title: GFP-USP7-H2AK119Ub-Rep2

description: DOX-inducible USP7-KO

data_processing:
FASTQ files were mapped against human genome (hg19) and Drosophila genome (Dm6) using bowtie2 (Langmead et al., 2009) and default parameters. SAM files were further filtered for uniquely mapped reads and high-quality mapping (-q 10) using SAMtools and PCR duplicates were removed using MarkDuplicates in PICARD tools. For quantitative ChIP-seq analysis with exogenous reference genome (ChIP-Rx), total reads in Drosophila BAM files were used to calculate the spike-in normalization factors and were used for downscaling the corresponding human BAM files as described (Orlando et al., 2014). Normalized human BAM files were further downscaled based on the BAM file with the lowest total read counts to normalize for sequencing depth. Next, BAM files were converted to BED files using BEDtools, and reads were extended by 160 nt and converted to BedGraph using bamCoverage tool from the deepTools suite. BeGraphs were converted to BigWig files using bedGraphToBigWig from UCSC tool suite for further visualization using Integrative Genomics Viewer (IGV) browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: H3K27me3 and H2AK119Ub ChIP-seq analysis using Sicer peak calling and follow up read counting

extract_protocol:
Biological duplicates of DLD1-KO-Dox-USP7, HAP1 wt and HAP1 RING1A/B-KO cells were grown in two 15 cm dishes per condition. GFP-USP7 expression in DLD1-KO-Dox-USP7 cells was induced by addition of doxycycline  (1 g/ml) for three days (+Dox). Two other plates were mock treated (-Dox). Cells were harvested by trypsinization, followed by cell counting. For crosslinking, 17 million cells were suspended in 10 ml PBS. Cells were fixed by the addition of 1% formaldehyde for 10 minutes on a roller mixer. Fixation was stopped by the addition of glycine (125 mM). Next, cells were washed twice with PBS and lysed in 1 ml 1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, supplemented with the following protease inhibitors. Cross-linked chromatin was sheared to approximately 200 bp of DNA length in a Bioruptor® Pico sonication system. The normalization reference exogenous genome was generated from 80 million Drosophila S2 cells (one 15 cm dish), which were harvested by “up-and-down” pipetting. Fixation was performed as above with 1% formaldehyde in PBS for 10 minutes. S2 cells were lysed in 1.2 ml  0.75 % SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, supplemented with protease inhibitors. Drosophila chromatin was sheared to 200-300 bp of DNA length. DLD1-KO-Dox-USP7 chromatin (180 µl) was combined with 20 µl of S2 chromatin and diluted 10-fold with dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20 mM Tris pH 8.0), cleared by centrifugation at 15,000 g for 20 min. The supernatant was transferred to a fresh tube and incubated overnight at 4 °C in the presence of either 10 µl anti-Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology #9733) or 5 µl anti-Ubiquityl-Histone H2A (Lys119) (Cell Signaling Technology #8240) on a rotating wheel. Next morning, 50 µl of Dynabeads™ protein A slurry (Invitrogen), which was blocked overnight with 1 % BSA in dilution buffer was added and followed by a 3 hour incubation on a rotating wheel. Next, beads were washed 4x with wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0) containing 150 mM NaCl and 1x with wash buffer containing 500 mM NaCl. DNA was eluted with 0.1 M NaHCO3, 1% SDS and 0.5 mg/ml proteinase K for two hours at 37 °C, followed by an overnight incubation at 65 °C. DNA was subsequently purified by double phenol/chloroform extraction, followed by ethanol precipitation.
KAPA Hifi kit according to manufacturer’s instruction
ChIP-Rx-seq

treatment_protocol: To generate DLD1-KO-Dox-USP7, DLD1-USP7-KO cells were transfected with the GFP-USP7-expressing pTREG-BI-USP7 and the Tet-ON pEF1α-Tet3G plasmids (table xx) linearized with Bsa1. cells were then selected in RPMI containing 400µg/mL G418. For USP7 induction, cells were treated with 1µg/ml doxycycline for 3 days.

value: H2AK119Ub (Cell Signaling; 8240)


title: CTL_Sperm_CTCF_Rep2_R1

status: Public on Nov 08 2022

type: SRA

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

country: USA

institute: Emory university

description: chromatin IP against CTCF

library_source: genomic

data_processing:
All reads were mapped to unique genomic regions using Bowtie2 (Langmead and Salzberg, 2012) and the mm10 genome. PCR duplicates were removed using Picard Tools.
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Sperm

extract_protocol: Cells were crosslinked with 1% formaldehyde in 1xPBS for 10 min at RT, and the reaction was quenched with 125 mM glycine for 10 min at RT. After washing with PBS, cells were lysed with 5 mM PIPES, 85 mM KCl, 0.5% NP40 and 1x protease inhibitors (P8107S, NEB) on ice for 15 min. After centrifugation, cells were resuspended in RIPA buffer (1x PBS; 1% NP40; 0.5% sodium deoxycholate; 0.1% SDS; 1x protease inhibitors) and incubated on ice for 20 min. The purified chromatin was sonicated to 300-500 bp using a Diagenode Bioruptor. After 25 cycles (30 seconds on and 60 seconds off), the supernatant containing sheared chromatin was collected. Immunoprecipitation was performed overnight at 4°C with antibodies. Libraries for Illumina sequencing were constructed using the following standard protocol. Fragment ends were repaired using the NEBNext End Repair Module and adenosine was added at the 3’ ends using Klenow fragment (3’ to 5’ exo minus, New England Biolabs). Precipitated DNA was incubated with adaptors at room temperature for 1 hr with T4 DNA ligase (New England Biolabs) and amplified with Illumina primers. Two independent biological replicates per sample were then sequenced using paired-end 50 bp on Illumina Hiseq2500 v4 or NovaSeq 6000 instruments.

tag: strain background

tag: chip-antibody

value: CTCF

tag: tissue

value: Sperm


title: TAU_ADAR1

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

library_source: transcriptomic

data_processing:
Reads aligned with STAR on hg19 genome
FeatureCounts was used to count reads per gene on FastDB 2018_1 annotations
Normalization was performed using DESeq2 on R.
Supplementary files format and content: Tab-delimited text files

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T cells

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany).  Circular RNA was enriched by removing rRNA (rRNA minus kit, Thermo Fisher) and digesting RNAs with RNAse R.
The libraries were sequenced from both ends of the fragments for a total of 150nt from each end a NovaSeq SP flow-cell (Illumina). The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA). The quality of the demultiplexed fastq files was evaluated with the FastQC software, which generates reports with the quality scores, base composition, k-mer, GC and N contents, sequence duplication levels and overrepresented sequences.
RNAseq of circular RNAs

tag: cell line

value: HEK293T cells

tag: genotype

value: TAU

tag: treatment


title: TRiP_M_2

city: Greenwood

first: Rebecca

middle: A

last: MacPherson

state: SC

address: 114 Gregor Mendel Circle, Dr. Trudy Mackay

department: Center for Human Genetics

institute: Clemson University

data_processing:
The default Illumina BaseSpace NovaSeq sequencing pipeline was used to demultiplex the barcoded sequencing reads. We then merged S1 flow cell lanes together, as well as reads from different flow cell runs.
Filtering: We filtered out short and low-quality reads using the AfterQC pipeline (v0.9.7) (Chen et al., 2017) and quantified remaining levels of rRNA via the bbduk command (Bushnell, 2014).
Alignment: Reads were aligned to the reference genome (D. melanogaster v6.13) using GMAP-GSNAP (Wu et al., 2016) and these unique alignments to Drosophila genes were counted using the featurecounts pipeline from the Subread package (Liao et al., 2013; Wu et al 2016).
Assembly: dm6 v6.13
Supplementary files format and content: read_counts_forGEO.csv

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Each sample contained 30 whole flash-frozen 3-5 day old flies, homogenized using a Fisherbrand™ Bead Mill (ThermoFisher Scientific, Waltham MA). RNA was extracted using the the Qiagen RNeasy Plus Mini Kit (Qiagen, Hilden, Germany), resuspended in RNase-free water, and kept at -80°C until further use.
Libraries were synthesized from RNA using the Universal RNA-seq with Nuquant + UDI kit (Tecan Genomics, Inc., CA) according to manufacturer recommendations. 100ng of total RNA was converted into cDNA using the integrated DNase treatment and sheared into 350bp fragments using the Covaris ME220 Focused-ultrasonicator (Covaris, Woburn, MA). We performed Ribosomal RNA depletion and bead selection using Drosophila AnyDeplete probes and RNAClean XP beads (Beckman Coulter, Brea, CA), respectively. Libraries were purified after 17 cycles of PCR amplification. We measured library fragment sizes on the Agilent Tapestation using the Agilent High Sensitivity DNA 1000 kit (Agilent Technologies) and quantified library concentration using the Qubit 1X dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific).

tag: background strain

value: whole body

tag: Sex

value: Male

tag: replicate

tag: molecule subtype

value: rRNA depleted RNA


title: TAU_GFP

value: GFP


title: TRiP_M_1


title: 60017-SMC3_F_3

value: Female


title: CTL_Sperm_CTCF_Rep1_R1

description: chromatin IP against CTCF


title: TRiP_F_2


title: DLD1-WT-Rep3

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

country: United Kingdom

institute: Queen's University Belfast

description: parental

data_processing:
FASTQ files were aligned against the human reference genome (hg19) using HiSat2 (version 2.1.0; Kim et al., 2019) and mapped reads were assigned to RNAs using HTseq-count with the following settings: -m union -s reverse -t exon. DESeq2 (Love et al., 2014) was used to normalize for library size and normalized reads were further corrected for batch variation between independent experiments using the SVA R package (Leek et al., 2012). Batch-corrected values were used in DESeq2 for differential gene expression analysis. Genes were considered differentially expressed if they fulfilled the following conditions: normalized log2 read counts ≥5, fold change ≥ 2 and FDR < 0.05 at one or more time points.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: deseq2_results

source_name: colorectal cancer cell line

growth_protocol: DLD1 cells were cultured in Roswell Park Memorial Institute 1640 medium (RPMI 1640; Gibco), 10% FBS and 1% Pen/Strep.

extract_protocol:
Each biological triplicate of DLD1 wt, DLD1-USP7-KO and DLD1-KO-Dox-USP7 were grown in a 10 cm2 plate. USP7 expression in DLD1-KO-Dox-USP7 cells was induced by the   GFP-USP7 expression was induced by addition of doxycycline  (1 µg/ml) for 24 hours, three days or 9 days (+Dox). For RNA isolation the medium was removed and 3 ml of TriPure isolation reagent (Roche) was added directly onto the cells.
Samples were prepped with the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting DNA libraries were sequenced according to the Illumina Truseq Rapid V2 protocol on an Illumina HiSeq2500 sequencer.

treatment_protocol: To generate DLD1-KO-Dox-USP7, DLD1-USP7-KO cells were transfected with the GFP-USP7-expressing pTREG-BI-USP7 and the Tet-ON pEF1α-Tet3G plasmids (table xx) linearized with Bsa1. cells were then selected in RPMI containing 400µg/mL G418. For USP7 induction, cells were treated with 1µg/ml doxycycline.

