title: MTJ_horse17

description:
H17MT
Mare

value: MTJ

value: Female


title: RKO_DMSO

status: Public on Jul 12 2021

type: SRA

city: Shanghai

first: Zhen

last: Xiang

state: Shanghai

address: No. 197, Ruijin er Road

country: China

institute: Department of Surgery of Ruijin Hospital

library_source: transcriptomic

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to grape genome using STAR
Read counts were calculated by using htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal cancer cell line

growth_protocol: Cancer cell lines were cultured in RPMI-1640 containing 10% FBS and 1% Penicillin-Streptomycin, and incubated at 37 °C in a humidified incubator at 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit 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: Cancer cell lines were treated by DMSO or Dex for 48 hours.

tag: cell line

value: RKO

tag: cell type

value: Colorectal cancer cell line

tag: treatment

value: DMSO; Control


title: SMMC-7721_Dex

source_name: Liver cancer cell line

value: Liver cancer cell line

value: dexamethasone (Dex)


title: MV3_DMSO

source_name: Melanoma cell line

value: Melanoma cell line


title: N-019: Pax_RNA_Normal_19

type: RNA

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

country: Japan

institute: Kanazawa University

description: Gene expression about healthy volunteer blood

hyb_protocol: 1.65 ug of Cy3-labelled 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 DNA microarray Whole Human Genome 4×44K Array kit G4112F (Agilent Technologies) 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 air dry.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slide

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207)to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral Blood, healthy volunteer No.19

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug total RNA using Quick Amp Labeling kit, One-Color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from PAXgene blood RNA tube using PAXgene Blood RNA Kit (PreAnalytix, Hombrechtikon, Switzerland) in accordance with the manufacturer’s protocol. total RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).

tag: diagnosis

value: healthy

tag: tissue

value: whole blood

tag: gender

value: female

tag: age


title: Tendon_horse16

city: Copenhagen

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

country: Denmark

institute: Bispebjerg Hospital

description:
H16T
Mare

data_processing:
Reads were filtered using SOAPnuke v1.5.2 and parameters: -n 0.01 -l 15 -q 0.5 -A 0.25 -Q 2
Clean reads were mapped to the horse genome (EquCab3.0) using Rsubread v2.0.0 and parameters: unique=TRUE
Clean reads were mapped to reference RNA using Rsubread v2.0.0 and parameters: countMultiMappingReads = FALSE
Expression levels were normalized with DESeq2 v1.26.0 resulting in rlog normalized values ("Count and rlog values.xlsx"). Only transcripts with count in at least 5 of the 15 samples were included.
Furthermore, increases in MTJ samples ("MTJ_changes.xlsx") were calculated by considering the background level of MTJ samples as a mix from muscle and tendon which can be estimated from muscle and tendon specific transcripts ("Reference genes for MTJ prediction.xlsx"), see article.
Genome_build: EquCab3.0
Supplementary_files_format_and_content: "Count and rlog values.xlsx" contains transcript read counts and DESeq2 regularized log transformation values.  "Reference genes for MTJ prediction.xlsx" contains muscle and tendon specific transcripts used for predicting muscle and tendon contribution to the MTJ samples, see article.  "MTJ_changes.xlsx" contains log2FC differences between measured and predicted counts in the MTJ samples.  All three files in Microsoft Excel Open XML format.

organism: Equus caballus

source_name: superficial digital muscle

extract_protocol:
Total RNA was purified with TriReagent
RNA was submitted to BGI Europa and analyzed according to their standard procedure:   1)mRNA enrichment: Oligo dT Selection or rRNA depletion;  2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random  primer;  3) End repair, add A tailing and adaptor ligation: The synthesized cDNA was subjected to end-repair  and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA  fragments;  4)PCR amplification:The ligation products were purified and many rounds of PCR amplification  were performed to enrich the purified cDNA template using PCR primer;  5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and  DNA ligase;  6) Sequencing on DNBseq platform.

treatment_protocol: These samples were obtained from the front limb of euthanized horses from which the SDF muscle was dissected and small samples of muscle with attached tendon were punched out using a 4 mm diameter biopsy puncher. The samples were mounted in TissueTeK (Sakura, Netherlands), tendon side down, frozen in liquid nitrogen-cooled isopentane, and stored at -80 °degrees C until analysis. By cryosectioning muscle, MTJ and tendon specific samples were obtained (approx. 200 micrometer each) and RNA purified using TriReagent.

value: Tendon

tag: horse number

tag: age (years)

tag: training

value: Trained


title: N-018: Pax_RNA_Normal_18

source_name: Peripheral Blood, healthy volunteer No.18


title: male_old_4dpi_1

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
After sequencing, perl script was used to filter the original data (Raw Data) to clean reads by removing contaminated reads for adapters and low-quality reads.
Clean reads were aligned to the mouse genome (Mus_musculus.GRCm38.99) using Hisat2 v2.1.0. The number of reads mapped to each gene in each sample was counted by HTSeq v0.6.0 and FPKM was then calculated  to estimate the expression level of genes in each sample.
Genome_build: Mus_musculus.GRCm38.99
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Mus musculus

source_name: lung

extract_protocol:
Total RNA from lung  were extracted using TRIzol (Invitrogen, Carlsbad, CA, USA)  and DNase I (NEB, USA) treated, respectively.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations

tag: strain

value: BALB/c

value: lung

value: 38 weeks

value: MASCp36 infected

value: male


title: N-022: Pax_RNA_Normal_22

source_name: Peripheral Blood, healthy volunteer No.22


title: SMMC-7721_DMSO


title: Muscle_horse17

description:
H17M
Mare

value: Muscle

value: Female

value: Sedentary


title: BxPC3_DMSO

source_name: Pancreatic cancer cell line

value: Pancreatic cancer cell line

value: DMSO; Control


title: Muscle_horse16

description:
H16M
Mare


title: N-014: Pax_RNA_Normal_14

source_name: Peripheral Blood, healthy volunteer No.14


title: male_old_1dpi_2


title: N-013: Pax_RNA_Normal_13

source_name: Peripheral Blood, healthy volunteer No.13


title: NCIH-747_DMSO

value: Colorectal cancer cell line


title: male_old_mock_3

value: mock


title: male_old_1dpi_1


title: MKN-45_DMSO

source_name: Gastric cancer cell line

value: Gastric cancer cell line


title: MTJ_horse16

description:
H16MT
Mare

value: MTJ


title: male_old_mock_2


title: MTJ_horse14

description:
H14MT
Mare


title: SGC-7901_DMSO


title: male_old_1dpi_3


title: Tendon_horse14

description:
H14T
Mare


title: Muscle_horse14

description:
H14M
Mare


title: male_old_mock_1


title: N-008: Pax_RNA_Normal_8

source_name: Peripheral Blood, healthy volunteer No.8

value: healthy

value: whole blood

value: female


title: Tcf1/Lef1-deficient CD8 RNAseq rep1

status: Public on Jul 11 2021

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

country: USA

institute: The George Washington University

data_processing:
The sequencing quality of RNA-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm10 from iGenome(http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FDR = 0.05). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Genome_build: mm9

source_name: CD8 T cells

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

tag: genotypes

value: splenocytes

tag: cell phenotype

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: Tcf1/Lef1-deficient CD8 RNAseq rep3


title: Tcf1/Lef1-deficient CD8 RNAseq rep2


title: N-012: Pax_RNA_Normal_12

source_name: Peripheral Blood, healthy volunteer No.12


title: WT CD8 RNAseq rep2

value: wild type


title: N-002: Pax_RNA_Normal_2

source_name: Peripheral Blood, healthy volunteer No.2


title: NZ9000-7.0

city: Wuxi

first: ming

middle: zheng

last: zhu

state: Jiangsu

address: 1800 Lihu Road

department: school of biotechnology

institute: Jiangnan University

data_processing:
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAPaligner/SOAP2
 QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis.
If alignment result passes QC, we will proceed with downstream analysis including gene expression. Results of gene expression include gene expression levels and differential expression analysis.
Further, we perform Gene Ontology (GO) enrichment analysis and Pathway enrichment analysis.
Genome_build: Lactococcus lactis subsp. cremoris NZ9000
Supplementary_files_format_and_content: tab-delimited .txt files include RPKM values for each Sample

organism: Lactococcus lactis

source_name: strain cells

growth_protocol: L. lactis cells were cultured in GM17 medium (M17 broth supplied with 0.5% glucose) at 30 oC without shaking

extract_protocol:
Total RNA was extracted using the RNAprep pure Bacteria Kit (TIANGEN, Beijing, China) in accordance with the instructions. Purified RNA was quantified by using NanoDrop ND-2000 (Thermo Scientific™, MA, USA). The RNA samples were stored at -80 oC before transcriptome analysis.
The samples were sent to BGI (Shenzhen, China) for transcriptome sequencing. rRNA removing, mRNA purification and fragmentation, cDNA synthesis, adapter ligation and then PCR amplification were performed to construct the cDNA library. The sample library quality was examined using Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, respectively.

treatment_protocol: The exponential phase cells were subjected to acid stress at pH 4.0 for 4 h.The cells were collected by centrifugation at 8000 * g for 2 min at 4 oC, then washed twice with ice-cold 50mM PBS (pH 7.4). The pellets were fully grinded with liquid nitrogen,

value: parent strain NZ9000

tag: stress

value: pH 7


title: WH101-4.0

value: genome mutagenesis strain WH101

value: pH 4


title: WH101-7.0


title: N-006: Pax_RNA_Normal_6

source_name: Peripheral Blood, healthy volunteer No.6

value: male


title: NZ9000-4.0


title: Tcf1/Lef1-deficient naive CD8+ input

description: H3K27ac_naive-dKO-CD8-W200-G400-FDR0.01-island.bed

library_source: genomic

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ChIP-Seq libraries, SICER (v1.1, Zang et al., 2008) was used for H3K27ac peak calling with the setting of FDR < 0.01, windows size = 200bps and gap size = 400bps.
Genome_build: mm9

molecule: genomic DNA

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, crosslinked and immunoprecipitated with anti-H3K27ac antibody
The DNA segments from DNase I digestion were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

tag: genotype

tag: antibody


title: Tcf1/Lef1-deficient naive CD8+, H3K27ac ChIP-Seq, rep1


title: WT naive CD8+ input

description: H3K27ac_naive-WT-CD8-W200-G400-FDR0.01-island.bed


title: IUE_sgPPM1D_exon6+H3K27M+PdgfraD842V_rep3

city: Boston

first: Prasidda

last: Khadka

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
DFCI MBCF VIPER pipeline is used for the analysis of RNAseq data
FASTQ files are aligned to BAM and then raw counts are obtained using STAR
Genome_build: mm10 for mouse tumors; hg38 for human patient-derived cell lines
Supplementary_files_format_and_content: Text file with sample names and raw gene counts

source_name: Brain tumor cells

growth_protocol: BT869 cells were cultured in ultra-low attachment flasks in culture medium with 1:1 ratio of DMEM/F-12 (Invitrogen, 11330-032) and Neurobasal A (Invitrogen, 10888-022) and ten percent each of HEPES Buffer Solution 1 M (Thermo Fisher, 15630080), Sodium Pyruvate solution 100 nM (Life Technologies, 11360070), MEM non-essential amino acids solution 10 mM (Thermo Fisher, 11140050), Glutamax-I Supplement (Thermo Fisher, 35050061), and Penicillin/Streptomycin solution (Life Technologies, 15140122). The media was supplemented with B27 Minus Vitamin A (Invitrogen, 12587-010), epidermal growth factor (EGF; StemCell Tech. Inc., 78006), fibroblast growth factor (FGF; GF003, StemCell Tech., Inc., 78003) and heparin solution, 0.2% (StemCell Tech. Inc., 07980), as well as PDGF-AA (Shenandoah Biotech, 100-16) and PDGF-BB (Shenandoah Biotech, 100-18). SF7761 cell line was cultured in medium with Neurobasal A (Invitrogen, 10888-022) and N-2 Supplement (Invitrogen, 17502), further supplemented with B27 Minus Vitamin A (Invitrogen, 12587-010), epidermal growth factor (EGF; StemCell Tech. Inc., 78006), fibroblast growth factor (FGF; GF003, StemCell Tech. Inc., 78003) and heparin solution, 0.2% (StemCell Tech. Inc., 07980). Cells were dissociated using Accutase (StemCell Tech. Inc., 07922) and passaged every 3 or 4 days.

