title: OMM 2.3 cells, NC_RIP

first: Hao

last: Tian

state: Shanghai

address: No.639, Zhizaoju Road

institute: Shanghai ninth people's hospital, Shanghai Jiaotong University school of medicine

description: NC.peak.annotation.txt

data_processing:
1 DATA TRIMMING Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic[1] software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Then randomly extract 250 thousand paired reads from clean data, use the blastn software to alignment with the NT database (ftp://ftp.ncbi.nih.gov/blast/db). And take the best result with evalue < 1e-10 and coverage > 80%.  2 DATA MAPPING Meanwhile, Use the SortMeRNA[2] software for ribosomal RNA reads removal. After discarded the rRNA reads, the remainly clean reads were mapped to the reference genome using HISAT2[3] with default parameters. Unique reads with high mapping quality were retained 3 RIP-QC To accessing the quality of methylated RNA immunoprecipitation sequencing data. Used the Guitar[4] R package and deeptools[5] software for evaluation of m6A-seq data quality. 4 PEAK CALLING The m6A-enriched peaks in each m6A immunoprecipitation sample were identified by MeTDiff[6] peak calling software with the corresponding input sample serving as control. MeTDiff was run with options (‘FRAGMENT_LENGTH=200, PEAK_CUTOFF_PVALUE = 0.01, PEAK_CUTOFF_FDR = 0.05’) for peak detection. Called peaks were annotated by intersection with gene architecture using ChIPseeker[7]  5 DIFFERENTIAL ANALYSIS Differential analysis for m6A-Seq identifies differences in RNA methylome in a case-control study, The differential peak were detected by MeTDiff with parameter (‘FRAGMENT_LENGTH = 200, PEAK_CUTOFF_PVALUE = 0.01, DIFF_PEAK_CUTOFF_FDR = 0.05, PEAK_CUTOFF_FDR = 0.05’), after which, differential peak were annotated by ChIPseeker 6 FUNCTION ANNOTATION GO enrichment and KEGG pathway enrichment analysis of peaks and differential peaks were performed respectively using R based on the hypergeometric distribution. 7 MOTIF ANALYSIS MEME[8] and DREME[9] were used to detect the sequence motif, after which, Tomtom software was performed to annotate the motifs.  Reference [1] BOLGER A M, LOHSE M, USADEL B. Trimmomatic: a flexible trimmer for Illumina sequence data [J]. Bioinformatics, 2014, 30(15): 2114-20. [2] KOPYLOVA E, NO L, TOUZET H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data [J]. Bioinformatics, 2012, 28(24): 3211-7. [3] KIM D, LANGMEAD B, SALZBERG S L. HISAT: a fast spliced aligner with low memory requirements [J]. Nature Methods, 2015, 12(4): 357-60. [4] CUI X, WEI Z, ZHANG L, et al. Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features [J]. BioMed research international, 2016, 2016(8367534). [5] RAMIREZ F, DUNDAR F, DIEHL S, et al. deepTools: a flexible platform for exploring deep-sequencing data [J]. Nucleic acids research, 2014, 42(Web Server issue): W187-91. [6] CUI X, ZHANG L, MENG J, et al. MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data [J]. IEEE/ACM Transactions on Computational Biology & Bioinformatics, 2018, 15(2): 526-34. [7] GUANGCHUANG Y, LI-GEN W, QING-YU H. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization [J]. Bioinformatics, 2015, 31(14): 2382-3. [8] BAILEY T L, MIKAEL B, BUSKE F A, et al. MEME SUITE: tools for motif discovery and searching [J]. Nucleic Acids Research, 2009, 37(Web Server): W202-W8. [9] SCHULZ M H, DEVANNY W E, GITTER A, et al. DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data [J]. Bmc Systems Biology, 2012, 6(1): 104-
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tap-delimited text files include RPKM values for each sample and bw files

source_name: OMM 2.3

extract_protocol:
A. Crush frozen tissue sample using the chilled mortar and pestle，and grind tissue sample for 5 minutes until sample becomes powdery. B. For 50-100mg of fresh weight of sample, add 1 mL of TRIzol to sample and mix vigorously. C. Add 200 ul of chloroform, and shake by hand for (at least) 15 seconds with increasing speed from slow to fast to vigorous. Incubate at room temperature for 5 minutes. D. Centrifuge for 15 minutes at 13000 rpm at 4° C.. E. Transfer the aqueous phase to a sterile 1.5 mL centrifuge tube. Add equal volume of 100% isopropanol to the aqueous phase, and incubate at room temperature for 10 minutes. F. Centrifuge for 15 minutes at 13000 rpm at 4° C, and remove the supernatant. G. Add 1 mL of cold 75% ethanol to wash the pellet. H. Centrifuge for 5 minutes at 13000 rpm at 4° C. Discard the wash, and dry the RNA pellet for 5–10 minutes. I. Dissolve RNA in RNase-free water, and incubating for 10 minutes at 55 to 60°C.
1. M6A RIP A. Each biological replicate for m6A-seq starts by using 400 μg of total RNA yielding approximately 10 μg of double poly(A) selected RNA. B. Resuspend each sample obtained from step 1 (10 μg of poly(A) RNA) in 50 μL of UltraPure H2O. C. Add 250 μL of fragmentation buffer to the 50 μL of isolated 2x poly(A) RNA to a final volume of 300 μL. 2. M6A RIP Fragmentation Step of the RIP A. Proceed to the fragmentation of the 300 μL Poly(A) RNA solution at 94°C for exactly 5 minutes using a thermocycler. B. Stop the fragmentation reaction by adding 50 μL of Stop Buffer to a final volume of 350 μL and immediately put on ice. 3. RNA binding to m6A-Dynabeads A. Add 150 μl of pre-equilibrated m6A-Dynabeads (see Notes 2 and 8) to the 350 μl of fragmented RNA from step 2 of section 3.2 to a final volume of 500 μl. B. Allow the fragmented RNA to bind to the m6A-Dynabeads at room temperature while rotating (tail-over-head) at 7 rotations per minute for 1 hour. C. Place the tubes containing the samples on a magnet allowing the bead complexes to cluster until the solution becomes clear. D. Discard the 500 μL liquid phase or supernatant as this fraction represents the m6A negative fragments not captured by the anti-m6A antibody. 4. Washing of m6A-Dynabeads A. Resuspend m6A-Dynabeads-RNA complexes in 500 μL of m6A Binding Buffer, incubate for 3 minutes at room temperature and remove clear supernatant after placing the beads in the magnet. B. Repeat step 1 with 500 μL of Low Salt Buffer. C. Repeat step 1 with 500 μL of High Salt Buffer. Do not exceed 3-minute incubation time for this step to prevent release of the RNA from the beads. D. Repeat step 1 twice with 500 μL of TET buffer. 5. Elution of m6A-positive RNA A. Add 125 μL of 42 °C pre-heated Elution Buffer to the m6A-Dynabead complexes from section 3D, step 4 and incubate at 42 °C for 5 minutes. B. At the end of the 5 minutes, vortex the beads gently and place them on the magnet. C. Collect the liquid phase and transfer to a fresh tube, kept on ice, as it represents the eluate fraction containing the m6A“enriched RNA”. D. Add an additional 125 μL of pre-heated Elution Buffer to the beads and process as described in step 1-3 above for 3 additional times, for a total of 4 elutions. E. Collect the liquid phase obtained at each elution step and pool with the previous ones. Keep sample on ice while working on the next elution. After the fourth round of elution, the final total eluate volume of the m6A positive RNA fraction is 500 μL. 6. Extraction and Cleanup Step of the RIP A. Extract the 500 μl of m6A positive RNA collected in previous step by adding 500 μL of acid phenol-chloroform. B. Centrifuged at 4 °C at 10,000g for 7.5 minutes. C. Carefully collected the upper phase making sure not to touch the inter-phase and transfer to a fresh 1.5 ml tube. D. Add 500 μL of previously tested RNAse free chloroform to the fresh tube, vortex briefly and centrifuged at 4 °C at 10,000g for 7.5 minutes. E. Transfer the upper phase to a fresh 1.5 mL tube and proceed to RNA precipitation (see Note 9) overnight at −20 °C. F. Centrifuged the sample at 4 °C for 20 minutes at 16,000g. G. Wash the pellet twice in 70% ethanol by centrifuging for 10 minutes at 4 °C at 16,000g. H. Dry the pellet at room temperature for 10 minutes prior to re-suspend it in the desired volume (typically 5-6 μl) of Ultra-Pure H20.
RIP Library Construction. We have generally utilized 100 ng of RNA (100 ng of input and 100 ng of post m6A-IP positive fraction) for library construction utilizing the Illumina TrueSeq Stranded mRNA. A. Add 13 μL of Fragment, Prime, Finish Mix to the 5 μl m6A positive fragmented RNA obtained (to final volume of 18 μL). B. Centrifuged at 4 °C at 10,000g for 7.5 minutes. Skip the fragmentation step in the Illumina protocol given the RNA has already been fragmented, and proceed immediately to the synthesis of the First Strand cDNA. C. Follow the Illumina protocol to the end. D. Verify the fragment sizes of each individual library on an Agilent BioAnalyzer 2100 or equivalent using High Sensitivity DNA chip. E. Quantify the library by qPCR on using the Kapa library quantification kit according to the manufacturer’s instructions. F. Submit the libraries for high-throughput sequencing
meRIP-seq

value: OMM 2.3

value: Uveal Melanoma cell line

value: wt

value: DMSO treated 24h


title: Normal liver tissue (Control) Rep2

status: Public on Mar 04 2025

type: SRA

city: Suwon-si

first: chanmo

last: yang

state: Gyeonggi-do

address: 206, World cup-ro, Yeongtong-gu, Song Jae-gwan 207-5

department: Department of Pathology

country: South Korea

institute: Ajou University School of Medicine

description: Library name: N3_1

library_source: transcriptomic

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Normal liver tissue

growth_protocol: Primary liver tumor and normal tissues (cHCC-CCC, HCC, CCC) were collected from patients, fixed in formalin, embedded in paraffin (FFPE), and stored until processing.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: FFPE tumor samples were deparaffinized with xylene, rehydrated in ethanol, digested with Proteinase K, and processed for RNA extraction.