tag: cell type

value: colorectal cancer cell line

value: No-treatment

value: parental


title: SAMPLE 36_MCF7_3D_R6

city: Singapore

first: Keng Hwee

last: Chiam

address: 30 Biopolis Street

country: Singapore

institute: Bioinformatics Institute

data_processing:
For the first batch, the libraries were run with BGI group’s in-house sequencing platform BGISEQ-500 (20M single-end reads). For the second batch, libraries were run on NovaSeq 6000 (Illumina, USA) to produce 6GB of raw data per sample (20M paired-end reads).
Kallisto version 0.46.0 with a precalculated human index from the ARCHS4 repository was used to obtain transcript counts, which were then mapped to gene-level counts using tximport version 1.22.0 and the GrCH38.87 human genome annotation.
Assembly: GrCH38.87 human genome annotation
Supplementary files format and content: comma-separated values (CSV) file includes read count values for each Sample

source_name: MCF7 spheroids

extract_protocol:
Total RNA was extracted from MCF7 and MCF10A cells in both 2D and 3D cultures using RNeasy plus kits (Qiagen, Germany) according to manufacturer’s instructions. Briefly, cells grown as monolayer were trypsinized and washed with PBS twice followed by RNA extraction using RNeasy Plus Kit. To collect spheroids, medium was removed from 3D cell culture followed by washing with PBS twice gently. Pre-chilled cell recovery solution (Corning, USA) at the volume of 200 μl were added to 8-well chamber slide (Ibidi, Germany). Matrigel matrix was fully depolymerized, and spheroids were released after 30 minutes incubation at 4°C. Suspended spheroids were collected and washed with PBS twice followed by RNA extraction using RNeasy Plus Kit (Qiagen). The integrity and quantity of RNA were determined with NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA) before sending out for RNA sequencing.
Library construction was performed using NEBNext Ultra II RNA Library Prep Kit (Illumina, USA) according to manufacturer’s protocols

value: MCF7 spheroids

tag: batch

value: Batch 2


title: 60017-SMC3_F_2


title: BPA_Sperm_CTCF_Rep2_R1

description: chromatin IP against CTCF


title: TAU_ADAR2


title: Tet6

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: mm10
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: primary neuron culture (in vitro)

extract_protocol:
RNA extracted using TRIzol (Thermo FIsher)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

tag: strain

tag: viral treatment

value: primary neuron culture


title: SAMPLE 35_MCF7_3D_R5


title: No-DOX-H2AK119Ub-Rep1

description: DOX-inducible USP7-KO


title: Single cell RNA-seq of Mouse dura cells

city: Beijing

first: Jiyan

last: Zhang

address: 27 Taiping Road

country: China

institute: Beijing Institute of Basic Medical Sciences

data_processing:
The Cell Ranger Single Cell Software Suite, version  was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. A detailed description of the pipeline and specific instructions to run it can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.
Cloupe files were generated using the Cell Ranger 6.0.0 version. A description of the pipeline and instructions can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/cellranger
The CellRanger count command was run on the individual Fastq datasets to produce expression data
R package Seurat v4.0.4 was used for cell filtration, normalization, principal component analysis, variable genes finding, clustering analysis, and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction.Data were then log-normalized for the subsequent analyses. Principal component analysis (PCA) was used for dimension reduction, followed by clustering analysis in principal component analysis space using a graph-based clustering approach. UMAP was then used for the two-dimensional visualization of the identified clusters.
Genome_build: NOT PROVIDED

source_name: Dura cells

extract_protocol:
To exclude intravascular leukocytes, FITC-labeled CD45 antibody was intravenously injected (CD45 IV) 5 min before intracardiac perfusion. We used mechanical isolation to get dura leukocytes lest enzymatic digestion makes hematopoietic progenitors undetectable. Dura cells from four 8 ~ 12-week-old mice were combined together. All leukocytes were stained with PE-labeled CD45 antibody and DAPI was used to exclude dead cells. CD45 IV−DAPI− CD45-PE+ singlets were then sorted
Libraries were prepared using the Chromium Single cell 3' Reagent Kits v3.1 (CG000204): Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000128), Chromium Single Cell 3’ Chip Kit v2 (PN-1000127) and Single Index Kit Set A (PN-1000213). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end sequencing with approximately >90% sequencing saturation.

value: dura leukocytes

tag: age

value: 8-12 weeks

tag: genotype/variation

value: WT


title: 60017-SMC3_F_1


title: 60017-SMC3_M_3


title: GFP-USP7-H3K27me3-Rep2

description: DOX-inducible USP7-KO

value: H3K27me3 (Active Motif; 39155)


title: Tet4


title: SAMPLE 33_MCF7_3D_R3


title: Tet5


title: GFP-USP7-H3K27me3-Rep1

description: DOX-inducible USP7-KO


title: 60017-SMC3_M_2


title: SAMPLE 34_MCF7_3D_R4


title: Tet3


title: no-DOX-H3K27me3-Rep2

description: DOX-inducible USP7-KO


title: SAMPLE 32_MCF7_3D_R2


title: SAMPLE 31_MCF7_3D_R1


title: 60017-SMC3_M_1


title: Tet2


title: no-DOX-H3K27me3-Rep1

description: DOX-inducible USP7-KO


title: GFP-USP7-H2AK119Ub-Rep1

description: DOX-inducible USP7-KO

value: H2AK119Ub (Cell Signaling; 8240)


title: SAMPLE 30_MCF7_2D_R6


title: KO_H3K27me3_Rep2

data_processing:
FASTQ files were mapped against human genome (hg19) and Drosophila genome (Dm6) using bowtie2 (Langmead et al., 2009) and default parameters. SAM files were further filtered for uniquely mapped reads and high-quality mapping (-q 10) using SAMtools and PCR duplicates were removed using MarkDuplicates in PICARD tools. For quantitative ChIP-seq analysis with exogenous reference genome (ChIP-Rx), total reads in Drosophila BAM files were used to calculate the spike-in normalization factors and were used for downscaling the corresponding human BAM files as described (Orlando et al., 2014). Normalized human BAM files were further downscaled based on the BAM file with the lowest total read counts to normalize for sequencing depth. Next, BAM files were converted to BED files using BEDtools, and reads were extended by 160 nt and converted to BedGraph using bamCoverage tool from the deepTools suite. BeGraphs were converted to BigWig files using bedGraphToBigWig from UCSC tool suite for further visualization using Integrative Genomics Viewer (IGV) browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: allH3K27me3 and H2AK119Ub normalized counts RING1A/B-DKO HAP1 cells (log2 FC < -1, Pval < 0.05)

source_name: Male Chronic Myelogenous Leukemia (CML) cell line derived from KBM-7

growth_protocol: HAP1 cells were cultured in Iscove′s Modified Dulbecco′s Medium (IMDM; Gibco) supplemented with 10% FBS and 1% Pen/Strep.

treatment_protocol: To generate HAP1-RING1B-KO and HAP1-RING1A/B-KO cells, we used CRISPR-Cas9-nickase-mediated genome editing. Oligonucleotides encoding the forward and reverse gRNAs were annealed, phosphorylated, and ligated into pSpCas9(Bb)-2APuro px459 v2 linearized with BbsI. Resulting in pX459-RNF2-guide1 and pX459-RNF2-guide 3. Another set of gRNA-encoding oligonucleotides targeting RING1B was cloned into the Esp3I site of pLentiCRISPRv2-GFP, resulting in pLentiCRISPRv2-GFP_ScRNF2. HAP1 wt and HAP1-RING1A-KO cells in 6 well plates were transfected with these three plasmids (2.5 g total DNA per well) using polyethyleneimine (PEI; at a ratio DNA:PEI of 1:3) to generate respectively, HAP1-RING1B-KO and HAP1-RING1A/B-KO cell lines. 48 h after transfection, high GFP-positive single cells were sorted by FACS into 96-well plates and cultivated until colonies were obtained. After 10 days, clones were duplicated  and screened for the absence of RING1B by immunoblotting.

value: HAP1 cell line


title: Tet1


title: 36786-vtd_F_2

value: whole body


title: No-DOX-H2AK119Ub-Rep2

description: DOX-inducible USP7-KO


title: Ctl6

value: shLuciferase - control


title: KO_H3K27me3_Rep1


title: 36786-vtd_F_1

value: rRNA depleted RNA


title: SAMPLE 28_MCF7_2D_R4


title: Ctl5


title: SAMPLE 29_MCF7_2D_R5


title: WT_H3K27me3_Rep2

value: Wild-type-control


title: WT_H3K27me3_Rep1


title: Ctl4


title: 36786-vtd_M_3

value: Male


title: 36786-vtd_M_2


title: KO_H2AUb_Rep2


title: SAMPLE 27_MCF7_2D_R3


title: Ctl3


title: SAMPLE 25_MCF7_2D_R1


title: SAMPLE 26_MCF7_2D_R2


title: Ctl2


title: KO_H2AUb_Rep1


title: SAMPLE 24_MCF10A_3D_R6

source_name: MCF10A spheroids

value: MCF10A spheroids


title: 36786-vtd_F_3

value: Female


title: Ctl1


title: 36786-vtd_M_1


title: SAMPLE 23_MCF10A_3D_R5


title: 34351-SMC1_F_3


title: 34351-SMC1_F_2


title: Sample-9-KO

source_name: hippocampal neuronal nuclei (in vivo)

value: CamKIIaCreERt2;Tet2 cKO

value: hippocampal neuronal nuclei


title: WT_H2AUb_Rep1


title: WT_H2AUb_Rep2


title: 34351-SMC1_F_1


title: SAMPLE 22_MCF10A_3D_R4

value: Batch 2


title: Sample-4-KO


title: 34351-SMC1_M_3


title: Pineal Gland, not active, animal 12 [36_PG_NA]

city: Zaragoza

first: Kenza

last: Lakhssassi

state: Zaragoza

address: Av Montañana, 930,

country: Spain

institute: CITA

data_processing:
All transcripts were analysed with bioinformatics tools implemented within OmicsBox v2.0.36 from BioBam
Checking quality control of the sequence with FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the Sliding Window Trimming option with a window size of 40 and a required quality of 20. The filtering configuration of reads was set to 20 and 35 for the average quality and the minimum length respectively
Clean reads were mapped against the ovine reference genome  using STAR v2.7.8a
Mapped reads were assembled by HTSeq. Gene quantification levels were analysed using the Union model.
Identification of differentially expressed genes with EdgeR
Assembly: Oar_rambouillet 1.0 (GCA_002742125.1)
Supplementary files format and content: Raw_gene_counts_matrix.txt: tab-delimited text file with raw gene counts for every gene and every sample

organism: Ovis aries

source_name: Pineal Gland

extract_protocol:
Samples from HT, PT and PG tissues were isolated and rapidly frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from tissue samples using RNeasy Lipid Tissue mini kit (QIAGEN, Madrid, Spain) according to the manufacturer’s instructions
Sequencing was carried out at the CNAG (Centro Nacional de Análisis Genómico, Spain; https://www.cnag.crg.eu/). The RNA-Seq library was prepared with KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche) following the manufacturer´s recommendations using Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies). The final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x151bp following the manufacturer’s protocol for dual indexing.

