title: C57_BMDM_ATAC_notx_rep2 [re-analyzed]

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description:
processed data file:
BMDM_ATAC_peaks.txt

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
For p300, SREBP and LXR ChIP-seq experiments peaks were called with HOMER for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Only peaks with > 16 normalized tags (normalized to total tags of 1e7) were kept. Overlapping peak sets were determined using mergePeaks command. The pooled tag directory from two replicates was used for track visualization. To annotate p300 signal in ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 200 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential p300 signal > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For H3K27ac analysis: To annotate H3K27ac signal around ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 1000 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal or chromatin accessibility with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For p65 and ATAC-Seq analysis of data from GSE79423 and GSE109965 respectively: Relevant raw FASTQ files were mapped to mm10 genome with Bowtie2 with default parameters (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010). For p65 peaks were called with HOMER findPeaks for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Peak files across various timepoints for vehicle and KLA treated timepoints were merged using HOMER mergePeaks. Merged peaks were annotated for H3K27ac and p300 signal as indicated. For ATAC-Seq, mm10 mapped, IDR defined peaks from GSE109965, for both vehicle and KLA treatment conditions, were used. Peaks were merged using HOMER mergePeaks, then merged peak file was used for further analysis as indicated in text.
To identify motifs enriched in peak regions over the background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. The background sequences were either from random genome sequences or from peaks from the comparing condition indicated in the main text and in the figure legends.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include peak text files (ChIP-Seq peak data, using default HOMER parameters). All genomic coordinates are relative to mm10 mouse assembly.

source_name: bone marrow derived macropages (BMDM)

growth_protocol: Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol:
Femur, tibia and iliac bones from the different mouse strains were flushed with DMEM high glucose (Corning) and red blood cells were lysed using red blood cell lysis buffer (eBioscience). After counting, 20 million bone marrow cells were seeded per 15cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS (Omega Biosciences), 30% L929-cell conditioned media (as source of M-CSF), 100 U/ml penicillin/streptomycin+L-glutamine (Gibco) and 2.5μg/ml Amphotericin B (HyClone). After 4 days of differentiation, 16.7 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM high glucose and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in DMEM high glucose containing 10% FBS, 100 U/ml penicillin/streptomycin+L-glutamine, 2.5μg/ml Amphotericin B and 16.7 ng/ml M-CSF. For KLA activation, macrophages were treated with 10 ng/mL KLA (Avanti Polar Lipids) for 1 or 6 hours.
ATAC-seq: To approximately 150k nuclei in 22.5ul GRO freezing buffer, isolated as described for GRO-seq above, 25ul DNA Tagmentation buffer was added, reaction mixed and 2.5uL DNA Tagmentation Enzyme mix (Nextera DNA Library Preparation Kit, Illumina) added. Mixture was incubated at 37°C for 30 minutes and subsequently purified using the Zymogen ChIP DNA purification kit as described by the manufacturer. DNA was amplified using the Nextera Primer Ad1 and a unique Ad2.n barcoding primers using NEBNext High-Fidelity 2X PCR MM for 10 cycles. PCR reactions were purified using 1.5 volumes of SpeedBeads in 2.5M NaCl, 20% PEG8000, size selected using PAGE/TBE gels for 160 – 280 bp and DNA eluted as described for GRO-seq.
For H3K27ac ChIP-seq, culture media was removed and plates were washed once with PBS and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For p300, LXR and SREBP ChIP-seq, cells were crosslinked with 3mM DSG (ProteoChem) in PBS for 30 minutes at room temperature, and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then pelleted at 700 X G for 5 minutes at 4°C. Crosslinked cells were stored at –80°C until ready for ChIP-seq library preparation. Fixed cells were thawed on ice, resuspended in either ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail, 1mM Na-Butyrate, for H3K27ac ChIP) or ice-cold RIPA-NR lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Na-Deoxycholate, 0.1% SDS, 1% NP-40, 1x protease inhibitors, for p300, LXR, and SREBP ChIP). Frozen crosslinked nuclei were resuspended in wash buffer (10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) for 5minutes on ice. Cells were spun down and then resuspended in RIPA-NR lysis buffer. Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles (samples in LB3) or 18 cycles (samples in RIPA-NR buffer) with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The LB3 lysate was diluted 1.1-fold with ice-cold 10% Triton X-100 after sonication. One percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 500,000 cells (for H3K27ac ChIP) or 1-2 million cells  (for p300, SREBP ChIP), 20 µl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein A/G (for p300, LXR, and SREBP ChIP) bound to specific antibodies for H3K27ac (2 μg, Active Motif, 39133), p300 (2 μg, Millipore, cat# 05-257,Diagenode, cat# C15200211), LXR (Santa Cruz Biotechnology: sc-1000X, sc- 133221X, sc-271064X) , and SREBP (2 μg, Santa Cruz Biotechnology: sc-8984X, Thermo Fisher Scientific: PA1-337, R&D Systems: AF7119) were combined and rotated overnight at 4°C. For H3K27ac ChIP, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). For p300, LXR and SREBP ChIP, beads were washed three times with RIPA-NR buffer (20 mM Tris-HCl/pH7.5, 150 mM NaCl, 0.1% SDS, 1% NP-40, 0.4 % Na-Deoxycholate, 1 mM EDTA, 0.5mM EGTA, 0.5mM DTT), six times with RIPA-LiCl buffer (10 mM Tris-HCl/pH 7.5, 250 mM LiCl, 1% NP-40, 0.7% Na-Deoxycholate, 1 mM EDTA), three times with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), and one time with IDTE (10mM Tris-HCl pH 8.0, 0.1mM EDTA). Bead complexes were resuspended in 25 μl TT (10 mM Tris/HCl pH 8.0, 0.05% Tween-20, 1x protease inhibitor cocktail) and sequencing libraries were prepared on-bead as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit with reaction volumes reduced by half, essentially as previously described (Heinz et al., 2018). Libraries were eluted and crosslinks reversed by adding to the 46.5 μl NEB reaction 20 μl water, 4 μl 10% SDS, 4.5 μl 5M NaCl, 3 μl 0.5 M EDTA, and 1 μl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 65C for 30 minutes to overnight in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries cleaned by adding 2 μl SpeedBeads 3 EDAC in 61 μl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 μl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 25 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 50 μl reaction volume using NEBNext Ultra II PCR master mix and 0.5 μM each Solexa 1GA and Solexa 1GB primers. Libraries were cleaned up with SpeedBeads as above using 36.5 μl 20% PEG 8000/1.5 M NaCl and 2 μl SpeedBeads. After ethanol washing and drying, PCR amplified libraries were eluted from the SpeedBeads using 20 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween- 20. Next, libraries were size selected 250-500 bp using gel extraction using 10% TBE acrylamide gels. Libraries were single-end sequenced using either a HiSeq 4000 or a NextSeq 500 to a depth of 10-20 million reads.

treatment_protocol: The following day after replating BMDMs, fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with or without 100 µg/ml 3'SL , with 10 ng/ml of LPS for 1 – 24 hours as indicated. For LXR and SREBP experiments cells were treated with 1uM GW3965.

value: 7 day cultured bone marrow derived macropages (BMDM)

value: no treatment


title: WTCHG_70485024_CT_MenACWY_+ve

status: Public on Mar 04 2024

type: SRA

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
The sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38 using STAR (version 2.7.3a).
Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92.
Genes with low counts across most libraries were removed by only retaining genes with abundance greater than 3 counts per million in 9 or more samples.
Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt file containing normalised expression (rpkm - reads per kilobase per million) for each gene for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
RNA was ribodepleted and globin depleted using Ribo-ZeroTM Gold rRNA removal Kit (Illumina, USA). RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and quality controlled before 150bp paired-end sequencing (NovaSeq6000).

tag: tissue

value: Whole blood

tag: timepoint

value: CT

tag: vaccine

value: MenACWY

tag: naat result

value: +ve

tag: age

tag: Sex

value: Female

tag: participant number


title: WTCHG_853846_207_CT+7_ChAdOx1_-ve

description:
small RNA
stage1

data_processing:
Alignments were performed using bowtie with up to 2 mismatches in best strata mode, and bowtie2 with 2 gaps permitted
Reads were first aligned to the non-coding transcriptome. The bowtie indexes for the non-coding RNAome were built by merging fasta files from the following databases: miRbase (miRNAs), SnOPY (snoRNAs), trRNA_db (tRNAs), RefSeq (snRNAs, yRNAs, vault RNAs, lncRNAs.
Non-aligned reads were then aligned to the mRNA transcriptome, and antisense to the non-coding and mRNA transcriptome
All other reads were collapsed using a "gene_union" approach like those employed in seqCluster and mmQuant.
sRNA features were removed if they did not have an abundance of at least 5 counts per million in at least 20% of samples.
Assembly: GRCh38
Supplementary files format and content: txt file containing raw read counts for each gene for each sample

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
Small RNA libraries were prepared with the NEBNext® Small RNA Library Prep Set for Illumina (catalog #E7330) and run on a single flow cell target of 300 million reads) on the NexTSeq platform using the 75SR configuration with the aim of achieving 5.2 million reads per sample.

value: -ve

value: Male


title: IMQ mouse deliveried EPIC repeat1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Remove low quality bases and adaptor sequences via Trimmomatic.
Align trimmed data to rRNA sequene to remove reads from ribosomal RNAs.
Align clean data to mm10 genome by HISAT2 then calculate FPKM of linear RNAs.
The unmapped reads were realignment to mm10 mouse genome by TopHat-Fusion and identify circRNAs via CIRCexplorer3.
Assembly: mm10
Supplementary files format and content: Text file cotains FPKM.

organism: Mus musculus

source_name: spleen

growth_protocol: Wild-type C57BL/6 mice received a daily topical dose of 62.5 mg IMQ cream (5%; Aldara; 3M Pharmaceuticals) on the shaved dorsal skin for 2 days, then EPIC-LNP was delivered (i.v.) at D1.5.

extract_protocol:
Total RNAs from spleens of mice were extracted with TRIzol (Life technologies) according to the manufacturer’s protocol.
For total RNA Ribo– RNA-seq libraries were prepared with TruSeq® Stranded Total RNA Library Prep Gold Kit. Deep sequencing was performed on Illumina NovaSeq.

treatment_protocol: Spleen samples were minced through a 70-μm mesh to obtain single-cell suspensions. Then obtained single-cell suspensions were treated with Red cell lysis buffer (TIANGEN) and washed with PBS for following experiments.

value: spleen

tag: strain

tag: genotype

value: WT

tag: treatment

value: IMQ (imiquimod) treatment at day 0 and day 1, and delivered (i.v.) EPIC by LNP at 1.5 day


title: C57_BMDM_ATAC_notx_rep1 [re-analyzed]

