title: SCID2 tumor

data_processing:
Reads were aligned to the mm10 reference genome using the Burrows–Wheeler Alignment tool version 0.7.17. Genome Analysis Toolkit (GATK) best practices were used for sorting, duplicate marking, and variant calling with the HaplotypeCaller. Variants were annotated using Ensemble-VEP version 90.9, and all possible 9-mer peptides that included a missense variant were identified using pVACtools version 1.0.8. MHC-I binding affinities (H-2-Db and H-2-Kb) were then predicted for each wild-type and corresponding mutant peptide with NetMHC 4.0. The following filtering steps were performed. Mutant peptides with predicted binding affinity > 500 nM were removed. Peptides from olfactory genes were excluded because they are prone to somatic mutations, are not highly expressed, and yield false-positives as cancer-associated genes. Mutations that corresponded to known polymorphic genes were also excluded. Peptides with low predicted agretopic indices, i.e., ratio of mutant to wild-type binding affinity < 4, were removed.
Genome_build: mm10
Supplementary_files_format_and_content: "neoantigen_predictions_GATK" file contains the list of neoantigens predected in all the samples. The file "neoantigen_predictions_filtered" lists the filtered putative neonatigens in the sample groups

source_name: mT3-2D sc SCID tumor

extract_protocol:
DNA was extracted using a DNeasy Blood and Tissue Kit (Qiagen, #69504).
Indexed, paired-end whole exome libraries were constructed from 1.0 µg gDNA using the Agilent SureSelect XT HS Mouse All Exon Library Kit.
Libraries were sequenced on an Illumina HiSeq 4000 using PE 150 bp (300 cycle) chemistry to a mean depth of 200x per sample.

treatment_protocol: mT3-2D cells were either grown in vitro or in SCID or WT mice

value: Immunodeficient

value: Cells grown in B6.CB17-Prkdcscid/SzJ (SCID) mice


title: SCID3 tumor

status: Public on Feb 26 2021

type: SRA

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Cells were grown in standard conditions and maintained in Dulbecco's Modified Eagle Medium (DMEM)(Fisher Scientific, # SH30022LS) supplemented with heat-inactivated fetal bovine serum (HI-FBS) to a final concentration of 10% and 2 mM L-glutamine

tag: cell type

value: Murine KPC cells

tag: original strain

tag: effect

tag: group (mouse strain)


title: SCID1 tumor


title: LW_2W_1_Spleen_H3K27ac

city: Wuhan

first: Shuhong

last: Zhao

address: No.1,Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

description: individual 1

data_processing:
The clean data was obtained after removing reads with adapter contamination or low quality.
ChIP reads and Input reads were aligned to susScr11.1 genome with BWA v0.7.15.
Low MAPQ reads (less than 25) and duplicated reads of mapped bam files were removed with SAMTools v1.2 and Picard v1.126. Then the filtered bam file of each sample were used to call peak.
The narrow peaks and the bedgraph files of -log10(p-value) signal tracks for each replicate were generated with MACS2 v2.1.0 (-g genome.size -p 0.01 --nomodel --shift 0 --extsize n --keep-dup 1 -B --SPMR). The “n” for –extsize parameter were automatically calculated by the ENCODE ChIP-seq pipeline which was downloaded from GitHub website (https://github.com/kundajelab/chipseq_pipeline).
The narrow peaks were filtered with the cutoff for P<1E-05. The bigwig files of signal tracks were generated with MACS2 v2.1.0 and bedGraphToBigWig command based on bedgraph files from the last step.
Genome_build: susScr11.1
Supplementary_files_format_and_content: Bigwig files of signal tracks and bed files of narrow peaks for each sample.

organism: Sus scrofa

source_name: Spleen

extract_protocol:
The frozen issues were ground to a fine powder with liquid nitrogen and fixed with 1% formaldehyde at room temperature for 20 min. Nuclear lysates were fragmented by Covaris S220 (Adaptive Focused Acoustics®). For each tissue, 300 μg of chromatin and 3 μg of H3K4me3 (Millipore-04-745) and H3K27ac (Abcam, ab4729) antibodies were used for ChIP-seq analysis.
ChIP–Seq libraries were constructed following Illumina protocols with minor modifications (Illumina, San Diego, CA), and sequenced on an illumina Hiseq X ten PE150 platform.

tag: breed

value: Large White

tag: tissue

value: spleen

tag: age

value: 2 weeks

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: LW_2W_2_Spleen_H3K27ac

description: individual 2


title: WT5 tumor

source_name: mT3-2D sc WT tumor

value: Immunocompetent

value: Cells grown in C57BL/6 (WT) mice


title: WT4 tumor


title: mT3-2D-GFP FACS cells from SCID tumors

library_source: transcriptomic

data_processing:
Raw reads were aligned to the mm9 reference genome with BWA and quantified into read counts with the annotation model (Partek E/M). All subsequent RNA-seq analyses were performed in R version 3.5.1. Read counts were variance-stabilized with the regularized log (rlog) function in the R/Bioconductor package DESeq2 version 1.20.0. Log fold-changes were computed on the rlog-transformed expression data, and genes with absolute log fold-changes greater than or equal to one were retained as significant.  FDR adjusted p-values below 0.05 were considered statistically significant.
Genome_build: mm9
Supplementary_files_format_and_content: Raw reads were aligned to the mm9 reference genome with BWA and the data is presented in the file "BWA-RAW10-FKPM-FOLD". Log fold-changes are presented in the file "FCResults"

molecule: total RNA

source_name: Murine KPC FACS tumor cells

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen). RNA concentration and quality were assessed using an Agilent BioAnalyzer (RINs >7). Equal amounts of RNA from each corresponding group were combined as one sample (1 WT sample, 1 SCID sample, and 1 cell line).
Indexed, paired-end sequencing libraries were prepared from 1.0 µg total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit (polyA cDNA synthesis) in the Genomics and Epigenomics Shared Resource (GESR) in the Lombardi Comprehensive Cancer Center at Georgetown University Medical Center.
Libraries were sequenced on an Illumina NextSeq550 using PE 75 bp (150 cycle) chemistry to a mean depth of 40M reads per sample

treatment_protocol: mT3-2D-GFP FACS cells were either grown in SCID mice or WT mice


title: LW_2W_2_Pancreas_H3K4me3

description: individual 2

source_name: Pancreas

value: pancreas

value: H3K4me3 (Millipore-04-745)


title: LW_2W_1_Pancreas_H3K4me3

description: individual 1


title: LW_2W_2_Thymus_H3K27ac

description: individual 2

source_name: Thymus

value: thymus


title: LW_2W_1_Thymus_H3K27ac

description: individual 1


title: SCID5 tumor


title: WT2 tumor


title: mT3-2D cell line

source_name: Murine KPC mT3-2D cell line

value: Basal level


title: DEX4

city: Shanghai

first: Yan

last: Lu

address: 180 Fenglin Road

department: Department of Endocrinology and Metabolism

institute: Zhongshan Hospital, Fudan University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by tophat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format: FPKM and count

source_name: mouse liver

extract_protocol:
Total RNA was harvested using Trizol reagent and used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

treatment_protocol: 10-week-old male C57BL/6J mice were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China).Dexamethasone (Sigma-Aldrich, St. Louis, MO, USA) or vehicle control (Saline) was administered daily at a dose of 1.0 mg/kg body weight by intraperitoneal injection for 14 days. Then, mice were sacrificed and livers were harvested for RNA extraction.

value: liver

tag: treatment

value: Dexamethasone treated

tag: strain

tag: Sex

value: male


title: LW_2W_1_Spleen_H3K4me3

description: individual 1


title: LW_2W_1_Thymus_H3K4me3

description: individual 1


title: DEX1


title: LW_2W_1_Lung_H3K4me3

description: individual 1

source_name: Lung

value: lung


title: SCID4 tumor

value: Immunodeficient


title: WT3 tumor


title: CON4

value: Vehicle control (Saline) treated


title: LW_2W_2_Pancreas_H3K27ac

description: individual 2


title: LW_2W_2_Spleen_H3K4me3

description: individual 2


title: LW_2W_2_Lung_H3K27ac

description: individual 2


title: LW_2W_2_Muscle_H3K4me3

description: individual 2

source_name: Muscle

value: muscle


title: WT1 tumor

source_name: mT3-2D subcutaneous (sc) WT tumor

value: Murine KPC cells


title: LW_2W_2_Muscle_H3K27ac

description: individual 2

value: Large White


title: DEX3


title: LW_2W_1_Muscle_H3K27ac

description: individual 1

value: 2 weeks


title: CON2


title: OT2-OVA5-3

city: Chicago

first: Jeffrey

last: Hubbell

state: Illinois

address: 5640 S. Ellis Ave

institute: University of Chicago

data_processing:
Fastq files were generated using bcl2fastq
kallisto (v0.46.1) was used to quantify abundances of transcripts from the fastq files.
Count tables were generated using R package tximport to import transcript-level estimates from kallisto output and summarize them at gene level
Genome_build: GRCm38.97
Supplementary_files_format_and_content: tab-delimited text file includes matrix table with raw gene count values for each sample

molecule: polyA RNA

source_name: CD4 T cells

extract_protocol:
Spleens and lymph nodes were pooled. OT-I and OT-i were sorted into Trizol using fluorescence activated cell sorting (FACS) and frozen at-80. RNA was extracted (Qiagen), and three mice were pooled per replicate.
Pooled samples were converted to cDNA using SmartSeq protocol

treatment_protocol: At 1 day post adoptive transfer of OTI and OTi cells, mice received either 1ug A8B1-OVA, the molar equivalent of OVA, a higher dose of OVA, or saline

value: OT-i

value: Higher dose OVA


title: CON3


title: OT2-OVA5-2


title: LW_2W_1_Lung_H3K27ac

description: individual 1

value: H3K27ac (Abcam, ab4729)


title: CON1


title: OT2-OVA0.5-3

value: Molar equivalent OVA


title: LW_2W_1_Liver_H3K4me3

description: individual 1

source_name: Liver

value: H3K4me3 (Millipore-04-745)


title: LW_2W_2_Kidney_H3K4me3

description: individual 2

source_name: Kidney

value: kidney


title: LW_2W_1_Pancreas_H3K27ac

description: individual 1

value: pancreas


title: OT2-OVA0.5-2


title: DEX2

value: liver


title: LW_2W_1_Liver_H3K27ac

description: individual 1


title: LW_2W_1_Kidney_H3K4me3

description: individual 1


title: OT2-saline-3

value: Saline


title: LW_2W_2_Kidney_H3K27ac

description: individual 2


title: LW_2W_2_Liver_H3K27ac

description: individual 2


title: LW_2W_1_Kidney_H3K27ac

description: individual 1


title: OT2-OVA0.5-1


title: LW_2W_1_Muscle_H3K4me3

description: individual 1


title: LW_2W_2_Liver_H3K4me3

description: individual 2


title: LW_2W_1_Heart_H3K4me3

description: individual 1

source_name: Heart

value: heart


title: LW_2W_2_Heart_H3K4me3

description: individual 2


title: LW_2W_2_Lung_H3K4me3

description: individual 2

value: lung


title: LW_2W_2_Heart_H3K27ac

description: individual 2


title: OT2-A8B1-2

value: 1ug A8B1-OVA


title: OT2-saline-1


title: OT2-saline-2


title: LW_2W_1_Heart_H3K27ac

description: individual 1


title: OT2-A8B1-1


title: LW_2W_2_Fat_H3K4me3

description: individual 2

source_name: Fat

value: fat


title: OT1-OVA5-3

source_name: CD8 T cells

value: OT-I


title: LW_2W_2_Duodenum_H3K4me3

description: individual 2

source_name: Duodenum

value: duodenum


title: OT1-OVA5-1


title: LW_2W_1_Fat_H3K27ac

description: individual 1

value: Large White


title: OT1-saline-3


title: LW_2W_1_Cerebrum_H3K4me3

description: individual 1

source_name: Cerebrum

value: cerebrum

value: 2 weeks


title: OT1-OVA0.5-3


title: LW_2W_2_Cerebrum_H3K4me3

description: individual 2


title: OT1-saline-1


title: LW_2W_2_Cerebrum_H3K27ac

description: individual 2


title: LW_2W_1_Duodenum_H3K4me3

description: individual 1


title: OT1-OVA5-2

value: Higher dose OVA


title: LW_2W_2_Fat_H3K27ac

description: individual 2

value: H3K27ac (Abcam, ab4729)


