title: LacNa_rep3

city: Bengbu

first: Xiang

last: Li

state: Anhui

address: First Affiliated Hospital of Bengbu Medical College, 287 Changhuai Road, Bengbu, China.

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 poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_count.txt: Tab-delimited text file includes gene counts.

source_name: Placental trophoblast

extract_protocol:
RNA from HTR-8/SVneo cells was harvested using Trizol reagent. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: treated with 25 mM sodium L-lactate


title: KO_RO-IP for meRIP-seq

status: Public on Dec 13 2021

type: SRA

city: nantong

first: hong

last: shihao

address: 19 Qixiu Road

country: China

institute: Nantong university

library_source: transcriptomic

data_processing:
Library strategy: MeRIP-seq
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For  MeRIP-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For MeRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: spermatogenic cells

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For MeRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2. Subsequently, the purified RNA was incubated with anti-m6A polyclonal antibody (Sigma-Aldrich, ABE572) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106). The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).

tag: strain

tag: tissue

value: testes

tag: age

tag: genotype

value: spermatogenic cells


title: BT474-P1_S1

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

country: USA

institute: New York University, NYU Langone Medical Center

data_processing:
scRNA-Seq Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
RNA-Seq Basecalls performed using CASAVA
RNA-Seq reads were mapped using STAR guided by GTF
RNA-Seq Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files, Count Tables, BAM files, gene names and genes-barcodes (tsv files) matrices (matrix file)

organism: Homo sapiens

extract_protocol:
Samples were prepared by the Princess Margaret Genomic Centre following the 10X Genomics Single Cell 3‚Äô Reagent Kits v2 user guide. Briefly, samples were washed two times in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. The cell suspension was loaded onto a 10X single cell A chip. After droplet generation, samples were transferred onto pre-chilled 96-well plates (Eppendorf), heat-sealed, and incubated overnight in a Veriti 96-well thermal cycler (Thermo Fisher) for reverse transcription (RT).
Following RT, cDNA was recovered using the Recovery Agent provided by 10X, and subsequently purified by using Silane DynaBead (Thermo Fisher) mix, as outlined by the user guide. Purified cDNA was amplified for 13 cycles before purification on SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA), and cDNA concentration was determined with a  Bioanalyzer (Agilent Technologies). cDNA libraries were prepared as outlined by the Single Cell 3‚Äô Reagent Kits v2 user guide with modifications to the PCR cycles based on the calculated cDNA concentration.

tag: treatment

value: untreated

tag: cell line

tag: cell type

value: HER2 positive breast cancer cells


title: BT474-Tuca-DTP-4_S4

value: 14 day tucatinib


title: Alveolar_Control_rep2

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 21.0.1 was used to demultiplex the raw sequencing reads according to the sample indices.
The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings. In short, the reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum reads length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2). They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs. Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton’s UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen). The reads were then mapped to the Human genome GRCh38
The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 21.0.1 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 (Small-sample estimation of negative binomial dispersion, with applications to SAGE data) and incorporated in the EdgeR Bioconductor package (Robinson et al., 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data).
Genome_build: Human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample

source_name: NCI-H441 (ATCC HTB-174) cell line

growth_protocol: As described in the paper. Briefly, the bro-ALI model was developed using PBEC. The PBEC were harvested from healthy bronchial tissues obtained from donors in connection with lobectomy following written and informed consent, and approval by the Swedish Ethical Review Authority (Institutional ethic committee reference number 99-357, approved on 10th January 2000 ). The detailed protocol and details of cellular differentiation (club cells, goblet cells, basal cells, ciliated cells, etc.) of the bro-ALI model have been described previously (PMID: 28107509) and have been used in several studies (PMID: 28107509, PMID: 31462114, PMID: 31381966). All experiments and methods were carried out in accordance with relevant guidelines and regulations.   The alveolar model was developed using NCI-H441 (ATCC HTB-174) cell line, known to express constitutively the mRNA and protein of the major surfactant apo-protein. NCI-H441 cells were co-cultured with HULEC-5a (ATCC CRL-3244) representative of human lung microvascular endothelial cells for this purpose. Details of the development of alv-ALI model and its characteristics have been described recently (PMID: 33235237).

extract_protocol:
RNeasy Micro (QIAGEN)
UPX 3’ RNA sequencing technology using Qiagen Genomic Services, Germany

treatment_protocol: As described in the paper. Briefly, S1 protein, 10nM (mixed in a small volume of cell culture media; 80µl) was added on the apical surface of both bro-ALI and alv-ALI and incubated for 24 hours (h). The exposure dose was determined following a dose gradient study using 5nM, 10nM, and 20nM S1 protein and corresponding assessment of cytotoxicity, surface expression of ACE2, TLR2 and TLR4 by flow cytometry.

value: control


title: Alveolar_Control_rep3


title: Alveolar_Control_rep4


title: KO_PA-input for meRIP-seq


title: LacNa_rep2


title: SA2SN

type: genomic

city: Lyon

first: Fazlur

middle: Rahman

last: Talukdar

state: Rhone Alps

address: 150 Cours Albert Thomas

department: Epigenetics

country: France

institute: International Agency for Research on Cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Processing and analysis was performed using standard protocol published online: https://github.com/IARCbioinfo/methylkey/find/master

label: Cy5 and Cy3

molecule: genomic DNA

source_name: normal esophageal mucosa

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor and normal tissue samples using AllPrep DNA/RNA Mini Kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: Fresh Frozen

tag: disease state

value: Adjacent normal


title: B3SN


title: SA4SN

value: Female


title: LacNa_rep1


title: TIGKs, siIRF1 HSV 3

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

data_processing:
Fastq files were downloaded from Illumina's BaseSpace for analysis.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1) for each sequencing sample. Quality trimming was not deemed necessary.
The concatenated sequences were directly aligned to the Homo sapiens hg38.p12 reference genome assembly using STAR (version 2.6), generating alignment files in bam format.
For the analysis using DESeq2, raw counts were obtained from the STAR aligned bam format files using HTSeq version 0.10.0
Genome_build: hg38.p12
Supplementary_files_format_and_content: tab-delimited text files with raw counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Telomerase-Immortalized Gingival Keratinocytes (TIGKs)

growth_protocol: TIGK cells were grown at 37℃ with 5% carbon dioxide.

extract_protocol:
RNA was extracted using QIAGEN Rneasy Plus Mini kit
Libraries were prepared using the TruSeqStranded mRNA Library Prep kit (Illumina Cat# 20020594),TruSeq RNA CD Index Plate (Illumina Cat# 20019792).

treatment_protocol: TIGK cells were grown to ~70-80% confluence and stimulated with IFN-β or IFN-λ for 24h.

value: siRNA against IRF1 (siIRF1)

tag: infection

value: HSV


title: BT474-LAP-DTP2_S4

value: 14 day lapatinib


title: TIGKs, siIRF1 HSV 2

value: Telomerase-Immortalized Gingival Keratinocytes (TIGKs)


title: B4SN


title: IR expressed in tancytes of NCD-fed animals IP3

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

description: NCD-fed lean WT mice

data_processing:
The pool was sequenced for 35 million reads using an Illumina NovaSeq6000 instrument and a PE100 sequencing protocol.
Data was processed using the nf-core/rnaseq v1.4.2 pipeline
Alignment to reference genome was done using STAR vSTAR_2.6.1d
Gene abundance estimation was done using Salmon 0.14.1
Differential gene expression analysis of IP samples was carried out using DESeq2 1.30.0
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary_files_format_and_content: Excel speadsheets containing raw salmon counts per sample as well as fold change and significance level for each annotated gene.

source_name: tancytes of mediobasal hypothalamus

growth_protocol: Mice were housed in groups of 3–5 at 22°C – 24°C using a 12 h light/1h dark cycle. Animals were fed ad libitum chow diet ssniff® (V1554, Sniff Spezialdiäten GmbH) containing 57% of calories from carbohydrates, 34% calories from protein and 9% calories from fat, or high-fat diet (HFD; EF D12492-(I), Sniff Spezialdiäten GmbH) containing 21% calories from carbohydrates, 19% calories from protein and 60% calories from fat, starting age of 4 weeks

extract_protocol:
Arcuate and median eminence regions were collected, frozen on dry ice and stored at -80°C.  Four to seven hypothalami were pooled per replicate. Further steps of the immunopurification of L10a-GFP tagged ribosomes and subsequent extraction of RNA were performed exactly as previously described94,96.  Protein A Dynabeads (375 µl per IP, Invitrogen) were washed three times (1mL) in 0.15M KCl IP wash buffer (20mM HEPES [pH 7.4], 5 mM MgCl2, 150 mM KCl, 1% NP40, 0.5 mM DTT and 100 mg/ml cycloheximide, resuspended in 275 µl 0.15M KCl IP wash buffer with 50 mg of 19C8 and 50 mg of 19F7 (Cat# Htz-GFP-19F7, RRID:AB_2716736 and Htz-GFP-19C8, RRID:AB_2716737, Memorial Sloan Kettering Monoclonal An-tibody Facility) and incubated with slow end-over-end mixing at 4°C overnight. Next day, beadswere washed three times (1 mL) in 0.15M KCl IP wash buffer to remove unbound anti-GFP antibody. Pooled hypothalami were homogenized in lysis buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 150 mM KCl, 0.5 mM DTT, 40 U/ml Rnasin, 100 mg/ml cycloheximide, protease and phosphatase inhibitor cocktails [1 tablet of cOmplete mini EDTA-free protease inhibitor cocktail/7 mL and 2 tablets of PhosS-TOP/10 ml]) using a handheld homogenization device at 4°C for 30 s. Homoge-nates were centrifuged at 2,000x g for 10 min at 4°C. The supernatant was trans-ferred to a new tube on ice, and 1/9 sample volume of  10% NP-40 (Applichem) and 300 mM DHPC (Avanti Polar Lipids) with final concentration 1% and 30 mM, re-spectively, incubated on ice for 2 min and then centrifuged at 17,000 x g for 10 min at 4°C. The resulting supernatant was transferred to a new tube, and a 30 µl aliquot of the supernatant was flash frozen separately on dry ice for purification as input RNA. Then, 200 µl of anti-GFP-coated  beads were added (800 -1000 ml superna-tant) and incubated at 4°C for one hour with end-over-end mixing. Beads were col-lected with a magnet and resuspended in 1000 µl of 0.35 M KCl IP wash buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 0.35 M KCl, 1% NP40, 0.5 mM DTT, 100 mg/ml cycloheximide). Beads were collected with MagnaRack (Invitrogen) and washed three times (1mL) with  0.35 M KCl IP wash buffer. The collected beads were incu-bated in  RLT buffer (350 µL at RT for 5 minutes. Input and IP RNA were isolated and purified subsequently using the Rneasy Micro Kit (QIAGEN). RNA was eluted in 10 µL in nuclease free water. RNA integrity was assessed using an Agilent 2100 bioanalyzer and RNA concentration was measured using Qubit fluorometer (Ther-mofisher Scientific).
Due to low amount of input material, pre-amplification using the Ovation RNASeq System V2 was performed as previously described. Total RNA was used for first strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input. After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System), transcriptome libraries were pooled. The pool was quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection and sequenced on an Illumina NovaSeq sequencing instrument with a 2 x 100 bp paired-end read length.

