title: Calu 1139


title: Calu 1142

status: Public on Sep 14 2021

type: SRA

city: Halifax

first: Paola

last: Marignani

state: Nova Scotia

address: 5850 College Street, Tupper Medical Building

department: Biochemistry & Molecular Biology

country: Canada

institute: Dalhousie University

library_source: transcriptomic

data_processing:
Basecalling performed using Real-Time Analysis (RTA) version 2.0
Fluidigm mRNA Sequencing High Throughput Demultiplexer Script (https://www.fluidigm.com/software) and Geneious Prime 2019.2.1 (https://www.geneious.com) were  used to demultiplex.
BBDuk Trimmer (a part of Bestus Bioinformatics Tools; RRID:SCR_016968) was used for quality trimming.
HISAT2 (RRID:SCR_015530) was used for read mapping to align processed reads to human reference genome (GRCh38.p13; NIH).
FeatureCounts (A part of Subread; RRID:SCR_009803) was used to count aligned reads per gene.
Genome_build: Human reference genome (GRCh38.p13; NIH)
Supplementary_files_format_and_content: Fastq containing 3'-end enriched scRNA-seq reads at single-end read

molecule: total RNA

organism: Homo sapiens

source_name: NSCLC

growth_protocol: Upon purchase, cells were stored at -80ºC freezer and then thawed just before directly loading to C1 HT mRNA-seq IFCs.

extract_protocol:
Individual cells were captured in chambers of Fluidigm HT mRNA-seq IFC. Total RNA extraction and preamplification of synthesized cDNAs were performed in Fluidigm C1 systems using the script of 'mRNA Seq HT:RT & Amp (1912x)’.
A total of 1,600 3'-end enriched scRNA-seq libraires (400 libraries per cell line) were constructed using Nextera XT index Kit v2 Set A/B and Nextera XT DNA library preparation kits.
3'-end enriched scRNA-seq using Fluidigm C1 system

treatment_protocol: Untreated

tag: tumour type

value: Lung adenocarcinoma

tag: cell type

value: Epithelial


title: Calu 1138


title: Calu 1137


title: Calu 1151


title: WT no drug rep1

city: Chapel Hill

first: Paul

middle: O

last: Grant

state: NC

address: 3105 Neuoscience Research Building

department: BARC

country: USA

institute: UNC SOM

data_processing:
Reads were  demultiplexed using the bcl2fastq.gz v2.2 conversion software (Illumina, RRID: SCR_015058).
The reads were adapter- and quality-trimmed using BBDuk and the optical duplicates removed using Clumpify, all part of the BBTools suite (RRID: SCR_016968).
Reads were aligned to either EV-A71 WT or Y276H variant reference genomes using bowtie2 (RRID: SCR_016368).
Unaligned reads were processed via BBMap
Genome_build: (GenBank) JN544419.1
Supplementary_files_format_and_content: The tsv (Table separated values) files contain the start and stop positions, the length and the nature of identified mutations for each sample. Scores are also given in order to appreciate the relevance of the mutations.

molecule: polyA RNA

source_name: Enterovirus A71-inefected RD cells

growth_protocol: RD cells were seeded in a 96-well tissue culture plate at 3.0 x 104 cells/well and incubated overnight at 37°C/5% CO2.

extract_protocol:
Total RNA was isolated with Direct-zol-96 RNA purification kit (Zymo Research) following manufacturer’s instructions. The recommended in-column DNase I treatment was also conducted to remove genomic DNA. Purified RNA was quantified with a microplate reader (Tecan M200 Infinite Pro) using the Quant-iT RNA assay kit (ThermoFisher). Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs).
Sequencing libraries were prepared using the NEBNext Ultra II RNA Library preparation kit for Illumina (New England Biolabs) and the pooled library was loaded in a NextSeq500/550 Mid Output kit v2.5 (Illumina) for sequencing in a NextSeq500 (151 cycles, 8 nucleotides of index).

treatment_protocol: RD cells were treated with T-1106 for 3 h before infection. T-1106-treated cells were then infected at an MOI of 10 with EV-A71-C2-MP4 in triplicate. Infection proceeded until cytopathic effect was observed (48 h.p.i.).

tag: cell line

value: RD cells (ATCC CAT#CCL-136, RRID:CVCL_1649)

tag: genotype

value: WT

tag: treatment

value: no drug


title: WT no drug rep2


title: WT no drug


title: WT 600 µM T-1106 rep1


title: WT 400 µM T-1106


title: WT 400 µM T-1106 rep2


title: WT 400 µM T-1106 rep1


title: WT 600 µM T-1106


title: HCA2 cell hAAT [R056]

city: Gainesville

first: Lei

last: Zhou

address: 2033 Mowry Rd, CGRC 261

institute: University of Florida

description:
Whole cell extraction
mRNA
AAT2
HCA2count.csv
HCA2Seq_DESeq2.csv
HCA2Seq_DESeq2_significant.csv

data_processing:
Illumina software used for basecalling. Quality assessment performed with FastQC.
Reads were mapped to dm6 or hg19 using tophat with default parameters.
Normalized expression value and differentially expressed genes were identified with CuffLinks and CuffDiffs.
Count data were further processed using DESeq2 to identify differentially expressed genes.
Genome_build: dm6 (Release 6 plus ISO1 MT), hg19 (GRCh37)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include un-normalized counts.
Supplementary_files_format_and_content: *.csv: Comma-separated text files.

source_name: HCA2 cell hAAT

growth_protocol: The UAS-hAAT flies were used for recombination with the lsp2-Gal4 flies to generate flies with genotype lsp2-Gal4:UAS-hAAT. The hAAT flies and genetic background matched control flies were incubated for 30-35 days for RNA-seq analysis. HCA2 cells were subjected to 10 Gy (2.56 Gy/min) of X-irradiation to introduce senescence, followed by 7-day incubation without interruption for senescence completion. The senescent cells were treated either with 2mg/mL hAAT or 1XPBS for 5 days.

extract_protocol: The RNA extracted for both Drosophila and HCA2 samples were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, Cat #: RS-122-2101).

value: 2mg/mL hAAT


title: HCA2 cell vehicle [R054]

description:
Whole cell extraction
mRNA
Ctr2
HCA2count.csv
HCA2Seq_DESeq2.csv
HCA2Seq_DESeq2_significant.csv

source_name: HCA2 cell vehicle


title: HCA2 cell vehicle [R053]

description:
Whole cell extraction
mRNA
Ctr1
HCA2count.csv
HCA2Seq_DESeq2.csv
HCA2Seq_DESeq2_significant.csv


title: HCA2 cell hAAT [R055]

description:
Whole cell extraction
mRNA
AAT1
HCA2count.csv
HCA2Seq_DESeq2.csv
HCA2Seq_DESeq2_significant.csv


title: TZM-bl_control_1

city: Moscow

first: Sergei

last: Funikov

state: Moscow

address: Vavilov str. 32

country: Russia

institute: Engelhardt Insitute of Molecular Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Preprocessing of data was performed using a PPLine script that includes Trimmomatic for the adapter, length and quality trimming, STAR for mapping reads to the human genome (hg38.97), and HTSeq-count for calculation of read counts aligned on genes
Genome_build: hg38.97
Supplementary_files_format_and_content: reads counts were made by feature counts

source_name: cell culture

extract_protocol:
Total RNA was extracted using the Extract RNA reagent (Evrogen). The concentration of RNA was measured with a Qubit Fluorometer (Invitrogen). The quality of RNA was determined with an Agilent BioAnalyzer 2100 using an RNA 600 nano kit. The RNA Integrity Number (RIN) of all RNA samples was not less than 8.
PolyA enriched libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.
Seventy-five bp single-end sequencing was conducted on an Illumina NextSeq 500 platform.

value: TZM-bl

value: original cells


title: Calu 1169


title: WT 600 µM T-1106 rep2


title: SW620B8_PSMB8-mCherry_1

value: mCherry knock-in cells


title: U937B8_PMSB8-mCherry_2


title: U937_control_2


title: U937_control_3


title: U937B8_PMSB8-mCherry_4


title: TZM-blB8_PSMB8-mCherry_1


title: U937_control_1


title: U937B8_PMSB8-mCherry_1


title: TZM-bl_control_2


title: SW620_control_2


title: U937B8_PMSB8-mCherry_3


title: TZM-blB8_PSMB8-mCherry_3


title: SW620_control_1


title: HepG2B8_PMSB8-mCherry_1


title: HepG2B8_PMSB8-mCherry_3


title: HepG2B8_PMSB8-mCherry_2


title: HepG2_control_1


title: HepG2_control_2


title: H460 774


title: H460 771


title: H460 769


title: H460 773


title: H460 772


title: H460 770


title: H460 768


title: H460 766


title: H460 765


title: H460 758


title: H460 756


title: H460 764


title: H460 763


title: H460 757


title: TZM-blB8_PSMB8-mCherry_2


title: H460 750


title: H460 752


title: H460 760


title: H460 751


title: H460 759


title: H460 761


title: H460 755


title: H460 754


title: H460 753


title: H460 749


title: SW620B8_PSMB8-mCherry_2


title: H460 748


title: H460 744


title: H460 747


title: H460 745


title: H460 743


title: H460 742


title: H460 741


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title: H460 435


title: H460 427


title: H460 448


title: H460 426


title: H460 428


title: Calu 1135


title: H460 430


title: Calu 1136


title: Calu 1134


title: Calu 1133


title: Calu 1130


title: Calu 1129


title: Calu 1128


title: Calu 1126


title: Calu 1127


title: Calu 1125


title: Calu 1122


title: H460 431


title: Calu 1124


title: Calu 1120


title: Calu 1121


title: Calu 1123


title: Calu 1117


title: Calu 1118


title: Calu 1115


title: Calu 1119


title: Calu 1114


title: Calu 1116


title: Calu 1113


title: Calu 1110


title: Calu 1132


title: Calu 1109


title: Calu 1111


title: Calu 1108


title: Calu 1105


title: Calu 1131


title: Calu 1104


title: Calu 1103


title: Calu 1106


title: A549 391


title: A549 389


title: A549 388


title: A549 387


title: A549 390


title: A549 385


title: A549 384


title: A549 382


title: A549 386


title: A549 380


title: A549 379


title: A549 381


title: Calu 1107


title: A549 371


title: A549 374


title: A549 372


title: A549 377


title: Calu 1112


title: A549 370


title: A549 383


title: A549 378


title: A549 364


title: A549 369


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title: A549 366


title: A549 363


title: A549 376


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title: A549 153


title: A549 170


title: db/db day 5 wound skin sodium butyrate replicate 4

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

description: dbdb_Day_0_Day_5_Vehicle_NaButyrate_fpkm_GEO_Upload.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was done using Hisat2
Cufflinks was used to assemble the transcripts
Cuffmerge was used to merged all the transcripts
Cuffdiff was for differential expression analysis
Genome_build: mm10 and grch38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Mus musculus

source_name: total skin

extract_protocol:
Total RNA from skin and macrophages was isolated using Rneasy kit (Qiagen)
rRNA removal was performed either by Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific). rRNA depleted RNA was subjected to preparation of Illumina compatible NEBNext Ultra II Directional RNA Library Preparation kit (NEB).

