPI (Sigma Cat. D9542), and the nuclei quality and density were evaluated using a hemocytometer under a microscope. The original nuclei were then diluted with DNB buffer to a final concentration of 3,200 nuclei per μL. Finally, 5 μL of nuclei (16,000 nuclei in total) were used as input for scATAC-seq library preparation.
scATAC-seq libraries were prepared using the Chromium scATAC v1.1 (Next GEM) kit from 10X Genomics (Cat# 1000175), following the manufacturer's instructions (10x Genomics, CG000209_Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v1.1_UserGuide_RevE). Libraries were sequenced on an Illumina NovaSeq 6000 in dual-index mode with eight and 16 cycles for i7 and i5 indexes, respectively.

value: root


title: scATAC-seq_Root.rep1


title: DBP9 at 75uM concentration replicate 1

source_name: DBP9 replicate 1


title: DBP35 at 100uM concentration replicate 1

source_name: DBP35 replicate 1


title: DBP48 at 75uM concentration replicate 1

source_name: DBP48 replicate 1


title: scATAC-seq_Pod.rep2

description:
Pod.soc.processed.rds
Gm_atlas_Pod_metav3_gene_sparse.rds
Gm_atlas_Pod_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Pod_ACR_4cpm_cellstates_counts.txt.gz

source_name: whole pod

value: whole pod


title: snRNA-seq_CS_seeds.rep1

description:
Gm_atlas_Cotyledon_stage_seeds.rna.seurat.obj.rds
Gm_atlas_Cotyledon_stage_seeds_RNA_gene_cellstate_counts.txt.gz


title: DBP6 at 200uM concentration replicate 1

source_name: DBP6 replicate 1


title: OCDC, scRNA

data_processing:
The Cell Ranger Software Suite v.6.1.2 was used to process the raw sequence data into gene expression profiles. The FASTQ files for each sample were processed with cell ranger count, which was used to mm10 reference genome alignment, filtering and quantifying the reads. The recovered cell parameter was set at 10,000, which is the expected number of cells for each library. The output files of Cell Ranger for each sample included the feature barcode and gene expression (in unique molecular identifier (UMI) format). Gene expression data were obtained using cellranger aggr, which performed an intersample normalization and merged the results of all samples into one file to remove potential sample variability.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
scRNA-seq was performed by the 10x Genomics single-cell 5′ V(D)J library platform.
scRNA-seq was performed by the 10x Genomics single-cell 5′ V(D)J library platform. The cell suspension was loaded into Chromium microfluidic chips with 30 (v2 or v3, depending on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). Single-cell gene expression and TCR libraries were generated according to the manufacturer’s instructions. RNA from the barcoded cells was subsequently reverse-transcribed, and sequencing libraries were constructed with reagents from a Chromium Single Cell 30 v2 (v2 or v3, depending on the project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq, on the project) according to the manufacturer’s instructions (Illumina).

value: lung cancer cells and immune cells

value: Mouse tumor sample treated with OCDC vaccine


title: scATAC-seq_Pod.rep4


title: NS, scRNA

value: Mouse tumor sample with no treat


title: T, scRNA

value: Mouse tumor sample treated with T cell transfer


title: scATAC-seq_Root.rep2


title: NooT, scRNA

value: Neoantigen-reactive T cells treated with OCDC


title: scATAC-seq_Pod.rep3


title: DBP5 at 300uM concentration replicate 1

source_name: DBP5 replicate 1


title: scATAC-seq_Pod.rep1


title: NeOT, scRNA


title: DBP3 at 75uM concentration replicate 1

source_name: DBP3 replicate 1


title: snRNA-seq_CS_seeds.rep2

value: seeds at cotyledon stage


title: scATAC-seq_Nodule.rep3

description:
Early_nodule.soc.processed.rds
Gm_atlas_Early_nodule_metav3_gene_sparse.rds
Gm_atlas_Early_nodule_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Early_nodule_ACR_4cpm_cellstates_counts.txt.gz

source_name: root with 1mm nodule

value: root with 1mm nodule


title: DBP1 at 300uM concentration replicate 1

source_name: DBP1 replicate 1


title: scATAC-seq_MMS_seeds.rep2

description:
Middle_maturation_stage_seeds.soc.processed.rds
Gm_atlas_Middle_maturation_stage_seeds_metav3_gene_sparse.rds
Gm_atlas_Middle_maturation_stage_seeds_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Middle_maturation_stage_seeds_ACR_4cpm_cellstates_counts.txt.gz