treatment_protocol: HFD-fed animals were fed HFD post-weaning (at ~4w) HFD

value: tancytes of mediobasal hypothalamus

tag: genotype/variation

value: NCD after weaning


title: Hy_rep3

value: incubated in 1% O2


title: TIGKs, siIRF1 HSV 1


title: BT474-LAP-DTP1_S3


title: Hy_rep2


title: IR expressed in tancytes of NCD-fed animals IP1

description: NCD-fed lean WT mice


title: TIGKs, SCR HSV 2

value: scramble siRNA (SCR)


title: TIGKs, SCR HSV 3


title: BT474_Untreated

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: hg19
Supplementary_files_format_and_content: gene names and genes-barcodes (tsv files) matrices (matrix file)

extract_protocol: Samples were prepared by the Princess Margaret Genomic Centre following the 10X Genomics Single Cell 3â Reagent Kits v2 user guide. Briefly, samples were washed two times in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. The cell suspension was loaded onto a 10X single cell A chip. After droplet generation, samples were transferred onto pre-chilled 96-well plates (Eppendorf), heat-sealed, and incubated overnight in a Veriti 96-well thermal cycler (Thermo Fisher) for reverse transcription (RT). Following RT, cDNA was recovered using the Recovery Agent provided by 10X, and subsequently purified by using Silane DynaBead (Thermo Fisher) mix, as outlined by the user guide. Purified cDNA was amplified for 13 cycles before purification on SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA), and cDNA concentration was determined with a  Bioanalyzer (Agilent Technologies). cDNA libraries were prepared as outlined by the Single Cell 3â Reagent Kits v2 user guide with modifications to the PCR cycles based on the calculated cDNA concentration.

tag: agent


title: IR expressed in tancytes of NCD-fed animals IP2

description: NCD-fed lean WT mice


title: EFM192A / SKBR3 / SUM225

description: scRNA-seq

source_name: EFM192A / SKBR3 / SUM225

value: EFM192A / SKBR3 / SUM225


title: IR expressed in tancytes of NCD-fed animals Input 3

description: NCD-fed lean WT mice


title: C_rep3

value: incubated in 21% O2


title: C_rep2


title: IR expressed in tancytes of NCD-fed animals Input 2

description: NCD-fed lean WT mice


title: C_rep1


title: HCC1419-DTP

tag: time point

value: 14 day

value: lapatinib

value: HER2 positive breast cancer cells


title: TIGKs, siIRF1 NI 3

value: NI


title: Hy_rep1


title: SA1SN

value: Male

value: Fresh Frozen


title: TIGKs, siIRF1 NI 2


title: HCC1419_6-hr


title: B2SN

value: Adjacent normal


title: B1SN


title: EFM192A-LAP-DTP1_S11


title: HCC1419_Untreated

value: untreated


title: BT474_6-hr


title: TIGKs, siIRF1 NI 1

value: siRNA against IRF1 (siIRF1)


title: TIGKs, SCR NI 3


title: IR expressed in tancytes of HFD-fed animals IP4

description: HFD-fed insulin resistant WT mice

value: HFD after weaning


title: SA5SN


title: K10T

source_name: tumor tissue

value: Female

value: Paraffin Embedded

value: Tumor


title: TIGKs, SCR HSV 1

value: Telomerase-Immortalized Gingival Keratinocytes (TIGKs)

value: HSV


title: amos mutant larval antennal disc 3

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.2.1, Martin 2011), and filtered for low complexity with Prinseq (v. 0.20.3, Schmieder and Edwards 2011).
Reads were aligned against Drosophila melanogaster (v. BDGP5) genome using TopHat2 (v. 2.0.9, Kim et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3, Anders et al. 2014) using D. melanogaster (Ensembl version 72) gene annotation.
Genome_build: Drosophila_melanogaster BDGP5
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

organism: Drosophila melanogaster

source_name: amos mutant larval antennal disc

growth_protocol: Animals (wild-type (w1118) and amos mutant (amos3; PMID:12925594)) were cultured on standard Drosophila medium under a 12 hour light:12 hour dark cycle at 22°C.

extract_protocol:
For mRNA extraction, both males and females were used. Eye-antennal discs were dissected from third instar larvae into ice-cold Schneider’s Drosophila medium (Life Technologies). 50 antennal discs were manually separated from the eye disc and immediately placed into 300 μl Trizol (Invitrogen). Adult antennae were collected from 0-4 h old flies by quickly freezing the animals in dry ice and separating the antennae from other tissues by shaking through a 20 μm sieve. Approximately 300 antennae were transferred into a 1.5 ml Eppendorf tube containing 20 μl Trizol. The antennae were homogenized with an RNase-free pestle until no intact cuticle could be detected, and the lysate was transferred into 300 μl Trizol. RNA purification was performed following a standard protocol (PMID:20516177) followed by column purification (RNeasy, QIAGEN).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol

value: amos mutant

tag: developmental stage

value: third-instar larvae

value: developing olfactory tissue


title: IR expressed in tancytes of NCD-fed animals Input 1

description: NCD-fed lean WT mice

value: tancytes of mediobasal hypothalamus

value: NCD after weaning


title: IR expressed in tancytes of HFD-fed animals IP3

description: HFD-fed insulin resistant WT mice


title: TIGKs, SCR NI 2

value: scramble siRNA (SCR)

value: NI


title: IR expressed in tancytes of HFD-fed animals IP2

description: HFD-fed insulin resistant WT mice


title: amos mutant larval antennal disc 2


title: TIGKs, TIGKs, SCR NI 1


title: BT474_DTP

value: 14 day

value: lapatinib

value: HER2 positive breast cancer cells


title: amos mutant larval antennal disc 1


title: RNA F. nucleatum 3

city: Chengdu

first: Jieyu

last: Zhou

address: No. 14, section 3, Renmin South Road

department: Department of Periodontics

institute: West China Hospital of Stomatology, Sichuan University

data_processing:
mRNAs, lncRNAs and circRNAs, Quality control of the sequencing raw data was conducted by Fast QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), including raw data filtering, sequencing error rate check and GC content distribution check.
mRNAs, lncRNAs and circRNAs, trimmomatic was applied to remove reads including adapter and low-quality reads from raw data and discard the sequences with N base before alignment
mRNAs, lncRNAs and circRNAs, Q20, Q30, and GC contents of the clean data were calculated.
The clean reads of mRNA were aligned to OryCun2.0 with HISAT2 program, and the mapped reads were assembled by using StringTie
mRNAs, lncRNAs and circRNAs, the cuffmerge software was used to merge and filter the transcripts, the criteria as follows: (a) The transcript does not have the coding potential (Software: cpc2, Pfam, CNCI); (b) the length of the transcript ≥ 200 bp; (c) exon number ≥ 2, filtering a large number of single exon transcripts with low expression level and low confidence in the splicing result of the transcriptome; (d) the transcripts are not indicated in the existing database as protein-coding transcripts
For miRNAs, library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced on the Illumina Novaseq 6000  platform.
For miRNA reads, alignment was performed with Bowtie. Meantime, miREvo and miRDeep2 was used to find novel miRNA with default parameters
All miRNAs were counted and normalized with TPM, and the correlation analysis of gene expression among samples was conducted
The aberrantly-expressed miRNAs between experimental and control groups were analyzed by DESeq2
Genome_build: reference genomes from NCBI for human
Supplementary_files_format_and_content: mRNAs, lncRNAs and circRNAs, tab-delimited text files include RPKM values for each Sample. For miRNAs, tab-delimited text files include TPM values for each Sample ...

source_name: THP-1 derived macrophages

growth_protocol: human monocyte cell line THP-1 (TIB-202) cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium, with 10%foetal bovine serum (FBS; HyClone,UT, USA) under 5% CO2 at 37°C.THP-1 monocytes were differentiated into macrophages (THP-1 derived macrophages, dTHP1) by treatment with 100nM PMA (phorbol 12-myristate 13-acetate, Sigma-Aldrich) for 48h.

extract_protocol:
Total RNA was extracted, and the RNA purity and concentration was inspected with a Nanodrop, and RNA integrity was measured with an Agilent 2100 bioanalyzer. Specific library (including lncRNA, mRNA and circRNA) was constructed by removing ribosomal RNA,Small RNA library was constructed by Small RNA Sample Pre-Kit following the manufacturer’s procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols.Using the special structure of 3 'and 5' ends of small RNA, we directly added the two ends of small RNA with connectors, and then reverse transcribed into cDNA. After PCR amplification, the target DNA fragment was separated by PAGE gel electrophoresis, and then the products recovered by gel cutting were small RNA library.

treatment_protocol: Macrophages were infected with live F.nucleatum at a multiplicity of infection (MOI) of 100. Infected Cells were harvested after 24h.

