title: Gro-seq-siBRD4-E2-MCF7

description: Nascent RNA sequencing

data_processing:
Library strategy: Gro-seq
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1.
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.
Genome_build: hg19

extract_protocol:
MCF7 cells were washed 3 times with cold phosphate buffered saline (PBS) buffer and then incubated in swelling buffer (10 mM Tris-Cl pH 7.5, 2 mM MgCl2, 3 mM CaCl2) for 5mins on ice and harvested. Cells were first re-suspended and lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 mL lysis buffer and then re-suspended in 100 μL of freezing buffer (50 mM Tris-Cl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA).
For run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 20 units of SUPERase In, 1% sarkosyl, 500 μM ATP, GTP, and Br-UTP, 2 μM CTP) and incubated for 5 mins at 30°C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent following manufacturer’s instructions. NRO-RNA was then subjected to base hydrolysis on ice for 40 mins and followed by treatment with DNase I and antarctic phosphatase. To purify the Br-UTP labeled nascent RNA, the NRO-RNA was immunoprecipitated with an anti-BrdU agarose beads in binding buffer (0.5 X SSPE, 1 mM EDTA, 0.05% tween-20) for 1hr at 4°C while rotating.  To repair the end, the immunoprecipitated BrU-RNA was re-suspended in 50μL reaction (43 μL DEPC water, 5.2 μL T4 PNK buffer, 1 μL SUPERase In and 1 μL T4 PNK) and incubated at 37 °C for 1hr. RNA was then extracted, precipitated using acidic phenol-chloroform and subjected to poly-A tailing reaction by using poly-A polymerase for 30 mins at 37 °C. Subsequently, reverse transcription was performed using oNTI223- primers (5’- pGATCGTCGGACTGTAGAACTCT; CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’) where the p indicates 5’ phosphorylation, ‘;’ indicates the abasic dSpacer furan and VN indicates degenerate nucleotides. Specifically, tailed RNA (8.0 μL) was subjected to reverse transcription using superscript III, after which the cDNA products were separated on a 10% polyacrylamide TBE-urea gel. The extended first-strand product (100-500 bp) was excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase and re-linearized by Ape1. Re-linearized single strand cDNA (sscDNA) was separated in a 10% polyacrylamide TBE gel as described above and the product of needed size was excised (~170-400 bp) for gel extraction. Finally, sscDNA template was amplified by PCR using the Phusion High-Fidelity enzyme according to the manufacturer’s instructions. Primers oNTI200 (5’-CAAGCAGAAGACGGCATA-3’) and oNTI201 (5’- AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3’) were used to generate DNAs for deep sequencing.

treatment_protocol: MCF7 cells were transfected with control siRNA or siRNA specifically targeting BRD4 and maintained in phenol red free DMEM (stripping medium) supplemented with 5% charcoal-treated FBS for three days, followed by treatemnt of either 10-7 M 17-β-estrodial or ethanol for 1 hr.


title: B6CBAF1/J RNA-seq_Ring1A_-/-_Ring1B_fl/fl_3

status: Public on Oct 19 2022

type: SRA

city: Yokohama-shi

first: Junichiro

last: Takano

state: Kanagawa-kwn

department: IMS

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm9) using Tophat (v2.0.13; https://ccb.jhu.edu/software/tophat/index.shtml).
Transcript levels (counts) were summarized per gene using Rsubread (Liao et al., 2013). Count per million (CPM) were calculated using edgeR (Robinson et al., 2010).
Assembly: mm9
Supplementary files format and content: bigwig files normalized using RPKM in each samples,

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Culture with TSt4 stroma cells by IMDM supplemented with IL7, SCF,Fl3L

extract_protocol:
Total RNA was extracted by RNeasy (74106; QIAGEN) following the manufacture’s protocol.
Poly(A) mRNA was isolated from total RNA by NEBNext poly(A) mRNA magnetic isolation module (E7490; New England Biolabs), and then library was prepared by NEBNext Ultra RNA library preparation kit for Illumina(E7530; New England Biolabs).

tag: strain

tag: cell type

value: Hemtopoietic progenitor cells (LMPP)

tag: passage

tag: genotype

value: Ring1A -/- 1B fl/fl


title: Day3_WT1_PRE

city: Bethesda

first: Michael

last: Bustin

state: MD

address: Building 37, Room 3122

department: NCI

country: USA

institute: NIH

data_processing:
Basecalling was performed using RTA version 2.4.11
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.18).
Mapping to the mouse genome (mm10) was performed using STAR 2.7.0f
Gene-level expression quantificiation was performed using RSEM (version 1.3.0).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited raw counts matrix

molecule: polyA RNA

source_name: Inguinal white adipose tissue

growth_protocol: Preadipocytes were isolated from inguinal white adipose tissue of WT and DKO mice and cultured on collagen coated plates. MEF were isolated from WT and DKO mouse embryo and cultured on tissue culture plates.

extract_protocol:
For RNA seq, cells were scrapped in  trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Proliferating preadipocytes and MEF were replated and grown until confluency. Two days after reaching confulency,  Preadipocytes were treated to differentiate into adipocytes using differentiation media (Insulin (0.5 μg/ml), dexamethasone (5 μM), IBMX (0.5 mM), T3 (1 nM), Rosiglitazone (1 μM)) for 4 days and maintained in maintenance medium (Insulin (0.5 μg/ml), T3 (1 nM)) for 4 days. MEFs were differentiated into adipocytes with differentiation medium (Insulin (0.5 μg/ml), dexamethasone (5 μM), IBMX (0.5 mM), T3 (1 nM), Rosiglitazone (1 μM)) for 8 days and then with maintenance medium (Insulin (0.5 μg/ml), T3 (1 nM)) for 4 days.

value: Wild type

value: differentiating  preadipocytes


title: primary AML cells isolated from bone marrow of mice treated with AC220 (quizartinib), replicate 2

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina adapters were removed and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl mouse transcriptome (hg38.p12, release 96)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Differential gene expression was calculated using the voom function in limma
Assembly: hg38
Supplementary files format and content: Text file containing STAR gene count values

organism: Homo sapiens

extract_protocol:
RNA was isolated using Rneasy Plus Mini Kit (Qiagen)
Poly-A-selected total RNA library construction was performed using Universal Plus mRNA-seq with NuQuant (Tecan)

treatment_protocol: NRG-S mice engrafted with primary FLT3-ITD+ AML were treated with either vehicle or 2.5mg/kg quizartinib for 16 hours

tag: tissue

value: Bone marrow

value: primary AML

tag: treatment

value: Quizartinib


title: Gro-seq-siBRD4-CTL-MCF7

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

country: China

institute: xiamen University

description: Nascent RNA sequencing

source_name: Michigan Cancer Foundation-7 cells(MCF-7 cells)

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

tag: cell line


title: primary AML cells isolated from bone marrow of mice treated with AC220 (quizartinib), replicate 1


title: Day0_KO3_PRE

value: Hmgn1-/- and Hmgn2-/-

value: white preadipocytes


title: Gro-seq-siCTL-E2-MCF7

description: Nascent RNA sequencing


title: B6CBAF1/J RNA-seq_Ring1A_-/-_Ring1B_fl/fl_2

value: Hemtopoietic progenitor cells (IdHPs)


title: B6CBAF1/J RNA-seq_Ring1A_-/-_Ring1B_fl/fl_1


title: primary AML cells isolated from bone marrow of mice treated with Vehicle, replicate 3

value: Vehicle


title: Day0_KO2_PRE


title: Gro-seq-siCTL-CTL-MCF7

description: Nascent RNA sequencing

value: siCTL-CTL


title: B6CBAF1/J RNA-seq_BCOR_deltaE9-10_3

value: Bcor delta E9-10


title: BE121_TNFaIL17_4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome of cells treated with TNFa+IL17 (TNFalpha 10 ng/ml;IL17 20ng/ml; 72 hours)

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: bronchial epithelial cells

growth_protocol: Primary bronchial epithelial cells were first cultured with LHC9/RPMI 1640 (Scudieri et al., J Physiol 590:6141-6155, 2012), to favor cell proliferation. To achieve mucociliary differentiation, cells were then plated on porous supports (Snapwell 3801) under air-liquid interface condition, with PneumaCult/ALI medium on the basolateral side.

extract_protocol:
RNA was quantified and diluted at 10ng/µl
For RNA-seq analysis, libraries were prepared according to manufacturer's instructions (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen GmbH) starting from 250ng of total RNA.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq6000 (Illumina) with a read length of 100 bp

treatment_protocol: Cells were treated with TNFalpha (10 ng/ml), IL-17 (20ng/ml) or TNFalpha+IL-17 (10ng/ml and 20ng/ml respectively) for 72 hours.

value: bronchial epithelial cells

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition, treated with TNFa+IL17 (TNFalpha 10 ng/ml;IL17 20ng/ml; 72 hours)


title: Day0_KO1_PRE


title: B6CBAF1/J RNA-seq_BCOR_deltaE9-10_2


title: BE121_TNFaIL17_3


title: RORB Overexpressing MG63 cells 3

city: Jupiter, FL 33458

first: Gogce

middle: Ceren

last: Crynen

state: Florida

address: 130 Scripps Way

department: Bioinformatics and Statistics Core

institute: UF Scripps Biomedical Research

data_processing:
star version 2.5.2a aligner
gene abundance was estimated with python version 2.7.11, and htseq version 0.9.1.
R version 3.4.0, and deseq2 version 1.16.1.
Assembly: H.sapiens-UCSC-GRCh38hg38
Supplementary files format and content: excel sheet with results from deseq2

source_name: bone

extract_protocol:
RNA was harvested using RNeasy mini  kit (Qiagen)
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA sample prep kit following manufacturer's protocols.

value: bone

value: MG 63

value: osteoblast like cell line

value: RORB OE


title: BE121_TNFaIL17_2


title: Day0_WT2_PRE

value: Wild type


title: RORB Overexpressing MG63 cells 1


title: B6CBAF1/J RNA-seq_BCOR_fl/y_3

value: Hemtopoietic progenitor cells (LMPP)

value: Bcor fl/y


title: Day0_WT3_PRE


title: RORB Overexpressing MG63 cells 2


title: B6CBAF1/J RNA-seq_BCOR_deltaE9-10_1


title: BE121_TNFaIL17_1


title: Day0_WT1_PRE


title: BE121_IL17_4

description: Transcriptome of cells treated with IL17 (20 ng/ml; 72 hours)

