title: 1000_10_10

value: intergeneric conjugation under the exposure of 10 mg/L 1000 nm PS


title: FB 18C, Rep 1, Day 4, ZT16

status: Public on Dec 05 2023

type: SRA

city: Evanston

first: William

last: Kath

state: IL

address: 2145 Sheridan Rd

department: Engineering Sciences and Applied Mathematics

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Basic quality checking of sequence files was performed with FastQC.   Paired-end reads were trimmed using Atropos version 1.1.31 using the options atropos trim --aligner insert -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length 50
Reads were aligned using STAR (2.7.10a_alpha_220818) with options --outFilterType BySJout --alignIntronMax 1000000 --outSAMmultNmax 1 --outSAMtype BAM to produce only uniquely mapped reads
Duplicate paired-end reads were removed using bamUtil with the options bam dedup --rmDups --excludeFlags 0xB04 --oneChrom
The resulting reads were then re-aligned with STAR to produce a BAM file with reads aligned to the transcriptome (--quantMode TranscriptomeSAM)
RSEM was then used with options --paired-end --strandedness none to produce tags-per-million (TPM) counts for each gene from transcriptome alignments.
Assembly: Ensembl Drosophila melanogaster BDGP6.32 reference (release 107)
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: fat body (FB)

growth_protocol: Age-matched female Iso31 flies (an isogenic w1118 strain) were collected and aged for 3 days with males before being transferred to an entrainment incubator for 3 days.

extract_protocol:
RNA was isolated from the abdominal fat bodies using Trizol LS (hermoFisher #10296028)
Non-stranded library preparation was carried out using the NEBNext Ultra II RNA Library Prep kit for Illumina according to manufacturer protocol.

treatment_protocol: The experimental group was shifted to 18 degrees C at seven days old while the control group was kept at 25 degrees C.

tag: tissue

value: fat body (FB)


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 5

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
10x Genomics
L1_sorghum_multiome_RNA_combined_with_ATAC.RData

library_source: genomic

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object
Library strategy: 10X-multiome (RNA + ATAC-seq)

molecule: genomic DNA

organism: Sorghum bicolor

source_name: seedling

growth_protocol: 5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.

extract_protocol:
Fresh tissue from each time point was finely chopped, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell Multiome ATAC Kit, 10x Genomics)

value: seedling

tag: age


title: byMM1832

city: Tianjin

first: Lifang

middle: Li

last: Yu

state: Tianjin

address: Wei Jin road

country: China

institute: Tianjin University

data_processing:
Data evaluation and quality control: 1) The quality of the original data of sequencing was evaluated by FastQC. 2) Trimmomatic is used for mass shearing, and relatively accurate and effective data are obtained.
RNAseq sequencing evaluation: 1) Compare the valid data of the sample with the reference genome by using HISAT2, and count the Mapping information. 2) According to the comparison results, RSeQC was used to perform redundant sequence analysis and insert fragment distribution analysis. 3) Using Qualimap to check the homogeneity distribution and analyze the genome structure distribution according to the comparison results. 4) statistical analysis of gene coverage and distribution of sequencing sequences on chromosomes were carried out by BEDTools.
Gene structure analysis: 1) Use BCFtools to find out possible SNP sites according to the Mapping results, and use SnpEff to determine the influence of SNP sites on genes.  2) Assemble the sequence Mapping to the genome with StringTie, and then compare it with the known gene model with GffCompare to find new transcription regions. 3) Perform variable shear analysis with ASprofier. 4) Use EricScript to analyze the fusion gene.
Expression level analysis: 1) Use StringTie and known gene models to evaluate the expression of genes. 2) Using WGCNA to analyze the co-expression of genes. 3) Multi-directional statistical analysis and exploration, such as comparative analysis of samples, are carried out based on the expression matrix of samples.
Analysis of expression differences: 1) Use DESeq2 to analyze gene expression difference, and visualize the results of expression difference analysis. 2) Mapping the differential genes to the STRING protein interaction network database to construct the protein interaction network. 3) Based on the results of difference analysis, Wayne diagram and heat map are drawn and cluster analysis is carried out.
Assembly: Saccharomyces cerevisiae S288C（NCBI）
Supplementary files format and content: One excel file includes Mean (PTM) of two strains (byMM1777 and byMM1827), log 2 fold changes, P-value, Q- value, results
Supplementary files format and content: One excel file includes Mean (PTM) of two strains (byMM1736 and byMM1832), log 2 fold changes, P-value, Q- value, results

organism: Saccharomyces cerevisiae

source_name: experimental strain contains dCas12e:ScRNA activator for GAL7 endogenous gene activation

extract_protocol:
toal RNA  was ectracted and quality from S. cereviase by using Total RNA Extractor (Trizol) and Qubit2.0 RNA examination kit
Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina®  kit

tag: cell type

value: eukaryocyte

tag: genotype

tag: treatment

value: Experimental strain included dCas12e, MCP-VP64 fusion protein, ScRNA that can target to pGAL7, the final result was activate the expression of GAL7 endogenous gene.


title: FB 18C, Rep 1, Day 4, ZT06


title: nlf_els_bap_SAP1

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

data_processing:
Reads were aligned using the Seq2Fun algorithm which translates raw reads to protein orthologs and maps them to a high-resolution protein-ortholog database - EcoOmicsDB available at www.expressanalyst.ca. The filtering parameters are provided below
Filtering: N. of amino acid mismatches was set at 2
Filtering: Minimum matching length was set at 19
Filtering: Minimum matching score was set at 80
Assembly: Mapping was species agnostic. Translated reads were mapped to the Vertebrate database
Raw fastq files were filtered as mentioned above and provided count matrices. These were analyzed for gene expression and pathway enrichment analysis.
Raw files and count files are provided as fastq files and .txt files, respectively.
Supplementary files format and content: Files here are from 49 datasets (datasets column below). Each dataset has a processed file which contains the counts for all samples within that dataset. Hence all samples (with unique title) from a dataset is present in the corresponding processed file. The title of the raw file for each sample is provided below as well. Some exposures were conducted together and hence had a common control exposure. Hence while 776 libraries are listed, they will correspond to fewer fastq files. But all fastq files are present.

organism: Lithobates pipiens

source_name: embryo

extract_protocol:
RNA was extracted from Japanese quail and Double-crested cormorant samples using the Qiagen RNeasy mini kits; RNA was extracted from the fathead minnow, rainbow trout, African-clawed frog and the northern leopard frog using the Qiagen RNeasy Universal Mini kit.
Library was prepared according to Illumina instructions for NovaSeq 6000 S4 PE100 or HiSeq 4000 PE100 101-bp paired-end reads.

tag: lifestage

value: els

value: embryo

tag: chemical

value: dmso

tag: concentration

value: CTRL


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 4


title: 1000_0.1_11

city: Shenzhen

first: Yuanyuan

last: Kang

address: No. 6 Pingshan 1st Road, Taoyuan Street, Nanshan District

department: School of Civil and Environmental Engineering

institute: Harbin Institue of Technology

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the A.baylyi ADP1 reference genome (NC_005966.1) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Assembly: NC_000913, NC_002947, L27758
Supplementary files format and content: Excel file includes FPKM values for each sample
Supplementary files format and content: Excel file includes LOG2FC values for each sample

organism:
Pseudomonas putida
Escherichia coli

source_name: Bacteria

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Total RNA was extracted using the Trizol method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed the donor (E. coli K-12 LE392) and intrageneric recipient or intergeneric recipient at a 1:1 ratio in PBS, and  incubation in triplicate for 8 h in 0.1 mg/L 20 nm PS, 10 mg/L 20 nm PS, 0.1 mg/L 120 nm PS, 10 mg/L 120 nm PS, 0.1 mg/L 1000 nm PS, 10 mg/L 1000 nm PS, at 25 °C

tag: strain 1

value: E. coli K-12 LE392

tag: strain 2

value: P. putida KT2440

value: Bacteria

value: intergeneric conjugation under the exposure of 0.1 mg/L 1000 nm PS with ROS scavenger


title: FB 25C, Rep 1, Day 5, ZT16


title: 1000_0.1_10

value: intergeneric conjugation under the exposure of 0.1 mg/L 1000 nm PS


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 3


title: nlf_els_bap_LDP4

value: bap

value: MED


title: 120_10_11

value: intergeneric conjugation under the exposure of 10 mg/L 120 nm PS with ROS scavenger


title: FB 25C, Rep 1, Day 5, ZT14


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 6


title: 120_10_10

value: intergeneric conjugation under the exposure of 10 mg/L 120 nm PS


title: nlf_els_bap_LCP3


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 5


title: nlf_els_bap_MEP5

value: HIGH


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 4

value: seedling


title: FB 25C, Rep 1, Day 5, ZT12

value: fat body (FB)


title: FB 25C, Rep 1, Day 5, ZT10


title: nlf_els_bap_LBP2


title: nlf_els_bap_MDP4


title: nlf_els_bap_LEP5


title: FB 25C, Rep 1, Day 5, ZT08


title: 120_0.1_10

value: intergeneric conjugation under the exposure of 0.1 mg/L 120 nm PS


title: nlf_els_bap_LAP1

value: els


title: FB 25C, Rep 1, Day 5, ZT18


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 5

molecule: nuclear RNA


title: FB 25C, Rep 1, Day 5, ZT06


title: FB 25C, Rep 1, Day 5, ZT04


title: nlf_els_bap_MCP3

value: embryo


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 3


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 4


title: 20_0.1_10

value: intergeneric conjugation under the exposure of 0.1 mg/L 20 nm PS


title: nlf_els_bap_SEP5

value: dmso

value: CTRL


title: FB 25C, Rep 1, Day 5, ZT02


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 6


title: 20_10_11

value: E. coli K-12 LE392

value: P. putida KT2440

value: intergeneric conjugation under the exposure of 10 mg/L 20 nm PS with ROS scavenger


title: nlf_els_bap_MBP2


title: FB 25C, Rep 1, Day 5, ZT00


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 5


title: nlf_els_bap_SDP4


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 3


title: 20_10_10

value: Bacteria

value: intergeneric conjugation under the exposure of 10 mg/L 20 nm PS


title: FB 25C, Rep 1, Day 4, ZT20


title: nlf_els_bap_SCP3


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 3


title: SKN-1gf Neurons Bio rep 4

city: Los Angeles

first: Chris

last: Turner

address: 3715 McClintock Ave

institute: University of Southern California

description: H

data_processing:
reads were quality trimmed, and adapter trimmed using timmomatic v0.39.
Quality trimmed reads were aligned to the C. elegans reference genome using STAR 2.7.6a.
Mapped reads were counted via HTseq v2.0.2 union mode.
Read counts were then used for differential expression (DE) analysis using the R package DESeq2 created using R version 3.5.2.
DESeq2 package used for differential expression analysis of counts files
Assembly: ce10
Supplementary files format and content: Tab delimited counts files

organism: Caenorhabditis elegans

source_name: Neuron

growth_protocol: C. elegans were raised on 6 cm nematode growth media (NGM) plates supplemented with streptomycin and seeded with OP50. All worm strains were grown at 20°C and unstarved for at least three generations before being used

extract_protocol:
Animals were homogenized and RNA extraction was performed via the Zymo Direct-zol RNA Miniprep kit (Cat. #R2052).
RNA libraries were prepped using the Ovation SoLo RNA library kit from Tecan Genomics

treatment_protocol: In brief, approximately 250,000 L4 synchronized WT and skn-1gf animals with GFP tagged ASI neurons (daf-7p::gfp) were washed with M9 6 times to remove residual bacteria. Animals were then pelleted and Cell Isolation Buffer (20mM HEPES, 0.25% SDS 200mM DTT 3% Sucrose pH8) was added to worms. Worms were incubated in Cell Isolation Buffer for 2min. Initial lysis was quenched by washing with M9 6 times. Worm pellet was resuspended in 20mg/ml Pronase and digested for 20 mins with vigorous pipetting every 5mins through a P1000 tip. Pronase digestion was quenched by resuspending in FBS. Cells were pelleted by centrifuging at 550rcf and resuspended in fresh FBS, Cells were passed through a 40-micron cell strainer. DAPI was added to cells to assess viability. Cells were then sorted on a Bio-Rad S3e FACS system.