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

tag: cell type


title: WTCHG_853846_209_CT_MenACWY_-ve

description:
small RNA
stage1


title: Ad_eGFP_2

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Quality control of sequence reads was performed using FastQC.
Sequence reads were trimmed to remove low-quality bases and adapters using Trimmomatic v0.39.
Trimmed sequence reads were mapped against the mouse reference genome (GRCm39) using the STAR aligner
Assembly: mm39
Supplementary files format and content: tab-delimited files including read counts for each sample

source_name: Articular cartilage

extract_protocol:
Total RNA was extracted 36 h after transduction using the TRI reagent (Molecular Research Center, Inc.).
RNA sequencing libraries were constructed by Macrogen using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Articular cartilage

tag: cell line

value: Primary culture

value: Chondrocyte

value: wild type

value: Ad-eGFP


title: C57_BMDM_ATAC_KLA_1h_rep2 [re-analyzed]

value: 7 day cultured bone marrow derived macropages (BMDM)

value: KLA 1h


title: WTCHG_70475023_CT_MenACWY_+ve

value: Whole blood


title: PBS_HUB

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Post sequencing, the 10x Genomics "cellranger" tool suite (v7.2) was used to generate expression counts per known gene (refdata-gex-mm10-2020-A) per sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: rostral rhinal hub

growth_protocol: All mice used in this study were handled in accordance with the guidelines established by the NIH Animal Care and Use Committee and the recommendations of AAALAC for the Care and Use of Laboratory Animals. The animal study protocol was approved by the NINDS Animal Care and Use Committee. Mice were bred and maintained within individually ventilated cages in the specific pathogen-free animal facilities at the NIH.

extract_protocol:
Meningeal rostral-rhinal hubs from twelve 15-week-old naïve or d8 VSV-infected mice B6 mice transcardially perfused with 20 ml of ice-cold PBS were carefully collected under a dissection microscope. Upon isolation, meningeal hub samples were pooled for each experimental group and dissociated with a mouse Tumor Dissociation Kit (Miltenyi Biotec) using the gentleMACS Octo Dissociator (Miltenyi Biotec). After dissociation, the samples were then filtered through 100µm meshes and washed with 2% fetal bovine serum in RPMI and resuspended in 0.05% BSA PBS solution. Cell number and viability were checked with the Luna-FX7 (Logos Bio).
cDNA libraries were prepared from single-cell suspensions following the 10x Genomics 3′ v3 protocol using either single indices or dual indicies (www.10xgenomics.com) and sequenced on a Illumina NextSeq 550 (www.illumina.com).

treatment_protocol: C57BL/6J mice were either uninfected or infected intranasally in each nostril with 10 ul of PBS containing 5x10^5 plaque forming units of VSV-OVA serotype Indiana

value: rostral rhinal hub

value: leukocytes

tag: infection

value: uninfected


title: WTCHG_853846_205_CT_MenACWY_-ve

description:
small RNA
stage1

value: CT

value: MenACWY


title: C57_BMDM_ATAC_KLA_1h_rep1 [re-analyzed]


title: Ad_eGFP_1


title: WTCHG_853846_206_CT_ChAdOx1_-ve

description:
small RNA
stage1

value: -ve

value: Male


title: WTCHG_853846_204_D0_MenACWY_-ve

description:
small RNA
stage1


title: WTCHG_853846_208_D0_MenACWY_-ve

description:
small RNA
stage1

value: Female


title: WTCHG_70505026_CT_ChAdOx1_+ve

value: +ve


title: Ad_Irf1_3

value: Articular cartilage


title: WT-rep3

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

data_processing:
The libraries were sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover v0.9.2.
Reads were mapped to the mouse genome (mm9) using Tophat v2.0.14 and Bowtie v2-2.1.0.
Quantification of gene expression was performed using HTSeq v0.6.1 and gene annotations from Ensembl release 67.
Assembly: mm9
Supplementary files format and content: Processed expression data were summarized in one single Excel file containing the following informations for each sample: gene name/ensemble_gene_id/raw read count/normalized read count/log2 fold change/p-value/p-value adjusted for multi-testing.

source_name: Tibialis anterior

extract_protocol:
To extract total RNA, 500 µl of TRI Reagent (Sigma) was added to frozen tibialis anterior and homogenized with PreCellys (Bertin Technologies) (6500 RPM, 3 × 10 s) in tube containing ceramics beads (Lysing Matrix D – MP biomedicals). After centrifugation, TRI Reagent was removed and beads were washed one time with 500 µl of TRI reagent. Total RNA was then extracted following provider’s instruction
Libraries of template molecules suitable for strand-specific high-throughput DNA sequencing were created using a TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit (RS-122-2301; Illumina)

value: Tibialis anterior

value: 12 months-old

value: H2A-Z.1flox/flox :H2A-Z.2 flox/flox HSA Cre WT


title: WTCHG_70455021_CT+7_ChAdOx1_+ve


title: WTCHG_853846_203_CT_MenACWY_-ve

description:
small RNA
stage1


title: GS_77_T12

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

description:
RNA-Seq of Sus scrofa : ex vivo lung sample treated by the gold standard EVLP protocol
design description: NextSeq 500 mid output kit v2

data_processing:
Demultiplexing (bcl2fastq2 v2.2.18.12)
Sequence cleaning (Cutadapt v1.15)
Mapping (tophat2 v2.0.14)
Gene counts (featureCounts - subread v1.6.0)
Differential analysis (DESEq2 v1.18.1)
Assembly: Sscrofa11.1 - Ensembl 101
Supplementary files format and content: tab delimited raw counts file

organism: Sus scrofa

source_name: Lung

extract_protocol:
Arcturus PicoPure RNA isolation kit or Trizol + NucleoSpin RNA kit
NextSeq 500 Mid output kit V2

treatment_protocol: EVLP with or without pediatric dialysis

value: Lung

value: EVLP gold standard


title: Ad_Irf1_2

value: Primary culture

value: Chondrocyte

value: wild type


title: WTCHG_70445020_CT_MenACWY_+ve

value: Whole blood


title: WTCHG_70435019_CT_ChAdOx1_+ve


title: WTCHG_853846_202_D0_MenACWY_-ve

description:
small RNA
stage1


title: Ad_Irf1_1


title: GS_44_T12


title: WTCHG_70425018_CT+7_ChAdOx1_+ve


title: WTCHG_853846_201_CT+7_ChAdOx1_-ve

description:
small RNA
stage1


title: WTCHG_70465022_CT+7_ChAdOx1_+ve


title: PKR KO mouse with 5 days IMQ treatment ,repeat2

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Remove low quality bases and adaptor sequences via Trimmomatic.
Align trimmed data to rRNA sequene to remove reads from ribosomal RNAs.
Align clean data to mm10 genome by HISAT2 then calculate FPKM of linear RNAs.
The unmapped reads were realignment to mm10 mouse genome by TopHat-Fusion and identify circRNAs via CIRCexplorer3.
Assembly: mm10
Supplementary files format and content: FPKM

growth_protocol: Wildtype C57BL/6 and PKR KO mice received a daily topical dose of 62.5 mg IMQ cream (5%; Aldara; 3M Pharmaceuticals) on the shaved dorsal skin for 1-5 days.

treatment_protocol: Spleen samples were minced through a 70-μm mesh to obtain single-cell suspensions, treated with Red cell lysis buffer (TIANGEN) and washed with PBS for following experiments.

value: spleen

value: PKR KO

value: IMQ Day5


title: WTCHG_70415017_CT_ChAdOx1_+ve

value: CT


title: GS_9_T12


title: PKR KO mouse with 5 days IMQ treatment ,repeat1

value: Male


title: GS_17_T12


title: VCOV_s06_P3,γδ scTCR-seq

city: Rozzano, Milan

first: Sara

last: Terzoli

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Research Hospital

description:
10x Genomics
Sample 28

data_processing:
*library strategy: scTCR-seq
The γδ TCR alignment and consensus annotations were performed using Cell Ranger VDJ tools v3.1.0
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0
Supplementary files format and content: Comma-separated values (csv) files

source_name: blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats of HDs (n=6) or from 6 healthy vaccinated subjects through Lympholyte®-H Cell Separation density gradient solution (Cedarlane Laboratories, Burlington, North Carolina, USA) according to the manufacturer’s instruction. In vitro experiments were performed on freshly isolated PBMCs, with a viability greater than 95%, while single-cell ones on PBMCs previously frozen in Fetal Bovine Serum (FBS) supplemented with 10% of the cryoprotective Dimethyl Sulfoxide (DMSO).
Thawed PBMC samples were evaluated for viability prior to scRNA-seq analysis, and all were ≥95% viable. Cells were resuspended in a volume equivalent to 10,000 target cells for each sample, and were individually loaded onto a Chromium single-cell controller (10X Genomics) to generate single-cell gel beads-in-emulsion (GEMs). Captured cells were then lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Complementary DNAs (cDNA) were generated and split to generate γδ scTCR-seq libraries. To this end, gene-specific primers 25 were used within the 5′ regions of the TRGC and TRDC segments for the enrichment of TCR transcripts (v1.1 chemistry) Complementary DNAs were amplified, and the quality was assessed using an Agilent 4200 Tapestation. The scTCR-seq libraries were sequenced on Illumina NextSeq 550 platform.