extract_protocol:
RNA extraction was performed from cell pellets using the RNAeasy kit (Qiagen, 74104)
Library prep was performed using Roche Kapa mRNA Hyper Prep

treatment_protocol: BT869 and SF776 were treated with vehicle control (DMSO) or 10 mM of PPM1D inhibitor GSK2830371 (MedChemExpress, 5140) for 1, 5, and 24 hours

value: Brain tumor cells from DIPG mouse model

value: untreated


title: WT CD8 RNAseq rep3


title: WT naive CD8+, H3K27ac ChIP-Seq, rep1


title: WT CD8 RNAseq rep1


title: control

city: Guangzhou

first: Yuting

state: China

address: No. 26, Yuancunerheng Road, Tianhe District, Guangzhou, China

institute: Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-Sen University

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Hisat2 (v2.0.1) was used to index reference genome sequence. Clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: hg19
Supplementary_files_format_and_content: xls file including gene counts and FPKM values for each Sample

source_name: HEK295T cells

growth_protocol: HEK293T cells were routinely maintained in high-glucose DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37℃ and 5% CO2 in a humidified atmosphere.

extract_protocol:
Total RNA of each sample was extracted using RNeasy Mini Kit(Qiagen). Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sample1 was transfected with plasmids overexpressing NAT10.

value: no treatment

value: wildtype


title: NAT10-binding

description: NAT10-binding RNA

source_name: HEK294T cells


title: NAT10-overexpressed

source_name: HEK293T cells


title: RPE IntS13 utr targeting knockdown replicate 3

city: Galveston

first: Nathan

middle: David

last: Elrod

state: TX

address: 1005 Strand Street

department: BMB

institute: University of Texas Medical Branch at Galveston

description: oligo-dT selected Total RNA isolated from RPE cells treated with siiRNA targeting IntS13 utr

data_processing:
adapters were trimmed and reads with Q<30 were sicarded using fastp ver 0.14.1
alignments were made using Hisat2 version 2.1.0
bedgraphs were generated using bedtools (ver 2.26.0) genomecoverage -split
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files of read alignments

source_name: retinal pigment epithial

growth_protocol: RPE cells were grown at 37°C with 5% CO2 in DMEM/F-12 50/50, supplemented with 10% (v/v) FBS and 1% (v/v) penicillin-streptomycin.

extract_protocol:
RPE cells were harvested and washed with PBS. Cells were counted, and 1 x 106 cells were resuspended in 1mL of Trizol and RNA was purified.
1 µg of RNA from each sample was diluted in 10uL of water. The input RNA was subjected to RNA-seq library generation using the  Click-Seq Total RNA (Jaworski et al. MiMB 2018), with Oligo-d(T) bead selection (NEB). The final libraries were amplified to 17 cycles and purified using AMPure XP beads (Beckman Coulter).

treatment_protocol: IntS13-utr-targeting siRNA treatment (120 hr) (Sigma Aldrich, SASI_Hs01_00134941/ASUN)

tag: sirna target

value: IntS13 utr


title: BT869_DMSO #1

tag: cell line

value: patient-derived DIPG cell line

value: DMSO


title: RPE IntS13 utr targeting knockdown replicate 1


title: RPE IntS13 gene body targeting knockdown replicate 3

description: oligo-dT selected Total RNA isolated from RPE cells treated with siiRNA targeting IntS13 gene body

treatment_protocol: IntS13-body-targeting siRNA treatment (120 hr) (Sigma Aldrich, SASI_Hs01_00134940/ASUN)

value: IntS13 gene body


title: RPE IntS13 gene body targeting knockdown replicate 2


title: D7 PbA CD11ahiCD49dlo, biological rep3

city: Nagasaki-shi

first: Mbaya

middle: Ntita

last: Felly

state: Nagasaki

address: Sakamoto

department: Molecular Microbiology and Immunology

institute: Nagasaki University

description: Gene expression from sorted CD11ahiCD49dlo 7 days after PbA infection

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The Affymetric Clariom S microarrays were analyzed with SST-RMA to detect the gene-level differential expression using the Affymetrix Transcriptome Anaylsis Console (TAC) 4.0 Software using default parameters. The significant genes (p<0.05) were ranked by fold-change with a cutoff of 2.

label: Biotin

source_name: D7 PbA CD11ahiCD49dlo_3 PbT-II

label_protocol: Synthesis of cDNA from the total RNA labeling were performed using GeneChip 3' IVT Pico Kit (Applied Biosystems) according to manufacturer’s instructions

growth_protocol: B6 mice were adoptively transferred with 1*10^6 PbT-II CD4 T cells , and then infected with PbA for 7 days

extract_protocol: Total RNA was prepared from purified T cell subpopulations using RNeasy Mini kit (Qiagen) according to manufacturer’s instructions

treatment_protocol: At D7 of PbA infection, mice spleen were harvested and CD45.1 PbT-II cells sorted based on their expression of CD11a and CD49d

value: 7 weeks

value: Spleen

tag: cell type

value: Antigen SP PbT-II CD4 T cells

tag: infection

value: PbA

tag: sorted subset of cells

value: sorted CD11ahiCD49dlo


title: CD4 T cell - αCD3/CD28+TRAIL_1 [a_CD328_TRA_1]

city: Taipei

first: I-Tsu

last: Chyuan

state: Outside of the US

address: No. 280, Sec. 4, Renai Rd.

department: Internal Medicine

country: Taiwan

institute: Cathay General Hospital

description:
a_CD328_TRA_1_S48_L003
processed data file: Diff_exprs_analysis_in vitro.xlsx

data_processing:
Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases.
Trimmed reads were aligned to the reference genome sequence using HISAT2 v2.1.0 aligner to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Differential expression analysis was performed using StringTie v2.1.4  and  DEseq2 v1.26.0 with genome bias detection/correction and Welgene Biotech's in-house pipeline.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Excel file include gene ID, gene type, gene name, gene length and TPM values for each samples.

source_name: CD4 T cell - αCD3/CD28+TRAIL

growth_protocol: Primary CD4 T cell isolated from C57/BL6 (4x10^7) culture in RPMI

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual.
All RNA sample preparation procedures were carried out according to the Illumina's official protocol. SureSelect XT HS2 mRNA Library Preparation kit (Agilent, USA)  was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

treatment_protocol: Treatment with medium, anti-CD3/CD28 antibodies (1mg/ml), or anti-CD3/CD28 antibodies (1mg/ml) plus TRAIL (10 ug/ml)

tag: tissue

value: lymph node

value: wild type

value: Primary CD4 T cell


title: D7 PbA CD11ahiCD49dlo, biological rep1

source_name: D7 PbA CD11ahiCD49dlo_1 PbT-II


title: CD4 T cell - αCD3/CD28+TRAIL_3 [a_CD328_TRA_3]

description:
a_CD328_TRA_3_S50_L003
processed data file: Diff_exprs_analysis_in vitro.xlsx


title: CD4 T cell - αCD3/CD28+TRAIL_2 [a_CD328_TRA_2]

description:
a_CD328_TRA_2_S49_L003
processed data file: Diff_exprs_analysis_in vitro.xlsx


title: D7 PbA CD11ahiCD49dhi, biological rep1

description: Gene expression from sorted CD11ahiCD49dhi 7 days after PbA infection

source_name: D7 PbA CD11ahiCD49dhi_1 PbT-II

value: sorted CD11ahiCD49dhi


title: D7 PbA CD11ahiCD49dlo, biological rep2

source_name: D7 PbA CD11ahiCD49dlo_2 PbT-II


title: IUE_sgPPM1D_exon6+H3K27M+PdgfraD842V_rep2

value: Brain tumor cells from DIPG mouse model

tag: treatment


title: D7 PbA CD11ahiCD49dhi, biological rep3

source_name: D7 PbA CD11ahiCD49dhi_3 PbT-II

tag: age


title: Tcf1-deficient CD8 T cells, Tcf1 ChIPseq

description: 22286_Sample_naiveCD8_TCF1_20160827000_peaks.xls

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ChIP-Seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a P value of < 1E-5, 4 fold enrichment  as identified Tcf1 binding peaks.
Genome_build: mm9

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, crosslinked and immunoprecipitated with anti-Tcf1 antiserum
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: naive CD8 T cells