title: LW_2W_2_Duodenum_H3K27ac

description: individual 2


title: LW_2W_1_Duodenum_H3K27ac

description: individual 1


title: OT1-OVA0.5-1

value: Molar equivalent OVA


title: OT1-saline-2


title: OT1-A8B1-3


title: LW_2W_1_Fat_H3K4me3

description: individual 1

value: H3K4me3 (Millipore-04-745)


title: OT1-A8B1-2


title: OT1-OVA0.5-2


title: LW_2W_1_Cerebrum_H3K27ac

description: individual 1


title: OT1-A8B1-1


title: LW_2W_2_Cerebellum_H3K4me3

description: individual 2

source_name: Cerebellum

value: cerebellum


title: Homozygous A178D left ventricle rep 3

city: Oxford

first: Katja

last: Gehmlich

address: Level 6, West Wing, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: Univeristy of Oxford

data_processing:
Illumina's bcl2fastq v2.18.0.12 was used for basecalling and demultiplexing.
Alignment to GRCm38 was performed with HISAT 2.1.0.
Alignment files were sorted and indexed with SAMtools 1.6.
Normalized counts were generated using DESeq2_1.26.0.
Genome_build: GRCm38.
Supplementary_files_format_and_content: Comma separated values file with raw counts for all samples as a matrix.
Supplementary_files_format_and_content: Comma separated values file with DESeq2 normalized counts for all samples as a matrix.

source_name: Left ventricle

extract_protocol:
LV tissue samples were powdered by freezing with liquid nitrogen and pulverised in a Biopulviser. Trizol Reagent and RNA Clean & Concentrator (Zymogen) were used to extract and purify the RNA
RNA-seq libraries were prepared as stranded mRNA using TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. Barcoded cDNA fragments of poly(A)+ RNA were then sequenced on a HiSeq 4000 instrument from Illumina with 2 × 76 + 7 bp paired end reads.

tag: genotype

value: Homozygous A178D

value: Left ventricle


title: Homozygous A178D left ventricle rep 2


title: OT2-A8B1-3

value: OT-i


title: LW_2W_2_Cerebellum_H3K27ac

description: individual 2


title: LW_2W_1_Cerebellum_H3K4me3

description: individual 1


title: Homozygous A178D left ventricle rep 4

data_processing:
Illumina's bcl2fastq v2.18.0.12 was used for basecalling and demultiplexing
Alignment to GRCm38 was performed with HISAT 2.1.0.
Alignment files were sorted and indexed with SAMtools 1.6.
Normalized counts were generated using DESeq2_1.26.0.
Genome_build: GRCm38.
Supplementary_files_format_and_content: Comma separated values file with raw counts for all samples as a matrix.
Supplementary_files_format_and_content: Comma separated values file with DESeq2 normalized counts for all samples as a matrix.


title: LW_2W_1_Cerebellum_H3K27ac

description: individual 1


title: ES_2W_1_Thymus_H3K4me3

description: individual 1

value: Enshi Black

value: thymus


title: Homozygous A178D left ventricle rep 1


title: WT left ventricle rep 4

data_processing:
Illumina's bcl2fastq v2.18.0.12 was used for basecalling and demultiplexing.
Alignment to GRCm38 was performed with HISAT 2.1.0.
Alignment files were sorted and indexed with SAMtools 1.6
Normalized counts were generated using DESeq2_1.26.0.
Genome_build: GRCm38.
Supplementary_files_format_and_content: Comma separated values file with raw counts for all samples as a matrix.
Supplementary_files_format_and_content: Comma separated values file with DESeq2 normalized counts for all samples as a matrix.

value: WT


title: WT.BMDM.curdlan.replicate.B

city: Durham

first: Mari

middle: L

last: Shinohara

state: NC

department: Immunology

institute: Duke University School of Medicine

data_processing:
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadapt to rim low-quality bases and Illumina squencing adaptors from the 3' end of the reads. Only reads that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool.
Gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Genome_build: GRCm38v73
Supplementary_files_format_and_content: tab-delimited text file with normalized gene expression values from output of DESeq2 analysis

source_name: Bone-marrow derived macrophages (BMDM)

growth_protocol: Cells were cultured in complete RPMI containing 10% FCS, penicillin/streptomycin, L-glutaime, and b-mercaptoethanol

extract_protocol:
Cells were lysed in Qiagen buffer RLT and homogenised with the QIAshredder kit. Total RNA was extracted using a Qiagen RNeasy Mini kit.  On-column DNase digestion was performed using Qiagen RNase-free DNase Set. RNA integrity was determined using the Agilent 2100 Bioanalyzer
KAPA Stranded mRNA-seq kit was used for construction of sequencing libraries.

treatment_protocol: Cells were treated with curdlan (100μg/ml) or PBS ("unstimulated") for 3hrs

value: curdlan

tag: cell preparation protocol

value: Bone-marrow derived macrophages (BMDM) were generated by culturing total bone-marrow cells for 6 days with 20ng/ml recombinant mouse M-CSF.

value: Bone-marrow derived macrophages (BMDM)


title: WT left ventricle rep 3


title: WT.BMDM.unstimulated.replicate.B

value: unstimulated


title: ES_2W_1_Pancreas_H3K4me3

description: individual 1

source_name: Pancreas

value: pancreas


title: Card9.Neutrophil.curdlan.replicate.C

source_name: Bone-marrow neutrophils

value: Neutrophils were isolated from total bone-marrow by positive selection with anti-Ly6G-biotinylated antibody and streptavidin beads using MACS Cell Separation (Milltenyi Biotec)

value: Bone-marrow neutrophils


title: WT left ventricle rep 1


title: ES_2W_1_Spleen_H3K4me3

description: individual 1

source_name: Spleen

value: spleen

value: 2 weeks


title: Card9.Neutrophil.curdlan.replicate.A


title: ES_2W_2_Spleen_H3K4me3

description: individual 2

value: H3K4me3 (Millipore-04-745)


title: ES_2W_1_Thymus_H3K27ac

description: individual 1

source_name: Thymus

value: H3K27ac (Abcam, ab4729)


title: Card9.Neutrophil.curdlan.replicate.B


title: ES_2W_1_Muscle_H3K27ac

description: individual 1

source_name: Muscle

value: muscle


title: ES_2W_2_Spleen_H3K27ac

description: individual 2


title: WT.BMDM.curdlan.replicate.A


title: ES_2W_1_Spleen_H3K27ac

description: individual 1


title: WT.BMDM.unstimulated.replicate.A


title: ES_2W_2_Muscle_H3K4me3

description: individual 2


title: ES_2W_1_Pancreas_H3K27ac

description: individual 1


title: ES_2W_1_Muscle_H3K4me3

description: individual 1


title: Card9.Neutrophil.unstimulated.replicate.A


title: Card9.Neutrophil.unstimulated.replicate.C


title: ES_2W_1_Lung_H3K27ac

description: individual 1

source_name: Lung

value: lung


title: ES_2W_2_Muscle_H3K27ac

description: individual 2


title: Card9.Neutrophil.unstimulated.replicate.B


title: ES_2W_1_Lung_H3K4me3

description: individual 1


title: WT.Neutrophil.curdlan.replicate.C


title: WT.Neutrophil.curdlan.replicate.B


title: ES_2W_1_Liver_H3K4me3

description: individual 1

value: liver


title: ES_2W_2_Liver_H3K4me3

description: individual 2

value: Enshi Black


title: WT.Neutrophil.curdlan.replicate.A


title: WT.Neutrophil.unstimulated.replicate.C


title: ES_2W_1_Liver_H3K27ac

description: individual 1


title: 9M_Tmem43-Het6

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

data_processing:
Samples were trimmed using Trim Galore! and then aligned using HISAT2 to the mm10 genome.
Genes were quantified using FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts are provided in a tab delimited file.

source_name: Cardiac Myocyte

extract_protocol:
RNA-Sequencing (RNA-Seq):  Total RNA was isolated from cardiac myocytes from  4 months old Wildtype (WT), Myh6-Cre:Tmem43W/F (Tmem43-Het) and 9 months old  Wildtype (9M_WT) and Myh6-Cre:Tmem43W/F (9M_Tmem43-Het)   mice. RNA-seq was performed on the ribosome-depleted RNA.
Samples with a RNA Integrity Number (RIN) read out of more than 8 were used to prepare sequencing library using the Illumina TruSeq stranded total RNA library preparation kit. The samples were sequenced on the Illumina HiSeq 4000 instrument using the paired-end sequencing reagents to generate 100 base pair runs.

value: Myocytes

tag: passages

value: Freshly isolated

value: 9 Month old

tag: genotype/variation

value: Myh6-Cre:Tmem43W/F (Tmem43-Het)


title: ES_2W_1_Kidney_H3K4me3

description: individual 1

value: kidney


title: WT.Neutrophil.unstimulated.replicate.B

value: WT

value: unstimulated


title: WT.Neutrophil.unstimulated.replicate.A

value: Neutrophils were isolated from total bone-marrow by positive selection with anti-Ly6G-biotinylated antibody and streptavidin beads using MACS Cell Separation (Milltenyi Biotec)


title: ES_2W_1_Kidney_H3K27ac

description: individual 1


title: 9M_Tmem43-Het3


title: 9M_Tmem43-Het5


title: ES_2W_1_Heart_H3K4me3

description: individual 1

value: heart


title: 9M_Tmem43-Het4


title: ES_2W_2_Heart_H3K4me3

description: individual 2


title: 9M_Tmem43-Het2


title: ES_2W_2_Fat_H3K4me3

description: individual 2

value: fat


title: 9M_WT6

value: Wildtype (WT)


title: ES_2W_1_Fat_H3K4me3

description: individual 1

value: 2 weeks

value: H3K4me3 (Millipore-04-745)


title: 9M_WT5


title: ES_2W_2_Fat_H3K27ac

description: individual 2

value: H3K27ac (Abcam, ab4729)


title: ES_2W_2_Heart_H3K27ac

description: individual 2


title: 9M_WT4


title: 9M_Tmem43-Het1


title: ES_2W_1_Fat_H3K27ac

description: individual 1


title: ES_2W_1_Duodenum_H3K4me3

description: individual 1

value: duodenum


title: 9M_WT3


title: ES_2W_1_Duodenum_H3K27ac

description: individual 1


title: ES_2W_1_Cerebrum_H3K4me3

description: individual 1

value: cerebrum


title: ES_2W_2_Liver_H3K27ac

description: individual 2

source_name: Liver

value: Enshi Black

value: liver


title: 9M_WT1

value: Myocytes

value: Freshly isolated

value: 4 month old


title: 9M_WT2

value: 9 Month old


title: ES_2W_1_Cerebrum_H3K27ac

description: individual 1


title: ES_2W_1_Heart_H3K27ac

description: individual 1


title: 4M_Tmem43-Het5

value: Myh6-Cre:Tmem43W/F (Tmem43-Het)