value: Neuron


title: nlf_els_bap_MAP1

value: bap


title: FB 25C, Rep 1, Day 4, ZT22


title: Control 10

value: intergeneric conjugation


title: FB 25C, Rep 1, Day 4, ZT18


title: SKN-1gf Neurons Bio rep 3

description: G


title: SKN-1gf Neurons Bio rep 2

description: F


title: FB 25C, Rep 1, Day 4, ZT16


title: FB 25C, Rep 1, Day 4, ZT14


title: Control 11

value: intergeneric conjugation with ROS scavenger


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC - replicate 2

value: seedling


title: 20_0.1_11

value: intergeneric conjugation under the exposure of 0.1 mg/L 20 nm PS with ROS scavenger


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome ATAC  - replicate 1


title: FB 25C, Rep 1, Day 4, ZT12

value: fat body (FB)


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 2


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome ATAC - replicate 1


title: FB 25C, Rep 1, Day 4, ZT08


title: 120_0.1_11

value: intergeneric conjugation under the exposure of 0.1 mg/L 120 nm PS with ROS scavenger


title: SKN-1gf Neurons Bio rep 1

description: E


title: JIMT-1 HUNK KD2_2

type: RNA

city: Indianapolis

first: Elizabeth

last: Yeh

state: Indiana

address: 635 Barnhill Drive, Medical Science Building A418

department: Pharmacology and Toxicology

institute: Indiana University School of Medicine

data_processing:
NanoString nSolver 4.0 software was used for analysis of gene expression values
Nanostring nSolver 4.0 software computed normalized log2 count and normalized linear count

organism: Homo sapiens

source_name: Human HER2+ Breast Cancer Cells (JIMT-1)

growth_protocol: Cells grown in DMEM (Corning 10-017-CV) supplemented with 10% fetal bovine serum, 200 nM glutamine (Thermo Scientific), and penicillin/streptomycin (Thermo Scientific). HUNK knockdown cells were grown in media with 1ug/ul puromycin

extract_protocol: Used GeneJET RNA purifcation kit (K0732) to isolate RNA from cells.

treatment_protocol: HSL samples were treated with 1ug/ul of HSL119

tag: cell line

value: HER2+ Breast Cancer


title: JIMT-1 HUNK KD2_4


title: JIMT-1 HUNK KD2_3


title: JIMT-1 HUNK KD2_1


title: FB 25C, Rep 1, Day 4, ZT10


title: N2 Neurons Bio rep 4

description: D

value: Wildtype


title: N2 Neurons Bio rep 2

description: B


title: FB 25C, Rep 1, Day 4, ZT06


title: N2 Neurons Bio rep 3

description: C


title: JIMT-1_HUNK KD1_3


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 2


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 2


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA  - replicate 1


title: hsSKM_ChIP_Normal Rabbit IgG _R1_rep2

first: kangjing

last: Li

address: 24-B3, Weijin Road Campus, Tianjin University

data_processing:
The fastq data were trimmed with Trim Galore (Galaxy Version 0.6.7), quality-checked by FastQC (Galaxy Version 0.73), and mapped to human genome hg38 using Bowtie2 (Galaxy Version 2.4.2) to generate bam file.
Bigwig file was generated from the bam file using bamCoverage (Galaxy Version 3.5.1.0.0).
A narrowPeak file was generated by MACS2 callpeak (Galaxy Version 2.2.7.1+galaxy0)  from the bam file.
Fasta file was generated by bedtools getfasta (Galaxy Version 2.30.0+galaxy1)  from the narrowPeak file.
Motif analysis was performed using MEME-ChIP (version 5.5.2) (https://meme-suite.org/meme/tools/meme-chip)

source_name: Skeletal muscle cell

growth_protocol: Human skeletal muscle cells were cultured in 10% FBS DMEM medium to 70-90% confluency on three 10cm tissue culture dishes for each sample.

extract_protocol:
Growth medium was replaced with 6 ml of PBS and cells were cross-linked with 10 mM dithiobis(succinimidyl propionate) (DSP) in 6 ml PBS at room temperature for 30 min. Unreacted DSP was quenched by adding 0.18 ml of 1 M Tris-HCl pH=8.0 at room temperature for 15 min and the cells were rinsed with PBS once. Fixed cells were lysed with 400uL RIPA-G buffer + protease inhibitor cocktail (PIC) +RNase to extract DNA-protein complexes. The extract was centrifuged at 15,000 x g for 10 min at 4°C. The pellet was rinsed with 400 uL PBS 5 times to remove the lysis buffer and then suspended in 400 uL PBS by pippeting. After centrifugation at 10,000 x g for 2 min at 4°C, the pellet was redissolved in 100 uL RIPA-T buffer +RNase by sonication (1s/1s, 5s). The redissolved DNA-protein complex was digested with 0.5 uL Micrococcal Nuclease (#10011, Cell Signaling Technologies) at 37°C for 30 min. After centrifugation at 20,000 x g for 30 min at 4°C, the supernatant was collected in a new tube. In total, 600 uL of supernatant from six 10 cm dishes (100 uL each) was pooled. The supernatant was incubated with 2 ug rabbit anti-CBF-beta antibody (#62184s Cell Signaling Technologies)，5 ug mouse anti-YAP1 antibody (63.7) (sc-101199, Santa Cruz Biotechnologies) or 2 ug rabbit normal IgG (a technical negative control, #2729, Cell Signaling Technologies) overnight with rotation, then incubated with 30 uL Protein G Magnetic Beads (#9006) for 2 hours with rotation in accordance with SimpleChIP Enzymatic Chromatin IP kit (#9003; Cell Signaling Technologies)  with slight modifications as follows. The magnetic beads were pelleted by magnetic separation rack, and then washed 3 times with 1 mL low-salt buffer at 4°C for 5 min with rotation. The magnetic beads were washed once with 1 mL of high salt buffer at 4°C for 5 min with rotation and then incubated with 150 uL 1xChIP Elution buffer at 65°C with vortexing briefly every 2-3 min for 30 min in total. The magnetic beads mixture was incubated with 2 uL Proteinase K (#10012, Cell Signaling Technologies) and 10 mM DL-Dithiothreitol (PE001, LEAGENE) at 65°C for 2 hours to remove the bound proteins. The eluted DNA fragments were purified using E.Z.N.A. R Cycle-Pure Kit (Omega_D6492-02; Omega BIO-TEK) and subjected for library construction.
The library construction used TruSeq DNA PCR-free prep kit (20015963, illumina). Library was sequenced by NovaSeq Sequencer.

treatment_protocol: no treatment

value: Primary Skeletal Muscle Cells, ATCC, PCS-950-010, adapted to 13% FBS in DMEM

tag: chip antibodies

value: Normal Rabbit IgG (#2729)

tag: antibody brand

value: CST

value: untreated


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X Multiome RNA - replicate 1


title: hsSKM_ChIP_CBFB_R1_rep2

value: Primary Skeletal Muscle Cells, ATCC, PCS-950-010, adapted to 10% FBS in DMEM

value: CBFβ (D4N2N) Rabbit mAb (#62184S)


title: hsSKM_ChIP_YAP1_R1

value: Primary Skeletal Muscle Cells, ATCC, PCS-950-010, adapted to 15% FBS in DMEM

value: Santa Cruz Biotechnologies


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 12h - 10X

description:
10x Genomics
L1_sorghum_combined.RData

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used. Enriched nuclei were then stained with Hoechst, before being FACS purified.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 8h - 10X

description:
10x Genomics
L1_sorghum_combined.RData


title: hsSKM_ChIP_Normal Rabbit IgG _R1_rep1

value: Primary Skeletal Muscle Cells, ATCC, PCS-950-010, adapted to 11% FBS in DMEM


title: N2 Neurons Bio rep 1

description: A

value: Neuron


title: JIMT-1_CTL_4


title: JIMT-1_HUNK KD1_2


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 6h - 10X

description:
10x Genomics
L1_sorghum_combined.RData


title: Cyc8-AA +Rap_3(Biol rep 3)

city: Dublin 2

first: Alastair

last: Fleming

address: College Green

department: Microbiology Dept.

country: Ireland

institute: Trinity College Dublin

data_processing:
Raw sequencing data was processed using fastp (version 0.20.0) software to remove poor quality bases (below Phred Quality 20) oradapter sequences.
Assembly: High quality sequence reads were mapped to the Saccharomyces cerevisiae S288c reference genome available on ENSEMBL using the STAR aligner(STAR v2.7.3). BAM files were generated as a result of this step.
Supplementary files format and content: Raw alignment counts for genes in a tab-delimited text file
Supplementary files format and content: Normalised counts and Differences in ratios (both generated using R/Bioconductor DESeq2 package) between the Flo+ Cyc8-AA experiment and the Flo- Cyc8-AA experiment. Provided in a tab-delimited text file

source_name: log phase yeast cells

growth_protocol: All samples were grown in YPD (2% glucose) media at 30° C.

extract_protocol: Total RNA was extracted using the hot phenol method, followed by DNase treatment and purification using the RNeasy Minelute Cleanup Kit (Qiagen).

treatment_protocol: Rapamycin (1μg/ ml) and/ or mannose (025M) were added to the relevant samples at early  exponential growth phase (OD600 = ~0.3) and samples for RNA isolation were taken after 4 hours.

value: log phase yeast cells

value: Cyc8-AA made in HHY221 background (Mata tor1-1 fpr1::loxP-LEU2-loxP RPL13A2xFKBP12::loxP CYC8-FRB::HIS3)

value: Grown for 4 hours after the addition of rapamycin (final concentration = 1μg/ ml)


title: JIMT-1_HUNK KD1_1


title: hsSKM_ChIP_CBFB_R1_rep1


title: JIMT-1_CTL_3


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 4h - 10X

description:
10x Genomics
L1_sorghum_combined.RData

value: seedling


title: Cyc8-AA +Rap_1 (Biol rep 1)


title: Cyc8-AA +Rap_2(Biol rep 2)


title: hsSKM_high_rep2

data_processing:
The fastq data were trimmed with Trim Galore (Galaxy Version 0.6.7), quality-checked by FastQC (Galaxy Version 0.73), and mapped to human genome hg38 using Bowtie2 (Galaxy Version 2.4.2).
The bigwig files were generated by bamCoverage (Galaxy Version 3.5.1.0.0) and peaks were visualized on integrative genomics viewer (IGV: ver. 2.9.4).
Heatmaps for score distributions across genomic regions were created using computeMatrix (Galaxy Version 3.5.1.0.0) and plotHeatmap (Galaxy Version 3.5.1.0.1).
Assembly: hg38
Supplementary files format and content: bigwig file

growth_protocol: Human skeleton muscle cells were cultured in 10% FBS DMEM medium to 50-70%  (low density) and 100% (high density) confluency on three 10cm tissue culture dishes for each sample.