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: naive CD8 T cells, Tcf1 ChIPseq


title: IUE_sgPPM1D_exon6+H3K27M+PdgfraD842V_rep1

value: untreated


title: RPE Control replicate 3

description: oligo-dT selected Total RNA isolated from RPE cells treated with control siiRNA

treatment_protocol: Nontargeting siRNA treatment (120 hr) (Sigma Aldrich, St. Louis MO, #SIC002)

value: non-targeting


title: D7 PbA CD11ahiCD49dhi, biological rep2

source_name: D7 PbA CD11ahiCD49dhi_2 PbT-II


title: SF7761_GSK_24hr #3

value: patient-derived DIPG cell line

value: GSK2830371 (10uM) for 24 hours


title: CD4 T cell - αCD3/CD28_3 [a_cd328_3]

description:
a_cd328_3_S47_L003
processed data file: Diff_exprs_analysis_in vitro.xlsx

source_name: CD4 T cell - αCD3/CD28


title: RPE Control replicate 2


title: SF7761_GSK_24hr #2


title: RPE Control replicate 1


title: CD4 T cell - αCD3/CD28_2 [a_cd328_2]

description:
a_cd328_2_S46_L003
processed data file: Diff_exprs_analysis_in vitro.xlsx


title: SF7761_GSK_24hr #1


title: RPE IntS13 gene body targeting knockdown replicate 1

value: IntS13 gene body


title: SF7761_GSK_5hr #3

value: GSK2830371 (10uM) for 5 hours


title: CD4 T cell - αCD3/CD28_1 [a_cd328_1]

description:
a_cd328_1_S45_L003
processed data file: Diff_exprs_analysis_in vitro.xlsx


title: CD4 T cell - medium_2 [medium_3]

description:
medium_3_S44_L003
processed data file: Diff_exprs_analysis_in vitro.xlsx

source_name: CD4 T cell - medium


title: AnTat1.1_input_2

city: Wuhan

first: chengjie

last: ma

address: luojiashan street 16

institute: Wuhan University

data_processing:
Raw data from Illumina Hiseq sequencing were analyzed by FastQC (v 0.11.5)
Low quality reads and adapter were removed to obtain clean data using the Trimmomatic software
Clean reads were aligned to the T. brucei reference genomes using BWA (v 0.7.12-r1039)
Peak calling was performed with MACS2 (v.2.1.1)
MEME-ChIP (v 4.11.2) was used for motif enrichment analysis
Genome_build: ASM244v1
Supplementary_files_format_and_content: bigwig files were generated using …;
Supplementary_files_format_and_content: peak bed files

organism: Trypanosoma brucei brucei

source_name: Trypanosoma brucei AnTat1.1

extract_protocol:
Purified trypanosomes were resuspended and lysed in SNET buffer (100 mM NaCl, 10 mM Tris–HCl, 25 mM EDTA, 0.5% SDS, pH 8.0) with 200 ng/µl proteinase K at 56°C for 3 h, followed by phenol-chloroform extraction and ethanol precipitation.
The enriched DNA fragments or the DNA fragments without enrichment (input) were end repaired and dA-tailed using Hieff NGS® Fast-Pace End Repair/dA-Tailing module (YEASEN Biotechnology Co., Ltd., Shanghai, China) according to the manufacture recommended protocol. As for the adapter ligation, end-repaired DNA, NEBNext adapter (15 μM), Fast-Pace DNA ligase and Fast-Pace DNA ligation Enhancer (YEASEN Biotechnology Co., Ltd., Shanghai, China) were incubated. The resulting DNA was purified with KAPA Pure beads (1.0× volume) (Kapa biosystems Pty Ltd., Cape Town, South Africa) to remove the excess adapter. The purified DNA was then amplified by PCR for 15 cycles. PCR products were sequentially purified using KAPA Pure beads (Kapa biosystems Pty Ltd., Cape Town, South Africa) and agarose gel using agarose gel extraction kit (Zymo Research). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The library was sequenced on an Illumina Hiseq platform and 150-bp paired-end reads were generated.

tag: pull-down


title: AnTat1.1_pull-down_2

value: pull-down with streptavidin beads


title: AnTat1.1_input_1


title: AnTat1.1_pull-down_1


title: SF7761_GSK_5hr #2


title: CD4 T cell - medium_1 [medium_1]

description:
medium_1_S43_L003
processed data file: Diff_exprs_analysis_in vitro.xlsx


title: SF7761_GSK_1hr #3

value: GSK2830371 (10uM) for 1 hour


title: SF7761_GSK_5hr #1


title: CD4 T cell - Lck Cre TRAIL-R f/f (TARIL)_2 [Cre_TRA_spleen_1]

description:
Cre_TRA_spleen_1_S48_L004
processed data file: Diff_exprs_analysis_in vivo.xlsx

value: spleen

value: Lck Cre TRAIL-R f/f


title: SF7761_GSK_1hr #2


title: CD4 T cell - Lck Cre TRAIL-R f/f (TARIL)_1 [Cre_spleen]

description:
Cre_spleen_S36_L002
processed data file: Diff_exprs_analysis_in vivo.xlsx


title: CD4 T cell - TRAIL-R f/f (TRAIL)_3 [TRA_spleen_2]

description:
TRA_R_flf_TRA_spleen_2_S45_L004
processed data file: Diff_exprs_analysis_in vivo.xlsx

source_name: CD4 T cell - TRAIL-R f/f (TRAIL)

value: TRAIL-R f/f


title: SF7761_GSK_1hr #1


title: Normal 1

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

description: rRNA-depleted total RNAs

data_processing:
The quality of sequence reads produced from the sequencer was checked by FastQC(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and sequences with low quality were trimmed using Trimmomatic (Bolger et al., 2014).
To analyze expression levels of mRNAs and lncRNAs, we utilized two different pipelines.
First, those trimmed sequences were aligned into mouse genome (mm10) using STAR aligner (Dobin et al., 2013). Normalized values of Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cuffnorm (Trapnell et al., 2012) based on recent basic gene annotation in GENCODE (Release M17, GRCm38.p6) (Harrow et al., 2006). We excluded genes from further analyses if their average FPKM values were less than 1 or FPKM was 0 in any sample. The t-test was applied to select those genes with significant expression change between normal and high fat diet groups.
Second, the same trimmed sequences were analyzed to quantify expression levels of transcripts using Salmon tool (Patro et al., 2017) and edgeR package (Robinson et al., 2010) was used to detect genes with significant expression changes.
Results from these two approaches were combined, and only those genes with significant expression changes in both pipelines were selected for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: The processed file contains the result from the first approach (normalized expression levels from cuffnorm algorithm) is provided with tab-delimited format.

growth_protocol: Male C57BL/6 mice (Orient) were obtained at 8 weeks of age. The mice were fed with either a conventional diet or a diet enriched with fat (60% wt/wt; Bio-Serv) for 8 weeks. At 16 weeks old, the high fat diet fed mice showed increased weight and impaired glucose tolerance. To obtain the brain cortexes, mice were sacrificed under ether anesthesia.

extract_protocol:
Total RNAs from brain cortexes were extracted using TRIzol reagent (Thermo Fisher) and a tissue homogenizer (Omni). The integrity of total RNA was checked using Agilent 2100 BioAnalyzer (Agilent). RNA integrity number (RIN) of all samples was greater than 9.
RNA samples were treated with Ribo-Zero Gold rRNA Removal Kit (Illumina) and library for RNA sequencing was prepared using TruSeq Stranded Total RNA Kit (Illumina).
The library was paired-end sequenced on HiSeq 2500 system (Illumina) with 100 sequencing cycles.

tag: diet

value: normal diet

value: cortex


title: HFD 3

description: rRNA-depleted total RNAs

value: high fat diet


title: Normal 3

description: rRNA-depleted total RNAs


title: HFD 4

description: rRNA-depleted total RNAs


title: Normal 4

description: rRNA-depleted total RNAs


title: HFD 2

description: rRNA-depleted total RNAs


title: Normal 2

description: rRNA-depleted total RNAs


title: CD4 T cell - TRAIL-R f/f (TRAIL)_2 [TRA_spleen_1]

description:
TRA_R_flf_TRA_spleen_1_S44_L004
processed data file: Diff_exprs_analysis_in vivo.xlsx

value: Primary CD4 T cell


title: CD4 T cell - TRAIL-R f/f (TRAIL)_1 [TRA_spleen]

description:
TRA_R_spleen_S34_L002
processed data file: Diff_exprs_analysis_in vivo.xlsx


title: SF7761_DMSO #3

value: DMSO


title: SF7761_DMSO #2


title: CD4 T cell - TRAIL-R f/f (Vehicle) [B6_spleen]

description:
B6_spleen_S32_L002
processed data file: Diff_exprs_analysis_in vivo.xlsx

source_name: CD4 T cell - TRAIL-R f/f (Vehicle)


title: SF7761_DMSO #1

source_name: Brain tumor cells


title: Tcf1/Lef1-deficient naïve CD8, DNase seq, rep2

data_processing:
Library strategy: Dnase-Seq
The sequencing quality of DNase-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Dnase-Seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a P value of < 1E-5, 4 fold enrichment  as identified binding sites.
Genome_build: mm9

source_name: CD8 T cells

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, lyzed and treated with DNase I
DNase libraries were prepared for sequencing using stardard Illumina protocol

value: splenocytes

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: HFD 1

description: rRNA-depleted total RNAs


title: Tcf1/Lef1-deficient naïve CD8, DNase seq, rep1


title: BT869_GSK_24hr #2


title: BT869_GSK_24hr #3


title: WT naïve CD8, DNase seq, rep3

value: wild type


title: NMZP rep2

city: Iowa City

first: Chen

last: Zhao

state: Iowa

address: 1163 Medical Laboratories

department: Pathology

institute: University of Iowa

description: pre-malignant cells

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 transcriptome index using kallisto v0.44.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts and TPM for each sample

source_name: Lymph Node

extract_protocol:
Control, singly-, doubly-activated B cells or transformed B cells were sort-purified and total RNA was extracted using standard Qiagen RNeasy columns
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lymph Node

value: marginal zone precursor B cells

value: Rosa-NIKdeltaT3flSTOP x CD19Cre

tag: activation

value: NF-kB-activated


title: RPE IntS13 utr targeting knockdown replicate 2

description: oligo-dT selected Total RNA isolated from RPE cells treated with siiRNA targeting IntS13 utr

value: IntS13 utr


title: NMZP rep1

description: pre-malignant cells

tag: strain


title: TMZP rep2

description: pre-malignant cells

value: Rosa-NIKdeltaT3flSTOP x Rosa-Notch2ICN x CD19Cre

value: doubly-activated


title: WT naïve CD8, DNase seq, rep2


title: BT869_GSK_5hr #3

value: patient-derived DIPG cell line

value: GSK2830371 (10uM) for 5 hours


title: BT869_GSK_24hr #1

value: GSK2830371 (10uM) for 24 hours


title: Tcf1/Lef1-deficient naive CD8+, H3K27ac ChIP-Seq, rep3

description: H3K27ac_naive-dKO-CD8-W200-G400-FDR0.01-island.bed


title: TMZP rep1

description: pre-malignant cells


title: Tcf1/Lef1-deficient naive CD8+, H3K27ac ChIP-Seq, rep2


title: BT869_GSK_5hr #2


title: BT869_GSK_5hr #1


title: CMZP rep2

description: pre-malignant cells

value: Wild-type

value: control


title: WT naive CD8+, H3K27ac ChIP-Seq, rep3

description: H3K27ac_naive-WT-CD8-W200-G400-FDR0.01-island.bed


title: WT naive CD8+, H3K27ac ChIP-Seq, rep4


title: CMZP rep1

description: pre-malignant cells


title: BT869_GSK_1hr #3

value: GSK2830371 (10uM) for 1 hour


title: IMZB rep2

description: pre-malignant cells

value: marginal zone B cells

value: Rosa-Notch2ICN x CD19Cre

value: Notch-activated


title: WT naive CD8+, H3K27ac ChIP-Seq, rep2

value: wild type

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: Tcf1/Lef1-deficient naive CD8+, HiC, rep2

data_processing:
The sequencing quality of Hi-C libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Hi-C libraries were mapped to mouse genome using hiclib (https://github.com/mirnylab/hiclib-legacy). UCSC genes for mouse mm9 from iGenome(http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
The resulting libraries were subject to further processing by Mirnylib (default parameters) and filterDuplicates (mode=’ram’) (https://github.com/mirnylab/hiclib-legacy) into hdf5 file.
The hdf5 files were converted into text files and then .hic files using Juicer (ref) pre function.
Genome_build: mm9