value: blood

value: PBMC

value: 25-50 years old

tag: gender


title: WTCHG_70405016_CT+7_ChAdOx1_+ve

value: +ve


title: VCOV_s06_P1,γδ scTCR-seq

description:
10x Genomics
Sample 27


title: WTCHG_70395015_CT+7_ChAdOx1_+ve

value: Female


title: PKR KO mouse with 2 days IMQ treatment ,repeat2

value: IMQ Day2


title: GS_77_T6

value: Lung


title: VCOV_s06_P0,γδ scTCR-seq

description:
10x Genomics
Sample 26


title: GS_55_T6

value: EVLP gold standard


title: GS_55_T12


title: PKR KO mouse with 2 days IMQ treatment ,repeat1


title: WTCHG_70385014_CT_MenACWY_+ve

value: MenACWY


title: VCOV_s05_P4,γδ scTCR-seq

description:
10x Genomics
Sample 25


title: GS_44_T6


title: VCOV_s05_P3,γδ scTCR-seq

description:
10x Genomics
Sample 24


title: PKR KO mouse with 1 day IMQ treatment ,repeat1

value: IMQ Day1


title: GS_9_T6


title: WTCHG_70365012_CT+7_MenACWY_+ve


title: VCOV_s05_P2,γδ scTCR-seq

description:
10x Genomics
Sample 23


title: PKR KO mouse with 0 day IMQ treatment ,repeat2

value: IMQ Day0


title: GS_17_T6


title: WTCHG_70355011_CT_ChAdOx1_+ve

value: Whole blood


title: PKR KO mouse with 0 day IMQ treatment ,repeat1

value: spleen


title: VCOV_s05_P1,γδ scTCR-seq

description:
10x Genomics
Sample 22


title: VCOV_s05_P0,γδ scTCR-seq

description:
10x Genomics
Sample 21


title: WTCHG_70345010_CT+7_MenACWY_+ve


title: GS_55_T0


title: WT mouse with 5 days IMQ treatment ,repeat2

value: WT


title: WTCHG_70335009_CT_ChAdOx1_+ve


title: PKR KO mouse with 1 day IMQ treatment ,repeat2

value: PKR KO


title: GS_44_T0


title: WTCHG_70375013_CT_ChAdOx1_+ve

value: CT


title: VCOV_s04_P3,γδ scTCR-seq

description:
10x Genomics
Sample 19


title: WT mouse with 2 days IMQ treatment ,repeat2

value: Male


title: VCOV_s04_P4,γδ scTCR-seq

description:
10x Genomics
Sample 20

value: blood


title: GS_9_T0


title: WT mouse with 5 days IMQ treatment ,repeat1

value: IMQ Day5


title: Ad_eGFP_3

value: Articular cartilage

value: Primary culture

value: Chondrocyte

value: wild type

value: Ad-eGFP


title: VCOV_s04_P2,γδ scTCR-seq

description:
10x Genomics
Sample 18

value: PBMC

value: 25-50 years old

value: Female


title: WTCHG_70315007_CT_MenACWY_+ve

value: MenACWY

value: +ve


title: WTCHG_70325008_CT_ChAdOx1_+ve

value: Whole blood


title: VCOV_s04_P1,γδ scTCR-seq

description:
10x Genomics
Sample 17


title: GS_17_T0

value: Lung

value: EVLP gold standard


title: WT mouse with 2 days IMQ treatment ,repeat1

value: spleen

value: WT

value: IMQ Day2


title: WTCHG_70305006_CT_ChAdOx1_+ve

value: CT


title: WT mouse with 1 day IMQ treatment ,repeat2

value: Male

value: IMQ Day1


title: WTCHG_70295005_CT_MenACWY_+ve


title: GS_77_T0


title: WT mouse with 1 day IMQ treatment ,repeat1


title: PD_4_T12

description:
RNA-Seq of Sus scrofa : ex vivo lung sample treated by a pediatric dialysis system
design description: NextSeq 500 mid output kit v2

value: EVLP with dialisys


title: VCOV_s03_P4,γδ scTCR-seq

description:
10x Genomics
Sample 15

value: blood


title: WTCHG_70285004_CT+7_MenACWY_+ve


title: WT mouse with 0 day IMQ treatment ,repeat2

value: IMQ Day0


title: WTCHG_70275003_CT_MenACWY_+ve


title: VCOV_s03_P3,γδ scTCR-seq

description:
10x Genomics
Sample 14

value: PBMC


title: PD_3_T12


title: WT mouse with 0 day IMQ treatment ,repeat1


title: WTCHG_70265002_CT_ChAdOx1_+ve


title: PD_2_T12


title: VCOV_s03_P2,γδ scTCR-seq

description:
10x Genomics
Sample 13

value: 25-50 years old


title: PD_5_T6


title: VCOV_s03_P1,γδ scTCR-seq

description:
10x Genomics
Sample 12


title: L28_Day 7 KDM5-C70 rep 3

city: Los Angeles

first: Karen

last: Reue

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
RNA-seq alignment was performed with STAR v2.7.2a to the mouse genome GRCm38.97.
The read-count per gene was quantified with STAR and Ensembl Mus_musculus.GRCm38.97 GTF file.
Differential gene analysis was performed with EdgeR (v3.26.8) with trimmed mean of M values (TMM) normalization. Significance was denoted as adjusted p value<0.05 and fold change>1.25.
Assembly: GRCm38.97
Supplementary files format and content: EdgeR_normalized counts_filtered dglist.csv, this processed data file contains the EdgeR processed counts for all samples, which are TMM normalized and filtered to removed low expression genes.

growth_protocol: 3T3-L1 cells were maintained in 3T3-L1 Preadipocyte medium (PM-1-L1, Zen-bio) until Day 0. 3T3-L1 Differentiation medium (DM-2-L1, Zen-bio) was used between Day 0 and Day 2. 3T3-L1 Adipocyte medium (AM-1-L1, Zen-bio) was used after Day 2.

extract_protocol:
At the specified timepoints, 3T3-L1 cells were lyzed with qiazol and RNA was isolated with Qiagen miRNeasy micro kit based on manufacturer's instructions.
Strand-specific RNA-seq libraries were constructed with the Universal plus mRNA-Seq Kit (NuGEN Technologies).

treatment_protocol: 3T3-L1 preadipocytes were treated with DMSO or 10 µM KDM5-C70 compound at differentiation Day –2 (100% confluent), until Day 0.

value: adipocyte


title: WTCHG_70255001_CT+7_MenACWY_+ve

value: MenACWY

value: Female


title: PD_4_T6


title: PD_5_T12


title: L29_Day 7 KDM5-C70 rep 4


title: VCOV_s04_P0,γδ scTCR-seq

description:
10x Genomics
Sample 16


title: WTCHG_70235095_CT_MenACWY_+ve

value: Whole blood

value: +ve


title: VCOV_s03_II_P0,γδ scTCR-seq

description:
10x Genomics
VCOV_s03_P0_filtered_contig_annotations.csv
Sample 11_2


title: WTCHG_70225094_CT_MenACWY_+ve


title: L26_Day 7 KDM5-C70 rep 1


title: L27_Day 7 KDM5-C70 rep 2


title: WTCHG_70215093_D0_ChAdOx1_D0_only


title: PD_2_T6

value: Lung


title: VCOV_s03_P0,γδ scTCR-seq

description:
10x Genomics
VCOV_s03_P0_filtered_contig_annotations.csv
Sample 11


title: VCOV_s02_P4,γδ scTCR-seq

description:
10x Genomics
Sample 10


title: VCOV_s02_II_P3,γδ scTCR-seq

description:
10x Genomics
VCOV_s02_P3_filtered_contig_annotations.csv
Sample 9_2


title: WTCHG_70205092_D0_ChAdOx1_D0_only


title: L24_Day 7 DMSO rep 3

value: DMSO


title: WTCHG_70195091_D0_ChAdOx1_D0_only


title: VCOV_s02_P3,γδ scTCR-seq

description:
10x Genomics
VCOV_s02_P3_filtered_contig_annotations.csv
Sample 9


title: L23_Day 7 DMSO rep 2


title: VCOV_s02_II_P2,γδ scTCR-seq

description:
10x Genomics
VCOV_s02_P2_filtered_contig_annotations.csv
Sample 8_2


title: WTCHG_70185090_D0_MenACWY_D0_only


title: PD_3_T0


title: PD_2_T0


title: L22_Day 7 DMSO rep 1


title: PD_3_T6


title: L21_Day 2 KDM5-C70 rep 4


title: VCOV_s02_P2,γδ scTCR-seq

description:
10x Genomics
VCOV_s02_P2_filtered_contig_annotations.csv
Sample 8


title: WTCHG_70165088_D0_MenACWY_D0_only


title: L20_Day 2 KDM5-C70 rep 3


title: PD_5_T0


title: WTCHG_70155087_D0_MenACWY_D0_only


title: KO, replicate 1, scRNAseq

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: danrer11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: embryo

extract_protocol:
The tissues of head regions from zebrafish embryos were washed in a phosphate-buffered solution before adding dispase I (Sigma, D4818) and incubated at 0.5U, 33 °C for 10 min, with 750 rpm shock (pipette every 30 s). After adding 100 μL of serum to stop digestion, tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer, pelleted by centrifugation at 4 °C, and washed twice with ice-cold HBSS adding 0.5 % BSA to remove debris.
Single cell suspensions were processed for library construction following the manufacturer’s instructions (Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide). Libraries were then sequenced by Illumina Novaseq 6000 platform.

value: embryo

value: 48 hpf

value: tet2/3 double knock out


title: L25_Day 7 DMSO rep 4


title: VCOV_s02_II_P1,γδ scTCR-seq

description:
10x Genomics
VCOV_s02_P1_filtered_contig_annotations.csv
Sample 7_2

value: Male


title: VCOV_s02_P1,γδ scTCR-seq

description:
10x Genomics
VCOV_s02_P1_filtered_contig_annotations.csv
Sample 7


title: WTCHG_70145086_D0_ChAdOx1_D0_only


title: VCOV_s02_P0,γδ scTCR-seq

description:
10x Genomics
Sample 6


title: L18_Day 2 KDM5-C70 rep 1


title: PD_4_T0


title: WTCHG_70135085_D0_MenACWY_D0_only


title: KO, replicate 2, scRNAseq


title: L17_Day 2 DMSO rep 3


title: VCOV_s01_P4,γδ scTCR-seq

description:
10x Genomics
Sample 5


title: WTCHG_70125084_D0_ChAdOx1_D0_only


title: L19_Day 2 KDM5-C70 rep 2


title: WTCHG_70175089_D0_ChAdOx1_D0_only


title: WT, replicate 1, scRNAseq

value: wild type


title: L16_Day 2 DMSO rep 2


title: VCOV_s01_P3,γδ scTCR-seq

description:
10x Genomics
Sample 4


title: Mesenchymal glioma stem cells with intact EGFR (scRNA-seq)

city: Montreal

first: Janusz

last: Rak

state: Quebec

address: 1001 Decarie Blvd. Room E01.4366

department: Department of Pediatrics

country: Canada

institute: McGill University

description:
10x Genomics 3' CellPlex Multiplexing single cell
scRNA
Human_Mouse_filtered.rds
Human_Mouse_unfiltered.rds

data_processing:
We used Cell Ranger v3.0.1 (10x Genomics) to demultiplex the raw sequencing reads to FASTQ files and align the reads to human and mouse reference hg19 and mm10 to quantify gene counts for each origin of species.
We loaded the gene count data using the Seurat package and separate the object to human and mouse ones for further quality controls.
Doublets were filtered out in each object, and cells were annotated based on consistent expression of lineage-specific markers.
Assembly: hg19, mm10
Supplementary files format and content: There are two forms of processed data: Gene count matrix by CellRanger (.tar) and Seurat analysis results (.rds). Each format of processed data include both unfiltered and filtered versions.