value: Pineal Gland

value: Adult ram

tag: breed

value: Rasa Aragonesa

tag: sexual behaviour_state

value: Not Active


title: Pineal Gland, not active, animal 11 [35_PG_NA]


title: Sample-6-WT

value: WT


title: SAMPLE 20_MCF10A_3D_R2


title: Pineal Gland, not active, animal 10 [34_PG_NA]


title: Pineal Gland, not active, animal 9 [33_PG_NA]


title: SAMPLE 18_MCF10A_2D_R6


title: 32372-Snr1_F_3


title: Sample-5-WT


title: Pineal Gland, not active, animal 8 [32_PG_NA]


title: SAMPLE 17_MCF10A_2D_R5


title: Sample-2-WT


title: Pineal Gland, not active, animal 7 [31_PG_NA]


title: 32372-Snr1_F_2


title: SAMPLE 16_MCF10A_2D_R4


title: 32372-Snr1_F_1


title: Sample-3-KO


title: SAMPLE 15_MCF10A_2D_R3


title: Pineal Gland, active, animal 6 [30_PG_A]

value: Active


title: 34351-SMC1_M_2


title: BPA_Sperm_m6A_Rep2

data_processing:
Library strategy: m6A-seq
All libraries were sequenced using Novaseq 6000 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm10 using HISAT2. For generating bigwig files, we combined each replicates.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

extract_protocol: Not provided

tag: strain background

value: Sperm

value: Bisphenol A (BPA)

tag: antibody


title: 32372-Snr1_M_3

tag: tissue

value: whole body


title: Pineal Gland, active, animal 5 [29_PG_A]


title: SAMPLE 14_MCF10A_2D_R2

tag: cell line


title: 34351-SMC1_M_1

tag: genotype

value: rRNA depleted RNA


title: SAMPLE 19_MCF10A_3D_R1


title: 32372-Snr1_M_2

tag: background strain


title: SAMPLE 13_MCF10A_2D_R1


title: Pineal Gland, active, animal 4 [28_PG_A]


title: BPA_Sperm_m6A_Rep1

tag: Sex

tag: treatment


title: SAMPLE 21_MCF10A_3D_R3


title: Pineal Gland, active, animal 3 [27_PG_A]


title: CTL_Sperm_m6A_Rep1

value: Control


title: 35211-brm_F_3

tag: replicate

tag: molecule subtype


title: Sample-1-WT

tag: cell type


title: Pineal Gland, active, animal 2 [26_PG_A]


title: 35211-brm_F_2


title: Cardiomyocyte differentiation, clone LC67, Nutlin

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description:
CM_67_N
67_CM_Nutlin
Library type: strand-specific

data_processing:
Signal processing, base-calling, and quality scoring were carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

molecule: polyA RNA

source_name: iPSC

growth_protocol: iPSCs were cultivated in mTeSR1 media supplemented with 1x antibiotic-antimycotic in a humidified atmosphere with 5% O2 & 5% CO2 at 37°C. iPSCs differentiation with 10µM retinoic acid for 5 days was carried out under the same conditions. iPSCs were induced into monolayer CMs using DMEF media supplemented with B27, GSKb inhibitors and WNT inhibitors for 45 days at 37οC and 5% CO2. CM were selected in glucose-free DMEM supplemented with 4 mM lactate in a humidified atmosphere with  5% CO2 at 37°C. 24h prior to RNA-seq CMs were incubated in mTeSR1 media at 37°C, 5% CO2 and 5% O2 for 24 hours prior to Nutlin-3 treatment.

extract_protocol:
TRI reagent
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA).

treatment_protocol: Cells were treated with 0.2% DMSO or 2.5µM Nutlin-3R for 12 hrs.

value: iPSC

tag: parental ipsc clone

tag: differentiation

value: Cardiomyocyte

value: 12 hrs 2.5uM Nutlin-3


title: Pineal Gland, active, animal 1 [25_PG_A]

tag: age


title: NB4_120h_atra_4

city: Sinagpore

first: Eleni

middle: G.

last: Christodoulou

address: 8 College Road

institute: Duke-NUS Medical School

data_processing:
Sequence reads were trimmed for adapter sequence using using trimmomatic software version 0.36, with parameters  MAXINFO:35:0.5 MINLEN:35. After trimming, the lanes (technical replicates) were concatenated.
The trimmed reads were mapped to the Genome Reference Consortium GRCh38 (hg38) using star aligner v2.5.2b, with the chimeric option. The ensembl-90 fasta sequence release was used for indexing, using parameter --runMode genomeGenerate. The fasta files for all chromosomes were downloaded from ftp://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/dna/ and were concatenated. The parameters for the chimeric star run were: --outFilterType BySJout --outFilterMultimapNmax 20 --twopassMode Basic --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax parameter 3 --limitBAMsortRAM 31532137230 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
To quantify the aligned reads of the genes, exons and promoters, Feature counts module from the Subread suite v1.5.1 was called, with parameters  -t exon -g gene_id -O -s 2 -J -T 8 -p -R -G c  GRCh38_r90.all.fa -a ensemble_hg38.gtf. The output file is the RNAseq_full_all.counts.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts were the output of Feature counts module above. They are provided in the txt file RNAseq_full_all.counts.

source_name: NB4 APL cell line

growth_protocol: NB4, NB4-LR2 and NB4-MR2 cells were cultured in RPMI 1640 (Nacalai Tesque) supplemented with 10% FBS (Biowest), 100U/mL penicillin-streptomycin and 2mM L-glutamine (Gibco).

extract_protocol:
Cells were harvested at the indicated timepoints and RNA was extracted using RNEasy Mini Kit (Qiagen) with on-column DNAse digestion. The RNA was further concentrated and purified with RNEasy Micro kit (Qiagen).
RNAseq libraries were prepared from 33 NB4 APL cell line samples using the Illumina Tru-Seq Stranded Total RNA kit protocol, according to the manufacturer’s instructions (Illumina, San Diego, California, USA). Library fragment size was determined using the DNA 1000 Kit on the Agilent Bioanalyzer (Agilent Technologies). Libraries were quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems).  Libraries were pooled in equimolar and cluster generation was performed on the Illumina cBOT system (Illumina). Sequencing (150bp pair-end) was performed on the Illumina HiSeq 3000 system at the Duke-NUS Genome Biology Facility (Singapore), according to manufacturer’s protocol (Illumina).

treatment_protocol: Cells were treated with 1µM of all-trans retinoic acid (ATRA) or DMSO control for 5 days in biological triplicate. Cultures were supplemented with media containing fresh drug on Day 3.

value: acute promyelocytic leukaemia (APL)

value: ATRA

tag: time


title: NB4_120h_atra_5


title: Cardiomyocyte differentiation, clone LC67, DMSO

description:
CM_67_D
67_CM_DMSO
Library type: strand-specific

value: 12 hrs 0.2% DMSO


title: CTL_Sperm_m6A_Rep2

value: Male


title: 35211-brm_F_1

value: Female


title: Cardiomyocyte differentiation, clone LC62, DMSO

description:
CM_62_D
62_CM_DMSO
Library type: strand-specific


title: Pars Tuberalis, not active, animal 12 [24_PT_NA]

source_name: Pars Tuberalis

value: Pars Tuberalis

value: Adult ram

tag: breed

value: Rasa Aragonesa


title: Cardiomyocyte differentiation, clone LC62, Nutlin

description:
CM_62_N
62_CM_Nutlin
Library type: strand-specific


title: 32372-Snr1_M_1


title: NB4_120h_dmso_5

value: DMSO


title: 35211-brm_M_3


title: Pars Tuberalis, not active, animal 11 [23_PT_NA]

tag: sexual behaviour_state

value: Not Active


title: Pars Tuberalis, not active, animal 9 [21_PT_NA]


title: Cardiomyocyte differentiation, clone LC42, DMSO

description:
CM_42_D
42_CM_DMSO
Library type: strand-specific


title: Cardiomyocyte differentiation, clone LC42, Nutlin

description:
CM_42_N
42_CM_Nutlin
Library type: strand-specific


title: NB4_120h_atra_2


title: 35211-brm_M_2


title: NB4_120h_dmso_4


title: NB4_120h_dmso_2


title: 5 days RA, clone LC67, Nutlin

description:
RA_67_N
67_RA_Nutlin
Library type: strand-specific

value: 5 days 10uM retinoic acid


title: Pars Tuberalis, not active, animal 10 [22_PT_NA]


title: Pars Tuberalis, not active, animal 8 [20_PT_NA]


title: 35211-brm_M_1

value: whole body


title: 35447-osa_F_2

value: rRNA depleted RNA


title: NB4_72h_atra_5


title: 35447-osa_F_3


title: NB4_72h_atra_4


title: Pars Tuberalis, not active, animal 7 [19_PT_NA]


title: 35447-osa_F_1


title: 5 days RA, clone LC62, Nutlin

description:
RA_62_N
62_RA_Nutlin
Library type: strand-specific


title: Pars Tuberalis, active, animal 6 [18_PT_A]

value: Active


title: NB4_72h_atra_2


title: 5 days RA, clone LC62, DMSO

description:
RA_62_D
62_RA_DMSO
Library type: strand-specific

value: iPSC


title: Pars Tuberalis, active, animal 5 [17_PT_A]


title: NB4_72h_dmso_5


title: 35447-osa_M_3


title: Pars Tuberalis, active, animal 4 [16_PT_A]


title: 5 days RA, clone LC42, DMSO

description:
RA_42_D
42_RA_DMSO
Library type: strand-specific


title: 35447-osa_M_1


title: Pars Tuberalis, active, animal 3 [15_PT_A]


title: 35447-osa_M_2


title: NB4_72h_dmso_4


title: NOR_T3

city: Qingdao

first: Mengqiang

last: Wang

state: Shandong

address: Nanhai Road

institute: The Institute of Oceanology, Chinese Academy of Science

description:
mRNA sequencing
processed data file: genes_fpkm_expression.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
A cDNA library constructed by technology from the total RNA was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: CfBase (http://mgb.ouc.edu.cn/cfbase/html/download.php , data from doi:10.1038/s41467-017-01927-0)
Supplementary_files_format_and_content: genes_fpkm_expression.txt: Tab-delimited text file includes counts and FPKM values for each Sample.

organism: Azumapecten farreri

source_name: hemocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA (5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001, RS-122-2002) (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing (2 x 150 bp) on Illumina Novaseq™ 6000 at LC Sciences (USA) following the vendor’s recommended protocol.

value: Hemocytes

tag: group

value: LPS stimulating exosomes


title: Pars Tuberalis, active, animal 2 [14_PT_A]


title: NB4_24h_atra_4

value: acute promyelocytic leukaemia (APL)


title: iPSC, clone LC67, DMSO

description:
PSC_67_D
67_iPSC_DMSO
Library type: strand-specific


title: NB4_72h_dmso_2


title: NOR_T1


title: NB4_24h_atra_5

value: ATRA


title: Pars Tuberalis, active, animal 1 [13_PT_A]


title: iPSC, clone LC67, Nutlin

description:
PSC_67_N
67_iPSC_Nutlin
Library type: strand-specific

value: 12 hrs 2.5uM Nutlin-3


title: Hypothalamus, not active, animal 12 [12_HT_NA]

source_name: Hypothalamus

value: Hypothalamus


title: NB4_24h_atra_2


title: LPS_T3

value: Normal exosomes


title: iPSC, clone LC62, Nutlin

description:
PSC_62_N
62_iPSC_Nutlin
Library type: strand-specific


title: Hypothalamus, not active, animal 11 [11_HT_NA]


title: LPS_T2


title: NB4_24h_dmso_4


title: iPSC, clone LC42, Nutlin

description:
PSC_42_N
42_iPSC_Nutlin
Library type: strand-specific


title: Hypothalamus, not active, animal 10 [10_HT_NA]


title: 5 days RA, clone LC42, Nutlin

description:
RA_42_N
42_RA_Nutlin
Library type: strand-specific


title: LPS_T1


title: iPSC, clone LC42, DMSO

description:
PSC_42_D
42_iPSC_DMSO
Library type: strand-specific

value: 12 hrs 0.2% DMSO


title: NB4_24h_dmso_2


title: NOR_T2


title: 5d-RAI DMSO replicate 2

description:
N2_RA_D
5dRAI_DMSO_2
Library type: strand-specific

growth_protocol: iPSCs were cultivated in mTeSR1 media supplemented with 1x antibiotic-antimycotic in a humidified atmosphere with 5% O2 & 5% CO2 at 37°C. iPSCs differentiation with 10µM retinoic acid for 5 days was carried out under the same conditions.

treatment_protocol: Cells were treated with 0.2% DMSO plus 4µM GSK343, 5µM 5-azacytidine (5-aza), or Combo (4µMGSK343 & 5µM 5-aza) for the final 48 hrs of differentiation.