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, crosslinked, digested with three restriction enzymes and underwent proximity ligation.
The biotinylated DNA segments were captured, and ligated to the Illumina Paired End Adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: splenocytes


title: BT869_GSK_1hr #1


title: IMZB rep1

description: pre-malignant cells

value: Lymph Node


title: CZTRIBDN rep2

source_name: Lymphoma Cells

value: Lymphoma

value: lymphoma cells


title: WT naïve CD8, DNase seq, rep1


title: BT869_GSK_1hr #2


title: Tcf1/Lef1-deficient naive CD8+, HiC, rep1


title: BT869_DMSO #3

value: DMSO


title: WT naïve CD8+, HiC, Rep2


title: BT869_DMSO #2


title: CZTRIBDN rep1

value: Rosa-NIKdeltaT3flSTOP x Rosa-Notch2ICN x CD19Cre

value: doubly-activated


title: WT naïve CD8+, HiC, Rep1


title: Seven days old, FruLexA/Fru440 mutant - replicate 1

city: Chapel Hil

first: Corbin

last: Jones

state: NC

address: 250 Bell Tower Dr

department: Biology

institute: UNC-CH

description:
FRULEXAFRU440_1
QC warning
nFRULEXAFRU440_1_new_sequence_update.vs_dm6main.dm6_genes.mapspliceMulti.MpBC.counts.txt

data_processing:
Sequenced reads were filtered/trimmed with FASTP
Filtered reads were aligned to the dm6 reference genome (consolidated chromosomes only) using Mapsplice2 with default parameters
Samtools was used to filter alignments for read duplication ( rmdup -rS) and quality ( view -bh -q 20 -F 0x0200 -F 0x04 -f 0x0002 )
Mapped reads were counted against the reference gene annotation using featureCounts ( -J —verbose -M -p -B -C  )
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: Seven days old, FruLexA/Fru440 mutant

growth_protocol: Flies were raised on standard fly food (containing yeast, cornmeal, agar, and molasses) at 25°C in a 12-hour light/12-hour dark cycle in cylindrical plastic vials (diameter, 24 mm and height, 94 mm).

extract_protocol:
KAPA HYPER mRNA , NON stranded
Illumina NovaSeq 6000

treatment_protocol: For single housing (SH) condition, 80-100 hour-old pupae were separated by sex and males were placed into individual vials, allowed to eclose alone, and aged to 7 days to deprive flies of pheromone interaction on ORNs. For group housing (GH) condition, 25-30 newly eclosed males were collected and placed into food vials. These were aged to 7 days and 180 antennae were dissected per sample.

tag: replicate

tag: Sex

value: male

tag: housing

value: group

value: antennae


title: P23H DMSO_9DIV_rep1

status: Public on Jul 10 2021

city: Pittsburgh

first: Abhishek

last: Vats

state: PA

address: BST-3, Room no. 10051, 3501 Fifth Avenue

department: Ophthalmology

institute: University of Pittsburgh

description:
DMSO_1
Matrix table_TMM counts_9DIV

data_processing:
150 bp PE (paired-end) reads were sequenced on Illumina HiSeq sequencer (Illumnia Inc., San Diego, CA).
The reads were trimmed and first mapped to the hg38 UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed.
Goseq was used to perform the GO enrichment analysis and Kobas was used to performed the pathway analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with TMM normalised read count per million_1DIV
Supplementary_files_format_and_content: Matrix table with TMM normalised read count per million_9DIV

source_name: Retinal explant

growth_protocol: Retinal explant culture were maintained in neurobasal medium containing 2% B27 supplement and 5ug/ml of plasmocin prophylactic.

extract_protocol:
Eyes were enucleated at post natal day 15 and retina were cultured for 24 hours followed by the treatment of YC-001 and DMSO. Retinas were extracted from transwell membrane and RNA was isolated using RNAzol reagent.
Total RNA was isolated and DNase I treated using Qiagen RNeasy Plus Mini Kit (Qiagen, Valencia, CA). The RNA integrity was checked by Agilent Bioanalyzer 2100 or Tapestation 4200 (Agilent, Santa Clara, CA) and samples with clean rRNA peaks (RIN>6) were used for library preparation. RNA-Seq library was prepared according to KAPA mRNA HyperPrep kit with 200-300 bp insert size (Roche, Wilmington, MA) using 250 ng of total RNAs as input. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 or Tapestation 4200 and Qubit 3.0 Fluorometer (Thermo Fisher Scientific Inc, Waltham, MA). 150 bp PE (paired-end) reads were sequenced on Illumina HiSeq sequencer (Illumnia Inc., San Diego, CA).

treatment_protocol: Retinal explant culture were treated with YC-001 dissolved in DMSO or DMSO vehicle control.

value: retinal explant

tag: days in vitro

tag: genotyping

tag: model

value: adRP model


title: P23H DMSO_9DIV_rep3

description:
DMSO_3
Matrix table_TMM counts_9DIV


title: P23H YC-001_9DIV_rep2

description:
YC001_2
Matrix table_TMM counts_9DIV


title: P23H YC-001_9DIV_rep3

description:
YC001_3
Matrix table_TMM counts_9DIV


title: P23H YC-001_9DIV_rep1

description:
YC001_1
Matrix table_TMM counts_9DIV


title: WT DMSO_1DIV_rep1

description:
WT_DMSO_1
Matrix table_TMM counts_1DIV


title: WT DMSO_1DIV_rep2

description:
WT_DMSO_2
Matrix table_TMM counts_1DIV


title: P23H YC-001_1DIV_rep3

description:
Mutant_compound_3
Matrix table_TMM counts_1DIV


title: P23H YC-001_1DIV_rep2

description:
Mutant_compound_2
Matrix table_TMM counts_1DIV


title: 103959-001-068

city: Leiden

first: Anita

last: van den Hoek

state: Zuid-Holland

address: Zernikedreef 9

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina fastq files was performed by TRIMMOMATIC software.
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Genome_build: Mus_musculus.GRCm38.gencode.vM19
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: muscle

growth_protocol: Fourteen-sixteen weeks old male Ldlr-/-.Leiden mice (TNO, Metabolic Health Research, Leiden, The Netherlands) were used. This substrain of the Ldlr-/- mouse has a 94% C57BL/6J background and 6% 129S1/SvImJ background. Mice were group housed in a temperature-controlled room on a 12 hour light-dark cycle and had free access to food and heat sterilized water. Mice were first matched on age, body weight, blood glucose, plasma cholesterol and triglycerides into two groups of mice: mice (n=10; healthy reference group) that were kept on a grain-based low (9%) fat chow diet (R/M-H chow, Ssniff Spezialdieten GmbH, Soest, Germany) or mice (n=60) that were given a high fat diet (HFD) containing 45 kcal% fat from lard, 35 kcal% from carbohydrates and 20 kcal% casein (D12451, Research Diets, new Brunswick, NJ, USA) for 30 weeks to induce obesity, NASH and atherosclerosis.

extract_protocol:
RNA extraction was performed as described previously in detail [29]. Total RNA was extracted from individual liver (lobus dexter lateralis) samples (n=10-11/group), perigonadal WAT samples (n=8-10/group) and quadriceps (n=7-10/group) samples using glass beads and RNA-Bee (Campro Scientific, Veenendaal, The Netherlands). RNA integrity was examined using the RNA 6000 Nano Lab-on-a-Chip kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands).
To assess the quality of the samples, the concentration of the sample was determined using the Fragment Analyzer. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).
Clustering and DNA sequencing using the Illumina Nextseq 500 V2 or NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.6pM (NextSeq) or 1.1 nM (NovaSeq) of amplicon DNA was used yielding 15-25 million sequencing clusters per sample as: 2x 150 bp Paired-End reads (PE) for Muscle or 1x 75bp Single-End reads for Liver and Perigonadal WAT. NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: After 30 weeks mice on the HFD, the mice were matched another time for age, body weight, blood glucose, plasma cholesterol and triglycerides into four groups of mice: mice that remained on the HFD for another 20 weeks (n=17; HFD control group), mice that remained on HFD and received a running-wheel in their cage (n=17; exercise group), mice that were switched to the low fat chow diet (n=18; dietary intervention group) and mice that received a running-wheel and were switched to low fat chow diet (n=18; combination group). In addition to the aforementioned groups, an additional chow reference group (n=9) and an additional HFD reference group (n=10) were added that were sacrificed after 30 weeks of diet feeding to determine liver pathology as a start-of-intervention reference. At t=50 weeks mice were sacrificed unfasted using gradual-fill CO2 asphyxiation. Terminal blood was collected through cardiac heart puncture to prepare EDTA plasma and livers, perigonadal and visceral white adipose tissue (WAT) and muscles (gastrocnemius and quadriceps) were collected.

value: HFD

value: Chow

value: Y

tag: mousenr


title: 103959-001-074


title: 103959-001-022


title: 103959-001-017


title: 103959-001-073


title: 103959-001-065


title: P23H YC-001_1DIV_rep1

description:
Mutant_compound_1
Matrix table_TMM counts_1DIV


title: P23H DMSO_1DIV_rep3

description:
Mutant_DMSO_3
Matrix table_TMM counts_1DIV

value: Rho+/+

value: Wild type


title: 103959-001-067


title: 103959-001-066


title: P23H DMSO_1DIV_rep2

description:
Mutant_DMSO_2
Matrix table_TMM counts_1DIV


title: 103959-001-024


title: P23H DMSO_9DIV_rep2

description:
DMSO_2
Matrix table_TMM counts_9DIV


title: 103959-001-071


title: 103959-001-078


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 50, line 3

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
small RNAs (polyphosphatase treated, 16-30 nt)
SetF_generation50_sRNA_counts.csv

data_processing:
Base calling and fastq file generation was done using Illumina software.
Other data processing steps added to SAMPLES section.
Genome_build: WS230

organism: Caenorhabditis elegans

source_name: gravid adults/whole animals, 20C

growth_protocol: Worms were grown at 20˚C on NGM containing E. coli (OP50).

extract_protocol:
Worms were washed from plates and rinsed with M9 3 times and flash frozed in liquid nitrogen. RNA was isolated using trizol/chloroform and isopropanol precipitation.
mRNA Libraries: RNA was depleted of rRNA using RiboZero and enriched for >200nt sizes with Zymo RNA clean and concentrator-5. Libraries were then prepared according to the NEBNext® Ultra™ II Directional RNA kit or Illumina TruSeq Stranded Total RNA kit protocol. Size selection and library purification was done using AMPure XP beads. Small RNA Libraries: Small RNAs (~16-30-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with RNA polyphosphatase to facilitate capture of 22G-RNAs. Libraries were then prepared according to the NEBNext® Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels.