tag: tissue

value: Normal liver tissue

tag: cell line

value: Patient-Derived Liver Cells

tag: cell type

value: Normal hepatocyte

tag: genotype

value: WT


title: H3A110C_SCEG1

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

country: USA

institute: UCLA

description:
Sample10_AC-EG-1_S15
H3A110C_SCEG1

data_processing:
FASTQ read 1 of the paired-end reads used for downstream analyses
Genomic alignment of FASTQ using HISAT2. Strand-specific alignment.
Assignment to open reading frames and counting using featureCounts. Strand-specific assignment.
Differential expression analysis performed with DESeq2
Assembly: sacCer3
Supplementary files format and content: csv

organism: Saccharomyces cerevisiae

source_name: whole yeast cells

growth_protocol: Cells were grown to 2-3 doublings before collection

extract_protocol:
RNA was extracted from whole yeast cells using hot acid phenol, followed by a further phenol-cholorform extraction and ethanol precipitation.
Prior to preparing RNA-seq libraries for Illumina NovaSeq sequencing, contaminating DNA was digested using Turbo DNase (Thermo Fisher). RNA quality was assessed by Agilent 2200 Tapestation. Stranded mRNA (Poly-A) libraries were constructed with automated NGS library construction and sequenced by UCLA Technology Center for Genomics & Bioinformatics

value: whole yeast cells

tag: treatment

value: SCEG (oxidative medium)


title: Liver, nuclei, snRNA-seq, chow diet, Plvap knockout, #C078

city: Odense M

first: Daniel

last: Hansen

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
To perform the abovementioned steps the features mkfastq and count were run.
The raw count matrix is provided as an mtx.gz file along with gene and barcode names as tsv.gz files
Assembly: mm10

organism: Mus musculus

source_name: Liver , Plvaptm1.1Salm-Tg(Lrat-cre)1Rshw (B6.126(Cg))

extract_protocol:
Chromium Next GEM Single Cell 3´ GEM, Library and Gel Bead kit v.3.1 (10x Genomics)
Chromium Next GEM Single Cell 3´ GEM, Library and Gel Bead kit v.3.1 (10x Genomics)
single-nucleus RNA-seq

treatment_protocol: 18 weeks old male mice given chow diet. Mice were fasted 12 hours o.n. before sac.

value: Liver

tag: strain

value: Plvap knockout

tag: fasting before_sac.

value: 12 hours o.n. before sac

tag: Sex

value: Male

value: Chow Diet


title: Normal liver tissue (Control) Rep1

description: Library name: N1


title: OMM 2.3 cells, NC_input

city: Shanghai

country: China


title: WT_SCEG3

description:
Sample9_WT-EG-3_S17
WT_SCEG3

value: Wild type


title: High_TnT_Group_4

city: Frankfurt

first: Jiaoyan

last: Han

state: Hessen

address: Theodor-Stern Kai 7

department: Department of Trauma Surgery and Orthopedics

country: Germany

institute: Goethe University Frankfurt, University Hospital

description:
Library name: SAMPLES 9
Plasma from polytrauma patient, high tnt group, replicate 4
TH4

data_processing:
Adapter and quality trimming were performed using Cutadapt. Unprocessed sequencing reads underwent adapter removal and low-quality trimming.
Unprocessed sequencing reads were trimmed to remove adapters and low-quality bases using Cutadapt. Deduplication was performed based on unique molecular identifiers using in-house scripts to ensure the accuracy of the data.
Quality checks were performed with FastQC.
Reads were then mapped to the reference genome using Bowtie2, and transcript quantification was conducted using HTSeq.
Assembly: ENSEMBL - GRCh38
Supplementary files format and content: Processed data is provided in a TSV file, containing raw counts across all samples.

source_name: plasma

extract_protocol:
miRNA was extracted from 200 µL of plasma (Low_TnT_Group, n=5; High_TnT_Group, n=5) using miRNeasy Serum/Plasma Advanced Kit (Qiagen, Hilden, Germany).
Small RNA libraries were prepared by GenXPro GmbH (Frankfurt, Germany). Sequencing was conducted on an Illumina NextSeq500 platform with 1x75 base pairs.

value: plasma


title: WT_SCEG2

description:
Sample8_WT-EG-2_S10
WT_SCEG2


title: High_TnT_Group_5

description:
Library name: SAMPLES 10
Plasma from polytrauma patient, high tnt group, replicate 5
TH5


title: WT_SCEG1

description:
Sample7_WT-EG-1_S9
WT_SCEG1


title: OMM 2.3 cells, MA_input

value: OMM 2.3

value: MA treated 24h


title: Liver, nuclei, snRNA-seq, chow diet, Plvap knockout, #C077


title: OMM 2.3 cells, MA_RIP

description: MA.peak.annotation.txt

value: Uveal Melanoma cell line

value: wt


title: H3A110C_SC3

description:
Sample6_AC-SC-3_S5
H3A110C_SC3

value: SC (synthetic complete, fermentative medium)


title: High_TnT_Group_3

description:
Library name: SAMPLES 8
Plasma from polytrauma patient, high tnt group, replicate 3
TH3


title: Liver, nuclei, snRNA-seq, chow diet, littermate control, #C074

value: Plvap Control


title: Liver, nuclei, snRNA-seq, chow diet, littermate control, #C075


title: High_TnT_Group_2

description:
Library name: SAMPLES 7
Plasma from polytrauma patient, high tnt group, replicate 2
TH2


title: H3A110C_SC2

description:
Sample5_AC-SC-2_S9
H3A110C_SC2


title: GLICO_320_negctrl

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine

data_processing:
CellRanger Pipeline 2.0.1
Assembly: hg38
Supplementary files format and content: CellRanger outputs, barcodes, matrix and features in tsv format

source_name: glioma-stem cell

growth_protocol: GSCs were cultured in Neurobasal medium A (NBE medium, Thermo Fisher Scientific) supplemented with N2 (Thermo Fisher Scientific), B27 (Thermo Fisher Scientific), human recombinant bFGF and EGF (25 ng/mL each, R&D Systems), heparin (2ng/ml, Sigma), Penicilin-Streptomycin solution (LifeTech), and L-glutamine (200 mM/100X. LifeTech).

extract_protocol:
After 1 week of co-culture, GLICOs were dissociated with trypsin and single-cell and GFP+/DAPI- cells were sorted. Cells from both samples were submitted for 10x scRNAseq.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Sorted GFP+/DAPI- GSCs 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 amplified by PCR and the apropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs and a sample index were added.

treatment_protocol: 100K cells each of the 320_negative guide_CRISPRi  and 320_GOLIM4_CRISPRi lines were co-cultured with 12 4.5-month-old cerebral organoids (GLICO). Organoids were plated one per well in a 96-well U-bottom plate, excess medium was removed and 100,000 GSCs in 150 uL of NBE were added to each well. After GLICO formation through stationary co-culture incubation at 37°C for 24h, 1ug/ml of doxycycline was added to the GLICO media and replenished with fresh media after 96h. After 1 week, GLICOs were dissociated and single-cell and GFP+/DAPI- cells were sorted. Cells from both samples were submitted for 10x scRNAseq.

value: glioma-stem cell

value: patient-derived glioma stem cells

value: guide for negative genomic region


title: GLICO_320_GOLIM4CRISPRi

value: guide targeting GOLIM4 enhancer region


title: Liver, bulk RNA-seq, chow diet, whole-body Cav1 knockout, rep D, (C962)

data_processing:
Reads were aligned using STAR v.2.7.8a to the mouse genome GRCm39 v.101
FeatureCounts (v.2.0) was employed for exon read counting
Quality of raw sequencing was assessed using FastQC (v.0.11.9) and MultiQC (v.1.10.1)
Assembly: GRCm39 v.101
Supplementary files format and content: Bulk RNA-seq data comparing 12h fasted Plvap knockout mice to littermate controls inclosed as txt.file
Supplementary files format and content: Bulk RNA-seq data comparing 2h refed Plvap knockout mice to littermate controls inclosed as txt.file
Supplementary files format and content: Bulk RNA-seq data comparing 6h fasted whole-body Cav1 knockout mice to wild-type controls inclosed as txt.file

source_name: Liver , STOCK Cav1tm1Mls/J

extract_protocol:
RNA was isolated using the Monarch® Total RNA Miniprep Kit (NEB #T2010S, New England BioLabs). Purified RNA was quantified using Qubit 3.0 Fluorometer and RNA quality was assessed using Fragment Analyzer 5200
NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, San Diego, CA)
Bulk RNA-seq

treatment_protocol: Mice were given normal chow diet and were fasted 12 hours o.n. before sac.

value: Liver

value: STOCK Cav1tm1Mls/J

value: Cav1 Knockout

value: 6 hours o.n. before sac

tag: tissue preservation

value: Snap frozen


title: High_TnT_Group_1

description:
Library name: SAMPLES 6
Plasma from polytrauma patient, high tnt group, replicate 1
TH1


title: Liver, nuclei, snRNA-seq, chow diet, littermate control, #C076

value: 12 hours o.n. before sac

value: Male

value: Chow Diet


title: H3A110C_SC1

description:
Sample4_AC-SC-1_S17
H3A110C_SC1

value: whole yeast cells


title: Skin_treatment_P3

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: 10x Genomics

data_processing:
CellRanger v6.0.2 used for demultiplexing + read mapping + barcode assignment + UMI counting
Seurat v4.1.1 used for quality control + normalization + sample integration + dimensionality reduction + cell clustering
CellChat v1.6 used for cell-cell interaction analysis
SCpubr v2.0.1 used for data visualization
Assembly: GRCh38.p13
Supplementary files format and content: Filtered feature-barcode count matrices from CellRanger

molecule: polyA RNA

source_name: skin

extract_protocol:
Enzymatic dissociation of skin samples according to the protocol published by Blaz et al., Front. Cell Dev. Biol. 2022 (https://doi.org/10.3389/fcell.2022.872688).
10 x Genomics Single Cell Gene Expression 3' v3.1

value: skin

tag: condition

value: on-treatment


title: Low_TnT_Group_5

description:
Library name: SAMPLES 5
Plasma from polytrauma patient, low tnt group, replicate 5
TL10

value: plasma


title: Skin_baseline_P3

description: 10x Genomics

value: baseline


title: Liver, bulk RNA-seq, chow diet, whole-body Cav1 knockout, rep B, (C960)


title: Low_TnT_Group_4

description:
Library name: SAMPLES 4
Plasma from polytrauma patient, low tnt group, replicate 4
TL9


title: Liver, bulk RNA-seq, chow diet, whole-body Cav1 knockout, rep C, (C961)


title: Skin_treatment_P2

description: 10x Genomics


title: WT_SC2

description:
Sample2_WT-SC-2_S13
WT_SC2

value: Wild type

value: SC (synthetic complete, fermentative medium)