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition, treated with IL17 (20 ng/ml; 72 hours)


title: MG63 cells 3

value: WT


title: Preadipocytes Day 0 ATAC seq DKO3

library_source: genomic

data_processing:
Basecalling was performed using RTA version 2.4.11
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.18).
Reads were mapped to UCSC mm10 reference genome using BowTie2 ver.2.3.4.3
Peak detection of enriched binding regions was performed using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: Bed file containing predicted peaks in narrowPeak format

molecule: genomic DNA

growth_protocol: Preadipocytes were isolated from inguinal white adipose tissue of WT and DKO mice and cultured on collagen coated plates.

extract_protocol:
Cells were collected as per omni-ATAC protocol
ATAC libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Proliferating preadipocytes were replated and grown until confluency. Two days after reaching confulency,  Preadipocytes were treated to differentiate into adipocytes using differentiation media (Insulin (0.5 μg/ml), dexamethasone (5 μM), IBMX (0.5 mM), T3 (1 nM), Rosiglitazone (1 μM)) for 4 days and maintained in maintenance medium (Insulin (0.5 μg/ml), T3 (1 nM)) for 4 days.

value: Hmgn1-/- and Hmgn2-/-


title: MG63 cells 2


title: B6CBAF1/J RNA-seq_BCOR_fl/y_1


title: BE121_IL17_3


title: Preadipocytes Day 0 ATAC seq DKO2


title: BE121_IL17_2


title: MG63 cells 1


title: B6CBAF1/J RNA-seq_Pcgf2/4_-/-_3


title: BE121_IL17_1


title: Preadipocytes Day 0 ATAC seq DKO1


title: B6CBAF1/J RNA-seq_Pcgf2/4_-/-_2


title: 21

city: Ningbo

first: Jia

last: Su

state: China

address: Liuting Street No.59

institute: Ningbo No. 1 Hospital

data_processing:
Trimmed reads (trimmed 5ÿ , 3ÿ -adaptor bases) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2
Based on alignment statistical analysis (mapping ratio, read length, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. If so, the expression profiling and differentially expressed tRFs & tiRNAs and miRNAs are calculated.
Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics
Assembly: GtRNAdb (http://gtrnadb.ucsc.edu/) and tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/)
Supplementary files format and content: txt

source_name: PBMC

extract_protocol:
After PBMC isolation, total RNA in samples were obtained by using TRIzol reagent, and the purity and concentration of them were determined with the instrument of NanoDrop ND-1000. If the OD was in the range of 1.8-2.0, the RNA was included in the follow-up experiment. According to rtStar tRF & tiRNA Pretreatment Kit protocols (Arraystar, USA), the total RNA samples were pretreated to remove RNA modifications
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter.  The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.

tag: disease

value: Heart Failure Patients after Acute Myocardial Infarction

tag: group

value: non sacubitril/valsartan resistance

value: PBMC


title: BE121_TNFalpha_4

description: Transcriptome of cells treated with TNFalpha (10 ng/ml; 72 hours)

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition, treated with TNFalpha (10 ng/ml; 72 hours)


title: 20

value: sacubitril/valsartan resistance


title: Preadipocytes Day 0 ATAC seq WT3


title: Preadipocytes Day 0 ATAC seq WT2


title: 19


title: B6CBAF1/J RNA-seq_Pcgf2/4_fl/fl_3

value: Hemtopoietic progenitor cells (IdHPs)

value: Pcgf2/4 fl/fl


title: Preadipocytes Day 0 ATAC seq WT1


title: 18


title: B6CBAF1/J RNA-seq_BCOR_fl/y_2


title: B6CBAF1/J RNA-seq_Pcgf2/4_fl/fl_2


title: cea9

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

data_processing:
Trim input file and remove adapters.
Tag reads with cell barcode and UMI
Align reads to PhiX, then to mouse.
Aggregate reads and de-duplicate UMIs.
Post-processing in R with custom scripts and Seurat.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Tab delimited file containing count values.

source_name: Central amygdala

extract_protocol:
Microdissect, dissociate, and pool cells across acute brain slices in B6 mice.
As in (Erwin*, Bristow*, … , Cembrowski; eLife 2021)

value: Central amygdala


title: 17


title: cea8


title: BE121_CTR_4

description: Transcriptome of cells kept under control conditions

value: bronchial epithelial cells

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition


title: 13


title: BE121_CTR_3


title: cea6


title: WtapBKO2

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of three groups (three biological replicates per group) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes  with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially  expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias wascorrected.  GO terms with corrected Pvalue less than 0.05 were considered significantly enriched  by differential expressed genes.
Assembly: Ensemble_ grcm38_p6
Supplementary files format and content: abundance measurements

source_name: BAT

extract_protocol:
iBATs were removed from BKO and f/f mice at 8 weeks old, flash frozen on liqid nitrogen, and total RNA was harvested using TriPure reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iBAT

tag: age

value: 8 weeks

value: WTAPflox/flox UCP1-iCre+/-


title: BE121_CTR_2


title: 8


title: cea7


title: WtapBKO3


title: B6CBAF1/J RNA-seq_Pcgf2/4_-/-_1


title: BE121_TNFalpha_2


title: WtapBKO1


title: 7


title: BE121_CTR_1


title: cea5


title: cea4


title: 5


title: BE121_TNFalpha_3


title: BE121_TNFalpha_1


title: B12475C

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

description: Total RNA with rRNA removal

data_processing:
alignment using HISAT2
compute FPKM using featureCounts after splitting strands
base count output by RepeatMasker program to caculate base coverage of interspersed repeats and low complexity DNA sequences
Assembly: hg19
Supplementary files format and content: tsv containing FPKM of gene expression as output by featureCounts

growth_protocol: SNU398, HepG2 and SNU475 cells were obtained form the American Type Culture Collection (ATCC; www.atcc.org).

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Zymo Direct-Zol RNA mini prep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
For directional RNA-seq with ribosomal RNA (rRNA) reduction, libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (KapaBiosystems) and sequenced as single-end (SE) 75 base reads on an Illumina NextSeq 500 instrument at the Van Andel Research Institute Genomics Core.
Total RNA sequencing with ribosomal RNA depleted

treatment_protocol: Each cell line was treated with daily doses of 100 nM 5-Aza-CdR (Sigma-Aldrich) at and/or of 500nM GSK-126 (Active Biochem, LTD, Hong Kong) for three days. SNU398 and HepG2 were harvested on day 14 after treatment, while SNU475 was harvested on day 21.

value: Liver hepatocellular carcinoma

value: Wildtype

value: 5-Aza-CdR + GSK-126


title: cea3

value: WT


title: BE111CF_TNFaIL17_2

description: Transcriptome of cells treated with TNFalpha+IL-17 (10 ng/ml and 20 ng/ml respectively; 72 hours)

growth_protocol: Primary bronchial epithelial cells were first cultured with LHC9/RPMI 1640 (Scudieri et al., J Physiol 590:6141-6155, 2012), to favor cell proliferation. To achieve mucociliary differentiation, cells were then plated on porous supports (Transwell 3470) under air-liquid interface condition, with PneumaCult/ALI medium on the basolateral side.

extract_protocol:
RNA was quantified and mixed at 10ng/µl
For RNA-seq analysis, libraries were prepared according to manufacturer's instructions (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen GmbH) starting from 100ng of total RNA.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq6000 (Illumina) with a read length of 100 bp

treatment_protocol: Cells were treated with TNFalpha+IL-17 (10 ng/ml and 20ng/ml respectively) for 72 hours.

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition, treated with TNFalpha+IL-17 (10 ng/ml and 20 ng/ml respectively; 72 hours)

tag: disease state

value: Cystic fibrosis


title: B6CBAF1/J RNA-seq_Pcgf2/4_fl/fl_1


title: Wtapff2

value: WTAPflox/flox


title: B11475G

description: Total RNA with rRNA removal


title: BE111CF_TNFaIL17_3


title: cea2


title: Wtapff1


title: cea1


title: 9

value: Heart Failure Patients after Acute Myocardial Infarction

value: non sacubitril/valsartan resistance

value: PBMC


title: DA10

city: Zhengzhou

first: Ruixue

last: Guo

state: Henan

address: No. 1 of Jianshe East Road

department: Nephrology

institute: the First Affiliated Hospital of Zhengzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering was performed using trimmomatic software. Then use bowtie2 software to remove rRNA reads. The specific filtering contents are as following: 1. Remove reads with adapters; 2. Remove reads containing N (N indicates that the base information cannot be determined); 3. Remove low-quality reads (Q < = 20 bases account for more than 50% of the entire read length; 4. Remove reads whose sequence length is less than 30. 5. Removal of rRNA.
Paired-end sequence files (fastq) were mapped to the reference genome using Hisat2 (Hierarchical Indexing for Spliced Alignment of   Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAM tools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05,  considered as significantly modulated, were retained for further analysis.
Assembly: mm10
Supplementary files format and content: The tab-delimited text files include the FPKM and count values for each sample.

source_name: renal cortex

growth_protocol: Intraperitoneal injection of STZ for 5 consecutive days caused mice to be in a high-glucose state, supplemented by high-fat diet for 3 months of continuous feeding

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following  TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

treatment_protocol: After developing into a hyperglycemic state, the diabetic mice were given dapagliflozin by gavage for one month.

value: renal cortex

value: post natal week18

value: diabetic with dapagliflozin


title: B10475D

description: Total RNA with rRNA removal


title: BE111CF_CTR3

value: bronchial epithelial cells

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition


title: DA7


title: DA5


title: B9475P

description: Total RNA with rRNA removal

value: DPBS


title: BE111CF_CTR2


title: Wtapff3

value: iBAT

value: 8 weeks


title: Control (nonlesion from cancer patient) and Crohn disease TFHS000053

city: Yokohama

first: Jonathan

last: Moody

address: 1-7-22 Suehiro-cho

institute: RIKEN Center for Integrative Medical Sciences

description:
Cells sorted with 7-AAD(-), CD45(+), TCRab(+)
10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the refdata-gex-GRCh38-2020-A reference using cellranger v5.0.0
Freemuxlet was used to demultiplex the individual cells using a refernce vcf of SNPs withim exons with  MAF>0.05 within East Asians from 1000genomes file ALL.wgs.shapeit2_integrated_v1a.GRCh38.20181129.sites.vcf.gz
Y chromosome gene RPS4Y1 expression within cells was used to assign freemuxlet ID with patient sample
Cells were processed with Seurat to filter cells >6 median absolute deviations in UMI or gene count from the mean, or mitochondrial UMI > 25% and integrated with Harmony.
Assembly: hg38
Supplementary files format and content: Tab or comma separated values files and matrix files

source_name: CD4+CD8A+ T cells

extract_protocol:
Dissected mucosa of small intestine or large intestine was cut into 5-mm pieces. Tissue was incubated with Ca2+, Mg2+-free HBSS containing 1 mM DTT (Invitrogen) and 5 mM EDTA (Thermo Fisher Scientific) at 37 °C for 30 minutes, then used as Intestinal epithelial lymphocytes (IELs). The rest of the supernatant was digested with 1 mg/mL collagenase (Wako) and 0.1 mg/mL DNase (Sigma-Aldrich) for 45 minutes. The dissolved solution was centrifuged at 1,700 rpm for 5 minutes. The pellet was resuspended in 40% Percoll (GE healthcare) and overlaid on 75% Percoll. Percoll gradient separation was performed by centrifugation at 2,000 rpm for 20 minutes at 20 C. Cells at the interface were LP mononuclear cells.
Library was performed according to the manufacter’s instructions (single cell 5’ v1.1 protocol, 10x Genomics).

