title: CC, untreated, rep4

status: Public on Nov 29 2022

city: Oxford

first: Amélie

last: Julé

address: Roosevelt Drive, Headington

institute: Kennedy Institute of Rheumatology (KIR)

data_processing:
Reads were aligned to NCBI build mm10 of the mouse genome (Mus musculus) using STAR aligner (version 2.6.1d)
Transcripts were quantified through a quasi-alignment approach using Salmon (version 0.14.2). Transcript-level counts were aggregated at the gene level and imported into R (version 4.1.0) using tximport.
Differential expression analyses and normalization (variance stabilization transformation) were performed with DESeq2 (version 1.34.0). Additional transcript-level information was sourced from Ensembl release 94.
Assembly: mm10
Supplementary files format and content: CSV file of raw counts for all samples, filtered for genes expressed in at least one sample (non-zero read count)
Supplementary files format and content: CSV file of normalized data (VST normalization) for all samples, filtered for genes expressed in at least one sample (non-zero read count)

source_name: optic nerve proper

extract_protocol:
HA-tagged risobosomes were isolated using anti-HA antibody and magnetic beads separation. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). 3.95-37.4 ng of RNA were used to make libraries.
mRNA was extracted with oligo-dT beads, capturing poly(A) tails, and cDNA libraries were made with the Smart-Seq HT Ultra-low input RNA kit (Takara Biosciences)

treatment_protocol: ONH, ONP and CC were micro-dissected on ice in chilled PBS. For ONH and ONP samples, tissue dissected from 4 distinct mice (2 males and 2 females) were pooled together to constitute one replicate.

value: B6J.129(Cg)-Rpl22tm1.1Psam/SjJ (The Jackson Laboratory, strain #029977) x B6.Cg-Tg (GFAP-Cre) 73.12Mvs/J (The Jackson Laboratory, strain #012886)

value: optic nerve proper

value: astrocyte

tag: developmental stage

value: 7-8 weeks

value: M


title: JY10767

status: Public on Dec 05 2022

type: SRA

city: Houston

first: Maria

last: Szwarc

address: One Baylor Plaza

country: USA

institute: Baylor College of MEdicine

library_source: transcriptomic

data_processing:
The pair-ended reads were mapped to the mouse genome using STAR (Dobin et al., 2013) with NCBI RefSeq genes as the reference. STAR generated read count for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: columns with counts for each sample (JY10337; JY10516; JY10772; JY10338; JY10767; JY10769) and with gene descriptors (EntrezGene; symbol; Description; Description2)

molecule: total RNA

organism: Mus musculus

source_name: thymus

extract_protocol:
Total RNA was extracted from thymus tissues using TRIzol reagent (ThermoFisher Scientific) and further purified with the RNeasy Plus Mini Kit (Qiagen). RNA purity was evaluated with a NanoDrop spectrophotometer (ThermoFisher Scientific) and RNA integrity was determined using a 2100 Bioanalyzer with RNA chips (Agilent Technologies).
Libraries for mRNA sequencing were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina) from 250 ng of RNA. Quality analysis of libraries was performed using Agilent 4200 TapeStation with D1000 ScreenTape assays (Agilent Technologies). Libraries were pooled and then quantified by two methods: 1) on a 2100 Bioanalyzer with DNA chips using High Sensitivity DNA Kit (Agilent Technologies); and 2) with KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).

treatment_protocol: Control and K5-rtTA:TetO-RANKL mice were administered doxycycline (in food and water) at 9-weeks of age for two weeks to induce transgenic RANKL expression.

tag: tissue

value: thymus

tag: genotype


title: CC, untreated, rep2

middle: M

country: United Kingdom

molecule: polyA RNA

tag: strain

tag: cell type

value: WT

tag: Sex

value: F

tag: treatment


title: BALB/c, mouse lung, uninfected, vehicle, rep1

status: Public on Dec 27 2022

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

data_processing:
CLC Genomics Workbench v12.0.3
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to either Mus_musculus.GRCm38.100 or Mus_musculus_balbcj.BALB_cJ_v1.100 using standard parameters.
Read counts extraction was performed using CLC Genomics Workbench.
Assembly: Mus_musculus.GRCm38.100 or Mus_musculus_balbcj.BALB_cJ_v1.100
Supplementary files format and content: tab-delimited text files include raw counts for each strain

source_name: lung

extract_protocol:
RNA was extracted from inferior lung lobes using TRIzol Reagent (ThermoFisher Scientific), precipitated overnight at -20 C overnight, and quantified using a NanoDrop (ThermoFisher Scientific). NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (New England Biolabs Inc.) was used to remove ribosomal RNA from 1000 ng total extracted RNA.RNA was harvested using Trizol (Illumina). 1 ug of total RNA was used in library construction.
RNA libraries were prepared using NEBNext Ultra II Directional Library Prep Kits following manufacturers protocol.

treatment_protocol:
Mice were lightly sedated with 50 mg/kg ketamine and 15 mg/kg xylazine and intranasally inoculated with 10E4 pfu of SARS-CoV-2-MA10.
Starting 1 day post infection (DPI) mice were administered vehicle (0.5% methylcellulose + 0.025% Tween + 2.5% DMSO) twice a day by oral gavage. Mice were euthanized by isoflurane overdose and lung tissues were collected.

value: BALB/c

value: lung

tag: virus

value: no

tag: dpi (day)


title: JY10338


title: CC, untreated, rep1


title: NGS02469b

status: Public on Dec 01 2022

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
Assembly: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary files format and content: File with raw counts for every gene and every sample

organism: Homo sapiens

source_name: Blood

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

value: CD4+ T-cell blasts

value: TCF3 wild-type / TCF3 S514X (HI)

tag: disease state

value: affected


title: JY10516

value: control


title: JY10337


title: NGS02466b

value: TCF3 wild-type / TCF3 G486Lfs*4 (Null)


title: ONP, untreated, rep1

value: pooled male and female


title: ONP, untreated, rep3

value: B6J.129(Cg)-Rpl22tm1.1Psam/SjJ (The Jackson Laboratory, strain #029977) x B6.Cg-Tg (GFAP-Cre) 73.12Mvs/J (The Jackson Laboratory, strain #012886)


title: ONP, untreated, rep5

value: optic nerve proper

value: 11-12 weeks


title: ONH, untreated, rep5

source_name: optic nerve head

value: optic nerve head

value: astrocyte


title: CC, untreated, rep5

value: 7-8 weeks

value: M


title: ONH, untreated, rep3

value: WT


title: ONH, untreated, rep4


title: CC, untreated, rep3

value: F


title: ONH, untreated, rep6

value: 9-10 weeks


title: ONP, untreated, rep4


title: ONH, untreated, rep2


title: ONH, untreated, rep1


title: sample.4

status: Public on Oct 14 2022

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

description: Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.0
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights
The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: mm10
Supplementary files format and content: tab delimited text files that include counts, counts per million and moderated log2 counts
Supplementary files format and content: tab delimited text file that include differential expression analysis between affected and control groups

source_name: spleen and lymph nodes

growth_protocol: Splenocytes with or without pooled peripheral lymph nodes (axillary, brachial, inguinal) were isolated and CD4+ T cells were purified with the MojoSort mouse CD4 T cell isolation kit (Cat#480005), then stained with anti-CD4-Pacific blue (Clone RM4-5, BD Biosciences Cat#558107) plus anti-CD45RB-alexa647 (Clone 16A, BD Biosciences Cat#562848) and sorted on the basis of Ab and EGFP fluorescence. All sorting was done on a BD FACS AriaFusion flow cytometer (BD Biosciences).

extract_protocol:
RNA was extracted from sorted cells using the RNeasy Mini Kit (Qiagen, Cat# 74014).
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol.. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: spleen and lymph nodes

value: sorted lymphocytes

tag: cell subtype

value: Foxp3 positive Tregs

value: Stat3 GOF G421R+/- Foxp3+

tag: dev state/age


title: sample.6

value: affected


title: sample.7

value: WT Foxp3+

value: control


title: sample.5


title: sample.8


title: sample.2


title: ONP, untreated, rep6

value: B6J.129(Cg)-Rpl22tm1.1Psam/SjJ (The Jackson Laboratory, strain #029977) x B6.Cg-Tg (GFAP-Cre) 73.12Mvs/J (The Jackson Laboratory, strain #012886)

value: pooled male and female


title: ONP, untreated, rep2

value: optic nerve proper


title: sample.1


title: P2s

library_source: transcriptomic single cell

data_processing:
Single-cell raw data was filtered, aligned and aggregated using Cellranger v6.0.0 (count and aggr functions)
The feature-barcode matrix analysis was performed using the R package Seurat v4. In total, 147,052 cells were present in the assay. Cells with more than 15% mithochondrial RNA and less than 200 expressed features were removed, along with cells with more than 4000 features (unstimulated cells) or 6000 features (stimulated cells), and 140,931 cells remained after filtering. Data matrices were split into lists based on affected status and normalized using SCTransform
Samples were integrated based on the expression of 3000 features, and the integration anchors were identified using reciprocal PCA (RPCA) reduction with k.anchor = 20 and 30 dimensions
Cell types were predicted using Azimuth’s human PBMC data (celltype.l2 gene list). Cells classified as anything other than T cells subsets were filtered out, and with that, 139,421 cells remained
Assembly: GRCh38
Supplementary files format and content: .h5 filtereded matrix A
Supplementary files format and content: .rds R object with filtered  single cell matrix and dimensional reduction
Supplementary files format and content: tab delimited text file with cell type prediction metadata

source_name: blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque Plus (Cytiva, Cat#17-1440-02) density gradient centrifugation, subjected to RBC lysis, and frozen at -80C before transferring for storage in liquid nitrogen. On the day of the experiment, PBMCs were thawed at 37C, incubated in DNase I solution, filtered and then isolated using the EasySep Human T cell Isolation Kit (Stemcell, Cat 17951) following the manufacturer’s instructions. Cells were seeded at 1x106 cells/ml in R10 media, and placed in a 37C incubator with or without stimulation. Cell stimulation was performed with 25ul/ml Immunocult Human CD3/CD28 activator reagent (Stemcell, Cat #10971) for 16 hours. Cells were filtered, washed with PBS/2% FBS/1mM EDTA, and resuspended in PBS/0.04% BSA solution for analysis
Samples were further processed by the Genome Technology Access Center at the McDonnell Genome Institute at Washington University School of Medicine where single-cell suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions.

value: blood

value: Thawed PBMC-purified CD3+ T cells

value: STAT3 GOF-Stim, p. F174S (c.521T>C)

value: anti-CD3/CD28 16h stim


title: C2s

value: Control-Stim


title: P2

value: STAT3 GOF-No Stim, p. F174S (c.521T>C)

value: F

value: No stim (16h media only)


title: C2

value: Control-No stim


title: MRL-Lpr

city: Brisbane

first: Zewen Kelvin

last: Tuong

state: QLD

address: 62 Graham Street, Centre for Children's Health Research (CCHR), South Brisbane, QLD, 4101

country: Australia

institute: The University of Queensland

description:
10x Genomics single-cell 3′ v2 kit
G7_171121

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: cellranger processed filtered h5 formats.