value: 48 hrs 0.2% DMSO


title: Hypothalamus, not active, animal 9 [9_HT_NA]

value: Adult ram

value: Rasa Aragonesa


title: Hypothalamus, not active, animal 8 [8_HT_NA]

value: Not Active


title: PBS_T2

value: Injected with PBS


title: Hypothalamus, not active, animal 7 [7_HT_NA]


title: NB4_12h_atra_4


title: Combo DMSO replicate 2

description:
N2_COMBO_D
COMBO_DMSO_2
Library type: strand-specific

value: 5 days 10uM retinoic acid

value: 48 hrs 0.2% DMSO + 5uM 5-azacytidine + 4uM GSK343


title: iPSC, clone LC62, DMSO

description:
PSC_62_D
62_iPSC_DMSO
Library type: strand-specific


title: GSK DMSO replicate 2

description:
N2_GSK_D
GSK_DMSO_2
Library type: strand-specific

value: 48 hrs 0.2% DMSO + 4uM GSK343


title: NB4_12h_atra_2


title: Hypothalamus, active, animal 6 [6_HT_A]

value: Active


title: NB4_24h_dmso_5

value: DMSO


title: Mesenchymal glioblastoma stem cell line 1312 (biol rep 2)

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Trimming reads with Trimmomatic 0-36
Alignment with STAR (STAR_2.5.3a)
Count reads with Gencode basic annotation (Gencode genome version: GRCh38)
Differential Expression analysis with DESeq2
GRCh38
Supplementary files format and content: xls file with raw counts generated using DESeq2 R-package.

growth_protocol: NeuroSphere Assay (NSA) conditions

extract_protocol:
RNA from PN and MES GSCs was extracted by using the RNeasy mini kit (Qiagen) according to manufacturer’s protocol.
The cDNA was synthesized starting from total RNA using SMART technology. After barcoding, the RNA libraries were pooled, denatured, and diluted to 2.4 pM final concentration.
RNA sequencing was performed by using NextSeq (Illumina) set for 76 cycles in single end (SE)

value: Mesenchymal glioblastoma stem cell


title: Hypothalamus, active, animal 5 [5_HT_A]


title: NB4_12h_dmso_5

value: acute promyelocytic leukaemia (APL)


title: Mesenchymal glioblastoma stem cell line 0315


title: 5d-RAI DMSO replicate 1

description:
N1_RA_D
5dRAI_DMSO_1
Library type: strand-specific

value: iPSC


title: Mesenchymal glioblastoma stem cell line 1312 (biol rep 1)


title: NB4_12h_dmso_4


title: Hypothalamus, active, animal 4 [4_HT_A]


title: NB4_12h_dmso_2


title: NB4_12h_atra_5

value: ATRA


title: GSK DMSO replicate 1

description:
N1_GSK_D
GSK_DMSO_1
Library type: strand-specific


title: Proneural glioblastoma stem cell line 0605 (biol rep 2)

value: Proneural glioblastoma stem cell


title: Hypothalamus, active, animal 3 [3_HT_A]

value: Hypothalamus


title: Combo DMSO replicate 1

description:
N1_COMBO_D
COMBO_DMSO_1
Library type: strand-specific


title: Hypothalamus, active, animal 2 [2_HT_A]


title: NB4_4h_atra_5


title: PBS_T3

value: Hemocytes


title: 5AZA DMSO replicate 1

description:
N1_5AZA_D
5AZA_DMSO_1
Library type: strand-specific

value: 48 hrs 0.2% DMSO + 5uM 5-azacytidine


title: 5AZA DMSO replicate 2

description:
N2_5AZA_D
5AZA_DMSO_2
Library type: strand-specific


title: NB4_4h_atra_4


title: Hypothalamus, active, animal 1 [1_HT_A]

value: Adult ram


title: Proneural glioblastoma stem cell line 0512 (biol rep 2)


title: 5 days RA, clone LC67, DMSO

description:
RA_67_D
67_RA_DMSO
Library type: strand-specific

value: 12 hrs 0.2% DMSO


title: S196096_D14_high_201805408

city: Auburn University

first: Xu

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

description:
Illumina mRNA-seq
S196096

data_processing:
FastQC (version 11.5) software was used for quality check.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.36), and masked for low-complexity or low-quality sequence.
The ramaining high-quality clean reads were mapped to swine reference genome (build Sus_scrofa11.1) using TopHat (version 2.1.1)
Cufflinks and bedtools were conducted to calculate the number of aligned reads of each gene overlapping its exons.
DESeq2 and edgeR were employed to calculate the log2-fold change (log2FC), a criterion with |log2FC| ≥ 1.5 and p-value < 0.05 was used as the threshold for evaluating the DEGs.
Genome_build: swine reference genome (build Sus_scrofa11.1)
Supplementary_files_format_and_content: Gzipped, comma delimiited text file inlcuding raw gene counts and RPKM for every transcript in each sample

organism: Sus scrofa

source_name: uterus

extract_protocol:
Total RNA was extracted from uterus tissue (~50 mg) for each sample using Zymo Quick-DNA/RNA Miniprep (Zymo Research, IRVINE, USA) according to the manufacturer’s  instructions.
RNA quantity was measured using a Qubit 4 Fluorometer (Invitrogen, Carlsbad, CA), and RIN (RNA Integrity Number) was detected by LabChip GX Touch HT Nucleic Acid Analyzer (PerkinElmer, USA). Stranded mRNA sequencing libraries were constructed with total RNA (1 μg) extracted from each uterus sample using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, New England Biolabs, USA). Stranded mRNA library quantities were assessed with a Qubit 4 Fluorometer (Invitrogen, Carlsbad, CA), and library quality was determined detected by LabChip GX Touch HT Nucleic Acid Analyzer (PerkinElmer, USA). 150 bp paired-end mRNAseq, at over 50 million reads per individual barcoded sample, was performed using the Illumina NovaSeq Platform (Illumina, Inc., San Diego, CA)

value: uterus

tag: developmental stage

value: 14 days after birth

value: sufficient lactocrine

tag: litter


title: ShESE_2

city: Wenzhou

first: Huijing

last: Xu

state: Zhejiang

address: Chashan University Park

institute: Wenzhou Medical unversity

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
StringTie and was used to estimate the expression levels of all transcripts.
Assembly: mm10
Supplementary files format and content: Gene expression abundance(FPKM) of each sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA).RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: cell line

value: pancreatic cancer cells

value: ESE1 knockdown


title: Con_1

value: no treatment


title: NB4_4h_dmso_5

value: DMSO


title: Proneural glioblastoma stem cell line 0512 (biol rep 1)


title: patient 2 rep3nodep

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

description:
processed data file:
TEFM fibro mitochounts nodepl

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to the human reference genome (GRCh38) with Salmon and to the human mtDNA only with HiSat2 for in depth analysis of the mitochondrial reads
Salmon mapped reads were further analysed DESeq2
HiSat2 mapped reads were split for each strand using Samtools and coverage between paired reads was obtained with Bedtools bamtobed and genomecov
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files are generated with DESeq2 and show the log2FC of patient versus control samples. Xlsx files contain the counts of each nucleotide for chrM (bedtools genomecov for both strands separately)

source_name: fibroblasts

growth_protocol: Patient and control fibroblasts were cultured in DMEM supplemented with 10% FBS

extract_protocol:
RNA from muscle tissue or cultured fibroblasts was extracted using Trizol
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

tag: subject status/id

value: patient 2

tag: tissue/cell type

value: fibroblasts

value: no rRNA depletion


title: Proneural glioblastoma stem cell line 0306


title: NB4_4h_dmso_4

value: acute promyelocytic leukaemia (APL)


title: S196008_D15_high_201801242

description:
Illumina mRNA-seq
S196008

tag: tissue

value: 15 days after birth


title: patient 2 rep2nodep


title: PBS_T1

description:
mRNA sequencing
processed data file: genes_fpkm_expression.txt

value: Injected with PBS


title: NB4_4h_dmso_2

tag: treatment


title: NB4_0h_notreatment_5

value: No Treatment

tag: replicate


title: S192644_D15_low_201803059

description:
Illumina mRNA-seq
S192644

value: insufficient lactocrine


title: OVCAR-5 H3K79Me3 ChIP-seq

city: Chicago

first: Daniela

last: Matei

state: Illinois

address: 303 E Superior St

department: Ob-Gyn

institute: Northwestern University

data_processing:
Quality of fastq files were checked by fastQC
Raw single-end 50bp sequencing reads were mapped to human genome build hg38 using Bowtie2 (v.2.2.6)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
FOXK2 ChIP-seq peaks were identified by HOMER (v.4.10)
Normalized read counts and differential enrichment statistics for each peak were analyzed by DESeq2 Software (Bioconductor).
Motif analysis was performed by HOMER (v.4.10)
Assembly: GRCh38
Supplementary files format and content: bigWig files

source_name: ascites

growth_protocol: OVCAR5 ovarian cancer cells were cultured in RPMI medium with 10% FBS, 1% Penicillin-Streptomycin at 37 degree with 5% CO2.

extract_protocol:
Chromatin in cells was crosslinked with 1% paraformaldehyde and fragmented to an average size of approximately 300-500 bp by sonication. 10 μg chromatin and 5 µg antibodies were proceeded to immunoprecipitation.
ChIP-seq libraries were prepared by using KAPA Hyper Prep kit (Roche Sequencing) with KAPA UDI Adaptor (Roche Sequencing).

value: OVCAR5 ovarian cancer cells

tag: tumor stage

value: high grade serous

tag: passage

tag: antibody


title: S196007_D15_low_201801242

description:
Illumina mRNA-seq
S196007

value: uterus


title: OVCAR-5 transduced with shDOT1L rep2

data_processing:
Trimmed reads were aligned to the ENSEMBL human genome version GRCh38 using STAR (2.5.2)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
Assembly: GRCh38
Supplementary files format and content: counts

extract_protocol:
RNA was harvested using Trizol reagent. DNA was removed by QIAGEN RNase-Free DNase Set. Total mRNA was isolated with Ambion Dynabeads mRNA purification kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.

treatment_protocol: OVCAR5 cells transduced with shRNA targeting DOT1L (shDOT1L) were prepared for RNA extraction.


title: Proneural glioblastoma stem cell line 0605 (biol rep 1)

tag: cell type

value: Proneural glioblastoma stem cell


title: patient 2 rep1nodep

tag: molecule subtype


title: S192640_D15_high_201803059

description:
Illumina mRNA-seq
S192640

value: sufficient lactocrine


title: NB4_0h_notreatment_4

tag: time


title: NB4_4h atra 2

value: ATRA


title: patient 3 rep3nodep

value: patient 3


title: NB4_0h_notreatment_2


title: S196091_D14_low_201805408

description:
Illumina mRNA-seq
S196091

value: 14 days after birth


title: S191579_D14_high_201802172

description:
Illumina mRNA-seq
S191579


title: patient 3 rep1nodep


title: OVCAR-5 Input ChIP-seq

value: input


title: OCI-mIDH1/N cells, ivosidenib + entospletinib, Day9, Replicate1

city: Toronto

first: AlexCH

last: Liu

state: Ontario

address: 101 College Street

department: Medical Biophysics

country: Canada

institute: University of Toronto

data_processing:
Adapter sequences were trimmed using Trimmomatic.
Reads were mapped to mm10 reference genome by STAR (v2.5; mismatch=2, RRID:SCR_004463).
Raw counts were quantified by HTSeq (v0.6.1; -m union, RRID:SCR_005514).
Assembly: mm10
Supplementary files format and content: readcount.csv: Comma-separated values of un-normalized gene counts.

source_name: Bone marrow

growth_protocol: Bone marrow cells from IDH1R132HNPM1c+ mice were gifted to us by the Mark Minden Lab (Princess Margaret Cancer Centre, University Health Network, Toronto, Canada). The bone marrow cells were cultured in X-VIVO 10 medium (Lonza, Cat# 04-380Q) supplemented with 20% (v/v) BIT 9500 serum substitute (Stem Cell Technologies, Cat # 09500), 2 mM Gluta-Plus (Wisent Bioproducts, Cat# 609-066-EL), and the following cytokines: 10 ng/mL hIL-6 (Peprotech), 10 ng/mL mIL-3 (Peprotech), 50 ng/mL mSCF (Peprotech), 50 ng/mL FLT3L (Peprotech) and 25 ng/mL TPO (Peprotech). Antimicrobial agents were not added to the culture medium.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were treated with DMSO (vehicle control), ivosidenib (5 uM) alone, fostamatinib (40 nM) alone, entospletinib (100 nM) alone, or the combination of ivosidenib with each of the two SYK inhibitors for 9 days.