value: CD4+CD8A+ T cells


title: DA4


title: Control (nonlesion from cancer patient) and Ulcerative colitis TFHS000025


title: B7398G

description: Total RNA with rRNA removal

value: Liver hepatocellular carcinoma

value: Wildtype


title: BE99 IL4_4

description:
Transcriptome of cells treated with IL-4 (10 ng/ml; 72 hours)
BE99 IL4_4

treatment_protocol: Cells were treated with IL-4 (10 ng/ml) for 72 hours.

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition, treated with IL-4 (10 ng/ml; 72 hours)


title: DA2


title: BE99 IL4_3

description:
Transcriptome of cells treated with IL-4 (10 ng/ml; 72 hours)
BE99 IL4_3


title: BE111CF_TNFaIL17_1

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition, treated with TNFalpha+IL-17 (10 ng/ml and 20 ng/ml respectively; 72 hours)

value: Cystic fibrosis


title: Unpaired training, Dam-Creb, rep1_TI2

city: Fribourg

first: Noemi

last: Sgammeglia

address: Chemin du Musee 10

country: Switzerland

institute: University of Fribourg

description:
UCB11-vs-Dam.gatc.gff
compared_PCB11vsUCB11_rep1.bedgraph
filtered_Compared_PCB_t2_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt

data_processing:
damidseq_pipeline (sequence alignment, read extension, binned counts, normalisation, pseudocount addition and final ratio file generation)
comparison pipeline (comparison between two paired and unpaired conditions)
Extraction of significant targets (q-values were assigned based on the signal from multiple GATC fragments and using a 0.01 false discovery rate (FDR) threshold)
Assembly: dmel_r6.22
Supplementary files format and content: .gff files include Dam-Creb vs Dam-Ony (from damidseq_pipeline)
Supplementary files format and content: .bedgraph files include compared Paired vs Unpaired
Supplementary files format and content: .txt files include significant target genes

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
Extraction of genomic DNA from the fly heads (50–100 per sample), amplification of methylated fragments, DNA purification, and sonication was performed according to Marshall et al. (2016). After sonication, DamID adaptors were removed by digesting overnight at 37° C with 5 units of Sau3AI (R0169S; NEB).
The sequencing libraries were prepared according to the Illumina TruSeq nano DNA library protocol.
llumina TruSeq nano DNA

treatment_protocol: Expression of Dam and Dam-CrebB was induced by shifting the flies to 29°C in two main time intervals (TIs). For TI-1, flies were moved to 29° C 3h before conditioning, trained at 25°  C, and moved back to 29° for 24 hr. For TI-2, animals were trained at 18° and shifted to 29° C 24–48h after conditioning. At the end of the 29°C-time interval, flies were frozen in liquid nitrogen and heads were collected.

value: brain

tag: developmental stage

value: adult

value: Mushroom body cells

tag: time

value: from 24h to 48h


title: Unpaired training, Dam-Creb, rep3_TI2

description:
UCB13-vs-Dam.gatc.gff
compared_PCB13vsUCB13_rep3.bedgraph
filtered_Compared_PCB_t2_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt


title: Unpaired training, Dam-Creb, rep2_TI2

description:
UCB12-vs-Dam.gatc.gff
compared_PCB12vsUCB12_rep2.bedgraph
filtered_Compared_PCB_t2_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt


title: DA1

value: renal cortex

value: post natal week18


title: DN10

value: diabetic


title: BE99 IL4_2

description:
Transcriptome of cells treated with IL-4 (10 ng/ml; 72 hours)
BE99 IL4_2

value: bronchial epithelial cells


title: BE99 IL4_1

description:
Transcriptome of cells treated with IL-4 (10 ng/ml; 72 hours)
BE99 IL4_1


title: B5398P

description: Total RNA with rRNA removal

value: DPBS


title: Unpaired training, Dam-Only, rep3_TI2


title: B4G2C

description: Total RNA with rRNA removal

value: 5-Aza-CdR + GSK-126


title: DN8


title: Unpaired training, Dam-Only, rep2_TI2


title: Unpaired training, Dam-Only, rep1_TI2


title: DN6


title: B3G2G

description: Total RNA with rRNA removal


title: B8398C

description: Total RNA with rRNA removal


title: B2G2D

description: Total RNA with rRNA removal


title: BE99 CTR_4

description:
Transcriptome of cells kept under control conditions
BE99 CTR_4

value: Bronchial epithelial cells differentiated on porous  membrane under air-liquid interface condition


title: BE99 CTR_3

description:
Transcriptome of cells kept under control conditions
BE99 CTR_3


title: DN4


title: BE111CF_CTR1


title: BE99 CTR_2

description:
Transcriptome of cells kept under control conditions
BE99 CTR_2


title: Paired training, Dam-Creb, rep3_TI2

description:
PCB13-vs-Dam.gatc.gff
compared_PCB13vsUCB13_rep3.bedgraph
filtered_Compared_PCB_t2_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt


title: B1G2P

description: Total RNA with rRNA removal


title: B6398D

description: Total RNA with rRNA removal


title: Paired training, Dam-Creb, rep2_TI2

description:
PCB12-vs-Dam.gatc.gff
compared_PCB12vsUCB12_rep2.bedgraph
filtered_Compared_PCB_t2_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt


title: DN2


title: A12475C

description: Total RNA with rRNA removal


title: BE99 CTR_1

description:
Transcriptome of cells kept under control conditions
BE99 CTR_1


title: DN1


title: Paired training, Dam-Creb, rep1_TI2

description:
PCB11-vs-Dam.gatc.gff
compared_PCB11vsUCB11_rep1.bedgraph
filtered_Compared_PCB_t2_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt


title: A11475G

description: Total RNA with rRNA removal


title: con9

value: healthy


title: nCoV 11 scRNA-seq reanalysis

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description:
nCoV 11 scRNA-seq
GSM4509030

data_processing:
Raw sequencing outputs were automatically converted to fastq file by the sequencer built-in software
raw fastq files were de-multiplexed into relative fastq files for each samples with truncated index sequence through splitBarcode version 0.1.6 provided by MGI Tech.
The demultiplexed files were aligned using cellranger count (v3.0.2; --r1-length 28 --r2-length 91) to cellranger reference GRCh38 (v 3.0.0).
Genome_build: hg38
Supplementary_files_format_and_content: gene expression count matrix, cell barcode information, and gene name list in gzfile format

extract_protocol:
polyA RNA was extracted using the Chromium Single Cell 3' Library & Gel Bead Kit v3.
The library was constructed using the Chromium Single Cell 3' Library & Gel Bead Kit v3.
droplet based single cell RNA seq

value: blood

tag: patient type

value: non-CHIP


title: Normal 4 scRNA-seq reanalysis

description:
Normal 4 scRNA-seq
GSM4509029


title: A10475D

description: Total RNA with rRNA removal

value: Liver hepatocellular carcinoma

value: Wildtype


title: Paired training, Dam-Only, rep2_TI2


title: con8


title: con7


title: A9475P

description: Total RNA with rRNA removal


title: Unpaired training, Dam-Creb, rep3_TI1

description:
UCB3-vs-Dam.gatc.gff
compared_PCB3vsUCB3_rep3.bedgraph
filtered_Compared_PCB_t1_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt

value: from -3h to 24h


title: A8398C

description: Total RNA with rRNA removal


title: Paired training, Dam-Only, rep1_TI2

value: brain


title: con5


title: nCoV 8 scRNA-seq reanalysis

description:
nCoV 8 scRNA-seq
GSM4509026


title: nCoV 10 scRNA-seq reanalysis

description:
nCoV 10 scRNA-seq
GSM4509028


title: nCoV 7 scRNA-seq reanalysis

description:
nCoV 7 scRNA-seq
GSM4509025


title: A7398G

description: Total RNA with rRNA removal


title: Unpaired training, Dam-Creb, rep2_TI1

description:
UCB2-vs-Dam.gatc.gff
compared_PCB2vsUCB2_rep2.bedgraph
filtered_Compared_PCB_t1_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt

value: adult


title: A6398D

description: Total RNA with rRNA removal


title: con4


title: con2


title: Unpaired training, Dam-Creb, rep1_TI1

description:
UCB1-vs-Dam.gatc.gff
compared_PCB1vsUCB1_rep1.bedgraph
filtered_Compared_PCB_t1_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt

value: Mushroom body cells


title: Normal 3 scRNA-seq reanalysis

description:
Normal 3 scRNA-seq
GSM4509024


title: A5398P

description: Total RNA with rRNA removal


title: Paired training, Dam-Only, rep3_TI2

value: from 24h to 48h


title: Normal 2 scRNA-seq reanalysis

description:
Normal 2 scRNA-seq
GSM4509023


title: Unpaired training, Dam-Only, rep3_TI1


title: A4G2C

description: Total RNA with rRNA removal


title: nCoV 6 scRNA-seq reanalysis

description:
nCoV 6 scRNA-seq
GSM4509022


title: P56_WT_YL12

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

description: transcriptome

data_processing:
10X Genomics CellRanger v3.0.2
Seurat v3 and v4
Supplementary files format and content: raw counts matrix for filtered cells/nuclei in H5AD format