tag: genotype


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 50, line 2


title: WT DMSO_1DIV_rep3

description:
WT_DMSO_3
Matrix table_TMM counts_1DIV


title: 103959-001-021


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 50, line 1


title: 103959-001-080


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 50, sRNA, line 2


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 50, sRNA, line 3


title: 103959-001-027


title: 103959-001-054


title: 103959-001-056


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 50, sRNA, line 1


title: 103959-001-077


title: SX922[prg-1(n4357) I], generation 50, sRNA, line 3


title: 103959-001-028


title: 103959-001-075


title: SX922[prg-1(n4357) I], generation 50, sRNA, line 2


title: 103959-001-076


title: wild type (N2), generation 50, sRNA, line 3

value: wild type (N2)


title: P23H DMSO_1DIV_rep1

description:
Mutant_DMSO_1
Matrix table_TMM counts_1DIV


title: 103959-001-009

value: N


title: wild type (N2), generation 50, sRNA, line 2


title: 103959-001-057


title: wild type (N2), generation 50, sRNA, line 1


title: WM161 [prg-1(tm872) I], sRNA, rep 3

description:
small RNAs (polyphosphatase treated, 16-30 nt)
SetE_prg-1_tm872_sRNA_counts.csv

source_name: gravid adults (68h)/whole animals, 20C


title: WM161 [prg-1(tm872) I], sRNA, rep 2


title: wild type (N2), sRNA, rep 3


title: 103959-001-064


title: WM161 [prg-1(tm872) I], sRNA, rep 1


title: 103959-001-059


title: 103959-001-061


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 1, sRNA, rep 3

description:
small RNAs (polyphosphatase treated, 16-30 nt)
SetD_generation1_sRNA_counts.csv

source_name: gravid adults (72h)/whole animals, 20C


title: wild type (N2), sRNA, rep 1


title: 103959-001-060


title: 103959-001-043


title: 103959-001-044


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 1, sRNA, rep 1


title: 103959-001-041


title: SX922[prg-1(n4357) I], generation 50, sRNA, line 1


title: 103959-001-047


title: wild type (N2), sRNA, rep 2


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 1, sRNA, rep 2


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 1, sRNA, rep 1


title: 103959-001-048


title: 103959-001-003


title: 103959-001-051


title: 103959-001-063


title: 103959-001-049


title: SX922[prg-1(n4357) I], generation 1, sRNA, rep 1


title: 103959-001-045


title: 103959-001-046


title: wild type (N2), generation 1, sRNA, rep 3


title: 103959-001-050


title: wild type (N2), generation 1, sRNA, rep 2


title: wild type (N2), generation 1, sRNA, rep 1


title: 103959-001-006


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 50, mRNA, line 3

description:
total RNA (rRNA-depleted, >200 nt)
SetC_generation50_mRNA_counts.csv


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 1, sRNA, rep 2


title: 103959-001-037


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 50, mRNA, line 1


title: 103959-001-039


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 50, mRNA, line 2


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 50, mRNA, line 1


title: SX922[prg-1(n4357) I], generation 1, sRNA, rep 3


title: 103959-001-040


title: 103959-001-035


title: SX922[prg-1(n4357) I], generation 1, sRNA, rep 2


title: 103959-001-042


title: SX922[prg-1(n4357) I], generation 50, mRNA, line 3


title: SX922[prg-1(n4357) I], generation 50, mRNA, line 2


title: 103959-001-086

source_name: eWAT


title: 103959-001-083


title: SX922[prg-1(n4357) I], generation 50, mRNA, line 1


title: wild type (N2), generation 50, mRNA,  line 2


title: 103959-001-081


title: 103959-001-082


title: wild type (N2), generation 50, mRNA,  line 3


title: 103959-001-036


title: wild type (N2), generation 50, mRNA,  line 1


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 1, mRNA, rep 3

description:
total RNA (rRNA-depleted, >200 nt)
SetB_generation1_mRNA_counts.csv


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 50, mRNA, line 2


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 1, mRNA, rep 2


title: 103959-001-088


title: 103959-001-092


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 50, mRNA, line 3


title: 103959-001-090


title: 103959-001-034


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 1, mRNA, rep 3


title: GR2070 [prg-1(n4357) I; mut-14(mg464) smut-1(tm1301) V], generation 1, mRNA, rep 1


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 1, mRNA, rep 2


title: Experiment 1 - Lvpl1

city: St. Louis

first: Steven

last: Bassnett

state: MO

address: McMillan Building, 517 S Euclid Ave

institute: WUSTL Ophthalmology

description: 3 sets of mouse eyes were used for this sample

data_processing:
Both data sets were base-called with Illumina Software Casava v1.8
Data was aligned to a mouse genome build (similar to mm10) by Cell Ranger
Cell Ranger filtered raw counts, eliminating background transcriptional noise
Both data sets were analyzed together as one large object in R with Seurat
Data was filtered downstream in R by Seurat's QC variables: percent mitochondrial genes, nfeature_RNA and nCount_RNA as specified in the manuscript's R script file
Genome_build: refdata - cell ranger - GRCm38 -2.0.1 -
Supplementary_files_format_and_content: txt files generated from raw count matrices show quantity of mRNA transcripts within the generated cDNA library for all genes within the genome build belonging to each cell, labeled by barcode.  Also provided: barcodes, features, matrix.

source_name: Ciliary Epithelium

growth_protocol: N/A - cells dissected from fresh samples

extract_protocol:
All tissue fragments were combined, then were treated with Collagenase 1(Sigma Aldrich, Cat. No. LS004196) and 3 (Worthington Biochem, Cat. No. LS004182) at 37˚C for a period of 20 minutes.  Both enzymes were applied at a concentration of 4.2 mg/mL in TESCA buffer (4.75 mL H20: 250 uL 1M TES: 7.2 uL 0.25 M CaCl2).  Then, 100 uL of DNase1 (0.5U/uL) was added and allowed 7 more minutes of incubation at 37˚C.  1.5 mL of DMEM/10% FBS was added to quench enzyme action after this.  The cell suspension was then transferred to room temperature and was triturated slowly and continuously with a 1mL capacity pipette with a wide-bored tip for 5 minutes.  Subsequently, 1 minute was allowed for large pieces of tissue to settle to the bottom of the tube, and supernatant containing the cell suspension was drawn off.  The suspension was centrifuged on a swinging bucket rotor centrifuge for 10 minutes at 100xg.  The cell pellet was resuspended in 220uL of PBS with 0.04% BSA and pressed through a 40um Flowmi cell strainer, leaving 200um of suspended single cell solution.
RNA libraries were prepared for sequencing using standard Illumina NovaSeq6000 protocols
scRNA-seq (GEM)

treatment_protocol: Tissue was dissected in 37 C DMEM and fragmented to increase surface area for enzyme digestion

value: Ciliary Epithelium

value: post natal day 35

tag: sample size


title: Experiment 2 - Lvpl3

description: 3 sets of murine eyes were used for this sample

value: 4 sets of murine eyes were used for this sample


title: KO10

city: Nalaga

first: Ramon

last: Muñoz-Chápuli

address: Campus de Teatinos

country: Spain

institute: University of Malaga

data_processing:
Quality control - Mapping to reference genome: Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were  based on the clean data with high quality.
Quantification: HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.

source_name: whole heart

extract_protocol:
Total RNA from each heart was extracted by using RNAqueous™-Micro Total RNA Isolation Kit (Ambion, AM1931) following manufacturer's instructions. Transcriptome analysis of total RNA was performed by Novogene (https://en.novogene.com/). Only RNA samples with RNA integrity number (RIN) higher than 8.5 were selected for libraries preparation.
200 ng of total RNA was subsequently used to prepare RNA-Seq library by using TruSeq RNA sample prep kit (Illumina) according to manufacturer's instructions. Paired-end (2x150) RNA sequencing was performed on Illumina NovaSeq 6000 plataform (Illumina).

tag: developmental stage

value: Cardiac tissue

value: C57BL/6 x DBA/2


title: KO5

tag: tissue


title: SX922[prg-1(n4357) I], generation 1, mRNA, rep 3


title: KO1


title: Wt5

value: wild type


title: SX922[prg-1(n4357) I], generation 1, mRNA, rep 1


title: 103959-001-087


title: Wt3


title: SX922[prg-1(n4357) I], generation 1, mRNA, rep 2


title: wild type (N2), generation 1, mRNA, rep 3


title: Wt2


title: wild type (N2), generation 1, mRNA, rep 1


title: wild type (N2), non-polyA-selected, mRNA, rep 3

description:
total RNA (rRNA-depleted, >200 nt)
SetA_polyA_vs_total_counts.csv


title: wild type (N2), non-polyA-selected, mRNA, rep 2


title: wild type (N2), non-polyA-selected, mRNA, rep 1


title: wild type (N2), polyA-selected, mRNA, rep 3

description:
polyA-selected total RNA (rRNA-depleted, >200 nt)
SetA_polyA_vs_total_counts.csv

molecule: polyA RNA


title: s103566-001-096


title: s103566-001-110


title: s103566-001-090


title: wild type (N2), polyA-selected, mRNA, rep 1


title: GR1948 [unc-119(ed3) III; mut-14(mg464) smut-1(tm1301) V], generation 1, mRNA, rep 1


title: wild type (N2), polyA-selected, mRNA, rep 2


title: s103566-001-109


title: s103566-001-082


title: SAMPLE 64:HC 34

type: genomic

city: Changsha

first: hy

last: long

address: xiangya road

institute: xiangya hospital

hyb_protocol: Samples were processed for array hybridization using Illumina provided array reagents.

scan_protocol: performed on the illumina iScan system following the manufacturer’s procedure.

data_processing: The array data (.IDAT files) was analyzed using ChAMP package in R for deriving the methylation level .

label: Cy5 and Cy3

source_name: peripheral blood

label_protocol: performed using  Illumina Human Methylation 850k BeadChip Kit

extract_protocol: Whole blood DNA was extracted from the blood samples of patients and control subjects using a commercial kit (Beijing Adly Biological Company, Beijing, China)

tag: disease state

value: normal

tag: gender

value: male

value: peripheral blood


title: SAMPLE 61:HC 31


title: SAMPLE 62:HC 32

value: female


title: SAMPLE 63:HC 33


title: SAMPLE 60:HC 30


title: s103566-001-080

value: HFD


title: SAMPLE 59:HC 29


title: wild type (N2), generation 1, mRNA, rep 2


title: s103566-001-081

value: Chow


title: s103566-001-079


title: s103566-001-077


title: SAMPLE 58:HC 28


title: s103566-001-085R


title: SAMPLE 57:HC 27


title: s103566-001-084R


title: s103566-001-106

value: Y


title: s103566-001-111


title: SAMPLE 56:HC 26


title: s103566-001-102


title: s103566-001-099


title: SAMPLE 55:HC 25


title: s103566-001-097


title: s103566-001-098


title: SAMPLE 54:HC 24


title: s103566-001-075


title: s103566-001-076


title: SAMPLE 52:HC 22


title: s103566-001-074


title: s103566-001-078


title: SAMPLE 53:HC 23


title: s103566-001-072


title: s103566-001-068


title: s103566-001-067


title: s103566-001-065


title: SAMPLE 49:HC 19


title: SAMPLE 51:HC 21


title: SAMPLE 50:HC 20


title: s103566-001-066


title: s103566-001-063


title: s103566-001-064


title: SAMPLE 47:HC 17


title: s103566-001-060


title: SAMPLE 48:HC 18


title: 2169-1_heart_WT

city: Baltimore

first: Mark

middle: E

last: Anderson

state: MD

address: Rangos 471, 855 N. Wolfe Street

department: Department of Medicine

institute: Johns Hopkins School of Medicine

description: wildtype

data_processing:
#Quality check: fastqc
#Trimming: (tests were done to decide that  trimming was not necessary.)
Reads alignment was done with Tophat using  mm10_refseq_nopseudo transcriptome index
ClassifyReads: #counts of how many reads are exonic, intronic, intergenic and overlaping a splice junction
Stringtie: assembly the reads into transcripts
Stringtie --merge :  # merging transcripts form all samples in one nonredundant file. Automatically filters a number of transfrags that are probably artfifacts. A reference annotation file  was used in order to merge novel isoforms and known isoforms and maximize overall assembly quality.  # This will be used further on, in the analysis (cuffdiff);
Cuffdiff  v2.2.1: # used to find significant changes in transcript expression.
Samtools: samtools index file.bam
IGV: # vizualize  alignments and assemblies
Genome_build: Genome version : mm10
Supplementary_files_format_and_content: .xlsx file of FPKM values. One biological sample per column.