value: F. nucleatum-infected


title: RNA F. nucleatum 2


title: IR expressed in tancytes of HFD-fed animals Input 4

description: HFD-fed insulin resistant WT mice

value: HFD after weaning


title: miRNA F. nucleatum 3


title: IR expressed in tancytes of HFD-fed animals Input 3

description: HFD-fed insulin resistant WT mice


title: RNA F. nucleatum 1


title: IR expressed in tancytes of HFD-fed animals Input 2

description: HFD-fed insulin resistant WT mice


title: amos mutant adult antenna 2

source_name: amos mutant adult antenna

value: adult

value: mature olfactory tissue


title: amos mutant adult antenna 3


title: TIGKs, IFN-λ 3

value: IFN-λ treated


title: TIGKs, IFN-λ 2

value: Telomerase-Immortalized Gingival Keratinocytes (TIGKs)


title: TIGKs, IFN-λ 1


title: miRNA F. nucleatum 2


title: miRNA Control 3

value: non-infected


title: IR expressed in tancytes of HFD-fed animals Input 1

description: HFD-fed insulin resistant WT mice


title: IR deleted in tanycytes of  IP 3

description: NCD-fed Insulin resitant IRΔTan mice

value: IRdelTan


title: RNA Control 3


title: amos mutant adult antenna 1

value: amos mutant


title: miRNA Control 2


title: IR expressed in tancytes of HFD-fed animals IP1

description: HFD-fed insulin resistant WT mice


title: TIGKs, IFN-β 3

value: IFN-β treated


title: TIGKs, IFN-β 2


title: ShMN-_Total_L002_R1

city: Suita

first: Shotaro

last: Tatekawa

state: Osaka

address: 2-2(D10), Yamadaoka, Suita-city

department: Departments of Radiation Oncology,

country: Japan

institute: The University of Osaka Graduate School of Medicine

data_processing:
library strategy: meRIP
After checking the quality of sequencing using FastQC and removing rRNA sequences using Bowtie2, reads were aligned to human reference genomes and transcriptomes using HISAT2 . Peak analysis was performed using MACS2  with some options: -q 0.01, --nomodel, and --extsize 100. We used input RNA sequencing data to perform expression analysis and calculated the reads using featureCounts. Read counting data were normalized and analyzed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: peak files; normalized read count data

source_name: Pancreatic cancer cell line

extract_protocol:
ISOGEN (NIPPON GENE)
RNA libraries were constructed following manufacturer instructions using the TruSeq stranded mRNA Library Prep Kit (Illumina, USA) except for the process of using oligo-dT beads.

value: epithelial cell

tag: tissue source

value: pancreas


title: ShMN-_Total_L001_R1


title: IR deleted in tanycytes of  IP 2

description: NCD-fed Insulin resitant IRΔTan mice

value: tancytes of mediobasal hypothalamus

value: NCD after weaning


title: TIGKs, IFN-β 1


title: IR deleted in tanycytes of  IP 1

description: NCD-fed Insulin resitant IRΔTan mice


title: ShMN-_m6A_L002_R1

data_processing:
library strategy: meRIP
library strategy: meRIP
After checking the quality of sequencing using FastQC and removing rRNA sequences using Bowtie2, reads were aligned to human reference genomes and transcriptomes using HISAT2 . Peak analysis was performed using MACS2  with some options: -q 0.01, --nomodel, and --extsize 100. We used input RNA sequencing data to perform expression analysis and calculated the reads using featureCounts. Read counting data were normalized and analyzed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: peak files; normalized read count data


title: TIGKs, Unstim 3

value: untreated


title: TIGKs, Unstim 2


title: miRNA Control 1


title: IR deleted in tanycytes of Input 2

description: NCD-fed Insulin resitant IRΔTan mice


title: IR deleted in tanycytes of Input 3

description: NCD-fed Insulin resitant IRΔTan mice


title: ShMN-_m6A_L001_R1


title: TIGKs, Unstim 1


title: RNA Control 1


title: IR deleted in tanycytes of Input 1

description: NCD-fed Insulin resitant IRΔTan mice


title: Wild type rep4

city: La Jolla

first: Maximiliano

middle: A

last: D'Angelo

state: CA

address: 10901 North Torrey Pines Road

department: Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Truseq adapter, polyA, and polyT sequences were trimmed using cutadapt v2.3
Trimmed reads were aligned to mouse genome version mm10 and Ensembl gene annotations version 84 using STAR aligner v2.7.0d_0221 with parameters according to ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). Gene expression levels were quantified using RSEM v1.3.1
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized expression (TPM) for every gene and every sample

source_name: quadriceps muscle

extract_protocol:
Quad muscles from four Nup210+/+ and four Nup210–/– mice were snap frozen and then homogenized in Trizol reagent (Thermo Fisher Scientific) using the Qiagen TissueLyser LT. RNA was transferred to the aqueous phase following Trizol manufacturer specifications. After the addition of 70% ethanol, the total RNA was purified using the PureLink RNA Mini kit (Thermo Fisher Scientific). RNA quality and integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module.
Barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

value: quadriceps muscle


title: ShcN-_Total_L002_R1

value: shRNA-Control


title: ShcN-_Total_L001_R1


title: EPCAM_rep2_ARID1A

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: ARID1A CUT&RUN library from 100,000 sorted EPCAM+ endometrial epithelial cells (biological replicate #2) from adult, wild-type mice.

library_source: genomic

data_processing:
library strategy: CUT&RUN
Raw paired-end reads for anti-ARID1A or IgG CUT&RUN were trimmed with cutadapt and Trim Galore! and analyzed for quality via FastQC.
Trimmed reads were aligned to mm10 genome assembly with bowtie2 using flag `--very-sensitive` and filtered for only properly-paired reads with samtools using flag `-f 3`.
Picard MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove PCR duplicates.
For each biological replicate, MACS2 was used to call ARID1A broad peaks against the respective IgG negative control as input, with FDR < 0.25 threshold.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
A naive replicate-overlapping peak set was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
Genome_build: mm10
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered CUTNRUN replicate broadPeaks (FDR < 0.25 MACS2 output) and naive replicate-overlapping broadPeaks.

source_name: EPCAM+ endometrial epithelial cells

growth_protocol: Mice were housed at the Van Andel Research Institute Animal Facility and the Michigan State University Grand Rapids Research Center in accordance with protocols approved by the Van Andel Research Institute and Michigan State University, under AUF# 01/16-099-00.

extract_protocol:
Concanavalin A magnetic beads (Bangs) were washed in Binding Buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) and incubated with either anti-ARID1A (D2A8U, Cell Signaling) or Rabbit IgG (2729, Cell Signaling). Purified cells were washed in Wash Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 5 mM sodium butyrate) then added to the conjugated antibody-bead slurry. After 10 minutes of nutating incubation at ambient temperature, Antibody Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 5 mM sodium butyrate, 2 mM EDTA, 0.05% digitonin) was added to cell bead mixtures, and nuclear permeabilization was confirmed with Trypan blue dye. Reactions then incubated overnight at 4°C. Reactions were washed with Digitonin Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 5 mM sodium butyrate, 0.05% digitonin) and incubated with pAG-MNase (CUTANA, EpiCypher) for one hour at room temperature, followed by an additional wash in Digitonin Buffer then Low-Salt Rinse Buffer (20 mM HEPES-NaOH pH 7.5, 0.5 mM spermidine, 5 mM sodium butyrate). Calcium Incubation Buffer (3.5 mM HEPES-NaOH pH 7.5, 10 mM CaCl2, 0.05% digitonin) was then added to activate the pAG-MNase enzyme, and the reaction was quenched after 3 minutes using EGTA-STOP buffer (170 mM NaCl, 20 mM EGTA, 0.05% digitonin, 20 µg/mL RNase A, 20 µg/mL glycogen, 0.8 pg/mL Saccharomyces cerevisiae nucleosomal DNA as spike-in). Fragments were then released into solution at 37°C followed by 5 minutes centrifugation at 16,000 x g. Eluted DNA were then purified with the NucleoSpin Gel and PCR Clean-up Kit (Takara).
Libraries for CUT&RUN samples were prepared by the Van Andel Genomics Core from 0.5-1 ng of IP material, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific) at a concentration of 500 nM. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp.), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S1, 100 cycle sequencing kit (Illumina Inc.) Each library was sequenced to an average depth of 50 million reads. Base calling was done by Illumina RTA3 and output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: Mouse uteri were surgically removed and minced using scissors. Tissues were digested using the MACS Multi Tissue Dissociation Kit II (Miltenyi Biotec). Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads.

value: Wild-type

tag: antibody

value: anti-ARID1A (D2A8U, Cell Signaling)


title: RNA Control 2


title: EPCAM_rep1_IgG

description: IgG CUT&RUN library from 100,000 sorted EPCAM+ endometrial epithelial cells (biological replicate #1) from adult, wild-type mice.

tag: strain

value: Rabbit IgG (2729, Cell Signaling)


title: EPCAM_rep2_IgG


title: ShcN-_m6A_L002_R1


title: ShcN-_m6A_L001_R1


title: Wild type rep2

tag: tissue


title: Wild type rep1


title: EPZ-3

city: Guangzhou

first: Chunsik

last: Lee

state: Guangdong

address: NO.7 Jinsui Rd.

institute: Sun Yat-Sen University

description: Experimental library 3 of triplicate samples

data_processing:
Standard Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, filtered for low-complexity or low-quality sequence, and then mapped to hg19 whole genome using Tophat2 and to reference genes using bowtie2
FPKM (fragments per kilobase of transcript per million mapped fragments) values were calculated using RSEM (v1.2.15).
Differentially expressed genes between DMSO or EPZ5676-treated cells were detected by EdgeR package for the genes represented by >1 FPKM with ≥ 2-fold difference and a FDR (false discovery rate) threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file of all genes showing the gene symbols, FPKM for each sample

source_name: Retina

extract_protocol:
After treatment with EPZ5676 or DMSO (vehicle control), total RNA from each sample was isolated using RNeasy Plus Mini kit (Qiagen, #74134), and processed for adapter ligation
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 µM EPZ5676 for 6 days in parallel with a vehicle control (DMSO); drugs were replenished every 2 days upon medium change of the culture

value: Y79 retinoblastoma cell line (ATCC HTB18)


title: Wild type rep3


title: R-NC-3

city: Shanghai

first: Yuan-Yuan

last: Luo

address: Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat(version:2.0.9).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample ...

source_name: liver cancer

growth_protocol: Huh7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.All cells were cultured in a 5% CO2 humidified atmosphere at 37˚C.