source_name: frontal cortex

extract_protocol:
Nuclei isolation protocol was modified from our previous work (Ayhan et al., 2021). Since homogenization of mouse cortex generated much fewer debris, we just did twice fltering through 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art) without doing sucrose-gradient centrifugation
The single-nuclei RNA-seq libraries were prepared using Chromium Single Cell 3ʹ Reagent Kits v3 (CG000185 Rev B) from 10x Genomics
Single nuclei RNA-seq was performed on Illumina NovaSeq 6000

value: WT

tag: gender

value: female

tag: rna preparation batch

tag: library preparation batch

tag: sequencing batch


title: Unpaired training, Dam-Only, rep2_TI1

tag: cell type


title: P56_WT_YL10

description: transcriptome

tag: strain


title: nCoV 5 scRNA-seq reanalysis

description:
nCoV 5 scRNA-seq
GSM4509021


title: A3G2G

description: Total RNA with rRNA removal

tag: genotype


title: P56_WT_YL08

description: transcriptome

value: male


title: P56_WT_YL01

description: transcriptome


title: A1G2P

description: Total RNA with rRNA removal


title: Lats1-CKO basal, BM8, ATAC-seq

city: Rehovot

first: Yael

last: Aylon

address: 234 Herzl St

department: MCB

country: Israel

institute: Weizmann Institute of Science

data_processing:
The cutadapt tool (versiom 1.10) [citation: http://dx.doi.org/10.14806/ej.17.1.200] was used to trim adapters (CTGTCTCTTATACACATCTCCGAGCCCACGAGAC from read 1 and   CTGTCTCTTATACACATCTGACGCTGCCGACGA from read 2). Reads which were shorter than 30 bases after the trimming were discarded.
The trimmed reads were aligned to the mouse mm10 genome using bowtie (version 1.0.0), using the options --maxins 2000, -m 1,  best, strata, and -n 1
Reads that were mapped to the mitochondrial chromosome were excluded
Duplicate reads were removed using Picard (version 2.3.0) MarkDuplicates
Fragments with lengths greater than 120 bases were excluded
Peaks were called using macs2 (version 2.1.1.20160309). Peaks that had an overlap with the mm10 blacklist regions (downloaded from the Encode) were excluded.
Genome_build: mm10
Supplementary_files_format_and_content: bed file of called peaks

source_name: PyMT tumor derived cell line, FACS purified basal population

growth_protocol: DMEM, P/S, FCS

extract_protocol:
Nuclei were incubated with 2ul of Nextera Tn5 enzyme (TDE1, Illumina) for 1h at 37°C. Enzyme inactivation was done by addition of 5ul Clean-up buffer (900mM NaCl, 30mM EDTA), 2ul of 5% SDS and 2ul of Proteinase K (NEB) and incubation for 30min at 40°C. Tagmented DNA was isolated using 2x SPRI beads cleanup.
two sequential 9-cycle and 5-cycle PCR were performed in order to enrich small tagmented DNA fragments. Libraries were prepared using KAPA HiFi HotStart ready mix. After the first PCR, the libraries were selected for small fragments using SPRI cleanup (0.65x). Then a second PCR was performed with the same conditions in order to obtain the final library.

treatment_protocol: samples were sterilely FACS separated into tubes containing complete medium, on a FACSAria III instrument (BD Biosciences) equipped with a 407, 488, 561 and 633 nm lasers, using a 100 um nozzle, controlled by BD FACS Diva software v8.0.1 (BD Biosciences).

value: PyMT tumor derived cell line

value: FBV/N

tag: facs purification

value: EpCAM-low; CD49f-high

tag: population

value: basal


title: Paired training, Dam-Creb, rep2_TI1

description:
PCB2-vs-Dam.gatc.gff
compared_PCB2vsUCB2_rep2.bedgraph
filtered_Compared_PCB_t1_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt

tag: tissue


title: At_H1_Drought_3

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

data_processing:
The paired-end reads of samples were first cleaned by Trimimomatic, then the cleaned reads were processed by HISAT with default parameters.
After mapping to Tair10 by HISAT, the reads mapped to each annotated gene were counted by HTseqcount.
Genome_build: tair 10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

extract_protocol:
Shoot of plants were frozen in liquid nitrigen, and RNA was harvested using RNA extraction kit from QIAGEN. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: shoot

tag: treatment

value: drought and Aeromonas sp. H1 treatment

tag: genotpye

value: wild type


title: Flu 5 scRNA-seq reanalysis

description:
Flu 5 scRNA-seq
GSM4509018

value: blood

value: non-CHIP


title: nCoV 3 scRNA-seq reanalysis

description:
nCoV 3 scRNA-seq
GSM4509019

value: CHIP


title: Paired training, Dam-Creb, rep1_TI1

description:
PCB1-vs-Dam.gatc.gff
compared_PCB1vsUCB1_rep1.bedgraph
filtered_Compared_PCB_t1_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt

value: brain

value: from -3h to 24h


title: At_H1_Drought_2


title: WT basal, BM6, ATAC-seq

tag: cell line


title: Lats1-CKO luminal, BM7, ATAC-seq

source_name: PyMT tumor derived cell line, FACS purified luminal population

value: EpCAM-high; CD49f-high

value: luminal


title: At_H1_Drought_1


title: Paired training, Dam-Only, rep3_TI1

description:
PCB3-vs-Dam.gatc.gff
compared_PCB3vsUCB3_rep3.bedgraph
filtered_Compared_PCB_t1_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt

tag: developmental stage

value: adult

value: Mushroom body cells


title: Flu 3 scRNA-seq reanalysis

description:
Flu 3 scRNA-seq
GSM4509016


title: Flu 4 scRNA-seq reanalysis

description:
Flu 4 scRNA-seq
GSM4509017


title: Normal 1 scRNA-seq reanalysis

description:
Normal 1 scRNA-seq
GSM4509015


title: Unpaired training, Dam-Only, rep1_TI1

tag: time


title: At_H1_3

value: Aeromonas sp. H1 treatment


title: nCoV 4 scRNA-seq reanalysis

description:
nCoV 4 scRNA-seq
GSM4509020

tag: patient type


title: Lats1-CKO basal, BM4, ATAC-seq

value: PyMT tumor derived cell line


title: WT luminal, BM5, ATAC-seq

value: FBV/N

value: WT


title: A2G2D

description: Total RNA with rRNA removal

value: Liver hepatocellular carcinoma

value: Wildtype


title: At_H1_2

value: shoot


title: Lats1-CKO luminal, BM3, ATAC-seq


title: Flu 1 scRNA-seq reanalysis

description:
Flu 1 scRNA-seq
GSM4509013


title: Flu 2 scRNA-seq reanalysis

description:
Flu 2 scRNA-seq
GSM4509014


title: Naives, no training, Dam-Creb, rep2

description:
NCB2-vs-Dam.gatc.gff
filtered_Naive_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt


title: WT basal, BM2, ATAC-seq

value: EpCAM-low; CD49f-high

value: basal


title: At_H1_1

value: wild type


title: Paired training, Dam-Creb, rep3_TI1


title: nCoV 2 scRNA-seq reanalysis

description:
nCoV 2 scRNA-seq
GSM4509012

value: blood

value: non-CHIP


title: Naives, no training, Dam-Creb, rep1

description:
NCB1-vs-Dam.gatc.gff
filtered_Naive_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt

value: brain


title: At_Drought_3

value: drought treatment


title: At_Drought_2


title: nCoV 1 scRNA-seq reanalysis

description:
nCoV 1 scRNA-seq
GSM4509011


title: Paired training, Dam-Only, rep2_TI1

value: from -3h to 24h


title: whisker pad 3 e12 IgG

city: Milan

first: Pierluigi Giuseppe

last: Manti

address: Via Festa del Perdono 7

institute: University of Milan

data_processing:
Library strategy: CUT&TAG
Bioinformatics analyses of CUT&Tag data were based on the tutorial published on Protocol.io by Zheng Y et al (2020).
The paired-end reads have been aligned against the mouse mm10 reference genome using Bowtie2 (v.2.3) with the following parameters (--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -l 10 -X 700).
Mapped paired reads were filtered (using Samtools v0.1.19) to only keep the read pairs located on the same chromosome and representing fragments of length less than 1kbp. Remaining fragments were converted to normalised counts using bedtools bamtobed and genomecov (v2.25.0) and to bigWig (using bedGraphToBigWig v4).
The peak calling was done per each replicate with SEACR v1.3 (Meers et al., 2019) using the norm and stringent parameters. Due to the poor distribution of fragment lengths of IgG replicate 1, resulting in a low reproduction rates,  we rather called the peaks without IgG by setting the top fraction of peaks considered to 1%, 2%, 3%, 4% and 5% to assess the overall behavior. Peaks represented in final Figures are the ones obtained from the top 1%.
Genome_build: mm10 (fasta files downloaded here: rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/)
Supplementary_files_format_and_content: bigWig files, scores represent the normalized fragment counts
Supplementary_files_format_and_content: peak bed files

source_name: whole adult kidney digested to single cells

extract_protocol:
Whisker pads or adult kidney were microdissected, digested to single cells and processed with the CUT&Tag protocol.
The DNA libraries were prepared for sequencing using standard Illumina protocols

value: murine primary cells freshly isolated

tag: cut&tag

value: IgG


title: At_Drought_1


title: Paired training, Dam-Only, rep1_TI1

value: adult

value: Mushroom body cells


title: Naives, no training, Dam-Creb, rep3

description:
NCB3-vs-Dam.gatc.gff
filtered_Naive_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt


title: Naives, no training, Dam-Only, rep1


title: Lung tissues with obvious pathological changes 2

city: Xi'an

first: Yan

last: Wang

address: 85 Xingqing Road, Beilin District

institute: Shaanxi Institute of Zoology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then we used HISAT2 for sequence alignment and Stringtie software was used for stitching
Library preparation for Transcriptome sequencing A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H - ). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Moschus berezovskii

source_name: Lung tissues

growth_protocol: Lung tissues with obvious pathological changes and normal lung tissues were collected from 3 dead forest musk deer that died within 3 days of the onset of respiratory symptoms

extract_protocol:
Lung tissues were removed, flash frozen, and RNA was harvested using Trizol reagent.
The cDNA libraries were constructed using the NEBNext UltraTM RNA Library Prep Kit for Illumina

tag: tissues

tag: disease state

value: Lung tissues with obvious pathological changes collected from 3 dead forest musk deer that died within 3 days of the onset of respiratory symptoms


title: Lung tissues with obvious pathological changes 1


title: whisker pad 2 e12 H3K4me1


title: At_mock_2

value: no-treatment


title: At_mock_1


title: whisker pad 3 e12 H3K4me1


title: Normal lung tissues 2

value: Normal lung tissues

value: Normal lung tissues collected from 3 dead forest musk deer that died within 3 days of the onset of respiratory symptoms


title: WT luminal, BM1, ATAC-seq

value: PyMT tumor derived cell line

value: FBV/N

value: EpCAM-high; CD49f-high

value: luminal

value: WT


title: whisker pad 1 e12 IgG

source_name: whole whisker pad digested to single cells


title: H3G34R RNAseq

city: Eugene

first: Elizabeth

middle: Toomey

last: Wiles

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

data_processing:
Reads were mapped and gene counts generated using RNA STAR (2.6.0)
DESeq2 version 1.18.1 was used to generate differential count files.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: Tabular files contain counts for every gene as outlined in process above. Excel workbook files (.xlsx) include the differential gene expression values for each mutant background as determined by DESeq2.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: Strains were grown, crossed, and maintained according to standard procedures (Davis RH, 2000). Briefly, polyA RNA was isolated from strains grown at 32°C with shaking for 18 hours in Vogel’s liquid medium.