tag: strain

value: db/db

tag: tissue

value: total skin


title: A549 147


title: db/db day 5 wound skin sodium butyrate replicate 5


title: A549 149


title: A549 150


title: A549 145


title: db/db day 5 wound skin sodium butyrate replicate 1


title: db/db day 5 wound skin sodium butyrate replicate 2


title: db/db day 5 wound skin sodium butyrate replicate 3


title: A549 163


title: A549 151


title: A549 143


title: db/db day 5 wound skin vehicle replicate 3


title: db/db day 5 wound skin vehicle replicate 5


title: A549 144


title: A549 146


title: A549 148


title: db/db day 5 wound skin vehicle replicate 4


title: A549 141


title: A549 142


title: db/db day 5 wound skin vehicle replicate 2


title: db/db day 5 wound skin vehicle replicate 1


title: A549 138


title: db/db day 0 wound skin sodium butyrate replicate 5


title: A549 139


title: db/db day 0 wound skin sodium butyrate replicate 3


title: A549 140


title: db/db day 0 wound skin sodium butyrate replicate 2


title: db/db day 0 wound skin sodium butyrate replicate 4


title: db/db day 0 wound skin vehicle replicate 5


title: A549 136


title: A549 137


title: A549 135


title: A549 133


title: db/db day 0 wound skin vehicle replicate 2


title: db/db day 0 wound skin vehicle replicate 4


title: A549 134


title: A549 132


title: A549 131


title: db/db day 0 wound skin sodium butyrate replicate 1


title: A549 128


title: Tamo_E2_3

city: Hangzhou

first: Xinyue

last: Guo

state: Zhejiang

address: 1 Xueshi Road

department: Department of Gynecology

country: China

institute: Women's hospital, School of Medicine, Zhejiang University

data_processing:
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Then these libraries were sequenced on the Illumina sequencing platform ( Illumina Novaseq 6000) and 150bp paired-end reads were generated.
Cutadapt software was used to remove the reads that contained adaptor contamination.
The reads containing poly-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read count and FPKM values for each Sample

source_name: P815 mouse mastocytoma cell line

growth_protocol: Mouse mastocytoma cell line P815 was cultured with RPMI-1640 (Gibco, USA) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
total RNA was extracted by TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: P815 cells (three duplicate samples in each group) were transfected with ESR1-specific shRNA vectors (SH) or the negative control vectors (NC) and treated with β-estradiol for 24 hours.  Other replicates were β-estradiol treatment with the administration of estrogen receptor inhibitors Tamoxifen or ICI-182780 for 24 hours.

value: mouse mastocytoma cell

value: treated with tamoxifen and Beta-estradiol for 24 hours


title: Tamo_E2_2


title: A549 129


title: A549 127


title: Tamo_3

value: treated with tamoxifen for 24 hours


title: Tamo_E2_1


title: Tamo_2


title: Tamo_1


title: A549 126


title: db/db day 0 wound skin vehicle replicate 3


title: SH_E2_3

value: transfected with mouse ESR1-specific shRNA and treated with Beta-estradiol for 24 hours


title: A549 124


title: SH_3

value: transfected with mouse ESR1-specific shRNA


title: SH_E2_2


title: peripheral blood Temra from healthy donor pTemra_004

city: Hwasun-eup, Hwasun-gun

first: Jae-Ho

last: Cho

state: Jeollanam-do

address: 264, Seoyang-ro

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY

description:
peripheral blood Temra from healthy donor
transcripts_1.fa.gz
raw_gene_counts_1.txt

data_processing:
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads whose average quality scores of each read is less than 20.The whole filtering process was performed using the in-house scripts.
Filtered reads were mapped to the human reference genome (Ensembl release 72, Flicek P. et al., 2013) using the aligner Tophat (Trapnell C et al. 2012).
Genome_build: Ensembl release 72
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: peripheral blood

growth_protocol: ex vivo

extract_protocol:
Tumor tissues were received directly from the operating room and processed immediately. Tissues were chopped into small pieces, then digested with 0.5 mg/ml Collagenase IV (Gibco) and 200 U DNase I (Roche) in a 37ºC magnetic stirrer. TILs were purified from the digested tissues using Percoll (Cytiva). Blood samples were harvested in BD Vacutainer (BD Biosciences). PBMCs were purified using Lymphoprep (Alere Technologies).
Library was constructed using TruSeq RNA Sample Prep Kit (Illumina) and sequenced with an Illumina HiSeq2500 sequencer (Illumina) according to manufacturer's protocols.

treatment_protocol: ex vivo

tag: phenotype

value: CD8+ CD3+ CCR7- CD45RA+


title: peripheral blood Temra from healthy donor pTemra_006

description:
peripheral blood Temra from healthy donor
transcripts_3.fa.gz
raw_gene_counts_3.txt


title: peripheral blood Temra from healthy donor pTemra_005

description:
peripheral blood Temra from healthy donor
transcripts_2.fa.gz
raw_gene_counts_2.txt


title: SH_E2_1


title: A549 130

value: Lung adenocarcinoma


title: A549 122

value: Epithelial


title: NC_E2_3

value: transfected with negative control vectors and treated with Beta-estradiol for 24 hours


title: A549 120


title: SH_2


title: SH_1


title: peripheral blood Temra from NSCLC patient pTemra_003

description:
peripheral blood Temra from NSCLC patient
transcripts_3.fa.gz
raw_gene_counts_3.txt


title: A549 123


title: NC_2

value: transfected with negative control vectors


title: A549 121


title: peripheral blood Temra from NSCLC patient pTemra_002

description:
peripheral blood Temra from NSCLC patient
transcripts_2.fa.gz
raw_gene_counts_2.txt


title: NC_E2_2


title: NC_E2_1


title: peripheral blood Temra from NSCLC patient pTemra_001

description:
peripheral blood Temra from NSCLC patient
transcripts_1.fa.gz
raw_gene_counts_1.txt


title: NC_3


title: tumor infiltrating Temra from NSCLC patient tilTemra_003

description:
tumor infiltrating Temra from NSCLC patient
transcripts_3.fa.gz
raw_gene_counts_3.txt

source_name: primary tumor


title: db/db day 0 wound skin vehicle replicate 1


title: A549 125


title: NC_1


title: tumor infiltrating Temra from NSCLC patient tilTemra_002

description:
tumor infiltrating Temra from NSCLC patient
transcripts_2.fa.gz
raw_gene_counts_2.txt


title: A549 119


title: ICI_3

value: treated with ICI-182780 for 24 hours


title: A549 118


title: ICI_E2_3

value: treated with ICI-182780 and Beta-estradiol for 24 hours


title: ICI_E2_1


title: NGS02743_AIII.1_B-cell

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr

department: Dept. of Lab Medicine

institute: NIH Clinical Center

data_processing:
Demultiplexed reads were mapped to the hg19 genome using the splice-aware aligner Tophat (Trapnell et al., 2009)
Read counts were variance stabilized (normalized) using DeSeq2
Genome_build: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary_files_format_and_content: File with raw counts for every gene and every sample

source_name: Blood

extract_protocol:
AmpliSeq for Illumina Transcriptome Human Gene Expression panel
Targeted Sequencing Library (>20,000 human RefSeq genes)

value: naive B-cells

value: AIOLOS N160S / AIOLOS wild-type

tag: disease state

value: primary immunodeficiency


title: ICI_E2_2


title: tumor infiltrating Temra from NSCLC patient tilTemra_001

description:
tumor infiltrating Temra from NSCLC patient
transcripts_1.fa.gz
raw_gene_counts_1.txt


title: A549 117


title: ICI_1


title: A549 116


title: mTBI2

city: San Francisco

first: Fiorella

middle: Carla

last: Grandi

address: 1650 Owens Street

institute: Gladstone

description: nuclear RNA

data_processing:
Library strategy: snRNA-seq
Cellranger (4.0.0) mkfastq was used to perform sample demultiplexing and generate fastq files
Cellranger (4.0.0) count was used to generate the single nucleus gen-UMI counting. Reads were mapped to mm10 (GENCODE vM23/Ensembl 98, from 10x).
The resulting data matrix was analyzed uisng Seurat (v3). Doublets were removed from each GEM reaction using DoubletFinder. In addition to doublets, we removed nuclei with more than 1% expression of mitochondrial RNAs. Expression was log scale normalized and the top 200- features were used for PCA and downstream clustering and UMAP. Harmony was used to combine the separate repliates.
Clusters were called using FindClusters (Seruat) and were annotated manually using key lineage markers.
For visualization of expression on UMAP projections, RNA expression values were imputed using Markov Affinity-based Graph Imputation of cells (MAGIC).
Genome_build: mm10
Supplementary_files_format_and_content: hdf5 files contain gene expression counts on a per nucleus basis for each sample; values represent filtered droplets (i.e. empty droplets removed) derived from cellranger
Supplementary_files_format_and_content: barcode.tsv.gz files contains list of barcodes for each sample; for import into Seurat
Supplementary_files_format_and_content: features.tsv.gz files contains list of features (genes) for each sample; for import into Seurat
Supplementary_files_format_and_content: matrix.mtx.gz files contains values of each feature for each barcode for each sample; for import into Seurat

source_name: micro-dissections of the nRT and the adjacent relay thalamic nuclei

extract_protocol:
Nuclei were isolated from the nRT/thalamus. Tissue samples were homogenized with 10 strokes of the loose "A" pestle and 15 strokes of the tight "B" sized pstle. The lysate was passed through a 40uM FlowMi strainer and nuclei were peleted at 500 RCF at 4C. Pelleted nuclei were resuspended in the homogenization buffer, purified using an iodixanol gradient and immidiately used for snRNA-seq.
SnRNA-seq libraries were processed using the Chromium Next GEM Single Cell 3'v3 library kit with dual indexing according ot the manufactuere's specifications. The chromium was loaded with 9,9000 nuclei.One GEM rxn was used for each sample. Replicate 1 and 2 nuclei were processed on different chromium runs.  Libraries were pooled based on their molar concentrations and sequenced on an Illumina NovaSeq 6000 system using an S1 flow cell and v1 300 cycle Reagent kit with 28 cycles for read 1, 90 cycles for read 2, 10 cycles for index1 (i7) and 10 cycles for index2 (i5).