title: 4M_Tmem43-Het4


title: ES_2W_1_Cerebellum_H3K27ac

description: individual 1

value: cerebellum


title: 4M_Tmem43-Het3


title: 4M_Tmem43-Het2


title: ES_2W_1_Cerebellum_H3K4me3

description: individual 1


title: 4M_WT5


title: 4M_Tmem43-Het1


title: Duroc_2W_2_Spleen_H3K4me3

description: individual 2

value: Duroc

value: spleen


title: Duroc_2W_1_Spleen_H3K4me3

description: individual 1


title: Duroc_2W_2_Spleen_H3K27ac

description: individual 2


title: 4M_WT4


title: Duroc_2W_1_Muscle_H3K4me3

description: individual 1

value: muscle


title: 4M_WT2

value: Wildtype (WT)


title: Duroc_2W_2_Muscle_H3K4me3

description: individual 2

value: 2 weeks


title: Duroc_2W_2_Muscle_H3K27ac

description: individual 2


title: Duroc_2W_1_Muscle_H3K27ac

description: individual 1


title: 4M_WT3


title: 4M_WT1


title: Duroc_2W_2_Liver_H3K4me3

description: individual 2

value: H3K4me3 (Millipore-04-745)


title: Duroc_2W_1_Liver_H3K27ac

description: individual 1

value: H3K27ac (Abcam, ab4729)


title: Duroc_2W_2_Liver_H3K27ac

description: individual 2


title: Duroc_2W_1_Liver_H3K4me3

description: individual 1


title: hyperloaded rep 6

city: Neustadt

first: Claudia

last: Klein

address: Höltystr. 10

country: Germany

institute: Friedrich-Loeffler-Institut, Institute of Farm Animal Genetics

description: Sample 12

data_processing:
Base calling and demultiplexing of transcriptome sequencing reads were performed using the Consensus Assessment of Sequence and Variance (CASAVA) v 1.6 and Novobarcode software.
Reads were mapped to the porcine genome Sscrofa11.1 using JMP Genomics 7.1, allowing two mismatches per read.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ventral annulus fibrosus

extract_protocol:
Annuli fibrosi were flash frozen and RNA was extracted using the RNeasy Fibrous Tissue Mini Kit. The TruSeq RNA sample Prep v2 LS protocol  was used for preparation of mRNA libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: repetitive in vivo manual loads on porcine intervertebral disc

value: hyperloaded

value: ventral annulus fibrosus


title: hyperloaded rep 4

description: Sample 10


title: hyperloaded rep 5

description: Sample 11


title: control rep 5

description: Sample 5

value: control


title: Duroc_2W_2_Heart_H3K4me3

description: individual 2

source_name: Heart

value: heart


title: hyperloaded rep 2

description: Sample 8


title: Duroc_2W_1_Heart_H3K4me3

description: individual 1


title: Duroc_2W_2_Fat_H3K4me3

description: individual 2

source_name: Fat

value: fat


title: control rep 3

description: Sample 3


title: Duroc_2W_1_Spleen_H3K27ac

description: individual 1


title: Duroc_2W_1_Heart_H3K27ac

description: individual 1


title: Duroc_2W_1_Fat_H3K4me3

description: individual 1


title: control rep 2

description: Sample 2


title: Duroc_2W_2_Fat_H3K27ac

description: individual 2


title: control rep 1

description: Sample 1


title: Duroc_2W_1_Fat_H3K27ac

description: individual 1


title: daf2_D9_3

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 97) by using STAR (v.2.7.0e). Aligned pairs on genes or transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
Differentially expressed genes (fold change > 1.5 and adjusted p value < 0.1) were identified by using DESeq2 (v.1.22.2). Wald test p values are adjusted for multiple testing using the procedure of BH.
Genome_build: WBcel235 (ce11)
Supplementary_files_format_and_content: txt files with read counts were generated by using RSEM (v.1.3.1)

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: Worms were grown on NGM plates as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.

extract_protocol:
RNA extraction was performed as previously described (Son et al., Nature Comm, 2017). Total RNA in the animals was extracted using RNAiso plus (Takara, Seta, Kyoto, Japan).
Libraries were constructed with TruSeq (unstranded) RNA Library Prep Kit v2 (Illumina, CA, USA) by Macrogen Inc. (Seoul, South Korea) following the manufacture’s instruction.

treatment_protocol: Synchronized wild-type(N2) and daf-2(e1370) animals were treated with 50 μM FUdR when worms reached L4 or young adult stage on OP50. At indicated ages (day 1 or day 9 adulthood), worms were harvested with M9 buffer, and washed 2-3 times, and frozen in liquid nitrogen. Three biological repeats of the samples were used for all conditions.

tag: development stage

value: adult at day9

value: Whole body


title: LW_2W_2_Thymus_RNA

description: individual 2

data_processing:
The adapter was firstly removed from the raw data and the clean data was obtained after removing low quality reads.
The reads were mapped to the susScr11.1 reference genome using TopHat (v2.1.1). The transcript assembly of each sample was separately performed by using BAM file as input file for Cufflinks (v2.2.1). The resulting individual transcript assemblies were further merged to a single transcript assembly using Cuffcompare.
To identify lncRNA of the pig genome, the transcripts from the single transcript assembly were filtered as the following steps: (i) the identified transcripts which must be with class code “x”, “i” or “.” in at least two samples, and do not overlap with any known transcripts or with class code “u” ; (ii) transcripts with length ≥ 200, exon number ≥ 2; (iii) transcripts with FPKM ≥ 1 and reads ≥ 5 in at least 2 replicates; (iv) the identified transcripts without potential coding regions which were filtered using CNCI and CPC2.
For identification of other types of novel transcripts, the transcripts which were assembled in two replicates in the transcript assembly file of each sample were selected firstly. Then the filtered transcript assembly files were merged by Cuffmerge. Next, Cuffcompare was applied again to integrate the merged transcript assembly file and the lncRNA gtf file. This new gtf was used to calculate transcript expression levels (FPKM value) by RSEM (v1.3.0). The last step was to filter the transcripts to identify novel transcripts by the following criteria: (i) transcripts on the same strand of known transcripts and exon overlapped with any known transcripts were omitted; (ii) lncRNAs which were identified before were removed; (iii) transcripts with class code “x”, “i” and “u” and with FPKM ≥ 5 at least in any 2 replicates.
Finally, The gtf file of lncRNA and novel transcripts was integrated with the annotation file from UCSC for calculating gene expression level(TPM value) by RSEM.
Genome_build: susScr11.1
Supplementary_files_format_and_content: Bed file of each Sample include TPM (Transcripts Per Million) values calculated by RSEM.

extract_protocol:
Total RNA was extracted from each tissue sample using TRIzol reagent, and RNA was further purified by removing the rRNA. These rRNA depleted RNA samples were used for the construction of sequencing libraries.
The strand-specific RNA-seq libraries using the protocol provided by Ilumina. The libraries were sequenced using the illumina Hiseq X ten PE150 platform.

value: Large White

value: thymus


title: LW_2W_1_Thymus_RNA

description: individual 1


title: LW_2W_2_Lung_RNA

description: individual 2

value: lung


title: daf2_D9_1


title: daf2_D1_3

value: adult at day1


title: daf2_D9_2


title: daf2_D1_2


title: Duroc_2W_2_Heart_H3K27ac

description: individual 2

value: Duroc


title: control rep 4

description: Sample 4


title: LW_2W_2_Kidney_RNA

description: individual 2

source_name: Kidney

value: kidney


title: daf2_D1_1


title: LW_2W_1_Kidney_RNA

description: individual 1


title: WT_D1_3

value: wild type


title: LW_2W_2_Cerebrum_RNA

description: individual 2

source_name: Cerebrum

value: cerebrum

value: 2 weeks


title: WT_D1_2


title: LW_2W_2_Duodenum_RNA

description: individual 2

source_name: Duodenum

value: duodenum


title: LW_2W_2_Cerebellum_RNA

description: individual 2

source_name: Cerebellum

value: cerebellum


title: WT_D9_1


title: LW_2W_1_Duodenum_RNA

description: individual 1


title: WT_D1_1


title: WT_D9_3


title: LW_2W_1_Cerebellum_RNA

description: individual 1


title: Fast-2

first: Ling

last: Wu

address: 639 Zhizaoju Road, Huangpu District, Shanghai.

department: Department of Assisted Reproduction

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by tophat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: mouse liver

growth_protocol: 10-week-old male C57BL/6J mice were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China). Mice were fed ad libitum or fasted for 16 hour. Then, mice were sacrificed and livers were harvested for RNA extraction.

value: fasted for 16 hour


title: LW_2W_2_Spleen_RNA

description: individual 2

value: spleen


title: Fast-3


title: LW_2W_1_Lung_RNA

description: individual 1


title: Fast-1


title: Fed-3

value: Fed ad libitum


title: Fed-1


title: LW_2W_2_Muscle_RNA

description: individual 2

value: muscle


title: Smad3+FoxL2mut+Foxo13A_5A

city: La Jolla

first: Christian

last: Secchi

state: CA

address: 9500 Gilman Drive, Biomedical Science Building, Room 5045

institute: University of California, San Diego

description:
FoxL2mut_Foxo13A_5A
Lipofectamine Transfection
raw_counts_salmon_hg38.csv

data_processing:
Transcript abundance for each sample was quantified using salmon (1.1.0) with default parameters and using hg38 as reference genome.
Gene-level quantification were obtained from the salmon transcript abundance files using the R package tximport with the gencode_v33 annotations and a matrix was created using DESeqDataSetFromTximport from the DESeq2 package.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.quant.sf: Abundance measurements files generated by salmon in each sample for each transcript.
Supplementary_files_format_and_content: raw_counts_salmon_hg38.csv: Comma-separated matrix table with raw gene counts for every gene and every sample.

organism: Homo sapiens

source_name: HGrC1 cell line

growth_protocol: HGrC1 cells were cultured in a standard incubator at 37°C in DMEM-F12 medium (catalog #12400-024, Thermo Fisher Scientific, Waltham, MA) complemented with antibiotics (penicillin and streptomycin) and 10% FBS (#F6178, Sigma-Aldrich). HGrC1 cells at passage 14 were used for all the experiments in this study.

extract_protocol:
After 4 hours transfection and additional culture for 24 hours in serum free DMEM-F12, HGrC1 cells were lysed using TRIzol reagent (catalog #15596026, Thermo Fisher Scientific) and RNA was extracted with Direct-zol RNA MiniPrep kit (#R2052, Zymo Research, Irvine, CA). RNA Quality control was performed by Agilent TapeStation.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina, catalog #20020595) and sequenced using an Illumina HiSeq4000 Platform using 75-bp single-end reads, to an average of 22.9 +/- 3.4 million reads per sample.

treatment_protocol: HGrC1 cells seeded into 6-well tissue culture plates (1 x 10^6 cells/well). Medium was replaced after 24 hours with serum-free DMEM-F12 (complemented with antibiotics), and transfection was performed using the above described plasmids for 4 hours with Lipofectamine 3000 reagents (catalog #L3000008, Thermo Fisher Scientific) following manufacturer’s procedures. After 4h, the medium was replaced with new serum free DMEM-F12 and transfected cells were cultured at 37°C for 24 hours.