source_name: Kidney

extract_protocol:
Fresh cells were flow-sorted from mouse kidneys based on differential F4/80 and CD11b expression and pooled, centrifuged at 1,300 rpm for 5 minutes. Supernatant was discarded and the pellet resuspended in PBS 0.05% BSA. Cells were loaded at an appropriate concentration to enable recovery of 10,000 cells. 10x single-cell 3’ v2 kit as per the manufacturer’s protocol. Libraries were produced using the manufacturer’s protocol and sequenced on a HiSeq 4000 (Illumina).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Kidney

value: mononuclear phagocytes

value: MRL-Lpr

tag: age

value: 16 weeks

tag: gender


title: P1s

value: STAT3 GOF-Stim, p. R70H (c. 209G>A)

value: M


title: C1s


title: P1

value: STAT3 GOF-No Stim, p. R70H (c. 209G>A)


title: C3


title: P3

value: STAT3 GOF-No Stim, p. T389S (c. 1165A>T)


title: P3s

value: blood

value: STAT3 GOF-Stim, p. T389S (c. 1165A>T)


title: C3s

value: Thawed PBMC-purified CD3+ T cells


title: C1


title: Puck_210412_29

status: Public on Oct 10 2022

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Demultiplexing, genome alignment and spatial matching was performed using Slide-seq tools github.com/MacoskoLab/slideseq-tools/releases/tag/0.1
Giotto (version 1.0.3) was used for data handling and RCTD (version 1.2.0) for the cell type deconvolution
Assembly: GRCh38 (hg38)
Supplementary files format and content: Giotto objects in RDS format containing bead location and count matrices and cell type weights after deconvolution; raw counts digital gene expression (DGE) matrix (.txt.gz) and a bead barcode locations file (.csv)

source_name: Kidney Medulla

extract_protocol:
Tissue pucks were prepared according to the step-by-step protocol: dx.doi.org/10.17504/protocols.io.bpgzmjx6
Sequencing libraries were prepared according to the step-by-step protocol: dx.doi.org/10.17504/protocols.io.bpgzmjx6

tag: patient

tag: condition

value: Reference

value: Kidney Medulla

tag: tissue source

value: Nephrectomy

tag: project

value: KPMP

tag: raw data location

tag: raw data id

tag: assay


title: Puck_210412_23

tag: tissue


title: Puck_210412_31


title: Puck_210412_24


title: Puck_210412_26

source_name: Kidney Cortex

value: Kidney Cortex


title: sample.3

value: spleen and lymph nodes

tag: cell type

value: sorted lymphocytes

value: Foxp3 positive Tregs

tag: genotype

value: WT Foxp3+

value: control


title: Puck_210412_27

source_name: Kidney Cortex / Medulla

value: Kidney Cortex / Medulla


title: Puck_210412_19


title: Puck_210412_17


title: Puck_210412_18


title: Puck_210412_21


title: Puck_210412_11


title: Puck_210412_10


title: Puck_210412_09


title: Puck_210412_13


title: Puck_210412_08


title: Puck_210412_16


title: Puck_210412_01


title: Puck_210412_03


title: Puck_201229_12


title: Puck_201229_08


title: Puck_201229_11


title: Puck_201229_07


title: Puck_210412_22


title: Puck_210412_02


title: Puck_201229_06


title: Puck_201229_05


title: Puck_210412_04


title: pNM-MS2-GlnZ_lysate_2

status: Public on Sep 28 2022

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: RNA sequencing library of total RNA from samples expressing MS2-GlnZ194 prior to performing the MAPS pulldown - Replicate 2

data_processing:
fastq records trimming (cutadapt 3.0)
short reads mapping (rilseq 0.60)
read counting (featureCounts/2.0.2)
Assembly: ecoli-k12-MG1655-NC_000913-3
Supplementary files format and content: Read counts in tab-delimited text file

organism: Escherichia coli K-12

growth_protocol: Bacterial strains were grown shaking at 250 rpm at 37˚C in Gutnick medium supplemented with HoLE, 0.4% glucose, 15 mM ammonium, and ampicillin, and samples were collected at stationary phase (9 hours of growth).

extract_protocol:
Standard TRIzol protocol was used for RNA extraction.
Library construction was carried out based on the RNAtag-Seq methodology (Shishkin et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018)

treatment_protocol: Cells were harvested by centrifugation, and cell pellets were snap frozen in liquid nitrogen.

tag: strain

tag: plasmid

tag: pulldown sample type

value: Lysate


title: Puck_201229_02


title: Puck_201229_01


title: Puck_201229_04


title: Puck_201229_03


title: Puck_210412_20


title: pNM-MS2-GlnZ_lysate_1

description: RNA sequencing library of total RNA from samples expressing MS2-GlnZ194 prior to performing the MAPS pulldown - Replicate 1


title: pNM-MS2-GlnZ_elute_1

description: RNA sequencing library after MAPS pulldown performed with MS2-GlnZ194 - Replicate 1

value: Eluate


title: pNM-MS2_elute_2

description: RNA sequencing library after MAPS pulldown performed with control MS2 vector - Replicate 2


title: pNM-MS2_elute_1

description: RNA sequencing library after MAPS pulldown performed with control MS2 vector - Replicate 1


title: pNM-MS2-GlnZ_elute_2

description: RNA sequencing library after MAPS pulldown performed with MS2-GlnZ194 - Replicate 2


title: TKD, Standard Culture, Untreated, Biol Rep 1 (TKD_S_P_1)

status: Public on Sep 23 2022

city: San Francisco

first: Ivana

last: Vasic

state: CALIFORNIA

address: 1650 Owens St

institute: Gladstone Institute

data_processing:
Adapters were trimmed using trimmomatic (v0.36) in paired end mode with the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Quality control was performed using FastQC (v0.11.9) and MultiQC (v1.9).
Transcripts were quantified using Salmon (v0.14.2) with parameters --validateMappings -l A with the GRCh38 reference transcriptome (downloaded from http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz).
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values for each Sample

source_name: WTC

extract_protocol:
Illumina's Stranded mRNA Prep kit protocol
Rneasy kit (Qiagen)

tag: cell line

value: WTC

value: hiPSC

value: ZO1 KD

tag: treatment

value: DOX treatment

tag: culture method

value: Standard Culture


title: TKD, Standard Culture, Untreated, Biol Rep 3 (TKD_S_P_3)


title: TWT, Standard Culture, Untreated, Biol Rep 2 (TWT_S_P_2)

value: WT

value: No treatment


title: TWT, Standard Culture, Untreated, Biol Rep 3 (TWT_S_P_3)


title: Puck_210412_07

value: Reference

value: Kidney Medulla

value: Nephrectomy

value: KPMP


title: TKD, Transwell Culture, BMP4 treated, Biol Rep 3 (TKD_T_B_3)

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis using dUTP
Rneasy kit (Qiagen)

value: DOX + BMP4 treatment

value: Transwell Culture


title: TKD, Standard Culture, BMP4 treated, Biol Rep 3 (TKD_S_B_3)


title: TKD, Transwell Culture, BMP4 treated, Biol Rep 1 (TKD_T_B_1)


title: TKD, Standard Culture, Untreated, Biol Rep 2 (TKD_S_P_2)


title: TKD, Standard Culture, BMP4 treated, Biol Rep 1 (TKD_S_B_1)


title: TKD, Transwell Culture, BMP4 treated, Biol Rep 2 (TKD_T_B_2)


title: TKD, Transwell Culture, Untreated, Biol Rep 1 (TKD_T_P_1)


title: TKD, Transwell Culture, Untreated, Biol Rep 2 (TKD_T_P_2)


title: TKD, Transwell Culture, Untreated, Biol Rep 3 (TKD_T_P_3)


title: TWT, Transwell Culture, BMP4 treated, Biol Rep 3 (TWT_T_B_3)

value: 48hr BMP4 treatment


title: TWT, Standard Culture, BMP4 treated, Biol Rep 3 (TWT_S_B_3)


title: TWT, Transwell Culture, BMP4 treated, Biol Rep 1 (TWT_T_B_1)


title: TWT, Standard Culture, BMP4 treated, Biol Rep 2 (TWT_S_B_2)


title: Puck_201229_10


title: TKD, Standard Culture, BMP4 treated, Biol Rep 2 (TKD_S_B_2)


title: TWT, Standard Culture, Untreated, Biol Rep 1 (TWT_S_P_1)


title: TWT, Standard Culture, BMP4 treated, Biol Rep 1 (TWT_S_B_1)


title: E2_6

status: Public on Aug 26 2022

city: Fukuoka

first: Kentaro

last: Nishi

address: 2-3-1 Matsukadai Higashi-ku

department: Life Science

country: Japan

institute: Kyushu sangyo university

data_processing:
The libraries was subjected to sequencing using the DNBSEQ-G400 (MGISEQ-2000RS, MGI Tech) instrument.
The obtained reads were aligned using splitBarcode (https://github.com/MGI-tech-bioinformatics/splitBarcode).
The read data were downsized to 20 M read pairs using seqkit v0.13.0.
The adopter sequences were cleaned with cutadapt ver.2.10, the read data were mapped with HISAT v2.2.1.
The value of FPKMs (reads per kilobase of transcript per million reads mapped) of each gene was estimated with Cuffdiff v2.2.1.
FPKMs of E2 and ctrl was used for the processed data files and E2/ctrl was used for caluculating log2.
Assembly: hg19

growth_protocol: MCF-7 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN).
The DNA libraries for sequencing were constructed with Truseq Stranded mRNA Library Prep (Illumina,  San Diego, CA) and MGIEasy Universal Library Conversion Kit (MGI Tech, Shenzhen, PRC).

value: breast cancer cells


title: E2_ICI


title: Ctrl_4


title: Ctrl_5


title: E2_3


title: Ctrl_3


title: E2_2


title: TWT, Transwell Culture, Untreated, Biol Rep 3 (TWT_T_P_3)


title: E2_5


title: E2_4


title: Non_vaccinated_donor_130

status: Public on Aug 02 2022

type: genomic

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

institute: Murdoch Children's Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Raw data was received as .iDAT files, which were pre-processed using the MissMethyl packages (available from Bioconductor) in R. Data was normalised for technical variation between and within arrays using the SWAN (Subset-quantile Within Array Normalization). Probes with poor average quality scores (p<0.01), cross-reactive probes and probes associated with single nucleotide polymorphisms (SNPs) were filtered from analysis, leaving 784,833 probes. Differential analysis was carried out using a linear regression model with limma and the DMRCate tool was used to determine differentially methylated regions (DMRs).
beta_values.csv: Normalized (SWAN) Average Beta and detP
signal_intensities_detP.csv: the Methylated and unmethylated signal intensities and detP

label: cy3, cy5

molecule: genomic DNA

source_name: Non vaccinated control_monocyte

label_protocol: Standard Illumina Protocol

extract_protocol: Monocytes were sorted (CD14+/-, CD16+/-) and placed in 500uL RLT buffer (Qiagen). Genomic DNA was extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.