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hsa_circ_0098181 overexpressing and control plasmid were transfected into Huh7 cells with Lipofectamine 2000. After 48 hours transfection, total RNA was extracted for further RNA sequencing.


title: R-NC-1


title: R-98181-3


title: R-NC-2


title: R-98181-2


title: EPZ-2

description: Experimental library 2 of triplicate samples


title: EPCAM_rep1_ARID1A

description: ARID1A CUT&RUN library from 100,000 sorted EPCAM+ endometrial epithelial cells (biological replicate #1) from adult, wild-type mice.


title: Nup210 knock-out rep4


title: Nup210 knock-out rep3


title: EPZ-1

description: Experimental library 1 of triplicate samples


title: R-98181-1


title: Nup210 knock-out rep2


title: m_KO1andKO2 [SC121952]

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm10 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq

molecule: polyA RNA

source_name: heart

extract_protocol:
Cell suspension was centrifuge (100 x g, 2min) three times to separate the cardiomyocytes and non-cardiomyocytes
One ng of purified cDNA was used to generate a sequencing library with the Nextera XT DNA sample preparation Kit

value: heart

value: KO; Mst1/2-deficient


title: CTL-2

description: Control library 2 of triplicate samples

value: DMSO (vehicle control)


title: NC-2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat(version:2.0.9).
Bowtie were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the RPKM value of each gene was calculated.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file include RPKM values for each Sample ...


title: m_WT1andWT2 [SC121925]

value: WT


title: CTL-3

description: Control library 3 of triplicate samples


title: 98181-3


title: Nup210 knock-out rep1


title: CTL-1

description: Control library 1 of triplicate samples


title: m_WT1andWT2 [SC121892]


title: 98181-2


title: Uwt32018 RNA

description: RNA library. Second flow cell. Cells from pooled mice. Retrieved from GEO accession GSE129784.

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting. Lexogen SIRVome was independently aligned and quantified for qualitative assessment of library concordancy.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file. Raw gene counts were combined with control cell data retrieved from GEO accession GSE129784.
Low count genes were filtered (at least 1 count per sample on average) prior to normalization factor calculation, dispersion estimation, negative binomial generalized linear model fitting, and Wald hypothesis testing in DESeq2 for differential gene expression analysis. For linear modeling, the design matrix was constructed from a single “condition” variable with the inclusion of an intercept term, in the form: ~ condition. Calculated differential gene expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including per-sample gene counts (STAR output) and non-thresholded DESeq2 differential gene expression analysis.

source_name: endometrial epithelium

extract_protocol:
Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Lexogen SIRV-set2 RNAs were spiked into RNA prior to library preparation at a concentration of 1% by mass. RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq Kit from 100 ng of total RNA material.

treatment_protocol: Mouse uteri were surgically removed and minced using scissors. Tissues were digested using the MACS Multi Tissue Dissociation Kit II (Miltenyi Biotec).

value: Control wild-type


title: nonapCAFs5

city: Vari

first: Maria

last: Tsoumakidou

state: Attica

address: 34 Fleming Street

country: Greece

institute: B.S.R.C. "Alexander Fleming"

data_processing:
base calling with alta-cyclic
fastq triming with trimgalore
alignement with bowtie2
downstream analysis with metaseqR2
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 natural normilized counts for each sample in txt
Supplementary_files_format_and_content: metaseqR2 table with DE and stats in txt

source_name: solid tumor

extract_protocol:
ApCAFs and nonapCAFs from tumor-bearing mice were FACS sorted as FSC-AhighCD45-CD31-EPCAM-mCherry-PDPL+PDGFRa+MHCII+ and FSC-AhighCD45-CD31-EPCAM-mCherry-PDPL+PDGFRa+MHCII- cells respectively. Total RNA was isolated by using Single Cell RNA Purification Kit (Norgen Biotek) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using NEB Next Ultra RNA Library Prep Kit.

value: lung tumor

tag: age

value: over 8-week-old

value: wt

value: CAFs

tag: cell subtype

value: nonapCAFs


title: wild-type larval antennal disc 5

source_name: wild-type larval antennal disc

tag: genotype

value: wild-type

value: third-instar larvae

value: developing olfactory tissue


title: Uwt12018 RNA


title: 98181-1

tag: cell line


title: wild-type larval antennal disc 2


title: apCAFs3

tag: cell type

value: apCAFs


title: nonapCAFs4


title: wild-type larval antennal disc 1


title: wild-type adult antenna 7

source_name: wild-type adult antenna

value: adult

value: mature olfactory tissue


title: Trp53flfl_Pik3caH1047R_rep3

description: RNA library from sorted EPCAM+ endometrial epithelial cells of an individual approximately 76-day old LtfCre^0/+; (Gt)R26^Pik3ca*H1047R; Trp53^fl/fl mouse biological replicate at time of vaginal bleeding.


title: m_KO1andKO2 [SC121949]


title: Input

city: Rome

first: Francesca

last: Rossi

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description: Total cell lysate

data_processing:
Basecalling was performed using RTA (Real Time Analysis) 2.11.3. Raw sequencing data processing (format conversion and demultiplexing) was performed using Bcl2Fastq version 2.0.2.
Adapter sequences and poor quality bases were removed from raw reads using Trimmomatic software with parameters ILLUMINACLIP:path/to/adapter:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18.
Alignment to human GRCh38 genome and Ensembl 90 transcriptome was performed using STAR aligner version 2.5.2b with parameters --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999.
Alignment files were further processed by filtering out reads mapping to rRNAs and tRNAs using BEDTools intersect, removing PCR duplicates using Picard MarkDuplicates and discarding the multi-mapped reads using bamtools. Properly paired reads were extracted using SAMtools.
GRCh38 genome was divided into 170 bp long non-overlapping bins using BEDtools makewindows tool. Properly paired fragments falling in each bin were counted using BEDtools intersect tool; this way, sample-specific count files were created. Such files were given as input to Piranha version 1.2.1 to call peaks for Odd and Even circRNA pull-down samples and LacZ pull-down sample, using Input sample counts as a covariate. Piranha parameters were set to -x -c -s.
Genome_build: GRCh38
Supplementary_files_format_and_content: Piranha output files (BED format) containing genomic coordinates of enriched read clusters. The last two columns represent the p-value and the covariate (Input) value, respectively.

source_name: Embryonal rhabdomyosarcoma cell line (RD)

growth_protocol: RD cells are cultured in DMEM high-glucose supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1x penicillin-streptomycin.

extract_protocol:
Total RNA was extracted with Qiazol reagent and miRNEasy spin columns according to the manufacturer’s specifications (QIAGEN).
Ovation RNA v2 followed by Ovation Ultralow v2 kit

treatment_protocol: The pull-down experiment was performed as described in Martone et al, 2020 with minor changes described in this work

value: RD

value: Embryonal rhabdomyosarcoma cancer cells


title: LacZ

description: Control pull-down

tag: target

value: control biotynilated antisense probes targeting LacZ bacterial mRNA


title: Uwt22018 RNA


title: apCAFs2


title: wild-type adult antenna 6


title: NC-1


title: circZNF609_Pull-Down_Odd

description: Specific pull-down

value: specific biotynilated antisense probes targeting ZNF609 exon 2


title: circZNF609_Pull-Down_Even

description: Specific pull-down


title: wild-type adult antenna 5


title: apCAFs1


title: Trp53flfl_Pik3caH1047R_rep1


title: assoL174

status: Public on Dec 12 2021

city: Hangzhou

first: Hengfu

last: Yin

state: Zhejiang

address: Daqiao 73

institute: Research Institute of Subtropical Forestry, Chinese Academy of Forestry

description:
L174
Transcriptomics Association Study in Camellia oleifera

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated  The number of reads falling in the exons of transcripts were counted and normalized by the size of the total transcript and by the size of the library.
Supplementary_files_format_and_content: abundance count
Supplementary_files_format_and_content: abundance FPKM value matrix

organism: Camellia oleifera

source_name: seed

growth_protocol: Under the natural condition in Hangzhou city, China.

extract_protocol:
Seed kenels were obtained, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: seed kernel

value: 12 years old

tag: cultivar


title: assoL175

description:
L175
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title: assoL182

description:
L182
Transcriptomics Association Study in Camellia oleifera


title: assoL176

description:
L176
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title: assoL180

description:
L180
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title: assoL178

description:
L178
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title: assoL177

description:
L177
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title: assoL164

description:
L164
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title: assoL163

description:
L163
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title: assoL167

description:
L167
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title: assoL165

description:
L165
Transcriptomics Association Study in Camellia oleifera


title: assoL170

description:
L170
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title: assoL15

description:
L15
Transcriptomics Association Study in Camellia oleifera


title: assoL166

description:
L166
Transcriptomics Association Study in Camellia oleifera


title: Trp53flfl_Pik3caH1047R_rep2


title: assoL168

description:
L168
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title: assoL162

description:
L162
Transcriptomics Association Study in Camellia oleifera


title: assoL153

description:
L153
Transcriptomics Association Study in Camellia oleifera


title: assoL160

description:
L160
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title: assoL161

description:
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title: assoL155

description:
L155
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title: assoL152

description:
L152
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title: assoL150

description:
L150
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title: assoL119

description:
L119
Transcriptomics Association Study in Camellia oleifera


title: assoL12

description:
L12
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title: assoL151

description:
L151
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title: assoL172

description:
L172
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title: assoL145

description:
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title: assoL173

description:
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title: assoL101

description:
L101
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title: assoL98

description:
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title: assoL99

description:
L99
Transcriptomics Association Study in Camellia oleifera


title: assoL100

description:
L100
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title: assoL102

description:
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title: assoL106

description:
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title: assoL96

description:
L96
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title: assoL95

description:
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title: assoL94

description:
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title: assoL89

description:
L89
Transcriptomics Association Study in Camellia oleifera


title: nonapCAFs6

value: lung tumor


title: assoL91

description:
L91
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title: assoL97