extract_protocol:
High-density (100% confluency) and low-density (50%-70%confluency) cells were cross-linked with 10mM dithiobis(succinimidyl propionate) (DSP) in PBS at room temperature for 30 min, quenched with 1 M Tris-HCl pH=8.0 at room temperature for 15 min and washed with PBS. Fixed cells were lysed with 400ul RIPA-G buffer + protease inhibitor cocktail (PIC ) +RNase to extract DNA-protein complex. Isolated DNA-protein complex was rinsed with 400ul PBS 5 times and then suspended in 400ul PBS. Ater centrifugation, the pellet was redissolved in 100 ul RIPA-T buffer +RNase by sonication (1s/1s,5s). The redissolved DNA-protein complex was digested with 0.5 ul Micrococcal Nuclease ( #10011,CST) at 37°C for 30 mins. After centrifugation, the supernatant was collected and 2 ul Proteinase K #10012 was added to digested bound protein  at 65°C for 2 hours. The DNA was loaded on 1.5% agarose gel, and then purified by E.Z.N.A. R Gel Extraction Kit (Omega_D2500-02; Omega BIO-TEK).The library construction was carried out using TruSeq DNA PCR-free prep kit (20015963, illumina). Library was sequenced by NovaSeq Sequencer.
The library construction was carried out using TruSeq DNA PCR-free prep kit (20015963, illumina). Library was sequenced by NovaSeq Sequencer.


title: hsSKM_high_rep1


title: Cyc8-AA -Rap_3(Biol rep 3)


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 1h - 10X

description:
10x Genomics
L1_sorghum_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 2h - 10X

description:
10x Genomics
L1_sorghum_combined.RData


title: JIMT-1_CTL_1


title: Cyc8-AA -Rap_2(Biol rep 2)


title: hsSKM_low_rep2


title: JIMT-1_HSL119 treated_3


title: Cyc8-AA -Rap_1 (Biol rep 1)


title: hsSKM_low_rep1


title: JIMT-1_HSL119 treated_2


title: JIMT-1_HSL119 treated_1


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X

description:
10x Genomics
L1_sorghum_combined.RData


title: Elongating spermatids, Prm1-EGFP sorted, replicate 1

status: Public on Dec 04 2023

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

description:
Prm_EGFP_ES
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz

data_processing:
SE 50 bp reads
TrimGalore + STAR
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR
Read count extraction and normalization were performed in R using the QuasR package
Assembly: mm10
Supplementary files format and content: comma separated text files include log2RPKM values for each Sample (counts performed on Gencode v19 or De Novo transcriptome assembly (see GTF file)); GTF file describing de novo transcriptome annotation

organism: Mus musculus

source_name: testes

growth_protocol: Single cell suspensions were generated from adult testis tissue by sequential digestion with collagenase and trypsin

extract_protocol:
Total RNA was extracted using a DirectZol kit (Zymo research)
RNA libraries for RNA-seq were prepared using the Illumina TruSeq kit following manufacturer's recommendations

treatment_protocol:
Single cell suspensions were then stained either with Hoechst 33342 alone (RS_23_dpp & Prm_EGFP_ES) or Hoechst 33342 and SYTO 16 (all other samples)
Stained cells were then isolated via FACS

tag: strain

value: 3 months

value: WT

tag: Sex

value: male

value: testes

value: Elongating spermatid


title: Round spermatids, Juvenile 23 dpp, replicate 1

description:
RS_23_dpp
Gill_RNA_Seq_log2RPKM_DeNovo.csv.gz
Gill_RNA_Seq_log2RPKM_Gencode.csv.gz

value: Round spermatid


title: Elongating spermatid H3K4me3

data_processing:
Trim Galore + STAR
Adapters were trimmed from sequences using Trim Galore
Sequences were aligned to mm10 using STAR
Reads within 2 kb of start sites of genes annotated in our de novo pipeline (see GTF file) were counted in R with the package QuasR
Assembly: mm10
Supplementary files format and content: Comma separated value text file with counts within 2 kb of start sites of genes annotated via de novo annotation pipeline (see GTF file)

growth_protocol: Single cell suspension were produced from adult mouse testes using sequential digestion with collagenase and trypsin

extract_protocol:
DNA was isolated using phenol/chloroform extaction
Libraries were prepared using Illumina ChIP-seq DNA Sample Prep Kit (Cat# IP-102-1001)

treatment_protocol: Single cells were lysed and digested with MNase, followed by immunoprecipitation with an antibody against H3K4me3

tag: chip antibody

value: Millipore 17-614


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0h - 10X Multiome RNA - replicate 4


title: Pachytene/Diplotene H3K4me3

value: Pachytene/Diplotene spermatocyte


title: JIMT-1_CTL_2

value: HER2+ Breast Cancer


title: Leptotene/Zygotene H3K4me3

value: Leptotene/Zygotene spermatocyte


title: Rnorvegicus_thymus_MAIT

city: Paris

first: Martin

last: MESTDAGH

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rnor6.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Thymus

extract_protocol:
4 thymi were maintained in CO2-independent medium (Gibco) at 4°c until processing. Sample processing started less than 6 hours after euthanasia. The 4 thymis were pooled together and minced with a sterile scalpel in a petri dish containing 5 mL of CO2-independent medium. Tissue pieces were then washed with 40 mL of FACS buffer (PBS supplemented with 2% fetal calf serum (FCS) and 2.5 mM EDTA) to recover single cell suspensions of thymocytes.   To generate scRNAseq data from R. norvegicus, 109 thymocytes were stained for 30 min at room temperature with PE-labeled mouse MR1:5-OP-RU tetramer, then washed and stained with 70 mL of anti-PE microbeads (Miltenyi).  Magnetic enrichment of tetramer-labeled thymocytes was then performed. Following magnetic enrichment, thymocytes were stained for 30 min at 4°C with the following primary antibodies: anti-rat TCRab FITC (clone R73, Biolegend 201105), anti-rat CD161 APC (clone 3.2.3, Biolegend 205606).  Cells were then washed with FACS buffer and stained with DAPI (Sigma). DAPI- Tetramer+ TCRab+ thymocytes were flow-sorted (Aria III, BD) into PBS supplemented with 0.35% BSA (Sigma). Sorted cells were centrifuged, counted and 5,000 – 10,000 cells were loaded onto the Chromium 3’ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer’s recommendations (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: MAIT

value: Thymus

tag: condition

value: Steady State


title: Mdomestica_thymus_MAIT

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: ASM229v1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Monodelphis domestica

source_name: thymus

extract_protocol:
A freshly isolated thymus was maintained in CO2-independent medium (Gibco) at 4°c until processing. Sample processing started less than 6 hours after euthanasia.  The thymus was minced with a sterile scalpel in a petri dish containing 5 mL of CO2-independent medium. Tissue pieces were then washed with 40 mL of FACS buffer (PBS supplemented with 2% fetal calf serum (FCS) and 2.5 mM EDTA) to recover single cell suspensions of thymocytes.  To generate scRNAseq data from M. domestica, 108 thymocytes were stained for 30 min at room temperature with a PE-labeled opossum MR1 tetramer loaded with 5-OP-RU, then washed and stained with 70 mL of anti-PE microbeads (Miltenyi).  Magnetic enrichment of tetramer-labeled thymocytes was then performed. Following magnetic enrichment, thymocytes were stained for 30 min at 4°C with the following primary antibodies: polyclonal rabbit anti-human CD3e (Dako A0452) and mouse anti-CD79A (clone HM57, GeneTex GTX74022) After washing with FACS buffer, opossum cells were further stained for 30 min on ice with the following secondary antibodies: donkey anti-rabbit IgG AF488 (Biolegend 406416) and anti-mouse IgG1 AF700 (clone RMG1-1, Biolegend 406631).  Cells were then washed with FACS buffer and stained with DAPI (Sigma). DAPI- Tetramer+ CD3+ thymocytes were flow-sorted (Aria III, BD) into PBS supplemented with 0.35% BSA (Sigma). Sorted cells were centrifuged, counted and 5,000 – 10,000 cells were loaded onto the Chromium 3’ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer’s recommendations (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: thymus


title: 7-day-old sorghum seedlings undergoing deetiolation - timepoint 0.5h - 10X

description:
10x Genomics
L1_sorghum_combined.RData

tag: age


title: Fusobacterium nucleatum infection 16 weeks Male Mice 7

city: gainesville

first: Kesavalu

middle: Lakshmyya

last: Naidu

state: Florida

address: 1600 SW Archer Road

department: Dentistry

institute: University of Florida

description:
Fusobacterium nucleatum
Infected 16 W
miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).

hyb_protocol: We used high-throughput nCounter® miRNA Expression Panels (Nanostring Technologies, Seattle, WA, USA) to effectively identify the DE of miRNA in both sexes. Nanos-  Int. J. Mol. Sci. 2022, 23, 5107 14 of 18  tring nCounter® analysis can identify 577 miRNAs in any sample, and by using molecular  barcodes, it can detect even a low number of miRNAs without the need for reverse transcription or amplification.  miRNA expression profiling was performed using the Nanostring nCounter® Mouse  miRNA Assay kit v1.5 (Nanostring Technologies). This assay is a highly sensitive multiplexed method that detects miRNAs using molecular barcodes called nCounter reporter  probes without the need for reverse transcription. Sample preparation involved annealing,  ligation, and purification. These steps were carried out based on the experimental procedure described in the nCounter® miRNA assay panel kit. Briefly, the annealing master  mix was prepared by combining 13 µL of annealing buffer, 26 µL of nCounter miRNA Tag  reagent, and 6.5 of diluted (1:500) miRNA assay controls. Next, 3.5 µL of the annealing master mix was aliquoted into each tube of the strip tube and 100 ng of the total RNA from six  left mandibles from each group (maximum 3-µL volume) with 260/280 and 260/230 ratios  of greater than 2 was added to the respective tubes. The strip tube was placed in the  Thermal Cycler with the following conditions: 94 ◦C for 1 min, 65 ◦C for 1 min, 45 ◦C for  1 min, and 48 ◦C for hold.  After annealing, 2.5 µL of the ligation master mix (19.5 µL of polyethylene glycol (PEG)  and 13 µL of ligation buffer) was added to all the tubes in the strip tube. The strip tube  was incubated at 48 ◦C for 5 min, followed by the addition of 1 µL of ligase into each tube  without removing the strip tubes from the Thermal Cycler. Ligation was performed with  the following conditions: 48 ◦C for 3 min, 47 ◦C for 3 min, 46 ◦C for 3 min, 45 ◦C for 3 min,  65 ◦C for 10 min, and 4 ◦C for hold. To remove the unligated tags, a purification step was  performed after adding 1 µL of ligation cleanup enzyme to all the tubes and incubating the  tubes at 37 ◦C for 1 h, 70 ◦C for 10 min, and 4 ◦C for hold. Forty microliters of RNase-free  water were added to each tube in the strip tube and the sample was ready for hybridization  with the nCounter reporter and capture probes. After denaturation at 85 ◦C for 5 min, a  5-µL aliquot from the miRNA sample preparation tube was taken along with the 10 µL of  miRNA reporter code, 10 µL of hybridization buffer, and 5 µL miRNA capture probe. The  strip tubes were incubated at 65 ◦C for 18 h in the Thermal cycler, and the samples were  immediately processed for post-hybridization with the nCounter analysis system at the  Molecular Pathology Core at the University of Florida.  The nCounter® Mouse miRNA Assay kit v1.5 provided six positive hybridization controls and eight negative control probes to monitor hybridization efficiency. All components  and reagents needed for sample preparation at the reparation station were taken from  the nCounter master kit (NanoString Technologies). Twelve samples per cartridge were  processed in a single run, which took 3 h. This was followed by digital analysis, which  involved the transfer of the cartridge to the multichannel epifluorescence digital analyzer.  A cartridge definition file with a maximum fields of view (FOV) count of 555 per flow cell  was taken for digital analysis. The number of images taken per scan corresponded to the  number of immobilized reporter probes on the cartridge. A separate Reporter Code Count  (RCC) file for each sample containing the count for each probe was downloaded and used  for data analysis.