title: Low_TnT_Group_3

description:
Library name: SAMPLES 3
Plasma from polytrauma patient, low tnt group, replicate 3
TL8


title: Liver, bulk RNA-seq, chow diet, WT C57BL/6N, rep D, (C958)

source_name: Liver , WT C57BL/6N

value: WT


title: Low_TnT_Group_2

description:
Library name: SAMPLES 2
Plasma from polytrauma patient, low tnt group, replicate 2
TL7


title: Liver, bulk RNA-seq, chow diet, whole-body Cav1 knockout, rep A, (C959)


title: Liver, bulk RNA-seq, chow diet, WT C57BL/6N, rep C, (C957)


title: Low_TnT_Group_1

description:
Library name: SAMPLES 1
Plasma from polytrauma patient, low tnt group, replicate 1
TL6


title: polyIC_TNF_3

city: Chicago

first: Savas

last: Tay

state: IL

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: University of Chicago

data_processing:
Basecalls performed using CASAVA
Sequenced reads were trimmed for adaptor sequence and aligned using STAR aligner with default settings
Transcript abundance was calculated using featureCounts
Assembly: GRCm38
Supplementary files format and content: featureCounts object with counts and annotations

source_name: BMDM

growth_protocol: Bone marrow stem cells were harvested from 6-12 week old RelA-V/V C57BL6 mice, differentiated in RPMI supplemented with 20 ng/mL m-CSF for 6 days and replated on day 7 in a 24 well plate at 150K/well

extract_protocol:
Cells were lysed using RLT buffer + 1% beta-mercaptanol
RT was done with poly-dT oligo + template switching, followed by second strand synthesis and library prep using the Nextera XT protocol

treatment_protocol: Media was aspirated and Stimulus A in complete media and m-CSF added. After 4 hours, Stimulus A was aspirated and Stimulus B in complete media and m-CSF added.

value: BMDM

value: RelA-mVenus


title: Skin_treatment_P1

description: 10x Genomics


title: Liver, bulk RNA-seq, chow diet, WT C57BL/6N, rep B, (C956)

value: Liver


title: Skin_baseline_P1

description: 10x Genomics


title: S351, scRNAseq

first: Patrick

last: Wilson

address: 413 E. 69th Street

department: gale and Ira Drukier Institute for Children's Health

description: 10x Genomics

data_processing:
Cellranger Single-Cell Software Suite (version 3.0) was used to perform sample de-multiplexing, barcode processing, and single-cell 5’ and V(D)J counting, and Cellranger mkfastq was used to de-multiplex raw base call (BCL) files into sample-specific fastq files. Subsequently, reads were aligned to the GRCh38 human genome. Cellranger counts and Cellranger vdj package within the Cellranger pipeline were used to identify gene expression and assemble V(D)J pairs of antibodies.
Assembly: GRCh38
Supplementary files format and content: compressed tar.gz file, has barcodes.tsv, genes.tsv, matrix.mtx 3 files, which are outputs from CellRanger pipeline

source_name: Blood Cells

extract_protocol:
cH5/1+ MBCs (CD19+CD27+HA+) were bulk sorted and partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) to achieve single cell resolution using the 10x Genomics Chromium Controller and according to the manufacturer’s instruction (10x Genomics).
The sorted single cells were processed according to 5’ gene expression and B cell Immunoglobulin (Ig) enrichment instruction to prepare the libraries for sequencing.
Libraries were sequenced using an Illumina HiSeq 4000 at Northwestern University or an Illumina NextSeq 500 at the University of Chicago.

value: Blood Cells


title: polyIC_TNF_1


title: polyIC_TNF_2


title: WT_SC3

description:
Sample3_WT-SC-3_S4
WT_SC3


title: Liver, bulk RNA-seq, chow diet, WT C57BL/6N, rep A, (C955)

value: 6 hours o.n. before sac


title: hiPSCs induced chondrocytes, HT, biological rep-3

city: Hong Kong

first: See Wing

last: Chan

address: Lo Kwee-Seong Integrated Biomedical Sciences  Building, Area 39, The Chinese University of Hong  Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Sequencing reads were checked by FastQC and aligned to hg38 using STAR. Read counts were generated using rsem and normalization was performed by EdgeR package in R.
Assembly: hg38
Supplementary files format and content: text file includes raw counts, TPM and FPKM values for each sample

source_name: iBC 1.2

extract_protocol:
Cells were dissolved in QIAzol Lysis Reagent. Chloroform was added, and the mixture was centrifuged to extract the aqueous phase. Total RNA was then extracted using the Direct-zol RNA Miniprep Kit by Zymo Research, following the manufacturer's instructions.
A total of 1 µg of RNA was used in the library preparation using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer's instructions.

value: male

value: iBC 1.2

value: hiPSC

value: chondrocyte differentiation


title: hiPSCs induced chondrocytes, HT, biological rep-2


title: Skin_baseline_P2

description: 10x Genomics


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep D, (C384)

value: Plvap Knockout

value: 10 hours fasting + 2 hour refed before sac

value: Male

value: Snap frozen

value: Chow Diet


title: polyIC_LPS_3


title: S347, scRNAseq

description: 10x Genomics


title: hiPSCs induced chondrocytes, HT, biological rep-1


title: S346, scRNAseq

description: 10x Genomics


title: polyIC_LPS_1


title: S343, scRNAseq

description: 10x Genomics


title: hiPSCs induced chondrocytes, WT, biological rep-2


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep B, (C382)


title: polyIC_LPS_2


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep A, (C381)


title: hiPSCs induced chondrocytes, WT, biological rep-3


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep C, (C383)


title: polyIC_media_1


title: polyIC_media_3


title: media_TNF_3


title: Liver, bulk RNA-seq, chow diet, littermate control, rep C, (C379)

value: Plvap Control


title: hiPSCs induced chondrocytes, WT, biological rep-1


title: HGC27_WT_H3K27acHiChIP_rep1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

library_source: genomic

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
Hi-C reads were processed using HiC-Pro
Assembly: hg19
Supplementary files format and content: .hic

molecule: genomic DNA

source_name: Gastric cancer cell line

growth_protocol: These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.

extract_protocol: Hi-C experiment were conducted in biological replicates using MboI, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).

value: uninfected control cell

tag: antibody

value: H3K27ac_ChIP (Active Motif, 91193, lot 22420004)


title: S334, scRNAseq

description: 10x Genomics


title: polyIC_media_2

value: BMDM


title: S336, scRNAseq

description: 10x Genomics


title: Liver, bulk RNA-seq, chow diet, littermate control, rep B, (C378)


title: S350, scRNAseq

description: 10x Genomics


title: S342, scRNAseq

description: 10x Genomics


title: WT_SC1

description:
Sample1_WT-SC-1_S8
WT_SC1

value: whole yeast cells

value: Wild type

value: SC (synthetic complete, fermentative medium)


title: media_TNF_2

value: RelA-mVenus


title: Liver, bulk RNA-seq, chow diet, littermate control, rep A, (C377)

value: Liver


title: S337, scRNAseq

description: 10x Genomics

value: Blood Cells


title: S327, scRNAseq

description: 10x Genomics


title: ago2-1(2014)

type: RNA

city: Guangzhou

first: Shaoyan

last: Zheng

address: Wushan Road No. 483

institute: South China Agricultural University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Oryza sativa

source_name: young panicles

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: RNA samples used for microarray analysis were prepared from young panicles before stage 5 in WT (ZH11) and ago2-1 (OsAGO2 antisense) plants grown under normal field conditions

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: normal field conditions

value: young panicles

tag: genotype/variation


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep D, (A432)

value: 12 hours o.n. before sac


title: S326, scRNAseq

description: 10x Genomics


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep E, (A433)

value: Plvap Knockout


title: KO Tfh4-2

city: New Haven

first: Ping-Min

last: Chen

state: CT

address: 333 Cedar Street

department: Immunobiology

institute: Yale University

data_processing:
Reads were aligned to the mm9 mouse genome using TopHat version 2.0.6 and Bowtie version 1.3.0, and differential expression computed with Cufflinks version 2.0.2
Analysis of RNA-seq data was done using the CummeRbund package version 2.0.0 in R.
Differentially expressed genes were filtered by keeping transcripts with at least 1 read from each population significant at FDR-adjusted p-value < 0.05 between 2 of the populations, and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were summed across isoforms to obtain data for all significant genes.
Genome_build: mm9
Supplementary_files_format_and_content: Stat6KO_Tfh_RNAseq.csv
Supplementary_files_format_and_content: Genelist_FPKM_pairwise-stats.xlsx

source_name: T follicular helper cells

growth_protocol: Ex vivo isolated Tfh cells from sorter

extract_protocol:
QIAGEN Rneasy Plus Mini Kit
Per Yale Center for Genomic Analysis

treatment_protocol: Two separate sorts were performed on different days, pooling 25-30 mice per genotype, per experiment.

value: T follicular helper cells

value: Stat6 KO

value: untreated


title: media_polyIC_3


title: KO Tfh4-1


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep C, (A431)

value: Male

value: Snap frozen

value: Chow Diet


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep B, (A430)


title: S319, scRNAseq

description: 10x Genomics


title: media_polyIC_1


title: KO Tfh21-2


title: S322, scRNAseq

description: 10x Genomics


title: S317, scRNAseq

description: 10x Genomics


title: media_polyIC_2


title: KO Tfh21-1


title: media_LPS_3


title: media_TNF_1


title: S324, scRNAseq

description: 10x Genomics


title: WT(2013)

value: wild type


title: Liver, bulk RNA-seq, chow diet, littermate control, rep F, (A427)

value: Plvap Control


title: Liver, bulk RNA-seq, chow diet, HSC Plvap knockout, rep A, (A429)


title: media_LPS_2

value: BMDM


title: WT(2014)


title: WT Tfh4-2

value: Stat6 WT


title: S311, scRNAseq

description: 10x Genomics


title: media_LPS_1


title: WT Tfh4-1


title: S310, scRNAseq

description: 10x Genomics


title: Liver, bulk RNA-seq, chow diet, littermate control, rep D, (A425)


title: WT Tfh21-2


title: ago2-1(2013)


title: Liver, bulk RNA-seq, chow diet, littermate control, rep B, (A423)


title: S308, scRNAseq

description: 10x Genomics


title: WT Tfh21-1


title: media_media_2


title: media_media_1


title: S301, scRNAseq

description: 10x Genomics


title: CD4+ T cells, STAT6KO-3

data_processing:
Reads were aligned to the mm9 mouse genome using Bowtie version 1.3.0
Peak-calling was performed using MACS v2.0
normalized using DE-Seq2 in R
Annotation of peaks was performed using HOMER
Differential expression was computed using a Poisson distribution method adapted from MAnorm
Genome_build: mm9
Supplementary_files_format_and_content: ATACseq_WT_Stat6KO_Il21e_result.txt

source_name: CD4+ T cells

growth_protocol: Ex vivo isolated naïve CD4+ T cells

extract_protocol:
50,000 cells of each type were subjected to the Nextera Tagmentation Enzyme reaction for 30 minutes at 37 degrees C, followed by DNA purification (MinElute PCR Purification Kit, Qiagen)
each library was amplified by PCR (KAPA HiFi HotStart ReadyMix, Kapa Biosystems) and barcoded using standard Illumina sequencing adaptors to normalize library size. Quality verification, library multiplexing, and sequencing were performed at the Yale Center for Genomic Analysis. Samples were sequenced on an Illumina HiSeq 2000 using 75-bp paired end reads.