description:
L97
Transcriptomics Association Study in Camellia oleifera


title: assoL88

description:
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title: assoL10

description:
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title: assoL77

description:
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title: assoL82

description:
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title: assoL86

description:
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title: assoL81

description:
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title: assoL72

description:
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title: assoL78

description:
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title: assoL76

description:
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title: assoL73

description:
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title: assoL9

description:
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title: assoL69

description:
L69
Transcriptomics Association Study in Camellia oleifera


title: assoL16

description:
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title: assoL185

description:
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title: assoL70

description:
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title: assoL90

description:
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title: assoL11

description:
L11
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title: assoL67

description:
L67
Transcriptomics Association Study in Camellia oleifera


title: assoL2

description:
L2
Transcriptomics Association Study in Camellia oleifera


title: assoL66

description:
L66
Transcriptomics Association Study in Camellia oleifera


title: assoL1

description:
L1
Transcriptomics Association Study in Camellia oleifera


title: assoL87

description:
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title: assoL65

description:
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Transcriptomics Association Study in Camellia oleifera


title: assoL63

description:
L63
Transcriptomics Association Study in Camellia oleifera


title: assoL8

description:
L8
Transcriptomics Association Study in Camellia oleifera


title: assoL59

description:
L59
Transcriptomics Association Study in Camellia oleifera


title: assoL60

description:
L60
Transcriptomics Association Study in Camellia oleifera


title: assoL61

description:
L61
Transcriptomics Association Study in Camellia oleifera


title: assoL58

description:
L58
Transcriptomics Association Study in Camellia oleifera


title: assoL55

description:
L55
Transcriptomics Association Study in Camellia oleifera


title: assoL54

description:
L54
Transcriptomics Association Study in Camellia oleifera


title: assoL71

description:
L71
Transcriptomics Association Study in Camellia oleifera


title: assoL53

description:
L53
Transcriptomics Association Study in Camellia oleifera


title: assoL44

description:
L44
Transcriptomics Association Study in Camellia oleifera


title: assoL46

description:
L46
Transcriptomics Association Study in Camellia oleifera


title: assoL49

description:
L49
Transcriptomics Association Study in Camellia oleifera


title: assoL43

description:
L43
Transcriptomics Association Study in Camellia oleifera


title: assoL45

description:
L45
Transcriptomics Association Study in Camellia oleifera


title: assoL4

description:
L4
Transcriptomics Association Study in Camellia oleifera


title: assoL39

description:
L39
Transcriptomics Association Study in Camellia oleifera


title: assoL40

description:
L40
Transcriptomics Association Study in Camellia oleifera


title: assoL42

description:
L42
Transcriptomics Association Study in Camellia oleifera


title: assoL32

description:
L32
Transcriptomics Association Study in Camellia oleifera


title: assoL64

description:
L64
Transcriptomics Association Study in Camellia oleifera


title: assoLyawu7

description:
Lyawu7
Transcriptomics Association Study in Camellia oleifera


title: assoL29

description:
L29
Transcriptomics Association Study in Camellia oleifera


title: assoL31

description:
L31
Transcriptomics Association Study in Camellia oleifera


title: assoLyawu4

description:
Lyawu4
Transcriptomics Association Study in Camellia oleifera


title: assoLyawu6

description:
Lyawu6
Transcriptomics Association Study in Camellia oleifera


title: assoLyawu2

description:
Lyawu2
Transcriptomics Association Study in Camellia oleifera


title: assoL56

description:
L56
Transcriptomics Association Study in Camellia oleifera


title: assoL52

description:
L52
Transcriptomics Association Study in Camellia oleifera


title: assoL30

description:
L30
Transcriptomics Association Study in Camellia oleifera


title: assoLyawu1

description:
Lyawu1
Transcriptomics Association Study in Camellia oleifera


title: assoLyajia8

description:
Lyajia8
Transcriptomics Association Study in Camellia oleifera


title: assoLyajia2

description:
Lyajia2
Transcriptomics Association Study in Camellia oleifera


title: assoLxiang7

description:
Lxiang7
Transcriptomics Association Study in Camellia oleifera


title: assoLxiang9

description:
Lxiang9
Transcriptomics Association Study in Camellia oleifera


title: assoLxiang6

description:
Lxiang6
Transcriptomics Association Study in Camellia oleifera


title: assoL28

description:
L28
Transcriptomics Association Study in Camellia oleifera


title: assoLxiang50

description:
Lxiang50
Transcriptomics Association Study in Camellia oleifera


title: assoLxiang5

description:
Lxiang5
Transcriptomics Association Study in Camellia oleifera


title: assoLxiang47

description:
Lxiang47
Transcriptomics Association Study in Camellia oleifera


title: assoLxiang4

description:
Lxiang4
Transcriptomics Association Study in Camellia oleifera


title: assoLxiang3

description:
Lxiang3
Transcriptomics Association Study in Camellia oleifera


title: assoLwupai5

description:
Lwupai5
Transcriptomics Association Study in Camellia oleifera


title: assoLwu5-2

description:
Lwu5-2
Transcriptomics Association Study in Camellia oleifera


title: assoLwuyiwu2

description:
Lwuyiwu2
Transcriptomics Association Study in Camellia oleifera


title: assoL3

description:
L3
Transcriptomics Association Study in Camellia oleifera


title: assoLyajia6

description:
Lyajia6
Transcriptomics Association Study in Camellia oleifera


title: assoLwu-1

description:
Lwu-1
Transcriptomics Association Study in Camellia oleifera


title: assoLwu5-1

description:
Lwu5-1
Transcriptomics Association Study in Camellia oleifera


title: assoLtong9

description:
Ltong9
Transcriptomics Association Study in Camellia oleifera


title: assoLwu

description:
Lwu
Transcriptomics Association Study in Camellia oleifera

value: assoLwu


title: pooled (20) whole embryos 47.2 µg/L FLX repB

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_47.2_vs_water.csv
flx-47.2-b

data_processing:
Raw files were trimmed using Trimmomatic v0.38
Trimmed fastq files were pseudoaligned to the referencefathead minnow transcriptome (NCBI Acc# GCA_016745375.1) using Kallisto
Only features with at least 5 counts per million in at least 3 samples were kept for differential expression analyses. Significance of differentially expressed genes were assessed using DESeq2 in R, with a cut-off FDR (Benjamini-Hochberg) < 0.05 and an effect size threshold |FC| ≥ 1.5
Genome_build: fathead minnow (Pimephales promelas) reference transcriptome NCBI Acc# GCA_016745375.1 from Martinson, J., Bencic, D.C., Toth, G.P., Kostich, M.S., Flick, R.W., See, M.J., Lattier, D., Biales, A.D., Huang, W., n.d. De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure. https://doi.org/10.1101/2021.02.24.432777
Supplementary_files_format_and_content: csv - raw counts of all samples
Supplementary_files_format_and_content: tabular - differential expression results using DESeq2

organism: Pimephales promelas

source_name: whole body tissue

growth_protocol: Fathead minnow embryos (<6 hrs post-fertilization; 20 embryos each replicates) were exposed to graded concentrations (measured concentrations: water control, 0.19, 0.74, 3.38, 10.2, 47.2 µg/L ) of FLX  in glass petri dishes, maintained at (23 oC, 16:8 light:dark cycle)

extract_protocol:
Total RNA was extracted from pools of 20 larvae using QIAGEN RNeasy plus universal mini kit following the manufacturer's protocol
Libraries were generated from 250 ng of total RNA. mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps were done using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Embryos were exposed (waterborne) from 6-hrs post-fertilization to 7-days post-fertilization in a static renewal condition (at least 50% test solution renewal per day)

value: 7-days post-fertilization

tag: treatment

value: 47.2 µg/L FLX

value: whole body tissue


title: pooled (20) whole embryos 47.2 µg/L FLX repC

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_47.2_vs_water.csv
flx-47.2-c


title: pooled (20) whole embryos 10.2 µg/L FLX repD

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_10.2_vs_water.csv
flx-10.2-d

value: 10.2 µg/L FLX


title: assoLtong40

description:
Ltong40
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 47.2 µg/L FLX repA

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_47.2_vs_water.csv
flx-47.2-a


title: assoLxiang8

description:
Lxiang8
Transcriptomics Association Study in Camellia oleifera


title: assoLtong41

description:
Ltong41
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 10.2 µg/L FLX repE

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_10.2_vs_water.csv
flx-10.2-e


title: pooled (20) whole embryos 10.2 µg/L FLX repB

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_10.2_vs_water.csv
flx-10.2-b


title: assoLtong6

description:
Ltong6
Transcriptomics Association Study in Camellia oleifera


title: assoLtong4

description:
Ltong4
Transcriptomics Association Study in Camellia oleifera


title: assoLyajia1

description:
Lyajia1
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 10.2 µg/L FLX repA

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_10.2_vs_water.csv
flx-10.2-a


title: assoLtong39

description:
Ltong39
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 3.38 µg/L FLX repE

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_3.38_vs_water.csv
flx-3.38-e

value: 3.38 µg/L FLX


title: assoLtong32

description:
Ltong32
Transcriptomics Association Study in Camellia oleifera


title: assoL27

description:
L27
Transcriptomics Association Study in Camellia oleifera


title: assoL26

description:
L26
Transcriptomics Association Study in Camellia oleifera


title: assoLtong30

description:
Ltong30
Transcriptomics Association Study in Camellia oleifera


title: assoLtong38

description:
Ltong38
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 10.2 µg/L FLX repC

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_10.2_vs_water.csv
flx-10.2-c


title: assoLtong29

description:
Ltong29
Transcriptomics Association Study in Camellia oleifera


title: assoLtong3

description:
Ltong3
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 0.74 µg/L FLX repE

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_0.74_vs_water.csv
flx-0.74-e

value: 0.74 µg/L FLX


title: assoLtong12

description:
Ltong12
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 3.38 µg/L FLX repA

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_3.38_vs_water.csv
flx-3.38-a


title: pooled (20) whole embryos 0.74 µg/L FLX repC

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_0.74_vs_water.csv
flx-0.74-c


title: assoLtong18

description:
Ltong18
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 0.74 µg/L FLX repD

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_0.74_vs_water.csv
flx-0.74-d


title: assoLtong10

description:
Ltong10
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 0.74 µg/L FLX repA

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_0.74_vs_water.csv
flx-0.74-a


title: assoLtong11

description:
Ltong11
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 3.38 µg/L FLX repD