data_processing: Initial data analysis was performed using nSolver 4.0. Initially, RCC files were imported into nSolver and imaging quality control (QC), binding density QC, positive control linearity QC, and positive control limit of detection QC were carried out as recommended in the system QC parameters. The lanes were flagged when the percent FOV registration was less than 75% for imaging QC. Binding density was outside the range from 0.1 to 2.25 for binding density QC, and the positive control R2 value was less than 0.95. All 24 samples passed the QC, and no flag lanes were observed. Raw data were generated after passing the QC. To reduce the background signal/noise, the background threshold count value was set to 52 and calculated by taking an average of eight negative control probe counts from all 24 samples. Codeset content normalization parameters were chosen, and the normalization was performed based on the top 100 miRNA genes expressed. The normalized factor was calculated based on the geometric mean values of the miRNA genes expressed in each sample. Fold changes in the genes were calculated based on the ratio of the difference in the means of the log-transformed normalized data to the square root of the sum of the variances of the samples in the two groups. The limma R library was used to calculate fold changes. Clustering of miRNA for the final heatmap of DE miRNA was done using the Partitioning Around Medoids method with the fpc R library.

label: NanoString

source_name: Infected 16 weeks

growth_protocol: Fusobacterium nucleatum was grown in Brucella Blood Agar with Hemin, and Vitamin K, Hardy Diagnostics - A30, 15×100 mm, Brucella Blood Agar with Hemin, and Vitamin K for three days in anaerobic growth chamber.

extract_protocol: Total RNA isolated from the mandible tissue using mirVana miRNA isolation kit (Ambion, Austin, TX, USA). mandibles from each mouse were entirely homogenized using the handheld rotor-stator homogenizer with sterile individual TissueRuptor disposable probes (Qiagen; Germantown, MD, USA) for each sample. After homogenization, each sample was lysed in a denaturing lysis solution that stabilized RNAs and inactivated RNases. The samples were subjected to an acid-phenol:chloroform extraction that removed all the cellular components such as protein, DNA, and other cellular products. The aqueous phase was removed, transferred to the fresh nuclease-free microcentrifuge tube, and 1.25 volume of 100% ethanol was added. This mixture was transferred to the filter cartridge placed into the collection tube and centrifuged for 15 s at 10,000× g. The filter cartridge was washed with 700 µL of wash solution-1 followed by washing with wash solution-2/3. After washing, the total RNA was eluted from the filter cartridge with 100 µL of nuclease-free water. RNA yield and purity were determined using a Take3 micro-volume plate in Epoch Microplate Spectrophotometer (BioTek), and quantification was performed in technical duplicates for each sample.

treatment_protocol: 100 million bacterial cells suspended in reduced transport fluid is mixed with equal volume of 6% carboxymethylcellulose (CMC) and administed orally. 0.1 ml cell suspension/mice.

value: Left Mandibles


title: Fusobacterium nucleatum infection 16 weeks Male Mice 10


title: Fusobacterium nucleatum infection 16 weeks Male Mice 8


title: Fusobacterium nucleatum infection 16 weeks Male Mice 3


title: Fusobacterium nucleatum infection 16 weeks Male Mice 4


title: Fusobacterium nucleatum infection 16 weeks Male Mice 6


title: Fusobacterium nucleatum infection 16 weeks Male Mice 5


title: Fusobacterium nucleatum infection 16 weeks Male Mice 2


title: Fusobacterium nucleatum infection 8 weeks male Mice 5

description:
Fusobacterium nucleatum
Infected 8W
miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).

source_name: Infected 8 weeks


title: Fusobacterium nucleatum  infection 8 weeks male Mice 6


title: Fusobacterium nucleatum  infection 8 weeks male Mice 7


title: Fusobacterium nucleatum infection 8 weeks male Mice 9


title: Fusobacterium nucleatum infection 16 weeks Male Mice 1


title: Fusobacterium nucleatum  infection 8 weeks male Mice 4


title: Fusobacterium nucleatum infection 8 weeks male Mice 10


title: Fusobacterium nucleatum  infection 8 weeks male Mice 2


title: Fusobacterium nucleatum  infection 8 weeks male Mice 3


title: JIMT-1_HUNK KD1_4

tag: cell type


title: Fusobacterium nucleatum infection 8 weeks male Mice 8


title: Fusobacterium nucleatum infection 8 weeks male Mice 1


title: SHAM 16 weeks female Mice (Fusobacterium nucleatum infection control) 10

description:
Sterile reduced transport Fluid and 6% CMC (1:1 ratio).
SHAM 16W
miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).

source_name: SHAM 16 WEEKS


title: SHAM 16 weeks female Mice (Fusobacterium nucleatum infection control) 7


title: SHAM 16 weeks female Mice (Fusobacterium nucleatum infection control) 8


title: SHAM 16 weeks female Mice (Fusobacterium nucleatum infection control) 9


title: Fusobacterium nucleatum infection 16 weeks Male Mice 9


title: SHAM 16 weeks Female Mice (Fusobacterium nucleatum infection control) 6


title: SHAM 16 weeks male Mice (Fusobacterium nucleatum infection control) 5


title: SHAM 16 weeks male Mice (Fusobacterium nucleatum infection control) 2


title: SHAM 8 weeks female Mice (Fusobacterium nucleatum infection control) 9

description:
Sterile reduced transport Fluid and 6% CMC (1:1 ratio).
SHAM 8W
miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).

source_name: SHAM 8 WEEKS


title: SHAM 16 weeks male Mice (Fusobacterium nucleatum infection control) 4


title: SHAM 16 weeks male Mice (Fusobacterium nucleatum infection control) 1


title: NK cells, co-culture with HDV-infected HepG2-hNTCP cells, replicate 2

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
FASTQ reads were aligned using the STAR aligner (version 2.5.3a) (doi: 10.1093/bioinformatics/bts635). Reads were aligned to a STAR index generated from the 1000 genomes assembly, gencode 19 gene models and for a sjbdOverhang of 200. Duplicate marking was done with Sambamba (version 0.6.5) (doi: 10.1093/bioinformatics/btv098). Read counting over exon features from gencode 19 gene models was performed with FeatureCounts (doi: 10.1093/bioinformatics/btt656). Both reads of a paired fragment (quality threshold of 255) were used for strand unspeciﬁc counting. The count data were transformed to TPM and FPKM expression values.
Assembly: 1000 genomes assembly, GRCh37
Supplementary files format and content: raw count matrix, FPKM + TPM normalized count matrix

source_name: NK cells

growth_protocol: NK cells were collected after 48 h of co-culture with HDV-infected or non-infected HepG2-hNTCP cells. To remove residual HepG2-hNTCP cells, NK cells were isolated through positive selection with magnetic beads according to the manufacturer’s instructions (purity > 85% as determined by ﬂow cytometry).

extract_protocol:
RNA was isolated from NK cells using the RNeasy Mini Kit (Quiagen, Cat.: 74104) according to the manufacturer’s instructions.
RNA libraries were prepared with the TruSeq Stranded Total RNA Gold with Ribo-Zero Plus protocol (Illumina, San Diego, USA).

value: NK cells

tag: co-culture condition

value: hdv-pos HepG2-hNTCP


title: NK cells, co-culture with non-infected HepG2-hNTCP cells, replicate 2

value: hdv-neg HepG2-hNTCP


title: NK cells, co-culture with HDV-infected HepG2-hNTCP cells, replicate 3


title: SHAM 8 weeks male Mice (Fusobacterium nucleatum infection control) 5


title: SHAM 8 weeks female Mice (Fusobacterium nucleatum infection control) 8


title: SHAM 8 weeks female Mice (Fusobacterium nucleatum infection control) 10


title: NK cells, co-culture with HDV-infected HepG2-hNTCP cells, replicate 1


title: SHAM 8 weeks male Mice (Fusobacterium nucleatum infection control) 2


title: SHAM 8 weeks female Mice (Fusobacterium nucleatum infection control) 6


title: NK cells, co-culture with HDV-infected HepG2-hNTCP cells, replicate 5


title: SHAM 8 weeks male Mice (Fusobacterium nucleatum infection control) 4


title: NK cells, co-culture with non-infected HepG2-hNTCP cells, replicate 5


title: NK cells, co-culture with HDV-infected HepG2-hNTCP cells, replicate 4


title: SHAM 8 weeks male Mice (Fusobacterium nucleatum infection control) 1


title: 1_mock

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: single cell RNA seq

data_processing:
The single cell library was sequenced with Illumina NovaSeq6000 platform. Sequencing reads were aligned to human GRCh38 reference genome with Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx, barcodes.tsv, genes.tsv

source_name: human ES-derived DA neuron

growth_protocol: Midbrain dopaminergic neuron differentiation were performed using H9, MEL1 and SCNA different copy numbers hPESCs, which include NURR1: GFP hPESC.  hESCs hPSCs were grown on VTN-N-coated 6-well plates in E8-essential medium. Cells were maintained at 37℃, 5% CO2. hPESCs were differentiated with an optimized protocol from a previously reported study.

extract_protocol:
This step was done by following the 10x Genomics single cell preparation protocol.
RNA libraries were prepared for sequencing using standard 10X Illumina single cell library preparation protocols

treatment_protocol: To purify DA neurons, DA neuron differentiated cells at day 25 from NURR1::GFP hPSC were sorted by GFP using a BDFACS Aria6 cell sorter in Flow Cytometry Core Facility of MSKCC. The GFP positive sorted cells were further in vitro cultured for subsequent experiments until use.

value: human ES-derived DA neuron

tag: agent

value: mock


title: 22Rv1_2024_androgen receptor targeting degrader_1

city: Seoul

first: TaeHyun

last: Bae

address: Yongeon 103 Daehangno, Jongno-gu

country: South Korea

institute: Seoul National University

data_processing:
The quality control analysis of raw reads was conducted, followed by a preprocessing step aimed at eliminating artifacts to reduce bias.
Processed reads underwent mapping to GRCh37 using HISAT2 during the preprocessing step.
Transcript assembly was conducted using StringTie, utilizing the information from reference-based aligned reads.
The expression profile is derived from the transcript quantification of each sample, utilizing FPKM/RPKM and TPM for expression level assessment.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file including raw counts for each samples

source_name: Prostate gland cancer cell

growth_protocol: 22Rv1 cells were maintained in RPMI-1640 medium with 10% FBS and antibiotics (100 units/mL penicillin and 100 mg/mL streptomycin) in a 5% CO2, 37℃ incubator.

extract_protocol:
RNA was harvested using Trizol (Sigma).
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, # 20020595).