treatment_protocol: controlled cortical impact; mild traumaic brain injury was perfomed with a CCI device using the following parameters: 3mm tip diamtere, 15 angle, depth 0.8mm from the dura, velocity 3m/s and dwell time 100ms. Sham animals recviered identical surgical prep and cranotomy, but the injury was not delivered.

value: reticular thalamic nucleus

value: WT

value: mild traumatic brain injury


title: NGS02740_HC1_B-cell

description: healthy control 1

value: AIOLOS wild-type / AIOLOS wild-type

value: apparently healthy


title: A549 115


title: A549 114


title: mTBI1

description: nuclear RNA


title: sham2

description: nuclear RNA

value: sham


title: A549 113


title: PBS [Spatial transcriptomics]

city: Boston

first: David

last: Zemmour

address: 77 avenue Louis Pasteur

institute: Harvard Medical Schol

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20.
Space Ranger software v1.0.0 (10X Genomics) was used for reads alignment, tissue detection, fiducial detection, and barcode/UMI counting with default parameters to obtain possorted_genome_bam.bam and processed data files
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix.csv, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5, tissue_hires_image.png
Supplementary_files_format_and_content: count matrix for all cells from all samples in matrix.mtx. Cell ID in barcodes.tsv. Genes in genes.tsv. Metadata in metadata.tsv

source_name: whole slide

extract_protocol:
WT mice were injected with either PBS or LCWE and one week later, heart tissues collected, embedded in OCT and sectioned on a cryostat at a thickness of 10µm. Tissue was enzymatically permeabelized accroding to the Visium protocol.
RNA libraries were prepared for sequencing using the Visium Spatial 3' V1, 10x Genomics protocol. Sequencing was done with NovaSeq 6000 using a custom paired-end sequencing protocol, consisting of: read 1, 28 cycles; index 1, 10 cycles; index 2, 10 cycles; read 2, 120 cycles.

tag: condition

value: PBS

value: heart

value: Visium, Spatial 3' V1, 10x Genomics


title: sham1

description: nuclear RNA


title: A549 112

value: Lung adenocarcinoma

value: Epithelial


title: NGS02738_2_HC3_B-cell

description: healthy control 3


title: PBS

data_processing:
CellRanger software (v3.0.2) (10X Genomics) (default parameters) mm10 genome
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file with cell x genes count matrix
Supplementary_files_format_and_content: count matrix for all cells from all samples in matrix.mtx. Cell ID in barcodes.tsv. Genes in genes.tsv. Metadata in metadata.tsv

source_name: all cells

extract_protocol:
WT mice were injected with PBS or LCWE and two weeks later, the abdominal aorta (from the left renal artery to the aortic bifurcation) was collected on ice cold PBS. The PBS group was composed of a pool of 9 abdominal aortas, whereas the LCWE group was composed of a pool of 7 abdominal aortas. A cell suspension of the freshly collected abdominal aorta tissues was prepared with the gentleMACS OCTO Dissociator with Heaters (Miltenyi Biotech) using the program “37_m_TDK2” and the Multi Tissue Dissociation Kit 1 (Miltenyi Biotech), according to the manufacturer’s instructions. The resulting cell suspension was washed in cold complete RPMI with 10% FBS and filtered through a 70μM cell strainer. For downstream application of scRNA-seq, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotech) according to the manufacturer’s instructions and viability was assessed with ViaStain AOPI staining solution (Nexcelom Bioscience)
RNA libraries were prepared for sequencing using standard 10X Genomics Single Cell 3′ Reagent Kit (V3 chemistry)

tag: condiition

value: aorta


title: NGS02739_AIII.1_B-cell


title: ICI_2

value: mouse mastocytoma cell

value: treated with ICI-182780 for 24 hours


title: LCWE [Spatial transcriptomics]

value: LCWE


title: NGS02738_1_HC3_B-cell

description: healthy control 3

value: naive B-cells


title: M72h rep3

city: Shanghai

first: Wenju

last: Liu

address: 1239  siping road

institute: University of Tongji

data_processing:
Illumina NovaSeq 6000 System was used for basecalling and 150 bp paired-end reads were generated.
Sequenced reads were trimed for adaptor and low-quality sequence using cutadapt v1.18 and then mapped to mm10 whole genome using HISAT2 v2.1.0 with parameters "--dta-cufflinks --no-discordant"
gene expression levels were quantified as FPKM by stringtie V1.3.4d.
Differences in expression were determined using Cuffdiff vV1.3.0.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted using the RNAiso Reagent (TaKaRa, Japan) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manual instructions and index codes were added to attribute sequences to each sample. Library fragments were purified with AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The 18 mice were divided into six groups, the Control group, the 10 min group, the 1 h group, the 6 h group, the 24 h group, and the 72 h group. They were anaesthetised by intraperitoneal injection of sodium pentobarbital (50 mg/kg). The MI model was performed by ligation of the proximal left anterior descending coronary artery.

tag: age

value: 8 weeks old


title: M24h rep2


title: M24h rep3


title: M24h rep1


title: NGS02737_2_HC2_B-cell

description: healthy control 2


title: M72h rep1


title: A549 108


title: NGS02737_1_HC2_B-cell

description: healthy control 2


title: NGS02736_HC1_B-cell

description: healthy control 1


title: A549 110


title: A549 111


title: NGS02677_HC1_T-blast

description: healthy control 1

value: T-cell blasts


title: NGS02678_HC2_T-blast

description: healthy control 2


title: LCWE

value: Single Cell 3′ Reagent Kit (V3 chemistry)


title: M6h rep3


title: M10m rep3


title: M1h rep3


title: M6h rep1


title: A549 109


title: M10m rep2


title: M72h rep2


title: A549 105


title: M10m rep1


title: M1h rep2


title: M1h rep1


title: M6h rep2


title: A549 104


title: A549 107


title: Mcon rep3


title: NGS02668_AIII.1_T-blast

value: AIOLOS N160S / AIOLOS wild-type

value: primary immunodeficiency


title: Mcon rep1


title: NGS02673_HC4_T-blast

description: healthy control 4

value: AIOLOS wild-type / AIOLOS wild-type

value: apparently healthy


title: Mcon rep2


title: NGS02667_AII.2_T-blast


title: A549 103


title: A549 102


title: NGS02665_HC3_T-blast

description: healthy control 3


title: Mtb_bcg_zdc_d15_2

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Sample demultiplexing, barcode processing, and single-cell 5’ counting was performed using the Cell Ranger Single-Cell Software Suite (10x Genomics, version 3). Cell ranger cell count was used to align samples to the reference mm10 genome, quantify and filter reads with a quality score below 30. The Seurat package (Butler et al., 2018) in R was used for subsequent analysis. Cells with mitochondrial content greater than 10% were removed. Filtered data were normalized using a scaling factor of 10,000 nUMI was regressed with a negative binomial model, and data was log transformed. The highly variable genes were selected using the FindVariableFeatures. Principal component analysis was performed using the top 3000 variable genes. Clustering was performed using the FindClusters function. UMAP was used to project cells into two dimensions using 15 first principal components. For T cell re-clustering we chose clusters that were identified as T cells (CD3+). For these 24758 cells we performed normalization, found variable genes and performed PCA, UMAP and clustering as described above. All visualization was done with ggplot2 R package (Wickham, 2016), heatmaps were done with Phantasus website (https://artyomovlab.wustl.edu/phantasus/). For TCR samples, sample demultiplexing and barcode processing was performed using the Cell Ranger Single-Cell Software Suite (10x Genomics). Cell Ranger VDJ v3 was used to align reads to the reference genome (vdj_GRCm38_alts_ensembl) and assemble TCRs. For downstream analysis, only TCRs with 1 productive rearrangement for TCR chain and 1 productive rearrangement for TCR chain were selected. Frequencies of clonotypes were calculated based on number of cells that pass quality control as described above and share both TCR and TCR nucleotide sequences. Gini coefficient was computed with "gini" function from tcR R package. To infer motifs, TCRdist tool was used (Dash et al., 2017). Motifs were visualized with ggseqlogo R package.
Genome_build: mm10

extract_protocol:
Lung single-cell suspensions from vaccinated or Mtb-infected mice were isolated as previously described (Griffiths et al., 2016). Briefly, mice were euthanized with CO2 and lungs were perfused with heparin in saline. Lungs were minced and incubated in Collagenase/DNAse for 30 minutes at 37°C. Lung tissue was pushed through a 70 µm nylon screen to obtain a single cell suspension. Red blood cells were lysed and the cells were resuspended in suitable media or buffer for further use.
Isolated total lung single cell suspensions were enriched for live cells using dead cell depletion kit according to manufacturer’s instruction (Milteny Biotec) and subjected to droplet-based massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ (v3) Reagent Kit as per manufacturer’s instructions (10x Genomics). Briefly, cell suspensions were loaded at 1,000 cells/uL with the aim to capture 10,000 cells/lane. The 10x Chromium Controller generated GEM droplets, where each cell was labeled with a specific barcode, and each transcript labeled with a unique molecular identifier (UMI) during reverse transcription. The barcoded cDNA was isolated and removed from the BSL-3 space for library generation. The cDNA underwent 11 cycles of amplification, followed by fragmentation, end repair, A-tailing, adapter ligation, and sample index PCR as per the manufacturer’s instructions. Libraries were sequenced on a NovaSeq S4 (200 cycle) flow cell, targeting 50,000 read pairs/cell.