extract_protocol:
RNA was isolated ( D), Dnase treated (ThermoFisher Scientific) and cleaned (Agencourt RNAClean XP beads; Beckman Coulter)
Poly-A+RNA-seq libraries were prepared using KAPA Stranded mRNA-seq kit (KAPA Biosystems)

tag: genotype/variation

value: mycelia


title: whisker pad 2 e12 IgG

tag: cell type


title: set-2_H3K27me2/3_ChIP-seq

data_processing:
All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012).
ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011) and bigwig files were generated using DeepTools (Ramirez et al., 2016) using a window size of 20 -200bp (tdf and bigwig files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV).

growth_protocol: Strains were grown, crossed, and maintained according to standard procedures (Davis RH, 2000). Briefly, tissue was harvested from strains grown at 32°C with shaking for 18 hours in Vogel’s liquid medium.

extract_protocol:
Tissue was cross-linked for 10 min in 0.5% formaldehyde. Tissue was disrupted by sonication and chromatin sheared using a biorupter (Diagenode).
Libraries were prepared using the NEBNext ChIP-seq Library Prep Master Mix for Illumina.

tag: antibody use

value: H3K27me2/3 (ActiveMotif, Cat#39535)


title: Naives, no training, Dam-Only, rep3

value: brain

tag: genotype


title: Lung tissues with obvious pathological changes 3


title: At_mock_3

value: shoot

value: wild type


title: SET-2; H3G34R RNAseq

value: SET-2; H3G34R


title: CD31 #58

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39)
Retained reads were mapped to the reference mouse genome, GRCm38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts (version 1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations, version M22
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD31+ sorted LSECs

extract_protocol:
Non parenchimal cells were isolated from the liver and CD31+ LSECs were facs sorted.  Total RNA was extracted using ReliaPrep RNA cell miniprep system (Promega). Illumina HighSeq 2000  was used to sequance RNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: IFNalpha

tag: age

value: 8 weeks


title: CD1dKO-1

city: London

first: Patricia

last: Barral

address: London

country: United Kingdom

institute: King's College London

data_processing:
Cutadapt with a quality threshold of 10
Counts quantified using RSEM (1.3.0) and STAR(2.5.2a)
Assembly: GRCm38 release 86
Supplementary files format and content: text files of rsem-star quantified counts

source_name: Peritoneal lavage

extract_protocol:
RNA was isolated using RNA Mini Kit (QIAGEN). RNAseq including cDNA library preparation was processed at the Advanced sequencing facility in the Francis Crick Institute (London, UK)
Libraries were created using a polyA KAPA mRNA HyperPrep kit (Roche)

value: Peritoneal lavage

value: Peritoneal macrophages

value: CD1dKO mice


title: whisker pad 1 e12 H3K4me1

value: murine primary cells freshly isolated

tag: strain


title: CD31 #55


title: CD1dKO-5

tag: tissue


title: WT-1

value: WT mice


title: Naives, no training, Dam-Only, rep2

value: adult

value: Mushroom body cells


title: MSR1_NoMag_TSS

city: Bayreuth

first: Cornelius

middle: Nicolas

last: Riese

address: Universitätsstraße 30

department: Microbiology

country: Germany

institute: University of Bayreuth

description:
5'-end enriched library
List_of_transcription_start_sites

data_processing:
The sequencing reads were trimmed for low quality bases prior to mapping.
Afterwards, reads were mapped to the M. gryphiswaldense genome (Accession No. CP027526) by using bowtie2 with default settings for single-end read mapping (Langmead and Salzberg, 2012).
TSS were automatically detected using the Cappable-tools with standard parameters as in Ettwiller et al., 2016.
The identified TSS were classified by the location in the genome into four groups: primary TSS (pTSS), intragenic TSS in sense orientation (iTSS), or antisense orientation (asTSS), and TSS positioned in the antisense direction in the intergenic regions were classified as "other" (oTSS).
The sequencing reads from all 15 libraries were trimmed for sequencing adapters and low-quality bases before mapping to the current M. gryphiswaldense genome (Accession No. CP027526) using the CLC Bio’s Genomic Workbench software package (Qiagen, Venlo, Netherlands) with a mapping efficiency between 93 to 98% (Table S 1). The resulting datasets were then visualized and investigated with ReadXplorer (Hilker et al., 2014).
The operon detection was performed with the automated prediction tool implemented in ReadXplorer (Hilker et al., 2014). When at least three reads connecting two coding sequences were counted the corresponding genes were assigned into a primary operon. This process was continued for the following genes until no more genes could be assigned to that operon.  Sub-operons were assigned, when a TSS (pTSS or iTSS) was identified within a primary operon.
Genome_build: CP027526
Supplementary_files_format_and_content: XLSX-file with all identified TSS in the genome
Supplementary_files_format_and_content: XLSX-file with the TPM-values
Supplementary_files_format_and_content: XLSX-file of identified operons

organism: Magnetospirillum gryphiswaldense

source_name: Bacteria, WT

growth_protocol: Cells of M. gryphiswaldense were cultivated in a 3L bioreactor at 28°C to early-growth phase.

extract_protocol: Cells were harvested by centrifugation at 4°C and flash frozen with liquid nitrogen prior total RNA isolation. RNA isolated from biological duplicates using the mirVana RNA isolation kit (Thermo Fisher Scientific, Waltham, USA) including DNase treatment was pooled and subsequently used for library preparation.

treatment_protocol: Cells were cultivated under anoxic (MaxMag), microoxic (MicroMag) and oxic (NoMagNO3) conditions. Growth under oxic conditions was also performed with ammoniun (NoMag).


title: Normal lung tissues 3

value: Normal lung tissues

value: Normal lung tissues collected from 3 dead forest musk deer that died within 3 days of the onset of respiratory symptoms


title: set-2_H3K36me3_ChIP-seq

value: H3K36me3 (Abcam, Cat#ab9050)


title: ash1(Y888F)_H3K9me3_ChIP-seq

value: H3K9me3 (ActiveMotif, Cat#39161)


title: set-2_H3K9me3_ChIP-seq


title: CD1dKO-2


title: CD1dKO-3


title: CD31 #54


title: CD31 #51


title: MSR1_WTSS

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_operons


title: MSR1_MaxMag_TSS


title: Normal lung tissues 1


title: MSR1_Term, 3'-end

description:
3'-end library
List_of_operons


title: WT-5


title: set-2; ash-1(Y888F)_H3K27me2/3_ChIP-seq

value: H3K27me2/3 (ActiveMotif, Cat#39535)


title: MSR1_NoMag, 3

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
NoMag_3

tag: condition

value: NoMag


title: WT-3


title: CD31 #49

tag: treatment

value: NaCl


title: CD31 #48


title: WT-2


title: SET2; H3G34R_H3K27me2/3_ChIP-seq

value: SET2; H3G34R


title: MSR1_NoMag, 2

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
NoMag_2

value: wild type


title: CD31 #44

value: 8 weeks


title: MSR1_MaxMag, 3

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
MaxMag_3

value: MaxMag


title: MSR1_NoMag, 1

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
NoMag_1


title: SET2; H3G34R_H3K9me3_ChIP-seq


title: KO no treatment replicate 1

city: Epalinges

first: Fabio

last: Martinon

address: 155 Ch. des Boveresses

department: Dept. of Biochemistry

institute: University of Lausanne

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.84.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.9.3). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus (v GRCm38) genome using STAR (v. 2.5.2b, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using M. musculus (Ensembl v 86) gene annotation.
Assembly: Mus musculus (v GRCm38)
Supplementary files format and content: Tab-delimited text files include gene counts for each Sample.

source_name: Liver

extract_protocol:
RNA was extracted from liver tissue using RNeasy mini kit (QIAGEN, Hilden, Germany) following standard protocols
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol

value: Liver


title: KO no treatment replicate 2


title: H3G34R_H3K36me3_ChIP-seq


title: CD31 #60

value: IFNalpha


title: set-2; ash-1(Y888F)_H3K9me3_ChIP-seq


title: H3G34R_H3K27me2/3_ChIP-seq


title: MSR1_MaxMag, 2

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
MaxMag_2


title: MSR1_MaxMag, 1

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
MaxMag_1


title: H3G34R H3K36me2 ChIP-seq

value: H3K36me2 (Abcam, Cat#ab9049)


title: WT no treatment replicate 1

value: WT


title: WT no treatment replicate 2


title: CD31 #57


title: CD31 #59


title: CD31 #50


title: MSR1_NoMagNO3, 3

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
NoMagNO3_3


title: lncRNA-Smad7-KO-ChIRP-CM3.3

city: Beijing

first: kong

last: xiaohui

state: Beijing

address: Zheng Yutong medical building

department: school of life science

data_processing:
Library strategy: ChIRP-seq
Illumina HiSeq 2000 software used for basecalling
RNA-seq, ChIP-seq, and ChIRP-seq reads were trimmed using TrimGalore for adaptor sequence, and masked for low-complexity or low-quality sequence.
RNA-seq reads were mapped to mm10 whole genome using hisat2 version 2.1.0 with parameters, reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Cufflinks (version 2.2.1). ChIP-seq, and ChIRP-seq reads mapped to mm10 genome assembly using Bowtie2 version 2.3.3.
Peaks were called using MACS2 for ChIP-seq and ChIRP-seq.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated from the bam files using the Coverage function in deepTools.