tag: subject id

tag: vaccination group

value: Non vaccinated control

value: Peripheral Blood

value: Monocyte


title: TWT, Transwell Culture, BMP4 treated, Biol Rep 2 (TWT_T_B_2)

value: WTC

value: hiPSC


title: Non_vaccinated_donor_129


title: Non_vaccinated_donor_121


title: Non_vaccinated_donor_120


title: TWT, Transwell Culture, Untreated, Biol Rep 1 (TWT_T_P_1)


title: Non_vaccinated_donor_122


title: Non_vaccinated_donor_116


title: Non_vaccinated_donor_125


title: Non_vaccinated_donor_127


title: Non_vaccinated_donor_117


title: Non_vaccinated_donor_126


title: Non_vaccinated_donor_128


title: Ctrl_2


title: Non_vaccinated_donor_114


title: Non_vaccinated_donor_113


title: Non_vaccinated_donor_123


title: Non_vaccinated_donor_124


title: Non_vaccinated_donor_110


title: Non_vaccinated_donor_119


title: Ctrl_6


title: Non_vaccinated_donor_107


title: Non_vaccinated_donor_112


title: Non_vaccinated_donor_111


title: Non_vaccinated_donor_115


title: Non_vaccinated_donor_102


title: Non_vaccinated_donor_109


title: Non_vaccinated_donor_99


title: TWT, Transwell Culture, Untreated, Biol Rep 2 (TWT_T_P_2)


title: Non_vaccinated_donor_97


title: Non_vaccinated_donor_108


title: Non_vaccinated_donor_105


title: Non_vaccinated_donor_106


title: Non_vaccinated_donor_118


title: Ctrl_1


title: Non_vaccinated_donor_92


title: Non_vaccinated_donor_104


title: Non_vaccinated_donor_100


title: Non_vaccinated_donor_103


title: Non_vaccinated_donor_87


title: Non_vaccinated_donor_98


title: Non_vaccinated_donor_86


title: Non_vaccinated_donor_94


title: Non_vaccinated_donor_96


title: Non_vaccinated_donor_95


title: Non_vaccinated_donor_93


title: Non_vaccinated_donor_91


title: Non_vaccinated_donor_84


title: Non_vaccinated_donor_82


title: Non_vaccinated_donor_90


title: Non_vaccinated_donor_89


title: Non_vaccinated_donor_88


title: Non_vaccinated_donor_79


title: Non_vaccinated_donor_85


title: Non_vaccinated_donor_83


title: Non_vaccinated_donor_101


title: Non_vaccinated_donor_81


title: Non_vaccinated_donor_73


title: Non_vaccinated_donor_74


title: Non_vaccinated_donor_70


title: Non_vaccinated_donor_69


title: Non_vaccinated_donor_76


title: Non_vaccinated_donor_78


title: Non_vaccinated_donor_77


title: Non_vaccinated_donor_75


title: BCG_vaccinated_donor_62

source_name: BCG vaccinated_monocyte

value: BCG vaccinated


title: Non_vaccinated_donor_72


title: Non_vaccinated_donor_71


title: Non_vaccinated_donor_68


title: BCG_vaccinated_donor_59


title: Non_vaccinated_donor_64


title: Non_vaccinated_donor_65


title: BCG_vaccinated_donor_63


title: BCG_vaccinated_donor_55


title: BCG_vaccinated_donor_53


title: BCG_vaccinated_donor_58


title: BCG_vaccinated_donor_60


title: Non_vaccinated_donor_67


title: BCG_vaccinated_donor_51


title: Non_vaccinated_donor_66


title: BCG_vaccinated_donor_49


title: Non_vaccinated_donor_80


title: BCG_vaccinated_donor_47


title: BCG_vaccinated_donor_50


title: BCG_vaccinated_donor_46


title: BCG_vaccinated_donor_54


title: BCG_vaccinated_donor_43


title: BCG_vaccinated_donor_44


title: BCG_vaccinated_donor_61


title: BCG_vaccinated_donor_42


title: BCG_vaccinated_donor_39


title: BCG_vaccinated_donor_38


title: BCG_vaccinated_donor_41


title: BCG_vaccinated_donor_40


title: BCG_vaccinated_donor_57


title: BCG_vaccinated_donor_37


title: BCG_vaccinated_donor_36


title: BCG_vaccinated_donor_35


title: BCG_vaccinated_donor_52


title: BCG_vaccinated_donor_33


title: BCG_vaccinated_donor_34


title: BCG_vaccinated_donor_32


title: BCG_vaccinated_donor_28


title: BCG_vaccinated_donor_45


title: BCG_vaccinated_donor_30


title: BCG_vaccinated_donor_29


title: BCG_vaccinated_donor_31


title: BCG_vaccinated_donor_48


title: BCG_vaccinated_donor_21


title: BCG_vaccinated_donor_26


title: BCG_vaccinated_donor_22


title: BCG_vaccinated_donor_25


title: BCG_vaccinated_donor_27


title: BCG_vaccinated_donor_20


title: BCG_vaccinated_donor_17


title: BCG_vaccinated_donor_15


title: BCG_vaccinated_donor_18


title: BCG_vaccinated_donor_13


title: BCG_vaccinated_donor_11


title: BCG_vaccinated_donor_10


title: BCG_vaccinated_donor_9


title: BCG_vaccinated_donor_24


title: BCG_vaccinated_donor_8


title: BCG_vaccinated_donor_6


title: BCG_vaccinated_donor_4


title: BCG_vaccinated_donor_5


title: BCG_vaccinated_donor_3


title: BCG_vaccinated_donor_2


title: BCG_vaccinated_donor_23


title: BCG_vaccinated_donor_7


title: BCG_vaccinated_donor_1


title: BCG_vaccinated_donor_16


title: BCG_vaccinated_donor_14


title: BCG_vaccinated_donor_12


title: E2_1


title: BCG_vaccinated_donor_19


title: Adult_1_d6_Denmark

data_processing:
BeadStudio software v3.2
Raw data was received as .iDAT files, which were pre-processed using the MissMethyl packages (available from Bioconductor) in R. Data was normalised for technical variation between and within arrays using the SWAN (Subset-quantile Within Array Normalization). Probes with poor average quality scores (p<0.01), cross-reactive probes and probes associated with single nucleotide polymorphisms (SNPs) were filtered from analysis, leaving 771,019 probes. Differential analysis was carried out using a linear regression model with limma and the DMRCate tool was used to determine differentially methylated regions (DMRs).

source_name: Adult Human Peripheral Blood

extract_protocol: Monocytes in culture were collected in 500uL RLT buffer (Qiagen). Genomic DNA was extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.

tag: individual

tag: condition

value: BCG Denmark exposed for 24 hours, culture for 5 days to macrophage


title: BCG_vaccinated_donor_56


title: Adult_3_24h_Bulgaria

value: BCG Bulgaria exposed, collected at 24 hours post exposure


title: Adult_5_d6_Bulgaria

value: BCG Bulgaria exposed for 24 hours, culture for 5 days to macrophage


title: Adult_3_d6_Bulgaria


title: Adult_5_d6_LPS

value: LPS exposed 24 hours, culture for 5 days to macrophage


title: Adult_5_24h_Bulgaria


title: Adult_1_d6_RPMI

value: RPMI media only for 6 days to macrophage


title: Adult_4_d6_Denmark


title: Adult_3_d6_RPMI


title: Adult_2_d6_Denmark


title: Adult_2_d6_Bulgaria


title: Adult_1_d6_LPS


title: Adult_5_d6_Denmark


title: Adult_2_d6_LPS


title: Adult_5_d6_RPMI


title: Adult_4_24h_Bulgaria


title: Adult_3_d6_Denmark


title: Adult_3_d6_LPS


title: Adult_2_d6_RPMI


title: Adult_1_d6_Bulgaria


title: Adult_4_24h_Denmark

value: BCG Denmark exposed, collected at 24 hours post exposure


title: Adult_1_24h_Bulgaria


title: Adult_5_24h_Denmark


title: Adult_2_24h_Bulgaria


title: A4_BCG_Denmark_d6_H3K4me1

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for histone marks at p-value of 10-5. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac peaks were called using the default (narrow) setting.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files for visualization

growth_protocol: Monocytes were differentiated into resting macrophages by ex vivo culture in RPMI 1640 medium (Sigma Aldrich) with 10% Human Serum. Trained immunity was induced by exposing cells to BCG vaccines for 24 hours, while a tolerance control was induced by LPS for 24 hours.

extract_protocol:
Ovation Ultralow DNA-seq library preparation kit
Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated and 1ug of chromatin (~1 million cells) was incubated with 1µg of H3K27ac or H3K4me1 antibodies (Diagenode) and incubated overnight at 4ºC with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 minutes at 4°C. Beads were washed with 400µl buffer for 5 minutes at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 minutes. Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C.Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB.
Library preparation was performed using the Ovation Ultralow DNA-seq library preparation kit and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 30 million reads per sample.

tag: chip antibody

value: H3K4me1 Antibody - ChIP-seq Grade (Diagenode, cat #C15210018)


title: A3_BCG_Denmark_d6_H3K4me1


title: Adult_3_24h_Denmark


title: A5_BCG_Denmark_d6_H3K4me1


title: Adult_4_d6_RPMI


title: A5_RPMI_d6_H3K4me1


title: A4_RPMI_d6_H3K4me1


title: Adult_4_d6_Bulgaria


title: A3_RPMI_d6_H3K4me1


title: A2_RPMI_d6_H3K4me1


title: A2_BCG_Denmark_d6_H3K27ac

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: A5_BCG_Denmark_d6_H3K27ac


title: A5_RPMI_d6_H3K27ac


title: A1_BCG_Denmark_d6_H3K27ac


title: Adult_1_24h_Denmark


title: A3_RPMI_d6_H3K27ac


title: A2_RPMI_d6_H3K27ac


title: A5_BCG_Bulgaria_d1_H3K27ac


title: A4_BCG_Bulgaria_d1_H3K27ac


title: A2_BCG_Denmark_d6_H3K4me1


title: A5_BCG_Denmark_d1_H3K27ac


title: Adult_4_d6_LPS


title: A3_BCG_Bulgaria_d1_H3K27ac


title: A1_BCG_Bulgaria_d1_H3K27ac


title: A2_BCG_Denmark_d1_H3K27ac


title: Adult_5_24h_LPS

value: LPS exposed, collected at 24 hours post exposure.