tag: cell line

value: Granulosa Cells

tag: transfected plasmids

value: Smad3 - FoxL2C134W - Foxo13A


title: Fed-2


title: PBMC WT SuHx 56d 3

city: Kishibe-Shinmachi,Suita

first: Takeshi

last: Masaki

state: Osaka

department: Vascular Physiology

country: Japan

institute: National Cerebral and Cardiovascular Center

data_processing:
A minimum 25M reads per library with 75 bp paired-ends reads were generated per sample.
Quality control of the resulting sequence data was performed using FastQC
Trimmed and filtered reads were aligned to rat genome version rn6 reference
Genome_build: Rn6
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

organism: Rattus norvegicus

source_name: Peripheral Blood

extract_protocol:
Cells and tissues were lysed in Trizol and RNA was extracted using PureLink RNA Mini Kit (Thermo Fisher Scientific,) and PureLink DNase (Thermo Fisher Scientific,) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral bloob mononucler cells (PBMC)

value: Sprague-Dawley

value: Wild type

value: Sugen-Hypoxia

tag: days


title: Smad3+FoxL2wt+Foxo13A_4C

description:
FoxL2wt_Foxo13A_4C
Lipofectamine Transfection
raw_counts_salmon_hg38.csv

tag: cell type

value: Smad3 - FoxL2wt - Foxo13A


title: Smad3+FoxL2mut+Foxo13A_5C

description:
FoxL2mut_Foxo13A_5C
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: LW_2W_1_Cerebrum_RNA

description: individual 1

value: Large White


title: LW_2W_1_Muscle_RNA

description: individual 1


title: WT_D9_2

value: wild type

value: adult at day9

value: Whole body


title: PBMC WT SuHx 56d 1


title: Smad3+FoxL2wt+Foxo13A_4B

description:
FoxL2wt_Foxo13A_4B
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: LW_2W_2_Liver_RNA

description: individual 2

value: liver

value: 2 weeks


title: PBMC WT SuHx 28d 1


title: Smad3+FoxL2wt+Foxo13A_4A

description:
FoxL2wt_Foxo13A_4A
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: PBMC WT SuHx 28d 3


title: PBMC WT SuHx 28d 2


title: LW_2W_1_Liver_RNA

description: individual 1


title: PBMC normoxia 3

value: Normoxia


title: Smad3+FoxL2mut+Foxo13A_5B

description:
FoxL2mut_Foxo13A_5B
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: Smad3+FoxL2mut_3C

description:
FoxL2mut_3C
Lipofectamine Transfection
raw_counts_salmon_hg38.csv

value: Smad3 - FoxL2C134W


title: Smad3+FoxL2mut_3B

description:
FoxL2mut_3B
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: LW_2W_1_Spleen_RNA

description: individual 1

source_name: Spleen

value: spleen


title: PBMC normoxia 1


title: Total Lung Tissue AhrKO SuHx 56d 3

value: Total Lung

value: Ahr-KO


title: LW_2W_2_Heart_RNA

description: individual 2

value: heart


title: Total Lung Tissue AhrKO SuHx 56d 2


title: PBMC WT SuHx 56d 2

value: Peripheral bloob mononucler cells (PBMC)


title: Total Lung Tissue WT SuHx 56d 3

value: Sprague-Dawley


title: Total Lung Tissue AhrKO SuHx 56d 1


title: LW_2W_1_Fat_RNA

description: individual 1

value: fat


title: LW_2W_2_Fat_RNA

description: individual 2


title: Total Lung Tissue WT SuHx 56d 2

value: Wild type

value: Sugen-Hypoxia


title: Smad3+FoxL2wt_2C

description:
FoxL2wt_2C
Lipofectamine Transfection
raw_counts_salmon_hg38.csv

value: Granulosa Cells

value: Smad3 - FoxL2wt


title: ES_2W_2_Spleen_RNA

description: individual 2

value: Enshi Black


title: Total Lung Tissue WT SuHx 56d 1


title: Smad3+FoxL2wt_2B

description:
FoxL2wt_2B
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: PBMC normoxia 2


title: Smad3+FoxL2wt_2A

description:
FoxL2wt_2A
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: ECs  normoxia3

value: Endothelial cells (ECs)


title: ECs  normoxia1


title: ES_2W_1_Spleen_RNA

description: individual 1


title: ECs  normoxia2


title: Total Lung Tissue AhrKO SuHx 4d 2


title: ES_2W_2_Muscle_RNA

description: individual 2

value: muscle


title: Total Lung Tissue AhrKO SuHx 4d 3


title: Smad3+FoxL2mut_3A

description:
FoxL2mut_3A
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: Total Lung Tissue AhrKO SuHx 4d 1


title: LW_2W_1_Heart_RNA

description: individual 1

value: Large White

value: 2 weeks


title: Total Lung Tissue WT SuHx 4d 3


title: ES_2W_1_Muscle_RNA

description: individual 1


title: Total Lung Tissue WT SuHx 4d 2


title: Vectors_1A

description:
Vectors_1A
Lipofectamine Transfection
raw_counts_salmon_hg38.csv

value: Vectors


title: Total Lung Tissue normoxia3

value: Normoxia


title: Total Lung Tissue normoxia2

value: Total Lung


title: Total Lung Tissue normoxia1


title: input

description: pooled lung samples from 3 rats

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings.
Only reads that pass illumina's pulify filter,  align with no more than 2 mismatches, and map uniquely to the rn6 genome are used in the subsequent analysis.
Peaks are called using  either MACS or SICER algorithms. MACS default cutoff is p value e-7 for narrow peaks and e^-1 for broad peaks,
and SICER default cutoff is FDR e^-10 with gap parameter of 600bp.
Genome_build: rn6
Supplementary_files_format_and_content: bw file

extract_protocol:
ChIP-seq was conducted using pooled  lung samples from SuHx rats at day4 , SuHx rats at 8weeks or normoxia control rats(day0) (3rats per group). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-AHR antibody(BML-SA210-0100, Enzo Life Sciences).
Libraries were prepared according to Illumina's instructions.


title: Sugen-Hypoxia 4 days

description: pooled lung samples from 3 rats

value: BML-SA210-0100, Enzo Life Sciences


title: Sugen-Hypoxia 8 wks

description: pooled lung samples from 3 rats


title: Vectors_1C

description:
Vectors_1C
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: ES_2W_1_Heart_RNA

description: individual 1

value: heart


title: normoxia

description: pooled lung samples from 3 rats


title: Vectors_1B

description:
Vectors_1B
Lipofectamine Transfection
raw_counts_salmon_hg38.csv


title: ES_2W_2_Fat_RNA

description: individual 2


title: ES_2W_2_Liver_RNA

description: individual 2

value: liver


title: ES_2W_1_Fat_RNA

description: individual 1


title: Total Lung Tissue WT SuHx 4d 1

value: Sprague-Dawley


title: ES_2W_1_Liver_RNA

description: individual 1


title: CLIP RNA From HeLa/Flag empty

city: St. Louis

first: Nima

last: Mosammaparast

state: MO

address: 660 S Euclid Ave

department: Pathology & Immunology

institute: Washington University in St. Louis

description:
Sample 1: CLIP RNA from HeLa/Flag empty vector cells (it serves as the background to remove false positivies and to generate other processed files.)
Processed data file(s): HeLa_rep1rep2_Overlap_All.xlsx

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads (length shorter than 20). Remaining reads were aligned to the human genome (hg19) using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) allowing at most three mismatches. The generated .bam files were sorted using Samtools and then processed with PIPE-CLIP tool to generate candidate cross-linking regions1. For the detailed parameters in PIPE-CLIP, CLIP type was set as 0, with minimum match length as 20 and maximum mismatch count as 3. PCR duplicates were removed according to sequence. Both FDR cutoffs for significant mutations and enriched clusters were set as 0.01. The pipeline was performed in both ‘input’ sample (transfected with empty vector) and ‘treated’ samples (overexpressed with RNF113A). All candidate cross-linking regions that appear in both ‘input’ and ‘treated’ cases were removed from the ‘treated’ samples, which serve as the background signal. The CLIP candidate cross-linking regions shared by two replicates of ‘treated’ sample were used for downstream analysis. For the CLIP clusters annotated to be within protein coding areas, their location relationship with 5’ splice site and 3’ splice site was further compared and studied by direct visualization through IGV software (https://software.broadinstitute.org/software/igv/). If one CLIP cluster of candidate cross-linking regions locates within +/- 50bp window around a 5’ splice site or a 3’ splice site, we regard this cluster as a 5’SS or 3’SS CLIP cluster.      1 Beibei Chen, Jonghyun Yun, Min Soo Kim, Joshua T Mendell, Yang Xie. PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. Genome Biol. 2014, 15(1):R18.
Supplementary_files_format_and_content: csv and xlsx files contain the CLIP-Seq read mapping and overlapping peaks between replicates

source_name: HeLa (ATCC CCL-2)

growth_protocol: Cells were grown in DMEM +10%FBS + Pen/Strep

extract_protocol:
Lysates were treated with Rnase T1, and immunoprecipitated with anti-Flag
NEB Next Small RNA Library Pret Set for Illumina Sequencing

treatment_protocol: Cells were treated with 5mM MMS and UV crosslinked

value: HeLa

tag: cell line origin

value: cervical adenocarcinoma

value: Wildtype

value: Treated with 5mM MMS

tag: ip antibody

value: anti-Flag


title: mRNA reference (Flag-RNF113A)

description:
Sample 4: mRNA isolated from HeLa/Flag-RNF113A cells, confirming the expressed mRNAs/genes when overexpressing RNF113A.
Processed data file(s): HeLa_rep1rep2_Overlap_Protein-coding.xlsx


title: CLIP RNA From HeLa/Flag RNF113A-1 (Sample 2, replicate 1)

description:
Sample 2: CLIP RNA from HeLa/Flag-RNF113A cells, rep1, misincorporation clusters
Processed data file(s): HeLa_CLIP2_Unique_Above20.csv, HeLa_CLIP_rep1_All.csv, HeLa_rep1rep2_Overlap_All.xlsx


title: CLIP RNA From HeLa/Flag RNF113A-2 (Sample 3, replicate 2)

description:
Sample 3: CLIP RNA from HeLa/Flag-RNF113A cells, rep2, misincorporation clusters
Processed data file(s): HeLa_CLIP3_Unique_Above20.csv, HeLa_CLIP_rep2_All.csv, HeLa_rep1rep2_Overlap_All.xlsx


title: MS_2W_2_Spleen_RNA

description: individual 2

tag: breed

value: Meishan

tag: tissue

value: spleen


title: ES_2W_2_Heart_RNA

description: individual 2

value: Enshi Black

tag: age


title: MS_2W_1_Spleen_RNA

description: individual 1


title: Normal human nasal epithelial cells (S. epidermidis)

city: Seoul

first: Hyun Jik

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of otorhinolaryngology

institute: Seoul National University

data_processing:
10x Genomics standard sequence protocol by trimming the barcode and unique molecular identifier (UMI) end to 26 bp and the mRNA end to 98 bp.
the FASTQ files were aligned to the human reference genome (GRCh38)
we applied Cell Ranger for preliminary data analysis and generated a file that contained a barcode table, a gene table, and a gene expression matrix. We used the WinSeurat v2.1 (Ebiogen Inc., Seoul, Korea) based on Seurat version 3 for QC, analysis, and exploration of single-cell RNA-seq data
Data mining and graphic visualization were performed using ExDEGA (Ebiogen Inc., Seoul, Korea)
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Normal human nasal epithelial cells

growth_protocol: passage-2 NHNE cells (1 x 10^5 cells/culture) were seeded in 0.25 ml of culture medium on Transwell-Clear culture inserts. Cells were cultured in a 1:1 mixture of basal epithelial growth medium and DMEM. Cultures were grown while submerged for the ﬁrst 9 days. The culture medium was changed on Day 1 and every other day thereafter. An air–liquid interface (ALI) was created on Day 9 by removing the apical medium and feeding the cultures from the basal compartment only. The culture medium was changed daily after establishment of the ALI.