extract_protocol:
To obtain high quality total RNA, the hearts were processed first in the Trizol reagent (ThermoFisher Scientific, Catalog # 15596018), and then by RNeasy mini columns (Qiagen, catalog # 74104) as follows. To avoid sampling bias, the entire hearts were homogenized in Trizol reagent at a weight (mg) to volume (µL) ratio of 1:15. Then, 1 mL of the homogenate was processed following the manufacturer's protocol until the step of phase separation. 0.5 mL of the aqueous phase was then mixed with an equal volume of 70% ethanol for subsequent RNA purification by the RNeasy mini kit. An on-column DNAse (RNase-Free DNase Set, Qiagen catalog # 79254) treatment step was included. The concentration of the RNA was determined by Qubit fluorometric quantitation (Qubit RNA BR Assay Kit, ThermoFisher Scientific, catalog # Q10210). The integrity of the total RNA was determined by a Fragment Analyzer (Advanced Analytical Technologies, Inc). The average RNA Quality Number (RQN) was 8.77 ± 0.07 (Mean ± SEM, n=24).
1 µg of total RNA from each sample was used for RNA sequencing library preparation with the TruSeq® Stranded mRNA Library Prep kit (Illumina, catalog # 20020594). The libraries were barcoded by TruSeq® RNA Unique Dual Indexes (Illumina, catalog # 20022371) and quantified by qPCR on a Bio-Rad CFX Connect Real-Time PCR detection system with the NEBNext Library Quant Kit for Illumina (New England Biolabs, catalog # E7630L). The libraries were normalized to 10 nM, pooled and sequenced.
RNA-seq. RNA sequencing was carried out at Johns Hopkins School of Medicine Genetic Resources Core Facility on a NovaSeq 6000 sequencing system (Illumina) with a S1 flow cell for 200 cycles, generating 100 bp paired-end reads.

treatment_protocol: No treatment

value: wildtype


title: s103566-001-058


title: s103566-001-057


title: 2168-4_heart_WT

description: wildtype


title: s103566-001-040

source_name: Liver


title: s103566-001-073


title: SAMPLE 46:HC 16


title: s103566-001-069


title: s103566-001-054


title: 2168-1_heart_WT

description: wildtype


title: SAMPLE 45:HC 15


title: s103566-001-036


title: s103566-001-039


title: SAMPLE 44:HC 14


title: 2048-4_heart_WT

description: wildtype


title: s103566-001-035


title: s103566-001-033


title: s103566-001-059


title: SAMPLE 43:HC 13


title: s103566-001-034


title: 2048-3_heart_WT

description: wildtype


title: s103566-001-053


title: 2298-4_heart_OGT_TG_x_OGA_TG

description: cardiac specific OGA x OGT double transgenic


title: 2047-4_heart_WT

description: wildtype


title: s103566-001-030R


title: SAMPLE 41:HC 11


title: 2298-1_heart_OGT_TG_x_OGA_TG


title: SAMPLE 40:HC 10


title: s103566-001-027


title: s103566-001-026


title: s103566-001-031


title: s103566-001-025


title: 2145-2_heart_OGT_TG_x_OGA_TG


title: SAMPLE 39:HC 9


title: s103566-001-023


title: SAMPLE 38:HC 8


title: s103566-001-024


title: s103566-001-022


title: s103566-001-021


title: 2010-3_heart_OGT_TG_x_OGA_TG


title: SAMPLE 37:HC 7


title: SAMPLE 42:HC 12


title: s103566-001-032


title: s103566-001-028R


title: 2007-1_heart_OGT_TG_x_OGA_TG


title: s103566-001-051


title: s103566-001-055


title: 2169-2_heart_OGT_TG

description: cardiac specific OGT transgenic


title: SAMPLE 36:HC 6


title: SAMPLE 34:HC 4


title: SAMPLE 35:HC 5


title: s103566-001-048


title: 2168-3_heart_OGT_TG

description: cardiac specific OGT transgenic


title: SAMPLE 33:HC 3


title: s103566-001-044


title: 2168-2_heart_OGT_TG

description: cardiac specific OGT transgenic


title: s103566-001-045


title: s103566-001-043


title: 2010-7_heart_OGT_TG_x_OGA_TG


title: 2048-5_heart_OGT_TG

description: cardiac specific OGT transgenic


title: s103566-001-042


title: s103566-001-029R


title: SAMPLE 32:HC 2


title: s103566-001-041


title: SAMPLE 31:HC 1


title: s103566-001-052


title: s103566-001-020


title: 2047-5_heart_OGT_TG

description: cardiac specific OGT transgenic


title: 2048-1_heart_OGT_TG

description: cardiac specific OGT transgenic


title: SAMPLE 30:ICH 30

value: ICH


title: s103566-001-050


title: SAMPLE 29:ICH 29


title: 2138-3_heart_OGA_TG

description: cardiac specific OGA transgenic


title: s103566-001-049


title: s103566-001-017


title: s103566-001-016


title: s103566-001-019


title: SAMPLE 28:ICH 28


title: s103566-001-018


title: s103566-001-015


title: s103566-001-013


title: 2138-2_heart_OGA_TG

description: cardiac specific OGA transgenic


title: SAMPLE 27:ICH 27


title: s103566-001-012


title: 2138-1_heart_OGA_TG

description: cardiac specific OGA transgenic


title: 2086-4_heart_OGA_TG

description: cardiac specific OGA transgenic


title: SAMPLE 26:ICH 26


title: s103566-001-010


title: 2086-2_heart_OGA_TG

description: cardiac specific OGA transgenic


title: s103566-001-009


title: s103566-001-008


title: s103566-001-007


title: SAMPLE 25:ICH 25


title: 2086-1_heart_OGA_TG

description: cardiac specific OGA transgenic


title: SAMPLE 24:ICH 24


title: jmj7-rep3

city: guangzhou city

first: Ding

last: xiaochun

state: guangdong

address: 723 xingke road, tianhe district

institute: SOUTH CHINA BOTANICAL GARDEN

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the tomato reference genome (version SL3.0) using HISAT2.2.4 with "-rna-strandness RF" and other parameters set as a default.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: Tomato reference genome (version SL3.0)
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

organism: Solanum lycopersicum

growth_protocol: Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.

extract_protocol:
Pericarp at the equatorial part of the fruit  were collected, immediately frozen in liquid nitrogen, and total RNA was extracted using Trizol reagent kit. mRNA Seq Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background

value: Ailsa Craig

tag: genotype/variation

value: At 38 days after anthesis (dpa)

value: Pericarp


title: s103566-001-005

value: N


title: jmj7-rep2


title: SAMPLE 23:ICH 23


title: SAMPLE 22:ICH 22


title: SAMPLE 21:ICH 21


title: jmj7-rep1


title: s103566-001-003


title: s103566-001-004


title: WT rep2

value: WT


title: WT rep3


title: s103566-001-002


title: s103566-001-011


title: s103566-001-001


title: SAMPLE 20:ICH 20


title: SAMPLE 19:ICH 19


title: WT rep1


title: SAMPLE 18:ICH 18


title: s103566-001-006


title: JMJ7-OE_GFP_ChIPSeq_Input rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to Tomato reference genome (version SL3.0) using the BWA program.
Peaks were called using MACS2 software with the following setting: MACS2 callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B –SPMR --broad --broad-cutoff 0.05.
Genome_build: Tomato reference genome (version SL3.0)
Supplementary_files_format_and_content: bigwig files were generated using MACS2 software.

extract_protocol:
Pericarp at the equatorial part of the fruit were collected, immediately cross-linked in 1% formaldehyde for chromatin isolation and Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: develpmental stage


title: GPN11897_10_R: Tumor_2_mRNA mixture

city: Cambridge

first: Joon Sang

last: Lee

state: MA

address: 270 Albany Street

department: Oncology

institute: Sanofi

description: cytokine mRNA mixture

data_processing:
STAR aligner
Cufflink
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

source_name: subcutaneous tumor

growth_protocol: 0.5 x 10^6 cells were injected subcutaneously into C57BL6/J mice.

extract_protocol:
Qiagen total RNA extraction with DNase treatment
RNA libraries were prepared for sequencing using stranded NuGEN protocols

treatment_protocol: Tumors were treated with a single intratumoral injection of 80 µg of mRNA.  Tumor tissue was collected for RNA extration 7 days following intratumoral mRNA injection.

value: murine melanoma

tag: tumor type

value: subcutaneous tumor


title: GPN11897_5_R: Tumor_1_Luc mRNA

description: Control mRNA


title: GPN11897_9_R: Tumor_2_mRNA mixture

description: cytokine mRNA mixture


title: GPN11897_7_R: Tumor_2_mRNA mixture

description: cytokine mRNA mixture


title: GPN11897_8_R: Tumor_2_mRNA mixture

description: cytokine mRNA mixture


title: GPN11897_4_R: Tumor_1_Luc mRNA

description: Control mRNA


title: BJAB cells, Infected with EBV, biological rep 3, input

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

description:
Input data for human B lymphoma cell line BJAB infected with EBV for 24 hours.
BJAB-EBV-3-peaks.xlsx
BJAB-EBV-3-INPUT

data_processing:
Raw data were processed using Trimmomatic(v0.32), the adaptor bases and the low quality reads were removed to obtain the clean reads.
The clean reads were aligned to genome reference sequences and EBV reference genome using HISAT2 software (v2.1.0).
Peak calling was performed using the exomePeak software(v2.13.2). The peaks were annotated according to the annotation information in Ensembl. The EBV reference genome and annotation were downloaded from https://www.ncbi.nlm.nih.gov/nuccore/NC_007605.1.
Genome_build: human GRCh37 and EBV reference genome(NC_007605.1)
Supplementary_files_format_and_content: xlsx files include peak information and annotations

source_name: B lymphoma

growth_protocol: The human B lymphoma cell lines BJAB were cultured in both RPMI 1640 medium supplemented with 10% fetal bovine serum. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

extract_protocol:
Intact mRNA was isolated from total RNA samples using Arraystar Seq-StarTM poly(A) mRNA Isolation Kit according to the manufacturer’s protocol. Isolated mRNA was chemically fragmented into 100-nucleotide-long fragments by incubation in fragmentation buffer. m6A methylated mRNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody, and also a part of the fragmented mRNAs was kept as input. The major procedures contained immunoprecipitation, wash and elution. Both m6A enriched mRNAs and input mRNAs were concentrated for RNA-seq library construction.
RNA-seq libraries of m6A antibody enriched mRNAs and input mRNAs were prepared using KAPA Stranded mRNA-seq Kit (Illumina).