treatment_protocol: Lung cells were isolated from Mtb-infected unvaccinated mice (Unvac), Mtb-infected BCG vaccinated mice (Vac), and Mtb-infected BCG vaccinated mice that received Z-DC transfer (Vac+Z-DC). M. bovis Bacille Calmette–Guerin (BCG Pasteur, Source: Trudeau Institute) and Mtb W. Beijing strain, HN878 (BEI Resources) were grown to mid-log phase in Proskauer Beck medium containing 0.05% Tween 80 and frozen in at -80º C. Mice were vaccinated with 1 X 106 colony forming units (CFU) BCG subcutaneous and 4 weeks later infected with ~100 CFU Mtb HN878 via aerosol route using a Glas-Col airborne infection system. At given time points following infection, lungs were collected, homogenized and the tissue homogenates were plated following serial dilutions on 7H11 agar (BD bioscience) to assess bacterial burden (Griffiths et al., 2016). Bone marrow-derived dendritic cells (BMDC) and bone marrow-derived macrophages (BMDMs) were generated as previously described (Griffiths et al., 2016). Briefly, cells isolated from the femur and tibia were cultured at 1 X 106 cells/ml in 10 ml of complete DMEM (cDMEM) supplemented with 4% recombinant mouse GM-CSF (Peprotech, Rocky Hill, NJ, USA) at 37°C in 7.5% CO2. After 3 days, 10 ml of cDMEM supplemented with 4% mouse GM-CSF was added and incubation continued till day 7. At day 7, non-adherent cells (BMDCs) were collected, counted, plated at 2 X 106 cells/ml in cDMEM and rested overnight at 37°C in 7.5% CO2 following which BMDCs were stimulated overnight with Ag85B (20 µg/ml) (New England Peptide) and Zymosan (25 µg/ml) (Sigma) to induce maturation and activation. Mature pulsed BMDCs were collected, washed and 1 X 106 cells in 50 ul PBS were instilled via intratracheal (IT) route at -1 and +4 dpi. For all the adoptive transfer of Z-DCs, Il10-/- BMDC were used.

tag: disease

value: Mycobacterium tuberculosis (Mtb)

value: dematricized lung cells

tag: infection strain

tag: cfu delivered

tag: vaccination

value: 1x10^6 CFU BCG


title: NGS02664_AIII.1_T-blast


title: A549 101

value: Lung adenocarcinoma


title: Mtb_bcg_zdc_d8_1

source_name: Mtb-infected BCG vaccinated mice that received Z-DC transfer


title: Mtb_bcg_2

source_name: Mtb-infected BCG vaccinated mice


title: Mtb_bcg_zdc_d15_1


title: NGS02663_AII.2_T-blast


title: A549 106

value: Epithelial


title: NGS02669_HC4_T-blast

description: healthy control 4


title: Mtb_unvaccinated_1

source_name: Mtb-infected unvaccinated mice


title: Mtb_bcg_1


title: Mtb_unvaccinated_2


title: Lgr5low-Itgb7 KO-4

first: Chen

last: Shiyang

address: Room 413, New biochemistry building, YueYang Road

institute: Shanghai Institute of Biochemistry and Cell Biology (CAS)

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
Itgb7-4-GFPlow

data_processing:
Basecalls performed using Real Time Analysis 3.4.4
Sequenced reads were trimmed for adaptor sequence and low-quality sequence
For mapping analysis using tophat2 software,tophat2 -a 8 -m 0 -i 50 -I 500000 -N 2 --read-gap-length 2 --read-edit-dist 2 -g --library-type fr-unstranded -p 8 -G -r 50 --microexon-search;For FPKM valuse analysis using RSEM software,RSEM --paired-end  --bowtie2 -p 8 --bowtie2-path.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: small intestine

extract_protocol:
The small intestine was dissected, flushed with cold PBS, opened longitudinally and cut into small fragments roughly 2-4 mm in length. Intestine fragments were washed twice with cold PBS and then incubated with 20 mM EDTA-PBS on ice for 30 min. The tissue was then shaken vigorously, and the supernatant was collected as fraction1 in a new conical tube. The tissue was incubated in fresh EDTA-PBS and a new fraction was collected every 30 min. Fractions were collected until the supernatant consisted almost entirely of crypts. The final fraction was filtered through a 70-μm cell strainer (enriched for crypts), washed twice in PBS, centrifuged at 300 g for 3 min, and dissociated with TrypLE Express (Invitrogen) at 37 ºC for 5 min. The single-cell suspension was then passed through a 40-μm cell strainer. Cells were stained with antibodies and gated on 7AAD- CD45- CD31-  TER119- EpCAM+, GFP high (stem cells) and GFP low (TA cells), and sorted by a BD AriaIII cell sorter. Sorted samples were processed by extracting RNA with RNeasy Micro Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: small intestine

value: Itgb7-/-  Lgr5-GFP

value: epithelial cell

tag: cell population

value: Lgr5-GFP low


title: NGS02659_HC1_T-blast

description: healthy control 1


title: A549 98

source_name: NSCLC

tag: tumour type


title: Lgr5high-Itgb7 KO -6

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
Itgb7-6-GFPhi

tag: cell type

value: Lgr5-GFP high


title: A549 96


title: Lgr5high-Itgb7 KO -5

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
Itgb7-5-GFPhi


title: NGS02661_HC3_T-blast

description: healthy control 3


title: Lgr5low-Itgb7 KO-3

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
Itgb7-3-GFPlow


title: adult bone marrow 1

city: Oxford

first: Supat

last: Thongjuea

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Raw sequencing data in the binary base call (BCL) format were demultiplexed. FASTQ files were then aligned to the human reference genome (GRCh38/hg38) using Cell Ranger software (version 3.0.1) from 10x Genomics. The CellRanger ‘‘count’’ standard pipeline was used to obtain the expression matrix of Unique Molecular Identifier (UMI) for each individual sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: MEX files were generated from the cellranger software. Cell information and UMI count were stored in the R object files.

source_name: CD34+ lineage negative HSPC

extract_protocol:
CD34+ lineage negative cells isolated by FACS for single cell RNA sequencing using the 10x Genomics 3' single cell platform.
Libraries were prepared as per the 10x Genomics Chromium Single Cell 3' Reagent kit user guide.

tag: sample type

value: Healthy donor


title: A549 99


title: Lgr5low-Itgb7 KO-5

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
Itgb7-5-GFPlow

tag: genotype


title: A549 97


title: paediatric bone marrow 2


title: Lgr5high-Itgb7 KO -4

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
Itgb7-4-GFPhi


title: Lgr5low-Itgb7 KO-2

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
Itgb7-2-GFPlow


title: A549 100


title: Lgr5high-Itgb7 KO -3

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
Itgb7-3-GFPhi


title: Lgr5low-WT-8

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
WT-8-GFPlow

value: Itgb7+/+  Lgr5-GFP


title: Lgr5high-Itgb7 KO -2

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
Itgb7-2-GFPhi


title: Lgr5low-Itgb7 KO-6

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
Itgb7-6-GFPlow


title: A549 94


title: A549 95


title: A549 93


title: Lgr5low-WT-7

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
WT-7-GFPlow


title: paediatric bone marrow 1


title: Lgr5low-WT-6

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
WT-6-GFPlow


title: NGS02660_HC2_T-blast

description: healthy control 2

value: T-cell blasts


title: fetal bone marrow 2


title: Lgr5low-WT-3

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
WT-3-GFPlow


title: Lgr5high-WT-7

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
WT-7-GFPhi


title: A549 92


title: fetal bone marrow 1


title: A549 91


title: Lgr5low-WT-1

description:
Lgr5-GFP_low_Itgb7_KO_vs_WT_count.txt
WT-1-GFPlow


title: Lgr5high-WT-3

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
WT-3-GFPhi


title: A549 90


title: A549 89


title: early fetal liver 2


title: Lgr5high-WT-6

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
WT-6-GFPhi


title: fetal liver 1


title: Lgr5high-WT-1

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
WT-1-GFPhi


title: A549 88


title: T2

city: Istanbul

first: Ozgur

last: Cakir

address: Vezneciler

country: Turkey

institute: Istanbul University

data_processing:
SOAPnuke software, http://soap.genomics.org.cn
BWA (Burrows-Wheeler Aligner) used for genome reference, BOWTIE used for gene reference
RSAM software
Possion Distribution method / Noiseq package / EBSeq package
http://www.yeastgenome.org/help/analyze/go-term-finder
Supplementary_files_format_and_content: xls files with FPKM values and fold change values

organism: Schizosaccharomyces pombe

source_name: wild type cells

growth_protocol: Initial cell density was 5 × 104 cells/ml and cells were grown up to mid-log phase in 25 ml of medium in a 100 ml flask at 30°C with orbital shaking at 180 rpm.,

extract_protocol:
Total RNAs were isolated from mid-log cells using GeneJET RNA Purification Kit (Thermo Fisher Scientific) following the manufacturer's instructions for each sample. The purity and quantity of RNAs were measured using a Nanodrop 2000 spectrophotometer (Nanodrop Technologies, USA). Total RNAs were then used in further analysis. Three replicates were used for each sample and replicates were then pooled for sequencing according to their concentrations.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. The library could be sequenced using Illumina HiSeq.