value: Bone marrow

value: AML cells

tag: genotype

value: IDH1-R132H, NPM1c

value: Ivosidenib + entospletinib


title: OCI-mIDH1/N cells, ivosidenib + entospletinib, Day9, Replicate2


title: control 1 rep3nodep

value: control 1

value: fibroblasts

value: no rRNA depletion


title: S191176_D14_low_201801581

description:
Illumina mRNA-seq
S191176

value: insufficient lactocrine


title: OCI-mIDH1/N cells, ivosidenib + fostamatinib, Day9, Replicate2

value: Ivosidenib + fostamatinib


title: starved fasn-1 mutant (D4)

city: New York

first: James

middle: Matthew

last: Jordan

state: NY

department: Medicine

institute: Weill Cornell Medical College, Cornell University

data_processing:
Bowtie2 2.3.3.1 was used to map paired-end reads to the WS273 genome with the parameter k set to 1.
HTSeq 0.12.4 was used to count reads.
edgeR 3.28.1 was used to filter and normalize read counts and perform differential expression analysis.
Library sizes were recomputed after filtering out lowly expressed genes.
The trimmed mean of M values (TMM) method was used to normalize for RNA composition. Tagwise dispersions were used to test for differentially expressed genes between all pairwise comparisons.
Genome_build: WS273
Supplementary_files_format_and_content: RNASeq 2_CPMs_forGEO.xlsx

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Worms were maintained without starvation at 20C on OP50 E.coli for at least 4 generations prior to being used in experiments.

extract_protocol:
RNA was extracted using 1ml TRIzol Reagent (Invitrogen# 15596026) according to the manufacturer’s protocol with the following exception - 100 uL of acid-washed sand (Sigma# 27439) was added to each sample at the beginning of the protocol to aid homogenization. RNA was eluted in nuclease-free water and stored at -80C until further use.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs# E7770) starting with 1 ug total RNA per library and 8 cycles of PCR.

treatment_protocol: 7 young adult animals were picked to large OP50 seeded plates x 6 plates and cultured at 20C for 72 hours. Plates were bleached to acquire embryos, which were resuspended in 5 ml virgin S-basal in test tubes at a density of 1 egg/ul. Worms were cultured on carousel at 20C for 8 days. 750 live animals were recovered on large 25 ug/ml Carb, 1mM IPTG, NGM plates seeded with empty vector HT115 bacteria. Worms were cultured at 20C until eggs appeared on plate ( ~68 hrs) before washing them off the plates with virgin S-basal. Worms were quickly washed twice in 10 ml virgin S-basal and snap frozen in liquid nitrogen.

tag: strain

value: early-life starvation

tag: Stage

value: early adult


title: control 1 rep2nodep


title: S191578_D14_low_201802172

description:
Illumina mRNA-seq
S191578

value: uterus

tag: developmental stage


title: OCI-mIDH1/N cells, ivosidenib + fostamatinib, Day9, Replicate1


title: control 1 rep1nodep


title: starved wild type (A3)

value: N2 (Bristol)

value: wild type


title: S191134_D14_high_201801054

description:
Illumina mRNA-seq
S191134

value: sufficient lactocrine

tag: litter


title: S191175_D14_high_201801581

description:
Illumina mRNA-seq
S191175

value: 14 days after birth


title: S191132_D14_low_201801054

description:
Illumina mRNA-seq
S191132


title: OCI-mIDH1/N cells, entospletinib, Day9, Replicate2

tag: cell line

value: Entospletinib alone


title: starved wild type (A4)


title: patient 2 rep2dep

description:
processed data file:
fibroblasts
TEFM fibro mitocounts

tag: subject status/id

value: patient 2

value: rRNA depleted RNA


title: ENT3-/- BMDM, IFN-b, 4hr, rep 3

city: Taipei

first: Chia-Lin

last: Hsu

address: R309, Biomedical Building, NYCU, No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
The sequencing was done by using a NextSeq 550 platform. The RNA concentration was measured by using a Qubit fluorometer with a Quant-iT RNA BR assay kit, and the RNA quality was examined on the Agilent Technologies 2100 Bioanalyzer with RNA nanochip. The library was prepared by using Illumina TruSeq Stranded mRNA Sample Prep Kit and sequenced by Illumina NextSeq High Output Kit v2.5-75 cycles on the sequencing platform. The raw data were aligned and analyzed following the CLC Genomics Workbench 20.0.4 pipeline. The sequence was annotated according to Mus musculus GRCm38 mm10 and calculated as RPKM.
The parameters in Trim sequences were set to Quality limit=0.01; Ambiguous limit=2; Remove 5' terminal nucleotides=12; Remove 3' terminal nucleotides=No; Maximum length=150.
CLC Genomics Workbench 20.0.4; Genome annotated with genes and transcripts
The parameters in RNA-seq analysis were set to Mismatch cos=2; Insertion cost=3; Deletion cost=3; Length fraction=0.8; Similarity fraction=0.8; Maximum number of hits for a read=10.
Assembly: GRCm38; mm10
Supplementary files format and content: Comma-separated values file. The file includes gene identifier, gene name, and chromosome region. Gene expression is shown in RPKM format.

source_name: Bone marrow-derived macrophages

extract_protocol: Bone marrow-derived macrophages generated from C57BL wild type and ENT3-/- mice were treated with or without 1000 U/mL IFN-β for 4 hr, then harvested for RNA extraction. Each sample represents a biological replicate. The library was prepared by using Illumina TruSeq Stranded mRNA Sample Prep Kit and sequenced by Illumina NextSeq High Output Kit v2.5-75 cycles on the NextSeq 550 platform.

value: Bone marrow-derived macrophages

value: 1000 U/mL IFN-b for 4 hr


title: starved fasn-1 mutant (D3)


title: patient 2 rep1dep

tag: tissue/cell type


title: ENT3-/- BMDM, IFN-b, 4hr, rep 2


title: ENT3-/- BMDM, IFN-b, 4hr, rep 1


title: OCI-mIDH1/N cells, fostamatinib, Day9, Replicate1

tag: tissue

value: Bone marrow

value: AML cells

value: IDH1-R132H, NPM1c

value: Fostamatinib alone


title: patient 3 rep3dep

value: patient 3

value: fibroblasts


title: OCI-mIDH1/N cells, ivosidenib, Day9, Replicate2

tag: treatment

value: Ivosidenib alone


title: OCI-mIDH1/N cells, fostamatinib, Day9, Replicate2


title: WT BMDM, IFN-b, 4hr, rep 3


title: patient 3 rep2dep


title: OCI-mIDH1/N cells, ivosidenib, Day9, Replicate1


title: patient 3 rep1dep


title: AD-ACD(+)_Atopy33

type: RNA

city: Kyoto City

first: Hiromi

last: Nishigaki

address: 465 Kajii-Cyo, Hirokouji, Kawaramachi doori, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

description: Collected with EDTA blood collection tube

hyb_protocol: Following fragmentation, Biotinylated RNA were hybridized for 16 hr at 48℃ on GeneChipTM miRNA 4.0 Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChipTM Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 (TAC 4.0) using robust multi-array analysis (RMA).

label: biotin

source_name: Human plasma of AD with severe ACD

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: Human plasma was obtained from all patients with informed consent.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Human plasma was collected using EDTA blood collection tubes.

tag: plasma

value: Human plasma

tag: group

value: AD with ACD


title: WT BMDM, IFN-b, 4hr, rep 2

value: wild type


title: OCI-mIDH1/N cells, DMSO Control, Day9, Replicate2

value: DMSO control


title: AD-ACD(+)_Atopy32


title: AD-ACD(+)_Atopy41


title: patient 2 rep3dep


title: patient 3 rep2nodep

value: no rRNA depletion


title: OCI-mIDH1/N cells, DMSO Control, Day9, Replicate1


title: control 1 rep2dep

value: control 1


title: OCI-mIDH1/N cells, entospletinib, Day9, Replicate1

value: Entospletinib alone


title: control 1 rep3dep

value: rRNA depleted RNA


title: WT BMDM, IFN-b, 4hr, rep 1

value: Bone marrow-derived macrophages


title: AD-ACD(-)_Atopy44

source_name: Human plasma of AD without severe ACD

value: AD without ACD


title: AD-ACD(-)_Atopy10


title: ENT3-/- BMDM, untreated, rep 3

value: untreated


title: mESCs rep3

city: Guangzhou

first: xuzhao

last: zhai

address: Kaiyuan avenue

institute: Guangzhou Laboratory

description: mESCs rep3

data_processing:
For bulk RNA-seq, trim_galore was used to trim the adapters,STAR was used for the alignment to the mm10 reference genome, RSEM was used to estimate Raw counts. For single cell RMA-seq, STAR was used for mapping , SEURAT and SCANPY was used for the downstream analysis.
Genome_build: mm10

source_name: mESCs

extract_protocol:
Libraries of bulk RNA-seq and single cell RNA-seq constructed according to the manufacturer's instructions.
transcriptomic

value: embryo

value: mESCs


title: mESCs rep2

description: mESCs rep2


title: ENT3-/- BMDM, untreated, rep 2


title: control 1 rep1dep


title: control 2 rep3nodep

value: control 2


title: ENT3-/- BMDM, untreated, rep 1


title: control 2 rep2nodep


title: WT BMDM, untreated, rep 3


title: mESCs rep1

description: mESCs rep1


title: mCMG-TBLCs rep3

description: mCMG-TBLCs rep3

source_name: mCMG-TBLCs

value: mCMG-TBLCs


title: WT BMDM, untreated, rep 2


title: mCMG-TBLCs rep2

description: mCMG-TBLCs rep2


title: control 2 rep1nodep

value: fibroblasts


title: mCMG-TBLCs rep1

description: mCMG-TBLCs rep1


title: patient 6 rep3nodep

value: patient 6


title: WT BMDM, untreated, rep 1


title: OVCAR-5 transduced with shDOT1L rep1

value: OVCAR5 ovarian cancer cells

tag: tumor stage

value: high grade serous

tag: passage


title: patient 6 rep2nodep


title: Control_N353

source_name: Normal Human plasma

value: Human plasma

value: healthy control


title: AD-ACD(-)_Atopy34


title: NMF Biological repetition 3

city: rehovot

first: Coral

last: Halperin

address: Herzel 234

country: Israel

institute: Weizmann institute of sciences

data_processing:
Raw reads were trimmed using Trimmomatic v0.36 and aligned against the mouse reference genome (mm10) utilizing bwa mem v0.7.8, invoking the parameter "-T 0". Alignment duplicates were marked by Picard MarkDuplicates (http://broadinstitute.github.io/picard) v1.125. Reads with coverage > 2 were sorted, and PCR duplicates were removed. Methylation calling was executed with MethylDackel (https://github.com/dpryan79/MethylDackel) v0.3.0. According to the M-bias plots, the first five base pairs at the two ends of the reads were excluded from methylation calling.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files include methylation calls and coverages per sample per CpG

source_name: Normal mammary fat pad

growth_protocol: 8 to 13 weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Normal mammary fat pad: Tissue was minced using scissors and placed and disrupted for 25 min at 37oC in a gentleMACS C tube using gentleMACS dissociator, in the presence of enzymatic digestion solution containing 1 mg ml-1 collagenase II, 1 mg ml-1collagenase IV and 70 unit ml-1 DNase. Primary tumor: Tissue was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase in RPMI 1640 for 20 min at 37oC, with pipetting every 3 min.
DNA from NMFs and pCAFs was processed for tWGBS as described in Weichenhan et al. 2018,  Briefly, we started with 25ng DNA for NMF, 8.5 ng for pCAFs. For the tagmentation reaction, we added 2µl of EZ-Tn5TMTransposase (Lucigen, cat# TNP92110), 1µl Unmethylated phage λ DNA and 5µl tagmentation buffer (20 mM Tris(hydroxymethyl)aminomethane, 10 mM MgCl2, 20% (vol/vol) dimethylformamide). DNA was purified using 46µl AMPure beads (Agencourt AMPure XP beads) following the manufacturer’s protocol. Next, we performed an Oligo Replacement/Gap Repair reaction using 2μl of dNTP mix. The bisulfite treatments were achieved by EZ DNA Methylation™ Kit (ZYMO Research) following the commercial kit protocol. The samples were divided into 4 technical replicates with different barcodes. We performed a qPCR reaction to amplify the libraries, followed by AMPure bead purification. The samples were eluted in 10μl of EB buffer (Tris-HCL pH8), library concentration was quantified with Qubit, and average fragment size was detected by Bioanalyzer. Libraries were sequenced using paired-end sequencing, 125 bps, on one lane of a HiSeq2000 v4 sequencer (Illumina, San Diego, CA, USA) per 4 technical replicates.