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_3.38_vs_water.csv
flx-3.38-d


title: pooled (20) whole embryos 0.19 µg/L FLX repB

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_0.19_vs_water.csv
flx-0.19-b

value: 0.19 µg/L FLX


title: pooled (20) whole embryos 0.74 µg/L FLX repB

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_0.74_vs_water.csv
flx-0.74-b


title: pooled (20) whole embryos 0.19 µg/L FLX repA

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_0.19_vs_water.csv
flx-0.19-a


title: pooled (20) whole embryos water control repD

description:
ME6_kallisto_countfile_fhm-els-flx.csv
flx-0-d

value: water control


title: assoLminyou60

description:
Lminyou60
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos water control repE

description:
ME6_kallisto_countfile_fhm-els-flx.csv
flx-0-e


title: assoLminyou9

description:
Lminyou9
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 3.38 µg/L FLX repC

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_3.38_vs_water.csv
flx-3.38-c


title: assoLminyou8

description:
Lminyou8
Transcriptomics Association Study in Camellia oleifera


title: assoLminyou6

description:
Lminyou6
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 3.38 µg/L FLX repB

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_3.38_vs_water.csv
flx-3.38-b


title: pooled (20) whole embryos water control repC

description:
ME6_kallisto_countfile_fhm-els-flx.csv
flx-0-c


title: assoLminyou5

description:
Lminyou5
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos 0.19 µg/L FLX repC

description:
ME6_kallisto_countfile_fhm-els-flx.csv
result_0.19_vs_water.csv
flx-0.19-c


title: assoLminyou4

description:
Lminyou4
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos water control repA

description:
ME6_kallisto_countfile_fhm-els-flx.csv
flx-0-a


title: assoLminyou2

description:
Lminyou2
Transcriptomics Association Study in Camellia oleifera


title: assoLminyou43

description:
Lminyou43
Transcriptomics Association Study in Camellia oleifera


title: assoL24

description:
L24
Transcriptomics Association Study in Camellia oleifera


title: assoLminyou10

description:
Lminyou10
Transcriptomics Association Study in Camellia oleifera


title: fecal_CRE_NEG_Late_8

city: Ann Arbor

first: Yatrik

last: Shah

state: Michigan

address: 500 S State Street

institute: University of Michigan

description:
518.4S
fecal_taxonomy_reads.txt

data_processing:
The V4 region of the 16S rRNA was amplified from freshly collected mouse feces using the Dual-indexing sequencing strategy. For tissue, colonic tissue was collected following dissection.
Sequencing was done on the Illumina MiSeq platform, using a MiSeq reagent kit V2 500 cycles, according to the manufacturer’s instructions.
Bacterial community analysis was performed using Mothur (v1.42.3) aligning to the full SILVA reference alignment (release 132) provided by Mothur
Genome_build: Mothur's Silva release 132
Supplementary_files_format_and_content: fecal_taxonomy_reads.txt and tissue_taxonomy_reads.txt representing annotated read counts

organism: feces metagenome

source_name: mouse feces

extract_protocol:
Feces were collected from the terminal colon at sacking. rRNA was extracted using the Qiagen MagAttract PowerMicrobiome kit.
Libraries were cleaned, normalized and underwent quality control before sequencing on Illumina MiSeq platform.

treatment_protocol: Mice were genotyped and DoubleMut, TripleMut and CRE-negative litter mate controls were induced with 1 dose of 100 mg/kg tamoxifen. Bedding was mixed daily throughout the experiment. Mice were euthanized on day 10. Feces were collected from the terminal colon at sacking.

value: feces; bacteria

tag: timepoint

value: Late

tag: cage


title: fecal_DoubleMut_Late_6

description:
519.1S
fecal_taxonomy_reads.txt

value: DoubleMut


title: fecal_TripleMut_Early_7

description:
519.3
fecal_taxonomy_reads.txt

value: TripleMut

value: Early


title: fecal_CRE_NEG_Early_8

description:
518.4
fecal_taxonomy_reads.txt


title: fecal_TripleMut_Late_7

description:
519.3S
fecal_taxonomy_reads.txt


title: fecal_DoubleMut_Early_5

description:
519.1
fecal_taxonomy_reads.txt


title: assoLminyou11

description:
Lminyou11
Transcriptomics Association Study in Camellia oleifera

value: seed kernel


title: assoLminyou1

description:
Lminyou1
Transcriptomics Association Study in Camellia oleifera

value: 12 years old


title: fecal_CRE_NEG_Early_7

description:
517.5
fecal_taxonomy_reads.txt


title: fecal_CRE_NEG_Late_7

description:
517.5S
fecal_taxonomy_reads.txt


title: assoL23

description:
L23
Transcriptomics Association Study in Camellia oleifera


title: pooled (20) whole embryos water control repB

description:
ME6_kallisto_countfile_fhm-els-flx.csv
flx-0-b


title: fecal_TripleMut_Late_5

description:
517.3S
fecal_taxonomy_reads.txt


title: assoLmin43

description:
Lmin43
Transcriptomics Association Study in Camellia oleifera


title: assoLmin48

description:
Lmin48
Transcriptomics Association Study in Camellia oleifera


title: assoLjiangxi23

description:
Ljiangxi23
Transcriptomics Association Study in Camellia oleifera


title: assoLmin60

description:
Lmin60
Transcriptomics Association Study in Camellia oleifera


title: fecal_TripleMut_Early_6

description:
517.4
fecal_taxonomy_reads.txt


title: fecal_TripleMut_Late_6

description:
517.4S
fecal_taxonomy_reads.txt


title: assoLguiruan23

description:
Lguiruan23
Transcriptomics Association Study in Camellia oleifera


title: assoLguiruan3

description:
Lguiruan3
Transcriptomics Association Study in Camellia oleifera


title: assoLminyou48

description:
Lminyou48
Transcriptomics Association Study in Camellia oleifera


title: fecal_TripleMut_Early_5

description:
517.3
fecal_taxonomy_reads.txt


title: assoLgui3

description:
Lgui3
Transcriptomics Association Study in Camellia oleifera


title: fecal_DoubleMut_Early_4

description:
517.2
fecal_taxonomy_reads.txt


title: fecal_DoubleMut_Late_4

description:
517.2S
fecal_taxonomy_reads.txt


title: fecal_DoubleMut_Late_5

description:
518.2S
fecal_taxonomy_reads.txt


title: fecal_TripleMut_Early_4

description:
516.1
low quality; fewer reads than Water negative control
fecal_taxonomy_reads.txt


title: fecal_TripleMut_Late_4

description:
516.1S
low quality; fewer reads than Water negative control
fecal_taxonomy_reads.txt