title: A3_BCG_Denmark_d1_H3K27ac


title: Adult_4_24h_LPS


title: A4_BCG_Denmark_d6_H3K27ac


title: A3_BCG_Denmark_d6_H3K27ac


title: A4_BCG_Denmark_d1_H3K27ac


title: Adult_2_24h_Denmark


title: A1_RPMI_d6_H3K27ac


title: A3_RPMI_d1_H3K27ac

value: RPMI media only, collected at 24 hours post culture


title: A4_RPMI_d1_H3K27ac


title: A1_BCG_Denmark_d1_H3K27ac


title: A2_RPMI_d1_H3K27ac


title: A5_RPMI_d1_H3K27ac


title: A1_RPMI_d1_H3K27ac


title: A5_d0_H3K27ac

value: Baseline monocyte, attached to dish for 1  hour


title: A4_d0_H3K27ac


title: A3_d0_H3K27ac


title: Adult_2_24h_LPS


title: A2_d0_H3K27ac


title: Adult_1_24h_RPMI


title: A1_d0_H3K27ac


title: Adult_4_0h


title: A5_d7B

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Genome_build: hg19
Supplementary_files_format_and_content: .gene.mmseq.txt files contain counts per gene

extract_protocol:
Total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

value: Adult Human Peripheral Blood

value: BCG Bulgaria exposed for 24 hours, culture for 5 days to macrophage, then LPS exposed for 4 hours


title: Adult_1_0h

value: Peripheral Blood

value: Monocyte


title: Adult_3_24h_LPS


title: Adult_1_24h_LPS


title: Adult_2_0h


title: A4_d7B


title: A3_d7B


title: Adult_5_24h_RPMI


title: A2_d7B


title: Adult_4_24h_RPMI


title: A1_D6_4h_Bul


title: A2_d7D

value: BCG Denmark exposed for 24 hours, culture for 5 days to macrophage, then LPS exposed for 4 hours


title: A3_d7D


title: A1_D6_4h_Den


title: A4_RPMI_d6_H3K27ac


title: A5_d7D


title: A5_d7L

value: LPS exposed 24 hours, culture for 5 days to macrophage, then LPS exposed for 4 hours


title: Adult_3_24h_RPMI


title: A4_d7D


title: A4_d7L


title: A2_d7L


title: A1_d7L


title: Adult_3_0h


title: A3_d7L


title: A3_d7R

value: RPMI media only for 6 days to macrophage, then LPS exposed for 4 hours


title: Adult_5_0h


title: A5_d7R


title: A2_d7R


title: A4_d7R


title: A3_d6B


title: A5_d6B


title: A1_D6_4h_RPMI


title: A4_d6B


title: A1_D6_Bul


title: A2_d6B


title: A4_d6D

value: BCG Denmark exposed for 24 hours, culture for 5 days to macrophage


title: A3_d6D


title: A5_d6L


title: A3_d6L


title: A2_d6D


title: A1_d6L


title: A2_d6L


title: A1_D6_Den


title: A4_d6L


title: A2_d1B

value: BCG Bulgaria exposed, collected at 24 hours post exposure


title: A5_d1B


title: A3_d1B


title: A2_d6R


title: A4_d1B


title: A1_D6_RPMI


title: A4_d6R


title: A3_d6R


title: A5_d6R


title: A5_d6D


title: Adult_2_24h_RPMI


title: A3_d1D


title: A1_24h_Bul


title: A5_d1D


title: A4_d1D


title: A4_d1L


title: A5_d1L


title: A2_d1D


title: A3_d1L


title: A2_d1L


title: A1_24h_LPS


title: A5_d1R


title: A4_d1R


title: A3_d1R


title: A1_24h_RPMI


title: A2_d1R


title: A5_B4h

value: BCG Bulgaria exposed, collected at 4 hours post exposure


title: A1_24h_Den


title: A4_B4h


title: A1_B4h


title: A1_D4h

value: BCG Denmark exposed, collected at 4 hours post exposure


title: A3_D4h


title: A2_L4h

value: LPS exposed, collected at 4 hours post exposure.


title: A4_L4h


title: A3_B4h


title: A2_D4h


title: A3_L4h


title: A5_L4h


title: A3_R4h

value: RPMI media only, collected at 4 hours post culture


title: A2_R4h


title: A4_R4h


title: A1_L4h


title: A5_d0


title: A4_d0


title: A3_d0


title: A2_d0


title: A1_0h


title: A2_B4h


title: A5_D4h


title: A4_D4h


title: SD8_LPS_IV_24h

status: Public on Jul 27 2022

type: RNA

first: Kieran

last: Hyslop

state: Queensland

address: Lvl 3, Clinical Sciences Building 627 Rode Road CHERMSIDE

department: Faculty of Medicine

institute: University of Queensland

description: ARDS phenotype 2 (Ph2, hyperinflammatry), induction using OA + intavenous LPS (LPS_IV), 24 hour observation time

hyb_protocol: Hybridizations reactionss were run at 67ºC for 18 hours in a T100 thermal cycler (Bio-rad laboratories). Lid temperature was maintained 5ºC above the block for the entire run.

scan_protocol: Digital detection of fluorescently-labelled molecular barcodes on an nCounter SPRINT profiler (NanoString Technologies)

data_processing: Raw data background subtraction (mean of the neagtive controls + 2 S.D) was performed in nSolver analysis 4.0 (NanoString). Raw counts were normalized to the top three reference genes (POLR2A, RPL19 and TBP) as determined by geNorm in the nCounter advanced analysis 2.0 plugin and log2 transfromed.

label: Fluorescent molecular barcodes

organism: Ovis aries

source_name: Lung Tissue_LPS_IV_24h

label_protocol: nCouter Elements Tagsets (NanoString) and custom oligonucleotide probe pairs (capture and reporter) designed by NanoString Technologies and supplied by Integrated DNA Technologies.

extract_protocol: 10 mg of lung tissue from each lobe of the right lung (upper, middle and lower) was homogenized in Trizol (Ambion) using a polytron PT 2100 (kinematica, AG) and used for total RNA isolation with a PureLink mini kit (Invitrogen). Following isolation a DNase treatment was performed using a DNA-free kit (Invitrogen) and sample concentrations were standardised to 100 ng/µL using Qubit prior to regions being pooled.

treatment_protocol: 3 mm cubes of right lung tissue (upper, middle and lower lobes) were stored in RNAlater (Invitrogen) overnight at 4ºC. Following overnight incubation, RNAlater was removed and tissue was transferred to -80ºC storage.

tag: phenotype

tag: study

value: STARDUST

tag: observation time

value: 24 hours

tag: Sex

value: Female


title: SD14_OA_24h

description: ARDS phenotye 1 (Ph1, hypoinflammatory), induction using Oleic aicd (OA), 24 hour observation time

source_name: Lung Tissue_OA_24h


title: SD11_LPS_IV_24h


title: A1_R4h

tag: tissue

tag: cell type


title: A5_R4h


title: SD9_LPS_IV_24h


title: SD7_OA_24h


title: SD10_OA_24h


title: SD2_OA_24h


title: G34_LPS_IV_12h

description: ARDS phenotype 2 (Ph2, hyperinflammatry), induction using OA + intavenous LPS (LPS_IV), 12 hour observation time

source_name: Lung Tissue_LPS_IV_12h

value: CELTIC

value: 12 hours


title: SD4_LPS_IV_12h


title: SD13_LPS_IV_12h


title: C19_OA_12h

description: ARDS phenotye 1 (Ph1, hypoinflammatory), induction using Oleic aicd (OA), 12 hour observation time

source_name: Lung Tissue_OA_12h


title: C4_LPS_IV_6h

description: ARDS phenotype 2 (Ph2, hyperinflammatry), induction using OA + intavenous LPS (LPS_IV), 6 hour observation time

source_name: Lung Tissue_LPS_IV_6h

value: 6 hours


title: C18_OA_12h


title: TR-Hindlimb-T3_2

status: Public on Jul 19 2022

data_processing:
Short reads mapping (Bowtie2 v2.3.4.1)
Peak calling (MACS2 v2.1.1.20160309)
Genome_build: Xenbase v9.1
Supplementary_files_format_and_content: peak txt files

organism: Xenopus tropicalis

source_name: Hindlimb of stage 54, TR knowckout, with T3 treatment

growth_protocol: Hindlimb samples were collected from WT and TRα (-/-) tadpoles which born from same parents.

extract_protocol:
Hindlimb chromatin DNA was extracted and IP was performed with TR antibody. After purification of ChIP-DNA, all purified DNA was used for the construction of sequencing libraries.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When tadpoles reached to around stage 54, tadpoles of T3 groups were treated with 10nM T3 for 18 hours.

value: Hindlimb

tag: genotype

value: TRalpha knockout

value: T3 treatment

tag: developmental stage


title: C11_OA_6h

description: ARDS phenotye 1 (Ph1, hypoinflammatory), induction using Oleic aicd (OA), 6 hour observation time

source_name: Lung Tissue_OA_6h


title: C5_LPS_IV_6h


title: C17_OA_12h


title: G33_LPS_IV_6h


title: C21_OA_12h


title: SD6_OA_6h


title: C1_OA_6h


title: C3_OA_6h


title: C2_OA_6h


title: TR-Hindlimb-T3_1


title: TR-Hindlimb-control_3

source_name: Hindlimb of stage 54, TR knockout, no T3 treatment

value: control


title: TR-Hindlimb-control_2


title: SD1_OA_24h


title: TR-Hindlimb-control_1


title: WT-in-control_2

data_processing:
Short reads mapping (Bowtie2 v2.3.4.1)
Peak calling (MACS2 v2.1.1.20160309)
Genome_build: Ensembl Xenopus_tropicalis.JGI_4.2 and Xenbase v9.1
Supplementary_files_format_and_content: peak text files

source_name: Intestine at stage 54, wild type, no T3 treatment

growth_protocol: Intestinal samples were collected from WT and TRα (-/-) tadpoles which born from same parents.

extract_protocol:
Intestinal chromatin DNA was extracted and IP was performed with TR antibody. After purification of ChIP-DNA, all purified DNA was used for the construction of sequencing libraries.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: stage 54

value: Intestine

value: wild type

value: no T3


title: WT-in-T3_1

source_name: Intestine at stage 54, wild type, with T3 treatment

value: with T3


title: WT-in-control_3


title: WT-in-T3_3


title: TR-in-T3_3

source_name: Intestine of stage 54, TR knowckout, with T3 treatment


title: TR-in-T3_2


title: WT-in-control_1


title: TR-in-control_3

source_name: Intestine of stage 54, TR knockout, no T3 treatment


title: TR-in-T3_1


title: TR-Hindlimb-T3_3


title: TR-in-control_2


title: TR-in-control_1


title: TRα(-/-)_Hindlimb_ T3-_rep2

data_processing:
Short reads mapping (STAR 2.5.3a)
Reads counting (featureCounts v1.4.6-p3)
Genome_build: Xenopus_tropicalis.JGI_4.2.90
Supplementary_files_format_and_content: Tab-delimited text file for reads counts of each gene.

source_name: Hindlimb

extract_protocol:
Hindlimb RNA was harvested by using RNeasy. One ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When tadpoles reached to around stage 54, tadpoles were treated ot nontreated with 10nM T3 for 18 hours.

value: TRalpha(-/-)

value: hindlimb


title: TRα(-/-)_Hindlimb_ T3+_rep2

value: TRalpha-/-_T3 treatment for 18 hours


title: TRα(-/-)_Hindlimb_ T3+_rep1


title: TRα(-/-)_Hindlimb_ T3-_rep3


title: TRα(-/-)_Hindlimb_ T3-_rep1


title: WT_Hindlimb_ T3+_rep1

value: WT

value: WT_T3 treatment for 18 hours


title: WT_Hindlimb_ T3-_rep2


title: WT_Hindlimb_ T3-_rep3


title: WT_Hindlimb_ T3-_rep1


title: TRα(-/-)_Hindlimb_ T3+_rep3


title: WT-Hindlimb-T3_3

source_name: Hindlimb at stage 54, wild type, with T3 treatment


title: WT_Hindlimb_ T3+_rep3


title: WT_Hindlimb_ T3+_rep2


title: WT-Hindlimb-T3_2


title: WT-in-T3_2


title: WT-Hindlimb-T3_1


title: WT-Hindlimb-control_3

source_name: Hindlimb at stage 54, wild type, no T3 treatment


title: WT-Hindlimb-control_1


title: T2389_PS54: Bronchoalveolar Lavage - Never-Smoker (89)

status: Public on Jul 13 2022

city: Columbus

first: Peter

last: Shields

state: OH

address: 420 West 12th Ave

institute: The Ohio State University

data_processing:
FASTQC was used for basecalling.
Sequences were trimmed for adaptor sequences by cutadapt and aligned to human genome (hg19) by TopHat version 2.1.0 with parameteres -p 8 --no-coverage-search --library-type fr-firststrand hg19.genome Read1.fastq.gz Read2.fastq.gz
Reads that were not mapped to the human genome were aligned to complete genomes of microbes downloaded from the NCBI Refseq database (dated March 2018). Kraken v. 1 was used for alignment with the parameters: kraken --preload –Kraken_Database --fastq-input --gzip-compressed --paired Microbiome_Read1.fastq.gz Microbiome_Read2.fastq.gz --output Microbial_alignment. Resulting alignment files were then converted into a read count table: kraken-report -Kraken_Database Microbial_alignment.
Aligned reads by Kraken were then provided to Bracken v.1 to align to bacterial species using the following parameters: python est_abundance.py -i BAL_Samples_Full_Kraken_subanalysis -k KMER_DISTR.txt
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw bacterial counts for each subject
Supplementary_files_format_and_content: Matrix table with raw gene counts with aligned bacteria species for every sample. One matrix table for saliva samples. One matrix table for BAL samples.