treatment_protocol: After24 hours from seeding, cells were treated with the indicated compounds

value: Prostate gland cancer cell

value: Prosate cancer cells

tag: genotype

value: WT

tag: treatment

value: Androgen receptor-targeting degrader


title: 22Rv1_1021_autophagy activating ligand_3

value: Autophagy-activating ligand


title: NK cells, co-culture with non-infected HepG2-hNTCP cells, replicate 3


title: SHAM 16 weeks male Mice (Fusobacterium nucleatum infection control) 3


title: 22Rv1_enzalutamide_2

value: Enzalutamide


title: NK cells, co-culture with non-infected HepG2-hNTCP cells, replicate 4


title: NK cells, co-culture with non-infected HepG2-hNTCP cells, replicate 1


title: infect

description: single cell RNA seq


title: 22Rv1_2024_androgen receptor targeting degrader_3


title: 22Rv1_2024_androgen receptor targeting degrader_2


title: SHAM 8 weeks male Mice (Fusobacterium nucleatum infection control) 3


title: 22Rv1_1021_autophagy activating ligand_2


title: 22Rv1_enzalutamide_3


title: A549, Control, 3 Days, R3

city: Odense

first: Paolo

last: Ceppi

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Quality control analysis of Fastq files were done using FastQC package.
Reads were then aligned to human reference genome with GRCh38 build (release 105) with the respective Ensembl GTF annotation file using STAR v2.7.9a aligner in a two-pass mode.
Read counts were measured with featureCounts function in Rsubread package using R 4.2.1
Differential gene expression analysis was performed using DESeq2 v1.36.0 pipeline.
Assembly: hg38; GRCh38 (release 105)
Supplementary files format and content: tab-delimited text file includes Raw count values from featureCounts for all samples

growth_protocol: A549 cell line was maintained in DMEM high glucose medium (Gibco) with 10% fetal bovine serum (FBS) and maintained at 37oC with 5% CO2 in a humidified incubator

extract_protocol:
Total RNA was isolated using miRNeasy kit (Qiagen) as per manufacturer's protocol. 500 ng of Total RNA was used for the library construction.
Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol (NEB).

treatment_protocol: A549 cell line was treated with brequinar (BRQ) at 1 µM for 72 hours.

value: NSCLC cell line

value: No treatment

tag: time

value: 3 Days


title: A549, Control, 3 Days, R1


title: A549, Control, 3 Days, R2


title: 22Rv1_1021_autophagy activating ligand_1


title: 22Rv1_enzalutamide_1


title: Sample 1 (coronary sample with plaque erosion from a 42-year-old white female)

city: GAITHERSBURG

first: Kenji

last: Kawai

state: MARYLAND

address: 19 FIRSTFIELD ROAD

institute: CVPath institute

data_processing:
library strategy: Spatial transcriptome sequencing
Raw FASTQ files for a given capture area and corresponding capture area histology images were processed with Space Ranger software version 1.3.0 (10X Genomics, Pleasanton CA).
Space Ranger Pipeline was used to align Fastq reads to human GRCh38 reference genome, and the probe set reference file specific only to human FFPE tissues because the synthetic probe DNA was sequenced rather than cDNA of a captured transcript. For FFPE samples, Space Ranger counts oligo ligation events to build the feature-barcode matrix.
Sequencing data was then imported into Partek Flow Enterprise Edition software (Partek Inc., Louis, MO) for generatig PCA and UMAP
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: feature-barcode matrix showing number of UMIs associated with gene expression (row) and barcodes (column) filtered only for cell-associated barcodes
Supplementary files format and content: spatial_enrichment.csv: Moran's I values, Gene Expression counts and p value in Spots under tissue in tabular format
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image: low-res image of tissue
Supplementary files format and content: tissue_positions: list of spatial barcodes and coordinates specifyig spots

source_name: coronary sample with plaque erosion

growth_protocol: Two histology sections (FFPE) from coronary artery with plaque erosion

extract_protocol:
Formalin-Fixed Paraffin-Embedded from coronary artery tissue
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium v1 kit
Visium Spatial Gene Expression Slide Kit, 16 rxns PN-1000185 | 4 rxns PN-1000188, Visium Human Transcriptome Probe Kit, Large PN-1000364 | Small PN-1000363

tag: tissue id

value: coronary sample with plaque erosion

tag: gender

value: female


title: A549, BRQ, 3 Days, R3

tag: cell line

value: BRQ 1 µM


title: Sample 2 (coronary sample with plaque erosion from a 46-year-old white female)


title: 22Rv1_vehicle_1

value: vehicle


title: 22Rv1_vehicle_3


title: A549, BRQ, 3 Days, R2


title: 22Rv1_vehicle_2


title: A549, BRQ, 3 Days, R1


title: SGI-1776-VHL-02 3750 nM Rep 2 (2)

city: Tucson

first: Marcas

last: Agostinelli

state: Arizona

address: 2690 W Avenida Azahar

department: Bioinformatics

institute: Novogene

data_processing:
Raw data of fastq format were  processed through in-house perl scripts. The clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
gene_count.xls generated using featureCounts 1.5.0-p3
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: gene_count.xls of raw gene counts

extract_protocol:
Total RNA was extracted with the Rneasy kit (Qiagen) according to the manufacturer's protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library ordTTP for non-directional library.

value: prostate


title: SGI-1776-VHL-02 3750 nM Rep 2 (1)


title: SGI-1776-VHL-02 3750 nM Rep 2 (3)


title: SGI-1776 3750 nM Rep 2 (3)


title: SGI-1776-VHL-02 3750 nM Rep 1 (2)


title: SGI-1776 3750 nM Rep 2 (2)


title: SGI-1776 3750 nM Rep 2 (1)


title: SGI-1776-VHL-02 3750 nM Rep 1 (3)


title: SGI-1776 3750 nM Rep 1 (3)


title: SGI-1776-VHL-02 1500 nM Rep 2 (2)


title: SGI-1776-VHL-02 1500 nM Rep 2 (1)


title: SGI-1776-VHL-02 1500 nM Rep 2 (3)


title: SGI-1776 3750 nM Rep 1 (1)


title: SGI-1776-VHL-02 1500 nM Rep 1 (3)


title: SGI-1776-VHL-02 1500 nM Rep 1 (2)


title: SGI-1776 1500 nM Rep 2 (3)


title: SGI-1776 1500 nM Rep 2 (1)


title: SGI-1776-VHL-02 1500 nM Rep 1 (1)


title: SGI-1776 1500 nM Rep 2 (2)


title: SGI-1776 1500 nM Rep 1 (2)


title: DMSO Rep 2 (1)

value: DMSO, 48 h


title: SGI-1776 1500 nM Rep 1 (1)


title: DMSO Rep 2 (3)


title: DMSO Rep 1 (3)


title: SGI-1776 3750 nM Rep 1 (2)


title: DMSO Rep 1 (2)


title: SGI-1776-VHL-02 3750 nM Rep 1 (1)


title: DMSO Rep 1 (1)


title: 3894_Striatopallidal-medium-spiny-neuron_HCT-17-HFG_CTRL

first: Kert

last: Matlik

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
The ATACseq reads were aligned with the hg38 genome from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.4.1) using Rsubread's align method in paired-end mode.
Normalized bigWigs were created with the rtracklayer package.
BSgenome.Hsapiens.UCSC.hg38
Assembly: BigWig files

source_name: gDNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1-, DRD2+) treated with Tn5 transposase

extract_protocol:
Genomic DNA was isolated with using MinElute Reaction Cleanup Kit (Qiagen, #28206)
Genomic DNA was used for PCR amplification with NEBNext® High-Fidelity 2X PCR Master Mix (New England Biolabs, #M0541S) and barcoded Nextera primers (Buenrostro JD et al., 2013, Nat Methods 10, 1213-1218. 10.1038/nmeth.2688). Libraries were pooled for sequencing on NovaSeq6000 (SP 2 x 150bp or SP 2 x 100bp).

treatment_protocol: Nuclei were isolated from fresh-frozen post-mortem human caudate nucleus and putamen, treated with Tagment DNA TDE1 Enzyme (Illumina, #15027865), labeled with cell type-specific probes and separated by FACS as described by Matlik et al 2023.

tag: application

value: ATAC-seq

value: Posterior caudate

value: Striatopallidal medium spiny neuron

tag: donor

value: M

tag: pmi (hrs)

tag: donor category

value: CTRL


title: 3602_Striatopallidal-medium-spiny-neuron_BEB20057_CTRL

value: Anterior caudate

tag: Sex


title: 3589_Striatopallidal-medium-spiny-neuron_BEB20057_CTRL

value: Posterior putamen


title: 3890_Striatopallidal-medium-spiny-neuron_BEB20057_CTRL

value: Anterior putamen


title: 3514_Striatopallidal-medium-spiny-neuron_HCTSU_CTRL

value: HCTSU

value: F


title: 3512_Striatopallidal-medium-spiny-neuron_BEB18117_CTRL


title: 3508_Striatopallidal-medium-spiny-neuron_HCTSU_CTRL


title: 3520_Striatopallidal-medium-spiny-neuron_BEB18116_CTRL


title: 3516_Striatopallidal-medium-spiny-neuron_BEB18117_CTRL


title: 3587_Striatopallidal-medium-spiny-neuron_BEB18135_CTRL


title: 3504_Striatopallidal-medium-spiny-neuron_HCTSU_CTRL


title: 3518_Striatopallidal-medium-spiny-neuron_BEB18116_CTRL


title: 3506_Striatopallidal-medium-spiny-neuron_HCTSU_CTRL


title: SGI-1776 1500 nM Rep 1 (3)


title: 3414_Striatopallidal-medium-spiny-neuron_BEB18135_CTRL


title: DMSO Rep 2 (2)


title: 3502_Striatopallidal-medium-spiny-neuron_BEB19051_CTRL


title: 3892_Striatopallidal-medium-spiny-neuron_BEB20057_CTRL


title: 3410_Striatopallidal-medium-spiny-neuron_BEB19051_CTRL


title: 3413_Striatopallidal-medium-spiny-neuron_BEB19051_CTRL


title: 3396_Striatopallidal-medium-spiny-neuron_BEB18135_CTRL


title: 3408_Striatopallidal-medium-spiny-neuron_BEB19025_CTRL


title: 3400_Striatopallidal-medium-spiny-neuron_HCT-17-HFG_CTRL


title: 3603_Striatopallidal-medium-spiny-neuron_BEB19051_CTRL


title: 3301_Striatopallidal-medium-spiny-neuron_BEB19025_CTRL


title: 3270_Striatopallidal-medium-spiny-neuron_BEB18135_CTRL


title: 3268_Striatopallidal-medium-spiny-neuron_HCT-17-HFG_CTRL


title: 3198_Striatopallidal-medium-spiny-neuron_BEB18116_CTRL


title: 3266_Striatopallidal-medium-spiny-neuron_HCT-17-HFG_CTRL


title: 3196_Striatopallidal-medium-spiny-neuron_BEB18117_CTRL


title: 3893_Striatonigral-medium-spiny-neuron_HCT-17-HFG_CTRL

source_name: gDNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-) treated with Tn5 transposase