organism:
Homo sapiens
Mus musculus

growth_protocol: 83 GSC WT and KO mesenchymal cells were maintained in DMEM-F12 supplemented with 100μg/ml EGF, 100μg/ml FGF, 0.2% Heparin, 1X B27 serum free supplement, 1% Glutamax and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Whole-tumor cells were dissociated and isolated using Collagenase/Dispase and resuspended in PBS for single-cell capture.
Following the Chromium Single Cell 3’ Reagent Kits v3 User Guide, a single-cell RNA library was generated using the GemCode Single-Cell Instrument.

treatment_protocol: The cells were injected in the brain of NSG mice.

value: mesenchymal glioma stem cells

value: WT

value: human 83 cells injected in brain of NSG mouse

tag: time

value: Day 15


title: WTCHG_70115083_D0_MenACWY_D0_only


title: WT, replicate 2, scRNAseq


title: L15_Day 2 DMSO rep 1


title: VCOV_s01_P2,γδ scTCR-seq

description:
10x Genomics
Sample 3

value: blood

value: PBMC

value: 25-50 years old


title: L14_Day 1 KDM5-C70 rep 4

value: adipocyte


title: VCOV_s01_P0,γδ scTCR-seq

description:
10x Genomics
Sample 1

value: Female


title: VAT_19

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

data_processing:
cDNA library was constructed using the ribosomal depletion methods, and reads were sequenced in 120 bp paired-end sequences per the Illumina 1.9 encoding Novogene protocols
Sample data integrity was examined using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, version 0.11.9) for quality control of fastq files.
Sequence reads were then mapped to the UCSC rn6 rat reference genome using HISAT2
Gene counts were generated from the BAM files using SummarizedExperiments (version 1.28.0) with the UCSC Rattus Norvegicus (rn6) reference genome
Assembly: Rn6
Supplementary files format and content: CSV file includes raw counts for each sample

organism: Rattus norvegicus

source_name: VAT

growth_protocol: 28-day-old male and female Sprague-Dawley rats (Charles River, Wilmington, MA) were allowed to acclimate for 8 days, followed by a 30 min. and a 2 hour training day in the nose-only apparatus. All rats were provided food (sterile Teklad 5% stock diet, Harlan, Madison, WI) and water ad libitum. 24 rats were weighed and assigned to the sham or PCB 52 exposure groups using a random number generator at 39 days of age for males 42 days of age for females to begin PCB 52 exposure.

extract_protocol:
Portions of the tissue (~100 mg) were rinsed with PBS and placed in a lysing matrix tube containing 1 mL of TRIzol. Sample solutions were then aliquoted to RNeasy spin columns, followed by the QIAGEN RNeasy Kits protocol to clean and isolate RNA from the tissue samples. Samples with RINs below 8 were excluded from further analysis.
mRNA enrichment: poly (A) capture or rRNA removal

treatment_protocol: Animals were exposed for 4 hours daily for 28 days to PCB 52 using a nose-only inhalation system by passing dried, high-efficiency particulate air (HEPA)-filtered air through the PCB 52-coated glass beads at a flow rate of 12 L/min.

value: VAT

value: Sprague-Dawley

value: PCB 52


title: VAT_23


title: VAT_17


title: L12_Day 1 KDM5-C70 rep 2


title: WTCHG_70105082_D0_ChAdOx1_D0_only

value: Whole blood


title: L13_Day 1 KDM5-C70 rep 3


title: WTCHG_70085080_D0_MenACWY_D0_only

value: MenACWY


title: Repli-seq-WT-for-q3C-S6

city: Beijing

first: Yang

last: Liu

address: Yiheyuan Road, No. 5

institute: School of life sciences, Peking University

data_processing:
Reads are mapped to hg19 with BWA-MEM
Assembly: hg19
Supplementary files format and content: bw files
Library strategy: Repli-seq

growth_protocol: Standard protocols for K562 cells, which has been provided in the ATCC database.

extract_protocol: Standard protocols with Proteinase K

treatment_protocol: It has been described in the experimental design


title: Mesenchymal glioma stem cells with depleted EGFR (scRNA-seq)

value: KO

value: Day 90


title: VAT_15

value: Male


title: WTCHG_70075079_D0_ChAdOx1_D0_only


title: Repli-seq-WT-for-q3C-S5


title: L11_Day 1 KDM5-C70 rep 1


title: WTCHG_70065078_D0_ChAdOx1_D0_only


title: Repli-seq-WT-for-q3C-S4


title: VAT_13


title: L10_Day 1 DMSO rep 3

value: DMSO


title: VAT_11

value: Sham


title: Repli-seq-WT-for-q3C-S3


title: WTCHG_70055077_D0_ChAdOx1_D0_only


title: L9_Day 1 DMSO rep 2


title: VAT_9


title: VCOV_s01_P1,γδ scTCR-seq

description:
10x Genomics
Sample 2


title: WTCHG_70045076_D0_ChAdOx1_D0_only


title: Repli-seq-WT-for-q3C-S2


title: VAT_7


title: WTCHG_70095081_D0_ChAdOx1_D0_only


title: L8_Day 1 DMSO rep 1


title: WTCHG_70035075_D0_MenACWY_D0_only


title: WTCHG_70025074_CT+7_ChAdOx1_+ve

value: +ve


title: L7_Day 0 KDM5-C70 rep 4


title: WTCHG_70015073_CT_ChAdOx1_+ve

value: CT


title: Proximal-q3C-S6-2

description: S6 phased cells

data_processing:
Illumina RTA software used for basecalling.
Both Illumina adapter sequences and ending low quality sequences (QC < 30) were trimmed by cutadapt (http://cutadapt.readthedocs.io/en/stable/); remaining reads shorter than 25bp were discarded.
The reported pipeline used in q3C-seq, termed PEM-Q (https://github.com/liumz93/PEM-Q), was applied to perform reads alignment and translocation break point detection.
The reported pipeline, PEM-Q, was applied to perform duplicates identification.
All samples were downsample to 16351 translocations by using bedtools sample -n .
Assembly: hg19
Supplementary files format and content: tab files indicating the junction site of chromatin interaction that downsampled from the original translocations
Library strategy: q3C-seq

growth_protocol: K562-FUCCI Cells were cultured in RPMI-1640 medium supplemented with 15% fetal bovine serum (FBS), 10 mM HEPES, 100 mM non-essential amino acids (NEAA), 50 U/mL penicillin, 50 mg/mL streptomycin, and 50 mM b-mercaptoethanol without further indication.

extract_protocol:
Standard protocols for genomic DNA extraction.
Genomic DNA was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced.

treatment_protocol: Asynchronized cells were incubated with 10 uM Hoechst33342 for 45 min and then subjected to FACS analysis. The G1 and S1-S6 cells were collected, fixed by 1% PFA, digested by DpnII, and then ligated in situ.

value: CML

value: with FUCCI knock-in at the AAVS1 locus

tag: cell cycle phase

tag: primer located within a fountain

value: Proximal


title: L5_Day 0 KDM5-C70 rep 2

value: adipocyte


title: Proximal-q3C-S5-2

description: S5 phased cells


title: Proximal-q3C-S4-2

description: S4 phased cells


title: WTCHG_72745250_CT+7_MenACWY_+ve

tag: tissue


title: VAT_5


title: VAT_1


title: VAT_3


title: L4_Day 0 KDM5-C70 rep 1


title: L3_Day 0 DMSO rep 3


title: Proximal-q3C-S3-2

description: S3 phased cells


title: WTCHG_72735249_CT_MenACWY_+ve

tag: timepoint


title: VAT_22

value: Female


title: WTCHG_72725248_CT_MenACWY_+ve

tag: vaccine


title: WTCHG_72715247_CT+7_MenACWY_+ve

tag: naat result


title: Proximal-q3C-S2-2

description: S2 phased cells


title: L2_Day 0 DMSO rep 2


title: L1_Day 0 DMSO rep 1


title: Proximal-q3C-S1-2

description: S1 phased cells


title: VAT_18

value: VAT


title: L6_Day 0 KDM5-C70 rep 3


title: VAT_20

value: Sprague-Dawley


title: VAT_16

value: PCB 52


title: WTCHG_72705246_CT_MenACWY_+ve

value: Whole blood

tag: age


title: WTCHG_72695245_CT+7_MenACWY_+ve

value: MenACWY

tag: Sex


title: MAC, siNC_3

extract_protocol:
Total RNA was extracted 36 h after transfection using the TRI reagent (Molecular Research Center, Inc.).
RNA sequencing libraries were constructed by Macrogen using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Articular cartilage

value: Primary culture

value: Chondrocyte

value: Control siRNA

value: control


title: VAT_14


title: VAT_24


title: WTCHG_72685244_CT_MenACWY_+ve

value: +ve

tag: participant number


title: MAC, siNC_2


title: Outside-q3C-S6-2

description: S6 phased cells

value: Outside


title: WTCHG_72675243_CT+7_ChAdOx1_+ve


title: Proximal-q3C-G1-2

description: G1 phased cells

value: CML


title: Repli-seq-WT-for-q3C-S1


title: Outside-q3C-S5-2

description: S5 phased cells

value: with FUCCI knock-in at the AAVS1 locus


title: MAC, siNC_1


title: MAC, siIRF1_3

value: Irf1 siRNA


title: VAT_12

tag: strain

value: Sham


title: Outside-q3C-S4-2

description: S4 phased cells

tag: genotype


title: VAT_10

value: Female

tag: treatment


title: Outside-q3C-S3-2

description: S3 phased cells

tag: cell type


title: MAC, siIRF1_2

tag: cell line


title: VAT_8

value: VAT


title: Outside-q3C-S2-2

description: S2 phased cells


title: WTCHG_72655241_CT+7_MenACWY_+ve

value: Male


title: MAC, siIRF1_1


title: VAT_6

value: Sprague-Dawley


title: WTCHG_72645240_CT_MenACWY_+ve

value: Whole blood

value: CT


title: Outside-q3C-S1-2

description: S1 phased cells


title: VAT_4


title: Tgfbr2_KO_10

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the mm39 reference genome using STAR and default parameters
Ensmebl v104 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method and differential gene expression conducted using LIMMA.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include VOOM adjusted cpms values for each Sample

source_name: lung

extract_protocol:
PureLink™ RNA Micro Kit
NEBNext®Single Cell/Low Input RNA Library Prep Kit for Illumina®