treatment_protocol: naïve CD4+ T cells were isolated by using the EasySep™ Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL).

value: Naive CD4+ T cells


title: media_CPG_3

value: RelA-mVenus


title: Liver, bulk RNA-seq, chow diet, littermate control, rep A, (A422)

value: Liver


title: media_CPG_1


title: CD4+ T cells, STAT6KO-1


title: media_CPG_2


title: CD4+ T cells, STAT6KO-2


title: Liver, bulk RNA-seq, chow diet, littermate control, rep C, (A424)


title: ChIP fully differentiated regulatory T cells (IRF4-Bio.Rosa26BirA)

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
ChIP-seq reads were aligned to UCSC mm10 genome using EaSeq version 1.2
For peak calling of Th17 cells following parameters were used: window size: 100bp, FDR: 1x10-15, p-value: 1x10-20, log2: 2.1, merge distance 0bp. For Treg cells the parameters were adjusted to: window size: 100bp, FDR: 1x10-10, p-value: 1E-10, log2: 1.5, merge distance: 100bp.
Peaks were annotated to nearest start or end of a gene.
Assembly: mm10
Supplementary files format and content: .wig.gz

source_name: Spleen

growth_protocol: IMDM supplemented with 10% fetal bovine serum, 1% sodium pyruvate, 1% glutamine. Th17 cells were induced by the addition of 1 ng/ml TGF-b, 40 ng/ml IL-6, 2.5 µg/ml anti-IFN-g, 10 µg/ml anti-IL-4 on anti-CD3 and anti-CD28 (each 4µg/ml) coat. Treg cells were induced by addition of 7.5 ng/ml TGF-b and 250 ng/ml IL-2 on anti-CD3 (4 µg/ml) and anti-CD28 (8 µg/ml) coat. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Chromatin from 1-1.5x10^7 1% formaldehyde fixed Th17/Treg cells was prepared using a lysis buffer containing 1% SDS, 50 mM Tris and 10 mM EDTA and with Bioruptor Plus (3 cycles each 30s/30s ON/OFF, high) before precipitation of chromatin by streptavidin beads
Sequencing libraries were prepared using 840pg (Th17)/880pg (Treg) decrosslinked and purified DNA employing the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® according to the manual (without size selection and 15 cycles of final PCR). All quality controls were done using Invitrogen’s Qubit HS assay and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay.Barcoded libraries weresequenced on a Illumina NovaSeq6000 (150 Cycles; paired-end) at Novogene (Cambridge; UK).For downstream analysis the software EaSeq (v1.2) was used.

value: Spleen

value: primary T cells

value: regulatory T cells


title: media_media_3


title: MDA-MB-231 cells, siC.3

city: LYON

first: Jean-Marc

last: Vanacker

address: 32-34 avenue Tony Garnier

country: France

institute: IGFL, ENS de Lyon, CNRS UMR 5242

data_processing:
Libraries were sequenced on Illumina NextSeq 500, giving 49-56 M single-end reads per sample. Read length was 86pb.
Sequencing quality was checked with FastQC. Then reads were aligned to the hg38 reference genome (hg38.refGene.gtf file) using STAR 2.7.3a with option --outSAMtype BAM Unsorted SortedByCoordinate.
Raw counts were calculated using the htseq-count Python 3.8 script with options --stranded reverse and --nonunique all, and the same gtf file as for alignment.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample.

source_name: MDA-MB-231; 3D-culture

growth_protocol: MDA-MB-231 cells were cultured in DMEM containing 4.5 g/L glucose, and supplemented with 10% fetal calf serum, 10 U/mL penicillin, 10 μg/mL streptomycin at 37°C and under 5% CO2.

extract_protocol:
RNA were extracted using Macherey-Nagel kit
RNA libraries were prepared using the LEXOGEN SENSE mRNA-Seq Library Prep Kit V2 designed to generate Illumina-compatible libraries.

treatment_protocol: siRNA were transfected using interferin under conditions recommended by the supplier (Ozyme)

value: breast cancer

value: breast cancer cells

value: siCtrl


title: ChIP fully differentiated regulatory T cells (Rosa26BirA)


title: Liver, bulk RNA-seq, chow diet, littermate control, rep E, (A426)

value: 12 hours o.n. before sac


title: MDA-MB-231 cells, siEi.3

value: siERRa-I


title: MDA-MB-231 cells, siEd.3

value: siERRa-D


title: CD4+ T cells, IL21KO-3

value: Il21e KO

value: untreated


title: CPG_TNF_3


title: MDA-MB-231 cells, siEi.2


title: ChIP fully differentiated T helper 17 cells (Rosa26BirA)

value: T helper 17 cells


title: CD4+ T cells, IL21KO-2


title: MDA-MB-231 cells, siEd.2


title: CPG_TNF_2

value: BMDM


title: CPG_TNF_1


title: CD4+ T cells, WT-3

value: WT


title: MDA-MB-231 cells, siEi.1


title: MDA-MB-231 cells, siC.2


title: CD4+ T cells, IL21KO-1

value: Naive CD4+ T cells


title: Liver, bulk RNA-seq, chow diet, littermate control, rep D, (C380)

value: Plvap Control

value: 10 hours fasting + 2 hour refed before sac

value: Male

value: Snap frozen

value: Chow Diet


title: KO_IP_3

city: Tianjin

last: Jiang

state: Tianjin

address: Weijin Road

institute: Tianjin university

description:
Library name: sample12
KO_IP_3

library_source: other

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.1), where low-quality reads were discarded and the reads with adaptor sequences were trimmed. Clean reads were further treated to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, grouping reads with the same UMI sequence into the same cluster. Reads within each cluster were compared using pairwise alignment, and then reads with over 95% sequence identity were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster. These steps eliminated errors and biases introduced by PCR amplification or sequencing. The sequences were then used for standard mRNA-seq analysis. They were mapped to the human genome hg38 using STAR software (version 2.7.6a). Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and RPKM values were calculated. Differentially expressed genes between groups were identified using the edgeR package (version 4.0.16), and a P-value cutoff of 0.05 and a FC cutoff of 2 were used.
Assembly: GRCh38
Supplementary files format and content: RPKM based "processed data.xls"

molecule: other

source_name: cell line

growth_protocol: HeLa cells were maintained with Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin (100 µg/mL) in a 5% CO2 incubator at 37 ℃.

extract_protocol:
Briefly, the protein G Dynabeads (Thermo Fisher Scientific) were washed and resuspended in the dsRIP lysis buffer (50 mM Tris-Cl, pH 7.4, 100 mM NaCl, 3 mM MgCl2, 0.5% IGEPAL CA-630). For each sample, 25 μL of beads were pre-bound to 5 μg of anti-dsRNA mAb (J2) by incubation for 2 h at 4 ℃. HeLa WT and KO cells were collected and washed with ice cold PBS for three times. Then, 3×10^7 cells for each group were lysed in 0.6 mL dsRIP lysis buffer for exactly 5 min on ice. Total RNA was harvested from the rest of cells using Trizol for both groups to serve as input samples and stored at -80 ℃. After that, the cell lysates were spin down by centrifugation at 13 000 g for 10 min at 4  ℃. For immunoprecipitation, 25 μL of J2-bound Protein G Dynabeads were added to the lysate and incubated for 1 h at 4 ℃ with rotation. Then, the beads were washed four times with dsRIP lysis buffer, and J2-bound dsRNA was harvested directly from beads with Trizol with a ratio of 1:5 of chloroform added.
Briefly, both the input and dsRIP samples were used for library generation. Sequencing libraries were prepared using the Ribo-clean rRNA Depletion Kit (Vazyme, China, Cat# RN416) and KCTM Digital Stranded mRNA Library Prep Kit (Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. Subsequently, the libraries were quantified by Qubit 3.0 and sequenced on a DNBSEQ-T7 platform (MGI) using the PE150 sequencing mode to generate paired-end reads.

value: cell line

value: cervical cancer cells

value: HeLa

value: ZNF385A KO


title: CPG_LPS_3

value: RelA-mVenus


title: KO_IP_2

description:
Library name: sample11
KO_IP_2


title: CPG_LPS_2


title: MDA-MB-231 cells, siEd.1

value: breast cancer

value: breast cancer cells

value: siERRa-D


title: CD4+ T cells, WT-2

value: untreated


title: KO_IP_1

description:
Library name: sample10
KO_IP_1


title: KO Tfh4 Cells

data_processing:
Reads were aligned to the mm9 mouse genome using Bowtie version 1.3.0
Peak-calling was performed using MACS v2.0
normalized using DE-Seq2 in R
Annotation of peaks was performed using HOMER
Differential expression was computed using a Poisson distribution method adapted from MAnorm
Genome_build: mm9
Supplementary_files_format_and_content: ATACseq_Tfh214_Stat6_result.txt

treatment_protocol: Tfh populations were sorted by flow cytometry, using 10 mice per genotype.