organism: human lung metagenome

source_name: Bronchoalveolar lavage

extract_protocol:
BAL and Saliva was stored in RNAlater solution at -80°C. Samples were thawed and spun to pellet cells, and supernatants were removed. RNA was extracted using QIAzol lysis reagent and miRNeasy Mini kit (Cat. # 217004). 200 ng total RNA was used to construct sequencing libraries
Total RNA was treated with Illumina TruSeq Stranded Total RNA Gold to remove rRNA, and libraries were prepared using Illumina TruSeq kit.

tag: smoking status

value: Never-Smoker

value: Cell from bronchoalveolar lavage fluid


title: T2383_PS48: Bronchoalveolar Lavage - E-cig User (101)

value: E-cig User


title: T2384_PS49: Bronchoalveolar Lavage - Smoker (96)

value: Smoker


title: T2380_PS45: Bronchoalveolar Lavage - E-cig User (77)


title: T2379_PS44: Bronchoalveolar Lavage - Smoker (99)


title: T2374_PS39: Bronchoalveolar Lavage - Never-Smoker (64)


title: T2376_PS41: Bronchoalveolar Lavage - Smoker (97)


title: T2390_PS55: Bronchoalveolar Lavage - Never-Smoker (53)


title: T2371_PS36: Bronchoalveolar Lavage - Smoker (62)


title: T2368_PS33: Bronchoalveolar Lavage - Never-Smoker (73)


title: T2366_PS31: Bronchoalveolar Lavage - E-cig User (79)


title: T2364_PS29: Bronchoalveolar Lavage - Never-Smoker (59)


title: T2360_PS25: Bronchoalveolar Lavage - Smoker (67)


title: T2359_PS24: Bronchoalveolar Lavage - Never-Smoker (60)


title: T2356_PS21: Bronchoalveolar Lavage - E-cig User (98)


title: T2354_PS19: Bronchoalveolar Lavage - E-cig User (87)


title: T2386_PS51: Bronchoalveolar Lavage - E-cig User (66)


title: T2351_PS16: Bronchoalveolar Lavage - Smoker (102)


title: T2344_PS9: Bronchoalveolar Lavage - E-cig User (58)


title: T2341_PS6: Bronchoalveolar Lavage - E-cig User (81)


title: T2352_PS17: Bronchoalveolar Lavage - Never-Smoker (63)


title: T2339_PS4: Bronchoalveolar Lavage - Never-Smoker (78)


title: T2348_PS13: Bronchoalveolar Lavage - Never-Smoker (70)


title: WT-Hindlimb-control_2

value: Hindlimb


title: mouse brown adipose tissue (denervation)

status: Public on Jul 03 2022

city: Daejeon

first: JUNGMO

last: KIM

state: -- None selected --

address: 291 Daehak-ro, Yuseong-gu

department: Center for Vascular Research

country: South Korea

institute: Institute for Basic Science

data_processing:
The BD Rhapsody™ WTA Analysis Pipeline of Seven Bridge Genomics is used to create sequencing libraries from single nucleus transcriptomes.
Aligned reads were then read by Seurat (v4.0.6) and cell-gene raw expression matrices were made. Then, ambient RNA were removed with DecontX function of Celda and DIEM package.
After quality control, expression matrices were log normalized and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Assembly: pre-mRNA GRCh38 (BD Seven Bridge Genomics supported)
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for mouse adipose tissue single nucleus data

molecule: nuclear RNA

source_name: brown adipose tissue

extract_protocol:
After tissue preparation and nuclear isolation using Nuclei EZ Prep(Sigma), single-nucleus suspensions were processed on the BD Rhapsody system following the manufacturer's protocols.
cDNA libraries were constructed using BD Rhapsody™ Whole Transcriptome Analysis (WTA) Amplification Kit (BD)

value: brown adipose tissue

tag: strain

tag: develomental stage

value: adult

value: denervation


title: T2342_PS7: Bronchoalveolar Lavage - Never-Smoker (44)


title: mouse brown adipose tissue (control)

tag: treatment

value: non-treatment


title: T2336_PS1: Bronchoalveolar Lavage - Smoker (84)


title: T2373_PS38: Bronchoalveolar Lavage - E-cig User (88)


title: mouse brown adipose tissue (sham operation)

value: sham operation


title: T2362_PS27: Bronchoalveolar Lavage - Smoker (100)


title: RNASeq_PROLIF_G_rep2.5

status: Public on Jun 17 2022

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
sequencing replicate of S7-KDNT_S19 (same extraction)
21-S7-KD6NT_S19
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab

data_processing:
RNA-Seq paired reads were aligned to the hg38 genome with Hisat2 (v2.1.0) using the Ensembl annotation (v95).
Reads in genes were counted using featurecounts, with multimapping reads fractionally assigned using --fraction and -M.
Low abundance genes were filtered out of further analysis using edgeR's function "filterByExpr".
Normalisation between library sizes to get FPKM values was done using the trimmed mean of M-values method.
Normalisation for differential expression was by limma-voom (Law et al. 2014) and tests calculated by lmFit and eBayes.
Calculations of changing expression over time were done pairwise Prolif  v day0, day0 v day1, day1 v day3 and day3 v day9; first within each donor and then combined across donors.
Transcript quantification from RNA-Seq reads was conducted with salmon v1.3.0 (--numBootstraps 20 --gcBias) on an index of the ensembl transcriptome plus additional HOTAIR transcripts from refseq (NR_003716.3, NR_047517.1, NR_047518.1) and from the lncRNA sections of the ucsc browser (TCONS_00079053_HOTAIR, TCONS_00079054_HOTAIR, TCONS_00079056_HOTAIR, TCONS_00079057_HOTAIR, TCONS_00079058_HOTAIR, TCONS_00079061_HOTAIR).
Genome_build: hg38 (GRCh38) ensembl95
Supplementary_files_format_and_content: *.bw: Bigwig RNAseq coverage file generated with deeptools bamCoverage (binsize 10bp).
Supplementary_files_format_and_content: Raw read counts per gene, one column per sample.
Supplementary_files_format_and_content: FPKM for each gene passing the filtering threshold in each sample.
Supplementary_files_format_and_content: TPM for each transcript in each gluteal sample.

source_name: Human primary adipose stem cells

growth_protocol: Human normal adipose tissue-derived mesenchymal stem cells were isolated from subcutaneous liposuction material. Cells were cultured under proliferative conditions in DMEM/F12 containing 10% fetal calf serum, 10 ng/ml epidermal growth factor (Sigma-Aldrich E9644) and 20 ng/ml basic fibroblast growth factor (FGF2; Sigma-Aldrich F5392). Cells at passage 5-7 were used in three independent differentiations into the adipocyte lineage.

extract_protocol:
For RNA-seq, total mRNA was isolated from cells at aforementioned stages of differentiation using the Qiagen RNeasy kit and processed for Illumina library preparation and sequencing.
Illumina sequencing libraries were generated as per Illumina protocols.

treatment_protocol:
Two days before induction of differentiation, proliferating cells (day-2 [day minus 2] stage) were harvested and processed for RNA extraction. For adipogenic differentiation, harvested day-2 cells were reseeded in DMEM/F12/10% serum without growth factors. Adipogenesis was induced 48 h later (on day 0; D0) by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was left with the cells for the 3 days of differentiation. Cells were collected on day0, day 1, day 3 and day9 (D0, D1, D3, D9) and processed for RNA extraction.
For transient knockdown, proliferating cells were electroporated with Nucleofector (Lonza) using the Human Mesenchymal Stem Cell NucleofectorTM Kit (Lonza). Two siRNAs (Silencer select from Ambion) were used - siHOTAIR 1: N272221, siHOTAIR 2: N272230. Electroporated cells were plated and cultured for 72 h in proliferative conditions before harvesting for RT-PCR and RNA-FISH.
For transient knockdown, proliferating cells were electroporated with Nucleofector (Lonza) using the Human Mesenchymal Stem Cell NucleofectorTM Kit (Lonza). Two siRNAs (Silencer select from Ambion) were used - siHOTAIR 1: N272221, siHOTAIR 2: N272230. Electroporated cells were plated and cultured for 72 h in proliferative conditions before harvesting for RT-PCR and RNA-FISH.

tag: time point

value: day-2 (proliferating)

tag: adipose depot

value: Gluteal

tag: culture

value: Cultured in vitro

tag: sirna probe


title: RNASeq_D1_A_rep3

description:
13-19197_S18
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab

value: Abdominal subcutaneous


title: RNASeq_D9_A_rep3

description:
15-19199_S2
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_D0_A_rep3

description:
12-19196_S15
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab

value: day0 (induction of differentiation)


title: RNASeq_D3_A_rep2

description:
9-19193_S6
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_D9_A_rep2

description:
10-19194_S9
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: T2346_PS11: Bronchoalveolar Lavage - E-cig User (55)


title: RNASeq_PROLIF_G_rep3.5

description:
sequencing replicate of S12-KDNT_S22 (same extraction)
22-S12-KD3NT_S22
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_D1_A_rep1

description:
3-19202_S11
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_PROLIF_A_rep3

description:
11-19195_S12
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_PROLIF_A_rep2

description:
6-19190_S20
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_D3_A_rep1

description:
4-19203_S14
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_D9_A_rep1

description:
5-19204_S17
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_D3_A_rep3

description:
14-19198_S21
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_D9_G_rep1

description:
6-P5D9_S6
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: RNASeq_D0_G_rep2

description:
8-P6D0_S8
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: RNASeq_PROLIF_G_rep2

description:
7-KD6NT_S7
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: RNASeq_D1_A_rep2

description:
8-19192_S3
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_PROLIF_G_rep1.5

description:
sequencing replicate of S2-KDNT_S16 (same extraction)
20-S2-KD5NT_S16
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: RNASeq_D3_G_rep1

description:
5-P5D3_S5
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: RNASeq_PROLIF_G_rep0

description:
extra replicate
1-KD4NT_S1
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: RNASeq_D1_G_rep1

description:
4-P5D1_S4
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: RNASeq_PROLIF_G_rep1

description:
2-KD5NT_S2
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: St63dNC-3

status: Public on Jun 14 2022

data_processing:
Short reads mapping (STAR 2.5.4a)
Reads counting (featureCounts v1.5.2)
Genome_build: Xenopus_tropicalis.JGI_4.2
Supplementary_files_format_and_content: Tab-delimited text file for reads counts of each gene.