value: lung

value: C57BL/6 CD1 mixed

value: HopxCreERT2+/-;Tgfbr2 fl/fl; eYFP-/-

value: No treatment


title: WTCHG_72635239_CT_ChAdOx1_+ve


title: Outside-q3C-G1-2

description: G1 phased cells


title: Tgfbr2_KO_9


title: WTCHG_72625238_CT+7_MenACWY_+ve

value: MenACWY


title: Distal-q3C-S6-2

description: S6 phased cells

value: Distal


title: SAT_23

source_name: SAT

value: SAT

value: PCB 52


title: WTCHG_72665242_CT_ChAdOx1_+ve

value: +ve


title: Tgfbr2_KO_8


title: WTCHG_72605236_CT_MenACWY_+ve


title: SAT_21


title: Tgfbr2_KO_7


title: WTCHG_72595235_CT+7_MenACWY_+ve


title: Distal-q3C-S5-2

description: S5 phased cells

value: CML

value: with FUCCI knock-in at the AAVS1 locus


title: SAT_17


title: Distal-q3C-S4-2

description: S4 phased cells


title: Distal-q3C-S3-2

description: S3 phased cells


title: SAT_19


title: Tgfbr2_het_4

value: HopxCreERT2+/-;Tgfbr2 fl/+; eYFP-/-


title: Tgfbr2_het_3


title: Distal-q3C-S2-2

description: S2 phased cells


title: Tgfbr2_het_2


title: WTCHG_72575233_CT+7_MenACWY_-ve

value: -ve

value: Female


title: SAT_15

value: Male

value: Sprague-Dawley


title: WTCHG_72585234_CT_MenACWY_+ve

value: Whole blood

value: CT


title: Distal-q3C-S1-2

description: S1 phased cells


title: Tgfbr2_het_1

value: lung

value: C57BL/6 CD1 mixed


title: VAT_2

value: VAT

value: Sham


title: WTCHG_72565232_CT_MenACWY_-ve

value: MenACWY


title: PTO017_ADT Neonate Liver

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

description:
Antibody-derived oligonucleotide (ADT)
PTO017_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
genome_build/assembly: n/a
The Cell Ranger pipeline (10x Genomics, version 3.1.0) was used to perform sample 996 demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene 997 expression and cell surface protein libraries.
Read 2 of the gene expression libraries was mapped to the mouse reference genome.
Subsequent barcode processing, unique molecular identifiers filtering and gene counting were performed using the Cell Ranger suite.
CITE-seq reads were quantified using the feature-barcoding functionality.
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format files as produced by the Cellranger pipeline of 10X Genomics
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Neonate Liver

growth_protocol: All mice were kept in individually ventilated GM500 cages (Techniplast) with a 14/10-hour light/dark cycle in a temperature-controlled (21°C). Mice were provided water and food ad libitum.

extract_protocol:
From adult 8-weeks-old Adult and P0.5 Neonatal mice from ex vivo extracted thymus, liver, spleen, and bone marrow, the following samples were used; Adult mice: 12 thymus, 4 spleens, 12 perfused livers, and bone marrow was collected from two hind legs (tibia and fibia) of 4 mice. For all adult organs, an equal number of male and female mice were used. Neonatal mice: 90 thymus, 45 spleen, 45 bone marrow samples (arm- and leg bones from 45 neonates), 30 livers.
Following sorting, both the NTOC supernatant cells and ex vivo tissue comparison cells were stained with mouse cell surface protein TotalSeq-A antibodies panels containing 9 isotype controls and 77 (NTOC) or 174 (tissue) oligo-conjugated antibodies (TotalSeq-A, Biolegend). The sorted single-cell suspensions were resuspended at a final estimated conc. of 1500 and 1100 cells/µl for NTOC and tissues, respectively. The cells were loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to create single-cell gel beads-in-emulsion (GEM). The scRNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library kit, version 3 (NTOC) and version NextGEM 3.1 (tissue) (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primer (3 nM, 5’CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos.

value: Neonate Liver

value: Enrichment for NK cells and stem cells


title: WTCHG_72615237_CT_MenACWY_+ve

data_processing:
The sequencing data were aligned against the whole human (Homo sapiens) genome build GRCh38 using STAR (version 2.7.3a).
Gene features were counted using HTSeq (version 0.11.1), using human gene annotation general transfer format version GRCh38.92.
Genes with low counts across most libraries were removed by only retaining genes with abundance greater than 3 counts per million in 9 or more samples.
Ribosomal RNA (rRNA), sex chromosome genes, mitochondrial RNA and haemoglobin genes were excluded from downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt file containing normalised expression (rpkm - reads per kilobase per million) for each gene for each sample

extract_protocol:
Peripheral blood (up to 2.5ml) was collected into a PAXgeneTM RNA tube at vaccination (D0), SARS-CoV-2 diagnosis (CT) and 7 days post diagnosis (CT+7). Total RNA was extracted using the PAXgene blood RNA kit (PreAnalytiX, Switzerland) on the QIAsymphony SP (Qiagen) with the PAX_RNA V5 protocol. Eluted RNA was quantified using the Agilent RNA ScreenTape assay on the 4200 TapeStation System (Agilent).
RNA was ribodepleted and globin depleted using Ribo-ZeroTM Gold rRNA removal Kit (Illumina, USA). RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and quality controlled before 150bp paired-end sequencing (NovaSeq6000).

value: +ve


title: Distal-q3C-G1-2

description: G1 phased cells

value: CML

value: Distal


title: SAT_11

value: SAT


title: Proximal-q3C-S6

description: S6 phased cells

value: with FUCCI knock-in at the AAVS1 locus

value: Proximal


title: WTCHG_72555231_CT+7_MenACWY_-ve

value: -ve

value: Male


title: PTO016_ADT Adult Liver

description:
Antibody-derived oligonucleotide (ADT)
PTO016_filtered_feature_bc_matrix.h5

source_name: Adult Liver

value: Adult Liver


title: SAT_9

value: Sprague-Dawley


title: PTO015_ADT Neonate Bone Marrow

description:
Antibody-derived oligonucleotide (ADT)
PTO015_filtered_feature_bc_matrix.h5

source_name: Neonate Bone Marrow

value: Neonate Bone Marrow


title: SAT_7


title: Proximal-q3C-S5

description: S5 phased cells


title: WTCHG_72535229_CT_MenACWY_-ve

value: Whole blood

value: CT

value: Female


title: Proximal-q3C-S4

description: S4 phased cells


title: PTO014_ADT Adult Bone Marrow

description:
Antibody-derived oligonucleotide (ADT)
PTO014_filtered_feature_bc_matrix.h5

source_name: Adult Bone Marrow

value: Adult Bone Marrow


title: SAT_5

value: Sham


title: WTCHG_72525228_CT+7_ChAdOx1_+ve


title: SAT_3


title: PTO013_ADT Neonate Spleen

description:
Antibody-derived oligonucleotide (ADT)
PTO013_filtered_feature_bc_matrix.h5

source_name: Neonate Spleen

value: Neonate Spleen

value: Enrichment for NK cells and stem cells


title: PTO012_ADT Adult Spleen

description:
Antibody-derived oligonucleotide (ADT)
PTO012_filtered_feature_bc_matrix.h5

source_name: Adult Spleen

value: Adult Spleen


title: Proximal-q3C-S2

description: S2 phased cells

value: CML


title: WTCHG_72505226_CT+7_ChAdOx1_+ve

source_name: Whole blood

value: +ve


title: SAT_1

value: SAT


title: Proximal-q3C-S1

description: S1 phased cells

value: with FUCCI knock-in at the AAVS1 locus

value: Proximal


title: PTO011_ADT Neonate Thymus

description:
Antibody-derived oligonucleotide (ADT)
PTO011_filtered_feature_bc_matrix.h5

source_name: Neonate Thymus

value: Neonate Thymus


title: SAT_24

value: PCB 52


title: SAT_13

value: Male

value: Sprague-Dawley


title: WTCHG_72495225_CT_ChAdOx1_+ve

value: Whole blood


title: SAT_22


title: PTO010_ADT Adult Thymus

description:
Antibody-derived oligonucleotide (ADT)
PTO010_filtered_feature_bc_matrix.h5

source_name: Adult Thymus

value: Adult Thymus


title: Proximal-q3C-G1

description: G1 phased cells


title: WTCHG_72545230_CT_MenACWY_-ve

value: CT

value: MenACWY

value: -ve


title: PTO017_RNA Neonate Liver

description:
poly A RNA
PTO017_filtered_feature_bc_matrix.h5

data_processing:
genome_build/assembly: GRCm38.99
The Cell Ranger pipeline (10x Genomics, version 3.1.0) was used to perform sample 996 demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene 997 expression and cell surface protein libraries.
Read 2 of the gene expression libraries was mapped to the mouse reference genome.
Subsequent barcode processing, unique molecular identifiers filtering and gene counting were performed using the Cell Ranger suite.
CITE-seq reads were quantified using the feature-barcoding functionality.
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format files as produced by the Cellranger pipeline of 10X Genomics
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: Neonate Liver


title: Outside-q3C-S6

description: S6 phased cells

value: Outside


title: SAT_20

value: Female


title: WTCHG_72485224_CT_ChAdOx1_+ve


title: PTO016_RNA Adult Liver

description:
poly A RNA
PTO016_filtered_feature_bc_matrix.h5

value: Adult Liver

value: Enrichment for NK cells and stem cells


title: Outside-q3C-S5

description: S5 phased cells

value: CML


title: SAT_18

value: SAT


title: WTCHG_72475223_CT+7_ChAdOx1_-ve


title: SAT_16


title: WTCHG_72465222_CT_ChAdOx1_-ve


title: WTCHG_72515227_CT_ChAdOx1_+ve

value: +ve


title: PTO015_RNA Neonate Bone Marrow

description:
poly A RNA
PTO015_filtered_feature_bc_matrix.h5

value: Neonate Bone Marrow


title: Proximal-q3C-S3

description: S3 phased cells

value: with FUCCI knock-in at the AAVS1 locus

value: Proximal


title: PTO014_RNA Adult Bone Marrow

description:
poly A RNA
PTO014_filtered_feature_bc_matrix.h5

value: Adult Bone Marrow


title: Outside-q3C-S4

description: S4 phased cells


title: SAT_14

value: Sprague-Dawley

value: PCB 52


title: WTCHG_72445220_CT+7_ChAdOx1_-ve

value: Whole blood

value: Male


title: PTO013_RNA Neonate Spleen

description:
poly A RNA
PTO013_filtered_feature_bc_matrix.h5

value: Neonate Spleen


title: Outside-q3C-S2

description: S2 phased cells


title: SAT_12

value: Sham


title: PTO012_RNA Adult Spleen

description:
poly A RNA
PTO012_filtered_feature_bc_matrix.h5

value: Adult Spleen


title: SAT_10

value: Female


title: Outside-q3C-S1

description: S1 phased cells

value: Outside


title: WTCHG_72425218_D0_ChAdOx1_-ve

value: -ve


title: Outside-q3C-G1

description: G1 phased cells

value: CML


title: SAT_8

value: SAT


title: PTO011_RNA Neonate Thymus

description:
poly A RNA
PTO011_filtered_feature_bc_matrix.h5

value: Neonate Thymus

value: Enrichment for NK cells and stem cells


title: WTCHG_72415217_CT_ChAdOx1_-ve

value: CT


title: Distal-q3C-S6

description: S6 phased cells

value: with FUCCI knock-in at the AAVS1 locus

value: Distal


title: WTCHG_72405216_CT_MenACWY_-ve

value: MenACWY


title: SAT_6

value: Sprague-Dawley


title: Distal-q3C-S5

description: S5 phased cells


title: WTCHG_72455221_D0_ChAdOx1_-ve

value: Whole blood


title: WTCHG_72395215_CT_MenACWY_-ve


title: Outside-q3C-S3

description: S3 phased cells


title: Muscle fibers (EDL), sham, rep 3

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
Adapter trimming was performed with CutAdapt v2.1 (-m 30 –a ADAPER-SEQUENCE).
FastQ files were mapped using Tophat v.2.1.0 (parameters: -x 1 -g 1 --no-coverage-search –no-convert-bam).
Reads per gene were counted with featureCounts v1.6.5 (-s 2).
RPKMs were calculated based on the gene length given by featureCounts.
Assembly: Ensembl: GRCm38.100
Supplementary files format and content: Excel sheet (xlsx) containing counts, RPMs and RPKMs