value: Striatonigral medium spiny neuron


title: 3891_Striatonigral-medium-spiny-neuron_BEB20057_CTRL


title: 3601_Striatonigral-medium-spiny-neuron_BEB20057_CTRL


title: 3519_Striatonigral-medium-spiny-neuron_BEB18116_CTRL


title: 3398_Striatopallidal-medium-spiny-neuron_BEB19025_CTRL


title: 3411_Striatopallidal-medium-spiny-neuron_BEB19025_CTRL


title: 3517_Striatonigral-medium-spiny-neuron_BEB18116_CTRL


title: 3598_Striatonigral-medium-spiny-neuron_BEB19025_CTRL


title: 3515_Striatonigral-medium-spiny-neuron_BEB18117_CTRL


title: 3511_Striatonigral-medium-spiny-neuron_BEB18117_CTRL


title: 3503_Striatonigral-medium-spiny-neuron_HCTSU_CTRL


title: 3889_Striatonigral-medium-spiny-neuron_BEB20057_CTRL


title: 3606_Striatonigral-medium-spiny-neuron_BEB18135_CTRL


title: 3409_Striatonigral-medium-spiny-neuron_BEB19051_CTRL


title: 3501_Striatonigral-medium-spiny-neuron_BEB19051_CTRL


title: 3202_Striatopallidal-medium-spiny-neuron_BEB18116_CTRL


title: 3586_Striatonigral-medium-spiny-neuron_BEB18135_CTRL


title: 3200_Striatopallidal-medium-spiny-neuron_BEB18117_CTRL


title: 3588_Striatonigral-medium-spiny-neuron_BEB20057_CTRL


title: 3507_Striatonigral-medium-spiny-neuron_HCTSU_CTRL


title: 3399_Striatonigral-medium-spiny-neuron_HCT-17-HFG_CTRL


title: 3395_Striatonigral-medium-spiny-neuron_BEB18135_CTRL


title: 3397_Striatonigral-medium-spiny-neuron_BEB19025_CTRL


title: 3300_Striatonigral-medium-spiny-neuron_BEB19025_CTRL


title: 3407_Striatonigral-medium-spiny-neuron_BEB19025_CTRL


title: 3505_Striatonigral-medium-spiny-neuron_HCTSU_CTRL


title: 3201_Striatonigral-medium-spiny-neuron_BEB18116_CTRL


title: 3267_Striatonigral-medium-spiny-neuron_HCT-17-HFG_CTRL


title: SHAM 8 weeks female Mice (Fusobacterium nucleatum infection control) 7

value: Left Mandibles


title: 3269_Striatonigral-medium-spiny-neuron_BEB18135_CTRL


title: 3513_Striatonigral-medium-spiny-neuron_HCTSU_CTRL


title: 3195_Striatonigral-medium-spiny-neuron_BEB18117_CTRL


title: 3199_Striatonigral-medium-spiny-neuron_BEB18117_CTRL


title: 3412_Striatonigral-medium-spiny-neuron_BEB19051_CTRL


title: 3197_Striatonigral-medium-spiny-neuron_BEB18116_CTRL


title: 3908_Oligodendrocyte_BEB20057_CTRL

source_name: gDNA extracted from striatal oligodendrocyte nuclei (EAAT1-, IRF8-, NeuN-, OLIG2+) treated with Tn5 transposase

value: Oligodendrocyte


title: 4856_Oligodendrocyte_BEB19051_CTRL


title: 3401_Oligodendrocyte_BEB18135_CTRL


title: 4844_Oligodendrocyte_BEB20057_CTRL


title: 3901_Oligodendrocyte_BEB18117_CTRL


title: 3307_Oligodendrocyte_BEB18116_CTRL


title: 3294_Oligodendrocyte_BEB19025_CTRL


title: 3265_Striatonigral-medium-spiny-neuron_HCT-17-HFG_CTRL


title: 4276_Oligodendrocyte_HCTSU_CTRL


title: 3304_Oligodendrocyte_BEB18117_CTRL


title: 3282_Oligodendrocyte_BEB18135_CTRL


title: 3274_Oligodendrocyte_HCT-17-HFG_CTRL


title: 3404_Oligodendrocyte_BEB18116_CTRL


title: 4277_Microglia_HCTSU_CTRL

source_name: gDNA extracted from striatal microglia nuclei (EAAT1-, IRF8+, NeuN-, OLIG2-) treated with Tn5 transposase

value: Microglia


title: 4845_Microglia_BEB20057_CTRL


title: 3899_Microglia_BEB18116_CTRL


title: 3405_Microglia_BEB18116_CTRL


title: 3298_Microglia_BEB19025_CTRL


title: 3283_Microglia_BEB18135_CTRL


title: 3305_Microglia_BEB18117_CTRL


title: 3271_Oligodendrocyte_BEB18117_CTRL


title: 3295_Microglia_BEB19025_CTRL


title: 3278_Microglia_HCT-17-HFG_CTRL


title: 3402_Microglia_BEB18135_CTRL


title: 3275_Microglia_HCT-17-HFG_CTRL


title: 3280_Microglia_BEB18116_CTRL


title: 3898_Oligodendrocyte_BEB18116_CTRL


title: 3272_Microglia_BEB18117_CTRL


title: 4859_Interneuron--Other_BEB19051_CTRL

source_name: gDNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-) treated with Tn5 transposase

value: Interneuron, Other


title: 3277_Oligodendrocyte_HCT-17-HFG_CTRL


title: 3297_Oligodendrocyte_BEB19025_CTRL


title: 4857_Microglia_BEB19051_CTRL


title: 4853_Interneuron--Other_BEB18116_CTRL


title: 4852_Interneuron--Non-Fast-Spiking_BEB19025_CTRL

source_name: gDNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-) treated with Tn5 transposase

value: Interneuron, Non-Fast Spiking


title: 4847_Interneuron--Other_BEB20057_CTRL


title: 4849_Interneuron--Non-Fast-Spiking_BEB20057_CTRL


title: 4854_Interneuron--Fast-Spiking_BEB18116_CTRL

source_name: gDNA extracted from striatal fast-spiking interneuron nuclei (TAC3-, ETV1+, PPP1R1B-) treated with Tn5 transposase

value: Interneuron, Fast Spiking


title: 4855_Interneuron--Non-Fast-Spiking_BEB18116_CTRL

value: ATAC-seq


title: 4851_Interneuron--Fast-Spiking_BEB19025_CTRL


title: 4860_Interneuron--Fast-Spiking_BEB19051_CTRL


title: 4848_Interneuron--Fast-Spiking_BEB20057_CTRL


title: 4278_Astrocyte_HCTSU_CTRL

source_name: gDNA extracted from striatal astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-) treated with Tn5 transposase

value: Posterior caudate

value: Astrocyte


title: 3903_Astrocyte_BEB18117_CTRL

value: M


title: 3909_Astrocyte_BEB20057_CTRL

value: CTRL


title: 4858_Astrocyte_BEB19051_CTRL


title: 3900_Astrocyte_BEB18116_CTRL


title: 3403_Astrocyte_BEB18135_CTRL


title: 3406_Astrocyte_BEB18116_CTRL


title: 3296_Astrocyte_BEB19025_CTRL


title: 3306_Astrocyte_BEB18117_CTRL

value: Anterior caudate


title: 3279_Astrocyte_HCT-17-HFG_CTRL

value: Posterior putamen


title: 4861_Interneuron--Non-Fast-Spiking_BEB19051_CTRL


title: 3299_Astrocyte_BEB19025_CTRL

value: Anterior putamen


title: 3276_Astrocyte_HCT-17-HFG_CTRL


title: 3281_Astrocyte_BEB18116_CTRL


title: 4850_Interneuron--Other_BEB19025_CTRL


title: 3273_Astrocyte_BEB18117_CTRL


title: Sequencing data for 5hmC from human normal lung tissue by DD-seq

city: Beijing

first: Nengbin

last: Xie

address: whu

institute: whu

description: SSD-seq sequencing data

data_processing:
library strategy: DD-seq/SSD-seq
the data quality was examined with FastQC (v0.11.8) software (https://www.bioinformatics.babraham.ac.uk).
Low-quality bases and adaptor sequences were removed from the raw reads using Trimmomatic (version 0.39)
The trimmed reads were mapped against the reference genomes (hg19) with Bismark (v0.23.0)
PCR duplicates and overlapping read pairs were removed and clipped using Bismark and BamUtil (version 1.0.14)
High-confidence 5hmC sites (depth ≥ 5) were called using a binomial distribution with q value cut-off of 0.01
Assembly: hg19
Supplementary files format and content: 5hmC signals from ACE-seq that calculated within tiled 10-kb genomic bins
Supplementary files format and content: 5hmC signals from SSD-seq that calculated within tiled 10-kb genomic bins

source_name: human normal lung tissue

extract_protocol:
Genomic DNA of human normal lung tissue was extracted using Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA)
SSD-seq：Genomic DNA of human normal lung tissue was extracted using Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA) according to the manufacturer's recommended procedure. The unmodified genomic DNA of lambda bacteriophage (Sangon Biotech, Shanghai, China) was added to the genomic DNA of human normal lung tissue as spike-in control (0.1% of spike-in DNA was added). The mixture was sheared to an average size of 250-400 bp using a JY92-II N Ultrasonic Homogenizer (Scientz Biotechnology Co., Ltd, China). The resulting fragmented DNA was end-repaired and adenylated using a Hieff NGS Ultima Endprep Mix kit (Yeasen Biotechnology Co., Ltd, Shanghai). Then, SSD-adaptor was ligated to both ends of repaired DNA using a Hieff NGS Ultima DNA Ligation Module kit (Yeasen) and the resulting DNA was purified using 0.8× KAPA Pure beads (Roche). To the resulting mixture, DNA-L-5mC and DNA-5hmC were added as spike-ins to evaluate the deamination rates of 5mC and 5hmC (0.1% of DNA-L-5mC and 0.1% DNA-5hmC were added). The DNA mixture was denatured followed by deamination using eA3A-v10. The deaminated DNA was amplificated by PCR with 5 cycles using pre-P5 primer, pre-P7 primer (Table S4) and Q5U Hot Start High-Fidelity DNA polymerase (New England Biolabs). After purification using 0.8× KAPA Pure beads, DNA products were then amplificated by PCR with 10 cycles using P5-index primer, P7-index primer and Q5 Hot Start High-Fidelity DNA polymerase (New England Biolabs). The PCR products were purified with 0.8× KAPA Pure beads and examined using 1.5% agarose gel electrophoresis.

value: human normal lung tissue


title: 8_022

city: Columbus

first: Jose

middle: Javier

last: Otero

state: Ohio

address: 333 W 10th Ave, 4170 Graves Hall

department: Pathology

institute: The Ohio State University

data_processing:
FASTQ files were processed through the GeoMx NGS pipeline, uploaded to the GeoMx, and standard QC applied to flag individual collections with <1000 raw reads, <80% aligned reads, <50% sequencing saturation, nuclei count <100, or No Template control counts are >1000. Additionally, segments were filtered out if they contained fewer than 10% of probes above threshold LOQ (=2*neg probe geomean or 2, whichever is higher), and probes were filtered out if they were above the LOQ in 10% of the segments or more.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the processed data file are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.
Library strategy: GeoMx Seq

source_name: Brain

extract_protocol:
hyb protocol: Slides were incubated with a cocktail of barcoded ISH probes overnight at 37C in a hybridization oven, and then at RT blocked for 30 minutes then incubated for 1 hour (also RT) with a cocktail of DNA stain (SYTO13) with fluorescent antibodies.
scan protocol: Slides were scanned at low resolution on the GeoMx to identify tissue regions, and then High-Resolution scans using the 20X objective were performed using the pre-built scanning conditions for the Fluorescent antibody kit from Nanostring.
Samples were pooled during library preparation. Individual FASTQ files were generated for each ROI, forward & reverse primers.