treatment_protocol: 3%, 5% and 8% glucose added to media from the beginning

tag: growth phase

value: mid-log

tag: treatment

value: grown in synthetic dextrose with 5percent  glucose


title: A549 87


title: early fetal liver 1


title: s9

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were firstly aligned to several mouse reference databases including mm10 mouse genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using HISAT alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript.  After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: mm10
Supplementary_files_format_and_content: txt files with read counts

source_name: kidney

extract_protocol: Paired-end sequencing at 150bp read length was performed on a HiSeq 4000 (Illumina, San Diego CA)

tag: diagnosis

value: Remission

tag: time

tag: tissue

value: kidney

tag: strain

value: NZB/W F1


title: s8


title: A549 86

data_processing:
Basecalling performed using Real-Time Analysis (RTA) version 2.0
Fluidigm mRNA Sequencing High Throughput Demultiplexer Script (https://www.fluidigm.com/software) and Geneious Prime 2019.2.1 (https://www.geneious.com) were  used to demultiplex.
BBDuk Trimmer (a part of Bestus Bioinformatics Tools; RRID:SCR_016968) was used for quality trimming.
HISAT2 (RRID:SCR_015530) was used for read mapping to align processed reads to human reference genome (GRCh38.p13; NIH).
FeatureCounts (A part of Subread; RRID:SCR_009803) was used to count aligned reads per gene.
Genome_build: Human reference genome (GRCh38.p13; NIH)
Supplementary_files_format_and_content: Fastq containing 3'-end enriched scRNA-seq reads at single-end read

extract_protocol:
Individual cells were captured in chambers of Fluidigm HT mRNA-seq IFC. Total RNA extraction and preamplification of synthesized cDNAs were performed in Fluidigm C1 systems using the script of 'mRNA Seq HT:RT & Amp (1912x)’.
A total of 1,600 3'-end enriched scRNA-seq libraires (400 libraries per cell line) were constructed using Nextera XT index Kit v2 Set A/B and Nextera XT DNA library preparation kits.
3'-end enriched scRNA-seq using Fluidigm C1 system


title: fetal liver 2


title: Lgr5high-WT-8

description:
Lgr5-GFP_high_Itgb7_KO_vs_WT_count.txt
WT-8-GFPhi


title: A549 85


title: s4


title: T3

value: grown in synthetic dextrose with 8percent  glucose


title: CRS_3RU

type: RNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genomestudio

label: biotin

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

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

value: nephritis

tag: time point


title: CRS_3LL


title: CRS_5RU


title: CRS_1RL


title: CRS_2LU


title: CRS_5O


title: A549 84

value: Lung adenocarcinoma


title: T1

value: grown in synthetic dextrose with 3percent  glucose


title: s3


title: A549 82

value: Epithelial


title: A549 83


title: RX11RU_repeat


title: RX12RU_repeat


title: A549 81


title: RX_10RL


title: HIL_5RU


title: A549 80


title: ZT0LU_repeat

value: Young


title: RX_8RU


title: ZT12RU_repeat


title: RX_9RL


title: CRS_1LL


title: CRS_1O


title: A549 79


title: CRS_2RL


title: CRS_2RU


title: A549 77


title: HIL_5LL


title: A549 78


title: s14


title: s12


title: CRS4O


title: mouse_protease_inhib_bc11

city: Vienna

first: Vera

last: Vorstandlechner

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38/mm10) and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: Genome_build: GrCh38/mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids), features.tsv: (gene ids)

source_name: scar 8 weeks bc11

extract_protocol:
Four mm biopsies were taken from human skin, human scar, and from mouse scar tissue, and enzymatically digested with MACS Miltenyi Whole Skin Dissociation Kit (Miltenyi Biotec, Bergisch-Gladbach, Germany) for 2.5h according to the manufacturer´s protocol. After processing on a GentleMACS OctoDissociator (Miltenyi), cell suspensions were passed through a 70 µm and a 40 µm filter and stained with DAPI nuclear dye. Cells were sorted on a MoFlo Astrios high speed cell sorting device (Beckman-Coulter, Brea, CA, USA), and only DAPI-negative cells, representing viable cells, were used for single cell RNAseq. Immediately after sorting, viable cells were loaded on a 10X-chromium instrument (Single cell gene expression 3‘v2/3, 10X Genomics, Pleasanton, CA, USA) to generate GEMs. GEM-generation, library preparation, RNA-sequencing, demultiplexing and counting were done by the Biomedical Sequencing Core Facility of the Center for Molecular Medicine (CeMM, Vienna, Austria). Sequencing was performed on an Illumina HiSeq 3000/4000 (Illumina, San Diego, CA, USA) with 3 samples per lane, 2x75bp, and paired-end sequencing.
Single-cell libraries were generated using the Chromium Controller and Single Cell 3− Library & Gel Bead Kit versions 2 and 3 (10x Genomics) according to the manufacturer’s protocol.

value: dermal scar cells

value: Balb/c

tag: molecule

value: total mRNA


title: s10


title: mouse_protease_inhib_ctrl

source_name: scar 8 weeks ctrl


title: CRS_1LU


title: CRS5LL


title: mouse_protease_inhib_sita

source_name: scar 8 weeks sita


title: s1


title: OGG1 inhibitor + RSV (72h)

city: GALVESTON

first: Xu

last: zheng

state: Texas

address: 301 University Boulevard Basic Science building, 3.142

department: Microbiology and Immunology

institute: University of Texas Medical

description:
Test
SAMPLE 15

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.qiagen.com/us/shop/genes-and-pathways/data-analysis-center-overview-page/.
For normalization, the average of five housekeeping genes (Gusb, Hprt, Hsp90ab1, Gapdh, Actb) were used.
Target gene signals normalized to housekeeping genes; 2^-delta CT, where delta CT = (Ct Target − Ct HKG)]
The web-based software package automatically performs all delta delta Ct based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., Solvent/OGG1 inhibitor/RSV challenge) ratios.

label: SYBR Green

source_name: Lung lysate

label_protocol: PCR assays were performed using the Mouse Inflammatory Cytokines & Receptors PCR array PAMM-011ZD (QIAGEN, Germantown, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1 µg total RNA using the Superscript® III First Strand Synthesis System (Invitrogen)

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Solvent, OGG1 inhibitor (30 mg per kg) was administered intra-peritoneally, challenge of lungs was performed by administration of RSV via  intranasal route.

tag: agent

value: OGG1 inhibitor + RSV

tag: Sex

value: Female+male (50%-50%)

tag: age

value: 8 weeks old

value: Balbc J


title: A549 74

first: Paola

last: Marignani

address: 5850 College Street, Tupper Medical Building

institute: Dalhousie University


title: CRS_4LL


title: RX110


title: A549 72


title: RX90


title: Solvent + RSV (72h)

description:
Test
SAMPLE 14

value: Solvent + RSV


title: RX8LU


title: CRS6LU


title: OGG1 inhibitor + RSV (48h)

description:
Test
SAMPLE 13


title: RX9RU


title: Solvent + RSV (48h)

description:
Test
SAMPLE 12


title: CRS_6RU


title: OGG1 inhibitor + RSV (24h)

description:
Test
SAMPLE 11


title: RX7LL


title: CRS_6LL


title: CR5_LU

value: young


title: A549 75


title: CR5_RL

value: kidney


title: CR5_LL

value: NZB/W F1


title: A549 70


title: RX8LL


title: Solvent + RSV (24h)

description:
Test
SAMPLE 10


title: A549 73


title: A549 69


title: A549 71


title: OGG1 inhibitor + RSV (12h)

description:
Test
SAMPLE 9


title: CR5_RU


title: CR4_LL


title: OGG1 inhibitor + RSV (6h)

description:
Test
SAMPLE 7


title: A549 67


title: RX9RL


title: RX8RU


title: CR4_RU


title: Solvent + RSV (3h)

description:
Test
SAMPLE 5


title: RX12RL


title: CR4_RL


title: A549 65


title: A549 64


title: A549 63


title: RX11RU


title: OGG1 inhibitor + RSV (2h)

description:
Test
SAMPLE 4


title: RX10RL


title: RX100


title: Solvent + RSV (12h)

description:
Test
SAMPLE 8


title: RX10RU


title: ZT_12LU


title: A549 68


title: Solvent + RSV (2h)

description:
Test
SAMPLE 3


title: A549 66


title: Solvent + RSV (1h)

description:
Test
SAMPLE 2


title: Solvent + RSV (6h)

description:
Test
SAMPLE 6


title: ZT_12RU


title: CR4_LU


title: RX7LU


title: CR3_LL


title: A549 61


title: A549 62


title: RX1OLL


title: A549 60


title: CR3_LU


title: A549 59


title: Vehicle (solvent)

description:
Control
SAMPLE 1

value: Vehicle (solvent)


title: RX11RL

value: nephritis


title: ZT_12RL


title: RX12LU


title: RX11LU


title: A549 58

value: Lung adenocarcinoma


title: RX12LL


title: A549 57


title: A549 56


title: RX12RU


title: A549 55


title: CR2_LL


title: RX11LL


title: A549 54


title: A549 76


title: A549 53


title: RX10LU


title: HIL5RU


title: CRS60


title: A549 50


title: HIL5LL


title: A549 51


title: CRS6LL


title: A549 49


title: CRS6LU


title: A549 47


title: Drosophila control [R038]

first: Lei

last: Zhou

institute: University of Florida

description:
Whole body extraction
mRNA

data_processing:
Illumina software used for basecalling. Quality assessment performed with FastQC.
Reads were mapped to dm6 or hg19 using tophat with default parameters.
Normalized expression value and differentially expressed genes were identified with CuffLinks and CuffDiffs.
Count data were further processed using DESeq2 to identify differentially expressed genes.
Genome_build: dm6 (Release 6 plus ISO1 MT), hg19 (GRCh37)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include un-normalized counts.
Supplementary_files_format_and_content: *.csv: Comma-separated text files.

organism: Drosophila melanogaster

source_name: Drosophila control

extract_protocol: The RNA extracted for both Drosophila and HCA2 samples were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, Cat #: RS-122-2101).

value: Whole body

value: Genetical background matched control


title: Drosophila control [R037]

description:
Whole body extraction
mRNA


title: CR3LL

value: Young


title: CR3LU


title: Drosophila hAAT expression [R036]

description:
Whole body extraction
mRNA

source_name: Drosophila hAAT expression

value: Transgenic hAAT expression


title: A549 52

value: Epithelial


title: CR3RL


title: A549 45


title: A549 46


title: root, PI5

city: Raleigh

first: Ramsey

last: Lewis

address: 101 Derieux PI

department: Crop and Soil Sciences Department

institute: North Carolina State University

data_processing:
Reads were mapped against tobacco K326 genome assembly Nitab4.5 using hisat2 version 2.1.0
Reads mapped to gene assembly were manipulated using samtools  for sorting/indexing
Raw count of reads mapped to annotated tobacco gene model (Nitab4.5 version) were extracted using bedtools version 2.25.0
Genome_build: Tobacco K326 genome assembly Nitab4.5
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample (geneIDs can be searched at https://solgenomics.net/jbrowse_solgenomics/?data=data/json/NitabEd17)

organism: Nicotiana tabacum

source_name: 42 hours after inoculation with Phytophthora nicotianae suspension

growth_protocol: Plants of each genotype were grown in sub-irrigated 8.3 cm square pots filled with calcined clay (Turface Athletics All Sport, Profile Products, Buffalo Grove, IL, USA) and maintained at 27C in a plant growth room with a 18 hours light: 6 hours dark photoperiod.