treatment_protocol: 8 weeks old BALB/c females were injected under anaesthesia with 100,000 4T1-luc cells suspended in PBS, directly into the lower left mammary fat pad. To obtain CAFs from primary tumors, mice were sacrificed and tumors were immediately excised post mortem.

value: BALB/c

value: Normal mammary fat pad

tag: cell type

value: Non-immune stromal cells

tag: selection marker

value: Ter119- CD45- EpCAM-

tag: mouse age

value: 12 weeks


title: Control_N316


title: patient 6 rep1nodep

tag: molecule subtype

value: no rRNA depletion


title: NMF Biological repetition 1

tag: strain


title: NMF Biological repetition 2


title: control 2 rep2dep

value: rRNA depleted RNA


title: High fat diet fed mice adipose tissue derived immune cells

city: Memphis

first: Udai

middle: P

last: Singh

state: TN

address: 881 Madison Avenue

department: Pharmacy

institute: University of Tennessee Health Science Center

description: microRNAs data from immune cells after 12 weeks of high fat diet feeding

hyb_protocol: Cocktails were hybridized for 16 hr at 45c on Gene chip miRNA4

scan_protocol: GeneChip 3000 7G

data_processing: RMA-DABG with Affymetrix Expression Console software

source_name: Immune cells isolated from Adipose tissue

label_protocol: Biotinylated miRNA were prepared according to the standard FlashTag Biotin HSR RNA labeling protocol, starting from 150ng total RNA

growth_protocol: Immune cells were isolated from adipose tissue of both HFD and ND feed mice by standard protocol in our laboratory.

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instruction from Qiagen

treatment_protocol: At 8 weeks of age, one group of animals was switched to a normal diet (ND) containing 10% fat (n = 6; D12450J, Research Diets, New Brunswick, NJ) that will serve as the control group, while the other half were switched to a high-fat diet containing 60% fat (HFD; n = 6; D12492, Research Diets). Both HFD and ND are calorie-matched diets.

value: Adiposse tissue derived immune cells


title: Experimental rat 2, SCI surgery was performed, 24h

city: Tian Jin

first: Jian an

last: Li

address: Jie fang road #406

institute: Tian Jin hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Blood exosomes

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Blood exosomes

tag: genotype

value: WT

value: SCI surgery, 24h


title: Day14_singlenuc_rep1

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

library_source: transcriptomic single cell

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Assembly: OryCun2.0

organism: Oryctolagus cuniculus

source_name: Retina

extract_protocol:
Papain dissociation to prepare single cell suspension or 0.01% Nonidet P40 lysis buffer to prepare single nuclei suspension
scRNA-Seq following 10x ver3.1 guideline

tag: condition

value: retinal cells


title: Hr4_singlenuc_rep2


title: Day14_singlenuc_rep2


title: Hr4_singlecell_rep1


title: control 2 rep1dep

value: control 2

value: fibroblasts


title: Normal Diet  Fed mice adipose tiuuse derived immune cells

description: microRNAs data from immune cells after 12 weeks of Normal diet feeding

value: Adipose tissue derived immune cells


title: Control_N306

value: Human plasma


title: Control_singlenuc_rep3

value: Control


title: patient 6 rep3dep

value: patient 6


title: Day14_singlecell_rep1


title: Control_singlenuc_rep2


title: Experimental rat 1, SCI surgery was performed, 24h


title: patient 6 rep2dep


title: mimic NC

hyb_protocol: Following fragmentation, Biotinylated cRNA were hybridized for 16 hr at 45℃ on ClarionTM S Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

source_name: THP-1 cell (JCRB0112.1)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: THP-1 cells were cultuerd in RPMI1640 medium containing 100ng/ml PMA for 2 days to differentiate into macrophage-like cells.

treatment_protocol: The mimic of hsa-let-7a-5p or negative contorl were mixed with lepofectamine RNAiMAX and added for 24hr to the THP-1 cells.

value: lymphocyte-like cells

tag: transfection

value: negative control


title: Control rat 2, the skin was injured, 24h

value: Skin injury, 24h


title: Control_singlenuc_rep1


title: Experimental rat 3, SCI surgery was performed, 24h


title: Control rat 1, the skin was injured, 24h


title: MOUSE_SPERM_BPA_HiC_Rep2

city: Atlanta

first: Yoonhee

last: Jung

address: 615 Michael Street

institute: Emory university

description: processed data file: MOUSE_SPERM_BPA_HiC.hic

data_processing:
For Hi-C, the paired end Hi-C reads were mapped independently using BWA mem and paired. Reads mapping to more than two genomic locations (one for each paired end or two for one paired end in agreement with its partner) were discarded. Reads were further filtered and normalized using HiFive v1.2.2 (Sauria et al., 2015) using the Express algorithm and the settings "--min-interactions 5 --min-distance 100000 --min-binsize 500 --num-bins 50 --express-iterations 5000 --min-change 0.00005 --remove-distance --express-reads cis".
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: MOUSE_SPERM_BPA_HiC.hic

source_name: Sperm

extract_protocol: We generated in-situ Hi-C libraries using DpnII restriction enzyme following the protocol as described (Rao et al., 2014). Briefly, 10 million sperm were crosslinked with 1% formaldehyde, quenched with glycine, washed with PBS, and permeabilized to obtain intact nuclei. Nuclear DNA was then digested with DpnII, the 5’-overhangs were filled with biotinylated dCTPs and dA/dT/dGTPs to make blunt-end fragments, which were then ligated, reverse-crosslinked, and purified by standard DNA ethanol precipitation. Purified DNA was sonicated to 200-500 bp small fragments and captured with streptavidin beads. Standard Illumina TruSeq library preparation steps including end-repairing, A-tailing, and ligation with universal adaptors were all performed on beads, washing twice in TWB between each step. DNA on the beads was PCR amplified with barcoded primers using KAPA SYBR FAST qPCR Master Mix for 5~12 PCR cycles to obtain enough DNA for sequencing. Generated libraries were paired-end sequenced on Illumina HiSeq2500 v4. Two sets of biological replicates were generated, and replicates were combined after ensuring high correlation.

tag: strain background

tag: Sex

value: Male

value: Sperm

value: Bisphenol A (BPA)


title: patient 6 rep1dep

tag: subject status/id

tag: tissue/cell type

value: rRNA depleted RNA


title: pCAF Biological repetition 3

source_name: PDPN+ CAFs

value: BALB/c

tag: tissue

value: Breast tumor

value: Non-immune stromal cells

value: Ter119- CD45- EpCAM- PDPN-

tag: treatment

value: Orthotopic breast injection of 4T1-luc cells

value: 8 weeks


title: MOUSE_SPERM_BPA_HiC_Rep1


title: MF6_112012_RS60_GF_Xbp1KO_2

status: Public on Nov 07 2022

city: Boston

first: Magdalena

middle: Barbara

last: Flak

state: MA

address: New Research Building, Room 641, 77 Avenue Louis Pasteur

department: Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine

institute: Brigham and Women’s Hospital, Harvard Medical School

data_processing:
Analysis performed using Partek Flow analysis pipeline (building version: 10.0.21.0201)
base trimming
STAR (v2.7.3a), HTSeq (v0.11. 0) and  Post-alignment QA/QC performed
Groups were filtered, data normalised, filtered by features, coversage assessed
differential gene expression analysis using DESeq2,
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text file of differential gene expression analysis including total count, ratios, fold-change, p-values

source_name: Paneth cells

extract_protocol:
Paneth cells were harvested by laser capture microdissection using an Arcturus PixCell II system and CapSure HS LCM caps (Arcturus). Total RNA was prepared from captured cells using the Arcturus PicoPure RNA Isolation Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: fastq

tag: colonisation status

value: germ-free

value: Vcre+/-; Xbp1fl/fl


title: Control_singlecell_rep1

value: Control

value: retinal cells


title: MF7_112012_RS62_GF_Xbp1KO_3


title: pCAF Biological repetition 2

value: Ter119- CD45- EpCAM- PDPN+


title: MF2_112012_RS51_GF_Xbp1WT_2

value: Vcre-/-; Xbp1fl/fl


title: Staphylococcus aureus gltS transposon biofilm 24h

first: Koichi

last: Yuki

address: 300 Longwood Avenue

institute: Boston Children's Hospital

data_processing:
CLC genomic benchwork
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36.
Trimmed sequence reads were mapped to USA300_FPR3757 reference genome using STAR aligner v.2.5.2b
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: USA300_FPR3757 reference genome (GCF_000013465.1)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Staphylococcus aureus

source_name: bacterial cells

extract_protocol:
RNA was purified using RiboPure RNA purification kit
Illumina Nextera XT library was used for sequencing library preparation

treatment_protocol: Biofilm culture in vitro

value: bacterial cells

value: GltS transposon

value: Biofilm culture 24h


title: Staphylococcus aureus gltS transposon baseline

value: No treatment


title: Staphylococcus aureus JE2 biofilm 48h

value: Biofilm culture 48h


title: pCAF Biological repetition 1

value: BALB/c


title: MF3_112012_RS52_GF_Xbp1WT_3


title: Staphylococcus aureus gltS transposon biofilm 48h


title: Staphylococcus aureus gltS transposon biofilm 4h

value: Biofilm culture 4h


title: Staphylococcus aureus JE2 biofilm 24h


title: nasal_epithelial_cell [0a13_43f4]

type: genomic

first: Emma

last: Thompson

state: IL

address: 920 E 58th St, CLSC Rm 501

institute: The University of Chicago

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

scan_protocol: Arrays were imaged using standard Illumina scanner settings

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5%) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using SWAN. Raw probe values were corrected for color imbalance and background by control normalization.
matrix processed value definition: SWAN normalized Beta values

label: cy3, cy5

label_protocol: Standard Illumina protocol.

extract_protocol: Samples were spun through a Qiashredder column and then extracted using AllPrep DNA/RNA mini kits (Qiagen) following the manufacturer's protocol.