value: T follicular helper cells

tag: cell population

value: Tfh4 Cells

value: Stat6 KO


title: MDA-MB-231 cells, siC.1

value: siCtrl


title: CPG_LPS_1

value: BMDM


title: KO_input_3

description:
Library name: sample9
KO_input_3


title: CD4+ T cells, WT-1

value: Naive CD4+ T cells

value: WT


title: HGC27_RUNX3KO_H3K4me3_rep1

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie1.0.1.
Duplication reads were removed from aligned file by using picard-tools-1.119.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

value: Gastric cancer cell line

tag: ChIP

value: H3K4me3_ChIP (Active Motif, 39159, lot 25817005)


title: KO_input_2

description:
Library name: sample8
KO_input_2

value: cell line

value: cervical cancer cells


title: HGC27_WT_H3K4me3_rep1


title: KO Tfh214 Cells

value: Tfh214 Cells


title: CPG_media_3

value: RelA-mVenus


title: WT_IP_3

description:
Library name: sample6
WT_IP_3

value: HeLa


title: WT Tfh4 Cells

value: Stat6 WT


title: WT_input_3

description:
Library name: sample3
WT_input_3


title: SmadKO4

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

data_processing:
alignment to mouse genome mm10 with Rsubread 2.2.6
quantification with FeatureCounts
differential expression with DESeq2 1.28
Genome_build: mm10
Supplementary_files_format_and_content: counts_mtx.txt: tab-delimited matrix of raw counts for all samples
Supplementary_files_format_and_content: diff_expression.txt: tab-delimited file with DESeq2 output

source_name: Sorted microglia P60

extract_protocol:
Rneasy Plus micro kit Qiagen
Nextera XT DNA Library Prep Kit Illumina, single-end unstranded

value: Brain

tag: age


title: WT_IP_2

description:
Library name: sample5
WT_IP_2


title: HGC27_RUNX3KO_Input_rep1

value: Input


title: HGC27_WT_H3K27ac_rep1

value: H3K27ac_ChIP (Active Motif, 91193, lot 22420004)


title: WT_input_2

description:
Library name: sample2
WT_input_2


title: WT_IP_1

description:
Library name: sample4
WT_IP_1


title: Wildtype replicate 1

city: Hamilton

first: Ted

last: Hackstadt

state: MT

address: 903 S 4th St

department: Rocky Mountain Laboratories (National Institute of Allergy and Infectious Disease)

institute: National Institutes of Health

description: Library name: genotype_WT_rep1

data_processing:
The reads were processed using the pipeline RNA-seek v1.9.5.
First, reads were trimmed using Cutadapt, and trimmed reads were aligned to the reference using STAR.
The splice junctions output from STAR were collected  across all samples and inserted into the genome indices to run STAR again.
Finally, RSEM was used to quantify gene and isoform expression.
Assembly: GCA_000018225
Supplementary files format and content: Tab-limited file includes RSEM expected counts for each sample.

organism: Rickettsia rickettsii str. 'Sheila Smith'

source_name: Vero76 cells (ATCC CCL-81TM) infected with R. rickettsii Sheila Smith (CP000848.1)

growth_protocol: Vero76 cells (ATCC CCL-81™) were grown in RPMI medium plus 5 % heat-inactivated fetal bovine serum (FBS) at 37˚C in a 5% CO2 atmosphere.  Rickettsia rickettsii Sheila Smith (CP000848.1) were grown at 34˚C in Vero76 cells in M199 medium plus 2% heat-inactivated FBS in a 5% CO2 atmosphere.

extract_protocol:
Samples were treated with Trizol. RNA was purified using the Direct-zol RNA miniprep Plus kit (Zymo) with the optional DNase I treatment. The RNA Clean and Concentration-100 kit (Zymo) with the optional DNase I treatment was used to purify the RNA.
For the genotype study, ribosomal RNA was depleted using the QIAseq FastSelect -rRNA HMR combined with -5S/16S/23S bacteria kit (Qiagen).  Sequencing libraries were generated from the rRNA-depleted RNAs using the Illumina Stranded mRNA Prep, Ligation kit, beginning at the first strand synthesis step (Illumina). For the temperature study, sequencing libraries were generated from total RNA using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus library preparation kit.

treatment_protocol: Vero cells at confluency were infected with rickettsia at an MOI of 0.5. The cultures were incubated at room temperature for 30 minutes, then incubated at 34ºC with additional media for 36 hours before harvesting. The lower-temperature samples were incubated at 22ºC for 2 hours before harvesting into Trizol.

value: Wildtype


title: CPG_media_2


title: Wildtype replicate 2

description: Library name: genotype_WT_rep2

value: Vero76 cells (ATCC CCL-81TM) infected with R. rickettsii Sheila Smith (CP000848.1)


title: SmadKO3


title: HGC27_RUNX3KO_Input_rep2


title: Truncated RoaM replicate 3

description: Library name: genotype_truncRoaM_rep3

value: Truncated RoaM


title: WT_input_1

description:
Library name: sample1
WT_input_1


title: Wildtype replicate 4

description: Library name: genotype_WT_rep4


title: Truncated RoaM replicate 4

description: Library name: genotype_truncRoaM_rep4


title: HGC27_RUNX3KO_H3K27ac_rep1


title: HGC27_WT_Input_rep2


title: KO Tfh21 Cells

value: T follicular helper cells

value: Tfh21 Cells

value: Stat6 KO

value: untreated


title: SmadKO2


title: CPG_media_1

value: BMDM


title: KO_input_1

description:
Library name: sample7
KO_input_1

value: cell line

value: ZNF385A KO


title: Wildtype replicate 3

description: Library name: genotype_WT_rep3


title: WT Tfh21 Cells


title: WT4


title: SmadKO1


title: Teatment_CPI-613_1

city: ATLANTA

first: Teng

last: Yong

state: Georgia

address: 1701 Uppergate Drive

department: Whinship Cancer INST

institute: Emory University

description: Cells treamented with CPI-613

data_processing:
CASAVA was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, reads containing N > 10% (N represents base that could not be determined) and  low-quality reads, then mapped to hg38 whole genome using STAR (v2.5).
The counts coincide with those produced by htseq-count with default parameters. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The read counts were adjusted by edgeR program package through one scaling normalized factor for each sequenced library. Differential expression analysis of two conditions was performed using the edgeR R package (v3.16.5).
Differential expression analysis between DMSO and CPI-613 was performed using the DESeq2 R package (v2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene of each sample
Supplementary files format and content: Tab-delimited text files including FPKM values for each Sample

growth_protocol: Human HN12 cells were grown in DMEM medium containing 10% FBS, 100 units/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Total RNA of cells was extracted with TRIzol™ reagent. NEBNext Ultra™ II RNA Library Prep Kit (Cat#NEB-E7765) was used with 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

treatment_protocol: HN12 cells were treated with DMSO or CPI-613 for 24 h.


title: Truncated RoaM replicate 2

description: Library name: genotype_truncRoaM_rep2


title: WT1


title: Control_2

description: Cells treamented with DMSO


title: Control_3

description: Cells treamented with DMSO


title: Teatment_CPI-613_2

description: Cells treamented with CPI-613


title: RoaM OE replicate 2

description: Library name: genotype_RoaMOE_rep2

value: Overexpressed RoaM


title: WT3


title: RoaM OE replicate 4

description: Library name: genotype_RoaMOE_rep4


title: RoaM OE replicate 3

description: Library name: genotype_RoaMOE_rep3


title: HGC27_WT_Input_rep1

value: Gastric cancer cell line


title: AKP1_ICG

city: Vienna

first: Dana

last: Krauß

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University of Vienna

description: Library name: Sample 13

data_processing:
Preprocessing and mapping of sequence reads to the mouse genome GRCm38/mm10 and GENECODE M25 annotations was achieved by the nf-core RNASeq pipeline version 3.2.
reads were mapped by STAR 2.6.1d and quantified by Salmon v1.4.0.
Assembly: GRCm38/mm10
Supplementary files format and content: csv file contains raw counts for each sample

source_name: colonic organoids

extract_protocol:
Total RNA was isolated from organoids cultured 48 hours after seeding using RNAeasy isolation kit following manufacturer instruction (Quiagen).
Library preparation and total transcriptome full-length mRNA sequencing was performed by Novogene UK using the NovaSeq 6000 Illumina Platform.

value: colonic organoids

value: APCmin, KRASG12D, p53


title: Control_1

description: Cells treamented with DMSO


title: WT2

value: Brain


title: AKPE2_ICG

description: Library name: Sample 17

value: APCmin, KRASG12D, p53, EGFR KO


title: Truncated RoaM replicate 1

description: Library name: genotype_truncRoaM_rep1


title: AKP3_ICG

description: Library name: Sample 15


title: AKPE1_ICG

description: Library name: Sample 16


title: AKP2_ICG

description: Library name: Sample 14


title: Teatment_CPI-613_3

description: Cells treamented with CPI-613


title: RoaM OE replicate 1

description: Library name: genotype_RoaMOE_rep1


title: AKPE3_ICG

description: Library name: Sample 18


title: WT Tfh214 Cells

value: Tfh214 Cells

value: Stat6 WT


title: HGC27_WT_RUNX3_rep1

value: RUNX3 ChIP (MBL, D235-3, lot 010 )


title: DRIVE 6mo + cHA 1yr TB ADT

address: 413 E 69th St

department: Drukier Institute

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, count, vdj)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes

extract_protocol:
MBCs (CD19+IgD-Probe+) were bulk sorted and partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) to achieve single cell resolution using the 10x Genomics Chromium Controller and according to the manufacturer’s instruction
The sorted single cells were processed according to 10x Genomics 5’ gene expression and B cell Immunoglobulin (Ig) enrichment protocol to prepare the libraries for sequencing.