tag: slide id

value: Slide 8 (case 23)

tag: roi number

tag: segment type

value: Full ROI

tag: diagnosis

value: glioblastoma

tag: disease state

value: PD

tag: histology

value: Hypercellular

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 8_019

description: Samples were pooled during library preparation. Individual FASTQ files were generated for each ROI, forward & reverse primers.


title: 8_024


title: 8_023


title: 8_021


title: 8_020


title: 8_016


title: 8_017


title: 8_018


title: 4846_Astrocyte_BEB20057_CTRL

tag: application

tag: tissue

tag: cell type

tag: donor

tag: age

tag: pmi (hrs)

tag: donor category


title: 8_014

tag: slide id

tag: roi number

tag: segment type

tag: diagnosis

tag: disease state

tag: histology

value: Inflammatory


title: 8_015

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: 8_013

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 8_010


title: 8_009


title: Sequencing data for 5hmC from human normal lung tissue by ACE-seq

description: ACE-seq sequencing data

data_processing:
library strategy: ACE-seq
the data quality was examined with FastQC (v0.11.8) software (https://www.bioinformatics.babraham.ac.uk).
Low-quality bases and adaptor sequences were removed from the raw reads using Trimmomatic (version 0.39)
The trimmed reads were mapped against the reference genomes (hg19) with Bismark (v0.23.0)
PCR duplicates and overlapping read pairs were removed and clipped using Bismark and BamUtil (version 1.0.14)
High-confidence 5hmC sites (depth ≥ 5) were called using a binomial distribution with q value cut-off of 0.01
Assembly: hg19
Supplementary files format and content: 5hmC signals from ACE-seq that calculated within tiled 10-kb genomic bins
Supplementary files format and content: 5hmC signals from SSD-seq that calculated within tiled 10-kb genomic bins

tag: tissue


title: 8_008


title: 8_011


title: 8_012


title: 8_004


title: 8_005


title: 8_002


title: 8_003


title: 8_007


title: 7_024

value: Slide 7 (case 56)

value: psPD

value: Control


title: 8_001


title: 7_023


title: 7_022


title: 7_021


title: 7_020


title: 7_019


title: 7_018


title: 7_012


title: 7_014


title: 7_015


title: 7_017


title: 7_013


title: 7_010


title: 7_016


title: 7_009


title: 7_011


title: 8_006


title: 7_008


title: 7_006


title: 7_003


title: 7_002


title: 7_005


title: 7_007


title: 7_001


title: 7_004


title: 6_024

value: Slide 6 (case 53)


title: 6_021


title: 6_022


title: 6_019


title: 6_023


title: 6_020


title: 6_018


title: 6_017


title: 6_016


title: 6_015


title: 6_013


title: 6_011


title: 6_012


title: 6_014


title: 6_010


title: 6_009


title: 6_008


title: 6_006


title: 6_007


title: 6_004


title: 6_005


title: 6_002


title: 6_001


title: 5_022

value: Slide 5 (case 7)


title: 5_021


title: 6_003


title: 5_019


title: 5_020


title: 5_015


title: 5_013


title: 5_018


title: 5_011


title: 5_017


title: 5_016


title: 5_014


title: 5_012


title: 5_009


title: 5_003


title: 5_010


title: 5_008


title: 5_005


title: 5_004


title: 5_006


title: 5_001


title: 5_002


title: 4_022

value: Slide 4 (case 4-10)


title: 4_021


title: 4_020


title: 4_024


title: 5_007


title: 4_019


title: 4_017


title: 4_013


title: 4_015


title: 4_016


title: 4_014


title: 4_012


title: 4_009


title: 4_010


title: 4_011


title: 4_008


title: 4_007


title: 4_004


title: 4_006


title: 4_005


title: 4_023


title: 4_002


title: 4_001


title: 4_003


title: 4_018


title: 3_022

value: Slide 3 (case 36-6)


title: 3_024


title: 3_018


title: 3_015


title: 5_023


title: 3_014


title: 3_021


title: 3_012


title: 3_011


title: 3_020


title: 3_019


title: 3_016


title: 3_023


title: 3_008


title: 3_010


title: normal oral mucosa, 20220412_Purdue 5_N5-A1_01

city: west lafayette

middle: F

last: Vanhaezebrouck

state: IN

address: 625 harisson

department: College of veterinary

institute: Purdue University

hyb_protocol: 16 hours at 65 celcius

scan_protocol: 280 field of view capture by the nanostring digital analyzer

data_processing: rosalin

label: not provided

organism: Canis lupus familiaris

source_name: normal oral mucosa

label_protocol: label with reporter and capture probe sets from canine immun-oncology panel

growth_protocol: pathology samples collected from surgical methods.

extract_protocol: qiagen rna extraction kit

treatment_protocol: metastatic vs normal vs local tumors

tag: breed

value: normal

value: normal oral mucosa


title: 3_013

tag: slide id


title: 3_017

tag: roi number


title: normal lung, 20220412_Purdue 4_N4-B1_11

source_name: normal lung

value: normal lung


title: normal lymph node, 20220412_Purdue 4_N4-C1_12

source_name: normal lymph node

value: normal lymph node


title: 3_004

tag: segment type


title: 3_007

tag: diagnosis


title: normal lymph node, 20220412_Purdue 4_N3-C1_09

tag: disease state


title: 3_006

tag: histology


title: normal lung, 20220412_Purdue 4_N3-B1_08


title: normal oral mucosa, 20220412_Purdue 4_N3-A1_07


title: 3_002

tag: area


title: 3_003

tag: roi x coordinate


title: normal oral mucosa, 20220412_Purdue 4_N2-A1_04


title: normal lymph node, 20220412_Purdue 4_N2-C1_06


title: normal lung, 20220412_Purdue 4_N2-B1_05


title: 3_001

tag: roi y coordinate


title: 3_009

tag: rawreads


title: normal lymph node, 20220412_Purdue 4_N1-C1_03


title: 2_023

value: Slide 2 (case 50-7)

tag: alignedreads


title: normal oral mucosa, 20220412_Purdue 4_N4-A1_10


title: 2_021

value: Full ROI

tag: deduplicatedreads


title: 2_022

value: glioblastoma

tag: trimmedreads


title: 3_005

tag: stitchedreads


title: oral cavity with potential spreading, 20211116_Purdue 3_M675-B1_02

source_name: oral cavity with potential spreading

value: scottish terrier

value: Oral melanoma

value: oral cavity with potential spreading


title: 2_019

tag: sequencingsaturation


title: 2_018


title: 2_017


title: 2_020


title: oral cavity with potential spreading, 20211116_Purdue 3_M675-A2_01

tag: tissue


title: normal oral mucosa, 20220412_Purdue 4_N1-A1_01

tag: breed


title: oral cavity with potential spreading, 20211116_Purdue 2_M570-A1_03

value: schnauzer


title: 2_016

tag: slide id

value: psPD

value: Inflammatory


title: oral cavity with potential spreading, 20211116_Purdue 2_M570-B1_04


title: oral cavity with potential spreading, 20211116_Purdue 2_M495-C1_10

value: Dachshund


title: 2_015

tag: roi number


title: oral cavity with potential spreading, 20211116_Purdue 2_M495-B1_09


title: normal lung, 20220412_Purdue 4_N1-B1_02


title: HeLa-R220A-atac-rep1

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
Paired-end reads were trimmed for adaptor sequence using cutadapt v4.3 with parameters: -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -e 0.1 -n 2 -m 35 -q 30 –pairfilter = any
Trimed reads were mapped to hg38 using Bowtie2 v2.5.1  with parameters: -I 10 -X 1000 -3 5 --local --no-mixed --no-discordant --no-unal.
Duplicates were marked using picard MarkDuplicates v2.27.5 with default parameters and removed using samtools view v1.17  with parameters: -f 2 -F 1024 -q 10.
ATAC peaks were detected with macs2 callpeak v2.2.7.1 with parameter -f BAMPE -m 10 50.
Signals within peaks were annotated using multiBigwigSummary, and heatmap was generated using plotHeatmap from deeptools v3.5.2.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Uterus; Cervix

extract_protocol:
nuclei were extracted in Nuclei Buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Triton X-100) with Roche Complete Protease Inhibitor EDTA-Free.
DNA were extracted with Phenol:Chloroform:Isoamyl Alcohol (25:24:1), and precipitated by cold ethanol. 25 µL Tris buffer (10 mM Tris-HCl, pH 7.5) were used to resolve the DNA pellet, and 11.5 µL were used for Nextera library amplification. The library was purified with 1X AMPure XP beads.

value: Uterus; Cervix

tag: cell line

value: HeLa

tag: cell type

value: epithelial cell

tag: genotype

tag: treatment

value: SUV420H1(Aa1-550)-R220A over-expression


title: HeLa-Aa63-550-atac-rep2


title: 2_014

tag: segment type

tag: diagnosis

tag: disease state

tag: histology

tag: area


title: oral cavity with potential spreading, 20211116_Purdue 2_M337-A2_07

value: Mixed ereed


title: HeLa-R220A-atac-rep2


title: oral cavity with potential spreading, 20211116_Purdue 2_M286-B2_06

value: Golden Retriever


title: oral cavity with potential spreading, 20211116_Purdue 2_M286-A1_05


title: oral cavity with potential spreading, 20211116_Purdue 2_M172-B1_02

value: Cocker


title: oral cavity with potential spreading, 20211116_Purdue 2_M172-A1_01


title: HeLa-Aa63-550-atac-rep1


title: 2_013

value: Slide 2 (case 50-7)

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: 2_012

value: Full ROI

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: HeLa-R357H-atac-rep2

tag: tissue

tag: cell line

value: SUV420H1(Aa1-550)-R357H over-expression


title: 2_011

tag: slide id

tag: roi number

value: glioblastoma


title: oral cavity with potential spreading, 20211116_Purdue 2_M074-A1_11

tag: breed

value: Labrador

value: Oral melanoma


title: oral cavity stay local, 20211116_Purdue 1_L998-A1_04

source_name: oral cavity stay local

value: non specified

value: oral cavity stay local


title: HeLa-R357H-atac-rep1

tag: cell type

tag: genotype

tag: treatment


title: oral cavity with potential spreading, 20211116_Purdue 2_M337-B1_08

value: Mixed

tag: disease state

value: oral cavity with potential spreading


title: 2_010

tag: segment type

tag: diagnosis

value: psPD

tag: histology

value: Inflammatory

tag: area

tag: roi x coordinate


title: 2_009

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: oral cavity stay local, 20211116_Purdue 1_L983-A1_10

tag: tissue


title: oral cavity stay local, 20211116_Purdue 1_L794-A1_05


title: HeLa-R352A-atac-rep2

value: Uterus; Cervix

tag: cell line

value: HeLa

value: epithelial cell

value: SUV420H1(Aa1-550)-R352A over-expression


title: HeLa-R352A-atac-rep1


title: oral cavity stay local, 20211116_Purdue 1_L614-A1_09

tag: breed


title: oral cavity stay local, 20211116_Purdue 1_L600-A1_01


title: oral cavity stay local, 20211116_Purdue 1_L237-A1_03


title: 2_007

tag: slide id

tag: roi number

value: Hypercellular

tag: stitchedreads

tag: sequencingsaturation


title: HeLa-Y349A-atac-rep1

tag: cell type

tag: genotype

tag: treatment

value: SUV420H1(Aa1-550)-Y349A over-expression


title: 2_006

value: Slide 2 (case 50-7)