tag: plate

tag: array

value: Male

tag: proportionpositiveskinpricktests

tag: percentciliatedepicells


title: nasal_epithelial_cell [d902_4698]


title: nasal_epithelial_cell [5498_40e4]


title: Staphylococcus aureus JE2 biofilm 4h

tag: cell type


title: nasal_epithelial_cell [d4a8_4b32]

value: Female


title: nasal_epithelial_cell [b5bf_44ef]


title: nasal_epithelial_cell [db7d_4d13]


title: nasal_epithelial_cell [cfea_470d]


title: MF4_112012_RS54_GF_Xbp1WT_4


title: MF1_112012_RS50_GF_Xbp1WT_1


title: nasal_epithelial_cell [62c5_4d11]


title: MF5_112012_RS57_GF_Xbp1KO_1


title: nasal_epithelial_cell [d1b2_42f1]


title: nasal_epithelial_cell [a706_4f38]


title: nasal_epithelial_cell [f66f_4cda]


title: nasal_epithelial_cell [b43a_4247]


title: nasal_epithelial_cell [81f8_457f]


title: nasal_epithelial_cell [cd72_4cbe]


title: nasal_epithelial_cell [b74e_49f1]


title: control 2 rep3dep

source_name: fibroblasts

value: control 2

value: fibroblasts

tag: molecule subtype

value: rRNA depleted RNA


title: nasal_epithelial_cell [a122_483d]


title: nasal_epithelial_cell [aacf_4181]


title: Hr4_singlenuc_rep1


title: nasal_epithelial_cell [a2aa_4f37]


title: nasal_epithelial_cell [2244_4759]


title: nasal_epithelial_cell [4438_4db6]


title: nasal_epithelial_cell [a567_4fc3]


title: nasal_epithelial_cell [4680_4b7c]


title: Control rat 3, the skin was injured, 24h

value: Blood exosomes

value: WT

value: Skin injury, 24h


title: nasal_epithelial_cell [9cb0_48bf]


title: nasal_epithelial_cell [c5dd_4ee6]


title: nasal_epithelial_cell [fa79_4cc3]


title: nasal_epithelial_cell [bf7c_4c07]


title: nasal_epithelial_cell [60c3_4cd8]


title: nasal_epithelial_cell [192f_4945]


title: nasal_epithelial_cell [e7cc_41d3]


title: nasal_epithelial_cell [d267_4880]


title: nasal_epithelial_cell [3206_422c]


title: nasal_epithelial_cell [540b_41ce]


title: nasal_epithelial_cell [4bcf_414d]


title: nasal_epithelial_cell [099a_4799]


title: nasal_epithelial_cell [eb8a_436e]


title: nasal_epithelial_cell [227d_4725]


title: nasal_epithelial_cell [8809_4320]


title: nasal_epithelial_cell [d1e7_402b]


title: nasal_epithelial_cell [770d_4553]


title: nasal_epithelial_cell [10e7_4e7b]


title: nasal_epithelial_cell [7e48_44cb]


title: nasal_epithelial_cell [8af4_407f]


title: nasal_epithelial_cell [ed75_4417]


title: nasal_epithelial_cell [e3c7_4cdd]


title: nasal_epithelial_cell [8d48_42c7]


title: nasal_epithelial_cell [ecad_4437]


title: nasal_epithelial_cell [4da9_4107]


title: nasal_epithelial_cell [5340_4c6e]


title: nasal_epithelial_cell [83a6_464b]


title: nasal_epithelial_cell [55d2_4cce]


title: nasal_epithelial_cell [365d_450b]


title: nasal_epithelial_cell [1f68_4160]


title: nasal_epithelial_cell [5ece_44ed]


title: nasal_epithelial_cell [8be9_46af]


title: nasal_epithelial_cell [917d_4410]


title: nasal_epithelial_cell [3450_4e8e]


title: nasal_epithelial_cell [65f1_447a]


title: nasal_epithelial_cell [c851_439a]


title: nasal_epithelial_cell [c005_446f]


title: nasal_epithelial_cell [219a_49ed]


title: nasal_epithelial_cell [03b3_4f8c]


title: nasal_epithelial_cell [7622_45fe]


title: nasal_epithelial_cell [e7de_4d41]


title: nasal_epithelial_cell [4193_4778]


title: nasal_epithelial_cell [3f3a_408c]


title: nasal_epithelial_cell [96f7_46dd]


title: nasal_epithelial_cell [e653_43c4]


title: nasal_epithelial_cell [73c8_4609]


title: nasal_epithelial_cell [6ace_4528]


title: nasal_epithelial_cell [da4b_43af]


title: nasal_epithelial_cell [2a21_497b]


title: nasal_epithelial_cell [fbf2_4f46]


title: nasal_epithelial_cell [6979_489c]


title: nasal_epithelial_cell [a812_455a]


title: nasal_epithelial_cell [1b47_432d]


title: mimic let-7a-5p

tag: cell line

value: lymphocyte-like cells

value: let-7a-5p mimic


title: nasal_epithelial_cell [f70a_47b0]


title: nasal_epithelial_cell [f4e1_42aa]


title: nasal_epithelial_cell [1796_4d1a]


title: nasal_epithelial_cell [0276_4d38]


title: nasal_epithelial_cell [4fe8_4e7f]


title: nasal_epithelial_cell [5831_458f]


title: nasal_epithelial_cell [a60f_493d]


title: nasal_epithelial_cell [a963_44d0]


title: nasal_epithelial_cell [c9f7_426d]


title: nasal_epithelial_cell [0235_44d9]


title: nasal_epithelial_cell [f972_4900]


title: nasal_epithelial_cell [45a5_4e0f]


title: nasal_epithelial_cell [f665_4e1b]


title: nasal_epithelial_cell [00d1_4cde]


title: nasal_epithelial_cell [1c92_4793]


title: nasal_epithelial_cell [d18f_4008]


title: nasal_epithelial_cell [c18f_4818]


title: nasal_epithelial_cell [7a6d_4bda]


title: nasal_epithelial_cell [4081_4b64]


title: nasal_epithelial_cell [5450_4370]


title: nasal_epithelial_cell [1f03_445a]


title: nasal_epithelial_cell [3e33_44a4]


title: nasal_epithelial_cell [e0e9_4dc6]


title: nasal_epithelial_cell [06f1_4902]


title: nasal_epithelial_cell [85aa_4e0f]


title: nasal_epithelial_cell [3867_4ee0]


title: nasal_epithelial_cell [b030_4319]


title: nasal_epithelial_cell [2a8d_46e8]


title: nasal_epithelial_cell [504c_425c]


title: nasal_epithelial_cell [e47c_4e9b]


title: nasal_epithelial_cell [60aa_40f1]


title: nasal_epithelial_cell [83cf_4f30]


title: nasal_epithelial_cell [32fa_4a92]


title: nasal_epithelial_cell [446a_413f]


title: nasal_epithelial_cell [a55c_472f]


title: nasal_epithelial_cell [9790_40b6]


title: nasal_epithelial_cell [4554_4bab]


title: nasal_epithelial_cell [85cd_4430]


title: nasal_epithelial_cell [628c_4467]


title: nasal_epithelial_cell [1723_4ac8]


title: nasal_epithelial_cell [5ef4_459d]


title: nasal_epithelial_cell [248d_4901]


title: nasal_epithelial_cell [99e1_4d92]


title: nasal_epithelial_cell [5ac0_4c3e]


title: nasal_epithelial_cell [2c93_4702]


title: nasal_epithelial_cell [cc7c_421d]


title: nasal_epithelial_cell [7804_4bab]


title: nasal_epithelial_cell [8e15_45ca]


title: nasal_epithelial_cell [3c61_4020]


title: nasal_epithelial_cell [294a_4d95]


title: nasal_epithelial_cell [5aeb_466f]


title: nasal_epithelial_cell [d9bd_448a]


title: nasal_epithelial_cell [5348_41b1]


title: nasal_epithelial_cell [6a3c_49d4]


title: nasal_epithelial_cell [6a32_47fc]


title: nasal_epithelial_cell [56bb_47e9]


title: nasal_epithelial_cell [fda4_4c5e]


title: nasal_epithelial_cell [3cde_4458]


title: nasal_epithelial_cell [12d8_4b2c]


title: nasal_epithelial_cell [7131_4332]


title: nasal_epithelial_cell [9e45_40b0]


title: nasal_epithelial_cell [5a30_4238]


title: nasal_epithelial_cell [8fc1_4c8c]


title: nasal_epithelial_cell [1455_4f52]


title: nasal_epithelial_cell [71e3_4eb8]


title: nasal_epithelial_cell [e083_4c15]


title: nasal_epithelial_cell [7a8b_490f]


title: old WT control mouse biorep 3

city: Tampa

first: Sami

last: Noujaim

state: FL

address: 12901 Bruce B Downs Blvd

department: Molecular Pharmacology and Physiology

institute: University of South Florida

data_processing:
Sequencing-quality was measured using fastqc v0.11.5, and quality reports were aggregated using Multiqc v1.7.
Resulting sequences were aligned against the Mus musculus reference genome GRCm38 (obtained from Ensembl; RefSeq ID: 5034988) using hisat2 v2.1.0 with RNA-strandedness set to paired-end.
Transcript-alignments were made against gene features annotated in Mus_musculus.GRCm38.95.gtf from Ensembl (default parameters).
Read count estimation and extraction were performed using FeatureCounts v1.5.0-p3.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample

source_name: atrial tissue

extract_protocol:
Atria from 3 WT old and 3 KO old male and female mice were isolated, flash-frozen then homogenized and lysed. mRNA was extracted from the tissue samples using the RNeasy kit from QIAGEN. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 following manufacturer's protocols.

tag: mouse line

tag: genotype

value: atrial tissue

tag: age

value: old (average age 20.9 ± 0.43 months)


title: nasal_epithelial_cell [303d_4f34]

department: Human Genetics


title: old WT control mouse biorep 2


title: old PKC-epsilon knockout mouse biorep 2

value: JAX stock #004189

value: PKC-epsilon knockout


title: nasal_epithelial_cell [2e3c_4388]


title: nasal_epithelial_cell [c21a_4a25]


title: nasal_epithelial_cell [ac8a_4da4]


title: old WT control mouse biorep 1


title: nasal_epithelial_cell [7a79_4237]


title: old PKC-epsilon knockout mouse biorep 1


title: nasal_epithelial_cell [8941_454a]


title: old PKC-epsilon knockout mouse biorep 3


title: nasal_epithelial_cell [d084_4cd9]


title: nasal_epithelial_cell [9df6_44a2]


title: 0731-047, NGN2, HCort, 1000nM

first: Carina

middle: of

last: Seah

state: New York

address: 1 Gustave L Levy Pl Fl 1

institute: Icahn School of Medicine at Mount Sinai

description:
EF11
RawCountMatrix_NGN2_Study2.txt

data_processing:
Short reads with Illumina adapters were trimmed and low-quality reads were filtered using TrimGalore92 (–illumina option). All high-quality reads were then processed for alignment using the hg38 reference and the ultrafast universal RNA-seq aligner STAR with default parameters93. Mapped bam files were sorted using Samtools and short read data were quantified using featureCounts94 with the following parameters: -T 5, -t exon and -g gene_id.
Assembly: Hg38
Supplementary files format and content: Read count files

source_name: Neuron

extract_protocol: For NGN2-neurons, RNA was harvested with an RNeasy Plus Micro Kit (Qiagen). For PBMCs, RNA was extracted from TRIzol-lysed PBMCs using the miRNAeasy Mini Kit (Qiagen).