source_name: Notochord-removed-tail of stage 63

extract_protocol:
Tails were removed, and RNA was harvested using SV Total RNA Isolation System kit (Promega, Madison, WI, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: notochord-removed-tail


title: RNASeq_D0_G_rep1

description:
3-P5D0_S3
mar19_rnaseq.multim.counts.txt
rpkm_tmm.tab
salmon_tpm_sum.txt


title: St63dNC-2


title: St60-3

source_name: Whole tail of stage 60

value: whole tail


title: RNASeq_D0_A_rep2

description:
7-19191_S1
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: St63-2

source_name: Whole tail of stage 63


title: St60-1


title: RNASeq_D0_A_rep1

description:
2-19201_S8
d13_rnaseq.multim.counts.txt
rpkm_tmm.tab


title: Hippocampus

status: Public on May 20 2022

city: New Haven

first: Yanxiang

last: Deng

state: CT

address: 55 Prospect Street

department: Biomedical Engineering

institute: Yale University

data_processing:
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 1, and the filtered sequences were transformed to Cell Ranger ATAC format (10x Genomics). The genome sequences were in the new Read 1, barcodes A and barcodes B were included in new Read 2. Resulting fastq files were aligned to the mouse reference (mm10) or human reference (GRCh38), filtered to remove duplicates and counted using Cell Ranger ATAC v1.2. The BED like fragments file were generated for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).
Assembly: mm10 (GRCm38), GRCh38
Supplementary files format and content: BED like fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).

source_name: Human hippocampus

extract_protocol: The fresh frozen tissue section on a standard aminated glass slide was first fixed with formaldehyde. Tn5 transposition was then performed, and adapters containing a ligation linker were inserted to transposase accessible genomic DNA. Afterwards, a set of DNA barcode A solutions were loaded via an array of microchannels 8 to the tissue section for in situ ligation of a distinct spatial barcode Ai (i = 1-50). Then, a second set of barcodes Bj (j = 1-50) were introduced on the tissue surface in microchannels perpendicularly to those in the first flow barcoding step. These barcodes were then ligated at the intersections, resulting in a mosaic of tissue pixels, each of which contains a distinct combination of barcodes Ai and Bj (i = 1-50, j = 1-50). During each flow or afterward, the tissue slides were imaged under the microscope such that spatially barcoded accessible chromatin can be correlated with the tissue morphology. After forming a spatially barcoded tissue mosaic (n = 2500), reverse crosslinking was performed to release barcoded DNA fragments and library construction was completed during the PCR. NGS sequencing was then performed using a HiSeq sequencer with pair-end 150 bp mode with custom read 1 primer.

value: Human hippocampus

tag: spatial resolution

value: 50 um


title: 5637 cells, siPOLD1-3

status: Public on Apr 22 2022

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

country: China

institute: Zhongnan Hospital of Wuhan University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: bladder

growth_protocol: 5637 cells were cultured and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
The RNA was isolated from 5637 cells using RNeasy Mini Kit (cat. #74101; Qiagen, Duesseldorf, Germany) followed the manufacturer’s protocol. In each RNA sample, contamination of genomic DNA is removed through DNase I digestion (cat. #79254; Qiagen). The NanoPhotometer (cat. #N60; Implen, Munich, Germany) was used to measure the quantity of each RNA sample.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: Transfection of siRNA and plasmid follows LipofectamineTM 3000 Reagent’s (L3000015, Invitrogen) protocol.

value: bladder

tag: cell line

value: bladder cancer cells

value: POLD1 knockdown

value: siRNA transfection


title: KO18 [pt42]

status: Public on Apr 12 2022

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

data_processing:
Data were analysed using the Lexogen's proprietary Bluebee sequence analysis platform. Trimming using Bbduk and quality control with FASTQC.
Genome_build: HGhg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: melanoma metastases

extract_protocol:
Qiagen Rneasy microRNA kit with Dnase treatment
Libraries were prepared according to Lexogen's instructions accompanying the Kit (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina)
RNA-Seq - 3' end RNA sequencing libraries were prepared using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD library.

value: melanoma metastases

value: POST LR

tag: drug

value: BRAFi+MEKi

tag: pt id-tm id (according to table s4, pubmed id 35643181)


title: KO17 [pt39]

tag: tissue

value: BRAFi


title: KO16 [pt29]


title: KO19 [pt42]

value: PRE LR


title: 5637 cells, siPOLD1-2

tag: cell type


title: 5637 cells, siPOLD1-1

tag: genotype


title: 5637 cells, siNC-3

value: WT


title: 5637 cells, siNC-2


title: KO14 [pt22]


title: KO13 [pt14]


title: KO12 [pt8]


title: KO11 [pt46]


title: St63dNC-1


title: FP60 [pt31]

value: PRE SR


title: KF62 [pt10]


title: FP59 [pt47]


title: FP57 [pt19]


title: FP68 [pt4]


title: St60-2


title: St63-1


title: FP53 [pt40]


title: St63-3


title: FP52 [pt32]


title: FO20 [pt15]


title: FO23 [pt24]


title: FO17 [pt44]


title: 5637 cells, siNC-1


title: KO15 [pt29]


title: FO13 [pt6]


title: FO11 [pt47]


title: FO08 [pt49]

value: POST SR


title: FO10 [pt50]


title: FO04 [pt49]


title: FO05 [pt49]


title: FN63 [pt41]


title: FN58 [pt48]


title: FN56 [pt48]


title: FN53 [pt18]


title: FN55 [pt18]


title: FN52 [pt26]


title: FN49 [pt7]


title: FN51 [pt7]


title: FN47 [pt35]


title: FN50 [pt12]


title: FN41 [pt7]


title: FL44 [pt28]


title: FN42 [pt12]


title: FN46 [pt35]


title: FO16 [pt47]


title: FL49 [pt7]


title: FL38 [pt30]


title: FL36 [pt23]


title: FL41 [pt43]


title: FN40 [pt7]


title: FB91 [pt20]


title: FB92 [pt20]


title: FN65 [pt18]


title: FB84 [pt34]


title: FN69 [pt49]


title: FB85 [pt34]


title: FB88 [pt10]


title: FB83 [pt34]


title: EY98 [pt1]


title: EY99 [pt34]


title: EY84 [pt21]


title: EY96 [pt1]


title: EY94 [pt34]


title: EY97 [pt8]


title: EY82 [pt8]


title: EY73 [pt13]


title: FL39 [pt25]


title: EY67 [pt16]


title: EY69 [pt2]


title: EY72 [pt13]


title: EY71 [pt13]


title: EY58 [pt3]


title: FB89 [pt10]


title: EY46 [pt28]


title: EY66 [pt3]


title: EY44 [pt11]


title: EY50 [pt36]


title: EY43 [pt11]


title: EY24 [pt17]


title: EY40 [pt43]


title: EY26 [pt9]


title: EY37 [pt9]


title: EY34 [pt33]


title: FB82 [pt27]


title: EY86 [pt37]


title: EY30 [pt10]


title: EY21 [pt11]


title: EY74 [pt13]


title: EY15 [pt38]


title: EY11 [pt38]


title: EY06 [pt43]


title: EY20 [pt25]


title: EX99 [pt5]


title: EY14 [pt36]


title: EY22 [pt38]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4780]

status: Public on Mar 20 2022

first: Chisato

last: Shimizu

address: 9500 Gilman Dr.

data_processing:
The RNA-Seq analysis pipeline consisted of: quality control using FastQC , MultiQC and alignment and read counting using STAR, Salmon, FeatureCounts and ensembl GCh38 genome and annotation. Normalisation was performed using the DESeq2 method for estimating scale factors with a subsequent log transformation.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole blood

growth_protocol: Not applicable

extract_protocol:
Total whole blood RNA from PAXgene tubes was isolated using PAXgene Blood miRNA Kit
polyA capture: Total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) paired end reads (PE100) to a depth of approximately 50 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA). ribosomal/globin depletion: Library preparation and sequencing of 30 million 75 or 100 bp paired end reads was conducted using the Illumina’s TruSeq RNA Sample Preparation Kit, ribosomal and globin RNA depletion was performed using the Illumina® Ribo-Zero Gold kit and HiSeq 4000 at The Wellcome Centre for Human Genetics.
Ribosomal depletion, globin depletion or poly-A capture

treatment_protocol: Not applicable

tag: disease

value: Febrile control

tag: disease stage

value: acute

tag: cdna prep

value: ribosomal/globin depletion


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4837]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4811]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4836]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4755]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4794]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4746]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4775]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4831]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4793]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4812]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4652]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4709]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4760]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4645]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4737]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4693]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4719]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4618]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4617]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4561]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4544]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4546]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4567]


title: EY00 [pt45]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4539]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4536]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4512]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4511]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4492]


title: KD patient, whole blood [UCSD-3904-C]

value: Kawasaki Disease

value: convalescent


title: KD patient, whole blood [UCSD-3947]


title: KD patient, whole blood [UCSD-3922]


title: KD patient, whole blood [UCSD-3931]


title: KD patient, whole blood [UCSD-3901-A]


title: KD patient, whole blood [UCSD-3901-C]


title: KD patient, whole blood [UCSD-3904-A]


title: KD patient, whole blood [UCSD-3929]


title: Febrile control (none-Kawasaki disease) patient, whole blood [UCSD-4476]


title: KD patient, whole blood [UCSD-3935]


title: KD patient, whole blood [UCSD-3895]


title: KD patient, whole blood [UCSD-3911]


title: KD patient, whole blood [UCSD-3899]


title: KD patient, whole blood [UCSD-3881]


title: KD patient, whole blood [UCSD-3877-A]


title: KD patient, whole blood [UCSD-3908]


title: KD patient, whole blood [UCSD-3877-C]


title: KD patient, whole blood [UCSD-3888]


title: KD patient, whole blood [UCSD-3868-A]


title: KD patient, whole blood [UCSD-3868-C]


title: KD patient, whole blood [UCSD-3856-C]


title: KD patient, whole blood [UCSD-3858]


title: KD patient, whole blood [UCSD-3853]


title: KD patient, whole blood [UCSD-3855]


title: KD patient, whole blood [UCSD-3867]


title: KD patient, whole blood [UCSD-3847]


title: KD patient, whole blood [UCSD-3848-C]


title: KD patient, whole blood [UCSD-3845]


title: KD patient, whole blood [UCSD-3838]


title: KD patient, whole blood [UCSD-3833-A]


title: KD patient, whole blood [UCSD-3836]


title: KD patient, whole blood [UCSD-3833-C]


title: KD patient, whole blood [UCSD-3826-C]


title: KD patient, whole blood [UCSD-3827-C]


title: KD patient, whole blood [UCSD-3827-A]


title: KD patient, whole blood [UCSD-3826-A]


title: KD patient, whole blood [UCSD-3815-A]


title: KD patient, whole blood [UCSD-3792-C]


title: KD patient, whole blood [UCSD-3824-A]


title: KD patient, whole blood [UCSD-3808-C]


title: KD patient, whole blood [UCSD-3848-A]


title: KD patient, whole blood [UCSD-3824-C]


title: KD patient, whole blood [UCSD-3811]


title: KD patient, whole blood [UCSD-3802]


title: MIS-C patient, whole blood [MC-203046]

value: MIS-C

value: polyA capture


title: MIS-C patient, whole blood [MC-204026]


title: KD patient, whole blood [UCSD-3808-A]