source_name: seeds at middle maturation stage

value: seeds at middle maturation stage


title: scATAC-seq_Nodule.rep1


title: DC, scRNA


title: scATAC-seq_MMS_seeds.rep1


title: scATAC-seq_Root.rep5


title: scATAC-seq_Root.rep4


title: Testis, Ythdc2 cKO, P16, rep 3

city: Stanford

first: Margaret

last: Fuller

state: California

address: 279 Campus Drive, Beckman Center B300

department: Developmental Biology

institute: Stanford University

data_processing:
Libraries were separated by barcode and adapters and low-quality bases were trimmed using trimGalore. Reads were mapped to the mouse genome (GRCm39/mm39) using STAR.
Reads for each transcript were extracted using HTSeq. Differential gene expression was calculated using DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include DEseq2 normalized counts

source_name: testes

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
Ribosomal RNAs were depleted from 1 µg of total RNA using NEBNext rRNA Depletion Kit v2 (New England Biolabs) according to the manufacturer’s protocol. Library preparation for high-throughput sequencing was performed on 100 ng of rRNA depleted RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Cre control andYthdc2 cKO mice were treated with 10 mg/ml Tamoxifen on P12 and P13.

value: testes

value: Ythdc2 conditional knockout

tag: developmental stage


title: ∆Snf-1 biol rep3

city: Bangkok

first: Pichamon

last: Kiatwuthinon

address: 50 Ngamwongwan Rd. Ladyao Jatujak

department: Biochemistry

country: Thailand

institute: Kasetsart University

data_processing:
Data analysis was performed on Galaxy platform (https://usegalaxy.org/) with default parameters. First, the sequence reads were trimmed for adapter sequence using Trimmomatic (Galaxy Version 0.38.0), followed by the alignment of the sequence reads against the reference genome assembly ASM252v1 using HISAT2 program (Galaxy Version 2.2.1+galaxy0). Then, the mapped sequences were assembled and quantified using StringTie and StringTie merge (Galaxy Version 2.1.7+galaxy1). The differentially expressed counts between wild-type and mutant assembled transcripts were estimated by DESeq2 (Galaxy Version 2.11.40.7+galaxy1). The differentially expressed genes were annotated using Annotate DESeq2/DEXSeq output tables (Galaxy Version 1.1.0). The false discovery rate was controlled with a p-value < 0.05.
Assembly: ASM252v1
Supplementary files format and content: tab-delimited text files include differentially expressed gene with p-value

organism: Yarrowia lipolytica

source_name: Yeast cell

growth_protocol: Two strains of Y. lipolytica including CXAU/AI (wild-type) and ∆Snf1 (mutant) were pre-cultured in 10 mL uracil-containing SG media and then grown at 30 °C, 220 rpm for 48 hr. Next, the cell densities were optically measured at 600 nm, adjusted to an OD of 0.05, and cultured in 150 mL uracil-containing SG media at 30 °C, 220 rpm for 24 hr at log phase. Subsequently, the cell pellets were then collected and washed with the YNB media twice at 25 °C, 5000 rpm for 10 min. Then, the cell pellets were further cultured in the media containing 2 % n-decane and 1 % uracil at 30 °C, 220 rpm for 1 hr. After that, 0.1 % triton-X was added into the media to separate the cell from n-decane droplet in medium. The cells were collected by centrifugation at 5000 rpm, 4 °C for 10 min. The cell pellets were washed with PBS buffer twice and kept at -80 °C until RNA extraction.

extract_protocol:
The cell pellets in Isogen (Nippo gene) were lysed by glass bead shocker. The RNA was extracted from the yeast cell lysates by chloroform extraction, followed by the removal of genomic DNA using an RNase-free DNase I Set (Omega biotek). The quality of extracted RNA was checked by a Nanodrop photometer (Thermo Fisher). High quality of RNA with the ratio for A260/280 (> 2.0) and A260/230 (> 2.0) was then proceeded to an RNA library preparation for RNA sequencing.
RNA libraries were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Cat No. 7420)

value: {delta}Snf1 (mutant)