extract_protocol:
Total RNA was isolated from NHNE cells which were inoculated with S. epidermidis at day one using TRIzol. cDNA was synthesized from 3 μg of RNA with random hexamer primers using Moloney murine leukemia virus reverse transcriptase.
Library construction was performed using 10X Chromium Single Cell 3’ reagent kits v3.1. Samples were sequenced using the Illumina NovaSeq 6000 platform, and preliminary sequencing results were converted to FASTQ files using the Cell Ranger pipeline.
Single cell RNA-seq

treatment_protocol: NHNE cells were inoculated with S. epidermidis (multiplicity of infection 0.25) for 24 hours.

value: cultured nasal epithelial cells

value: Human

tag: treatment

value: S. epidermidis inoculation


title: MS_2W_2_Muscle_RNA

description: individual 2

source_name: Muscle

value: muscle

value: 2 weeks


title: GEP profile of BM-MSC HD4 primed with SUDHL4 cells

type: RNA

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

description:
Initial lab ID: T4SUD
mRNA

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Human U133Plus2 arrays.

scan_protocol: GeneChips were scanned using the GeneChip Scanner Affymetrix 3000.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed by using the RMA algorithm. Dataset was then filtered by eliminating PS with no expression in all dataset and/or no gene symbol annotations.

label: biotin

source_name: Stromal cells from HD primed with SUDHL4 cells

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA).

growth_protocol: Stromal cells were obtained as previously described (Guilloton F, Blood 2012).

extract_protocol: RNA extraction was performed using RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Stromal cells were expanded from lymph node mononuclear cells in aphaMEM+10%FBS+FGF2 (1ng/mL).

tag: diagnosis

value: Healthy

value: BM-MSC

value: Primed with SUDHL4 cell line


title: GEP profile of BM-MSC HD6 primed with FL4 B cells

description:
Initial lab ID: T6FL4ns
mRNA

source_name: Stromal cells from HD primed with FL cells

value: Primed with primary follicular lymphoma B cells


title: GEP profile of BM-MSC HD6 primed with FL3 B cells

description:
Initial lab ID: T6FL3ns
mRNA


title: GEP profile of BM-MSC HD5 primed with SUDHL4 cells

description:
Initial lab ID: T5SUD
mRNA


title: H9 human embryonic stem cells line (WA09) passage 200s [P3-1]

city: Busan

first: Haeseung

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

institute: Pusan National University

data_processing:
Quality check and subsequent trimming (removal of adapters and low-quality bases) of raw RNA-seq fastq files were conducted via FastQC and TrimGalore, respectively (https://www.bioinformatics.babraham.ac.uk/).
The reads were mapped to the GRCh38 reference genome using the STAR aligner (v2.7.3a).
Transcripts per million (TPM) and expected read counts were calculated using RSEM v.1.3.3. with assembly GRCh38.84.
Genome_build: Genome Reference Consortium Human Build 38 (hg38)
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcript_id, gene_length, effective_length, expected_count, TPM, and FPKM values for each Sample.

source_name: human blastocysts

growth_protocol: hESCs (H9; Wicell Research Institute) were maintained in mTeSR1 medium (StemCell Technologies) on plates coated with Matrigel (Corning, #354277) diluted at 1:80 in hESC basal medium (DMEM/F12 supplemented with 1% non-essential amino acids, 0.1% -mercaptoethanol, and 0.1% gentamycin, Gibco) for feeder-free conditions. The medium was replaced every day up to passaging, and the cells were enzymatically dissociated using a dispase solution (Gibco, #17105041).

extract_protocol:
Total RNA was isolated using Easy-blue reagent (Intron, #17061) according to the manufacturer’s instructions.
To construct a sequencing library, we used a TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Briefly, the steps for the strand-specific protocol are as follows: first strand cDNA synthesis; second strand synthesis using dUTPs instead of dTTPs; end repair, A-tailing, and adaptor ligation; and PCR amplification.

tag: developmental stage

value: passage 200s


title: H9 human embryonic stem cells line (WA09) passage 300s [P4-2 ]

value: passage 300s


title: MS_2W_1_Muscle_RNA

description: individual 1


title: H9 human embryonic stem cells line (WA09) passage 300s [P4-1]


title: GEP profile of BM-MSC HD5 primed with FL1 B cells

description:
Initial lab ID: T5FL1ns
mRNA


title: GEP profile of BM-MSC HD4 primed with FL1 B cells

description:
Initial lab ID: T4FL1ns
mRNA


title: H9 human embryonic stem cells line (WA09) passage 200s [P3-2]


title: H9 human embryonic stem cells line (WA09) passage 100s [P2-2]

value: passage 100s


title: H9 human embryonic stem cells line (WA09) passage 100s [P2-1]


title: H9 human embryonic stem cells line (WA09) passage 40s [P1-2]

value: passage 40s


title: Normal human nasal epithelial cells (control)

tag: strain

value: untreated


title: H9 human embryonic stem cells line (WA09) passage 40s [P1-1]


title: MS_2W_2_Liver_RNA

description: individual 2

source_name: Liver

value: Meishan

value: liver


title: MS_2W_2_Heart_RNA

description: individual 2

source_name: Heart

value: heart


title: MS_2W_1_Liver_RNA

description: individual 1


title: Illumina_WT-24-replicate 4_short_read_reanalyzed

city: Middleton

first: Allan

last: Brasier

state: WI

address: 715 Highland

institute: university of Wissconsin

description:
Sample 20
GSM4915889

data_processing:
ccs <input.subreads.bam> --noPolish --min-rq 0.9 <ccs output> (CCS Version: 4.2.0)
lima --isoseq --peek-guess --dump-clips --no-pbi <input.ccs.bam> <clonetech_primers> <demux output> (lima Version: 1.10.0)
isoseq3 refine <input.demux.bam> <clonetech_primers> <flnc output> (Isoseq3 Version: 3.3.0)
dataset create --type TranscriptSet <all flnc output> <single merged.flnc output> (SMRTLink v9.0.0 command line)
isoseq3 polish <merged.flnc> <polished flnc output>  (Isoseq3 Version: 3.3.0)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: PacBio samples: fastq of polished flnc transcripts (available in tar archive on series record).
Supplementary_files_format_and_content: master_count_table.xlsx: read counts of re-analyzed samples aligned to PacBio data. GTF file included.

source_name: hSAEC wild type

growth_protocol: hSAECs were grown in SAGM small airway epithelial cell growth medium (Lonza, cc-3118).

extract_protocol:
Cells were harvested for RNA isolation using RNeasy kit with on-column DNase digestion (Qiagen).
Iso-Seq SMRTbell libraries containing circular templates were generated using NEBNext Single Cell RT Enzyme Mix and recommendations by the manufacturers recommendations for long-read transcripts using the Iso-Seq™ Express Template (PN: 101-901-700) and indicated quality control steps.  Sequencing was performed using the Pac Bio Sequel II system with SMRT Cell 8M.

treatment_protocol: The human RSV Long strain was grown in Hep-2 cells and prepared by sucrose cushion

value: small airway epithelial cells

tag: genotype

value: WT

value: infected (24 h)


title: Illumina_WT-24-replicate 3_short_read_reanalyzed

description:
Sample 19
GSM4915888


title: GEP profile of BM-MSC HD1 primed with FL3 B cells

description:
Initial lab ID: T1FL3ns
mRNA


title: MM-5610-31: Wh Tum Rapa 3

city: Nashville

middle: C

last: Rathmell

state: Tennessee

address: 1161 21st Ave S

department: PMI

institute: Vanderbilt University Medical Center

hyb_protocol: According to manufacturer's instructions

data_processing: Raw transcript counts of 768 genes were analyzed using NACHOv1.0.17, an R package for parsing, visualization, quality control, and normalization designed for NanoString nCounter data. While parsing raw transcript counts, manufacturer-designated housekeeping genes were used to normalize between samples: Abcf1, Agk, Cog7, Dhx16, Dnajc14, Edc3, Fcf1, G6Pdx, Mrps5, Nrde2, Oaz1, Polr2a, Sap130, Shda, Stk11ip, Tbc1d10b, Tbp, Tlk2, Ubb, Usp39. Sample quality was evaluated based on normal ranges provided by the manufacture for 1) binding density (0.1-2.25), 2) Field of View (<75), 3) Positive Control Linearity (<0.95), and 4) limit of detection (<2). Samples were excluded if they failed any of the four conditions. The third replicates of M-MDSC Rapa and CD4 Rapa were excluded as outliers for abnormal positive control linearity and limit of detection, respectively. Normalization was performed using geometric means based on housing genes, positive, and negative controls.

source_name: Whole tumor single cell suspension, rapamycin treated mouse, replicate 3

growth_protocol: 1 million MC38 cells were injected subcutaneously on day 0 into the flanks of male 6-12wk old wild-type C57BL/6J mice (000664 Jackson Laboratory). Mice were euthanized at day 14 of tumor growth after 4 days of treatment with vehicle or rapamycin.

extract_protocol: Tumors were chopped, mechanically dissociated on the Miltenyi gentleMACS™ Octo Dissociator with Heaters (setting implant tumor one) and digested in 435U/mL deoxyribonuclease I (Sigma-Aldrich, D5025) and 218U/mL collagenase (Sigma-Alrich, C2674) at 37°C for 30min. After enzyme treatment, tumors were passed through a 70μm filter and ACK-lysed. Cells were resuspended in MACS buffer (PBS +2% FBS +2mM EDTA) and counted using trypan blue with the TC20™ Automated Cell Counter (Bio-Rad). CD45 negative and CD45 positive cells were isolated using CD45+ positive selection microbeads (Miltenyi 130-110-618), stained for surface markers and viability, and sorted on a BD FACSAria III cell sorter. RNA was isolated from tumor cell populations and unstained whole tumor single cell suspensions using the Quick-RNA™ Microprep Kit (Zymo R1050) according to manufacturer’s instructions.

treatment_protocol: On days 10, 11, 12, and 13, tumor-bearing mice were intraperitoneally injected with vehicle or rapamycin 2mg/mL.