extract_protocol:
Root samples were collected and frozen and ground in liquid nitrogen, and RNA was purified using Plant Rneasy mini kit of Qiagen.
100 ng total RNA samples was used for RNA-seq library construction using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA)  followed the protocol for long size insertions.

treatment_protocol: The roots of each of eighteen 33-day old plants of each genotype were inoculated with 10 mL of a 1×103 zoospores mL-1 suspension of a P. nicotianae race 0 isolate maintained at N.C. State University. A separate set of eighteen plants of each plant genotype was treated with 10 mL of the suspension buffer (without zoospores) and maintained as uninoculated control plants. All plants were maintained with sub-irrigation for 42 hours post-inoculation, at which time roots were carefully rinsed to remove growth media, excised, transferred to liquid nitrogen for rapid freezing, and eventually stored at -80°C until RNA purification.

tag: cultivar

value: Hicks

value: Hicks + Phn7.1 NIL

value: Phytophthora nicotianae suspension

value: Root


title: CR6LL


title: CR6RL


title: A549 48

city: Halifax


title: CR6RU


title: root, PI4


title: A549 43


title: A549 42


title: A549 44


title: root, PI3


title: ZT200


title: Drosophila hAAT expression [R035]

address: 2033 Mowry Rd, CGRC 261

description:
Whole body extraction
mRNA


title: A549 41


title: ZT20LU


title: A549 40


title: CR2_LU


title: A549 38


title: ZT20RU


title: ZT20RL


title: A549 39


title: root, PI2


title: root, HI3


title: root, PI1


title: CR1_RL


title: ZT160


title: A549 37


title: root, HI1


title: ZT16LL


title: ZT16LU


title: IgG DNA for EMF2b ChIP

city: Wuhan

first: Fengquan

last: Tan

address: Hongshan

institute: HZAU

library_source: genomic

data_processing:
Adaptors were trimmed off from raw reads with Trimmomatic (version 0.36) :ILLUMINACLIP:FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15
Map to the genome “MSU7.0” with Bowtie2 (version 2.4.2) using default parameters.
Duplicate reads were removed with picard-tools (MarkDuplicates) using default setting (version 2.23.3).
Genome_build: MSU7.0
Supplementary_files_format_and_content: *.bw: bigWig files were generated using bamCoverage (deeptools) with parameters ‘--bam --binSize 10 --effectiveGenomeSize 4e8 --ignoreDuplicates --extendReads -normalizeUsing RPKM’

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: shoot meristem enriched tissue of 5-day-old seedling

growth_protocol: Rice seeds were surface-sterilized and germinated in media containing 0.8% agar supplemented with 3% (w/v) sucrose at 28°C (in light) and 24°C (in dark) with a 14-h-light/10-h-dark cycle. Five-day-old seedlings were used for the collection of shoot meristem enriched tissue.

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (Potok et al., 2019, Nature Communications, 10: 3352). About 2 g SAM enriched tissue of 5-day-old seedling were used.
DNA from chromatin immunoprecipitation was used to construct sequencing libraries following the protocol provided by the Illumina TruSeq ChIP Sample Prep Set A.

value: wild type (ZH11)

tag: Stage

value: 5-day-old seedling

value: shoot meristem

tag: chip antibody

value: IgG


title: CR2_RL

value: NZB/W F1

value: kidney

value: young


title: pap1 EMF2b-rep2

value: mutant (pap1)


title: CR1_LL


title: A549 35

tag: tumour type

value: Lung adenocarcinoma

tag: cell type


title: root, PC2

source_name: 42 hours after treated with suspension buffer without pathogen

tag: genotype

value: control


title: CR6_LU


title: CR3_RU


title: root, PC3


title: CR1_LU


title: A549 34


title: A549 36


title: pap1 EMF2b-rep1


title: CR6_RL


title: CR6_LL


title: CR2_RU


title: CR1_RU


title: CR6_RU


title: root, PC1


title: ZT16RU

value: Young


title: ZH11 EMF2b-rep2


title: ZT12LU


title: A549 33


title: ZT120


title: A549 31


title: root, HC3


title: ZH11 EMF2b-rep1


title: root, HC2


title: ZT12RU


title: pap1 H3K27me3-rep2


title: input DNA for H3K27me3 ChIP


title: pap1 H3K27me3-rep1


title: ZT8LU


title: ZH11 H3K27me3-rep2


title: root, HC1


title: A549 28


title: A549 30


title: A549 29


title: ZT8LL


title: A549 27


title: WT

city: Nantong

first: Yinchuan

last: Li

state: Jiangsu

address: 16 wenfeng road, Chongchuan

department: Medical School

institute: Nantong University

data_processing:
Libraries were sequenced on the Illumina HiSeq X using 150 bp paired end reads. Raw data were processed by: FastQC (V0.11.7) (FastQC, RRID:SCR_014583) for quality evaluation, fastp (v1) (fastp, RRID:SCR_016962) for trimming, STAR aligner (v2.5.3a) (STAR, RRID:SCR_015899) for alignment, and featureCounts (v1.6.2) (featureCounts, RRID:SCR_012919) for transcript counting.
Cells were integrated and filtered under Seurat 3.2.3 (nFeature_RNA > 200, nFeature_RNA < 7000, percent.mt < 20 and min.cells=3). Batch effects were removed by sctransform 0.3.1 in Seurat.

source_name: Normal adult testes

extract_protocol: none provided by the submitter

tag: sample type

value: whole testicle cell populations digested with collagenase I


title: ZH11 H3K27me3-rep1


title: ZT8RL


title: O50t

data_processing:
Libraries were sequenced on the Illumina HiSeq X using 150 bp paired end reads. Raw data were processed by: FastQC (V0.11.7) (FastQC, RRID:SCR_014583) for quality evaluation, fastp (v1) (fastp, RRID:SCR_016962) for trimming, STAR aligner (v2.5.3a) (STAR, RRID:SCR_015899) for alignment, and featureCounts (v1.6.2) (featureCounts, RRID:SCR_012919) for transcript counting.
Cells were integrated and filtered under Seurat 3.2.2 (nFeature_RNA > 200, nFeature_RNA < 7000, percent.mt < 20 and min.cells=3). Batch effects were removed by sctransform 0.3.1 in Seurat.

source_name: Orchitic textes

value: whole testicle cell populations digested with trypsin/EDTA


title: T13

source_name: Tex13a-knocked-out testes


title: Nt


title: A549 32

value: Epithelial


title: ZT8RU


title: ZT40


title: ZT12RL


title: Macrophage GMCSF+IFNg+LPS+sodium palmitate

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

institute: University of Ulm

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was done using Hisat2
Cufflinks was used to assemble the transcripts
Cuffmerge was used to merged all the transcripts
Cuffdiff was for differential expression analysis
Genome_build: mm10 and grch38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Macrophage

extract_protocol:
Total RNA from skin and macrophages was isolated using Rneasy kit (Qiagen)
rRNA removal was performed either by Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific). rRNA depleted RNA was subjected to preparation of Illumina compatible NEBNext Ultra II Directional RNA Library Preparation kit (NEB).

value: Macrophage


title: ZT4LU


title: Macrophage GMCSF


title: A549 26

source_name: NSCLC


title: A549 23


title: A549 25


title: ZT4RL


title: Macrophage GMCSF+IFNg+LPS


title: ZT00


title: A549 24


title: RNA_seq_4175_miR339

first: Ying

last: Liang

state: Shanghai

address: Room 416, West Building 13, Dong'an Road 130, Xuhui District

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: peak text files; matrix table with raw gene counts for every gene and every sample

source_name: Breast cancer cells

growth_protocol: human breast cancer MDA-MB-231 derived LM2-4175 cells  and 293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, HyClone) supplemented with 10% fetal calf serum (HyClone). All cells were incubated in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP seq; Total RNA extract was harvested using Trizol reagent for RNA seq.
For ChIP-seq, libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Transfecting miR-339 expression lentivirus into 4175 cells.

value: MDA-MB-231 derived LM2-4175 cells

tag: treatment

value: overexpressing miR-339


title: A549 22


title: ZT4RU

tag: diagnosis


title: A549 21


title: RNA_seq_4175_Control


title: 293T_H3K27ac_KO

value: knockout miR-339


title: ZT0RL

tag: time


title: ZT0LU

tag: tissue


title: 293T_H3K27ac_OE

tag: strain


title: 293T_H3K27ac_Control


title: ZT0RU


title: CSF32

city: Chicago

last: Gate

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
Real-Time Analysis (RTA) software called RTA2 used for basecalling.
Base call files were demultiplexed using cellranger mkfastq version 3.0.2
RNA-seq reads were mapped alligned to the GRCh38 3.0.0 genome assembly available from 10X Genomics using cellranger count version 3.0.2
Gene expression matrices were generated using cellranger count version 3.0.2
Gene expression matrices for each sample were loaded into the R package 'Seurat' v3.0 and all samples  were merged into one Seurat object
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: fodlers for each sample containing expression matrix, cellbarcodes, and genes

source_name: cerebrospinal fluid derived cells

extract_protocol:
CSF cells were Live cell sorted using an LSRFortessa (BD Biosciences). RNA was extracted according to the 10x v2 5' Expression library kit.
Libraries were prepared  according to the 10x v2 5' Expression library kit.
single cell RNA-seq

value: cerebrospinal fluid

value: immune cells

value: healthy control


title: OE33_H3K27me3_ChIPseq

city: Guangzhou

first: Yongsheng

last: Huang

address: 107 Yan Jiang West Road

institute: Sun Yat-Sen University

data_processing:
Sequencing reads were aligned to reference human genome (GRCh37/hg19) with BWA (0.7.12),with the removal of reads within the ENCODE blacklisted regions.
Peaks were identified with MACS2 (v2.2.6), using parameters --bdg --SPMR --nomodel  --extsize 200 -q 0.01 (Zhang et al., 2008).
Bigwig files were generated by bamCompare in DeepTools (v3.1.3),using parameters --binSize 10 --numberOfProcessors 5 --scaleFactorsMethod None --normalizeUsing CPM --ignoreDuplicates --extendReads 200 (Ramirez et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated

source_name: Esophageal adenocarcinoma cells

growth_protocol: RPMI1640/DMEM +10% FBS

extract_protocol:
Cells were cross-linked with 1% formaldehyde and then neutralized by 1.25M glycine. Cells were sonicated in a Bioruptor Sonicator (Diagenode, USA), followed by cell lysis. Sonicated lysates were incubated overnight at 4 °C with indicated antibody and then were incubated with magnetic beads for an additional 4 h. DNAs were eluted from precipitated immune-complex and subjected to standard Illumina library construction.
Libraries were prepared  for sequencing using standard Illumina protocols.