value: Yeast cell

value: homologous recombination method


title: scATAC-seq_Hypocotyl.rep3

description:
Hypocotyl.soc.processed.rds
Gm_atlas_Hypocotyl_metav3_gene_sparse.rds
Gm_atlas_Hypocotyl_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Hypocotyl_ACR_4cpm_cellstates_counts.txt.gz

source_name: hypocotyl

value: hypocotyl


title: scATAC-seq_Leaf.rep2

description:
Leaf.soc.processed.rds
Gm_atlas_Leaf_metav3_gene_sparse.rds
Gm_atlas_Leaf_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Leaf_ACR_4cpm_cellstates_counts.txt.gz

source_name: leaf

value: leaf


title: Testis, Cre control, P16, rep 2

value: Cre control


title: scATAC-seq_HS_seeds.rep2

description:
Heart_stage_seeds.soc.processed.rds
Gm_atlas_Heart_stage_seeds_metav3_gene_sparse.rds
Gm_atlas_Heart_stage_seeds_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Heart_stage_seeds_ACR_4cpm_cellstates_counts.txt.gz

source_name: seeds at heart stage

value: seeds at heart stage


title: Testis, Cre control, P16, rep 4


title: scATAC-seq_Hypocotyl.rep2


title: ∆Snf-1 biol rep2


title: scATAC-seq_Hypocotyl.rep1


title: ∆Snf-1 biol rep1


title: scATAC-seq_Nodule.rep2


title: Testis, Cre control, P16, rep 1


title: scATAC-seq_GS_seeds.rep4

description:
Globular_stage_seeds.soc.processed.rds
Gm_atlas_Globular_stage_seeds_metav3_gene_sparse.rds
Gm_atlas_Globular_stage_seeds_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Globular_stage_seeds_ACR_4cpm_cellstates_counts.txt.gz

source_name: seeds at globular stage

value: seeds at globular stage


title: CXAU-AI biol rep3

value: CXAU/AI (wild-type)


title: scATAC-seq_HS_seeds.rep1


title: scATAC-seq_GS_seeds.rep3


title: CXAU-AI biol rep2


title: CXAU-AI biol rep1


title: scATAC-seq_GS_seeds.rep1


title: Testis, Ythdc2 cKO, P14, rep 3


title: Testis, Cre control, P14, rep 2


title: scATAC-seq_GS_seeds.rep2


title: scATAC-seq_EMS_seeds.rep2

description:
Gm_Early_maturation_stage_seeds.soc.processed.rds
Gm_atlas_Early_maturation_stage_seeds_metav3_gene_sparse.rds
Gm_atlas_Early_maturation_stage_seeds_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Early_maturation_stage_seeds_ACR_4cpm_cellstates_counts.txt.gz

source_name: seeds at early maturation stage

value: seeds at early maturation stage


title: 02008

city: Wuhan

first: Qinglei

last: Gao

state: Hubei

address: Jiefang Avenue

department: Department of Gynecological Oncology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology

data_processing:
For scRNA-seq data, FASTQ files were processed using the CeleScope (https://github.com/singleron-RD/CeleScope) “rna” workflow, designed for transcriptome sequencing data generated through the Singleron platform, to obtain gene-level UMI counts for each droplet, with GENCODE v37 human genome as the reference. Briefly, after using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and cutadapt (Martin, 2011) to quality control and filter the data, reads were compared with the reference genome using STAR (Dobin et al., 2013). Finally, featureCounts (Liao et al., 2014) was used to output the gene count matrices.
For paired same-cell scTCR-seq data, FASTQ files were processed using CeleScope “flv_CR” workflow, designed for full-length VDJ enrichment sequencing data generated through the Singleron platform, to obtain TCR alpha and beta-chain CDR3 nucleotide sequences.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: High-grade serous ovarian carcinoma