source_name: Muscle fibers

extract_protocol:
TA muscles or EDL myofibers were homogenized in TRIzol reagent and RNA was isolated according to the manufacturer`s protocol (VWR, 30-2010)
Library preparation was performed using the NEBNext Ultra II directional RNA kit with polyA molecule selection and unique dual indexing.

treatment_protocol: Sham/ DEN for 21 days

value: Muscle fibers

value: sham


title: Distal-q3C-S4

description: S4 phased cells


title: BAT_23

source_name: BAT

value: BAT

value: Male

value: PCB 52


title: Muscle fibers (EDL), sham, rep 2


title: WTCHG_72385214_D0_MenACWY_-ve

value: Female


title: SAT_2

value: Sham


title: BAT_21


title: Distal-q3C-S3

description: S3 phased cells

value: CML


title: Muscle fibers (EDL), sham, rep 1


title: Distal-q3C-S2

description: S2 phased cells


title: BAT_17


title: PTO010_RNA Adult Thymus

description:
poly A RNA
PTO010_filtered_feature_bc_matrix.h5

value: Adult Thymus


title: WTCHG_72355211_D0_ChAdOx1_+ve

value: +ve


title: Distal-q3C-S1

description: S1 phased cells


title: WTCHG_72375213_CT+7_ChAdOx1_+ve


title: WTCHG_72365212_CT_ChAdOx1_+ve


title: WTCHG_72435219_CT_ChAdOx1_-ve

value: -ve


title: Distal-q3C-G1

description: G1 phased cells


title: Muscle fibers (EDL), DEN, rep 3

value: DEN


title: Muscle fibers (EDL), sham, rep 4


title: Muscle fibers (EDL), DEN, rep 4


title: BS-seq-GEMS65

first: Wang

last: Zi

address: NO2 Yuanmingyuan West Road, Haidian

department: ational Maize Improvement Center  of China

institute: China Agricultural University

data_processing:
Sequenced reads of each samples were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73.v4 whole genome and de duplicated using bismark. Calculated the sequencing conversion efficiency and methylation level of each sample based on the results generated from the previous step.
Merge the sequenced reads of same genotype and perform the same analysis as above, then calculate the differentially methylated regions based on the results generated.
Assembly: B73.v4
Supplementary files format and content: tab files, matrix, bw

organism: Zea mays

source_name: ear

extract_protocol:
Genomic DNA was isolated from the developing ear (<0.5 cm in length) with the traditional CTAB method.
Samples were fragmented and ligated with TruSeq-methylated adapters. Bisulfite conversion was performed on 500 ng of adaptor-ligated DNA using the MethylCode bisulfite conversion kit (Zymo Research, Orange, CA, USA). Converted DNA was amplified for 14 cycles.

value: ear

value: developing ear (<0.5 cm in length)

value: natural population line


title: WTCHG_72345210_CT+7_MenACWY_-ve

value: MenACWY


title: BAT_15

value: Sprague-Dawley


title: BAT_11


title: Muscle fibers (EDL), DEN, rep 2

value: Muscle fibers


title: BS-seq-DE.EX


title: WTCHG_72325208_D0_MenACWY_-ve

value: Whole blood


title: BAT_13

value: BAT


title: Whole muscle (TA), sham, rep 4

source_name: Whole muscle

value: Whole muscle

value: sham


title: BS-seq-CML171


title: BAT_19

value: Male

value: PCB 52


title: BS-seq-GEMS55


title: WTCHG_72335209_CT_MenACWY_-ve

value: CT

value: Female


title: Muscle fibers (EDL), DEN, rep 1


title: Whole muscle (TA), sham, rep 3


title: WTCHG_72315207_CT+7_ChAdOx1_-ve


title: BAT_9

value: Sham


title: BS-seq-CIMBL52


title: WTCHG_72295205_CT_MenACWY_-ve

value: -ve


title: Whole muscle (TA), sham, rep 2


title: BS-seq-CIMBL40


title: BAT_5


title: BAT_3


title: Whole muscle (TA), sham, rep 1


title: BS-seq-CIMBL20


title: WTCHG_72285204_D0_MenACWY_-ve


title: Whole muscle (TA), DEN, rep 4

value: DEN


title: BAT_1


title: WTCHG_72275203_CT_MenACWY_-ve


title: WTCHG_72265202_D0_MenACWY_-ve


title: BAT_22


title: WTCHG_72305206_CT_ChAdOx1_-ve


title: BS-seq-CIMBL19

value: ear


title: BS-seq-CIMBL12

value: developing ear (<0.5 cm in length)


title: BAT_24


title: Whole muscle (TA), DEN, rep 3


title: Whole muscle (TA), DEN, rep 2


title: BAT_7


title: Whole muscle (TA), DEN, rep 1


title: BAT_20


title: BS-seq-CIMBL119

value: natural population line


title: BAT_18


title: E14.5, cochlea, rep2, scRNAseq

city: Ann Arbor

first: Joerg

last: Waldhaus

state: MI

address: Medical Sciences I Building, Rm. 5315A, 1150 West Medical Center Drive

department: Department of Otolaryngology–Head and Neck Surgery, Kresge Hearing Research Institute

institute: University of Michigan

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Next, the data set included YFP-positive cells from a different experiment. To exclude the YFP-positive cells from analysis, we removed all cells with no GFP expression and positive YFP expression values detected.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cochlear duct

extract_protocol:
Embroynic cochlea samples were dissected, dissociated and flow sorted for GFP expression. Next, cells were encapsulated using 10x Genomics platform for scRNA-seq library preparation following the manufacturer’s instructions.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3 protocol, 10x Genomics).

value: Cochlear duct

value: Auditory cells

value: Embryonic day 14.5 (E14.5)


title: WTCHG_72245200_CT_ChAdOx1_-ve

first: Irina

last: Chelysheva

address: Roosevelt Dr

institute: University of Oxford

value: Whole blood


title: BS-seq-BY4944


title: WTCHG_72235199_D0_ChAdOx1_-ve


title: BAT_14

value: BAT

value: Sprague-Dawley


title: E14.5, cochlea, rep1, scRNAseq

description: 10x Genomics


title: BAT_16


title: WTCHG_72225198_CT+7_MenACWY_+ve

value: MenACWY

value: +ve


title: WTCHG_72255201_CT+7_ChAdOx1_-ve


title: WTCHG_72215197_CT_MenACWY_+ve


title: BS-seq-zmet2-rep 3

value: zmet2 mutant


title: E12.5, cochlea, rep1, scRNAseq

description: 10x Genomics

value: Embryonic day 12.5 (E12.5)


title: E12.5, cochlea, rep2, scRNAseq

description: 10x Genomics


title: BAT_12

value: Female


title: BS-seq-zmet2-rep 2


title: WTCHG_72205196_D0_MenACWY_+ve


title: WT, replicate 2, bulk RNAseq

city: Durham

first: Mari

last: Shinohara

state: NC

address: 207 research drive

department: Immunology

institute: Duke University Medical School

data_processing:
TrimGalore v0.4.0 for initial processing of fastq files
STAR v2.4.1d was used to align the reads ('--outFilterMultimapNmax 1' and '--alignSJoverhangMin 500' were the non-default parameters used)
HTSeq v0.6.1p1 to quantify gene expression ('-s reverse' was the non-default parameter used)
Genes were removed prior to normalization if they didn't have at least 10 reads in any one sample
Normalization and differential expression was carried out using the DESeq26 Bioconductor package with the R statistical programming environment
Assembly: ENSEMBL release GRCm38v68 of the mouse genome and transcriptome
Supplementary files format and content: Tab separated text files (.tsv) that contain the raw HTSeq counts as well as the EdgeR normalized expression values

growth_protocol: Obtained from mice

extract_protocol:
Alveolar macrophages of wild type (WT) and osteopontin knock-out (OPNKO) mice were isolated by Fluorescence-activated cell sorting (FACS) according to the cell surface markers and analyzed using scRNAseq.
We built 10 stranded mRNA libraries. We pooled libraries to equimolar concentration and sequenced the pool on one lane of  S-Prime Flow Cell

treatment_protocol: No treatment in vivo and ex vivo

value: lung

value: Alveolar Macrophages

value: C57BL6 OPNKO

value: Bleomycin


title: BAT_10

value: Sham


title: BS-seq-zmet2-rep 1

value: ear

value: developing ear (<0.5 cm in length)


title: OPNKO, replicate 2, bulk RNAseq

description: We built 10 stranded mRNA libraries. We pooled libraries to equimolar concentration and sequenced the pool on one lane of  S-Prime Flow Cell


title: OPNKO, replicate 1, bulk RNAseq

value: C57BL6 WT


title: BS-seq-WT-rep 2

value: WT


title: BS-seq-WT-rep 3


title: BS-seq-4F1

value: natural population line


title: WTCHG_72175193_D0_ChAdOx1_+ve

city: Oxford

value: Whole blood


title: BAT_6

value: BAT

value: Sprague-Dawley


title: WTCHG_72185194_CT_ChAdOx1_+ve

value: CT

value: +ve


title: BS-seq-WT-rep 1


title: WTCHG_72195195_CT+7_ChAdOx1_+ve


title: BAT_8


title: BAT_4


title: zmet2-rep 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73.v4 whole genome using bowtie2
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using stringtie. DGEs werw using DEseq2 in R-project.
Assembly: B73.v4
Supplementary files format and content: tab files, matrix, bw

value: zmet2 mutant


title: BAT_2

value: Female


title: D4_INF_a1_24h

city: Paris

first: Ludovic

last: Tailleux

state: non-US Resident

address: 25-28 rue du Dr Roux, 75015 Paris, France

institute: Institut Pasteur

data_processing:
Raw reads derived from the sequencing instrument are clipped for adapter sequence, trimmed for minimum quality (Q30) in 3' and filtered for minimum length of 32 bp using Trimmomatic [PMID: 24695404]. Surviving read pairs were aligned to GRCh38 by the ultrafast universal RNA-seq aligner STAR [PMID: 23104886] using the recommended two passes approach. Aligned RNA-Seq reads were assembled into transcripts and their relative abundance was estimated using Stringtie [PMID: 25690850]. All of the above processing steps were accomplished through the GenPipes framework [PMID 31185495].
Assembly: GRCh38
Supplementary files format and content: The raw counts were generated using Stringtie [PMID: 25690850].