treatment_protocol: Cells were grown in RPMI 1640 medium (with 10% serum), and was uninfected or infected with EBV for 24 hours.

tag: cell line

value: B lymphoma cell line BJAB

tag: infection

value: EBV

tag: merip antibody


title: SAMPLE 17:ICH 17


title: BJAB cells, Infected with EBV, biological rep 3, m6A-RIP

description:
MeRIP data of human B lymphoma cell line BJAB infected with EBV for 24 hours.
BJAB-EBV-3-peaks.xlsx
BJAB-EBV-3-IP

value: anti-N6-methyadenosine (m6A) antibody (Synaptic Systems, catalog# 202003, lot# 2-89)


title: GPN11897_3_R: Tumor_1_Luc mRNA

description: Control mRNA


title: BJAB cells, Infected with EBV, biological rep 2, input

description:
Input data for human B lymphoma cell line BJAB infected with EBV for 24 hours.
BJAB-EBV-2-peaks.xlsx
BJAB-EBV-2-INPUT


title: JMJ7-OE_GFP_ChIPSeq_Input rep2


title: SAMPLE 16:ICH 16

value: male

value: peripheral blood


title: SAMPLE 15:ICH 15


title: GPN11897_6_R: Tumor_2_mRNA mixture

description: cytokine mRNA mixture


title: BJAB cells, Infected with EBV, biological rep 2, m6A-RIP

description:
MeRIP data of human B lymphoma cell line BJAB infected with EBV for 24 hours.
BJAB-EBV-2-peaks.xlsx
BJAB-EBV-2-IP


title: GPN11897_2_R: Tumor_1_Luc mRNA

description: Control mRNA


title: JMJ7-OE_GFP_ChIPSeq_Input rep1


title: GPN11897_1_R: Tumor_1_Luc mRNA

description: Control mRNA


title: BJAB cells, Infected with EBV, biological rep 1, input

description:
Input data for human B lymphoma cell line BJAB infected with EBV for 24 hours.
BJAB-EBV-1-peaks.xlsx
BJAB-EBV-1-INPUT


title: JMJ7-OE_GFP_ChIPSeq_IP rep3

tag: chip antibody

value: GFP (ab290, Abcam)


title: JMJ7-OE_GFP_ChIPSeq_IP rep2


title: BJAB cells, Infected with EBV, biological rep 1, m6A-RIP

description:
MeRIP data of human B lymphoma cell line BJAB infected with EBV for 24 hours.
BJAB-EBV-1-peaks.xlsx
BJAB-EBV-1-IP


title: SAMPLE 13:ICH 13

value: female


title: SAMPLE 14:ICH 14


title: G4: GSK343

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
Illumina Hi-Seq 2500 platform was used for RNA-sequencing
Sequenced reads were trimmed using Trimmomatic version 0.33 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15; and then mapped to mouse reference genome version mm10 using HISAT2 version 2.1.0 with parameters --mp 6,2 --rdg 5,3--rfg 5,3
Transcriptome assembly and gene expression quantification were performed using StringTie version 1.3.3b with default parameters to calculate FPKM values
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for each gene

source_name: Mouse HEPA1-6 Tumors

growth_protocol: HEPA1-6 cells were subcuteneously injected into C57/BL6 and tumors were grown for 4 weeks.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.

treatment_protocol: C57/BL6 tumors injected with Control antibody or Anti-AsilaoGM1 antibody was treated with or without EZH2 inhibitor GSK343

tag: strain

value: Mouse HEPA1-6 Tumor


title: BJAB cells, Uninfected, biological rep 3, input

description:
Input data for human B lymphoma cell line BJAB uninfected for 24 hours.
BJAB-Control-3-peaks.xlsx
BJAB-Control-3-INPUT


title: JMJ7-OE_GFP_ChIPSeq_IP rep1


title: G5: GSK343


title: SAMPLE 12:ICH 12


title: BJAB cells, Uninfected, biological rep 3, m6A-RIP

description:
MeRIP data of human B lymphoma cell line BJAB uninfected for 24 hours.
BJAB-Control-3-peaks.xlsx
BJAB-Control-3-IP


title: G2: GSK343


title: G3: GSK343


title: SAMPLE 10:ICH 10


title: G1: GSK343


title: jmj7_H3K4me3_ChIPSeq_Input rep1


title: jmj7_H3K4me3_ChIPSeq_Input rep2


title: SAMPLE 11:ICH 11


title: SAMPLE 9:ICH 9


title: SAMPLE 8:ICH 8


title: BJAB cells, Uninfected, biological rep 2, m6A-RIP

description:
MeRIP data of human B lymphoma cell line BJAB uninfected for 24 hours.
BJAB-Control-2-peaks.xlsx
BJAB-Control-2-IP


title: BJAB cells, Uninfected, biological rep 1, input

description:
Input data for human B lymphoma cell line BJAB uninfected for 24 hours.
BJAB-Control-1-peaks.xlsx
BJAB-Control-1-INPUT


title: C6


title: SAMPLE 7:ICH 7


title: jmj7_H3K4me3_ChIPSeq_IP rep2

value: H3K4me3 (ab8580, Abcam)


title: C3


title: C5


title: KOCK_3

first: Chenmi

last: Mo

address: Shizishan street 1st

institute: HuaZhong Argriculture university

data_processing:
Illumina Hiseq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Purpureocillium linacinum strain PLFJ-1 whole genome using HISAT2 v2.0.1
The counts were normalized by HTSeq v0.6.1, and differential expression genes were screened using the edgeR package with the false discovery rate (FDR) < 0.05.
Genome_build: Purpureocillium linacinum strain PLFJ-1
Supplementary_files_format_and_content: raw counts

organism: Purpureocillium lilacinum

source_name: Fungal mycelia

extract_protocol:
Mycelia were collected, flash frozen on dry ice, and RNA was 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 protocol

value: Mycelia

value: PlCYP5 gene mutant


title: BJAB cells, Uninfected, biological rep 1, m6A-RIP

description:
MeRIP data of human B lymphoma cell line BJAB uninfected for 24 hours.
BJAB-Control-1-peaks.xlsx
BJAB-Control-1-IP


title: jmj7_H3K4me3_ChIPSeq_IP rep1

value: Ailsa Craig

value: At 38 days after anthesis (dpa)


title: C2


title: SAMPLE 6:ICH 6

value: ICH


title: SAMPLE 5:ICH 5


title: KOCK_2


title: C1


title: jmj7_H3K4me3_ChIPSeq_Input rep3

value: Pericarp


title: BJAB cells, Uninfected, biological rep 2, input

description:
Input data for human B lymphoma cell line BJAB uninfected for 24 hours.
BJAB-Control-2-peaks.xlsx
BJAB-Control-2-INPUT


title: WT_H3K4me3_ChIPSeq_Input rep2

value: WT


title: WT_H3K4me3_ChIPSeq_Input rep3


title: 8505C-PTX

city: Udine

first: Giuseppe

last: Damante

address: via chiusaforte, E

department: Medical Area

country: Italy

institute: University of Udine

data_processing:
Bcl2Fastq version 2.20 in the Illumina pipeline was used for processing the raw data (format conversion and de-multiplexing).
Adapter sequences were masked with Cutadapt2 version 1.11 from raw fastq data and the ERNE software was used to remove lower quality bases and adapters.
Assembly and quantitation of full-length transcripts representing multiple spliced variants for each gene locus was performed using the Stringtie tool.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.tab: Tab-delimited text files include FPKM and TPM values for each Sample.

source_name: 8505C-PTX cell line

growth_protocol: SW1736 and 8505C cells, derived from ATC, were grown in RPMI-1640 medium supplemented with 10% FBS, 2 mM L-glutamine and 50 mg/ml gentamicin, in a humidified incubator (5% CO2, 95% air, at 37°C).

extract_protocol:
RNA of SW1736 and 8505C cells, wt or PTX-resistant, was extracted using a RNeasy Mini kit according to the manufacturer's instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the Universal Plus mRNA-Seq kit, according to the manufacturer's instructions.

treatment_protocol: To obtain ATC paclitaxel-resistant cell lines (SW1736-PTX and 8505C-PTX), the two parental cell lines were treated with increasing doses of paclitaxel arising from 1 nM to 1.5 μM for 6 months. Resistance to pacitaxel was considered to be acquired when a 1.5 μM dose resulted in no effect in terms of cell viability. Resistant cells have been cultured in RPMI-1640 medium supplemented with 10%, 2 mM L-glutamine, 50 mg/ml gentamicin and paclitaxel 1.5 μM.

tag: cell type

value: anaplastic thyroid cancer (ATC) cells

tag: phenotype

value: paclitaxel resistant


title: WT_H3K4me3_ChIPSeq_IP rep3


title: SAMPLE 3:ICH 3


title: WT_H3K4me3_ChIPSeq_Input rep1


title: 8505C wt

source_name: 8505C cell line

value: paclitaxel sensititve


title: jmj7_H3K4me3_ChIPSeq_IP rep3


title: WTCK_2

tag: genotype

value: wildtype


title: SAMPLE 2:ICH 2

value: male


title: SW1736-PTX

source_name: SW1736-PTX cell line


title: WTCK_1


title: WT_H3K4me3_ChIPSeq_IP rep1


title: SW1736 wt

source_name: SW1736 cell line


title: WT_H3K4me3_ChIPSeq_IP rep2


title: SAMPLE 1:ICH 1

value: peripheral blood


title: miR-155-5p_rep5

status: Public on Jul 09 2021

city: Seoul

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

institute: Seoul National University

description: hsa-miR-155-5p-transfected mRNA-seq in HepG2

data_processing:
1. Base-calling by RTA(Real Time Analaysis) software within HiSeq 2500 (mRNA-Seq) or HiSeq 2000 (sRNA-Seq)
2. Quality trimming by the highest scoring path algorithm (hsptrim-1.2.6)
3. Adapter trimming by cutadapt-1.2.1
4. Remove tRNA, rRNA-derived reads by Bowtie2 alignment
5. Remove sequencing artifacts by fastx_artifacts_filter of fastx_toolkit
6. Alignment of filtered reads to human reference genome by Tophat2 (mRNA-Seq) or Bowtie2 (sRNA-Seq)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Tab-delimited text file (*.quants.txt) contains expression levels for individual genes. Columns: (1) id: Gene identifier (e.g. NM_000000), (2) symbol: Gene symbol (e.g. GAPDH), (3) readcount: Number of mapped reads, (4) exlev: Expression level (RPM or RPKM), (5) expct: Expression percentile rank
Supplementary_files_format_and_content: BED file (*.dmscount.{plus,minus}.txt) contains RT truncation counts by DMS treatment in single nucleotide resolution