value: Blood Cells

value: B cells

value: Influenza vaccination


title: AKPE3_CHIRR

description: Library name: Sample 12


title: RoaM KO replicate 4

description: Library name: genotype_RoaMKO_rep4

value: Vero76 cells (ATCC CCL-81TM) infected with R. rickettsii Sheila Smith (CP000848.1)

value: RoaM knockout


title: DRIVE 6mo + cHA 1yr TB RNA

description: 10X Genomics


title: RoaM KO replicate 2

description: Library name: genotype_RoaMKO_rep2


title: AKPE1_CHIRR

description: Library name: Sample 10


title: AKPE2_CHIRR

description: Library name: Sample 11


title: ChIP fully differentiated T helper 17 cells (IRF4-Bio.Rosa26BirA)

value: Spleen

value: primary T cells

value: T helper 17 cells


title: DRIVE 6mo + cHA 1yr AS ADT

description: 10X Genomics


title: AKP3_CHIRR

description: Library name: Sample 9


title: AKP1_CHIRR

description: Library name: Sample 7


title: AKP2_CHIRR

description: Library name: Sample 8


title: RoaM KO replicate 1

description: Library name: genotype_RoaMKO_rep1


title: DRIVE 6mo + cHA 1yr AS RNA

description: 10X Genomics


title: cHA 1yr TB ADT

description: 10x Genomics


title: Fermented grains,durig pretreatment,Day3,Fungus

city: Lanzhou

first: Zemin

last: Wang

state: Gansu

address: Lanzhou university

institute: Lanzhou university

description: Library name: Fungus_Y3

data_processing:
The qualified sequences with more than 97% similarity thresholds were allocated to one operational taxonomic unit (OTU) using USEARCH (version 10.0). Taxonomy annotation of the OTUs/ASVs was performed based on the Naive Bayes classifier in QIIME2[6] using the SILVA database[7] (release 138.1) with a confidence threshold of 70%.Alpha was performed to identify the complexity of species diversity of each sample utilizing QIIME2 software. Beta diversity calculations were analyzed by principal coordinate analysis (PCoA) to assess the diversity in samples for species complexity. One-way analysis of variance was used to compare bacterial abundance and diversity. Linear discriminant analysis (LDA) coupled with effect size (LEfSe) was applied to evaluate the differentially abundant taxa.The online platform BMKCloud (https://www.biocloud.net) was used to analyze the sequencing data.
Assembly: 338F: 5'- ACTCCTACGGGAGGCAGCA-3'  806R: 5'- GGACTACHVGGGTWTCTAAT-3' ITS-F:CTTGGTCATTTAGAGGAAGTAA; ITS-R:GCTGCGTTCTTCATCGATGC
Supplementary files format and content: Three replicates were performed for each group, and samples from each group were grouped into a single library on a single day
Library strategy: ITS-seq

molecule: cytoplasmic RNA

organism: fermentation metagenome

source_name: Fermented grains

extract_protocol:
Total genomic DNA was extracted from *** samples using the TGuide S96 Magnetic Soil /Stool DNA Kit (Tiangen Biotech (Beijing) Co., Ltd.) according to manufacturer’s instructions. The hypervariable region V3-V4 of the bacterial 16S rRNA gene were amplified with primer pairs 338F: 5'- ACTCCTACGGGAGGCAGCA-3' and 806R: 5'- GGACTACHVGGGTWTCTAAT-3'.PCR products were checked on agarose gel and purified through the Omega DNA purification kit (Omega Inc., Norcross, GA, USA). The purified PCR products were collected and the paired ends (2 × 250 bp) was performed on the Illumina Novaseq 6000 platform. (Please adjust the primer according to the actual amplification sub region)
Total genomic DNA was extracted from *** samples using the TGuide S96 Magnetic Soil /Stool DNA Kit (Tiangen Biotech (Beijing) Co., Ltd.) according to manufacturer’s instructions. The hypervariable region V3-V4 of the bacterial 16S rRNA gene were amplified with primer pairs 338F: 5'- ACTCCTACGGGAGGCAGCA-3' and 806R: 5'- GGACTACHVGGGTWTCTAAT-3'.PCR products were checked on agarose gel and purified through the Omega DNA purification kit (Omega Inc., Norcross, GA, USA). The purified PCR products were collected and the paired ends (2 × 250 bp) was performed on the Illumina Novaseq 6000 platform. (Please adjust the primer according to the actual amplification sub region)

value: Fermented grains


title: DRD1 + L-Dopa _6903016019_F

city: Toronto

first: Naomi

middle: P

last: Visanji

state: ON

address: Tanz CRND, 60 Leonard Ave

country: Canada

institute: University of Toronto

hyb_protocol: The cDNA samples were  hybridized to four Mouse WG-6 V2.0 BeadChips. BeadChips were incubated at 48°C with a rotation speed of 5 for 18.0 hrs of hybridization. BeadChips were then washed and stained as per Illumina protocol

scan_protocol: BeadChips were scanned on the iScan (Illumina).

data_processing: Data was imported in Genespring v11.5.1 for analysis.  During import, the data was normalized using a standard (for Illumina arrays) quantile normalization followed by a “per probe” median centered normalization.

source_name: mouse striatum

label_protocol: cDNA samples were biotin label according to Nugen Illumina Solution application Note #2

extract_protocol: RNA was extracted  and purified according to the manufacturer`s instructions using an Absolutely RNA nanoprep kit (Stratagene, La Jolla, CA) with in column DNA digestion. One nanogram of RNA was amplified following WT-Ovation Pico RNA amplification System Version 1.0 (Lot # 1012202-A) to generate cDNA.

value: striatum

value: 71 days old

tag: bacterial artificial chromosome promotor

tag: ldopa treatment

value: Chronic


title: AKPE3_BPTES

description: Library name: Sample 12

value: colonic organoids

value: BPTES


title: cHA 1yr TB GEX

description: 10x Genomics

tag: tissue


title: DRD2 + saline _6903016019_E

value: Acute


title: DRD2 + L-Dopa _6903016019_A


title: DRD1 + L-Dopa _6903016019_D


title: RoaM KO replicate 3

description: Library name: genotype_RoaMKO_rep3

tag: cell line


title: DRIVE 6mo + cHA 1yr AS VDJ

description: 10X Genomics

tag: cell type


title: Fermented grains,durig pretreatment,Day0,Fungus

description: Library name: Fungus_Y0


title: AKPE2_BPTES

description: Library name: Sample 11

tag: genotype

value: APCmin, KRASG12D, p53, EGFR KO


title: DRD1 + L-Dopa _6903024019_E


title: Fermented grains,durig pretreatment,Day7,Fungus

description: Library name: Fungus_Y7


title: DRD1 + L-Dopa _6903016019_C


title: DRD1 + saline _6903016019_B


title: DRD2 + saline _6903024019_F


title: Fermented grains,pretreatment,Day13,Fungus

description: Library name: Fungus_G13


title: cHA 1yr AS GEX

description: 10x Genomics

tag: treatment


title: AKPE1_BPTES

description: Library name: Sample 10


title: cHA 1yr AS VDJ

description: 10x Genomics


title: Fermented grains,pretreatment,Day4,Fungus

description: Library name: Fungus_G4


title: DRD1 + L-Dopa _6903024019_D

tag: strain


title: Fermented grains,pretreatment,Day0,Fungus

description: Library name: Fungus_G0


title: DRD1 + L-Dopa _6903024019_C


title: cHA 1yr AS ADT

description: 10x Genomics


title: sample2_AKPE

description:
Library name: Sample 2
10X Genomics PN-1000269

data_processing:
Processing raw binary base call (BCL) sequence files were converted to FASTQ files and processed with the 10X Genomics Cell Ranger pipeline version-8.0.1 using the GRCm39-2024-A reference genome.
Assembly: GRCm39-2024-A
Supplementary files format and content: fastq

extract_protocol:
AKP and AKPE organoids were seeded at 10E4/100 µL Matrigel for 48h, trypsinized, and to single cell suspension were subjected to scRNA-seq using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index) (10X Genomics PN-1000269) and sequenced with the NovaSeq X Plus System (PE150-10B).
10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index) (10X Genomics PN-1000269)


title: Fermented grains,pretreatment,Day26,Fungus

description: Library name: Fungus_G26


title: sample1_AKP

description:
Library name: Sample 1
10X Genomics PN-1000269

value: APCmin, KRASG12D, p53


title: AKP1_BPTES

description: Library name: Sample 7


title: AKP2_BPTES

description: Library name: Sample 8


title: dRoaM 34º replicate 4

description: Library name: temp_dRoaM_34_rep4

value: RoaM deletion


title: Fermented grains,control,Day13,Fungus

description: Library name: Fungus_C13


title: AKPE3_MRTX

description: Library name: Sample 12


title: DRD2 + L-Dopa _6903024019_A


title: Fermented grains,control,Day4,Fungus

description: Library name: Fungus_C4


title: AKPE1_MRTX

description: Library name: Sample 10


title: AKPE2_MRTX

description: Library name: Sample 11


title: AKP3_MRTX

description: Library name: Sample 9


title: dRoaM 34º replicate 3

description: Library name: temp_dRoaM_34_rep3


title: Fermented grains,control,Day0,Fungus

description: Library name: Fungus_C0


title: Fermented grains,durig pretreatment,Day7,Bacteria

description: Library name: Bacteria_Y7


title: dRoaM 34º replicate 1

description: Library name: temp_dRoaM_34_rep1


title: AKP2_MRTX

description: Library name: Sample 8


title: dRoaM 34º replicate 2

description: Library name: temp_dRoaM_34_rep2


title: Fermented grains,control,Day26,Fungus

description: Library name: Fungus_C26


title: AKP1_MRTX

description: Library name: Sample 7


title: DRD1 + saline _6903016014_D


title: DRD2 + saline _6903016014_F


title: DRD1 + L-Dopa _6903016014_E


title: DRD2 + saline _6903016014_C


title: AKP3_BPTES

description: Library name: Sample 9


title: dRoaM 22º replicate 4

description: Library name: temp_dRoaM_22_rep4


title: DRD1 + saline _6903024019_B


title: AKPE1_SMOC2_KO.2

description: Library name: b12

value: APCmin, KRASG12D, p53, EGFR KO, SMOC2 KO


title: Fermented grains,durig pretreatment,Day3,Bacteria

description: Library name: Bacteria_Y3

data_processing:
The qualified sequences with more than 97% similarity thresholds were allocated to one operational taxonomic unit (OTU) using USEARCH (version 10.0). Taxonomy annotation of the OTUs/ASVs was performed based on the Naive Bayes classifier in QIIME2[6] using the SILVA database[7] (release 138.1) with a confidence threshold of 70%.Alpha was performed to identify the complexity of species diversity of each sample utilizing QIIME2 software. Beta diversity calculations were analyzed by principal coordinate analysis (PCoA) to assess the diversity in samples for species complexity. One-way analysis of variance was used to compare bacterial abundance and diversity. Linear discriminant analysis (LDA) coupled with effect size (LEfSe) was applied to evaluate the differentially abundant taxa.The online platform BMKCloud (https://www.biocloud.net) was used to analyze the sequencing data.
Assembly: 338F: 5'- ACTCCTACGGGAGGCAGCA-3'  806R: 5'- GGACTACHVGGGTWTCTAAT-3' ITS-F:CTTGGTCATTTAGAGGAAGTAA; ITS-R:GCTGCGTTCTTCATCGATGC
Supplementary files format and content: Three replicates were performed for each group, and samples from each group were grouped into a single library on a single day
Library strategy: 16S rRNA-seq