source_name: mouse embryonic stem cell

growth_protocol: mESCs were cultured on gelatin coated plates with 15% serum ESC culture medium. Cardiac progenitor cells (CM3.3) were induced from mESCs and cultured by hanging drops for 2 days, then cultured on bacterial plates in 15% serum-containing ESC culture medium withdrawal LIF for 1.3 days. WT and lncRNA-Smad7 KIpA (4x polyA knock-in) mESCs and cardiac progenitor cells (CM3.3) were harvested for RNA extraction.

extract_protocol:
Total RNA was extracted by commerical RNA extraction Kit. Lysates for ChIP and ChIRP assays were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody or antisense probes.
RNA libraries were prepared for sequencing using standard Illumina protocols, and the libraries were sequenced on Illumina HiSeqXten-PE150 following the manufacturer's protocols. For ChIP-seq and ChIRP DNA-seq, libraries were prepared according to Illumina's instructions and the libraries were sequenced on the Illumina HiSeq-PE150 following the manufacturer's protocols.

treatment_protocol: There is no other treatment for the mESCs. The cardiac progenitor cells were treated with activin A, hBMP4, L-Ascorbic Acid, and hVEGF from day 2 to day 3.3. WT and lncRNA-Smad7 KIpA cardiac progenitor cells (CM3.3) were cross-linked and harvested for H3K27me3 ChIP-seq. WT and lncRNA-Smad7 KO (knock-out) mESCs were cross-linked and harvested for lncRNA-Smad7 ChIRP-seq.

value: mouse embryonic stem cell

tag: chip antibody

tag: chirp probe

value: lncRNA-Smad7 probes (BGI tech)


title: lncRNA-Smad7-WT-ChIRP-CM3.3


title: MSR1_NoMagNO3, 2

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
NoMagNO3_2


title: set-2; ash1(Y888F)_5mC

data_processing:
The BRAT-BW software package (compbio.cs.ucr.edu/brat/) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping.
BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged.
To display the bisulfite sequencing data, the average 5mC level was determined for specified step-wise window sizes across the genome using the MethPipe program (smithlabresearch.org/software/methpipe/). The resulting file was renamed with an .igv file extension to allow display on the Integrated Genome Viewer.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: The igv and bigwig files were generated for display of average 5mC levels on IGV (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011). "bigwig" files were generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp. "igv" files were generated using MethPipe (smithlabresearch.org/software/methpipe/) using a window size of 25bp.

growth_protocol: Strains were grown, crossed, and maintained according to standard procedures (Davis RH, 2000). Briefly, genomic DNA was isolated from strains grown at 32°C with shaking for 48 hours in Vogel’s liquid medium.

extract_protocol:
Genomic DNA isolation was performed as previously described (Honda & Selker, 2008).
50ng of genomic DNA was treated with bisulfite using the EZ DNA Methylation Lightning kit (ZYMO Research). Libraries were prepared for sequencing with the EpiGnome Methyl-Seq Kit and EpiGnome Index PCR Primers (Epicentre), purified with Agencourt AMPure XP beads (Beckman Coulter), Qubit HS Assay quantified (Life Technologies), visualized on the Fragment Analyzer (Advanced Analytical), and sequenced on a Illumina HiSeq 2000  or HiSeq4000 (www.illumina.com) at the UO Genomics Core Facility as single-end 75 or 100nt reads.

tag: tissue type

value: mycleia

tag: bisulfite treated

value: bisulfite


title: nAb-CM3.3

data_processing:
Illumina HiSeq 2000 software used for basecalling
RNA-seq, ChIP-seq, and ChIRP-seq reads were trimmed using TrimGalore for adaptor sequence, and masked for low-complexity or low-quality sequence.
RNA-seq reads were mapped to mm10 whole genome using hisat2 version 2.1.0 with parameters, reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using  Cufflinks (version 2.2.1). ChIP-seq, and ChIRP-seq reads mapped to mm10 genome assembly using Bowtie2 version 2.3.3.
Peaks were called using MACS2 for ChIP-seq and ChIRP-seq.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated from the bam files using the Coverage function in deepTools.

value: ES-derived cardiomyocyte progenitor cells


title: CD31 #46


title: CD31 #43


title: MSR1_NoMagNO3, 1

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
NoMagNO3_1


title: BKO_m6A MeRIP-Seq input

first: Zheng

last: Chen

address: 92 Xidazhijie  Harbin Institute of Technology

data_processing:
library strategy: meRIP-seq
Raw data (raw reads) of fastq format were firstly processed using fastp (version  0.19.11). In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low-quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using BWA v0.7.12 and clean  reads were aligned to the reference genome using BWA mem v 0.7.12.
After mapping reads to the reference genome, exomePeak R package (version 2.16.0)  was used for the m6A peak identification in each anti-m6A immunoprecipitation group  with the corresponding input samples serving as a control, and q-value threshold of  enrichment of 0.05 was used for all data sets. The m6A-enriched motifs of each group  were identified by HOMER (version 4.9.1).
In the peak calling result, each peak was corresponding on gene, in which the peak was  located in its exon. These genes were supposed as peak related genes, and then Gene  Ontology (GO) enrichment analysis was performed to identify the function enrichment  results. GO enrichment analysis was implemented by the GOseq R package, in which  gene length bias was corrected. GO terms with corrected P-value less than 0.05 were  considered significantly enriched by peak related genes. KEGG is a database resource  for understanding high-level functions and utilities of the biological system, such as the  cell, the organism and the ecosystem, from molecular-level information, especially  large-scale molecular datasets generated by genome sequencing and other high-through  put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS  software (version 3.0) to test the statistical enrichment of peak related genes in KEGG  pathways.  Besides, the distribution of peak on different function regions, such as 5’ UTR, CDS,  3’UTR was performed.
Differential peak calling was performed using exomePeak R package (version 2.16.0)  with parameters of P-value less than 0.05 and fold change more than 1. Using the same  method, genes associated with different peaks were identified and also do GO and  KEGG enrichment analysis.
Assembly: Ensemble_ grcm38_p6
Supplementary files format and content: peaks

organism: Mus

source_name: brown adipose tissue

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany) from iBAT of Wtapflox/flox and BKO mice .
Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Fragmented poly(A)+ RNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation. Then, immunoprecipitated mRNAs or Input was used for library construction with NEBNext ultra RNA library prepare kit  for Illumina (New England Biolabs). The library preparations were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols.

treatment_protocol: Wtapflox/flox and BKO mice were fed with normal chow diet for 8 weeks old

value: BKO (Wtapflox/flox UCP1-iCre)


title: FF_m6A MeRIP-Seq input

value: Wtapflox/flox


title: MSR1_MicroMag, 3

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
MicroMag_3

value: MicroMag


title: H3K27me3-KIpA-2-1-CM3.3


title: H3K27me3-KIpA-2-2-CM3.3


title: MSR1_MicroMag, 2

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
MicroMag_2


title: CD31 #45

value: NaCl


title: H3K27me3-KIpA-1-1-CM3.3


title: H3K27me3-KIpA-1-2-CM3.3


title: BKO_m6A MeRIP-Seq

value: m6A antibody (Synaptic System, 202003)

value: BKO (Wtap flox/flox UCP1-iCre)


title: H3K27me3-WT-2-CM3.3


title: FF_m6A MeRIP-Seq


title: Tumour organoid, scramble control, replicate 3

status: Public on Oct 18 2022

city: Umea

first: Cedric

last: Patthey

address: Analysvägen 1,

country: Sweden

institute: Umeå University

data_processing:
FASTQ files were generated with bcl2fastq version 2.20.0 with default parameter.
Adapter sequences were removed with Cutadapt version 4.0 including 5 iterations (-n 5), 20% mismatch allowed (-e 0.2), at least 2 base pairs matching for trimming (-o 2) and a cut-off for keeping the read of 18 bp (-m 18).
For rRNA removal, reads were mapped to 45S rRNA (NR_046233.2) and 5S rRNA (NR_030686.1) sequences using Bowtie2 version 2.3.5.1 with default parameters. Identified rRNA reads were removed.
Reads were mapped to the reference genome with STAR version 2.9.9a with adjusted stringency for mapping score cut-off --outFilterScoreMinOverLread 0.5 and  --outFilterMatchNminOverLread 0.5. Read mapped as primary alignments were selected using Samtools version 1.14 with flag parameters -F4 and -F256.
Reads mapping to exons of coding genes were counted to generate a raw read count matrix using HTseq version 0.12.4. The gene models were extracted from the Ensemble release 104 annotation (GTF) file, keeping exons from transcript with biotype=protein_coding annotation.
TPM was calculated as described in Wagner et al, 2012 (PMID 22872506).
Assembly: Mus musculus genome assembly GRCm39 (mm10) primary assembly
Supplementary files format and content: The file Bulk_raw_read_count.xlsx has a single tab with raw read count per gene. First column contains the official gene symbol, second column contains the Ensembl gene accession number. Following columns contain the raw read count for the six samples
Supplementary files format and content: The file Bulk_TPM.xlsx has a single tab with normalized expression values (TPM) per gene. First column contains the official gene symbol, second column contains the Ensembl gene accession number. Following columns contain the raw read count for the six samples

source_name: mT5 organoid

extract_protocol:
500 cells were FACS sorted directly into 5.5 µl of lysis buffer containing 0.2% triton and 2 U/µl RNase inhibitor (Takara Bio #2314B) before freezing on dry ice. The samples were thawed and RNA sequencing libraries were generated using the Smart-seq2 protocol according to Picelli et al, 2014 (PMID 24385147).
Smart-Seq2 as described in Picelli et al, 2014 (PMID 24385147)

tag: cell line

value: mT5 organoid

value: Ductal adenocarcinoma

value: scambled control

tag: flow cytometry_run

value: Run 3


title: Tumour organoid, Galectin 4 KD, replicate 3

value: Galectin 4 knock-down


title: set-2_5mC


title: H3K27me3-WT-1-CM3.3

value: WT


title: Tumour organoid, scramble control, replicate 1

value: Run 1


title: Gal4KD, scRNA-seq

data_processing:
Single cell sequencing data was processed with Cell Ranger version 6.1.2. FASTQ files were generated with the mkfastq function with default parameter. The reads were mapped on the refdata-gex-mm10-2020-A reference genome. Cellranger count was run with default parameters, yielding 7677 cells.
For cell annotation, the UMI count was loaded into Seurat vesion 4.1.0 and processed with a standard pipeline. Briefly, cells were annotated QC-pass based on percent mitochondrial reads (percent.mt<10),  number of UMI detected (2000<nCount_RNA<50000), number of genes genes detected (800<nFeature_RNA<8000). The two samples (Gal4KD and scramble) were normalized, scaled and integrated using the IntegrateData function. Clustering was performed with default methods. Clusters identified as CAF or immune cells were separated and the integration and clustering were reiterated on CAF or immune cells individually. Clusters representing cross contaminations of CAF and immune cells were identified and excluded, yielding 3811 CAF and 1618 immune cells. Clusters of CAF and immune subtypes were annotated using lists of markers derived using the FindMarkers function with default parameters comparing each cluster versus all others.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Cell_Annotation_7677_cells.csv contains a coma separated table. The first column contains the cell name; second column contains the shRNA group (scramble vs Gal4KD); the third column indicates quality control result (pass or fail); the fourth column contains a broad annotation (CAF vs Immune); The fifth column indicates cell subtype annotation

source_name: Pancreas tumour

extract_protocol:
Single cell suspensions in 0.2% BSA in PBS at a concentration of 1000 cells/µl were used to load a total of 7500 cells per well into a 10x Chromium cartridge.
cDNA and sequencing libraries were prepared according to the manufacturer’s instructions following the 10x Chromium Single Cell 3’ dual indexing v3.1 protocol.