source_name: Blood mononuclear cells - donor 4

growth_protocol: Blood mononuclear cells from 4 healthy volunteers (named D1, D2, D3 and D4; Etablissement Français du Sang, Paris, France) were isolated by Lymphocytes Separation Medium centrifugation (Eurobio). CD14+ monocytes were isolated by positive selection using CD14 microbeads (Miltenyi Biotec). Recovered cells were cultured at 37°C and 5% CO2 in RPMI-1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Dutscher), 2 mM L-glutamine (Gibco) and macrophage colony stimulating factor (M-CSF, 20 ng/mL; Miltenyi Biotec). Cultures were fed every 2 days with complete medium containing full doses of cytokine. Monocytes were allowed to differentiate into macrophages for 6 days at 37°C in 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was extracted using QIAzol reagent (Life Technologies) and purified over RNeasy columns (Qiagen). The quality of all samples was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies) to verify RNA integrity. Only samples with a good RNA yield and no RNA degradation (ratio of 28S to 18S, > 1.7; RNA integrity number > 9) were used for further experiments. All samples were sequenced two times, in two different lanes (named L001 and L002 in the file names).
cDNA libraries were prepared with the Illumina TruSeq Stranded mRNA and the IDT for Illumina TruSeq UD Indexes, and were sequenced on an Illumina NovaSeq 6000 systems at the CHU Sainte-Justine Integrated Centre for Pediatric Clinical Genomics (Montreal, Canada).

treatment_protocol: Mycobacterium tuberculosis H37Rv (MTB) was grown from a frozen stock to mid-log phase in 7H9 medium (Becton Dickinson), supplemented with albumin-dextrose-catalase (ADC, Becton Dickinson). Before infection, MTB were washed and resuspended in 4 mL PBS. Clumps were eliminated by passing through a 10 µm filter. The density of bacteria in the supernatant was verified by measuring the OD600 and aliquot volumes defined to allow one bacterium-per two cell infections. After 2 h of incubation at 37 °C, infected cells were washed three times in PBS and treated with amikacin (50 µg/ml). After 1 h, cells were washed and incubated in fresh complete medium. After 24h, cells were treated with MC3465 or MC3209 (10 μM) during 4 h and 24 h.

tag: subject

value: Donor 4

value: human monocyte-derived macrophage

tag: infection statut

value: Infected


title: D4_INF_40_24h


title: zmet2-rep 1


title: PT286-WT

city: Hefei

first: Bingbing

last: Ren

state: Anhui

address: University  of  Science  and  Technology  of  China,  443  Huangshan  Road, Hefei, Anhui

data_processing:
Libraries were sequenced using PE150 (Pair End 150bp) on an Illumina HiSeq 6000 instrument (Novogene, China). Low quality reads (one end low quanlity base > 50%), N-containing reads (unidentified reads ratio > 0.002) and reads with adapters are removed from the raw data to generate clean reads for further analysis.
Clean reads were mapped onto the fission yeast genome released on Pombase using HISAT2
The expressions of mRNA and lncRNA were evaluated with Stringtie followed by the annotation references
Genome_build: reference sequence based on Pombase(https://www.pombase.org/)

organism: Schizosaccharomyces pombe

growth_protocol: Strain PT286 was grown at 30℃ to mid-log phase in YES medium.

extract_protocol:
Total RNA was extracted from harvested cells using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured in YES medium and harvested at 16h. Then cultured in YES medium and harvested at 8h.

value: wild type


title: PT286-Phl

institute: University of Science and Technology of China

data_processing:
Libraries were sequenced using PE150 (Pair End 150bp) on an Illumina HiSeq 6000 instrument (Novogene, China). Low quality reads (one end low quanlity base > 50%), N-containing reads (unidentified reads ratio > 0.002) and reads with adapters are removed from the raw data to generate clean reads for further analysis.
Clean reads were mapped onto the fission yeast genome released on Pombase using HISAT2
The expressions of mRNA and lncRNA were evaluated with Stringtie followed by the annotation references
Genome_build: reference sequence based on Pombase(https://www.pombase.org/)
Supplementary_files_format_and_content: FPKM

treatment_protocol: For the stress experiments, cells were cultured in YES medium and harvested at 16h. Then changed medium to induce stress and harvested at 8h after addition of different DNA damage-inducing agents to the culture. Different DNA damage conditions were induced as follows. Camptothecin (APExBIO) was added to a fifinal concentration of 20 μM. Hydroxyurea (Sigma) was added to a fifinal concentration of 10 mM. Methyl methanesulfonate (Sigma) was added to a fifinal concentration of 0.02%. Phleomycin (APExBIO) was added to a fifinal concentration of 5 μg/mL.

value: phleomycin (5 μg/mL) for 8h


title: OV33604 Ovarian cancer tumor nest CD68- ROI 6

city: South San Francisco

first: Lee

middle: Benjamin

last: Rivera

address: 333 Oyster Point Blvd.

department: Biology

institute: NGM Bio

description: Spatial transcriptomics by GeoMx Digital Spatial Prolifer

data_processing:
Raw fastq files were converted to DCC files by the Nanostring geomxngspipeline software.
The DCC files were uploaded to the DSP software and the read counts file was exported for furthere analysis.
Assembly: hg38
Supplementary files format and content: DCC files generated by the Nanostring geomxngspipeline software
Supplementary files format and content: Read count files exported from Nanostring GeoMx DSP software

source_name: tumor

extract_protocol:
Probes (photocleaved oligos containing a readout tag sequence identifier and unique molecule identifier) were aspirated by the GeoMx instrument for library preparation.
Following collection on the GeoMx instrument, the probes were subjected to polymerase chain reaction amplification during which i5 and i7 indexing sequences were added. Following subsequent pooling, purification, and qualtity control, the library was sequenced on an Illumina HiSeq4000.
Spatial Transcriptomics

value: tumor

value: CD68 neg


title: WT-rep 2

value: ear

value: developing ear (<0.5 cm in length)


title: PT286-MMS

value: methyl methanesulfonate (0.02%) for 8h


title: OV33604 Ovarian cancer tumor nest CD68+ ROI 6

value: CD68 pos


title: D4_INF_DMSO_24h

value: DMSO


title: D4_UNF_a1_24h

value: Uninfected


title: PT286-HU

value: hydroxyurea (10 mM) for 8h


title: OV33604 Ovarian cancer tumor nest CD68- ROI 5


title: WT, replicate 1, bulk RNAseq

source_name: lung

value: lung

value: Alveolar Macrophages

value: C57BL6 WT

value: Bleomycin


title: PT286-CPT

value: camptothecin (20 μM) for 8h


title: OV33604 Ovarian cancer tumor nest CD68+ ROI 4


title: OV33604 Ovarian cancer tumor nest CD68+ ROI 5


title: D3_INF_40_24h

source_name: Blood mononuclear cells - donor 3

value: Donor 3

value: human monocyte-derived macrophage

value: Infected


title: mouse, feces, M4

city: Dalian

first: Hong

middle: xu

address: 1 Light Industry Garden, Ganjingzi District, Dalian City, Liaoning Province, China

institute: Dalian Polytechnic University

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads were normalized by calculated CPM value
Differential expression analysis of miRNAs between groups was performed using edgeR with settings of 1.5-fold difference, p-value < 0.05 and within-group CPM mean of 1 to screen for differentially expressed miRNAs.
Assembly: mm10
Supplementary files format and content: Microsoft excel file includes the counts per million (CPM) reads of miRNAs in all samples.
Supplementary files format and content: Differential expression analysis of miRNAs between groups was performed using edgeR. For differentially expressed miRNA were screened with the significant threshold to 1.5-fold difference, p-value ≤ 0.05 and the mean CPM within the group ≥ 1

source_name: feces

extract_protocol:
Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: feces

tag: condition

value: Model


title: mouse, feces, M2


title: OV33604 Ovarian cancer stroma CD68- ROI 3

value: tumor

value: CD68 neg


title: mouse, feces, M5


title: mouse, feces, M1


title: D3_INF_DMSO_24h


title: WT_3_If

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Sequences were mapped to W275 C elegans genome
The htseq-count were further analyesd for the differentially expressed features from count tables using DESeq2
Genome_build: Genome_build: Caenorhabditis elegans genome WS275
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample

organism: Caenorhabditis elegans

source_name: C elegans whole animal

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to L4 larval stage at 20oC. The animals were infected with S. aureus for 8 hours.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Purification of Total RNA was done using the TURBO DNase.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were washed off the plates with M9 and frozen in QIAzol by ethanol/dry ice and stored at -80 prior to RNA extraction.