value: Neuron

tag: diagnosis

value: Control

value: 1000 nM HCort


title: 0731-047, NGN2, HCort, 100nM

description:
CD11
RawCountMatrix_NGN2_Study2.txt

value: 100 nM HCort


title: 0731-047 NGN2, HCort, 0nM

description:
AB11
RawCountMatrix_NGN2_Study2.txt

value: 0 nM HCort


title: nasal_epithelial_cell [68f8_4d10]

tag: Sex

value: Female


title: nasal_epithelial_cell [3844_44af]

value: Male


title: nasal_epithelial_cell [7527_417c]


title: nasal_epithelial_cell [75a1_4e15]


title: 0731-036 NGN2, HCort, 0nM

description:
AB7
RawCountMatrix_NGN2_Study2.txt


title: 0731-036, NGN2, HCort, 1000nM

description:
EF7
RawCountMatrix_NGN2_Study2.txt


title: 0731-035, NGN2, HCort, 1000nM

description:
EF5
RawCountMatrix_NGN2_Study2.txt


title: 0731-036, NGN2, HCort, 100nM

description:
CD7
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [ead4_485e]


title: nasal_epithelial_cell [19c1_493c]


title: 0731-035, NGN2, HCort, 100nM

description:
CD5
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [e32e_430b]


title: nasal_epithelial_cell [1822_46c3]


title: nasal_epithelial_cell [ce4e_4ee7]


title: 0731-024, NGN2, HCort, 100nM

description:
CD3
RawCountMatrix_NGN2_Study2.txt


title: 0731-035 NGN2, HCort, 0nM

description:
AB5
RawCountMatrix_NGN2_Study2.txt


title: 0731-024, NGN2, HCort, 1000nM

description:
EF3
RawCountMatrix_NGN2_Study2.txt


title: 0731-024 NGN2, HCort, 0nM

description:
AB3
RawCountMatrix_NGN2_Study2.txt


title: 0731-016, NGN2, HCort, 1000nM

description:
EF9
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [9747_46ec]


title: nasal_epithelial_cell [eaa4_49a1]


title: nasal_epithelial_cell [c9ed_47e4]


title: nasal_epithelial_cell [45f8_4239]


title: 0731-016 NGN2, HCort, 0nM

description:
AB9
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [9ea6_469e]


title: nasal_epithelial_cell [c9c3_41ae]


title: 0731-016, NGN2, HCort, 100nM

description:
CD9
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [cf5a_43e2]


title: 0731-013, NGN2, HCort, 100nM

description:
CD10
RawCountMatrix_NGN2_Study2.txt

value: PTSD


title: nasal_epithelial_cell [debb_4963]


title: nasal_epithelial_cell [2ca0_46f0]


title: 0731-013, NGN2, HCort, 1000nM

description:
EF10
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [56e0_4dbf]


title: 0731-013 NGN2, HCort, 0nM

description:
AB10
RawCountMatrix_NGN2_Study2.txt


title: 0731-011 NGN2, HCort, 0nM

description:
AB8
RawCountMatrix_NGN2_Study2.txt


title: 0731-010, NGN2, HCort, 1000nM

description:
EF6
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [94db_415e]


title: 0731-011, NGN2, HCort, 1000nM

description:
EF8
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [4fd7_42e0]


title: 0731-011, NGN2, HCort, 100nM

description:
CD8
RawCountMatrix_NGN2_Study2.txt


title: 0731-010 NGN2, HCort, 0nM

description:
AB6
RawCountMatrix_NGN2_Study2.txt


title: nasal_epithelial_cell [797f_4a4f]


title: nasal_epithelial_cell [a102_4294]


title: 0731-010, NGN2, HCort, 100nM

description:
CD6
RawCountMatrix_NGN2_Study2.txt


title: 0731-004, NGN2, HCort, 100nM

description:
CD4
RawCountMatrix_NGN2_Study2.txt


title: 0731-004 NGN2, HCort, 0nM

description:
AB4
RawCountMatrix_NGN2_Study2.txt


title: 0731-115, NGN2, HCort, 100nM

description:
P3C11
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [56b6_49db]


title: 0731-114, NGN2, HCort, 100nM

description:
P3C7
RawCountMatrix_NGN2_Study1.txt


title: 0731-115 NGN2, HCort, 0nM

description:
P3B11
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [849c_424f]


title: nasal_epithelial_cell [cb8c_4f8c]


title: nasal_epithelial_cell [61ab_4b98]


title: 0731-114 NGN2, HCort, 0nM

description:
P3B7
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [835d_496e]


title: nasal_epithelial_cell [c327_4fff]


title: 0731-113, NGN2, HCort, 1000nM

description:
P3D10
RawCountMatrix_NGN2_Study1.txt


title: 0731-113, NGN2, HCort, 100nM

description:
P3C10
RawCountMatrix_NGN2_Study1.txt


title: 0731-108, NGN2, HCort, 1000nM

description:
P1D11
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [a768_4b98]


title: 0731-113 NGN2, HCort, 0nM

description:
P3B10
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [91ff_4ca7]


title: nasal_epithelial_cell [2bcd_4835]


title: 0731-108, NGN2, HCort, 100nM

description:
P1C11
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [4ca7_42b1]


title: nasal_epithelial_cell [f1e1_45c6]


title: nasal_epithelial_cell [61a2_48bb]


title: 0731-108 NGN2, HCort, 0nM

description:
P1B11
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [1644_43b3]


title: nasal_epithelial_cell [cfa6_4e5f]


title: 0731-106, NGN2, HCort, 1000nM

description:
P3D5
RawCountMatrix_NGN2_Study1.txt


title: 0731-106, NGN2, HCort, 100nM

description:
P3C5
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [78f3_41a8]


title: 0731-115, NGN2, HCort, 1000nM

description:
P3D11
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [a894_4adc]


title: 0731-106 NGN2, HCort, 0nM

description:
P3B5
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [e454_4e68]


title: 0731-097, NGN2, HCort, 1000nM

description:
P1D10
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [aae5_4276]


title: nasal_epithelial_cell [f5de_46e9]


title: 0731-097, NGN2, HCort, 100nM

description:
P1C10
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [d7bb_48eb]


title: nasal_epithelial_cell [67a8_4cad]


title: nasal_epithelial_cell [b6f6_4619]


title: 0731-101, NGN2, HCort, 1000nM

description:
P1G11
RawCountMatrix_NGN2_Study1.txt


title: 0731-097 NGN2, HCort, 0nM

description:
P1B10
RawCountMatrix_NGN2_Study1.txt


title: 0731-101, NGN2, HCort, 100nM

description:
P1F11
RawCountMatrix_NGN2_Study1.txt


title: 0731-101, NGN2, HCort, 0nM

description:
P1E11
RawCountMatrix_NGN2_Study1.txt


title: 0731-099, NGN2, HCort, 100nM

description:
P1F10
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [68ad_4244]


title: nasal_epithelial_cell [cc03_400c]


title: 0731-099, NGN2, HCort, 1000nM

description:
P1G10
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [dc0b_4294]


title: 0731-099, NGN2, HCort, 0nM

description:
P1E10
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [8dab_416d]


title: nasal_epithelial_cell [4781_40a3]


title: nasal_epithelial_cell [5b26_42a3]


title: 0731-098, NGN2, HCort, 0nM

description:
P1B9
RawCountMatrix_NGN2_Study1.txt


title: 0731-098, NGN2, HCort, 1000nM

description:
P1D9
RawCountMatrix_NGN2_Study1.txt


title: 0731-095, NGN2, HCort, 0nM

description:
P3B8
RawCountMatrix_NGN2_Study1.txt


title: 0731-095, NGN2, HCort, 100nM

description:
P3C8
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [180e_47a6]


title: nasal_epithelial_cell [975b_4857]


title: nasal_epithelial_cell [fae2_422f]


title: nasal_epithelial_cell [ca71_44ab]


title: nasal_epithelial_cell [26f6_4a54]


title: 0731-096, NGN2, HCort, 100nM

description:
P3C9
RawCountMatrix_NGN2_Study1.txt


title: 0731-096, NGN2, HCort, 0nM

description:
P3B9
RawCountMatrix_NGN2_Study1.txt


title: 0731-093, NGN2, HCort, 1000nM

description:
P3D4
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [f173_43c7]


title: nasal_epithelial_cell [fb23_478a]


title: nasal_epithelial_cell [e217_4562]


title: nasal_epithelial_cell [9b22_452c]


title: 0731-093, NGN2, HCort, 0nM

description:
P3B4
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [9854_46d3]


title: 0731-093, NGN2, HCort, 100nM

description:
P3C4
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [cdd3_4282]


title: 0731-098, NGN2, HCort, 100nM

description:
P1C9
RawCountMatrix_NGN2_Study1.txt


title: 0731-059, NGN2, HCort, 100nM

description:
P1F9
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [62a4_487e]


title: 0731-090, NGN2, HCort, 100nM

description:
P3C2
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [f947_445f]


title: nasal_epithelial_cell [5f28_4154]


title: nasal_epithelial_cell [e013_484e]


title: 0731-090, NGN2, HCort, 0nM

description:
P3B2
RawCountMatrix_NGN2_Study1.txt


title: 0731-096, NGN2, HCort, 1000nM

description:
P3D9
RawCountMatrix_NGN2_Study1.txt


title: 0731-086, NGN2, HCort, 1000nM

description:
P1D8
RawCountMatrix_NGN2_Study1.txt


title: 0731-086, NGN2, HCort, 0nM

description:
P1B8
RawCountMatrix_NGN2_Study1.txt


title: 0731-084, NGN2, HCort, 1000nM

description:
P1G8
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [80e0_4fa8]


title: nasal_epithelial_cell [d3d0_4867]


title: nasal_epithelial_cell [8207_47b9]


title: 0731-084, NGN2, HCort, 100nM

description:
P1F8
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [8fed_4797]


title: 0731-084, NGN2, HCort, 0nM

description:
P1E8
RawCountMatrix_NGN2_Study1.txt


title: 0731-059, NGN2, HCort, 1000nM

description:
P1G9
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [baf5_4b60]


title: 0731-059, NGN2, HCort, 0nM

description:
P1E9
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [42b8_4d34]


title: 0731-072, NGN2, HCort, 1000nM

description:
P1D7
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [819d_425d]


title: nasal_epithelial_cell [5a5e_4c64]


title: 0731-090, NGN2, HCort, 1000nM

description:
P3D2
RawCountMatrix_NGN2_Study1.txt


title: 0731-072, NGN2, HCort, 100nM

description:
P1C7
RawCountMatrix_NGN2_Study1.txt


title: 0731-074, NGN2, HCort, 100nM

description:
P1C6
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [ad65_430b]


title: nasal_epithelial_cell [57aa_42ac]


title: 0731-072, NGN2, HCort, 0nM

description:
P1B7
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [87f4_4ec7]


title: 0731-074, NGN2, HCort, 1000nM

description:
P1D6
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [e3fe_4b4e]


title: 0731-074, NGN2, HCort, 0nM

description:
P1B6
RawCountMatrix_NGN2_Study1.txt


title: 0731-086, NGN2, HCort, 100nM

description:
P1C8
RawCountMatrix_NGN2_Study1.txt


title: 0731-071, NGN2, HCort, 100nM

description:
P1C5
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [083e_47e3]


title: nasal_epithelial_cell [8b6b_436d]


title: 0731-071, NGN2, HCort, 0nM

description:
P1B5
RawCountMatrix_NGN2_Study1.txt


title: 0731-069, NGN2, HCort, 100nM

description:
P1C4
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [b0f0_4248]


title: 0731-069, NGN2, HCort, 1000nM

description:
P1D4
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [6229_4f52]


title: nasal_epithelial_cell [f408_46cc]


title: nasal_epithelial_cell [4e16_40e8]


title: 0731-067, NGN2, HCort, 1000nM

description:
P1G7
RawCountMatrix_NGN2_Study1.txt


title: 0731-067, NGN2, HCort, 100nM

description:
P1F7
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [f22c_4753]


title: 0731-066, NGN2, HCort, 1000nM

description:
P1D3
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [a280_4aa3]


title: nasal_epithelial_cell [dc7f_4ede]


title: 0731-067, NGN2, HCort, 0nM

description:
P1E7
RawCountMatrix_NGN2_Study1.txt


title: 0731-066, NGN2, HCort, 100nM

description:
P1C3
RawCountMatrix_NGN2_Study1.txt


title: 0731-071, NGN2, HCort, 1000nM

description:
P1D5
RawCountMatrix_NGN2_Study1.txt


title: nasal_epithelial_cell [65d9_411e]


title: nasal_epithelial_cell [28f6_409a]