extract_protocol:
Fresh tumor samples were shipped in Mylteni Biotec® Tissue Storage Solution and maintained at 4°C until processing. A volume of 8 cm3 (2 x 2 x 2 cm) tumor tissue derived from one patient would be cut into three pieces, one of which was dissociated as single-cell suspensions for paired scRNA/TCR-seq.
For the generation of single-cell suspension, tumor tissues were dissociated using the gentleMACS™ Dissociator with Heaters and the Tumor Dissociation Kit, human, as per the manufacturer’s instructions, right after they were received by the laboratory. Immediately following dissociation, all single-cell suspensions were filtered using MACS Smart Strainers (70µm and 40µm). They were then treated with Red Blood Cell Lysis Solution and one or two rounds of dead cell removal using the Dead Cell Removal Kit, depending on the number of dead cells in each sample. All samples were processed as per the manufacturer’s instructions. Finally, the cell pellets were re-suspended with 1 x PBS for paired scRNA/TCR-seq.
For sorting of CD3+ T cells from tumors, these single-cell suspensions dissociated from tumor tissues (derived from P35-P44) were preincubated with Fixable Viability Dye (Biolegend, 423105) to mark alive cells within 1 x PBS for about 30 min, and then labeled with surface antibodies including CD45-PE (Biolegend, 3685110), CD3-APC (Biolegend, 300312), and CD19-FITC (Biolegend, 302206). Sorting for paired scRNA/TCR-seq was performed using a FACSAria (BD Biosciences).
The scTCR-seq library was generated using the sCircle® Single Cell Full-Length Immunoreceptor Library Kit (Singleron) according to the manufacturer’s instructions. In brief, the sorted CD3+ T cells from 10 patients were resuspended in cold PBS at a concentration of ~ 3 × 105 cells/mL. Approximately 100 μL of homogenous cell suspension was injected into a prepared microchip via the inlet port slowly and let stand for 5 min at room temperature, allowing the suspension to fully enter the microwells. Following cell loading, 60 μL of the barcode beads suspension was loaded onto the microchip and incubated for 1 min. After three washes with PBS, 100 μL of prepared Lysis Mix was injected into the microchip to lyse the cells, leading to the released mRNA binding to the barcode beads. Immediately following mRNA capture, barcode bead retrieval was performed with a Singleron Magnetic Rack and pre-chilled wash buffer A (supplied by the Library Kit) to obtain the barcode beads with bound mRNA. The mRNA was reverse transcribed on a thermal mixer preheated to 42 °C at 1300 rpm for 90 min, followed by cDNA amplification using a T100 Thermal Cycler (Bio-Rad). A portion of the purified cDNA was subjected to scRNA-seq library preparation. The remaining cDNA was used for scTCR-seq library preparation and programmed at cDNA circularization, digestion, and purification initially. After three rounds of TCR enrichment, the immune receptor enriched library was prepared through fragmentation, adapter ligation, purification of the adapter-ligated cDNA, enriched library amplification, and purification and size selection of the amplified enriched libraries. Lastly, the prepared libraries were sequenced on an Illumina NovaSeq 6000 Sequencer.

value: High-grade serous ovarian carcinoma

value: T cells


title: scATAC-seq_CS_seeds.rep2

description:
Gm_Cotyledon_stage_seeds.soc.processed.rds
Gm_atlas_Cotyledon_stage_seeds_metav3_gene_sparse.rds
Gm_atlas_Cotyledon_stage_seeds_ACR_4cpm_rmcds_ACR_sparse.rds
Gm_atlas_Cotyledon_stage_seeds_ACR_4cpm_cellstates_counts.txt.gz

source_name: seeds at cotyledon stage

value: seeds at cotyledon stage


title: scATAC-seq_EMS_seeds.rep1


title: Testis, Cre control, P14, rep 1


title: scATAC-seq_Leaf.rep1


title: Testis, Cre control, P16, rep 3


title: scATAC-seq_CS_seeds.rep1


title: H3 HAR Perturb-seq CRISPR-Capture Batch 3, Lane 8

city: New Haven

first: Mark

middle: Alan

last: Noble

state: CT

address: 22 Gold Street, APT 102

institute: Yale University

description: Feature Barcoding forCRISPR guide direct capture

data_processing:
Demultiplexing was performed using Illumina DRAGEN v3.9. Read alignment, gene counting, and aggregation was performed using CellRanger v7.0.1. Guide assignment was performed by thresholding guide count distributions by the 99.6th percentile across cells, and by filtering for guides captured at 2x higher rates than other detected guides within each cell. Doublets were removed using scDblFinder (Germain et al, 2021). Cells with fewer than 2500 features and/or more than 10% mitochondrial reads were removed. Only cells with a single guide assignment were retained.
Assembly: Hg38
Supplementary files format and content: Count matrices (Gene Expression and CRISPR counts) readable by Seurat, as RDS
Library strategy: Perturb-seq (Direct CRISPR sgRNA capture)