value: Pancreas tumour

value: Pdpn+ fibroblast & Cd45+ immune cells

value: wt

tag: transplanted line

value: Galectin 4 shRNA tumour cells


title: Tumour organoid, Galectin 4 KD, replicate 2

value: Run 2


title: Tumour organoid, scramble control, replicate 2


title: Tumour organoid, Galectin 4 KD, replicate 1


title: head, 5-days flies, control group, ancestors fed with normal food diet [ND_1]

city: hangzhou

first: JIE

last: YANG

state: ZheJiang

address: Yuhangtang Road No.388,Zhejiang Province, Zijingang Campus of Zhejiang University, nano building 560 room

department: science life institute

institute: ZheJiang Univeristy

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
Removing reads containing sequencing adapter
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5)  was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: Dm6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: head

extract_protocol:
RNA was harvested using Trizol. >1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared  following RNA-Seq Library Preparation Protocol (DNBSEQ).mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads.PCR products were purified with Ampure XP Beads (AGENCOURT).

value: head

value: 5-days flies

value: W+VDRC

value: the flies' mother fed with normal food (contains 10% sucrose) diet from egg to adult


title: head, 5-days flies, ancestors exposed in high sugar diet [F1_1]

value: the flies' mother fed with high sugar diet  (contains 20% sucrose)  from egg to adult


title: head, 5-days flies, control group, ancestors fed with normal food diet [ND_2]


title: head, 5-days flies, ancestors exposed in high sugar diet [F1_2]


title: head, 5-days flies, control group, ancestors fed with normal food diet [ND_3]


title: Scramble, scRNA-seq

value: Scramble shRNA tumour cells


title: MSR1_MicroMag, 1

description:
Ribo-depleted whole transcriptome shotgun sequencing library
List_of_TPM_values
MicroMag_1

value: wild type

value: MicroMag


title: head, 5-days flies, ancestors exposed in high sugar diet [F1_3]


title: SubjectC_Pre-1_Exp2

type: RNA

city: Tsukuba

first: Masaya

last: Seki

state: Ibaraki

address: Sengen 2-1-1

department: JEM Utilization Center

institute: Japan Aerospace Exploration agency

description:
C_Pre-1_2
Gene expression in Pre -1 human whole blood.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 0.1ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 0.1 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression 4x44K v2 Microarray Kit (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B).

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

source_name: Whole blood, Pre -1, SubjectC, Experiment2

label_protocol: Cyanine-3 (Cy3) labeled aRNA was prepared from RNA using the Low Input Quick Amp Labeling Kit and the RNA Spike-In Kit (1 color) (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using the PAXgene Blood RNA System Kit (Qiagen, Tokyo, Japan) according to the manufacturer’s guidelines.

treatment_protocol: Blood samples were collected in tubes at 15:00-16:00 on 1 day before staying at isolation and confinement facility and day 14th during. Whole blood samples were incubated at room temperature for 24 hours after collecting and stored at -80℃ until analysis.

value: Whole blood

tag: gender

value: male

value: pre-confinement

tag: subject

value: C


title: SubjectG_C14_Exp2

description:
G_C14_2
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectG, Experiment2

value: confinement for 14 days

value: G


title: SubjectF_C14_Exp1

description:
F_C14_1
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectF, Experiment1

value: F


title: SubjectD_C14_Exp2

description:
D_C14_2
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectD, Experiment2

value: D


title: SubjectF_Pre-1_Exp2

description:
F_Pre-1_2
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectF, Experiment2


title: SubjectA_Pre-1_Exp2

description:
A_Pre-1_2
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectA, Experiment2

value: A


title: SubjectE_C14_Exp2

description:
E_C14_2
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectE, Experiment2

value: E


title: SubjectH_Pre-1_Exp2

description:
H_Pre-1_2
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectH, Experiment2

value: H


title: SubjectB_Pre-1_Exp2

description:
B_Pre-1_2
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectB, Experiment2

value: B


title: SubjectE_Pre-1_Exp2

description:
E_Pre-1_2
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectE, Experiment2


title: SubjectD_C14_Exp1

description:
D_C14_1
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectD, Experiment1


title: SubjectA_C14_Exp1

description:
A_C14_1
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectA, Experiment1


title: SubjectG_Pre-1_Exp1

description:
G_Pre-1_1
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectG, Experiment1


title: SubjectC_C14_Exp1

description:
C_C14_1
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectC, Experiment1


title: SubjectA_C14_Exp2

description:
A_C14_2
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectA, Experiment2


title: SubjectB_C14_Exp1

description:
B_C14_1
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectB, Experiment1


title: SubjectD_Pre-1_Exp2

description:
D_Pre-1_2
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectD, Experiment2


title: SubjectC_C14_Exp2

description:
C_C14_2
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectC, Experiment2


title: SubjectH_C14_Exp2

description:
H_C14_2
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectH, Experiment2


title: SubjectE_C14_Exp1

description:
E_C14_1
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectE, Experiment1


title: SubjectB_C14_Exp2

description:
B_C14_2
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectB, Experiment2


title: SubjectF_C14_Exp2

description:
F_C14_2
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectF, Experiment2


title: SubjectG_Pre-1_Exp2

description:
G_Pre-1_2
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectG, Experiment2


title: SubjectF_Pre-1_Exp1

description:
F_Pre-1_1
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectF, Experiment1


title: SubjectG_C14_Exp1

description:
G_C14_1
Gene expression in C14 human whole blood.

source_name: Whole blood, C14, SubjectG, Experiment1


title: SubjectE_Pre-1_Exp1

description:
E_Pre-1_1
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectE, Experiment1


title: SubjectD_Pre-1_Exp1

description:
D_Pre-1_1
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectD, Experiment1


title: SubjectB_Pre-1_Exp1

description:
B_Pre-1_1
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectB, Experiment1


title: SubjectC_Pre-1_Exp1

description:
C_Pre-1_1
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectC, Experiment1


title: NALM-6 cells, low dex (50 nM), Rep 2

city: Iowa City

first: Miles

last: Pufall

state: IA

address: 51 Newton Rd., BSB Rm 4-430

department: Biochemistry

institute: University of Iowa

data_processing:
Adapters were trimmed using TrimGalore v0.4.0
Trimmed reads were mapped to Gencode Fasta transcriptome GRCh38
Counts were imported into R using tximeta, with differential expression performed using DESeq2
Assembly: Gencode GRCh38
Supplementary files format and content: Gene level raw count table for all samples in csv format

source_name: B cells

growth_protocol: NALM-6 cells were grown in RPMI + 10% FBS, 5% CO2

extract_protocol:
RNA was extracted from 2 million cells using miRNeasy Mini Kit (Qiagen cat#217004),
Illumina TruSeq v2 mRNA

treatment_protocol: Cells were treated for 24 hours with the drug or vehicle combination indicated

tag: cell type

value: B cell acute lymphoblastic leukemia

value: t(5;12) ETV6/PDGFRB

value: 50 nM Dexamethasone


title: NALM-6 cells, low dex (50 nM), Rep 3


title: NALM-6 cells, low dex (5 nM), Rep 3

value: 5 nM Dexamethasone


title: NALM-6 cells, low dex (5 nM),  Rep 1


title: NALM-6 cells, ldelalisib (250 nM), Rep 3

value: 250 nM Idelalisib


title: NALM-6 cells, high dex (50 nM), idelalisib (250 nM), Rep 2

value: 50 nM Dexamethasone, 250 nM Idelalisib


title: NALM-6 cells, low dex (5 nM), idelalisib (250 nM), Rep 1

value: 5 nM Dexamethasone, 250 nM Idelalisib


title: NALM-6 cells, high dex (50 nM), idelalisib (250 nM), Rep 1


title: NALM-6 cells, low dex (5 nM), idelalisib (250 nM), Rep 2


title: NALM-6 cells, idelalisib (250 nM), Rep 1


title: NALM-6 cells, idelalisib (250 nM), Rep 2


title: NALM-6 cells, low dex (5 nM), Rep 2


title: SubjectA_Pre-1_Exp1

description:
A_Pre-1_1
Gene expression in Pre -1 human whole blood.

source_name: Whole blood, Pre -1, SubjectA, Experiment1

value: Whole blood

value: male

value: pre-confinement


title: NALM-6 cells, low dex (5 nM), idelalisib (250 nM), Rep 3


title: NALM-6 cells, high dex (50 nM), idelalisib (250 nM), Rep 3


title: NALM-6 cells, vehicle, Rep 1

value: 0.1percent DMSO


title: NALM-6 cells, vehicle, Rep 3


title: NALM-6 cells, vehicle, Rep 2


title: iNeurons non-targeting shRNA rep1

city: Stanford

first: Caitlin

last: Rodriguez

state: CA

address: 279 Campus Dr.

department: Genetics

institute: Stanford University

description: non-targeting shRNA (Mission) for

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Assembly: Genome_build: hg38 for human samples, mm10 for mouse samples
Supplementary files format and content: Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: iPSC-derived neurons

extract_protocol:
RNA extracted using a PureLink RNA Mini Kit (Ambion)
polyA selected libraries were derived using the TruSeq Stranded mRNA kit from Illumina.