tag: cell line

value: H3K27me3 (Abcam;ab6002)

value: Esophageal


title: A549 18


title: A549 19


title: CSF31_DLB

first: David

value: Dementia with Lewy Bodies


title: OE33_H3K4me3_ChIPseq

value: H3K4me3 (Abcam;ab8580)


title: CSF30_PD

value: Parkinson's Disease


title: OE33_Input


title: A549 15

value: Lung adenocarcinoma


title: CSF28_HC


title: A549 16


title: CAL27_Input

source_name: Head and neck squamous cells

value: Head and neck


title: A549 20


title: KYSE140_H3K27me3_ChIPseq

source_name: Esophageal squamous cells


title: KYSE140_Input


title: CSF26_PD


title: KYSE140_siDLX5_2

data_processing:
Reads were aligned to the genome using HISAT2 (v2.0.4),using parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000 ( Kim, D.et al., 2015), and Bowtie2 (v2.2.5) with the default parameter settings.
RSEM (v1.2.12) and DESeq (v3.4) was used for differential gene expression analysis with the default parameter settings.
Genome_build: hg19
Supplementary_files_format_and_content: txt files - tab-delimited files containing FPKM values for RefSeq genes in each sample, and fold change as well as p values relative to the control group.

extract_protocol:
Total RNA was extracted from cell lines using Trizol reagent (Invitrogen) and purified using the RNAeasy Plus kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The siRNA that target DLX5 was transfected in KYSE140 cell line.

value: KYSE140 cell line

value: knockdown DLX5 by siRNA2


title: A549 17

value: Epithelial


title: CSF27_PD


title: CSF__HC15

data_processing:
Real-Time Analysis (RTA) software called RTA2 used for basecalling.
Base call files were demultiplexed using cellranger mkfastq version 3.0.2
RNA-seq reads were mapped alligned to the GRCh38 3.0.0 genome assembly available from 10X Genomics using cellranger count version 3.0.2
Gene expression matrices were generated using cellranger count version 3.0.2
Gene expression matrices for each sample were loaded into the R package 'Seurat' v3.0 and all samples were merged into one Seurat object
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: tar archive for each sample containing expression matrix, cellbarcodes, and genes; filtered & raw expression matrix

extract_protocol:
CSF cells were Live cell sorted using an LSRFortessa (BD Biosciences). RNA was extracted according to the 10x v2 5' Expression library kit.
Libraries were prepared according to the 10x v2 5' Expression library kit.


title: CSF29_PD


title: A549 9


title: A549 11


title: root, HI2

value: Hicks

value: Phytophthora nicotianae suspension

value: Root


title: CSF__HC14


title: A549 10


title: CAL27_DLX5_ChIPseq

value: DLX5 (Abcam;ab109737)


title: CSF__HC17

value: cerebrospinal fluid


title: CSF25_DLB

value: immune cells


title: A549 7


title: A549 8


title: A549 13


title: KYSE140_Control

value: Negative control


title: CAL27_TP63_ChIPseq


title: CSF__HC16

value: healthy control


title: KYSE140_H3K4me3_ChIPseq


title: A549 6


title: A549 12


title: CSF__HC13


title: A549 14


title: KYSE140_siDLX5_1

value: knockdown DLX5 by siRNA1


title: CSF__HC12


title: KYSE140_TP63_ChIPseq


title: CSF__HC10


title: KYSE140_DLX5_ChIPseq


title: A549 5


title: Mouse seminal vesicle tissue transcriptomics data - Acrylamide treated (25mg/kg bw/day) 5

city: Callaghan

first: John

middle: Even

last: Schjenken

state: NSW

address: Life Sciences Building, Level 4, Office 39. The University of Newcastle, University Drive

country: Australia

institute: University of Newcastle, Australia

data_processing:
All of the generated raw sequencing reads were filtered using SOAPnuke [116] to remove reads with adaptors, reads with more than 0.1% unknown bases, and low quality reads (more than 40% base quality < 20). Trimmed reads counted for > 93.5% total raw reads and were stored in FASTQ format
Reads were mapped onto the mouse reference genome (mm10) using Hisat2
Novel genes were predicted using Stringtie and Cuffcompare (Cufflinks tools), and CPC was used to predict the coding potential of novel genes before obtaining a complete reference to be used in downstream analyses by merging coding novel genes with reference genes. Autosomal gene expression levels were calculated using RSEM
To assess the impact of acrylamide exposure on the seminal vesicle transcriptome, differential regulation of genes was assessed between acrylamide and control groups using DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: The file "SkerrettByrne_DESeq list_Geo dataset.xlsx" contains a combined analysis of acrylamide and control mouse seminal vesicle tissue using DEseq2 identified a total 17,258 assessable genes. These data were assessed and  a comparative analysis of the seminal vesicle transcriptome from acrylamide versus control (PBS treated) animals was also completed . Genes were defined as differentially expressed when they met the criteria of a fold-change ≥ 1.5 or ≤ 0.67, an adjusted p value < 0.1, and at least one group had an average expression ≥ 1. Data includes gene symbol (GeneID), control expression (DESeq2 calculated values), acrylamide expression (DESeq2 calculated values), fold-change, adjusted p values (p.adj), log10 p.adj, un-adjusted p.value (p value) and gene symbol.

source_name: Seminal vesicle tissue

extract_protocol:
Seminal vesicle samples were homogenised using the FastPrep-24 5G homogeniser (MP Biomedicals, Irvine, CA) with the Cool Prep Adaptor (2 × 1min, 4.0m/s, at 4 °C) in Trizol reagent (ThermoFisher Scientific, Waltham, MA). Total RNA was extracted using the Trizol RNA method and DNase treated using RQ1 RNase free DNase (Promega, Madison, WI), following the manufacturer’s instructions. RNA was quantified using a Nano-Drop Lite Spectrophotometer (ThermoFisher Scientific) and RNA integrity was assessed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA with a RIN > 7 was used in this study. RNA sequencing was completed at BGI (Shenzen, China).
RNA-sequencing analysis was performed at BGI Genomics (Shenzhen, China) using DNBseq technology. Poly-A libraries were constructed by initially purifying poly-A mRNAs using poly-T oligo attached magnetic beads. Poly-A mRNAs were fragmented using divalent cations and the cleaved RNA was processed through first strand cDNA synthesis using reverse transcriptase and random primers, followed by second strand cDNA synthesis using polymerase I and RNase H. Second strand cDNA was then purified, and DNA nanoballs were generated with the libraries by rolling circle replication and samples were loaded into patterned nanoarrays to generate 100 bp paired end reads through the DNBseq platform. For each library, a minimum of 67 million paired end raw reads were produced.

treatment_protocol: Mice (8–12 weeks old, n = 4 / group) received an intra-peritoneal injection of acrylamide (25mg/kg body weight) or vehicle alone (phosphate buffered saline (PBS) 137mM NaCl, 2.7mM KCl, 8mM Na2HPO4, and 2mM KH2PO4, pH 7.4) each morning for five consecutive days. Mice were euthanised 72 h following the final injection and seminal vesicles were dissected following careful removal of prostate tissue. Seminal vesicle tissue was weighed and washed thoroughly in Tris-buffered saline (TBS, 50mM Tris-Cl, 150mM NaCl, in mass spectrometry (MS) grade H2O, pH 7.6). Seminal vesicle fluid was removed by gently squeezing seminal vesicle tissue using curved forceps. Tissue was snap frozen in liquid nitrogen and stored at − 80 °C for transcriptomic analysis.

tag: tissue type

value: Seminal vesicle tissue

value: Male outbred Swiss mice

value: Acrylamide treated (25 mg/kg bw/day)

tag: injection type

value: intra-peritoneal


title: A549 3

value: Lung adenocarcinoma


title: Mouse seminal vesicle tissue transcriptomics data - Acrylamide treated (25mg/kg bw/day) 3


title: Mouse seminal vesicle tissue transcriptomics data - Acrylamide treated (25mg/kg bw/day) 4


title: CSF__HC11


title: CSF__HC9


title: A549 4


title: A549 1


title: CSF7_PD

value: Parkinson's Disease


title: CSF24_PD


title: CSF21_PD


title: CSF10_PD


title: Mouse seminal vesicle tissue transcriptomics data - Acrylamide treated (25mg/kg bw/day) 2


title: Mouse seminal vesicle tissue transcriptomics data - Control vehicle (PBS treated) 5

value: Vehicle control treated (PBS)


title: CSF14_PD


title: Mouse seminal vesicle tissue transcriptomics data - Control vehicle (PBS treated) 3


title: A549 2

value: Epithelial


title: SNU638_WT_1

city: Seongnam-si

first: Minwook

last: Lee

state: Gyeonggi

address: 335 Pangyo-ro, Bundang-gu

institute: CHA University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Gastric cancer (STAD)

growth_protocol: The human gastric cancer cell line SNU638 were obtained from the Korean Cell Line Bank (KCLB, Seoul, S. Korea) and were cultured in RPMI-1640 (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (Gibco/Life Technologies, Grand Island, NY, USA) and 5% penicillin-streptomycin (Gibco/Life Technologies).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The human gastric cancer cell line SNU638 were transfected with siELK3 (50 nM) using Lipofectamine 2000

value: human gastric cancer cell line

value: 48hrs after NC mimic transfection


title: SNU638_WT_2


title: Mouse seminal vesicle tissue transcriptomics data - Control vehicle (PBS treated) 1


title: DATB

status: Public on Sep 13 2021

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were adapter-trimmed and quality-filtered with Trimmomatic.
High-quality fastq files were aligned to the mouse genome by using STAR.
Gene read counts were calculated with featureCounts.
Differential gene expression was performed with DESeq2.
Downstream analysis was performed within the R environment.
Genome_build: mm10

source_name: Substantia nigra

extract_protocol:
Fresh brain tissue was collected from saline-perfused animals. Once the brain was removed, the nigral tissue was manually dissected and lysated in Trizol for the RNA isolation.
RNA libraries were generated starting from 1 microgram of total RNA whose quality was assessed by using a Tape Station instrument (Agilent). To avoid over-representation of 3’ ends, only high-quality RNA with an RNA Integrity Number (RIN) ≥ 9 was used. RNA was processed according to either TruSeq Stranded mRNA Library Prep Kit. The libraries were sequenced on Illumina HiSeq 3000 with 76 bp stranded reads using Illumina TruSeq technology. Image processing and base calling were performed using the Illumina Real-Time Analysis Software.