growth_protocol: Induced human pluripotent stem cells were maintained in feeder-free conditions with mTeSR medium. Cells were transduced with lentiviral particles containing KRAB:dCas9 driven by eF1A and blasticidin resistance. Cells were selected using blasticidin for 2 weeks to generate polyclonal lines. Cells were differentiated to neural stem cell state using dual SMAD inhibition and ROCK inhibitor for 72 hours, then transduced (MOI 0.3) with lentiviral paricles containing an sgRNA library targeting 180 Human Accelerated Regions, 5 non-targeting controls, and 6 postive controls, as well as a BFP fluorescence marker. Cells were grown in differentiation media for 48 hours, then sorted for BFP expression. Cells recovered in differentiation media for an additional 4 days before collection.

extract_protocol:
Cells were washed 2x in Dulbecco's PBS, then released with Accutase for 4 minutes. Cells were resuspended in ice cold DPBS with 0.4% Bovine Serum Albumin and placed on ice prior to single cell partitioning. Cells were encapsulated in gel beads in emulsion (GEMs) using a 10X Controller with 10X Chromium 3' v3.1 reagents, using the manufacturer's protocol.
Library construction was performed according to the manufactuerer's protocol (Chromium s3' single cell v3.1 with Feature Barcoding for CRISPR, Dual Index; 10X Genomics). Two libraries are made per GEM lane (gene expression and CRISPR capture).

value: Neural Stem Cell


title: 01056


title: Control, scRNA-seq

city: St. Louis

first: Ashraf Ul

last: Kabir

state: Missouri

address: 660 S Euclid Ave, BJCIH 8th floor, room 8302

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
For data processing, 10x Genomics CellRanger software version 7.2 was used for demultiplexing and gene counting
Assembly: mm10
Supplementary files format and content: Raw and filtered .tsv and .mtx files containing features, barcodes and count matrices.

extract_protocol:
Tumor were harvested from 5 individual mice in each treatment group and pulled together to digest and process for signle cell suspension with a cocktail of Collagenase-III, Dispase-II, and Deoxyribonuclease. Following enzymatic digestion, the cells were FACS sorted as live non-tumor (GFP-) population. For multiplexing, cells were split into separate tubes as either mCherry+ or mCherry- cells (mCherry is a fluorescence reporter included in both the empty vector and Zbtb46 overexpressing vector), marked with distinctive hashtags (Hashtag-B0301 for mCherry+ and Hashtag-B0302 for mCherry- cells), and pulled back to make two samples: control and treatment. The cells were then processed for single-cell library generation using version 3.1 Chromium Single Cell 3' v3.1 HT library, Gel Bead & Mutiplex Kit (10X Genomics), and sequenced with Illumina NovaSeq 6000
The library construction protocol was the 10X Genomics single cell 3` version 3.1 HT kit performed according to manufacturer’s protocol

value: Tumor

value: Non-tumor cells


title: H3 HAR Perturb-seq CRISPR-Capture Batch 3, Lane 6


title: 01054


title: Alveolar macrophages from Cpt1a-KO mouse (sample #6)

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM25)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Lung

extract_protocol:
Cell as input and lysis accroding to manufacturer's instructions of SMART-Seq Stranded Kit (Takara)
Libraries were prepared using the SMART-Seq Stranded Kit (Takara)

value: Lung

value: Primary alveolar macrophages

value: Cpt1a-KO (AT2 cell-specific)


title: Treatment, scRNA-seq


title: Alveolar macrophages from Cpt1a-KO mouse (sample #5)


title: H3 HAR Perturb-seq CRISPR-Capture Batch 3, Lane 4


title: H3 HAR Perturb-seq CRISPR-Capture Batch 3, Lane 3


title: H3 HAR Perturb-seq CRISPR-Capture Batch 3, Lane 5


title: H3 HAR Perturb-seq CRISPR-Capture Batch 3, Lane 2


title: 01053


title: H3 HAR Perturb-seq CRISPR-Capture Batch 3, Lane 1


title: H3 HAR Perturb-seq Gene Expression, Batch 3, Lane 8


title: Alveolar macrophages from Cpt1a-KO mouse (sample #4)


title: Alveolar macrophages from Cpt1a-KO mouse (sample #3)