treatment_protocol: iNeurons were transduced with virus (Mission® shRNA, non-targeting or human RTN4R: TRCN0000061558). 24hr later, a half media change was performed. iNeurons were maintained for 3 days before being re-transduced with a half dose of virus, then maintained for another 5 days prior to harvesting for experimentation.

value: Control


title: iNeurons non-targeting shRNA rep2

description: non-targeting shRNA (Mission) for


title: iNeurons RTN4R shRNA rep2

description: RTN4R shRNA (Mission) for 8 days

value: RTN4R shRNA


title: iNeurons RTN4R shRNA rep1

description: RTN4R shRNA (Mission) for 8 days


title: NALM-6 cells, low dex (50 nM),  Rep 1


title: HepG2, HBx-overexpressing, biol rep 3

first: Jian

last: Yu

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

data_processing:
The libraries were sequenced on an Illumina HiSeq 4000 platform (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions, and 150-bp paired-end reads were generated.
Cutadapt (V1.9.3) (Kechin et al., 2017) was used to acquire high-quality reads.
The high-quality reads were then mapped to the Homo sapiens Hg19 genome using STAR (V2.5.1b)(Dobin et al., 2013).
CircRNAs were identified by DCC (V0.4.4)(Cheng et al., 2016) and annotated by circBase(Glažar et al., 2014) and Circ2Traits(Ghosal et al., 2013).
Assembly: hg19
Supplementary files format and content: CircRNA Expression Profiling: circRNAs identified by DCC, including  their junction reads, logCPM, coordinates, sources, best_transcripts etc.

extract_protocol:
Total RNA was extracted from HBx-overexpressing (HBx-oe) and NC (negative control) HepG2 cells using Trizol reagent (Invitrogen, CA) following the manufacturer’s protocol. The RNA concentration and quality were evaluated with the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies).
Firstly, rRNA was depleted by NEBNext rRNA Depletion Kit（New England Biolabs, Inc., Massachusetts, USA）according to the manufacturer’s protocol. Secondly, sequencing libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit（New England Biolabs, Inc., Massachusetts, USA）. BioAnalyzer 2100 system（Agilent Technologies, USA）was used in quality control.

value: human hepatocellular carcinoma cell line

value: HBx-overexpressing

value: Day 10


title: HepG2, negative control, biol rep 1

value: WT


title: HepG2, negative control, biol rep 2


title: HepG2, negative control, biol rep 3


title: HepG2, HBx-overexpressing, biol rep 2


title: E2 iMO Naïve rep2

city: Huntingdon Valley

first: Carolina

last: Rezende Melo da Silva

state: Pennsylvania

address: 2527 Morgan run

department: Microbiology and Immunology

institute: Thomas Jefferson University

data_processing:
pseudo alignment using Kallisto (v0.46.1) and Sleuth R package (v0.30.0)
Assembly: Mus Musculus GRCm38.p6 and ECTV Moscow GCA_000841905.1
Supplementary files format and content: Excel spreadsheet showing transcripts abundance normalized to transcripts per million for all libraries

source_name: spleen

extract_protocol:
B-cells and iMO were sorted directly into Trizol. Total RNA was purified with the RNA Clean and Concentrator with DNase I treatment (Zymo Research).
mouse Ovation SoLo RNA-Seq Systems, including DNaseI and Insert-Dependent Adaptor Cleavage (InDA-C) treatments.

value: spleen

tag: sample group

value: iMO Naïve

value: iMO

tag: strain background

value: infected subcutaneously with GFP-expressing ECTV


title: G1 iMO Naïve rep3


title: C3 iMO Naïve rep1


title: E1 iMO GFP pos rep3

source_name: lymph node

value: lymph node

value: iMO GFP pos


title: C2 iMO GFP pos rep2


title: A3 iMO GFP pos rep1


title: HepG2, HBx-overexpressing, biol rep 1

tag: genotype


title: B3 iMO GFP neg rep1

value: iMO GFP neg


title: D2 iMO GFP neg rep2


title: F1 iMO GFP neg rep3


title: H2 B cell Naïve rep3

value: B cell Naïve

value: B cell


title: B2 B cell Naïve rep1


title: H1 B cell GFP pos rep2

value: B cell GFP pos


title: A2 B cell GFP neg rep1

value: B cell GFP neg


title: D1 iMO Ifnar1-/- GFP pos rep1

extract_protocol:
iMO were sorted directly into Trizol. Total RNA was purified with the RNA Clean and Concentrator with DNase I treatment (Zymo Research).
mouse Ovation SoLo RNA-Seq Systems, including DNaseI and Insert-Dependent Adaptor Cleavage (InDA-C) treatments.

value: iMO Ifnar1-/- GFP pos


title: G2 B cell GFP neg rep3


title: F3 B cell Naïve rep2


title: D3 B cell GFP pos rep1


title: H3 iMO Ifnar1-/- Naïve rep2

value: iMO Ifnar1-/- Naïve


title: C1 iMO Ifnar1-/- GFP neg rep1

value: iMO Ifnar1-/- GFP neg


title: G1 iMO Ifngr-/- GFP neg rep2

value: iMO Ifngr-/- GFP neg


title: B3 iMO Ifngr-/- GFP pos rep1

value: iMO Ifngr-/- GFP pos


title: E2 iMO Ifnar1-/- GFP neg rep2


title: H1 iMO Ifngr-/- GFP pos rep2


title: F2 iMO Ifnar1-/- GFP pos rep2


title: A3 iMO Ifngr-/- GFP neg rep1


title: F1 iMO WT GFP pos rep3

value: iMO WT GFP pos


title: B2 iMO Ifngr-/- Naïve rep1

value: spleen

value: iMO Ifngr-/- Naïve


title: D2 iMO WT GFP pos rep2

value: iMO


title: B1 iMO WT GFP pos rep1

value: infected subcutaneously with GFP-expressing ECTV


title: F3 iMO Ifngr-/- Naïve rep2


title: E3 B cell GFP neg rep2

value: lymph node


title: H2 iMO WT GFP pos rep4


title: G2 iMO WT GFP neg rep4

value: iMO WT GFP neg


title: C3 iMO WT Naïve rep2

value: iMO WT Naïve


title: E1 iMO WT GFP neg rep3


title: A2 iMO WT Naïve rep1


title: A1 iMO WT GFP neg rep1


title: C2 iMO WT GFP neg rep2


title: D3 iMO Ifnar1-/- Naïve rep1


title: GTML, DMSO, RNA, Rep2

city: San Francisco

first: Duygu

last: Kuzuoglu Ozturk

state: California

address: 1450 3rd Street, Helen Diller Cancer Building

institute: UCSF

data_processing:
For Riboseq and RNAseq analyses, the sequences were processed as described previously (Ingolia, 2012).
Only-adapter containing reads were used, the first nucleotide of the reads were trimmed.
rRNA-aligned reads were excluded.
Assembly: GRCm38/mm10
Supplementary files format and content: Each dataset contains analysis compared to Control (DMSO) condition. Total RNAseq dataset are labelled as "mrna"; RPFs are labelled as ''ribo" and Translation efficiency calculations are labelled as "trleff"
Supplementary files format and content: Raw read numbers for Riboseq and RNAseq samples were included in 'exprtable-all' file. RNAseq data are labelled as "total", Riboseq as "RP"

source_name: Brain

growth_protocol: GTML cells were cultured in complete neurobasal culture media (Gibco) supplemented with B27 (2%), L-Glutamine (1x), EGF (20 µg/L), bFGF (20 µg/L) and Penicillin-streptomycin at 37C. Accutase (Innovate Cell Tech) was used to dissociate the cells.

extract_protocol:
Cells were lysed and a small aliquot was removed for total RNA extraction for RNAseq samples, using Zymo RNA Clean&Concentrator Kit.
The Riboseq and RNAseq libraries were prepared by using ARTseq Ribosome Profiling Kit (Epicentre)

treatment_protocol: 3 hour treatment

value: Brain

value: GTML

value: Human MYCN overexpressed

value: Control


title: GTML, Rapamycin, RNA, Rep1

description:
GTML5_Rapamycin-1_total_3_hr_S13
mrna-rapa-all.csv

value: Rapamycin (5 nM)


title: GTML, Rapalink, RNA, Rep2

description:
GTML5_M1071-2_total_3_hr_S5
mrna-m1071-all.csv

value: Rapalink-1 (50nM)


title: GTML, DMSO, RNA, Rep1


title: GTML, Rapamycin, RNA, Rep2

description:
GTML5_Rapamycin-2_total_3_hr_S14
mrna-rapa-all.csv


title: GTML, Rapamycin, RNA, Rep3

description:
GTML5_Rapamycin-3_total_3_hr_S15
mrna-rapa-all.csv


title: GTML, Rapamycin, RP, Rep3

description:
GTML5_Rapamycin-3_RP_3_hr_S18
ribo-rapa-all.csv
trleff-rapa-all.csv

data_processing:
For Riboseq and RNAseq analyses, the sequences were processed as described previously (Ingolia, 2012).
Only-adapter containing reads were used, the first nucleotide of the reads were trimmed.
rRNA-aligned reads were excluded.
Assembly: GRCm38/mm10
Supplementary files format and content: Each dataset contains analysis compared to Control (DMSO) condition. Total RNAseq dataset are labelled as "mrna"; RPFs are labelled as ''ribo" and Translation efficiency calculations are labelled as "trleff"
Supplementary files format and content: Raw read numbers for Riboseq and RNAseq samples were included in 'exprtable-all' file. RNAseq data are labelled as "total", Riboseq as "RP"
Library strategy: Ribo-seq


title: GTML, Rapamycin, RP, Rep2

description:
GTML5_Rapamycin-2_RP_3_hr_S17
ribo-rapa-all.csv
trleff-rapa-all.csv


title: GTML, Rapalink1, RP, Rep3

description:
GTML5_M1071-_3_RP-B_3_hr_S12
ribo-m1071-all.csv
trleff-m1071-all.csv


title: GTML, Rapalink1, RP, Rep1

description:
GTML5_M1071-1_RP-B_3_hr_S10
ribo-m1071-all.csv
trleff-m1071-all.csv


title: GTML, Rapalink1, RP, Rep2

description:
GTML5_M1071-2_RP-B_3_hr_S11
ribo-m1071-all.csv
trleff-m1071-all.csv


title: GTML, DMSO, RP, Rep2


title: GTML, DMSO, RP, Rep1