tag: segment type

value: Full ROI

tag: diagnosis

tag: disease state

tag: histology

tag: area


title: HeLa-S283L-atac-rep2

value: SUV420H1(Aa1-550)-S283L over-expression


title: oral cavity stay local, 20211116_Purdue 1_L194-A1_02


title: oral cavity with potential spreading, 20211116_Purdue 2_M074-C1_12

value: Labrador


title: Nc-4,Day14

city: Kunming

first: Yuan

last: Zhao

state: Yunnan

address: No. 212, Daguan Road, Xishan District, Kunming City, Yunnan Province, China

institute: 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China

data_processing:
The adapter and low-quality reads were filtered out through cutadapt (version 1.11). Clean reads were mapped to the reference genomes by Hisat2 (version 2.1.0), allowing up to two mismatches
These genes were subjected to alignment against public protein databases;NR(RefSeq non-redundant proteins). Featurecount(v1.6.0) was used for transcript abundance estimation and normalization of expression values as FPKM (Fragments per kilobase of transcript per million fragments mapped)
Differentially expressed genes were identified with edgeR with a filter threshold of FDR<0.05 and |log2FoldChange| > 1
Assembly: Oryctolagus_cuniculus

organism: Oryctolagus cuniculus

source_name: bone

extract_protocol:
total RNA was extracted using the RNAprep Pure Kit DP432 (TIANGEN Biotech Co.,Ltd., Beijing, China), following the manufacturer’s instructions.
All the RNA samples were assessed for their integrity using Qsep1 instrument. To construct RNA libraries with the MGIEasy mRNA Library Prep Kit, 3 μg of total RNA was used

value: bone

value: healthy control


title: Nc-3,Day14


title: oral cavity stay local, 20211116_Purdue 1_L031-A1_12

value: Non specified

value: Oral melanoma

value: oral cavity stay local


title: oral cavity stay local, 20211116_Purdue 1_L088-A1_07

value: non specified


title: Nc-2,Day14


title: 2_005

value: glioblastoma

value: psPD

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Nc-1,Day14

tag: tissue


title: 2_004

tag: slide id

tag: roi number

tag: trimmedreads


title: HeLa-S283L-atac-rep1

city: Shenzhen

value: Uterus; Cervix

tag: cell line

value: HeLa

tag: cell type


title: Inf-3,Day14

tag: treatment

value: infectious bone defect


title: oral cavity stay local, 20211116_Purdue 1_L700-A1_06

tag: breed


title: HeLa-S255F-atac-rep2

value: epithelial cell

tag: genotype

value: SUV420H1(Aa1-550)-S255F over-expression


title: 2_003

value: Slide 2 (case 50-7)

tag: segment type

tag: diagnosis

tag: disease state

value: Hypercellular

tag: stitchedreads

tag: sequencingsaturation


title: Inf-1,Day14


title: 2_002

value: Full ROI

tag: histology

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: 2_008

tag: slide id

tag: roi number

tag: alignedreads

tag: deduplicatedreads


title: HeLa-Y349A-atac-rep2

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: SUV420H1(Aa1-550)-Y349A over-expression


title: oral cavity stay local, 20211116_Purdue 1_L562-A1_08

tag: breed


title: HeLa-K258E-atac-rep2

tag: genotype

value: SUV420H1(Aa1-550)-K258E over-expression


title: oral cavity stay local, 20211116_Purdue 1_L080-A1_11

tag: disease state


title: HeLa-K258E-atac-rep1


title: HeLa-WTOE-atac-rep2

value: SUV420H1(Aa1-550) over-expression


title: 1_024

value: Slide 1 (case 12-10)

tag: segment type

tag: diagnosis

value: PD

value: Control

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 1_023

tag: histology

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: blank_1

organism: blank sample

source_name: blank sample

tag: slide id

value: No Template Control

tag: roi number

value: Blank

tag: alignedreads

tag: deduplicatedreads


title: Vehicle_mice_V2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Gene expression from WT mouse CXCL12-abundant reticular cells

hyb_protocol: Labeled fragments were hybridized to Applied Biosystems Clariom S Mouse Arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization Oven 645

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: vehicle mice ( allogenic transplant + PBS)

label_protocol: We used the Applied Biosystems GeneChipTM 3' IVT Pico Kit (catlog n.: 902789) for cDNA synthesis, amplification, cRNA synthesis, second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin according to manufacturer's instructions.

extract_protocol: RNA was isolated using the picopure RNA Isolation kit according to the manufacturer's instructions

treatment_protocol: after 4 days, injected i.p for 10 days with 100µl ROCK-Inhibitor 8mg/kg or 100µl PBS (vehihicle)

tag: cell type

tag: tissue

value: spleen

value: Wildtype


title: Vehicle_mice_V4

tag: genotype


title: 1_022

tag: segment type

value: glioblastoma

tag: disease state


title: HeLa-KO-atac-rep2

value: Uterus; Cervix

tag: cell line

value: HeLa


title: HeLa-S255F-atac-rep1

value: epithelial cell

tag: treatment

value: SUV420H1(Aa1-550)-S255F over-expression


title: Vehicle_mice_V3


title: blank_2

tag: diagnosis

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: ROCK_mice_R2

source_name: ROCK mice (allogenic transplant + ROCK-Inhib 8mg/kg)


title: 2_6_CD4_PanCK_WTA | 036 | CD4

city: Palo Alto

first: Audrey

last: Lee

address: 240 Pasteur Dr. 1500 BMI

institute: Stanford University

description: GeoMx DSP

data_processing:
FASTQ files generated upon sequencing were converted to Digital Count Conversion (DCC) files using the NanoString Technologies publicly available pipeline (v2.0.21) (GeoMx® NGS Pipeline (illumina.com)). Through the pipeline, individual probe alignment was performed using identification of read tag sequences (RTS), and duplicate counts of probes generated during the library preparation polymerase chain reaction were removed through evaluation of the probe unique molecular identifier (UMI) sequences.
Supplementary files format and content: DCC files
Library strategy: GeoMx DSP

molecule: polyA RNA

source_name: FFPE lung tissue section

extract_protocol:
Murine lungs were harvested, formalin-fixed and paraffin-embedded. FFPE tissues were sectioned for GeoMx digital spatial profiling (DSP).
For library preparation, Illumina i5 and i7 dual indexing primers were added to the oligonucleotide tags during PCR to uniquely index each AOI. Next generation sequencing (NGS) library preparation was performed according the NanoString Technologies published protocol (GeoMx DSP NGS Readout User Manual (nanostring.com)).

value: Lungs

value: CD4 and PanCK+ cells

tag: stained with

tag: slide

tag: region of_interest_id

value: ROI 036

tag: strain

value: unimmunized


title: 2_6_CD4_PanCK_WTA | 035 | PanCK

description: GeoMx DSP

value: PanCK

value: ROI 035


title: 2_6_CD4_PanCK_WTA | 036 | PanCK

description: GeoMx DSP


title: ROCK_mice_R4


title: 2_001

tag: slide id

value: Slide 2 (case 50-7)

tag: roi number

value: Full ROI

value: psPD

tag: histology

value: Hypercellular

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: ROCK_mice_R3

tag: cell type

tag: tissue

value: spleen

tag: genotype


title: 2_6_CD4_PanCK_WTA | 034 | CD4

description: GeoMx DSP

value: ROI 034

tag: treatment


title: 1_020

value: Slide 1 (case 12-10)

tag: segment type

tag: diagnosis

value: glioblastoma

tag: disease state

value: PD

value: Control

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 2_6_CD4_PanCK_WTA | 034 | PanCK

description: GeoMx DSP

tag: stained with

tag: slide

tag: region of_interest_id

tag: strain


title: HeLa-WT-atac-rep2

value: Uterus; Cervix

tag: cell line

value: HeLa

value: epithelial cell

value: wild type


title: Inf-2,Day14

value: bone

value: infectious bone defect


title: 2_6_CD4_PanCK_WTA | 033 | PanCK

description: GeoMx DSP

value: Lungs

value: CD4 and PanCK+ cells

value: PanCK

value: ROI 033

value: unimmunized


title: HeLa-WTOE-atac-rep1

value: SUV420H1(Aa1-550) over-expression


title: 1_019

tag: slide id

tag: roi number

value: Full ROI

tag: histology

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: HeLa-WT-atac-rep1

tag: tissue

tag: cell type

tag: genotype


title: 1_021

value: Slide 1 (case 12-10)

tag: segment type

tag: diagnosis

tag: disease state

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 2_6_CD4_PanCK_WTA | 032 | CD4

description: GeoMx DSP

tag: stained with

tag: slide

tag: region of_interest_id

value: ROI 032

tag: strain

tag: treatment


title: HeLa-KO-atac-rep1

tag: cell line


title: 2_6_CD4_PanCK_WTA | 031 | PanCK

description: GeoMx DSP

value: ROI 031


title: 2_6_CD4_PanCK_WTA | 033 | CD4

description: GeoMx DSP


title: 1_018

tag: slide id

tag: roi number

value: glioblastoma

value: PD

tag: histology

value: Control

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: 2_6_CD4_PanCK_WTA | 032 | PanCK

description: GeoMx DSP

tag: tissue

tag: cell type


title: 1_014

tag: segment type

tag: diagnosis

tag: disease state

value: Inflammatory

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 2_6_CD4_PanCK_WTA | 026 | PanCK

description: GeoMx DSP

tag: stained with

tag: slide

tag: region of_interest_id

value: ROI 026

tag: strain

tag: treatment


title: 2_6_CD4_PanCK_WTA | 027 | PanCK

description: GeoMx DSP

value: ROI 027


title: ROCK_mice_R1

value: spleen

tag: genotype

value: Wildtype


title: 2_6_CD4_PanCK_WTA | 031 | CD4

description: GeoMx DSP

value: Lungs

value: CD4 and PanCK+ cells


title: scRNA-seq_Irf4-/- NKP cell

city: HOUSTON

first: Xiaolong

last: Zhang

state: Texas

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

description: 10x Genomics

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

source_name: from bone marrow

extract_protocol:
WT and Irf4-/- mice bone marrow cells were staining with fluorochrome-conjugated antibodies, NKP cells were sorted from bone marrow cells by a cell sorter
Single cell Gene Expression Library was prepared according toChromium Next GEM Single Cell 3' Reagent Kits v3(10x Genomics). In Brief, single nuclei suspension, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: from bone marrow

tag: cell line

value: primary NKP cells

value: NKP cells


title: scRNA-seq_WT NKP cell

description: 10x Genomics


title: 1_013

tag: slide id

tag: roi number

value: Full ROI

tag: histology

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: 2_6_CD4_PanCK_WTA | 029 | PanCK

description: GeoMx DSP

tag: tissue

tag: cell type

value: PanCK

value: ROI 029


title: 1_017

value: Slide 1 (case 12-10)

tag: segment type

tag: diagnosis

tag: disease state

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 2_6_CD4_PanCK_WTA | 022 | PanCK

description: GeoMx DSP

tag: stained with

tag: slide

tag: region of_interest_id

value: ROI 022

tag: strain

tag: treatment


title: 2_6_CD4_PanCK_WTA | 028 | PanCK

description: GeoMx DSP

value: ROI 028


title: 2_6_CD4_PanCK_WTA | 025 | PanCK

description: GeoMx DSP

value: ROI 025


title: 1_015

tag: slide id

tag: roi number

value: glioblastoma

value: PD

tag: histology

value: Inflammatory

tag: area

tag: roi x coordinate

tag: roi y coordinate