title: assoLgui4

description:
Lgui4
Transcriptomics Association Study in Camellia oleifera


title: assoLgui1

description:
Lgui1
Transcriptomics Association Study in Camellia oleifera


title: assoL22

description:
L22
Transcriptomics Association Study in Camellia oleifera


title: assoLganwu2

description:
Lganwu2
Transcriptomics Association Study in Camellia oleifera


title: fecal_CRE_NEG_Late_6

description:
515.4S
fecal_taxonomy_reads.txt


title: assoLgan5

description:
Lgan5
Transcriptomics Association Study in Camellia oleifera


title: fecal_CRE_NEG_Early_6

description:
515.4
fecal_taxonomy_reads.txt


title: assoLgan9

description:
Lgan9
Transcriptomics Association Study in Camellia oleifera


title: assoLgan4

description:
Lgan4
Transcriptomics Association Study in Camellia oleifera


title: fecal_DoubleMut_Late_3

description:
515.3S
fecal_taxonomy_reads.txt


title: assoLgan2

description:
Lgan2
Transcriptomics Association Study in Camellia oleifera


title: fecal_TripleMut_Late_2

description:
515.1S
fecal_taxonomy_reads.txt


title: assoLgan3

description:
Lgan3
Transcriptomics Association Study in Camellia oleifera


title: fecal_TripleMut_Early_2

description:
515.1
fecal_taxonomy_reads.txt


title: fecal_TripleMut_Late_3

description:
515.2S
fecal_taxonomy_reads.txt


title: fecal_CRE_NEG_Late_5

description:
514.4S
fecal_taxonomy_reads.txt


title: fecal_TripleMut_Early_3

description:
515.2
fecal_taxonomy_reads.txt


title: fecal_CRE_NEG_Early_4

description:
514.4
fecal_taxonomy_reads.txt


title: assoLgan12

description:
Lgan12
Transcriptomics Association Study in Camellia oleifera


title: assoLgan1

description:
Lgan1
Transcriptomics Association Study in Camellia oleifera


title: assoLguiruan2

description:
Lguiruan2
Transcriptomics Association Study in Camellia oleifera


title: fecal_CRE_NEG_Late_4

description:
514.3S
fecal_taxonomy_reads.txt


title: assoLFy9

description:
LFy9
Transcriptomics Association Study in Camellia oleifera


title: assoLgui2

description:
Lgui2
Transcriptomics Association Study in Camellia oleifera


title: assoL21

description:
L21
Transcriptomics Association Study in Camellia oleifera


title: assoLFy7

description:
LFy7
Transcriptomics Association Study in Camellia oleifera


title: fecal_CRE_NEG_Early_3

description:
514.3
fecal_taxonomy_reads.txt


title: assoLFy2

description:
LFy2
Transcriptomics Association Study in Camellia oleifera


title: assoLFy5

description:
LFy5
Transcriptomics Association Study in Camellia oleifera


title: fecal_CRE_NEG_Late_3

description:
514.2S
fecal_taxonomy_reads.txt


title: fecal_CRE_NEG_Early_2

description:
514.2
fecal_taxonomy_reads.txt


title: fecal_DoubleMut_Early_3

description:
515.3
fecal_taxonomy_reads.txt


title: fecal_CRE_NEG_Late_2

description:
514.1S
fecal_taxonomy_reads.txt


title: fecal_DoubleMut_Late_2

description:
513.4S
fecal_taxonomy_reads.txt


title: fecal_CRE_NEG_Early_5

description:
514.1
fecal_taxonomy_reads.txt


title: assoLbendiCK

description:
LbendiCK
Transcriptomics Association Study in Camellia oleifera

value: assoLbendiCK


title: assoLDe1

description:
LDe1
Transcriptomics Association Study in Camellia oleifera


title: fecal_DoubleMut_Early_2

description:
513.4
fecal_taxonomy_reads.txt


title: assoLFy1

description:
LFy1
Transcriptomics Association Study in Camellia oleifera


title: fecal_DoubleMut_Late_1

description:
513.3S
fecal_taxonomy_reads.txt


title: assoL164-1

description:
L164-1
Transcriptomics Association Study in Camellia oleifera


title: assoL213-1

description:
L213-1
Transcriptomics Association Study in Camellia oleifera


title: assoL3014

description:
L3014
Transcriptomics Association Study in Camellia oleifera


title: fecal_CRE_NEG_Early_1

description:
513.2
fecal_taxonomy_reads.txt


title: assoL20

description:
L20
Transcriptomics Association Study in Camellia oleifera


title: fecal_CRE_NEG_Late_1

description:
513.2S
fecal_taxonomy_reads.txt


title: fecal_TripleMut_Late_1

description:
513.1S
fecal_taxonomy_reads.txt


title: assoL3038

description:
L3038
Transcriptomics Association Study in Camellia oleifera


title: assoL3012

description:
L3012
Transcriptomics Association Study in Camellia oleifera


title: fecal_TripleMut_Early_1

description:
513.1
fecal_taxonomy_reads.txt


title: assoL3011

description:
L3011
Transcriptomics Association Study in Camellia oleifera


title: assoL3007

description:
L3007
Transcriptomics Association Study in Camellia oleifera


title: Zebrafish Intestine - FE

city: Bandung

first: Indra

last: Wibowo

state: West Java

address: Jl. Ganesha No. 10

department: School of Life Sciences and Technology

country: Indonesia

institute: Institut Teknologi Bandung

description: 2 x 150 bp paired-end sequence reads

data_processing:
Raw paired-end reads were examined for base score, adapter content, and overrepresented sequences with FastQC v0.11.5
Clean reads were aligned to zebrafish genome reference using Tophat2 v2.1.0 with default parameters
Transcriptome assembly and gene expression quantification were calculated with Cufflink v2.2.1 in default parameters. Abundance were calculated in fragments per kilobase of transcript per million reads (FPKM).
Genes were considered differentially expressed if log2FC>1.5
Genome_build: Danio rerio GRCz11 (GCA_000002035.4)
Supplementary_files_format_and_content: tab-deliminated files containing gene ID, gene short name, locus, and FPKM

organism: Danio rerio

source_name: intestine

growth_protocol: Healthy adult zebrafish of 6-9 months old were maintained under established protocols (Avdesh et al., 2012). Lightning conditions were 14:10 hour (light:dark).

extract_protocol:
Zebrafish from each feeding group were fasted for 24 hours. Zebrafish were euthanized with 0.4% MS-222. Intestines were isolated and immersed in RNALater until extraction of RNA. Total RNA was isolated using GeneJET RNA Purification kit according to manufacturer's protocol (ThermoFisher Scientific).
1µg of total RNA with RIN values above 7 were used for library preparation. Poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module. NGS library preparation were constructed with NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Zebrafish were divided into 3 treatment groups, i.e. control, Cavendish diet, and Fe'i diet. Control zebrafish (CO) were fed commercial feed Tetramin (Tetra, Germany). Zebrafish in Cavendish diet group (CV) received Cavendish-containing granule. Similarly, zebrafish in Fe'i diet group (FE) were fed Fe'i-containing granule. Banana-containing granule were prepared from fruit pulp according to Tanaika et al. (2011). The resulting granule contains 50% banana fruit pulp to Tetramin. All feeds were given as much as 4% of body weight per day, divided into three daily feedings.

tag: Stage

value: Day 56 of diet treatment

value: Fe'i diet (50% Tetramin, 50% Fe'i fruit pulp)

tag: organ

value: intestine


title: assoL3009

description:
L3009
Transcriptomics Association Study in Camellia oleifera


title: Zebrafish Intestine - CV

description: 2 x 150 bp paired-end sequence reads

value: Cavendish diet (50% Tetramin, 50% Cavendish fruit pulp)


title: Zebrafish Intestine - CO

description: 2 x 150 bp paired-end sequence reads

value: Control (Tetramin)


title: assoL3001

description:
L3001
Transcriptomics Association Study in Camellia oleifera


title: assoL561

description:
L561
Transcriptomics Association Study in Camellia oleifera


title: fecal_DoubleMut_Early_1

description:
513.3
low quality; fewer reads than Water negative control
fecal_taxonomy_reads.txt


title: WT_preGC_3

city: Tokyo

first: Michelle Sue Jann

state: Tokyo

address: Minato-ku, Shirokanedai 4-6-1, Building 1, 3F, Room 333

department: Institute of Medical Science

institute: The University of Tokyo

data_processing:
TopHat version 2.0.13
Bowtie2 version 2.2.3
SAMtools version 0.1.19
Cufflinks version 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

source_name: Wild-type Pre-GC B cells

growth_protocol: Mb1cre/wt Tbk1f/f mice and Mb1wt/wt Tbk1f/f mice on a C57BL/6 background were infected with Plasmodium yoelii Non-Lethal parasites at 1x10 infected erythrocytes. On day 9, splenic Pre-GC B cells (B220+ IgD- CD38+ GL7+) were enriched by MACS separation and sorted by FACS for RNA preparation. Total RNA was purified from 1 x 10^5 sorted cells.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen)
DNA library was constructed using TruSeq Stranded mRNA Sample Prep Kit

value: Spleen

value: Mb1cre(WT/WT) Tbk1(flox/flox)

value: Germinal center precursor B cells (Pre-GC)

tag: agent

value: Plasmodium yoelii

tag: time point

value: Day 9


title: WT_preGC_4


title: WT_preGC_2


title: WT_preGC_1


title: assoL19

description:
L19
Transcriptomics Association Study in Camellia oleifera


title: KO_preGC_2

source_name: TBK1-deficient Pre-GC B cells

value: Mb1cre(cre/WT) Tbk1(flox/flox)


title: assoL559

description:
L559
Transcriptomics Association Study in Camellia oleifera


title: assoL547

description:
L547
Transcriptomics Association Study in Camellia oleifera


title: KO_preGC_4


title: assoL548

description:
L548
Transcriptomics Association Study in Camellia oleifera


title: assoL564

description:
L564
Transcriptomics Association Study in Camellia oleifera


title: KO_preGC_1


title: AB13296

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Note: Second read contained only cell and molecule barcodes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: Mars seq run of mouse Organs

growth_protocol: Experiments were performed in the Weizmann Institute of Science specific-pathogen free facility, and animals of both sexes were used between the ages of 8-10 weeks. MC38 (2×10^6) cell line were implanted subcutaneously on the right flank of mice and tumor volumes were measured every 2–3 days with an electronic caliper.

extract_protocol:
Isolation of tumor infiltrating leukocytes:  Tumor bearing mice were sacrificed 7 days days after treatment injection inoculation. The tumors underwent mechanical (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA) and enzymatic digestion (0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640) for 15 min at 37°C. Cells then filtered through 100µm cell strainer, washed with ice cold sorting buffer, centrifuged (5 min, 4°C, 300g), and stained with fluorophores conjugated antibodies. LN and spleen were harvested 3 hours after treatment injection.Lymph nodes and spleen were dissected through a 70 µm nylon cell strainer and washed with PBS.
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: When the sum of tumor length and width reached approximately 50 mm3, mice were randomized by tumor size (day 0), and received treatment by intraperitoneal injection as described for each experiment. CD40 mAb or CD40/CD11c bsAb at their respective MTDs (0.175 mg/kg, or 2.5 mg/kg respectively) on days 0, 2, 4, and 6 and/or with 50 ug of both Abs for in-vivo preferential binding. Organs were harvested at day 8 for TME analysis or 3 hours post treatment for in-vivo preferential binding experiment.

value: LN

tag: selection marker

value: CD40 bi

tag: mouse id

value: 3 hours post injection

tag: mouse age

value: 8 weeks


title: assoL540

description:
L540
Transcriptomics Association Study in Camellia oleifera

tag: tissue

value: seed kernel

tag: age

value: 12 years old


title: KO_preGC_3

tag: strain

tag: genotype


title: assoL543

description:
L543
Transcriptomics Association Study in Camellia oleifera


title: AB13297


title: assoL539

description:
L539
Transcriptomics Association Study in Camellia oleifera


title: assoL545

description:
L545
Transcriptomics Association Study in Camellia oleifera


title: AB13280


title: AB13281


title: AB13295


title: assoL536

description:
L536
Transcriptomics Association Study in Camellia oleifera


title: assoL3003

description:
L3003
Transcriptomics Association Study in Camellia oleifera


title: assoL534

description:
L534
Transcriptomics Association Study in Camellia oleifera


title: assoL531

description:
L531
Transcriptomics Association Study in Camellia oleifera


title: AB13294


title: assoL504

description:
L504
Transcriptomics Association Study in Camellia oleifera


title: AB13279


title: AB13278


title: AB13306

value: CD40 mono


title: assoL18

description:
L18
Transcriptomics Association Study in Camellia oleifera


title: assoL530

description:
L530
Transcriptomics Association Study in Camellia oleifera


title: assoL299

description:
L299
Transcriptomics Association Study in Camellia oleifera


title: AB13290


title: AB13292


title: assoL298

description:
L298
Transcriptomics Association Study in Camellia oleifera


title: AB13291


title: AB13293


title: AB13276


title: assoL297

description:
L297
Transcriptomics Association Study in Camellia oleifera


title: assoL233

description:
L233
Transcriptomics Association Study in Camellia oleifera


title: AB13277


title: assoL229

description:
L229
Transcriptomics Association Study in Camellia oleifera


title: assoL232

description:
L232
Transcriptomics Association Study in Camellia oleifera


title: AB13304


title: AB13305


title: AB13288


title: assoL227

description:
L227
Transcriptomics Association Study in Camellia oleifera


title: assoL228

description:
L228
Transcriptomics Association Study in Camellia oleifera


title: AB13289


title: assoL226

description:
L226
Transcriptomics Association Study in Camellia oleifera


title: AB13303


title: assoL17

description:
L17
Transcriptomics Association Study in Camellia oleifera


title: AB13302


title: assoL222

description:
L222
Transcriptomics Association Study in Camellia oleifera


title: AB13286


title: assoL501

description:
L501
Transcriptomics Association Study in Camellia oleifera


title: assoL252

description:
L252
Transcriptomics Association Study in Camellia oleifera


title: AB13300


title: AB13287


title: assoL219

description:
L219
Transcriptomics Association Study in Camellia oleifera


title: assoL220

description:
L220
Transcriptomics Association Study in Camellia oleifera


title: assoL217

description:
L217
Transcriptomics Association Study in Camellia oleifera


title: AB13284


title: assoL214

description:
L214
Transcriptomics Association Study in Camellia oleifera


title: assoL212

description:
L212
Transcriptomics Association Study in Camellia oleifera


title: assoL186

description:
L186
Transcriptomics Association Study in Camellia oleifera


title: AB13299


title: AB13298


title: assoL213

description:
L213
Transcriptomics Association Study in Camellia oleifera


title: AB13282


title: Aged

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

data_processing:
demultiplexing with cellranger mkfastq v2.1.1
alignment to GRCm38 reference and counting with cellranger count v2.1.1
aggregation of runs with cellranger aggr v2.1.1
count processing with Seurat v3.1.0
Genome_build: 10X Reference 2.1.0 (GRCm38, Ensembl 84)
Supplementary_files_format_and_content: comma-separated text files containing count matrices as output by Seurat