value: Wild type (N2)

value: whole animal


title: OV33604 Ovarian cancer stroma CD68+ ROI 3

value: CD68 pos


title: D3_UNF_a1_24h

value: Uninfected


title: WT_2_If


title: mouse, feces, LSFP5

value: LSFP


title: WT_1_If


title: OV33604 Ovarian cancer stroma CD68- ROI 2


title: WT-rep 1

value: ear

value: developing ear (<0.5 cm in length)

value: WT


title: D3_UNF_40_24h


title: npr15_3_If


title: D4_UNF_DMSO_24h

value: Donor 4

value: DMSO


title: OV33604 Ovarian cancer stroma CD68+ ROI 2


title: D3_UNF_DMSO_24h

value: Donor 3


title: OV33604 Ovarian cancer tumor nest CD68- ROI 4


title: mouse, feces, LSFP3


title: D4_UNF_40_24h

value: human monocyte-derived macrophage


title: D3_INF_a1_24h

value: Infected


title: OV33604 Ovarian cancer stroma CD68- ROI 1


title: mouse, feces, M3

value: feces


title: npr15_2_If


title: npr15_1_If


title: D2_INF_a1_24h

source_name: Blood mononuclear cells - donor 2

value: Donor 2


title: mouse, feces, LSFP1


title: OV33604 Ovarian cancer stroma CD68+ ROI 1

value: tumor


title: D2_INF_DMSO_24h


title: WT_3_Nof

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Sequences were mapped to W275 C elegans genome
The htseq-count were further analyesd for the differentially expressed features from count tables using DESeq2
Genome_build: W275 C elegans genome
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample

source_name: C elegans whole animal_wild type

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to L4 larval stage at 20oC

tag: strain background

tag: genotype/variation

value: wild type


title: mouse, feces, LSFP2

tag: tissue


title: D2_UNF_a1_24h


title: mouse, feces, C5

value: Control


title: 43881 Lung cancer tumor nest CD68- ROI 6

value: CD68 neg


title: mouse, feces, C4


title: mouse, feces, LSFP4


title: 43881 Lung cancer tumor nest CD68+ ROI 6

value: CD68 pos


title: D2_UNF_40_24h

value: Uninfected


title: npr15_3_Nof

source_name: C elegans whole animal_npr-15(tm12539)

value: whole animal


title: mouse, feces, C3


title: D2_UNF_DMSO_24h


title: 43881 Lung cancer tumor nest CD68+ ROI 5


title: D2_INF_40_24h


title: 43881 Lung cancer tumor nest CD68- ROI 4


title: mouse, feces, C2


title: 43881 Lung cancer tumor nest CD68- ROI 5


title: npr15_2_Nof


title: mouse, feces, C1


title: D1_INF_a1_24h

source_name: Blood mononuclear cells - donor 1

value: Donor 1


title: npr15_1_Nof


title: prosIR-ATAC

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

institute: National Institute of Biological Sciences, Beijing

data_processing:
Raw data were processed to remove low quality reads, and the clean data were then subjected to Cutadapt software to remove index sequences. These raw sequencing data were filtered and qualified reads were mapped to the D. melanogaster genome (BDGP6),   using bowtie2 (version 2.2.4). PCR duplicates are removed by picard MarkDuplicates function, multimaped reads are removed by samtools, regions in blacklist are removed by bedtools intersect function.
bw files are generated by deepTools bamCoverage function using BPM normalization method, peaks are called by MACS3.
Assembly: D. melanogaster genome (BDGP6)
Supplementary files format and content: bigwig, narrowPeak

organism: Drosophila melanogaster

source_name: progenitor like cell

growth_protocol: All crosses were performed at 18℃, and 5-7d old adult F1 progenies with correct genotypes would be collected and transferred to 29 ℃ to induce gene expression.

extract_protocol:
For each sample, around 40,000 PI- GFP+ (DAPI-; GFPweek ; mCherry+) cells were FACS sorted into ice-cold PBS and collected by centrifugation. Cell lysis, DNA Tagmentation by Tn5 were carried out using the ATAC-Seq Kit (Active motif, Catalog No. 53150), following the manufacturer’s instructions.
Tagmented DNA were amplified with N50x, N70x index to construct the sequencing library, also using the ATAC-Seq Kit (Active motif, Catalog No. 53150), following the manufacturer’s instructions. Amplified sequencing library is then purfied using 1.2x magnetic beads, and sequenced on a Hiseq platform.

treatment_protocol: 100-150 guts for each sample were dissected in ice-cold DEPC-PBS within 2 hours, and were digested in 1mg/ml elastase solution (Sigma, cat. no. E0258) for 1 hour at room temperature. Cell suspension were then used to sort GFP+ cells via FASC. These sorted GFP+ cells were then used for library preperation for ATAC-seq

value: intestine

value: pros-depletion induced EE to progenitor transformed cell

value: prosV1-Gal4ts, UAS- GFP>UAS-pros-RNAi


title: 43881 Lung cancer tumor nest CD68+ ROI 4


title: WT_2_Nof


title: 43881 Lung cancer stroma CD68- ROI 3


title: D1_INF_DMSO_24h

value: DMSO


title: bleo_navi_scRNAseq

city: San Francisco

first: Jaymin

middle: J

last: Kathiriya

address: 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

description: 10X Genomics

data_processing: Reads were aligned to mm10 mouse genome and quantified using Cell Ranger Single-Cell Software.The matrix outputs were generated with barcodes (cell IDs), genes (gene names).

source_name: Lung

extract_protocol:
single cells were extracted from lungs of mice treated with bleomycin and vehicle or bleomycin and navitoclax. Lungs of mice in respective groups were harvested 21 days after bleomycin injury and enzymatically digested followed by flow sorting for total epithelial and stromal cells.
Libraries were constructed using the Chromium Single-Cell 3' library kit (10X Genomics)

treatment_protocol: Mice were injured with Bleomycin at day 1 and subsequently treated with Navitoclax (ABT-263) from Day 15 to Day 20.

value: Lung

value: Lung epithelial and stromal cells

value: Bleomycin + Navitoclax


title: ttkIR-ATAC

source_name: EE-like cell

value: ttk-depletion induced EC to EE transformed cell


title: D1_INF_40_24h

value: human monocyte-derived macrophage

value: Infected


title: Muscle stem cells (MuSCs), sham, rep 4

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
Adapter trimming was performed with CutAdapt v2.1 (-m 30 –a ADAPER-SEQUENCE).
FastQ files were mapped using Tophat v.2.1.0 (parameters: -x 1 -g 1 --no-coverage-search –no-convert-bam).
Reads per gene were counted with featureCounts v1.6.5 (-s 0).
RPKMs were calculated based on the gene length given by featureCounts.
Assembly: Ensembl: GRCm38.100
Supplementary files format and content: Excel sheet (xlsx) containing counts, RPMs and RPKMs

source_name: Muscle stem cells

extract_protocol:
MuSCs were FACS-isolated and sorted directly into lysis buffer containing β-mercaptoethanol from the RNeasy Micro Kit (Qiagen).
Library preparation was performed with a two-step approach: 1) introducing 4 ng of total RNA to the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara) for full-length cDNA synthesis was followed by 2) introducing 300 pg of full-length cDNA to the Nextera XT DNA Library Preparation Kit (Illumina).

value: Muscle stem cells

value: sham


title: D1_UNF_40_24h


title: WT_1_Nof

value: wild type


title: 43881 Lung cancer stroma CD68+ ROI 3

value: tumor

value: CD68 pos


title: D1_UNF_a1_24h

value: Uninfected


title: 43881 Lung cancer stroma CD68- ROI 2

value: CD68 neg


title: EC-ATAC

source_name: EC

value: intestine

value: enterocyte

value: Myo1A-Gal4ts, UAS-GFP


title: Muscle stem cells (MuSCs), sham, rep 3


title: 43881 Lung cancer stroma CD68+ ROI 2


title: EE-ATAC

source_name: EE

value: enteroendocrine cell

value: prosV1-Gal4ts, UAS-GFP


title: D1_UNF_DMSO_24h

value: Donor 1

value: DMSO


title: esg-ATAC

source_name: esg

value: progenitor cell

value: esg-Gal4ts, UAS-GFP


title: Muscle stem cells (MuSCs), sham, rep 2


title: bleo_veh_scRNAseq

description: 10X Genomics

value: Lung

value: Lung epithelial and stromal cells

value: Bleomycin + Vehicle


title: D4_INF_a1_4h

source_name: Blood mononuclear cells - donor 4

value: Donor 4

value: human monocyte-derived macrophage

value: Infected


title: 43881 Lung cancer stroma CD68- ROI 1

source_name: tumor

value: tumor


title: Muscle stem cells (MuSCs), sham, rep 1

value: Muscle stem cells

value: sham


title: D4_INF_40_4h


title: Muscle stem cells (MuSCs), DEN, rep 4

value: DEN


title: 43881 Lung cancer stroma CD68+ ROI 1

value: CD68 pos


title: D4_INF_DMSO_4h


title: 43728 Lung cancer tumor nest CD68- ROI 6

value: CD68 neg


title: Muscle stem cells (MuSCs), DEN, rep 3


title: 43728 Lung cancer tumor nest CD68+ ROI 6


title: Muscle stem cells (MuSCs), DEN, rep 1


title: D4_UNF_DMSO_4h

value: Uninfected


title: 43728 Lung cancer tumor nest CD68+ ROI 5


title: D3_INF_a1_4h

value: Donor 3


title: 43728 Lung cancer tumor nest CD68- ROI 5


title: D4_UNF_40_4h


title: IBD, SAMPLE 43

type: RNA

city: Herlev

first: Jaslin

middle: P

last: James

address: Borgmester Ib Juuls vej 1

department: Department of Pathology

country: Denmark

institute: Herlev hospital

hyb_protocol: Genechip Fluidics Station 450

scan_protocol: Affymetrix GeneChip 7G scanner

data_processing: analysis was done using RStudio with R version 4.2.2. Preprocessing were performed using robust multichip average (RMA) algorithm.  Lowly expressed probe sets were removed, and batch correction was performed using ComBat batch correction.

label: biotin

source_name: FFPE IBD

label_protocol: FlashTag Biotin HSR

growth_protocol: Formalin fixed paraffin embedded tissue biopsies stored at room temperature

extract_protocol: Total RNA was extracted using MagMAX™ FFPE DNA/RNA Ultra Kit from Applied Biosystems

tag: disease classification

value: UC

tag: age group

value: Adult

value: Mucosal tissue biopsies


title: IBD, SAMPLE 41


title: IBD, SAMPLE 40

value: CD


title: 43728 Lung cancer tumor nest CD68- ROI 4


title: IBD, SAMPLE 42


title: 43728 Lung cancer tumor nest CD68+ ROI 4


title: IBD, SAMPLE 39


title: D3_INF_40_4h

source_name: Blood mononuclear cells - donor 3


title: D3_INF_DMSO_4h

value: DMSO


title: 43728 Lung cancer stroma CD68+ ROI 3


title: 43728 Lung cancer stroma CD68- ROI 3


title: D3_UNF_40_4h


title: Muscle stem cells (MuSCs), DEN, rep 2


title: 43728 Lung cancer stroma CD68- ROI 2


title: D3_UNF_a1_4h


title: 43728 Lung cancer stroma CD68+ ROI 2


title: D4_UNF_a1_4h


title: D3_UNF_DMSO_4h


title: IBD, SAMPLE 38


title: IBD, SAMPLE 37


title: 43728 Lung cancer stroma CD68- ROI 1


title: IBDU, SAMPLE 34

source_name: FFPE IBDU


title: IBDU, SAMPLE 35


title: 43728 Lung cancer stroma CD68+ ROI 1


title: D2_INF_40_4h

value: Donor 2