title: KD patient, whole blood [UCSD-3792-A]


title: KD patient, whole blood [UCSD-3790-C]


title: MIS-C patient, whole blood [MC-203063]


title: MIS-C patient, whole blood [MC-203064]


title: KD patient, whole blood [UCSD-3786-A]


title: KD patient, whole blood [UCSD-3790-A]


title: KD patient, whole blood [UCSD-3815-C]


title: KD patient, whole blood [UCSD-3829-A]


title: MIS-C patient, whole blood [MC-203060]


title: MIS-C patient, whole blood [MC-203055]


title: KD patient, whole blood [UCSD-3780-C]


title: MIS-C patient, whole blood [MC-203050]


title: KD patient, whole blood [UCSD-3775-A]


title: MIS-C patient, whole blood [MC-203040]


title: KD patient, whole blood [UCSD-3777]


title: KD patient, whole blood [UCSD-3768]


title: KD patient, whole blood [UCSD-3775-C]


title: KD patient, whole blood [UCSD-3780-A]


title: KD patient, whole blood [UCSD-3786-C]


title: KD patient, whole blood [UCSD-3764]


title: KD patient, whole blood [UCSD-3758]


title: KD patient, whole blood [UCSD-3752-A]


title: KD patient, whole blood [UCSD-3755-C]


title: MIS-C patient, whole blood [MC-203061]


title: KD patient, whole blood [UCSD-3753]


title: KD patient, whole blood [UCSD-3720]


title: KD patient, whole blood [UCSD-3829-C]


title: KD patient, whole blood [UCSD-3740]


title: KD patient, whole blood [UCSD-3821]


title: KD patient, whole blood [UCSD-3718]


title: KD patient, whole blood [UCSD-3783]


title: KD patient, whole blood [UCSD-3757-C]


title: KD patient, whole blood [UCSD-3704]


title: MIS-C patient, whole blood [MC-203041]


title: KD patient, whole blood [UCSD-3698-C]


title: KD patient, whole blood [UCSD-3698-A]


title: KD patient, whole blood [UCSD-3755-A]


title: KD patient, whole blood [UCSD-3696]


title: KD patient, whole blood [UCSD-3693]


title: KD patient, whole blood [UCSD-3752-C]


title: KD patient, whole blood [UCSD-3675]


title: KD patient, whole blood [UCSD-3674-A]


title: KD patient, whole blood [UCSD-3749]


title: KD patient, whole blood [UCSD-3682]


title: KD patient, whole blood [UCSD-3641]


title: KD patient, whole blood [UCSD-3665]


title: KD patient, whole blood [UCSD-3667]


title: KD patient, whole blood [UCSD-3645]


title: KD patient, whole blood [UCSD-3659]


title: KD patient, whole blood [UCSD-3637-C]


title: KD patient, whole blood [UCSD-3639]


title: KD patient, whole blood [UCSD-3637-A]


title: KD patient, whole blood [UCSD-3633]


title: KD patient, whole blood [UCSD-3627-C]


title: KD patient, whole blood [UCSD-3625]


title: KD patient, whole blood [UCSD-3627-A]


title: KD patient, whole blood [UCSD-3612]


title: KD patient, whole blood [UCSD-3620]


title: KD patient, whole blood [UCSD-3615]


title: KD patient, whole blood [UCSD-3610]


title: KD patient, whole blood [UCSD-3607]


title: KD patient, whole blood [UCSD-3674-C]


title: KD patient, whole blood [UCSD-3604-A]


title: KD patient, whole blood [UCSD-3662]


title: KD patient, whole blood [UCSD-3604-C]


title: KD patient, whole blood [UCSD-3602]


title: KD patient, whole blood [UCSD-3596]


title: KD patient, whole blood [UCSD-3598]


title: KD patient, whole blood [UCSD-3589]


title: KD patient, whole blood [UCSD-3581]


title: KD patient, whole blood [UCSD-3572]


title: KD patient, whole blood [UCSD-3591]


title: KD patient, whole blood [UCSD-3518]


title: KD patient, whole blood [UCSD-3528]


title: KD patient, whole blood [UCSD-3553-A]


title: KD patient, whole blood [UCSD-3318]


title: KD patient, whole blood [UCSD-3553-C]


title: KD patient, whole blood [UCSD-3386-A]


title: KD patient, whole blood [UCSD-3386-C]


title: KD patient, whole blood [UCSD-3291-C]


title: KD patient, whole blood [UCSD-3290-C]


title: KD patient, whole blood [UCSD-3290-A]


title: KD patient, whole blood [UCSD-3237-C]


title: KD patient, whole blood [UCSD-3094-C]


title: KD patient, whole blood [UCSD-3237-A]


title: KD patient, whole blood [UCSD-3578]


title: KD patient, whole blood [UCSD-3094-A]


title: KD patient, whole blood [UCSD-3188]


title: KD patient, whole blood [UCSD-163028]


title: KD patient, whole blood [UCSD-153079]


title: KD patient, whole blood [UCSD-3573]


title: KD patient, whole blood [UCSD-153035]


title: KD patient, whole blood [UCSD-153030]


title: KD patient, whole blood [UCSD-153017]


title: KD patient, whole blood [UCSD-153027]


title: KD patient, whole blood [UCSD-153007]


title: KD patient, whole blood [UCSD-153039]


title: KD patient, whole blood [UCSD-153023]


title: KD patient, whole blood [UCSD-153005]


title: AB13_24hr_LPS_RNA

status: Public on Mar 06 2022

source_name: Adult Human Peripheral Blood

tag: individual

value: Monocyte

value: LPS exposed, collected at 24 hours post exposure.


title: AB13_24hr_T3_LPS_RNA

value: T3 and LPS co-exposed, collected at 24 hours post exposure.


title: AB13_24hr_T3_RNA

value: T3 exposed, collected at 24 hours post exposure.


title: AB13_24hr_RPMI_RNA

value: RPMI media only, collected at 24 hours post culture


title: AB13_4hr_T3_RNA

value: T3 exposed, collected at 4 hours post exposure.


title: AB13_4hr_T3_LPS_RNA

value: T3 and LPS co-exposed, collected at 4 hours post exposure.


title: AB13_4hr_LPS_RNA

value: LPS exposed, collected at 4 hours post exposure.


title: AB13_T0_RNA

value: Baseline monocyte, attached to dish for 1  hour


title: AB12_24hr_T3_LPS_RNA


title: AB12_24hr_T3_RNA


title: AB12_4hr_T3_LPS_RNA


title: AB12_24hr_LPS_RNA


title: AB12_4hr_T3_RNA


title: AB12_T0_RNA


title: AB12_4hr_RPMI_RNA

value: RPMI media only, collected at 4 hours post culture


title: AB13_4hr_RPMI_RNA


title: AB11_24hr_T3_LPS_RNA


title: AB12_24hr_RPMI_RNA


title: AB11_24hr_T3_RNA


title: AB11_4hr_T3_RNA


title: AB11_4hr_T3_LPS_RNA


title: AB12_4hr_LPS_RNA


title: AB11_4hr_RPMI_RNA


title: AB11_4hr_LPS_RNA


title: AB11_T0_RNA


title: cDNA6530_S5: human islets- IL1B with FK506- rep 1

status: Public on Mar 01 2022

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

institute: Baylor Research Institute

data_processing:
RNAseq reads were trimmed and aligned to human genome using hisat2 and counted using htseq-count
Normalization and differential gene  expression (DGE) analysis was performed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file includes raw counts

source_name: islet

growth_protocol: Human islets were provided by the Integrated Islet Distribution Program at City of Hope. Islets were cultured overnight at 5 mM glucose RPMI media supplemented with sodium pyruvate, HEPES, FBS, and penicillin-streptomycin. cultured at 37°C, 5% CO2. Islets were separated 300 islets per well in a 6 well plate. Each well contained one treatment with conditions done in duplicate.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each treatment was performed in duplicate wells. Control duplicate samples were treated with 0.1% DMSO for 2 hr, IL1B duplicate samples were treated with 50 ng/mL IL-1β and high glucose (11 mM) for 2 hr, and IL1B with FK506 duplicate samples were pretreated with 30 min 1 uM FK506 then 50 ng/mL IL-1β and high glucose (11 mM) added for 2 hr

tag: condition

value: FK506 inhibitor+IL1B

tag: tissue type

value: islet

tag: treatment

value: 1 uM FK506


title: cDNA6531_S6: human islets- IL1B with FK506- rep 2


title: AB11_24hr_RPMI_RNA


title: cDNA6529_S4: human islets- IL1B- rep 2

value: IL1B cytokine stimulation

value: 50 ng/mL IL1B


title: cDNA6527_S2: human islets-DMSO-rep 2

value: control

value: 0.1% DMSO


title: cDNA6526_S1: human islets-DMSO-rep 1


title: KD patient, whole blood [UCSD-3727]

value: Kawasaki Disease

value: acute

value: ribosomal/globin depletion


title: WT1-control: Wildtype mouse-no treatment- rep 1

description: Wildtype: in vivo tamoxifen treatment without resultant gene knockout

data_processing:
RNAseq reads were trimmed and aligned to mouse genome using hisat2 and counted using htseq-count
Normalization and differential gene  expression (DGE) analysis was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file includes raw counts

source_name: pancreatic islet

growth_protocol: Mouse islets were isolated from C57BL/6 mice from Jackson Laboratories (JAX) and NFATc2βKO transgenic mice. Briefly, pancreases were extracted from mice after collagenase perfusion and digested for 10 min at 37°C. Islets were separated from digested pancreas preparations by centrifugation on a 1.077 and 1.100 g/mL Ficoll gradient solution. The separated islet tissue layer was collected and washed with Hanks’ balanced salt solution. Intact islets were hand-selected from the purified prep by pipette and cultured overnight at 5.5 mM glucose RPMI, 5% CO2, and 37°C.

treatment_protocol: Islets were treated in duplicates. Control samples were left untreated in culture for two hours. Cytokine cocktail samples were treated with 5 ng/mL IL1β, 10 ng/mL TNFα, 50 ng/mL IFNγ and high glucose (11 mM) for 2 hr

tag: strain

value: Wildtype

value: pancreatic islet

value: untreated for 2 hr


title: WT2-CC: Wildtype mouse-cytokine cocktail- rep 2

value: treated with cytokine cocktail and high glucose for 2 hr


title: KO2-CC: NFATc2βKO mouse islets-cytokine cocktail-rep 2

description: NFATc2βKO: in vivo knockout of NFATc2 in INS-1 expressing cells of adult mice

value: NFATc2beta KO


title: WT1-CC: Wildtype mouse-cytokine cocktail- rep 1


title: KO1-control: NFATc2βKO mouse islets-no treatment-rep 1

description: NFATc2βKO: in vivo knockout of NFATc2 by tamoxifen in INS-1 expressing cells of adult mice


title: cDNA6528_S3: human islets- IL1B- rep 1


title: Multi_FA_15_unstim

status: Public on Feb 28 2022

data_processing:
BeadStudio software v3.2
Normalized (SWAN) Average Beta and detP
The Methylated and unmethylated signal intensities and detP

label: Cy3 and Cy5

source_name: CD3+CD4+CD45RA+CCR7+ T cell

extract_protocol: Total nCD4T cell populations were sorted; and cultured for 72 hours in RPMI alone, or RPMI supplemented with anti-CD3/CD28 beads. DNA and total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.