title: dRoaM 22º replicate 3

description: Library name: temp_dRoaM_22_rep3


title: dRoaM 22º replicate 1

description: Library name: temp_dRoaM_22_rep1


title: AKPE1_SMOC2_KO.1

description: Library name: b11


title: Fermented grains,pretreatment,Day4,Bacteria

description: Library name: Bacteria_G4


title: DRD1 + L-Dopa _6903016014_A


title: Fermented grains,pretreatment,Day13,Bacteria

description: Library name: Bacteria_G13


title: AKP1_SMOC2_KO.1

description: Library name: b9

value: APCmin, KRASG12D, p53, SMOC2 KO


title: Wildtype 34º replicate 4

description: Library name: temp_WT_34_rep4

value: Vero76 cells (ATCC CCL-81TM) infected with R. rickettsii Sheila Smith (CP000848.1)

value: Wildtype


title: dRoaM 22º replicate 2

description: Library name: temp_dRoaM_22_rep2


title: AKP1_SMOC2_KO.2

description: Library name: b10


title: Wildtype 34º replicate 2

description: Library name: temp_WT_34_rep2


title: Fermented grains,pretreatment,Day0,Bacteria

description: Library name: Bacteria_G0


title: Wildtype 34º replicate 3

description: Library name: temp_WT_34_rep3


title: DRD1 + saline _6903016008_E


title: Fermented grains,durig pretreatment,Day0,Bacteria

description: Library name: Bacteria_Y0


title: Fermented grains,pretreatment,Day26,Bacteria

description: Library name: Bacteria_G26


title: AKPE1_SMOC_KO

description: Library name: b8


title: DRD1 + saline _6903016008_C


title: Fermented grains,control,Day26,Bacteria

description: Library name: Bacteria_C26


title: AKP1_SMOC2_KO

description: Library name: b7


title: Mouse cecal contents, Gastric administration of edible alcohol, Bacteria

description: Library name: Bacteria_S

organism: mouse metagenome

source_name: Mouse cecal content

value: Mouse cecal content


title: DRD1 + saline _6903016008_B


title: Fermented grains,control,Day13,Bacteria

description: Library name: Bacteria_C13


title: Mouse cecal contents, Gastric administration of distilled pretreatment liquor, Bacteria

description: Library name: Bacteria_G


title: Wildtype 34º replicate 1

description: Library name: temp_WT_34_rep1


title: Wildtype 22º replicate 4

description: Library name: temp_WT_22_rep4


title: Wildtype 22º replicate 3

description: Library name: temp_WT_22_rep3


title: Fermented grains,control,Day0,Bacteria

description: Library name: Bacteria_C0


title: Mouse cecal contents, Gastric administration of distilled control liquor, Bacteria

description: Library name: Bacteria_C


title: Mouse cecal contents, Gastric administration of distilled water, Bacteria

description: Library name: Bacteria_B


title: Wildtype 22º replicate 2

description: Library name: temp_WT_22_rep2


title: AKPE3_ctrl

description: Library name: b6


title: DRD2 + L-Dopa _6903016008_A


title: LW_LN12

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: A doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/)
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Allium cepa

source_name: Onion bulb

growth_protocol: Transcriptomic analysis of onion bulbs collected from field study under managed stress conditions was performed using the variety Matahari. Field was managed under normal (optimal) waterand nitrogen fertilizer treatments and stressed conditions with sub-optimal water and nitrogen. The plots within treatments were replicated four times. The bulb tissue samples were collected as 3 replicates for both time points and flash-frozen in liquid nitrogen before storing at -80℃ for further processing.

extract_protocol:
Total RNA was extracted from each sample using the QIAseq fastSelect kits. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Onion bulb

value: Onion bulb cells

value: outer and inner sheath

value: Matahari

value: Treated


title: LW_LN11

treatment_protocol: Field was managed under normal (optimal) waterand nitrogen fertilizer treatments and stressed conditions with sub-optimal water and nitrogen. The plots within treatments were replicated four times.


title: AKPE2_ctrl

description: Library name: b5


title: Wildtype 22º replicate 1

description: Library name: temp_WT_22_rep1


title: Detached leaf Col0 ABA+diacetyl_rep2

city: shanghai

first: li

last: peng

institute: PSC

data_processing:
the low quality (Q < 17) sequences of raw reads were removed using SolexaQA (verison 2.2)
the adapter sequences were trimmed by Cutadapt (version 1.4)
after trimming, the short reads (length < 25bp) were discarded by SolexaQA (verison 2.2)
paired-end reads were mapped to the genome of Arabidopsis thaliana (TAIR 10) using Tophat
the mapped reads on each gene were counted by htseq-count
the differentially expressed genes (DEGs) were identified using the R package edgeR (FDR < 0.05, FoldChange > 1.5)
the Gene Ontology enrichment analysis of DEGs was performed by R package topGO
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample
Genome_build: TAIR 10

organism: Arabidopsis thaliana

source_name: Mature Leaf

extract_protocol:
RNeasy Plant Mini Kit (Qiagen) was used for total RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The fourth rosette leaves from 30-day-old plants were placed on in I-plates, which contained wet filter paper on one part. Diacetyl, was added to the I-plates in the half part without leaves, so as to allow the leaves perceive the volatile compounds through airborne exposure. A volume of 300 µL water (mock) or 10 mM diacetyl solution were used for each plate. The plates were wrapped in aluminum foil for dark incubation immediately after the chemical treatments.

value: Fourth rosette leaf

value: Detached leaves kept on 3ml 100 uM ABA soaked tissue and 300 ul 10mM diacetyl on non leaf side of I-plate for 30 min

value: DARK


title: Detached leaf Col0 ABA+diacetyl_rep3


title: AKP3_ctrl

description: Library name: b3

value: colonic organoids


title: AKP2_ctrl

description: Library name: b2


title: LW_LN10


title: Detached leaf Col0 ABA+diacetyl_rep1


title: Post_0W_29_biol rep2

city: Waltham

first: Sebastian

last: Kadener

state: Massachusetts

address: 415 South Street

institute: Brandeis University

data_processing:
Data was aligned using STAR to Drosophila melanogaster genome version dm6.
Counting number of reads for each gene was done using featureCounts (Liao et al., 2014).
circRNAs were detected by searching unaligned reads for head-to-tail splice junctions as previously described (Memczak et al., 2013).
Assembly: dm6
Supplementary files format and content: Excel sheet with normalized counts of linear and circular RNA for each sample.

organism: Drosophila melanogaster

source_name: head

growth_protocol: Flies were grown at 25C in 12:12 Light:dark.

extract_protocol:
Trizol RNA extraction (SIGMA) followed by DNase I (NEB) treatment following manufacturer's instructions.
1 ug of RNA was ribodepleted using Hybridase thermostable RNaseH (Epicentre, H39500) and total libraries were prepared using NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (PerkinElmer) as recommended by the manufacturer.

treatment_protocol: Male flies were exposed to 18, 25, or 29 °C for ten days and flash frozen in liquid nitrogen right before or after treatment.

value: head

value: CS

value: WT

value: male

value: 10 days exposure to 29 C


title: AP_REP3

value: APCmin, p53


title: DRD2 + L-Dopa _6903016008_D

value: striatum

value: 71 days old

value: Chronic


title: Post_0W_29_biol rep1


title: LW_HN9

value: Onion bulb

value: Onion bulb cells

value: Control


title: Detached leaf Col0 ABA_rep3

value: Detached leaves kept on 3ml 100 uM ABA soaked tissue for 30 min


title: AKP1_ctrl

description: Library name: b1

value: APCmin, KRASG12D, p53


title: LW_HN8

value: outer and inner sheath

value: Matahari


title: Post_0W_25_biol rep2

value: 10 days exposure to 25 C


title: Detached leaf Col0 ABA_rep2

value: Fourth rosette leaf

value: DARK


title: AP_REP2

value: colonic organoids


title: LW_HN7


title: AKPE1_ctrl

description: Library name: b4

value: APCmin, KRASG12D, p53, EGFR KO


title: Detached leaf Col0 ABA_rep1


title: HW_LN6

value: Treated


title: Detached leaf Col0 diacetyl_rep3

value: 30 min 300 ul 10mM diacetyl on non leaf side of I-plate


title: Post_0W_18_biol rep3

value: head

value: CS

value: WT

value: male

value: 10 days exposure to 18 C


title: Post_0W_29_biol rep3

value: 10 days exposure to 29 C


title: Post_0W_25_biol rep1


title: AKPE_REP3


title: Detached leaf Col0 diacetyl_rep2


title: Post_0W_18_biol rep2


title: HW_LN5

value: Onion bulb

value: Onion bulb cells


title: AKPE_REP2


title: Post_0W_18_biol rep1


title: HW_LN4

value: outer and inner sheath


title: Detached leaf Col0 diacetyl_rep1


title: AKPE_REP1


title: DRD1 + saline _6903016008_F

value: striatum

value: 71 days old

value: Acute


title: Detached leaf Col0 Mock_rep3

value: Fourth rosette leaf

value: 30 min 300 ul double distilled water on non leaf side of I-plate

value: DARK


title: Pre_biol rep3

value: pre-treatment


title: HW_HN2

value: Matahari

value: Control


title: Detached leaf Col0 Mock_rep2


title: HW_HN1


title: AKP_REP2

value: colonic organoids

value: APCmin, KRASG12D, p53


title: Pre_biol rep1

value: head

value: CS

value: WT

value: male


title: Detached leaf Col0 Mock_rep1


title: AKP_REP3


title: Pre_biol rep2


title: HW_HN3

value: Onion bulb

value: Onion bulb cells


title: AKP_REP1


title: Fermented grains,control,Day4,Bacteria

description: Library name: Bacteria_C4

value: Fermented grains


title: AP_REP1

value: APCmin, p53


title: h04d00i [200055410097_D]

status: Public on Mar 03 2025

city: Helsinki

first: Esko

last: Kankuri

address: Haartmaninkatu 8

department: Department of Pharmacology

country: Finland

institute: University of Helsinki

hyb_protocol: The cDNA and cRNA products were purified with a GeneChip sample cleanup module (Affymetrix). The cRNA products were then used for fragmentation reaction and hybridized onto the Illumina Human HT-12 GeneChips (Illumina Inc., San Diego, CA).