value: Substantia nigra

tag: genotype/variation

value: 3xDAT-Cre (infected with Synuclein-expressing vector)


title: DATA


title: SNU638_siELK3_2

value: 48hrs after siELK3 transfection


title: CX3A

value: 3xCX3-Cre (infected with Synuclein-expressing vector)


title: SOCS1-HTO-dil10

city: Rouen

first: Chervin

last: Hassel

address: GRAM2.0 - EA2656 - UFR Santé - 22 Boulevard Gambetta - CS 76183 - 76183 ROUEN Cedex 1

department: UFR Santé

country: France

institute: Université de Rouen

data_processing:
Sorted sequencing reads were converted from BCL2 to FASTQ files and demultiplexed using bcl2fastq converter (v2.20.0.422).
Reads were aligned to the Mm10 mouse genome using STAR, filtered, and normalized and UMI counting and production of the gene/barcode matrix were performed for all libraries (RNA and HTO, TotalSeq hashtag) using CellRanger pipeline software (v 3.0.2).
HTO tags were then counted in all HTO libraries using the Python script CITE-seq-Count (v 1.4.2) with TotalSeq Hashtag (Biolegend) parameters, which allows creation of a hashtag count matrix.
Downstream analyses were then performed using R package Seurat v 4.0.0.
Genome_build: Mouse mm10

source_name: Immune cells (CD45pos) from lactating mammary gland

extract_protocol: The fourth pair of lactating mammary glands were harvested from the mice and the inguinal lymph nodes carefully removed from the tissue preparation. Each mammary gland was finely sliced and digested with Liberase at and DNAse I. Lactating mammary gland cell suspensions of each mouse were labeled using TotalSeq™ anti-mouse hashtag 1-3 antibodies A301-303 (Biolegend, UK) and were pooled and stained with anti-IgG2b-Vioblue antibody to specifically label CD45 cells. Doublet, 7AADpos and FITCpos cells were gated out to sort only viable resident CD45pos immune cells using a BD FACS Influx instrument (BD Biosciences).

tag: age

value: 8-12 weeks

value: Mammary gland

tag: tissue state

value: Lactation


title: CX3C


title: SOCS2-dil10_S2


title: SNU638_siELK3_1


title: Mouse seminal vesicle tissue transcriptomics data - Control vehicle (PBS treated) 4

value: Seminal vesicle tissue


title: SOCS2-HTO-dil10


title: SOCS1-dil10_S1


title: CTRA

value: GFP (control)


title: CX3B


title: CTRC


title: CTRB


title: DATC


title: Drosophila S2R+ cells_H2Av RNAi_30°C_Rep 1

city: Zurich

first: Christian

middle: F.

last: Lehner

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

description: Gene expression after treatment with His2Av dsRNA and 24 hours at 30°C

hyb_protocol: The hybridization mix (55 µl) contained 1.65 µg of fragmented cRNA, 2.2 µl of 25x hybridization buffer, 11 µl of 10x blocking agent and RNase-free water. For hybridization, we used single-color gene-expression microarrays purchased from Agilent.

scan_protocol: After microarray hybridization and washing, signal intensities were recorded with Agilent Feature Extraction Software

data_processing: Signal intensities were background-corrected with normexp convolution method and quantile-normalized

source_name: Drosophila S2R+ cells_H2Av RNAi_30°C

label_protocol: For generation of Cyanine 3 (Cy3)-labelled complementary RNA (cRNA) probes, we used the Low-Input QuickAmp kit (Agilent, Santa Clara, CA, USA). The resulting cRNA was purified using the Absolute RNA Nanoprep kit (Agilent).

growth_protocol: S2R+ cells were cultured in Schneider’s medium (Gibco, cat# 21720, Thermo Fisher Scientific, Waltham, MA), supplemented with 10% fetal bovine serum (Gibco, cat# 10500-064) and 1% Penicillin-Streptomycin (Gibco, cat# 15140).

extract_protocol: Total RNA was isolated with the NucleoSpin RNAII kit (Macherey-Nagel, Oensingen, Switzerland)

treatment_protocol: Aliquots of cells were plated into 60 mm culture dishes. The numbers of cells that were plated were adjusted to the temperature, to which they were shifted eventually (30°C: 0.4x106; 25°C: 0.65x106; 14°C: 0.7x106) so that comparable cell densities were present at the end of the temperature treatment. Twenty-four hours after seeding, we added 30 µg dsRNA per dish, derived from either His2Av or lacZ for control. Four days after dsRNA addition, aliquots were shifted to different temperatures (14, 25 and 30°C) for 24 hours.

value: S2R+ cells

value: H2Av RNAi

value: 24 hours at 30°C


title: Drosophila S2R+ cells_H2Av RNAi_25°C_Rep 3

description: Gene expression after treatment with His2Av dsRNA and 24 hours at 25°C

source_name: Drosophila S2R+ cells_H2Av RNAi_25°C

value: 24 hours at 25°C


title: Drosophila S2R+ cells_H2Av RNAi_30°C_Rep 3


title: Drosophila S2R+ cells_lacZ RNAi_30°C_Rep 3

description: Gene expression after treatment with lacZ dsRNA and 24 hours at 30°C

source_name: Drosophila S2R+ cells_lacZ RNAi_30°C

value: lacZ RNAi


title: Drosophila S2R+ cells_H2Av RNAi_14°C_Rep 3

description: Gene expression after treatment with His2Av dsRNA and 24 hours at 14°C

source_name: Drosophila S2R+ cells_H2Av RNAi_14°C

value: 24 hours at 14°C


title: Drosophila S2R+ cells_H2Av RNAi_25°C_Rep 1


title: Drosophila S2R+ cells_H2Av RNAi_30°C_Rep 2


title: Drosophila S2R+ cells_H2Av RNAi_25°C_Rep 2


title: Drosophila S2R+ cells_lacZ RNAi_25°C_Rep 1

description: Gene expression after treatment with lacZ dsRNA and 24 hours at 25°C

source_name: Drosophila S2R+ cells_lacZ RNAi_25°C


title: Drosophila S2R+ cells_H2Av RNAi_14°C_Rep 2


title: Drosophila S2R+ cells_lacZ RNAi_30°C_Rep 2


title: Drosophila S2R+ cells_lacZ RNAi_25°C_Rep 2


title: female liver 7week PpargΔ/Δ rep1

city: Lausanne

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

institute: University of Lausanne

description: gene expression data

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 2.5μg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package

data_processing: Affymerix Expression Console 1.1.2637.26569, RMA normalization

source_name: mouse LIVER

label_protocol: For each sample, 100ng of total RNA were amplified using the WT Expression kit (Invitrogen, Carlsbad, USA; catalogue no. 4411974); the resulting sense cDNA was fragmented using UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labelling kit (Affymetrix, Santa Clara, USA; catalogue no. 900671, Santa Clara, USA).

growth_protocol: mice were housed in standard 12h Light/12h dark light regimen

extract_protocol: Trizol extraction of total RNA, followed by purification with MagMax (Applied Biosystems) .

treatment_protocol: at the indicated developmental stage mice were decapitated and liver was collected for RNA extraction

value: Mixed C57BL6/SV129

tag: developmental stage

value: 7 weeks

value: liver

value: Pparg delta/delta

tag: Sex

value: female


title: female liver 7week PpargΔ/Δ rep3

description: gene expression data


title: female liver 7week control rep1

description: gene expression data

value: control


title: female liver 7week PpargΔ/Δ rep2

description: gene expression data


title: Drosophila S2R+ cells_lacZ RNAi_25°C_Rep 3


title: male liver 7week PpargΔ/Δ rep2

description: gene expression data

value: male


title: Drosophila S2R+ cells_lacZ RNAi_30°C_Rep 1


title: Drosophila S2R+ cells_H2Av RNAi_14°C_Rep 1


title: Drosophila S2R+ cells_lacZ RNAi_14°C_Rep 1

description: Gene expression after treatment with lacZ dsRNA and 24 hours at 14°C

source_name: Drosophila S2R+ cells_lacZ RNAi_14°C


title: female liver 7week control rep3

description: gene expression data


title: male liver 7week control rep1

description: gene expression data


title: male liver 7week control rep3

description: gene expression data


title: male liver 7week PpargΔ/Δ rep3

description: gene expression data


title: female liver 7week control rep2

description: gene expression data


title: male liver 7week PpargΔ/Δ rep1

description: gene expression data


title: Drosophila S2R+ cells_lacZ RNAi_14°C_Rep 3


title: male liver 7week control rep2

description: gene expression data


title: Drosophila S2R+ cells_lacZ RNAi_14°C_Rep 2


title: female liver 20week PpargΔ/Δ rep1

description: gene expression data

value: 20 WEEKS


title: female liver 20week PpargΔ/Δ rep2

description: gene expression data


title: female liver 20week control rep1

description: gene expression data


title: female liver 20week control rep2

description: gene expression data


title: female liver 20week PpargΔ/Δ rep3

description: gene expression data


title: male liver 20week PpargΔ/Δ rep1

description: gene expression data