tag: indiidual

value: CD4 T cells

value: U

tag: Sex

value: F

value: MULTI FA (PN + TN)

value: DNAme


title: KO2-control: NFATc2βKO mouse islets-no treatment-rep 2


title: KO1-CC: NFATc2βKO mouse islets-cytokine cocktail- rep 1


title: Single_FA_13_stim

value: S

value: M

value: PEANUT ONLY


title: WT2-control: Wildtype mouse-no treatment- rep 1


title: Multi_FA_14_unstim

value: MULTI FA (PN + TN + sesame)


title: Non_FA_17_unstim

value: control

value: NO FA


title: Single_FA_12_unstim


title: Single_FA_12_stim


title: Multi_FA_14_stim


title: Non_FA_17_stim


title: Multi_FA_13_stim


title: Non_FA_16_stim


title: Non_FA_16_unstim


title: Non_FA_15_unstim


title: Non_FA_15_stim


title: Non_FA_14_stim


title: Non_FA_14_unstim


title: AB11_24hr_LPS_RNA

value: Monocyte

value: LPS exposed, collected at 24 hours post exposure.


title: Single_FA_11_unstim


title: Single_FA_9_unstim


title: Multi_FA_13_unstim


title: Multi_FA_15_stim


title: Non_FA_13_stim


title: Non_FA_12_stim


title: Single_FA_11_stim


title: Single_FA_10_stim


title: Single_FA_13_unstim


title: Single_FA_9_stim


title: Non_FA_10_unstim


title: Non_FA_11_stim


title: Non_FA_10_stim


title: Single_FA_8_unstim


title: AB13_24hr_T3_DNAme

data_processing: BeadStudio software v3.2. Raw data was received as .iDAT files, which were pre-processed using the MissMethyl packages (available from Bioconductor) in R. Data was normalised for technical variation between and within arrays using the SWAN (Subset-quantile Within Array Normalization). Probes with poor average quality scores (p<0.01), cross-reactive probes and probes associated with single nucleotide polymorphisms (SNPs) were filtered from analysis, leaving 771,019 probes. Differential analysis was carried out using a linear regression model with limma and the DMRCate tool was used to determine differentially methylated regions (DMRs).

label: Cy3, Cy5

extract_protocol: Monocytes in culture were collected in 500uL RLT buffer (Qiagen). Genomic DNA was extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.

value: T3 exposed, collected at 24 hours post exposure.


title: AB12_24hr_T3_LPS_DNAme

value: T3 and LPS co-exposed, collected at 24 hours post exposure.


title: Single_FA_8_stim


title: Non_FA_11_unstim


title: Multi_FA_12_unstim


title: Non_FA_9_stim


title: Single_FA_7_unstim


title: AB11_24hr_LPS_DNAme


title: Multi_FA_11_unstim

value: MULTI FA (PN + TN + milk)


title: Non_FA_9_unstim


title: Non_FA_13_unstim


title: AB12_24hr_RPMI_DNAme

value: RPMI media only, collected at 24 hours post culture


title: Multi_FA_12_stim

value: CD4 T cells


title: Single_FA_6_unstim

value: U


title: Non_FA_8_unstim

value: F


title: Multi_FA_11_stim


title: AB11_24hr_T3_LPS_DNAme


title: AB12_T0_DNAme

value: Baseline monocyte, attached to dish for 1  hour


title: Non_FA_8_stim

value: DNAme


title: AB13_T0_DNAme


title: Non_FA_7_stim

value: S


title: Multi_FA_10_unstim

value: M

value: MULTI FA (PN + TN)


title: Multi_FA_9_unstim


title: Non_FA_7_unstim


title: AB13_24hr_LPS_DNAme


title: Multi_FA_9_stim


title: AB12_24hr_T3_DNAme


title: Single_FA_6_stim

value: PEANUT ONLY


title: Multi_FA_8_unstim


title: Non_FA_5_unstim

value: control


title: Non_FA_4_unstim

value: NO FA


title: Non_FA_6_stim


title: Non_FA_4_stim


title: Non_FA_3_stim


title: Non_FA_5_stim


title: AB13_24hr_RPMI_DNAme

value: Monocyte


title: Single_FA_1_unstim 3


title: Multi_FA_7_unstim

value: MULTI FA (PN + TN + egg)


title: Single_FA_5_stim


title: Non_FA_3_unstim


title: Multi_FA_6_unstim


title: Multi_FA_6_stim


title: AB11_24hr_RPMI_DNAme


title: AB13_24hr_T3_LPS_DNAme


title: Non_FA_2_stim


title: Multi_FA_8_stim


title: Non_FA_1_unstim


title: Multi_FA_4_unstim

value: MULTI FA (PN + TN + shrimp)


title: Non_FA_1_stim


title: Multi_FA_5_unstim

value: MULTI FA (PN + egg)


title: Multi_FA_5_stim


title: Multi_FA_4_stim


title: Single_FA_1_unstim 2


title: Single_FA_4_stim 1


title: Single_FA_4_unstim


title: Multi_FA_7_stim


title: Single_FA_4_stim 2


title: Multi_FA_3_unstim


title: Multi_FA_3_stim


title: Non_FA_2_unstim


title: AB11_T0_DNAme


title: Single_FA_3_stim


title: Single_FA_3_unstim


title: Multi_FA_2_unstim


title: AB11_24hr_T3_DNAme

value: T3 exposed, collected at 24 hours post exposure.


title: Multi_FA_1_stim


title: AB12_24hr_LPS_DNAme

value: LPS exposed, collected at 24 hours post exposure.


title: Single_FA_2_unstim

value: CD4 T cells


title: Single_FA_2_stim


title: Single_FA_1_stim


title: Multi_allergic_17

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. Genes with low expression (mean reads per kilobase of transcript, per million of mapped reads (RPKM) <1 across all samples) were removed from analysis, leaving expression data for 20,025 genes. DESeq  was used to normalise count data and determine gene expression differences between group comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: .counts files contain counts per gene

growth_protocol: PBMCs were viably thawed and total B cell populations (CD3-CD19+) were isolated using fluorescence activated cell sorting (BD FACS-ARIA Fusion cell sorter).

extract_protocol:
Total nCD4T cell populations were sorted; and cultured for 72 hours in RPMI alone, or RPMI supplemented with anti-CD3/CD28 beads. DNA and total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 100ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

value: CD4+ T cells

value: RNA-seq

value: activated with anti-CD3/CD28


title: Multi_allergic_16

value: MULTI FA (PN + TN + sesame)


title: Multi_allergic_15

value: F


title: Multi_allergic_13


title: Multi_allergic_14


title: Multi_allergic_11

value: M


title: Multi_allergic_12

value: MULTI FA (PN + TN + milk)


title: Multi_allergic_10


title: Multi_allergic_8


title: Multi_allergic_7

value: MULTI FA (PN + TN)


title: Multi_allergic_6


title: Multi_allergic_4


title: Multi_FA_2_stim

value: S

value: DNAme


title: Multi_allergic_2


title: Multi_FA_1_unstim

value: U


title: Multi_allergic_1


title: Single_allergic_13

value: PEANUT ONLY


title: Single_allergic_12


title: Multi_allergic_3


title: Single_allergic_11


title: Single_allergic_10


title: Single_FA_1_unstim 1


title: Single_allergic_8


title: Single_allergic_7


title: Single_allergic_6


title: Single_allergic_5


title: Single_allergic_4


title: Single_allergic_3


title: Single_allergic_2


title: Multi_allergic_9


title: Non_allergic_18

value: Control

value: NO FA


title: Multi_allergic_5

value: MULTI FA (PN + TN + shrimp)


title: Non_allergic_17


title: Single_allergic_1


title: Non_allergic_16


title: Non_allergic_13


title: Non_allergic_12


title: Non_allergic_15


title: Non_allergic_10


title: Non_allergic_9


title: Non_allergic_8


title: Non_allergic_11


title: Non_allergic_6


title: Non_allergic_7


title: Non_allergic_4


title: Single_allergic_9


title: Non_allergic_1


title: Non_allergic_2


title: Non_allergic_3


title: Non_allergic_14


title: Non_allergic_5


title: Multi_FA_10_stim


title: M_to_F_Donor_13_12m

status: Public on Feb 17 2022

data_processing:
BeadStudio software v3.2
Raw data was received as .iDAT files, which were pre-processed using the MissMethyl packages (available from Bioconductor) in R. Data was normalised for technical variation between and within arrays using the SWAN (Subset-quantile Within Array Normalization). Probes with poor average quality scores (p<0.01), cross-reactive probes and probes associated with single nucleotide polymorphisms (SNPs) were filtered from analysis. Differential analysis was carried out using a linear regression model with limma and the DMRCate tool was used to determine differentially methylated regions (DMRs).

extract_protocol: Genomic DNA was extracted from concentrated whole blood (buffy coat) using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.

value: Whole blood

value: 12 months following feminizing GAHT


title: M_to_F_Donor_12_6m

value: 6 months following feminizing GAHT


title: M_to_F_Donor_9_baseline

value: Baseline, before feminizing GAHT


title: M_to_F_Donor_13_6m


title: M_to_F_Donor_9_12m


title: M_to_F_Donor_13_baseline


title: M_to_F_Donor_11_6m


title: M_to_F_Donor_11_12m


title: M_to_F_Donor_11_baseline


title: M_to_F_Donor_9_6m


title: M_to_F_Donor_10_12m


title: M_to_F_Donor_10_6m


title: M_to_F_Donor_8_12m


title: M_to_F_Donor_10_baseline


title: M_to_F_Donor_5_6m


title: M_to_F_Donor_5_12m


title: M_to_F_Donor_5_baseline


title: M_to_F_Donor_6_6m


title: M_to_F_Donor_4_6m


title: M_to_F_Donor_12_baseline


title: M_to_F_Donor_6_baseline


title: M_to_F_Donor_8_6m


title: M_to_F_Donor_7_12m


title: M_to_F_Donor_4_12m


title: M_to_F_Donor_7_6m


title: M_to_F_Donor_6_12m


title: M_to_F_Donor_7_baseline


title: M_to_F_Donor_8_baseline


title: M_to_F_Donor_12_12m


title: M_to_F_Donor_4_baseline


title: M_to_F_Donor_3_6m


title: M_to_F_Donor_3_12m


title: M_to_F_Donor_2_6m


title: F_to_M_Donor_12_12m

value: 12 months following masculinizing GAHT


title: F_to_M_Donor_12_6m

value: 6 months following masculinizing GAHT


title: F_to_M_Donor_12_baseline

value: Baseline, before masculinizing GAHT


title: F_to_M_Donor_13_12m


title: M_to_F_Donor_3_baseline


title: F_to_M_Donor_11_baseline


title: F_to_M_Donor_11_12m


title: M_to_F_Donor_1_baseline


title: F_to_M_Donor_8_6m


title: F_to_M_Donor_9_12m


title: F_to_M_Donor_13_6m


title: F_to_M_Donor_13_baseline


title: F_to_M_Donor_10_baseline


title: F_to_M_Donor_8_baseline


title: M_to_F_Donor_1_12m


title: F_to_M_Donor_7_6m


title: F_to_M_Donor_9_baseline


title: F_to_M_Donor_6_12m


title: F_to_M_Donor_7_12m


title: F_to_M_Donor_7_baseline


title: F_to_M_Donor_8_12m