value: Rapamycin

tag: cell population

value: Whole tumor single cell suspension


title: MS_2W_1_Heart_RNA

institute: Huazhong Agricultural University

description: individual 1

value: 2 weeks


title: GEP profile of untreated BM-MSC from HD6

description:
Initial lab ID: T6p2
mRNA

source_name: Untreated stromal cells from HD

value: Healthy

value: BM-MSC

value: Untreated


title: MS_2W_2_Fat_RNA

description: individual 2

source_name: Fat

value: fat


title: Illumina_WT-0-replicate 4_short_read_reanalyzed

description:
Sample 4
GSM4915881

value: uninfected (0h)


title: Illumina_WT-24-replicate 1_short_read_reanalyzed

description:
Sample 17
GSM4915886


title: GEP profile of untreated BM-MSC from HD3

description:
Initial lab ID: T3p2
mRNA


title: GEP profile of untreated BM-MSC from HD5

description:
Initial lab ID: T5p2
mRNA


title: GEP profile of untreated BM-MSC from HD2

description:
Initial lab ID: T2p2
mRNA


title: MS_2W_1_Fat_RNA

description: individual 1


title: Illumina_WT-0-replicate 3_short_read_reanalyzed

description:
Sample 3
GSM4915880


title: GEP profile of untreated BM-MSC from HD4

description:
Initial lab ID: T4p2
mRNA


title: MM-5610-19: Wh Tum Rapa 2

scan_protocol: According to manufacturer's instructions

source_name: Whole tumor single cell suspension, rapamycin treated mouse, replicate 2


title: Duroc_2W_2_Spleen_RNA

description: individual 2

value: Duroc

value: spleen


title: MM-5610-25: Wh Tum Veh 3

source_name: Whole tumor single cell suspension, vehicle treated mouse, replicate 3

value: Vehicle


title: MM-5610-07: Wh Tum Rapa 1

source_name: Whole tumor single cell suspension, rapamycin treated mouse, replicate 1


title: MM-5610-13: Wh Tum Veh 2

source_name: Whole tumor single cell suspension, vehicle treated mouse, replicate 2


title: Duroc_2W_1_Spleen_RNA

description: individual 1

source_name: Spleen


title: Illumina_WT-0-replicate 2_short_read_reanalyzed

description:
Sample 2
GSM4915879


title: Illumina_WT-24-replicate 2_short_read_reanalyzed

description:
Sample 18
GSM4915887


title: MM-5610-01: Wh Tum Veh 1

source_name: Whole tumor single cell suspension, vehicle treated mouse, replicate 1


title: Duroc_2W_2_Muscle_RNA

description: individual 2

value: muscle


title: Duroc_2W_1_Liver_RNA

description: individual 1

value: liver


title: Duroc_2W_2_Heart_RNA

description: individual 2

value: heart


title: CUcovID_0007

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

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

description:
globin-depleted, poly(A)+ RNA from whole blood
Counts_for_GEO.txt.gz
FPKMs_for_GEO.txt.gz

data_processing:
Signal processing, base-calling, and quality scoring was 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.
Genome_build: 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).

source_name: whole blood

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Universal Plus mRNA-Seq with NuQuant, Human Globin AnyDeplete (Tecan). Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the Genomics Shared Resource at the University of Colorado Anschutz Medical Campus.

value: whole blood

tag: Sex

value: Male

tag: sars-cov2 status

value: Positive

tag: library type

value: strand-specific


title: CUcovID_0001

institute: University of Colorado Anschutz Medical Campus


title: CUcovID_0107


title: CUcovID_0005


title: MM-5610-12: CD4 Rapa 1

source_name: CD4 T cell, rapamycin treated mouse, replicate 1

value: Rapamycin

value: CD4 T cell


title: MM-5610-18: CD4 Veh 2

source_name: CD4 T cell, vehicle treated mouse, replicate 2


title: MM-5610-30: CD4 Veh 3

source_name: CD4 T cell, vehicle treated mouse, replicate 3


title: Illumina_WT-0-replicate 1_short_read_reanalyzed

description:
Sample 1
GSM4915878

value: small airway epithelial cells

value: WT


title: CUcovID_0060

value: Female


title: GEP profile of untreated BM-MSC from HD1

description:
Initial lab ID: T1p2
mRNA

value: Healthy

value: BM-MSC

value: Untreated


title: MM-5610-06: CD4 Veh 1

source_name: CD4 T cell, vehicle treated mouse, replicate 1


title: CUcovID_0010


title: Duroc_2W_1_Heart_RNA

city: Wuhan

first: Shuhong

last: Zhao

description: individual 1

value: Duroc

value: 2 weeks


title: MM-5610-35: CD8 Rapa 3

source_name: CD8 T cell, rapamycin treated mouse, replicate 3

value: CD8 T cell


title: MM-5610-24: CD4 Rapa 2

source_name: CD4 T cell, rapamycin treated mouse, replicate 2


title: GEP profile of BM-MSC HD5 primed with FL2 B cells

description:
Initial lab ID: T5FL2ns
mRNA

source_name: Stromal cells from HD primed with FL cells

value: Primed with primary follicular lymphoma B cells


title: IK-mock cells

city: Tokyo

first: Izumi

last: Suzuki

state: 東京都

address: 2-1-1 Hongo Bunkyo-ku

institute: Juntendo University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole human Genome Array (4x44K) ver 2.0 (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color MicroArray-Based Gene Expression Analysis(Low Input Quick Amp Labeling) . Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was purified with an RNeasy Plus Mini Kit (Qiagen, Valencia, CA) following the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: IK

value: endometrial cancer cell

tag: genotype/variation

value: control/mock


title: IK-YBX2 C1 cells

tag: cell type

value: overexpressed YBX2


title: MM-5610-11: CD8 Rapa 1

first: Jeffrey

source_name: CD8 T cell, rapamycin treated mouse, replicate 1


title: MM-5610-23: CD8 Rapa 2

source_name: CD8 T cell, rapamycin treated mouse, replicate 2


title: CUcovID_0108

value: whole blood

value: Male

value: Positive

value: strand-specific


title: IK-YBX2 C3 cells


title: Duroc_2W_1_Fat_RNA

description: individual 1

source_name: Fat

value: fat


title: Duroc_2W_2_Liver_RNA

description: individual 2

source_name: Liver

value: liver


title: IK-YBX2 C1 SP cells


title: Duroc_2W_1_Muscle_RNA

description: individual 1

source_name: Muscle

value: muscle


title: CUcovID_0013


title: CUcovID_0033

value: Female


title: LW_2W_1_Muscle_HiC

description:
individual 1
LW_2W_1_Muscle_HiC_Lib1
LW_2W_1_Muscle_HiC_Lib2

data_processing:
The configuration file for Hi-C processing was prepared with corresponding BOWTIE2_IDX_PATH, GENOME_SIZE and GENOME_FRAGMENT (BIN_SIZE = 40000; LIGATION_SITE = GATCGATC).
The paired-end Hi-C reads from different libraries were separately mapped to susScr11.1 genome using the HiC-Pro (Servant et al., 2015) pipeline v2.9.0 with the parameter “-s mapping” (https://github.com/nservant/HiC-Pro).
After mapping, the singleton, multi mapped, dumped, dangling and self-circle paired-end reads and PCR duplication were all removed by HiC-Pro with the parameter “-s proc_hic”. Next, files with.bwt2pairs.validPairs suffix from different libraries were moved to a new folder as the input data for subsequent analysis. And then merging multiple libraries, building raw inter-/intra-chromosomal contact maps and running ICE normalization on contact maps were performed using the programs in order of HiC-Pro parameter “-s merge_persample”, “-s build_contact_maps” and “-s ice_norm”.
The bed files of TAD structures (insulation/boundaries) were defined by the insulation method construction which was developed by previous studies (Crane et al., 2015; Giorgetti et al., 2016). The insulation score of ICE matrix was calculated by the following options: -is 480000 –ids 320000 -im iqrMean -ss 160000.
The BAM files of read1 and read2 from different libraries were merged as single one read1 BAM and read2 BAM using SAMTools v1.9, respectively. The makeTagDirectory command of HOMER (Heinz et al., 2010) with default parameters was used to process the alignment file into HOMER-style tag directory. For chromatin compartments identification, Principal Component Analysis (PCA) was performed to reveal active and inactive chromatin regions along the genome with runHiCpac.pl command of HOMER following the parameters “-res 40000 -genome susScr11”. The output file with .PC1.bedgraph suffix were used to view partition of chromatin compartments.
Genome_build: susScr11.1
Supplementary_files_format_and_content: BedGraph file for partition of chromatin compartments, bed files of TAD and TAD boundaries.

extract_protocol:
Skeletal muscle tissue samples from Large White pigs were ground up in liquid nitrogen, and then fixed with 1% formaldehyde at room temperature for 20 min. In suit Hi-C was performed mainly as described (Rao et al., 2014). Briefly, the pulverized tissues were mixed with 250 μl of ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2 % Igepal CA630), and incubated on ice for 20 min. Chromatin was digested with 100 U of Mbo I restriction enzyme (NEB, R0147) overnight followed by labeling of the DNA fragment ends with biotin through incubation at 37 °C for 45 min. DNA ligation was performed with T4 DNA ligase (NEB, M0202) by incubating the reaction at room temperature for 4 hours with slow rotation. The biotinylated DNA was sheared to a size of 300–500 bp.
Libraries were constructed following Illumina protocols (Illumina, San Diego, CA), and sequenced on an Illumina Hiseq X ten PE150 platform.

value: Large White


title: Illumina_WT-24-replicate 4_PacBio

description: Sample 20

source_name: hSAEC wild type

value: small airway epithelial cells

value: WT

value: infected (24 h)


title: Illumina_WT-24-replicate 3_PacBio

description: Sample 19


title: CUcovID_0042


title: CUcovID_0020


title: Illumina_WT-24-replicate 1_PacBio

description: Sample 17


title: CUcovID_0016


title: Duroc_2W_2_Fat_RNA

description: individual 2

value: Duroc

value: 2 weeks


title: Illumina_WT-24-replicate 2_PacBio

description: Sample 18


title: MM-5610-29: CD8 Veh 3

source_name: CD8 T cell, vehicle treated mouse, replicate 3

value: Vehicle

value: CD8 T cell


title: RLTRE2

city: Philadelphia

first: Wasik

middle: A

last: Mariusz

state: Pennsylvania

address: 422 Curie Blvd

institute: University of Pennsylvania

data_processing:
RTA (Illumina)was used for base calling and CASAVA (version 1.8) for converting BCL to fastq format, coupled with adaptor trimming.
Reads were trimmed to remove the adapter sequences and low quality bases.
RNA-seq reads were aligned to the human refference genome (hg19) using BWA software
Gene expression (RPKM) were calculated using Partek Genomics Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA)
Genome_build: Human genome (hg19, GRCh37)
Supplementary_files_format_and_content: Gene expression and change folds in excel
Supplementary_files_format_and_content: FPKM, read counts

source_name: MCL Cell line cells

growth_protocol: RL cells and Jeko-1 cells were cultured at 37 °C and 5% CO2 in RPMI medium 1640, supplemented with 2-mM L-glutamine, 10% heat-inactivated FBS (FBS), 1% penicillin/streptomycin mixture

extract_protocol:
Cells with or without treatment were washed and RNA were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RL cells and JeKo cells were treated with BTK inhibitor for 6 hours

value: RL

tag: agent

value: BTK inhibitor


title: CUcovID_0055

source_name: whole blood

value: whole blood


title: MM-5610-17: CD8 Veh 2

source_name: CD8 T cell, vehicle treated mouse, replicate 2


title: MM-5610-22: M-MDSC Rapa 2

source_name: Monocytic myeloid derived suppressor cell, rapamycin treated mouse, replicate 2

value: Rapamycin

value: Monocytic myeloid-deprived suppressor cell


title: MM-5610-05: CD8 Veh 1

source_name: CD8 T cell, vehicle treated mouse, replicate 1


title: MM-5610-28: M-MDSC Veh 3

source_name: Monocytic myeloid derived suppressor cell, vehicle treated mouse, replicate 3


title: MM-5610-10: M-MDSC Rapa 1

source_name: Monocytic myeloid derived suppressor cell, rapamycin treated mouse, replicate 1


title: RLTRE1


title: CUcovID_0008

value: Positive

value: strand-specific


title: Illumina_WT-0-replicate 3_PacBio

description: Sample 3

value: uninfected (0h)


title: CUcovID_0051

value: Male

value: Negative


title: Illumina_WT-0-replicate 2_PacBio

description: Sample 2

value: small airway epithelial cells


title: RLCTR2


title: CUcovID_0100

value: Female


title: MM-5610-16: M-MDSC Veh 2

source_name: Monocytic myeloid derived suppressor cell, vehicle treated mouse, replicate 2