scan_protocol: After 16 hours, the chips were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix), followed by chip scanning with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Background correction of the array signals and the normalization were applied through neqc function in limma package of R. Principal component analysis (PCA) was applied to the normalized signals through prcomp function in stat package of R. For the gene set enrichment analysis of the genes regulated both in the untreated wound healing time-course and by the treatment, (i) pairs of the fold-change values of each microarray probe were projected to the second diagonal line, (ii) were ranked by distance from the origin on the projected line, and (iii) applied to the GseaPreranked analysis on GSEA software with Gene Ontology gene sets. For the classifier of the skin tissue biopsies, probes were selected by WGCNA after batch bias correction by ComBat function in sva package of R. The classifier was established by support vector machine with nu classification and Radial Basis kernel through ksvm function in kernlab package of R.
The Matrix tables  include normalized (scaled) and non-normalized signal count data and detection p-value

source_name: Patient 4 0 day intact skin sample

label_protocol: A Bioarray High Yield RNA transcript labeling kit (Affymetrix) was then used to synthesize the complementary RNA (cRNA)

extract_protocol: Tissue homogenization and RNA extraction— After harvesting the harvested tissue biopsies were immediately immersed in RNAlater® buffer according to the manufacturer’s instructions (Qiagen GmbH, Hilden, Germany). They were then incubated at +4 °C for 1 day, and subsequently stored at – 80 °C until RNA isolation. Before isolation of total RNA, the samples were homogenized, using the Precellys 24-tissue homogenizer with a Cryolys temperature controller unit (Bertin Technologies SA, Montigny-le-Bretonneux, France). The frozen samples were placed in the hard tissue-homogenizing tubes (Bertin Technologies) with small ceramic beads and 350 µl of RLT lysis buffer (Qiagen). The biopsies were processed 3 × 23 s at 6,000 rpm. The temperatures ranged between −5 °C and +10 °C during the homogenization. Thereafter, the total RNA was extracted from the homogenized tissue samples with an RNeasy® Mini Kit (Qiagen), according to the manufacturer’s protocol. The RNA quality was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA) to ensure RNA integrity. After the RNA isolation, the RNA integrity was measured for each sample to ensure that the RNA quality was adequate for the microarray process.

treatment_protocol: The wounds were divided into treatment side and control side using a silicone dressing (CICA-CARE®, Smith&Nephew, United Kingdom) having a 2–3-cm-wide healthy skin strip between the study sites (Figure 1B). The cell suspension was sprayed onto the treatment side (80,000 cells/cm2). Before that, a thin layer of fibrin sealant (1ml of Artiss®, Baxter, IL, USA) was sprayed to both wound areas using an EasySpray pressure regulator device (Baxter). Subsequently, the donor site wounds were covered with OpSite® polyurethane dressing

tag: subject

value: skin

tag: day

tag: type

value: intact

tag: batch


title: h02d14c [200058720010_J]

source_name: Patient 2 14 day control skin sample

value: control


title: h03d14t [200055410097_B]

source_name: Patient 3 14 day treatment skin sample

value: treatment


title: h01d00i [200058720010_A]

source_name: Patient 1 0 day intact skin sample


title: h01d14c [200058720010_E]

source_name: Patient 1 14 day control skin sample


title: h01d07c [200058720010_C]

source_name: Patient 1 7 day control skin sample


title: h02d00i [200058720010_F]

source_name: Patient 2 0 day intact skin sample


title: h03d07t [200058720010_L]

source_name: Patient 3 7 day treatment skin sample


title: h02d07t [200058720010_G]

source_name: Patient 2 7 day treatment skin sample


title: h03d07c [200055410097_A]

source_name: Patient 3 7 day control skin sample


title: h04d07t [200055410097_G]

source_name: Patient 4 7 day treatment skin sample


title: h04d14c [200055410097_F]

source_name: Patient 4 14 day control skin sample


title: h03d00i [200058720010_K]

source_name: Patient 3 0 day intact skin sample


title: h03d14c [200055410097_C]

source_name: Patient 3 14 day control skin sample


title: h04d07c [200055410097_H]

source_name: Patient 4 7 day control skin sample


title: h02d14t [200058720010_I]

source_name: Patient 2 14 day treatment skin sample


title: h01d07t [200058720010_B]

source_name: Patient 1 7 day treatment skin sample


title: h02d07c [200058720010_H]

source_name: Patient 2 7 day control skin sample


title: h04d14t [200055410097_E]

source_name: Patient 4 14 day treatment skin sample


type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

description:
tumor DNA from breast cancer patient S011782.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC beadchip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing:
Beta values, representing the level of methylation, were computed in a sample-by-sample context using the minfi R package v1.44 function preprocessNoob() and next Infinium probe normalized using the approach described by PMID:26923702
processed value definition: beta-value

label: Cy3 and Cy5

source_name: breast cancer

label_protocol: Standard Illumina protocol

extract_protocol: Tumor DNA was extracted from RNAlater preserved tissue using Qiagen AllPrep kit according to manufacturer's instructions.

value: breast cancer

value: TNBC

tag: Sex

value: Female


description:
tumor DNA from breast cancer patient S011707.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


title: h14d21c [F]

source_name: Patient 14 21 day control skin sample


title: h13d00i [A]

source_name: Patient 13 0 day intact skin sample


description:
tumor DNA from breast cancer patient S010986.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


title: h15d21c [I]

source_name: Patient 15 21 day control skin sample


title: h14d14c [E]

source_name: Patient 14 14 day control skin sample


title: h15d14c [H]

source_name: Patient 15 14 day control skin sample


title: h01d14t [200058720010_D]

source_name: Patient 1 14 day treatment skin sample


title: h13d14c [B]

source_name: Patient 13 14 day control skin sample


title: h13d21c [C]

source_name: Patient 13 21 day control skin sample


title: h15d00i [G]

source_name: Patient 15 0 day intact skin sample


description:
tumor DNA from breast cancer patient S011081.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S010782.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S010855.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S010473.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S010173.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009574.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009557.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009555.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009543.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009556.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009533.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S010006.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009509.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009374.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009421.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009373.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009369.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009362.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S010659.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009251.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009119.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009210.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009100.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009082.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009077.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008932.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


title: h14d00i [D]

source_name: Patient 14 0 day intact skin sample


description:
tumor DNA from breast cancer patient S008930.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009319.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009815.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S009263.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008665.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008710.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008823.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008589.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008511.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008429.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008242.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008104.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008221.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007697.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007681.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007538.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008926.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008431.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007851.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007992.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007534.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007518.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007970.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S008847.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007395.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007285.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007504.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007190.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007427.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S007083.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S006999.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S006989.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S006862.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S006950.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S006936.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S006321.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S006860.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S005117.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S004053.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S005019.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S003344.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S003496.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S003585.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S000710.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


description:
tumor DNA from breast cancer patient S000766.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


title: Bulk sample for Individual 106

city: Exeter

first: Alice

last: Franklin

address: Stocker Road

country: United Kingdom

institute: University of Exeter

hyb_protocol: Nuclei samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Nuclei samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing:
Raw data (IDAT files) were imported using the watermelon R package readEPIC function. Data was then pre-processed using dasen function.
Normalized beta values

label: Cy5 and Cy3

source_name: Pre-frontal cortex

label_protocol: 500 ng DNA from each nuclei sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gold Kit (Cambridge Bioscience, UK) according to the manufacturer's standard protocol.

extract_protocol: Genomic DNA was extracted from frozen nuclei aliquots using a modified proteinase K-based extraction method.

value: Bulk

value: Pre-frontal cortex

tag: ID

value: M

tag: basename


title: Bulk sample for Individual 105

value: F


title: Bulk sample for Individual 107


title: Bulk sample for Individual 104


title: Bulk sample for Individual 103


description:
tumor DNA from breast cancer patient S006918.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


title: Bulk sample for Individual 102


description:
tumor DNA from breast cancer patient S005001.l.d.mth.tsv
ProcessedData_LUepic_V1.txt
RawData_LUepic_v1.txt


title: Bulk sample for Individual 100


title: Bulk sample for Individual 98


title: Bulk sample for Individual 96


title: Bulk sample for Individual 99


title: Bulk sample for Individual 97


title: Bulk sample for Individual 95


title: Bulk sample for Individual 91


title: Bulk sample for Individual 101


title: Bulk sample for Individual 92


title: Bulk sample for Individual 90


title: Bulk sample for Individual 93


title: Bulk sample for Individual 89


title: Bulk sample for Individual 84


title: Bulk sample for Individual 86


title: Bulk sample for Individual 87


title: Bulk sample for Individual 85


title: Bulk sample for Individual 81


title: Bulk sample for Individual 82


title: Monocytes, mandible derived S23

city: Minneapolis

first: Kim

last: Mansky

state: MN

address: 515 Delaware St SE

institute: University of Minnesota

description:
Library name: Mansky23
Kmansky23

data_processing:
Sequencing reads were mapped to the mouse reference genome (GRCm38 v94) via Hisat2 (v2.1.0).
Quality control on raw sequence data for each sample was performed with FastQC
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed between WT and conditional KO were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: mouse (GRCm38 v94)
Supplementary files format and content: RawReadCounts.txt

source_name: bone marrow

growth_protocol: Monocytes were isolated from the bone marrow of femur and mandible from 1 year old mice

extract_protocol:
RNA was isolated using RNA Plus Mini Kit (Qiagen)
Libraries were constructed by UMN Genomic Center

treatment_protocol: Monocytes were isolated using Milentyi Biotec mouse monocyte isolation kit

value: bone marrow

value: monocytes


title: Bulk sample for Individual 79


title: Monocytes, mandible derived S16

description:
Library name: Mansky16
Mansky016


title: Monocytes, mandible derived S19

description:
Library name: Mansky19
Mansky019


title: Bulk sample for Individual 78


title: Monocytes, femur derived S18

description:
Library name: Mansky18
Mansky018


title: Monocytes, femur derived S15

description:
Library name: Mansky15
Mansky015


title: Bulk sample for Individual 77


title: Bulk sample for Individual 83


title: Bulk sample for Individual 76


title: Bulk sample for Individual 88


title: Bulk sample for Individual 94


title: Bulk sample for Individual 75


title: tumor DNA from breast cancer patient S012322.l.d.mth.tsv


title: Bulk sample for Individual 74


title: tumor DNA from breast cancer patient S011990.l.d.mth.tsv


title: Monocytes, femur derived S13

description:
Library name: Mansky13
Mansky013


title: tumor DNA from breast cancer patient S011904.l.d.mth.tsv


title: Bulk sample for Individual 73


title: Bulk sample for Individual 72


title: tumor DNA from breast cancer patient S011496.l.d.mth.tsv


title: Bulk sample for Individual 71


title: tumor DNA from breast cancer patient S011174.l.d.mth2.tsv


title: Bulk sample for Individual 70