source_name: dentate gyrus

extract_protocol:
After cervical dislocation, brains were isolated from hGFAP-eGFP mice (2-14 month-old) and the dentate gyri were dissected in ice-cold HBSS or PBS. Tissue was enzymatically dissociated with 0.25 % Trypsin/EDTA (Gibco) in HBSS containing 2 mM Glucose at 37°C for 30 min. Before and after incubation, the tissue was repeatedly triturated with a fire polished Pasteur pipette. Enzyme activity was stopped by addition of equal volume of 4 % BSA in Earle's Balanced Salt Solution (EBSS, Gibco). The cell suspension was filtered through a 70?m cell strainer and centrifuged at 1200 rpm for 5 min and the pellet was re-suspended in 0.9 M sucrose in 0.5 x HBSS (Gibco). After further centrifugation for 10 min at 2000 rpm the cell pellet was re-suspended in 2 ml of Solution 3 and placed on top of 10 ml Solution 3, centrifuged again for 7 min at 1500 rpm. The resulting pellet was then resuspended filtered PBS.
Libraries were prepared using the Chromium Controller and the Chromium Single Cell 3' Reagent Kit v2 (10X Genomics, Pleasanton, CA) according to the manufacturer's instructions.

treatment_protocol: Adult animals (8-week-old) held under standard conditions served as controls, and were compared to littermates that had access to a running wheel for 12 days as well as to 14-month-old hGFAPeGFP animals (non-running conditions).

value: hGFAP-eGFP

value: primary cells

value: aging adult

value: standard housing conditions


title: AB13035

value: Spleen


title: LC_UVR_24hr_3_RNA-seq

city: London

first: Duncan

last: McKenzie

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt -1.9.1
Reads were aligned and quantified using RSEM-1.3.0/STAR-2.5.2
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited file containing matrix table with raw gene counts for every gene and every sample

source_name: FACS sorted CD45+ CD3- MHCII+ LCs

growth_protocol: Ear tissue was processed immediately following sacrifice of mice, at indicated timepoints following UV radiation

extract_protocol:
Ears were split and floated upon Trypsin-GNK (2.5mg/ml trypsin (Sigma), 7.35mg/ml NaCl, 0.35mg/ml KCl, 0.85mg/ml glucose) for 1 hr at 37 degrees C. Epidermis was separated and digested in trypsin-GNK with 100 ug/ml DNase I (Roche) and 1X Dnase buffer (1.21 mg/ml Tris base, 0.5mg/ml MgCl2, 73ug/ml CaCl2) for 20 min at 37 degrees C with agitation. Isolated cells were washed in medium and stained with Live/Dead Fixable Near-IR Dye (Molecular Probes), followed by mouse Fc block (BD) and anti-EpCAM-PE, anti-Sca1-FITC, anti-CD3-PerCPCy5.5, anti-CD45-APC, anti-TCRd-BV421, anti-MHC-II(I-A/I-E)-BV605. Cells were then washed and sorted on a BD FACS Aria Fusion directly into buffer RLT+.
RNA was isolated from sorted cells using RNeasy Micro Plus Kit (Qiagen). cDNA was prepared with Ovation RNA-Seq System V2 (NuGEN) and libraries were constructed with Ultralow Library System V2 (NuGEN). Resulting libraries were pooled and sequenced on an Illumina HiSeq 2500 platform with single ended 75 bp reads.

treatment_protocol: Ear epidermis was separated and digested to yield a single cell suspension, from which epidermal populations were FACS purified

tag: cell type

value: Langerhans cells (LC)

value: 8 week old

tag: Sex

value: Female

value: WT

value: Treated 24hr prior with 300mJ/cm2 UVB


title: Young non-runner (control)

value: adult


title: AB13034

value: CD40 bi


title: LC_UVR_24hr_2_RNA-seq


title: AB13036

value: LN

value: 3 hours post injection


title: AB13301

value: 8 weeks


title: IF_KC_UVR_24hr_3_RNA-seq

source_name: FACS sorted CD45- MHCII- EpCAM lo Sca1+ interfollicular keratinocytes

value: interfollicular keratinocytes (KC)


title: AB13285

value: CD40 mono


title: LC_UVR_24hr_1_RNA-seq


title: AB13032


title: AB13033


title: AB13030


title: IF_KC_UVR_24hr_2_RNA-seq


title: IF_KC_UVR_24hr_1_RNA-seq


title: AB13031


title: AB13029


title: AB13028


title: DETC_UVR_24hr_2_RNA-seq

source_name: FACS sorted CD45+CD3+TCRgd+ DETC

value: Dendritic epidermal T cells (DETC)


title: AB13283


title: AB13026


title: Young runner

value: hGFAP-eGFP

value: primary cells

value: 12 days access to running wheel


title: DETC_UVR_24hr_1_RNA-seq


title: AB13027

value: Spleen


title: AB13025


title: AB13024


title: LC_UVR_4hr_1_RNA-seq

value: Langerhans cells (LC)

value: Treated 4hr prior with 300mJ/cm2 UVB


title: LC_UVR_4hr_3_RNA-seq

value: 8 week old

value: Female


title: LC_UVR_4hr_2_RNA-seq

value: WT


title: AB13023


title: IF_KC_UVR_4hr_2_RNA-seq


title: AB13021


title: AB13022


title: IF_KC_UVR_4hr_1_RNA-seq


title: DETC_UVR_24hr_3_RNA-seq

value: Treated 24hr prior with 300mJ/cm2 UVB


title: DETC_UVR_4hr_2_RNA-seq


title: DETC_UVR_4hr_1_RNA-seq


title: AB12961


title: DETC_UVR_4hr_3_RNA-seq


title: AB13020


title: AB12959

value: CD40 bi


title: AB12957


title: AB12958


title: AB12956


title: IF_KC_normal_3_RNA-seq

value: Unchallenged


title: LC_normal_3_RNA-seq


title: LC_normal_2_RNA-seq


title: LC_normal_1_RNA-seq


title: IF_KC_normal_2_RNA-seq


title: AB12954

value: 3 hours post injection


title: AB12955

value: 8 weeks


title: IF_KC_UVR_4hr_3_RNA-seq

value: interfollicular keratinocytes (KC)


title: DETC_normal_3_RNA-seq


title: DETC_normal_1_RNA-seq


title: AB12952

value: CD40 mono


title: DETC_normal_2_RNA-seq

value: Dendritic epidermal T cells (DETC)


title: AB12951


title: AB12950


title: AB12949

value: LN


title: AB12960


title: M28_Liver_met_H_6

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
Raw BCL read files were demultiplexed and FASTQ files were generated using bcl2fastq and trimmed using Trimmomatic (Bolger et al., 2014).
Next, the reads were aligned to the mouse mm10 reference genome using STAR to generate BAM files (Dobin et al., 2013).
HTSeq was used to count reads in the exons of genes (Anders et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: counts_tables.xlsx is an Excel spreadsheet that contains processed counts data for all samples

source_name: Liver Tissue

growth_protocol: No treatments

extract_protocol:
Whole RNA was extracted using a QIAGEN RNeasy Plus Mini Kit. Tissues were homogenized in RLT Plus Buffer + BME with a QIAGEN TissueRuptor II handheld rotor-stator homogenizer. After tissue homogenization, QIAshredder spin columns were used followed by gDNA elimination columns and an on column DNase digestion with Ambion RNase-free Dnase during the RNeasy RNA preparation manufacturer protocol.
RNA was quantified and QC was checked using an Agilent 4200 TapeStation RNA ScreenTape. mRNA libraries were prepared using NEBNext Ultra Kit with polyA selection (New England BioLabs).

treatment_protocol: mice were either treated with 200mg/kg metformin for 8 hours or were not treated as indicated

value: NDUFS2 hemizygous

value: young

value: metformin 200mg per kg 8 hours


title: M28_Kidney_met_H_6

source_name: Kidney Tissue


title: AB12948


title: M27_Liver_met_W_6


title: AB12946


title: M27_Kidney_met_W_6


title: M26_Liver_met_H_5


title: AB12945


title: AB12944


title: IF_KC_normal_1_RNA-seq


title: M25_Liver_met_W_5


title: M26_Kidney_met_H_5


title: M25_Kidney_met_W_5


title: AB13010

source_name: MARS seq run of mouse MC38 tumor

value: Tumor

value: TCRb

value: 7 days post injection


title: AB12953

value: Spleen


title: AB13009


title: AB13007

value: PBS


title: M23_Kidney_met_H_3


title: AB13008


title: M24_Liver_met_H_4


title: M24_Kidney_met_H_4


title: AB13006


title: M22_Kidney_met_W_4

value: WT


title: AB12947

value: CD40 bi


title: M19_Kidney_met_W_1


title: AB13002