title: MM-5610-04: M-MDSC Veh 1

source_name: Monocytic myeloid derived suppressor cell, vehicle treated mouse, replicate 1


title: RLCTR1


title: Illumina_WT-0-replicate 1_PacBio

description: Sample 1

value: WT


title: MM-5610-33: TAM Rapa 3

source_name: Tumor-associated macrophage, rapamycin treated mouse, replicate 3

value: Tumor-associated macrophage


title: CUcovID_0106


title: Sample_Plate13_B9

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: rawcounts_dengue_samples.txt and filtered_normalized_counts_dengue_samples.txt

data_processing:
Sequencing and mapping were controlled for quality using standard tools provided in the FastQC software.
Raw reads were mapped to the reference human genome (hg19_ens_GRCh37) using tophat 2.0.11. Read counts per gene were calculated for each sample using HTseq version 0.6.1 (only genes with the “gene_biotype” type “protein coding” were considered for quantification).
Lowly expressed genes were removed, and genes with a total number of less than 5 counts across all samples were discarded (the total number of remaining genes was 10,238). Read counts per gene were further normalised across all samples using the “trimmed mean of M-value” (TMM) approach.
Genome_build: hg19_ens_GRCh37
Supplementary_files_format_and_content: rawcounts_dengue_samples.txt: abundance measurements at the gene level for protein coding genes (HTSeq output gene counts)
filtered_normalized_counts_dengue_samples.txt: library size normalized and low expression filtered abundance measurements
metadata_dengue_samples.txt: technical covariates

source_name: dendritic cell

growth_protocol: CD14+ cells were isolated by positive selection from PBMCs using MACS CD14 microbeads (Miltenyi Biotec). PBMCs were centrifuged at 1500 rpm for 5 minutes and cell pellet. Primary human DCs or monocytes were collected in 50 ml falcon tubes, centrifuged and infected with DENV at a MOI of 1 or 5 FFU/cell, as determined based on the viral titre and number of cells, for 2 hours at 37 °C at 5% CO2. Excess DENV was washed off three times with RPMI 1640. Cells were then resuspended in R10 (5x10^5 cells/ml) and plated in 24 or 48 well plate at 37 °C, for an overnight period.  The antibody dependent enhancement assay was performed using a monoclonal antibody against the DENV precursor membrane protein prM (1H10; produced in house as described in [17]). Anti-prM antibody was diluted to a final concentration of 0.2 μg/ml in R10 in a volume of 100 μl. DENV, at (MOI 1 or 5 FFU/cell), was then mixed with the diluted antibody in a final volume of 200 μl for 1 hour at 37 °C to allow immune complex formation. After incubation, the antibody-virus mixture was added to human monocyte-derived macrophages and incubated for 2 hours at 37 °C at 5% CO2. To remove residual ICs, supernatants were discarded from the monolayer and cells were carefully rinsed 3 times with RPMI 1640 before incubating cells in R10 at 37 °C, overnight. The infection rates in macrophages and DCs were measured by flow cytometry using an antibody against DENV protein NS3, 24 hours following infection. was resuspended in 80 μl of MACS buffer with the addition of 10 μl CD14 microbeads per 107 cells. After incubation at 4 °C for 30 minutes, labelled cells were resuspended in 12 ml MACS buffer and applied onto a LS column (Miltenyi Biotec). Cells were flushed out mechanically by adding 5 ml of R10, centrifuged and resuspended in R10. The purity of CD14+ cells was determined with an anti CD14-APC antibody (BD Biosciences) by flow cytometry.  To generate monocyte derived macrophages, 7x10^6 CD14+ cells were plated in a 60mm dish and cultured in 5 ml R10 with 100 ng/ml recombinant human M-CSF (Peprotech). After 5 days, adherent cells were gently washed with RPMI 1640 and detached with cell dissociation solution non-enzymatic (Sigma-Aldrich). Cells were then resuspended in R10 and cultured at 5x10^5 cells/ml in 24 or 48 well plate for additional 24 hours at 37 °C in a 5% CO2 incubator. Monocyte-derived dendritic cells (DCs) were generated by culturing CD14+ cells in R10 (5x10^5 cells/ml) with 20 ng/ml human recombinant GM-CSF (First Link) and 25 ng/ml human recombinant IL-4 (eBioscience) for 5 to 6 days at 37 °C in a 5% CO2 incubator. On day 3, half of the culture media was carefully replaced with fresh media containing 40 ng/ml human recombinant GM-CSF and 50 ng/ml human recombinant IL-4. Immature DCs were harvested and confirmed with anti CD14-APC (BD Biosciences) and anti CD209-PE (Miltenyi Biotec) by flow cytometry.

extract_protocol:
The cDNA synthesis, labelling and subsequent hybridization were performed according to the manufacturer’s protocol using the TruSeq® Stranded mRNA Low Sample Preparation Guide (Illumina). Briefly, 500 ng total RNA was purified to obtain polyA containing mRNA using poly-T oligo attached magnetic beads. PolyA RNA was fragmented and primed with random hexamers for cDNA synthesis. After synthesis of the first strand cDNA, remaining RNA was removed and a second strand cDNA was synthesised to obtain blunt-ended double stranded cDNA.
RNA sequencing was performed using an ultra-high-throughput sequencing system HiSeq 2500 (Illumina).

treatment_protocol: Primary human DCs and macrophages were infected with DENV or IC for 6 or 24 hours. As a control, cells were treated with medium only (DCs) or anti-prM only (macrophages). After incubation time, cells were washed with warm PBS before adding 500 µl TRIzol® reagent (Invitrogen) and RNA was isolated using the RNeasy mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quantification and quality were assessed using NanoDrop 2000 and stored at -80 °C until further use.

tag: infection

value: control

value: dendritic cell

tag: infection time (hours)

tag: treated with

value: medium

tag: biological replicate


title: CUcovID_0061

tag: tissue

tag: age


title: MM-5610-21: TAM Rapa 2

source_name: Tumor-associated macrophage, rapamycin treated mouse, replicate 2

tag: treatment


title: CUcovID_0068


title: Sample_Plate13_B8


title: CUcovID_0030


title: Sample_Plate13_B6


title: MM-5610-27: TAM Veh 3

source_name: Tumor-associated macrophage, vehicle treated mouse, replicate 3

value: Vehicle


title: Illumina_WT-0-replicate 4_PacBio

description: Sample 4


title: Sample_Plate13_B5


title: CUcovID_0014


title: B3_Clean_Data1

city: Hefei

first: shuo

last: chen

address: Meishan Road#81

institute: Anhui Medical University

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from StringTie et al. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with FPKM value for every gene and every sample

source_name: normal kidney

extract_protocol:
The total RNA was extracted using TRIzol reagent. RNA-Seq was conducted according to a previously reported method. Briefly, after quality control and purification, the total RNA from each sample was used to enrich mRNA. The mRNA was fragmented and reverse-transcribed to cDNA. The cDNA was then purified, linked with the adaptor, size selected, and PCR amplified to obtain the cDNA library. After the quality check, libraries were sequenced through the Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Normal

value: Kidney


title: B1_Clean_Data1


title: A2_Clean_Data1

source_name: kidney tumor

value: Tumors


title: B2_Clean_Data1


title: CUcovID_0064

value: whole blood


title: MM-5610-15: TAM Veh 2

source_name: Tumor-associated macrophage, vehicle treated mouse, replicate 2


title: Sample_Plate13_B4


title: A1_Clean_Data1


title: Sample_Plate13_B3


title: 786-0 shGLUD1-2

city: Shanghai

first: Jialiang

last: Shao

address: No. 100 Haining Road, Hongkou District, Shanghai

institute: Department of Urology, Shanghai General Hospital, Jiaotong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human renal-carcinoma cell line

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS (HyClone, Logan, UT, USA)

extract_protocol:
1 ug of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated by amino acid starvation for 12 hours before sequencing.

value: amino acid starvation

value: 786-0 cells

tag: condition

value: GLUD1 knockdown


title: MM-5610-03: TAM Veh 1

source_name: Tumor-associated macrophage, vehicle treated mouse, replicate 1

tag: cell population


title: CUcovID_0054

source_name: whole blood

tag: Sex

value: Male

value: Positive

value: strand-specific


title: Sample_Plate13_B2


title: CUcovID_0050

value: Female

tag: sars-cov2 status


title: 786-0 shGLUD1-1


title: MM-5610-09: TAM Rapa 1

source_name: Tumor-associated macrophage, rapamycin treated mouse, replicate 1

value: Rapamycin


title: CUcovID_0066

tag: library type


title: Sample_Plate13_B12


title: Sample_Plate13_B1

source_name: macrophage

value: macrophage

value: anti-prM dengue protein


title: 786-0 shNT-1

tag: cell line

value: Control


title: 786-0 shNT-2


title: CUcovID_0025


title: Sample_Plate13_A9

value: control


title: Sample_Plate13_B11

value: dendritic cell

value: medium


title: h+ dis2∆::NatMX_rep3

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: lab strain number

tag: genotype

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: CUcovID_0076

value: whole blood

value: Negative


title: Sample_Plate13_A8

tag: infection

tag: cell type

tag: infection time (hours)


title: h+ dis2∆::NatMX_rep2


title: Sample_Plate13_B10

tag: treated with

tag: biological replicate


title: CUcovID_0037

tag: tissue

tag: age


title: PAS-seq_8hpi_27LacZ_Hela

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Rd

institute: University of California, Irvine

data_processing:
Library strategy: PAS-seq
Reads were trimmed to remove the primers and polyA tails.
Aligned to human(hg19) genome using STAR. Multi-mapping was not allowed.
Mapped reads were converted to bigwig files using deepTools.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

source_name: cervical carcinoma

extract_protocol:
Total RNA from each sample was extracted by Trizol (Invitrogen) according to instructions.
10 μg total RNA was fragmented with fragmentation reagent (Ambion) at 70 oC for 10 minutes followed by precipitation with ethanol. After centrifugation, RNA was dissolved and Reverse transcription was performed with PASSEQ7-2 RT oligo: [phos]NNNNAGATCGGAAGAGCGTCGTGTTCGGATCCATTAGGATCCGAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTT[V-Q] and Superscript III. cDNA was recovered by ethanol precipitation and centrifugation. 120-200 nucleotides of cDNA was gel-purified and eluted from 8% Urea-PAGE. Recovered cDNA was circularized with CircligaseTM II (Epicentre) at 60 oC overnight. Buffer E (Promega) was added in cDNA and heated at 95 oC for 2 minutes, and then cool to 37 oC slowly. Circularized cDNA was linearized by adding BamH I (Promega). cDNA was centrifugated after ethanol precipitation. PCR was carried out with primers PE1.0 and PE2.0 containing index. Around 200 bp of PCR products was gel-purified and submitted for sequencing (single read 100 nucleotides).

treatment_protocol: (1) For infection: HeLa cells with 100% confluence in 10 cm dish were washed once with PBS plus MgCl2. Add 5 ml PBS plus MgCl2 containing HSV-1 (MOI=10) and incubate cells at 37 oC for 45 min. Remove viral suspension and add 8 ml fresh growth media to culture until cells were harvested. (2) For transfection, 10 μg plasmid (for 10-cm dish) was incubated with 30 μl of 1 mg/ml PEI in 1 ml DMEM for 20 min at RT, and then PEI/DNA complex was added in Hela cells. Transfected cells were harvested 2 days post transfection. (3) For U1 AMO treatment: 50 uM U1 AMO treated 293 cells for 48h.