title: 01060


title: H3 HAR Perturb-seq Gene Expression, Batch 3, Lane 6


title: H3 HAR Perturb-seq Gene Expression, Batch 3, Lane 7


title: H3 HAR Perturb-seq Gene Expression, Batch 3, Lane 5


title: Alveolar macrophages from Cpt1a-KO mouse (sample #2)


title: 01050


title: H3 HAR Perturb-seq Gene Expression, Batch 3, Lane 4


title: H3 HAR Perturb-seq Gene Expression, Batch 3, Lane 3


title: H3 HAR Perturb-seq CRISPR-Capture Batch 3, Lane 7


title: 01055


title: Alveolar macrophages from Cpt1a-KO mouse (sample #1)


title: 01049


title: H3 HAR Perturb-seq Gene Expression, Batch 3, Lane 2


title: Alveolar macrophages from control mouse (sample #5)


title: HSC3_anti-Flag

city: Hubei

first: Yang-Ying-Fan

last: Feng

address: Luonan stress

institute: wuhan university

data_processing:
Raw data were preprocessed by fastp. Alignment was performed with BWA. Peak calling was performed with MACS3.
Assembly: GRCh38
Supplementary files format and content: narrowPeak file contains peak location and intensity.
Library strategy: CUT&Tag

growth_protocol: Human HNSCC cell lines HSC3 were cultured in DMEM supplemented with 10% fetal bovine serum and 100 U/mL penicillin, and 100 mg/mL streptomycin. Cells were cultured under standard conditions at 37 °C with 5% CO2.

extract_protocol:
Cells were lysed and incubated with concanavalin A-coated magnetic beads. Then, the bead-bound cells were washed and incubated with the primary antibody (DYKDDDDK Tag/Anti-Flag, #14793, Cell Signaling Technology, RRID: AB_2572291) or control IgG on a rotating platform for 2 h at room temperature (RT). After incubation with the secondary antibody for 30 min, the beads were treated with the proteinA-Tn5 transposome for 1 h at room temperature. Next, to stop tagmentation and solubilize DNA fragments, 1.67 μL 0.5 M EDTA, 0.5 μL 10% SDS and 0.42 μL 20 mg/mL Proteinase K (20 mg/mL) was added to each sample.
The CUT&Tag sequencing was carried out as previously described by Kaya-Okur (2019), the DNA of samples was dissolved in 22 μL of 1 mM Tris–HCl pH 8, 0.1 mM EDTA buffer and utilized as template for library generation with Universal i5 Primer and Uniquely Barcoded i7 Primers for Illumina.

value: human tongue squamous carcinoma cell line

value: HSC3-PD-L1 KO-PD-L1 overexpression-Flag

value: Cells were lysed and incubated with concanavalin A-coated magnetic beads. Then, the bead-bound cells were washed and incubated with the primary antibody (DYKDDDDK Tag/Anti-Flag, RRID:AB_2572291) on a rotating platform for 2 h at room temperature


title: HSC3_αIgG

value: Cells were lysed and incubated with concanavalin A-coated magnetic beads. Then, the bead-bound cells were washed and incubated with the control IgG on a rotating platform for 2 h at room temperature


title: H3 HAR Perturb-seq CRISPR-Capture Batch 2, Lane 5


title: H3 HAR Perturb-seq CRISPR-Capture Batch 2, Lane 7


title: 01052


title: Alveolar macrophages from control mouse (sample #3)


title: H3 HAR Perturb-seq CRISPR-Capture Batch 2, Lane 6


title: H3 HAR Perturb-seq CRISPR-Capture Batch 2, Lane 3


title: HSC3_Blank

value: HSC3-PD-L1 KO-PD-L1 overexpression


title: H3 HAR Perturb-seq CRISPR-Capture Batch 2, Lane 8


title: H3 HAR Perturb-seq CRISPR-Capture Batch 2, Lane 4


title: 01051


title: H3 HAR Perturb-seq CRISPR-Capture Batch 2, Lane 1


title: Alveolar macrophages from control mouse (sample #2)


title: H660_siPLX2

city: Sacramento

first: Chengfei

last: Liu

state: CA

address: 4645 2nd Ave Research III building, suite2300

institute: University of California, Davis

data_processing:
Data analysis was performed using a Top Hat-Cufflinks pipeline and sequence read mapping/alignment using HISAT
Assembly: hg18
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
An mRNA-Seq paired-end library was prepared using Illumina NovaSeq 6000:2 × 150 cycles/bases (150bp, PE).