source_name: liver hepatocellular carcinoma

extract_protocol:
For mRNA-seq, total RNA was extracted with Trizol reagent (Qiagen) according to the manufacturer's instructions. After total RNA extraction, mRNA was selected using Dynabead (Thermofisher). Isolated mRNA was then randomly fragmented using fragmentation reagent (Invitrogen). Size-selected RNA fragments (200-400nt) were used for library preparation.
poly(A)-selected RNA-seq
Both of the library preparations (mRNA-Seq and sRNA-Seq) were done based on the Illumina Truseq small RNA library preparation protocol (TruSeq Small RNA Library Prep Guide, Part # 15004197 Rev. G). DMS-seq libraries were prepared using adaptors from a previous study (PMID: 30605524) following procedures from Rouskin et al., 2014 (PMID: 24336214).
mRNA-seq, sRNA-seq, DMS-seq

tag: treatment

value: hsa-miR-155-5p transfection

tag: concentration

tag: incubation


title: miR-155-5p_rep4


title: miR-155-5p_rep3


title: miR-155-5p_rep2


title: miR-155-5p_rep1


title: SAMPLE 4:ICH 4

tag: disease state

tag: tissue


title: miR-129-2-3p_rep3

description: hsa-miR-129-2-3p-transfected mRNA-seq in HepG2

value: hsa-miR-129-2-3p transfection


title: miR-129-2-3p_rep2


title: KOCK_1


title: WTCK_3


title: miR-129-2-3p_rep1


title: miR-451a_rep2

description: hsa-miR-451a-transfected mRNA-seq in HepG2

value: hsa-miR-451a transfection


title: miR-451a_rep1


title: OCCM Conrol

city: Beijing

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: cementum

growth_protocol: Immortalized mouse cementoblast-like cells (OCCM-30) were cultured in Dulbecco’s modified Eagle’s medium plus 10% fetal bovine serum and 1% penicillin/streptomycin.

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

treatment_protocol: The cells were exposed to compressive force

value: cementum

value: wild type

value: control


title: miR-142-5p_rep2

description: hsa-miR-142-5p-transfected mRNA-seq in HepG2

value: hsa-miR-142-5p transfection


title: miR-142-5p_rep1


title: miR-193b-3p_rep1

description: hsa-miR-193b-3p-transfected mRNA-seq in HepG2

value: hsa-miR-193b-3p transfection


title: miR-193b-3p_rep2


title: miR-142-3p_rep4

description: hsa-miR-142-3p-transfected mRNA-seq in HepG2

value: hsa-miR-142-3p transfection


title: miR-142-3p_rep3


title: miR-142-3p_rep2


title: miR-142-3p_rep1


title: OCCM Force

value: Immortalized mouse cementoblast-like cells (OCCM-30)

value: compressive force


title: miR-1-3p_rep2

description: hsa-miR-1-3p-transfected mRNA-seq in HepG2

value: hsa-miR-1-3p transfection


title: miR-365a_rep2

description: hsa-miR-365a-3p-transfected mRNA-seq in HepG2

value: hsa-miR-365a-3p transfection


title: miR-365a_rep1


title: miR-217_rep1

description: hsa-miR-217-transfected mRNA-seq in HepG2

value: hsa-miR-217 transfection


title: miR-216a-5p_rep1

description: hsa-miR-216a-5p-transfected mRNA-seq in HepG2

value: hsa-miR-216a-5p transfection


title: miR-217_rep3


title: miR-218-5p_rep3

description: hsa-miR-218-5p-transfected mRNA-seq in HepG2

value: hsa-miR-218-5p transfection


title: miR-216a-5p_rep2


title: miR-142-5p_rep3


title: miR-217_rep4


title: miR-217_rep2


title: miR-199b-3p_rep2

description: hsa-miR-199b-3p-transfected mRNA-seq in HepG2

value: hsa-miR-199b-3p transfection


title: miR-199b-3p_rep3


title: miR-218-5p_rep1


title: miR-218-5p_rep2


title: miR-140-3p_rep1

description: hsa-miR-140-3p-transfected mRNA-seq in HepG2

value: hsa-miR-140-3p transfection


title: miR-199b-3p_rep1


title: miR-101-3p_rep4

description: hsa-miR-101-3p-transfected mRNA-seq in HepG2

value: hsa-miR-101-3p transfection


title: miR-140-3p_rep3


title: miR-101-3p_rep3


title: miR-199b-3p_rep4


title: miR-218-5p_rep4


title: miR-1-3p_rep1


title: miR-133a-3p_rep3

description: hsa-miR-133a-3p-transfected mRNA-seq in HepG2

value: hsa-miR-133a-3p transfection


title: miR-1-3p_rep3


title: miR-101-3p_rep1


title: miR-133a-3p_rep2


title: miR-140-5p_rep2

description: hsa-miR-140-5p-transfected mRNA-seq in HepG2

value: hsa-miR-140-5p transfection


title: miR-140-5p_rep3


title: miR-133a-3p_rep1


title: miR-140-3p_rep2


title: miR-137_rep4

description: hsa-miR-137-transfected mRNA-seq in HepG2

value: hsa-miR-137 transfection


title: miR-140-5p_rep1


title: miR-137_rep3


title: miR-137_rep2


title: miR-137_rep5


title: miR-137_rep1


title: miR-18a-5p_rep2

description: hsa-miR-18a-5p-transfected mRNA-seq in HepG2

value: hsa-miR-18a-5p transfection


title: miR-18a-5p_rep3


title: miR-211-5p_rep3

description: hsa-miR-211-5p-transfected mRNA-seq in HepG2

value: hsa-miR-211-5p transfection


title: miR-133a-3p_rep4


title: miR-101-3p_rep2


title: mock_rep11

description: mock-transfected mRNA-seq in HepG2

value: mock transfection


title: mock_rep10

description: mock-transfected mRNA-seq in HepG2


title: miR-18a-5p_rep1


title: mock_rep9

description: mock-transfected mRNA-seq in HepG2


title: mock_rep8

description: mock-transfected mRNA-seq in HepG2


title: miR-211-5p_rep4


title: miR-211-5p_rep2


title: mock_rep7

description: mock-transfected mRNA-seq in HepG2


title: mock_rep5

description: mock-transfected mRNA-seq in HepG2


title: mock_rep4

description: mock-transfected mRNA-seq in HepG2


title: mock_rep6

description: mock-transfected mRNA-seq in HepG2


title: mock_rep3

description: mock-transfected mRNA-seq in HepG2


title: mock_rep2

description: mock-transfected mRNA-seq in HepG2


title: miR-18a-5p_rep5


title: miR-18a-5p_rep4


title: mock_rep1

description: mock-transfected mRNA-seq in HepG2


title: mRNA_HCT116

description: mRNA-seq in HCT116

source_name: human colorectal carcinoma


title: mRNA_HepG2

description: mRNA-seq in HepG2


title: miR-211-5p_rep1


title: mRNA_HeLa

description: mRNA-seq in HeLa

source_name: human cervical carcinoma

value: HeLa


title: mRNA_HEK293T

description: mRNA-seq in HEK293T

source_name: human embryonic kidney


title: SCAB1-2

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

data_processing:
library strategy: amplicon-seq
Basecalls performed using CASAVA
The 29 bp vector sequence was determined and removed from the 5’ end of the Read_1 by using the Cutadapt 1.18.
The trimmed reads were then mapped to genomic DNA, cDNA and CDS by using HISAT2.1.0 with default parameters.
The in-frame reads were collected into a new SAM file by using a home-made python script.
The number of gene mapped reads and unique read were calculated by using a home-made python script.
Genome_build: Arabidopsis_tair10
Supplementary_files_format_and_content: Tab-delimited text file includes reads count and number of unique read for each samples.

organism: Arabidopsis thaliana

source_name: cDNA library for Y2H screening

extract_protocol:
Plasmids were extracted according to the manual of TIANprep yeast plasmid kit (TIANGEN, China). The prey inserts were amplified by PCR.
The PCR products were sheared into 200-300 bp DNA fragments by Bioruptor Plus (Diagenode). End repair and adaptor ligation were performed by using NEBNext Ultra II End Repair/dA-Tailing Module and NEBNext Ultra II Ligation Module (NEB). The sequencing libraries were constructed by using PCR.

value: selected by SD-Trp-Leu-His medium with 1 mM 3-AT

tag: recovery time

value: 2 hours

tag: sample info

value: Interacting partners of SCAB1

tag: molecule subtype

value: amplified DNA


title: SOS2-3

value: 4 hours

value: Interacting partners of SOS2


title: SOS2-2


title: SCAB1-1

value: 0 hour


title: SOS2-1


title: SCAB1-3


title: PKS5-2

value: Interacting partners of PKS5


title: PKS5-1


title: Ascities

city: montreal

first: Yojiro

last: Yamanaka

state: Quebec

address: 1160 Pine Avenue West, room 416

department: Human Genetics

country: Canada

institute: McGill University (Goodman Cancer Research Centre)

description: Acites_cluster_markers.xlsx and CNVs_ascites.xlsx

data_processing:
For WGS - Raw reads were trimmed using Skewer and the resulting reads were aligned to the GRCm38 mouse reference genome using BWA-MEM. Duplicates were marked using Picard (http://broadinstitute.github.io/picard/).
Copy number variants (CNVs) were identified using CNVKit at default parameters in each tumour sample and normal tissue as reference. Heatmaps were generated using CNVKit’s heatmap command on all .cns segment files.
For scRNAseq - Raw BCL files from the Illumina HiSeq were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the mouse reference transcriptome (mm10) containing the Tdtomato-WPRE-polyA transcript, and transcript counts quantified for each annotated gene within every cell.
The resulting UMI count matrix (genes × cells) were then provided as input to Seurat suite (version 2.3.4)
Cells were first filtered to remove those that contain less than 200 genes detected and those in which > 10% of the transcript counts were derived from mitochondrial-encoded genes.
Clustering was performed using the “FindClusters” function and Uniform Manifold Approximation and Projection (UMAP) visualization for all cells.
Cluster-specific gene markers were identified using Seurat’s FindMarkers with cutoffs avg_logFC > 0.5 and FDR < 0.05. CNV analysis was performed using the inferCNV package (10.18129/B9.bioc.infercnv)
Genome_build: GRCm38 for WGS and mouse reference transcriptome (mm10) containing the Tdtomato-WPRE-polyA transcript
Supplementary_files_format_and_content: Excel files containing CNAs and cluster gene markers.

source_name: Ovarian tumor Ascities 50822

growth_protocol: Mice were housed under standard conditions on B6 background.

extract_protocol:
DNA was extracted from FFPE samples using Qiagen GeneRead DNA FFPE kit. RNA was isolated from the cell portion of ascities fluid after red blood cell removal
DNA libraries were prepared for sequencing using standard Illumina protocols. scRNA library was made using the Chromium Single Cell 3' kit V2.

treatment_protocol: Tumor formation was induced by in vivo electroportation of mouse fallopian tube epithelial cells with plasmids expressing Cas9, guide RNA and Cre.

value: Ascities fluid, red blood cells removed

tag: lkb1 status

value: Deletion

tag: pax8 expression