value: Hela + ICP27-deleted KOS

tag: treatment

value: ICP27-deleted HSV-1 infection


title: PAS-seq_U1AMO_293

source_name: 293 cells

value: U1 antisense morpholino oligonucleotide (AMO) treatment


title: PAS-seq_ICP27-overexpression_293

value: ICP27 overexpression


title: PAS-seq_293-WT

value: no treatment


title: h+ dis2∆::NatMX_rep1


title: h+ swd22::HygMX_rep3


title: CUcovID_0027

value: Female

value: strand-specific


title: CUcovID_0036

value: Male

value: Positive


title: PAS-seq_8hpi_KOS_Hela

value: Hela + KOS

value: HSV-1 infection


title: Sample_Plate13_A7

value: control

value: macrophage

value: anti-prM dengue protein


title: h+ swd22::HygMX_rep2

value: log phase culture, YES medium

value: vegetative growth


title: PAS-seq_HSV-12hpi_Hela


title: CUcovID_0023

value: whole blood

value: Negative


title: MM-5610-32: CD45- Rapa 3

source_name: CD45- cancer cell, rapamycin treated mouse, replicate 3

value: Rapamycin

tag: cell population

value: CD45- cancer cell


title: CUcovID_0097

tag: Sex


title: MM-5610-20: CD45- Rapa 2

source_name: CD45- cancer cell, rapamycin treated mouse, replicate 2


title: MM-5610-14: CD45- Veh 2

source_name: CD45- cancer cell, vehicle treated mouse, replicate 2

value: Vehicle


title: MM-5610-26: CD45- Veh 3

source_name: CD45- cancer cell, vehicle treated mouse, replicate 3


title: MM-5610-08: CD45- Rapa 1

source_name: CD45- cancer cell, rapamycin treated mouse, replicate 1


title: MM-5610-02: CD45- Veh 1

source_name: CD45- cancer cell, vehicle treated mouse, replicate 1


title: CUcovID_0048

tag: sars-cov2 status


title: PAS-seq_8hpi_mock_Hela

value: Hela

value: no treatment


title: CUcovID_0073

tag: library type

value: strand-specific


title: h+ swd22::HygMX_rep1


title: Sample_Plate13_A5


title: Sample_Plate13_A6


title: Sample_Plate13_A3


title: h+ ppn1∆::HygMX_rep3


title: CUcovID_0044

value: Female


title: PAS-seq_HSV-6hpi_Hela


title: PAS-seq_HSV-2hpi_Hela


title: Sample_Plate13_A2


title: PAS-seq_HSV-0hpi_Hela


title: Sample_Plate13_A4


title: h+ ppn1∆::HygMX_rep2


title: h+ ppn1∆::HygMX_rep1


title: CUcovID_0006


title: Sample_Plate13_A1


title: JekoTRE2

source_name: MCL Cell line cells

tag: cell line

tag: agent

value: BTK inhibitor


title: JekoTRE1


title: Sample_Plate13_A12


title: CUcovID_0017


title: h+ _rep3

source_name: WT

tag: lab strain number

tag: genotype

value: WT


title: CUcovID_0094


title: CUcovID_0093

value: Male


title: h+ _rep1

tag: growth conditions

tag: developmental stage


title: JekoCTR1


title: h+ _rep2


title: Sample_Plate11_B9

source_name: dendritic cell

tag: infection

value: dengue

tag: cell type

value: dendritic cell


title: CUcovID_0038


title: CUcovID_0021

value: Positive


title: Sample_Plate11_B7

tag: infection time (hours)

tag: treated with


title: Sample_Plate13_A10

value: control

value: macrophage

value: anti-prM dengue protein

tag: biological replicate


title: CUcovID_0079

tag: tissue

value: whole blood

tag: age

value: Negative


title: Sample_Plate11_B8


title: Sperm miRNA

city: Oxford

first: Yue

last: Du

state: Oxford

address: NDCLS, RDM, JR hospital, head

institute: University of Oxford

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and the dataset was further processed with an in‐house program called ACGT101‐miR (LC Sciences, Houston, TX) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats.
Unique sequences with lengths of 18–26 nts were subsequently mapped to specific‐species precursors in miRBase 20.0 by BLAST searching to identify known miRNAs and novel 3p‐ and 5p‐derived miRNAs.
Lengths varying at both 3′‐ and 5′‐ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapped to specific‐species mature miRNAs in hairpin arms were identified as known miRNAs.
Unique sequences that mapped to the arm of known, specific‐species precursor hairpins complementary to the annotated mature miRNA‐containing arm were considered to be novel 5p‐ or 3p‐derived miRNA candidates
The mapped pre‐miRNAs were further BLASTed against the genomes of specific species to determine their genomic locations. Sequences that mapped to existing regions were classified as known miRNAs.
Supplementary_files_format_and_content: excel

organism: Bos taurus

source_name: diced cauda epididymis

extract_protocol:
Sperm were filtered from the diced cauda epididymis, and extracted by trituration at room temperature. Spermatozoa from whole pieces were removed and collected using the swim‐up method in BO solution pre‐warmed to 37°C. After incubating the sample for 30 min at 37°C with the tube slanted at an approximate angle of 45°, the motile overlying fraction (1 ml liquid) was pipetted into a clean tube containing 1 ml of HEPES‐buffered Tyrode's lactate sperm medium (100 mM NaCl, 25 mM NaHCO3, 10 mM HEPES, 0.3 mM NaH2PO4, 3.11 mM KCl, 0.035 mM sodium lactate, 2 mM CaCl2·2 H2O, 4 mM MgCl2·6 H2O [pH 7.3]) (Parrish et al., 1995). This mixture was centrifuged at 800g for 5 min at 30°C. The pelleted sperm were evaluated (see below), and then frozen at −80°C until RNA isolation.
RNA libaries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Bull

value: diced cauda epididymis

value: 1 yr


title: ChIPseq_H4K20me1_TX1072_24h_Dox_Rep2

city: Leuven

first: Aurélie

last: Bousard

address: Herestraat 49, bus 912

country: Belgium

institute: VIB/KULeuven

data_processing:
Adapters and low quality bases (< Q20) have been removed with TrimGalore (v0.4.4; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and Cutadapt (1.12) {Martin et al, 2011}. Moreover, for PE150 samples, last 50 pb were trimmed to allow unbiased comparison of the data with PE100 samples.
An ‘N-masked” genome has been generated with SNPSplit (0.3.2) {Krueger, 2016 #2319} which is a version of the mouse reference genome mm10 where all the polymorphic sites for the hybrid strain Mus musculus CAST/EiJ and Mus musculus C57BL/6 are masked by ambiguity nucleobase ‘N’. For all samples, reads were then mapped to the ‘N-masked” genome with STAR (2.5.3a) with options [--outFilterMultimapNmax 1 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.03 --alignIntronMax 1 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD] (Dobin et al., 2013)}.
Duplicates were discarded with Picard MarkDuplicates (1.65) with options [REMOVE_DUPLICATES = true] (https://broadinstitute.github.io/picard/) and reads mapped on blacklisted regions from Encode Consortium were discarded.
SNPSplit (0.3.2) {Krueger et al, 2016} was then used to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST and B6) based on SNPs information downloaded from Sanger.
Bigwig files were created with bedtools genome CoverageBed (2.27.1) {Quinlan et al, 2010}, using a scale factor calculated on the total library (10.000.000/total reads) for both allele specific bigwigs, and loaded on UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: TX1072 ESC lines were cultured on gelatine-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% foetal bovine serum, 2-mercaptoethanol (0.1mM), LIF(1000u/mL) and 2i (PD0325901 [0.4 mM], CHIR99021 [3 mM]). Cells were incubated at 37°C with 8% CO2. After 24hrs of culture in DMEM/15%FCS+LIF+2i the medium was supplemented with doxycycline (1ug/ml).

extract_protocol:
Cells were collected using Accutase (Thermo Fisher Scientific), washed twice in ice-cold PBS and counted.
Native ChIP-seq was performed as previously described {Zylicz, 2019}. Cells were collected using Accutase (Thermo Fisher Scientific), washed twice in ice-cold PBS and counted. Typically, 10 mln cells were used per immunoprecipitation (IP). A fraction of cells was always used for RNA/FISH verification of Xist induction. Cell pellet was resuspended in 90 μL (per 10 mln cells) of Lysis Buffer (50 mM Tris-HCl, pH7.5; 150mM NaCl; 0.1% sodium deoxycholate; 1% Triton X-100; 5mM CaCl2; Protease Inhibitor Cocktail; 5 mM sodium butyrate). After lysing cells on ice for 10 min we added 62 μL (per 10 mln cells) of Lysis Buffer with MNase (500 μL buffer + 0.5 μL MNase). Chromatin was digested for exactly 8 min at 37°C and reaction was stopped by the addition of 20 mM EGTA. To remove undigested debris the lysates were centrifuged at 13000 rpm for 5 min at 4°C. Supernatant was transferred to a fresh tube, an equal volume of STOP Buffer (50 mM Tris-HCl, pH7.5; 150mM NaCl; 0.1% sodium deoxycholate; 1% Triton X-100; 30 mM EGTA; 30 mM EDTA; Protease Inhibitor Cocktail; 5 mM sodium butyrate) was added, samples were stored on ice. 5 μL of lysate was digested in 45 μL of ProtK Digestion Buffer (20 mM HEPES; 1 mM EDTA; 0.5% SDS) for 30 min at 56°C. 50 μL of AMPure XP beads were added to the digested lysate together with 60 μL of 20% PEG8000 1.25M NaCl. After mixing the samples were incubated for 15 min at RT. Beads were separated on a magnet and washed twice with 80% Ethanol for 30sec. DNA was eluted in 12 μL of Low-EDTA TE. DNA isolated in this step was used as the input sample. The volume of each undigested lysate was adjusted to obtain 1mL per IP using a 1:1 mix of Lysis Buffer and STOP Buffer. Anti-mouse Dynabeads (25ul/IP) were washed twice in Blocking Buffer (0.5% BSA; 0.5% Tween in PBS). Beads were then resuspended in Blocking buffer and coated with antibodies for 4hrs at 4°C (H4K20me1 [0.5ug/IP], Active Motif cat. 39727). Once coated beads were magnet-separated and resuspended in 1mL of lysate. Samples were left rotating overnight at 4°C. Following day beads were magnet-separated and washed quickly with ice-cold washing buffers. IPs were washed 4-times with Low Salt Buffer, 2-times with High Salt Buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA; 20 mM Tris-HCl, pH 8.1; 360 mM NaCl; 0.1% sodium deoxycholate) and 2-times with LiCl buffer (0.25 M LiCl; 1% NP40;1.1% sodium deoxycholate; 1 mM EDTA; 10 mM Tris-HCl pH 8.1). Prior to elution all samples were rinsed once in TE. ChIP-DNA was eluted in ProtK-Digestion buffer for 15 min at 56°C. Beads were separated and the supernatant was further digested for another 2 hr at 56°C. DNA was isolated using AMPure XP beads as described for the input sample.  For each nChIP-seq, 0.5 μL of each sample was used for qPCR validation of enrichment at control regions. 0.5 μL of input samples were also used to verify the digestion efficiency using D1000 tapestation. Remaining DNA concentration was adjusted and used for library preparation using Ovation® Ultralow Library System V2 following suppliers protocol. Amplified libraries were size-selected for dinucleotide fraction (350-600bp fragments) using agarose gel-separation and MinElute Gel Extraction Kit (QIAGEN). Sample quality was inspected using D1000 tapestation. S

value: CAST / C57BL/6

tag: condition

value: 24h Dox

tag: replicate

tag: antibody


title: Input_TX1072_0h_Dox_Rep2

source_name: Input

tag: cell line

value: 0h Dox


title: Sample_Plate11_B6