value: Prostate cancer cell line

value: PLXND1 knockdown


title: H3 HAR Perturb-seq Gene Expression, Batch 2, Lane 8


title: H660_siPLX1


title: H3 HAR Perturb-seq Gene Expression, Batch 2, Lane 7


title: H3 HAR Perturb-seq CRISPR-Capture Batch 2, Lane 2


title: Alveolar macrophages from control mouse (sample #1)


title: H3 HAR Perturb-seq Gene Expression, Batch 2, Lane 6


title: H660_siCon

value: Control siRNA


title: H3 HAR Perturb-seq Gene Expression, Batch 3, Lane 1


title: P14_male_mct8_fl_cre_cko_inf_C6

city: Bethesda

first: Hong

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
Libraries were multiplex sequenced. Some samples were sequenced on Illumina HiSeq2500 and 3000 Sequencers (NIDDK Genomics Facility), and some with an Illumina NovaSeq6000  (NHLBI Genomics Facility).
Single-end, 50 base reads were collected and converted by bcl2fastq (version 2) into fastq files and aligned on (GRCm38/mm10) using STAR (version 2.7.10b)
Reads were counted by FeatureCounts (subread v2.0.6) and normalized as counts per million mapped reads (cpm). To compare transcript abundance, data were quantified using Kallisto (v0.46.0) as transcripts per million reads (TPM).
Assembly: GRCm38/mm10
Supplementary files format and content: comma-separated text file includes transcripts per kilobase million for RPE and counts-per-million for retina and single-cone sample

source_name: retina

extract_protocol:
For single cell analyses, cones labeled with a Thrb2Cre driver were dissociated from superior and inferior pieces of retina of Mct8-KO and control male mice at 2 months of age. Cones were isolated individually by micromanipulator to minimize contamination by rods, then examined visually for cone morphology and integrity before library construction. For dissected retina and isolated RPE cells, all samples were taken from superior and inferior areas around the vertical mid-line of the eye, then incubated in RNAprotect Cell reagent before RNA extraction with Qiagen RNeasy kit.
Single cell RNA-seq library library construction with SMART-Seq v4 Ultra Low Input RNA kit and ThruPLEX DNA-Seq Kit, purified RNA from different retina and RPE samples were constructed into RNA-seq libraries with SMARTer stranded total RNA sample prep kit and ThruPLEX DNA-Seq Kit.

value: retina

value: Mct8 fl/y;Best1cre

tag: age


title: H3 HAR Perturb-seq Gene Expression, Batch 2, Lane 5


title: Alveolar macrophages from control mouse (sample #4)


title: P14_male_mct8_fl_cre_cko_inf_C5


title: MDVR_siPLX2

source_name: C4-2B MDVR

value: C4-2B MDVR


title: H3 HAR Perturb-seq Gene Expression, Batch 2, Lane 4

value: Neural Stem Cell


title: P14_male_mct8_fl_cre_cko_inf_B4


title: H3 HAR Perturb-seq Gene Expression, Batch 2, Lane 2


title: P14_male_mct8_fl_cre_cko_inf_A3


title: H3 HAR Perturb-seq CRISPR-Capture Batch 1, Lane 8


title: MDVR_siCon


title: MDVR_siPLX1


title: H3 HAR Perturb-seq Gene Expression, Batch 2, Lane 1


title: H3 HAR Perturb-seq CRISPR-Capture Batch 1, Lane 2


title: P14_male_mct8_fl_cre_cko_inf_A1


title: P14_male_mct8_fl_cre_cko_inf_A2


title: H3 HAR Perturb-seq CRISPR-Capture Batch 1, Lane 1


title: H3 HAR Perturb-seq CRISPR-Capture Batch 1, Lane 7


title: H3 HAR Perturb-seq Gene Expression, Batch 1, Lane 5


title: P14_male_mct8_fl_ctrl_retina_inf_C5

value: Mct8 fl/y


title: H3 HAR Perturb-seq Gene Expression, Batch 1, Lane 4


title: P14_male_mct8_fl_ctrl_retina_inf_B3


title: H3 HAR Perturb-seq Gene Expression, Batch 1, Lane 7


title: Sample49

city: Aurora

first: Sunita

last: Sharma

address: 13001 East 17th Place

institute: University of Colorado - Anschutz Medical Campus

data_processing:
examined the quality of the sequencing reads (FastQC) and removed adaptors and low quality base calls (Cutadapt).
Sequences were aligned to the human genome (GENCODE GRCh37)
Read counts overlapping each gene were reported using STAR
Removed genes detected with 0 reads in greater than or equal to 75% of samples or with a range of reads less than or equal to 100.
Corrected for unwanted technical effects using two normalization factors estimated using Removal of Unwanted Variance using Residuals (RUVr) using RUVSeq (ver.
Assembly: GENCODE GRCh37
Supplementary files format and content: Filename: seq_express_filter.csv; Format: Raw gene counts aligned to the genome and filtered to remove those with 0 reads in greater than or equal to 75% of samples or with a range of reads less than or equal to 100.
Supplementary files format and content: Filename: seq_express_norm.csv; Format: Normalized gene counts from DESeq2 Model adjusting for vape status, age, sex, recruitment center, and two normalization (RUVr) factors.

source_name: Nasal-epithelial

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) and sequenced using Illumina chemistry (Nugen Universal Plus mRNASEQ kit [Redwood City, CA]; NovaSeq6000 [Illumina: San Diego, CA]) through the Genomics and Microarray Core at the University of Colorado Anschutz Medical Campus.
Sequencing libraries will be prepared using the standard TruSeq RNA Sample Prep Kit v2 Protocol (Illumina, San Diego, CA).

value: Nasal-epithelial

tag: vape 6mo_lab

value: Female

tag: age (yrs)

tag: ruv k1

tag: ruv k2


title: H3 HAR Perturb-seq CRISPR-Capture Batch 1, Lane 4


title: P14_male_mct8_fl_ctrl_retina_inf_C4

tag: strain

tag: tissue


title: Sample48

tag: Sex

value: Male


title: H3 HAR Perturb-seq Gene Expression, Batch 1, Lane 8

tag: cell type


title: H3 HAR Perturb-seq Gene Expression, Batch 1, Lane 6


title: H3 HAR Perturb-seq Gene Expression, Batch 1, Lane 3


title: P14_male_mct8_fl_ctrl_retina_inf_A2

tag: genotype


title: H3 HAR Perturb-seq Gene Expression, Batch 2, Lane 3


title: H3 HAR Perturb-seq CRISPR-Capture Batch 1, Lane 5


title: H3 HAR Perturb-seq CRISPR-Capture Batch 1, Lane 6


title: H3 HAR Perturb-seq CRISPR-Capture Batch 1, Lane 3


title: P14_male_mct8_fl_ctrl_retina_inf_A1


title: P14_male_mct8_fl_cre_cko_sup_C6


title: H3 HAR Perturb-seq Gene Expression, Batch 1, Lane 1


title: Sample46


title: Sample47


title: P14_male_mct8_fl_cre_cko_sup_C5


title: Sample-CuS-7

city: Shanghai

first: Qimin

last: Zheng

address: 131 Dongan Road,Xuhui District

department: Institutes of Brain Science

institute: Fudan University

data_processing:
StringTie
Assembly: mm9
Supplementary files format and content: xls. Contains GO and KEGG analysis

source_name: Brain

extract_protocol:
The brain tissue was dissected and processed for simultaneous isolation of total RNA, pro- tein, and gDNA using the Transzol Up Plus RNA kit (Beijing, CHN) following the manufacturer's directions.
Sample libraries were prepared with Illumina mRNA sample preparation kits.

value: Brain

value: WT

value: MCAO operation+Cu9S8-SNAP injection


title: Sample-CuS-9


title: P14_male_mct8_fl_cre_cko_sup_B4


title: Sample-CuS-10


title: Sample45


title: Sample-CuS-8


title: P14_male_mct8_fl_cre_cko_sup_A2


title: Sample-MCAO-5

value: MCAO operation


title: Sample-MCAO-6


title: Sample-C57-2

value: Naïve


title: P14_male_mct8_fl_cre_cko_sup_A3


title: P14_male_mct8_fl_ctrl_retina_sup_C5


title: Sample-MCAO-4


title: Sample44


title: H3 HAR Perturb-seq Gene Expression, Batch 1, Lane 2


title: Sample-C57-3


title: Sample43


title: P14_male_mct8_fl_ctrl_retina_sup_C4


title: Sample-C57-1

value: Naïve,


title: Sample42


title: Sample40